ChemOffice.Com - CambridgeSoft

ChemOffice.Com
®
ChemOffice
®
Enterprise, Workgroup and Database

User’s Guide
ChemOffice Enterprise 2005
for Windows
ChemOffice Enterprise is an Enterprise and Workgroup solution including:
Knowledge Management: E-Notebook, CombiChem and Reaction Planner
Chemical Informatics: Registration Enterprise and Inventory Enterprise
Biological Informatics: BioAssay Enterprise, BioSAR and BioViz
Scientific Databases: The Merck Index and ChemACX Database
ChemOffice
®
Enterprise, Workgroup and Databases

License Information
ChemOffice, ChemDraw, Chem3D, ChemFinder, and ChemInfo programs, all resources in the ChemOffice,
ChemDraw, Chem3D, ChemFinder, and ChemInfo application files, and this manual are Copyright © 1986-2004
by CambridgeSoft Corporation (CS) with all rights reserved worldwide. MOPAC 2000 and MOPAC 2002 are
Copyright © 1993-2004 by Fujitsu Limited with all rights reserved. Information in this document is subject to
change without notice and does not represent a commitment on the part of CS. Both these materials and the right
to use them are owned exclusively by CS. Use of these materials is licensed by CS under the terms of a software license
agreement; they may be used only as provided for in said agreement.
ChemOffice, ChemDraw, Chem3D, CS MOPAC, ChemFinder, Inventory, E-Notebook, BioAssay, and ChemInfo
are not supplied with copy protection. Do not duplicate any of the copyrighted materials except for your personal
backups without written permission from CS. To do so would be in violation of federal and international law, and
may result in criminal as well as civil penalties. You may use ChemOffice, ChemDraw, Chem3D, CS MOPAC,
ChemFinder, Inventory, E-Notebook, BioAssay, and ChemInfo on any computer owned by you; however, extra
copies may not be made for that purpose. Consult the CS License Agreement for Software and Database Products
for further details.
Trademarks
ChemOffice, ChemDraw, Chem3D, ChemFinder, ChemInfo and ChemACX are registered trademarks of
CambridgeSoft Corporation (Cambridge Scientific Computing, Inc.).
The Merck Index is a registered trademark of Merck & Co., Inc. ©2001 All rights reserved.
MOPAC 2000 and MOPAC 2002 are trademarks of Fujitsu Limited.
Microsoft Windows, Windows NT, Windows 95, and Microsoft Word are registered trademarks of Microsoft Corp.
Apple Events, Macintosh, Laserwriter, Imagewriter, QuickDraw and AppleScript are registered trademarks of Apple
Computer, Inc. Geneva, Monaco, and TrueType are trademarks of Apple Computer, Inc.
The ChemSelect Reaction Database is copyrighted © by InfoChem GmbH 1997.
AspTear is copyrighted © by Softwing.
Copyright © 1986-2004 CambridgeSoft Corporation (Cambridge Scientific Computing, Inc.) All Rights Reserved.
Printed in the United States of America.
All other trademarks are the property of their respective holders.
CambridgeSoft End-User License Agreement for Software Products
Important: This CambridgeSoft Software License Agreement (“Agreement”) is a legal agreement between you, the
end user (either an individual or an entity), and CambridgeSoft Corporation (“CS”) regarding the use of CS Software
Products, which may include computer software, the associated media, any printed materials, and any “online” or
electronic documentation. By installing, copying, or otherwise using any CS Software Product, you signify that you
have read the CS End User License Agreement and agree to be bound by its terms. If you do not agree to the
Agreement’s terms, promptly return the package and all its contents to the place of purchase for a full refund.

CambridgeSoft Software License
1. Grant of License. CambridgeSoft (CS) Software Products are licensed, not sold. CS grants and you hereby accept
a nonexclusive license to use one copy of the enclosed Software Product (“Software”) in accordance with the terms
of this Agreement. This licensed copy of the Software may only be used on a single computer, except as provided
below. You may physically transfer the Software from one computer to another for your own use, provided the
Software is in use (or installed) on only one computer at a time. If the Software is permanently installed on your computer
(other than a network server), you may also use the Software on a portable or home computer, provided that
you use the software on only one computer at a time. You may not (a) electronically transfer the Software from one
computer to another, (b) distribute copies of the Software to others, or (c) modify or translate the Software without
the prior written consent of CS, (d) place the software on a server so that it is accessible via a public network such as
the Internet, (e) sublicense, rent, lease or lend any portion of the Software or Documentation, (f) modify or adapt
the Software or merge it into another program, (g) modify or circumvent the software activation, or (h) reverse engineer
the software activation so as to circumvent it. The Software may be placed on a file or disk server connected to
a network, provided that a license has been purchased for every computer with access to that server. You may make
only those copies of the Software which are necessary to install and use it as permitted by this agreement, or are for
purposes of backup and archival records; all copies shall bear CS’s copyright and proprietary notices. You may not
make copies of any accompanying written materials.
With a fixed license, the software cannot be installed on more than the number of computers equivalent to the number
of fixed licenses purchased. For example, a 10-user fixed license means the software can be installed on no more
than 10 different computers. A fixed license cannot be installed on a server. With a concurrent license, the software
can be installed on any number of computers at the organization, but the number of computers using the software
at any one time cannot exceed the number of concurrent licenses purchased. For example, a 10-user concurrent
license can be installed on 20 computers, but no more than 10 users can be using it at any one time. If the number
of users of the software could potentially exceed the number of licensed copies, then Licensee must have a reasonable
mechanism or process in place to assure that the number of persons using the software does not exceed the number
of copies. CambridgeSoft reserves the right to conduct periodic audits no more than once per year to review the
implementation of this agreement at the Licensee’s site. At CambridgeSoft’s request, Licensee will provide a knowledgeable
employee to assist in said audit
2. Ownership. The Software is and at all times shall remain the sole property of CS. This ownership is protected by
the copyright laws of the United States and by international treaty provisions. Upon expiration or termination of this
agreement, you shall promptly return all copies of the Software and accompanying written materials to CS. You may
not modify, decompile, reverse engineer, or disassemble the Software.
3. Assignment Restrictions. You may not rent, lease, or otherwise sublet the Software or any part thereof. You may
transfer on a permanent basis the rights granted under this license provided you transfer this Agreement and all copies
of the Software, including prior versions, and all accompanying materials. The recipient must agree to the terms of
this Agreement in full and register this transfer in writing with CS.
4. Use of Included Data. All title and copyrights in and to the Software product, including but not limited to any
images, photographs, animations, video, audio, music, text, applets, Java applets, and data files and databases (the
“Included Data”), are owned by CS or its suppliers.
· You may not copy, distribute or otherwise make the Included Data publicly available.

· Licensed users of ChemOffice Enterprise and Workgroup and the accompanying Plugin software products may
access, search, and view the Included Data and may transmit the results of any search of the Included Data to other
users of the licensed ChemOffice Enterprise and Workgroup software products within your organization only, provided
that such transmission is via an internal corporate (or university) network and is not accessible by the public.
· You may not install the Included Data on non-licensed computers nor distribute or otherwise make the Included
Data publicly available.
· You may use the Software to organize personal data, and you may transmit such personal data over the Internet provided
that the transmission does not contain any Included Data.
· All rights not specifically granted under this Agreement are reserved by CS.
5. Separation of Components. The Software is licensed as a single product. Its component parts may not be separated
for use on more than one computer, except in the case of ChemOffice Enterprise. ChemOffice Enterprise
includes licenses for ChemDraw ActiveX and licenses for Chem3D ActiveX. The ActiveX software products may be
installed on computers other than that one on which ChemOffice Enterprise is installed. However, each copy of the
ActiveX is individually subject to the provisions of Paragraphs 1 through 4 of this Agreement.
6. Educational Use Only of Student Licenses. If you are a student enrolled at an educational institution, the CS
License Agreement grants to you personally a license to use one copy of the enclosed Software in accordance with the
terms of this Agreement. In this case the CS License Agreement does not permit commercial use of the Software nor
does it permit you to allow any other person to use the Software.
7. Termination. You may terminate the license at any time by destroying all copies of the Software and documentation
in your possession. Without prejudice to any other rights, CS may terminate this Agreement if you fail to comply
with its terms and conditions. In such event, you must destroy all copies of the Software Product and all of its
component parts.
8. Confidentiality. The Software contains trade secrets and proprietary know-how that belong to CS and are
being made available to you in strict confidence. ANY USE OR DISCLOSURE OF THE SOFTWARE, OR USE OF ITS
ALGORITHMS, PROTOCOLS OR INTERFACES, OTHER THAN IN STRICT ACCORDANCE WITH THIS LICENSE
AGREEMENT, MAY BE ACTIONABLE AS A VIOLATION OF OUR TRADE SECRET RIGHTS.
CS Limited Warranty
Limited Warranty. CS’s sole warranty with respect to the Software is that it shall be free of errors in program logic
or documentation, attributable to CS, which prevent the performance of the principal computing functions of the
Software. CS warrants this for a period of thirty (30) days from the date of receipt.
CS’s Liability. In no event shall CS be liable for any indirect, special, or consequential damages, such as, but not
limited to, loss of anticipated profits or other economic loss in connection with or arising out of the use of the software
by you or the services provided for in this agreement, even if CS has been advised of the possibility of such damages.
CS’s entire liability and your exclusive remedy shall be, at CS’s discretion, either (A) return of any license fee,
or (B) correction or replacement of software that does not meet the terms of this limited warranty and that is returned
to CS with a copy of your purchase receipt.
NO OTHER WARRANTIES. CS DISCLAIMS OTHER IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, AND IMPLIED WAR-
RANTIES ARISING BY USAGE OF TRADE, COURSE OF DEALING, OR COURSE OF PERFORMANCE. NOTWITH-

STANDING THE ABOVE, WHERE APPLICABLE, IF YOU QUALIFY AS A “CONSUMER” UNDER THE MAGNUSON-
MOSS WARRANTY ACT, THEN YOU MAY BE ENTITLED TO ANY IMPLIED WARRANTIES ALLOWED BY LAW FOR
THE PERIOD OF THE EXPRESS WARRANTY AS SET FORTH ABOVE. SOME STATES DO NOT ALLOW LIMITATIONS
ON IMPLIED WARRANTIES, SO THE ABOVE LIMITATION MIGHT NOT APPLY TO YOU. THIS WARRANTY GIVES
YOU SPECIFIC LEGAL RIGHTS, AND YOU MAY ALSO HAVE OTHER RIGHTS WHICH VARY FROM STATE TO STATE.
No Waiver. The failure of either party to assert a right hereunder or to insist upon compliance with any term or condition
of this Agreement shall not constitute a waiver of that right or excuse a similar subsequent failure to perform
any such term or condition by the other party.
Governing Law. This Agreement shall be construed according to the laws of the Commonwealth of Massachusetts.
Export. You agree that the Software will not be shipped, transferred, or exported into any country or used in any manner
prohibited by the United States Export Administration Act or any other export laws, restrictions, or regulations.
End-User License Agreement for CambridgeSoft Database Products
Important: This CambridgeSoft End-User License Agreement is a legal agreement between you (either an individual
or a single entity) and CambridgeSoft Corporation for the CambridgeSoft supplied database product(s) and may
include associated media, printed materials, and “online” or electronic documentation. By using the database product(s)
you agree that you have read, understood and will be bound by this license agreement.
Database Product License
1. Copyright Notice. The materials contained in CambridgeSoft Database Products, including but not limited to,
ChemACX, ChemIndex, and The Merck Index, are protected by copyright laws and international copyright treaties,
as well as other intellectual property laws and treaties. Copyright in the materials contained on the CD and internet
subscription products, including, but not limited to, the textual material, chemical structures representations,
artwork, photographs, computer software, audio and visual elements, is owned or controlled separately by
CambridgeSoft Corporation (“CS”).
CS is a distributor (and not a publisher) of information supplied by third parties. Accordingly, CS has no editorial
control over such information. Database Suppliers (“Supplier”) individually own all right, title, and interest, including
copyright, in their database—and retain all such rights in providing information to Customers.
The materials contained in The Merck Index are protected by copyright laws and international copyright treaties, as
well as other intellectual property laws and treaties. Copyright in the materials contained on the CD and internet
subscription products, including, but not limited to, the textual material, chemical structures representations, artwork,
photographs, computer software, audio and visual elements, is owned or controlled separately by the Merck &
Co., Inc., (“Merck”) and CambridgeSoft Corporation (“CS”).
2. Limitations on Use. Except as expressly provided by copyright law, copying, redistribution, or publication,
whether for commercial or non-commercial purposes, must be with the express permission of CS and/or Merck. In
any copying, redistribution, or publication of copyrighted material, any changes to or deletion of author attribution
or copyright notice, or any other proprietary notice of CS, Merck, or other Database producer are prohibited.
3. Grant of License, CD/DVD Databases. CambridgeSoft Software Products are licensed, not sold. CambridgeSoft
grants and you hereby accept a nonexclusive license to use one copy of the enclosed Software Product (“Software”)
in accordance with the terms of this Agreement. This licensed copy of the Software may only be used on a single

computer, except as provided below. You may physically transfer the Software from one computer to another for your
own use, provided the Software is in use (or installed) on only one computer at a time. If the Software is permanently
installed on your computer (other than a network server), you may also use the Software on a portable or home computer,
provided that you use the software on only one computer at a time. You may not (a) electronically transfer the
Software from one computer to another, (b) distribute copies of the Software to others, or (c) modify or translate the
Software without the prior written consent of CambridgeSoft, (d) place the software on a server so that it is accessible
via a public network such as the Internet, (e) sublicense, rent, lease or lend any portion of the Software or
Documentation, or (f ) modify or adapt the Software or merge it into another program. The Software may be placed
on a file or disk server connected to a network, provided that a license has been purchased for every computer with
access to that server. You may make only those copies of the Software which are necessary to install and use it as permitted
by this agreement, or are for purposes of backup and archival records; all copies shall bear CambridgeSoft’s
copyright and proprietary notices. You may not make copies of any accompanying written materials.
4. Assignment Restrictions for CD/DVD databases. You may not rent, lease, or otherwise sublet the Software or
any part thereof. You may transfer on a permanent basis the rights granted under this license provided you transfer
this Agreement and all copies of the Software, including prior versions, and all accompanying materials. The recipient
must agree to the terms of this Agreement in full and register this transfer in writing with CambridgeSoft.
5. Revocation of Subscription Access. Any use which is commercial and/or non-personal is strictly prohibited, and
may subject the Subscriber making such uses to revocation of access to this Paid Subscription Service, as well as any
other applicable civil or criminal penalties. Similarly, sharing a Subscriber password with a non-Subscriber or otherwise
making this Paid Subscription Service available to third parties other than the Authorized User as defined above
is strictly prohibited, and may subject the Subscriber participating in such activities to revocation of access to the Paid
Subscription Services; and, the Subscriber and any third party, to any other applicable civil or criminal penalties
under copyright or other laws. In the case of an authorized site license, a Subscriber shall cause any employee, agent
or other third party which the Subscriber allows to use the Paid Subscription Service materials to abide by all of the
terms and conditions of this Agreement. In all other cases, only the Subscriber is permitted to access the Paid
Subscription Service materials. Should CambridgeSoft become aware of any use that might cause revocation of the
license, they shall notify the Subscriber. The Subscriber shall have 90 days from date of notice to correct such violation
before any action will be taken.
6. Trademark Notice. THE MERCK INDEX ® is a trademark of Merck & Company Incorporated, Whitehouse
Station, New Jersey, USA and is registered in the United States Patent and Trademark Office. CambridgeSoft ® and
ChemACX are trademarks of CambridgeSoft Corporation, Cambridge,Massachusetts, USA and are registered in the
United States Patent and Trademark Office, the European Union (CTM) and Japan.
Any use of the marks in connection with the sale, offering for sale, distribution or advertising of any goods and services,
including any other website, or in connection with labels, signs, prints, packages, wrappers, receptacles or
advertisements used for the sale, offering for sale, distribution or advertising of any goods and services, including any
other website, which is likely to cause confusion, to cause mistake or to deceive, is strictly prohibited.
7. Modification of Databases, Websites, or Subscription Services. CS reserves the right to change, modify, suspend
or discontinue any or all parts of any Paid Subscription Services and databases at any time.
8. Representations and Warranties. The User shall indemnify, defend and hold CS, Merck, and/or other Supplier
harmless from any damages, expenses and costs (including reasonable attorneys’ fees) arising out of any breach or
alleged breach of these Terms and Conditions, representations and/or warranties herein, by the User or any third
party to whom User shares her/his password or otherwise makes available this Subscription Service. The User shall
cooperate in the defense of any claim brought against CambridgeSoft, Merck, and/or other Database Suppliers.

In no event shall CS, Merck, and/or other Supplier be liable for any indirect, special, or consequential damages, such
as, but not limited to, loss of anticipated profits or other economic loss in connection with or arising out of the use
of the software by you or the services provided for in this agreement, even if CS, Merck, and/or other Supplier has
been advised of the possibility of such damages. CS and/or Merck’s entire liability and your exclusive remedy shall
be, at CS’s discretion a return of any pro-rata portion of the subscription fee.
The failure of either party to assert a right hereunder or to insist upon compliance with any term or condition of this
Agreement shall not constitute a waiver of that right or excuse a similar subsequent failure to perform any such term
or condition by the other party.
This Agreement shall be construed according to the laws of the Commonwealth of Massachusetts, United States of
America.

Q: IS IT OK TO COPY MY COLLEAGUE’S
SOFTWARE
NO, it’s not okay to copy your colleague’s
software. Software is protected by federal copyright law,
which says that you can't make such additional copies
without the permission of the copyright holder. By
protecting the investment of computer software
companies in software development, the copyright law
serves the cause of promoting broad public availability of
new, creative, and innovative products. These companies
devote large portions of their earnings to the creation of
new software products and they deserve a fair return on
their investment. The creative teams who develop the
software–programmers, writers, graphic artists and
others–also deserve fair compensation for their efforts.
Without the protection given by our copyright laws, they
would be unable to produce the valuable programs that
have become so important to our daily lives: educational
software that teaches us much needed skills; business
software that allows us to save time, effort and money;
and entertainment and personal productivity software
that enhances leisure time.
Q: That makes sense, but what do I get out of
purchasing my own software
A: When you purchase authorized copies of software
programs, you receive user guides and tutorials, quick
reference cards, the opportunity to purchase
upgrades, and technical support from the software
publishers. For most software programs, you can read
about user benefits in the registration brochure or
upgrade flyer in the product box.
Q: What exactly does the law say about copying
software
A: The law says that anyone who purchases a copy of
software has the right to load that copy onto a single
computer and to make another copy “for archival
purposes only” or, in limited circumstances, for
“purposes only of maintenance or repair.” It is illegal
to use that software on more than one computer or to
make or distribute copies of that software for any
other purpose unless specific permission has been
obtained from the copyright owner. If you pirate
software, you may face not only a civil suit for
damages and other relief, but criminal liability as well,
including fines and jail terms of up to one year
Q: So I'm never allowed to copy software for any other
reason
A: That’s correct. Other than copying the software you
purchase onto a single computer and making another
copy “for archival purposes only” or “purposes only of
maintenance or repair,” the copyright law prohibits
you from making additional copies of the software for
any other reason unless you obtain the permission of
the software company.
Q: At my company, we pass disks around all the time.
We all assume that this must be okay since it was
the company that purchased the software in the
first place.
A: Many employees don’t realize that corporations are
bound by the copyright laws, just like everyone else.
Such conduct exposes the company (and possibly the
persons involved) to liability for copyright
infringement. Consequently, more and more
corporations concerned about their liability have
written policies against such “softlifting”. Employees
may face disciplinary action if they make extra copies
of the company’s software for use at home or on
additional computers within the office. A good rule to
remember is that there must be one authorized copy
of a software product for every computer upon which
it is run
Q: Can I take a piece of software owned by my
company and install it on my personal computer at
home if instructed by my supervisor
A: A good rule of thumb to follow is one software
package per computer, unless the terms of the license
agreement allow for multiple use of the program. But
some software publishers’ licenses allow for “remote”
or “home” use of their software. If you travel or
telecommute, you may be permitted to copy your
software onto a second machine for use when you are
not at your office computer. Check the license carefully
to see if you are allowed to do this.
Q: What should I do if become aware of a company
that is not compliant with the copyright law or its
software licenses
A: Cases of retail, corporate and Internet piracy or noncompliance
with software licenses can be reported on
the Internet at http://www.siia.net/piracy/report.asp
or by calling the Anti-Piracy Hotline:
(800) 388-7478.

Q: Do the same rules apply to bulletin boards and user
groups I always thought that the reason they got
together was to share software.
A: Yes. Bulletin boards and user groups are bound by the
copyright law just as individuals and corporations.
However, to the extent they offer shareware or public
domain software, this is a perfectly acceptable
practice. Similarly, some software companies offer
bulletin boards and user groups special demonstration
versions of their products, which in some instances
may be copied. In any event, it is the responsibility of
the bulletin board operator or user group to respect
copyright law and to ensure that it is not used as a
vehicle for unauthorized copying or distribution.
Q: I'll bet most of the people who copy software don't
even know that they're breaking the law.
A: Because the software industry is relatively new, and
because copying software is so easy, many people are
either unaware of the laws governing software use or
choose to ignore them. It is the responsibility of each
and every software user to understand and adhere to
copyright law. Ignorance of the law is no excuse. If
you are part of an organization, see what you an do to
initiate a policy statement that everyone respects.
Also, suggest that your management consider
conducting a software audit. Finally, as an individual,
help spread the word that users should be “software
legal.”
Q: What are the penalties for copyright infringement
SIIA also offers a number of other materials designed to
help you comply with the Federal Copyright Law. These
materials include:
"It's Just Not Worth the Risk" video.
This 12–minute video, available $10, has helped over
20,000 organizations dramatize to their employees the
implications and consequences of software piracy.
“Don’t Copy that Floppy” video
This 9 minute rap video, available for $10, is designed
to educate students on the ethical use of software.
Other education materials including, “Software Use
and the Law”, a brochure detailing the copyright law
and how software should be used by educational
institutions, corporations and individuals; and several
posters to help emphasize the message that unauthorized
copying of software is illegal.
To order any of these materials, please send your request to:
“SIIA Anti-Piracy Materials”
Software & Information Industry Association
1090 Vermont Ave, Sixth Floor,
Washington, D.C. 20005
(202) 289-7442
We urge you to make as many copies as you would like
in order to help us spread the word that unauthorized
copying of software is illegal.
A: The Copyright Act allows a copyright owner to
recover monetary damages measured either by: (1) its
actual damages plus any additional profits of the
infringer attributable to the infringement, or (2)
statutory damages, of up to $150,000 for each copyrighted
work infringed. The copyright owner also has
the right to permanently enjoin an infringer from
engaging in further infringing activities and may be
awarded costs and attorneys’ fees. The law also
permits destruction or other reasonable disposition of
all infringing copies and devices by which infringing
copies have been made or used in violation of the
copyright owner’s exclusive rights. In cases of willful
infringement, criminal penalties may also be assessed
against the infringer.

A Guide to CambridgeSoft Manuals
And Databases
ChemDraw
Chemical Structure
Drawing Standard
ChemOffice
Chem3D, ChemFinder
ChemOffice
Enterprise Solutions
Manuals
& E-Notebook
Includes
ChemDraw
Chem3D
Databases Desktop Applications Software
Tips Enterprise Solutions
ChemFinder
E-Notebook Desktop
Inventory Desktop
BioAssay Desktop
ChemDraw/Excel
ChemFinder/Office
CombiChem/Excel
ChemSAR/Excel
MOPAC, MM2
CS Gaussian, GAMESS Interface
ChemOffice WebServer
Oracle Cartridge
E-Notebook Workgroup, Enterprise
Document Manager
Registration Enterprise
Formulations & Mixtures
Inventory Workgroup, Enterprise
Discovery LIMS
BioAssay Workgroup, Enterprise
BioSAR Enterprise
ChemDraw/Spotfire
The Merck Index
ChemACX, ChemSCX
ChemMSDX
ChemINDEX, NCI & AIDS
ChemRXN
Ashgate Drugs
Structure Drawing Tips
Searching Tips
Importing SD Files

Contents
ChemOffice Enterprise Workgroup &
Databases . . . . . . . . . . . . . . . . . . . . . . . . . ix
About the Manual . . . . . . . . . . . . . . . . . . . . . . . . . .ix
Manual Organization . . . . . . . . . . . . . . . . . . . . . . .ix
Helpful CambridgeSoft Links . . . . . . . . . . . . . . . .ix
Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix
Section I: Knowledge Management . . . 1
Chapter 1: Document Manager . . . . . . . . . .3
Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Logging In . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Submitting Documents . . . . . . . . . . . . . . . . . . . . . . 4
Add Document Details. . . . . . . . . . . . . . . . . . . . . 4
Batch Submission . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Recent Activities . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Searching for Documents . . . . . . . . . . . . . . . . . . . . 5
Performing a Search . . . . . . . . . . . . . . . . . . . . . . . 6
Manage Users and Roles . . . . . . . . . . . . . . . . . . . . 6
Section II: Chemical Informatics . . . . .7
Chapter 2: Registration System . . . . . . . . . .9
Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Registration System Workflow . . . . . . . . . . . . . . . 9
Chemical Registry Number Assignment . . . . . . . 9
Starting Registration System . . . . . . . . . . . . . . . . . 9
Add to Temporary . . . . . . . . . . . . . . . . . . . . . . . . . 10
Adding a Compound. . . . . . . . . . . . . . . . . . . . . . 10
Adding a Batch/Lot . . . . . . . . . . . . . . . . . . . . . . 11
Registration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Searching and Viewing Records in the Temporary Table.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Registering Records in the Temporary Table . . . 13
Editing Records in the Temporary Table . . . . . 13
Deleting Records in the Temporary Table . . . . 13
Registering a Record . . . . . . . . . . . . . . . . . . . . . . 13
Adding Identifier Information to Records. . . . . 14
Adding Analytics Data to a Record . . . . . . . . . . 15
Query and Reporting. . . . . . . . . . . . . . . . . . . . . . . 16
Searching for Registered Compounds . . . . . . . . 16
Analytics Spreadsheets . . . . . . . . . . . . . . . . . . . . 16
Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Managing Tables. . . . . . . . . . . . . . . . . . . . . . . . . .17
Defining Projects . . . . . . . . . . . . . . . . . . . . . . . .17
Defining Sequences . . . . . . . . . . . . . . . . . . . . . .18
Defining Structure Comments . . . . . . . . . . . . . .19
Defining Registration System People . . . . . . . . .20
Defining Salts . . . . . . . . . . . . . . . . . . . . . . . . . .21
Defining Solvates . . . . . . . . . . . . . . . . . . . . . . . .22
Managing Users and Roles. . . . . . . . . . . . . . . . . .23
Defining New Experiments. . . . . . . . . . . . . . . . .23
Managing Analytics Data . . . . . . . . . . . . . . . . . . .23
Defining Result Type . . . . . . . . . . . . . . . . . . . . .24
Defining Experiment Type . . . . . . . . . . . . . . . .24
Defining Parameter Type . . . . . . . . . . . . . . . . . .25
Managing Workgroups. . . . . . . . . . . . . . . . . . . . .25
Importing SDFiles . . . . . . . . . . . . . . . . . . . . . . . . .25
Steps to Import a SDFile . . . . . . . . . . . . . . . . . . .26
Choosing Input and Output Databases. . . . . . . .26
Matching Fields in the Input and Output Databases. . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27
View Matches and Import . . . . . . . . . . . . . . . . . .27
Optional Features . . . . . . . . . . . . . . . . . . . . . . . . . .29
Row Level Security (RLS) . . . . . . . . . . . . . . . . . .29
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .29
The User Interface . . . . . . . . . . . . . . . . . . . . . . .29
How are Projects linked to People . . . . . . . . . . .29
The Unspecified Project . . . . . . . . . . . . . . . . . .29
Duplicate Checking . . . . . . . . . . . . . . . . . . . . . .29
Activating RLS . . . . . . . . . . . . . . . . . . . . . . . . .30
Salt and Solvate Recognition . . . . . . . . . . . . . . . .30
Customizable Fields . . . . . . . . . . . . . . . . . . . . . . .30
Choosing Preferences. . . . . . . . . . . . . . . . . . . . . . .30
Printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .30
Logging Off. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .31
Chapter 3: Formulations & Mixtures . . . . 33
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Registration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Adding a Structure . . . . . . . . . . . . . . . . . . . . . . . .33
Adding a Product/Substance. . . . . . . . . . . . . . . .34
Adding a Sample . . . . . . . . . . . . . . . . . . . . . . . . .34
Adding Analytics Data . . . . . . . . . . . . . . . . . . . . .34
Query and Reporting . . . . . . . . . . . . . . . . . . . . . . .35
Viewing Details of a Record . . . . . . . . . . . . . . . .35
Marking Records . . . . . . . . . . . . . . . . . . . . . . . . .36
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Viewing Marked Records . . . . . . . . . . . . . . . . . .36
Clearing Marked Records . . . . . . . . . . . . . . . . . .36
Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . .36
Managing Tables. . . . . . . . . . . . . . . . . . . . . . . . . .36
Defining Projects . . . . . . . . . . . . . . . . . . . . . . . .36
Defining Prefix/Sequence . . . . . . . . . . . . . . . . .37
Defining Labs . . . . . . . . . . . . . . . . . . . . . . . . . .37
Defining Safety Phrases . . . . . . . . . . . . . . . . . . .38
Defining Risk Phrases . . . . . . . . . . . . . . . . . . . .38
Defining Conditions . . . . . . . . . . . . . . . . . . . . .38
Defining Units . . . . . . . . . . . . . . . . . . . . . . . . . .39
Defining Business Units . . . . . . . . . . . . . . . . . .39
Defining Status . . . . . . . . . . . . . . . . . . . . . . . . .39
Defining Shelf Life . . . . . . . . . . . . . . . . . . . . . .40
Defining Physical State . . . . . . . . . . . . . . . . . . .40
Managing Users & Roles . . . . . . . . . . . . . . . . . . .40
Defining People . . . . . . . . . . . . . . . . . . . . . . . . .40
Changing Passwords. . . . . . . . . . . . . . . . . . . . . . .41
Managing Analytics Data . . . . . . . . . . . . . . . . . . .41
Defining Experiment Types . . . . . . . . . . . . . . . .41
Defining Parameter Types . . . . . . . . . . . . . . . . .42
Defining Result Types . . . . . . . . . . . . . . . . . . . .42
Chapter 4: Inventory . . . . . . . . . . . . . . . . . 45
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .45
Terminology . . . . . . . . . . . . . . . . . . . . . . . . . . . . .45
Location . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .46
Substance . . . . . . . . . . . . . . . . . . . . . . . . . . . . .46
Container . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .46
Logging in. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .46
The User Interface . . . . . . . . . . . . . . . . . . . . . . . . .47
Forms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .48
Locations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .48
Containers . . . . . . . . . . . . . . . . . . . . . . . . . . . . .49
Substances . . . . . . . . . . . . . . . . . . . . . . . . . . . . .49
Managing an Inventory . . . . . . . . . . . . . . . . . . . . .50
Managing Locations . . . . . . . . . . . . . . . . . . . . . . .50
Location Tree . . . . . . . . . . . . . . . . . . . . . . . . . .51
Creating a New Location . . . . . . . . . . . . . . . . . .51
Editing a Location . . . . . . . . . . . . . . . . . . . . . . .51
Moving a Location . . . . . . . . . . . . . . . . . . . . . . .52
Deleting a Location . . . . . . . . . . . . . . . . . . . . . .52
Saving a Default Location . . . . . . . . . . . . . . . . .53
Refreshing the Location Tree . . . . . . . . . . . . . . .53
Managing Substances . . . . . . . . . . . . . . . . . . . . . .53
Creating a New Substance . . . . . . . . . . . . . . . . .53
Mixtures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .54
Conflict Resolution . . . . . . . . . . . . . . . . . . . . . .54
Editing a Substance . . . . . . . . . . . . . . . . . . . . . .56
Deleting a Substance . . . . . . . . . . . . . . . . . . . . .57
Synonym Management . . . . . . . . . . . . . . . . . . . 57
Managing Containers. . . . . . . . . . . . . . . . . . . . . . 58
Creating a New Container . . . . . . . . . . . . . . . . . 58
Editing a Container . . . . . . . . . . . . . . . . . . . . . . 59
Moving a Container . . . . . . . . . . . . . . . . . . . . . 59
Order Container . . . . . . . . . . . . . . . . . . . . . . . . 61
Update Contents . . . . . . . . . . . . . . . . . . . . . . . . 62
Rectify Contents . . . . . . . . . . . . . . . . . . . . . . . . 63
Multi Select . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Managing Plates. . . . . . . . . . . . . . . . . . . . . . . . . . 64
Creating New Plates . . . . . . . . . . . . . . . . . . . . . 64
Searching for Plates . . . . . . . . . . . . . . . . . . . . . 65
Viewing the Contents of a Plate . . . . . . . . . . . . 65
Creating Daughter Plates . . . . . . . . . . . . . . . . . 66
Create Plate Map . . . . . . . . . . . . . . . . . . . . . . . 67
Create a Plate Map Location . . . . . . . . . . . . . . . 67
Edit Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Move Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Retire Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Delete Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Searching Inventory. . . . . . . . . . . . . . . . . . . . . . . . 68
Searching for Containers. . . . . . . . . . . . . . . . . . . 69
Simple Search . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Advanced Search . . . . . . . . . . . . . . . . . . . . . . . 70
Substructure Search . . . . . . . . . . . . . . . . . . . . . 70
Searching for Substances. . . . . . . . . . . . . . . . . . . 72
Searching for Plates. . . . . . . . . . . . . . . . . . . . . . . 73
Global Search . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Viewing Results from a Global Search . . . . . . . 74
Global Search - Registration System Substances 75
Printing Labels and Reports . . . . . . . . . . . . . . . . 76
Labels. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Inventory Tasks . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Managing Users and Roles . . . . . . . . . . . . . . . . . 78
Managing Tables . . . . . . . . . . . . . . . . . . . . . . . . . 79
Custom Fields . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Record Locking . . . . . . . . . . . . . . . . . . . . . . . . 81
Managing the Container list display . . . . . . . . . . 81
Analyze Audit Trail . . . . . . . . . . . . . . . . . . . . . . . 82
Standard Audit Report . . . . . . . . . . . . . . . . . . . 82
Aggregate Audit Report . . . . . . . . . . . . . . . . . . 82
Chapter 5: Discovery LIMS . . . . . . . . . . . . 85
Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Searching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Browsing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Expand All. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
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Contract All . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Test Details . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Material On/Off . . . . . . . . . . . . . . . . . . . . . . . . . 86
New Request . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
New Action . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Search. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Home. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Working with Requests and Actions . . . . . . . . . . 88
Creating a New Request . . . . . . . . . . . . . . . . . . . 89
Creating a Request Short-cut . . . . . . . . . . . . . . . 89
Creating a New Action . . . . . . . . . . . . . . . . . . . . 89
Adding and Modifying Results . . . . . . . . . . . . . . 90
Viewing Request Details . . . . . . . . . . . . . . . . . . . 91
Deleting Requests . . . . . . . . . . . . . . . . . . . . . . . . 91
Administration and Configuration . . . . . . . . . . . . 91
Actions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Labs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Test Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Test Attributes. . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Users and Security Level Definitions . . . . . . . . . 95
Setting Up Email Features . . . . . . . . . . . . . . . . . . 96
Section III: Biological Informatics . . . 97
Chapter 6: BioAssay . . . . . . . . . . . . . . . . . .99
Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Versions of BioAssay . . . . . . . . . . . . . . . . . . . . . 99
Logging in to BioAssay . . . . . . . . . . . . . . . . . . . . . 99
Terminology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Navigation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Resizing and Moving Columns . . . . . . . . . . . . . 101
Sorting Data . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
Filtering Data. . . . . . . . . . . . . . . . . . . . . . . . . . . 102
Tips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Refreshing the Data View . . . . . . . . . . . . . . . . . 103
Printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Exporting Data to Excel. . . . . . . . . . . . . . . . . . 103
Getting Help . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Protocols. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Viewing Protocols in the Navigator . . . . . . . . . 104
Moving a Protocol or Project . . . . . . . . . . . . . 104
Duplicating a Protocol . . . . . . . . . . . . . . . . . . 104
Viewing a Protocol’s Properties (Renaming) . . 104
Protocol Data and Definitions . . . . . . . . . . . . . 105
Tasks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .105
Protocol Data . . . . . . . . . . . . . . . . . . . . . . . . .107
Protocol Definitions . . . . . . . . . . . . . . . . . . . .109
Designing a New Protocol. . . . . . . . . . . . . . . . .111
Defining Tables and Fields . . . . . . . . . . . . . . .113
Assigning a Calculation to a Field . . . . . . . . . .116
Summary Tables . . . . . . . . . . . . . . . . . . . . . . .124
Defining Security . . . . . . . . . . . . . . . . . . . . . .124
Importing and Viewing Data. . . . . . . . . . . . . . .125
File Import Templates . . . . . . . . . . . . . . . . . . .125
Importing Data . . . . . . . . . . . . . . . . . . . . . . . .128
Searching for and Viewing Data in Tables . . . .129
Validating Protocol Data . . . . . . . . . . . . . . . . .129
Data Manipulation and Curve Fitting . . . . . . . .129
Plotting Data using a Graph Template . . . . . . .130
Fitting Data to a Curve . . . . . . . . . . . . . . . . . .130
Curve Fit Templates . . . . . . . . . . . . . . . . . . . .131
Viewing the Plotted Data . . . . . . . . . . . . . . . . .131
Invalidating Data Points . . . . . . . . . . . . . . . . .132
Graphing Options . . . . . . . . . . . . . . . . . . . . . .132
Compound Lists . . . . . . . . . . . . . . . . . . . . . . . . . .134
Manipulating Compound Lists . . . . . . . . . . . . .134
Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .134
Editing the settings tables . . . . . . . . . . . . . . . . .135
Adding an entry . . . . . . . . . . . . . . . . . . . . . . . .135
Deleting an entry . . . . . . . . . . . . . . . . . . . . . . .135
Canceling/Discarding Changes . . . . . . . . . . . .135
Plate Formats . . . . . . . . . . . . . . . . . . . . . . . . . . .135
Defining a Plate Format . . . . . . . . . . . . . . . . .135
Defining Attributes of the Plate . . . . . . . . . . . .135
Well Formats . . . . . . . . . . . . . . . . . . . . . . . . . . .136
Protocol Picklist . . . . . . . . . . . . . . . . . . . . . . . . .136
Adding a Picklist to the Picklist Table . . . . . . .136
Adding Picklist Options . . . . . . . . . . . . . . . . . .137
Using a Picklist . . . . . . . . . . . . . . . . . . . . . . . .137
Administration . . . . . . . . . . . . . . . . . . . . . . . . . . .137
Publishing Tables in BioSAR Enterprise. . . . . .137
Security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .137
Managing Users . . . . . . . . . . . . . . . . . . . . . . . . .137
Managing Groups. . . . . . . . . . . . . . . . . . . . . . . .138
Creating New Groups . . . . . . . . . . . . . . . . . . .139
Adding a User to a Group . . . . . . . . . . . . . . . .139
Chapter 7: BioSAR Enterprise . . . . . . . . 141
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .141
Terminology . . . . . . . . . . . . . . . . . . . . . . . . . . . . .141
Schema . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .141
Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .141
View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .141
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Formgroup . . . . . . . . . . . . . . . . . . . . . . . . . . . . .141
Login to BioSAR Enterprise . . . . . . . . . . . . . . . .142
Schema Management. . . . . . . . . . . . . . . . . . . . . .142
Refreshing Tables . . . . . . . . . . . . . . . . . . . . . . . .142
Add/Remove Schemas. . . . . . . . . . . . . . . . . . . .143
Add a Schema . . . . . . . . . . . . . . . . . . . . . . . . .143
Remove a Schema . . . . . . . . . . . . . . . . . . . . . .143
Edit Schema Description/Password . . . . . . . . .144
Schema Display Name . . . . . . . . . . . . . . . . . . .144
Schema Password . . . . . . . . . . . . . . . . . . . . . .144
Edit Exposed Tables . . . . . . . . . . . . . . . . . . . . .144
Edit Table Fields . . . . . . . . . . . . . . . . . . . . . . . .145
Edit a Table's Primary Key . . . . . . . . . . . . . . .145
Edit a Table's Default Column Order . . . . . . .146
Edit Table Display Name . . . . . . . . . . . . . . . .146
Table Fields . . . . . . . . . . . . . . . . . . . . . . . . . . .146
Manage Your Forms. . . . . . . . . . . . . . . . . . . . . . .148
Create a New Form . . . . . . . . . . . . . . . . . . . . . .149
Selecting a Base Table . . . . . . . . . . . . . . . . . . .149
Selecting Child Tables . . . . . . . . . . . . . . . . . . .152
Form Roles and Users . . . . . . . . . . . . . . . . . . .152
Editing a Form . . . . . . . . . . . . . . . . . . . . . . . . . .152
Renaming a Form . . . . . . . . . . . . . . . . . . . . . .153
Duplicating a Form . . . . . . . . . . . . . . . . . . . . . .153
Delete an Existing Form . . . . . . . . . . . . . . . . . .153
Opening a Form/Searching Using a Form . . . .154
Searching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .155
Search Using a Saved Query . . . . . . . . . . . . . . .155
Searching Using the History . . . . . . . . . . . . . . .155
Viewing Search Results . . . . . . . . . . . . . . . . . . .156
Sorting Results . . . . . . . . . . . . . . . . . . . . . . . . .156
Dynamically Editing a Form . . . . . . . . . . . . . .156
List View Options . . . . . . . . . . . . . . . . . . . . . .156
Details View Options . . . . . . . . . . . . . . . . . . .157
Generating Reports . . . . . . . . . . . . . . . . . . . . . .157
Create a New Profile . . . . . . . . . . . . . . . . . . . .159
Edit a Profile . . . . . . . . . . . . . . . . . . . . . . . . . .161
View a Profile . . . . . . . . . . . . . . . . . . . . . . . . .162
Delete a Profile . . . . . . . . . . . . . . . . . . . . . . . .162
Ordering Fields and Changing Label Sizes in Reports. . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .163
Manage Users and Roles . . . . . . . . . . . . . . . . . . .163
Section IV: ChemOffice WebServer . 165
ChemOffice WebServer . . . . . . . . . . . . . . . . . . . .165
CS Oracle Cartridge . . . . . . . . . . . . . . . . . . . . . . .165
Chapter 8: ChemOffice WebServer . . . . . 167
Installation and Administration . . . . . . . . . . . . 167
Global Login and Security. . . . . . . . . . . . . . . . . . 167
Logging In . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
Manage Users and Roles . . . . . . . . . . . . . . . . . . 167
Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
Roles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
Searching ChemOffice WebServer Applications 168
Accessing a ChemOffice WebServer Application. . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
The Query Input Form User Interface . . . . . . 169
The Navigation Toolbar . . . . . . . . . . . . . . . . . 169
Search Input Form . . . . . . . . . . . . . . . . . . . . . 171
Performing a Simple Search . . . . . . . . . . . . . . . 172
Searching by Different Query Methods . . . . . . 173
Searching With Text . . . . . . . . . . . . . . . . . . . . 173
Searching With Structures . . . . . . . . . . . . . . . . 173
Searching With Molecular Formulas . . . . . . . . 174
Searching With Numerical Ranges . . . . . . . . . 175
Combination Searching . . . . . . . . . . . . . . . . . . 175
Search Results . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
Viewing Search Results . . . . . . . . . . . . . . . . . . . 176
Viewing Results in List View . . . . . . . . . . . . . 176
Viewing Results in Form View . . . . . . . . . . . . 176
Browsing Other Records . . . . . . . . . . . . . . . . 177
Viewing All Records . . . . . . . . . . . . . . . . . . . . 177
Marking and Unmarking Records . . . . . . . . . . 178
Manipulating Queries . . . . . . . . . . . . . . . . . . . . 178
Restoring Queries . . . . . . . . . . . . . . . . . . . . . . 178
Saving Queries . . . . . . . . . . . . . . . . . . . . . . . . 179
Managing Queries . . . . . . . . . . . . . . . . . . . . . . 180
Manipulating Hit Lists. . . . . . . . . . . . . . . . . . . . 181
Restoring Hit Lists . . . . . . . . . . . . . . . . . . . . . 181
Saving Hit Lists . . . . . . . . . . . . . . . . . . . . . . . 181
Managing HIt Lists . . . . . . . . . . . . . . . . . . . . . 181
Refining Search Results . . . . . . . . . . . . . . . . . . . 182
Refining Over Current Records Found . . . . . . 183
Undoing a Refined Search . . . . . . . . . . . . . . . 183
Exporting Search Results . . . . . . . . . . . . . . . . . 183
Histories. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
Setting Your Display and Search Preferences . . 184
Server Information. . . . . . . . . . . . . . . . . . . . . . . . 185
Logging Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
Chapter 9: CS Oracle Cartridge . . . . . . . 187
Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
Minimum Requirements . . . . . . . . . . . . . . . . . . 187
Supported Platforms. . . . . . . . . . . . . . . . . . . . . 187
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Before installation . . . . . . . . . . . . . . . . . . . . . . . 187
Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
Un-installation . . . . . . . . . . . . . . . . . . . . . . . . . . 188
Re-installation . . . . . . . . . . . . . . . . . . . . . . . . . . 188
Security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
DDL Considerations . . . . . . . . . . . . . . . . . . . . . . 188
Fast Substructure Search. . . . . . . . . . . . . . . . . . 189
Example. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
DML Considerations. . . . . . . . . . . . . . . . . . . . . . 190
Fast Substructure Search. . . . . . . . . . . . . . . . . . 190
Simple Example. . . . . . . . . . . . . . . . . . . . . . . . . 191
Querying large structures . . . . . . . . . . . . . . . . . 191
Safe querying of large structures . . . . . . . . . . . 192
Formula query . . . . . . . . . . . . . . . . . . . . . . . . . . 192
MolWeight query. . . . . . . . . . . . . . . . . . . . . . . . 193
Migration Recommendations. . . . . . . . . . . . . . . 193
Support functions . . . . . . . . . . . . . . . . . . . . . . . . 193
Using data maintained by the cartridge . . . . . . 194
Error Handling . . . . . . . . . . . . . . . . . . . . . . . . . . 196
Performance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . 197
Checking the presence of the cartridge . . . . . . 197
Checking the version of the cartridge. . . . . . . . 197
Checking for fields indexed by the cartridge . . 198
What to do if creating an index fails . . . . . . . . . 198
Setup problems . . . . . . . . . . . . . . . . . . . . . . . . . . 199
ORA-28575 unable to open RPC connection to external
procedure agent . . . . . . . . . . . . . . . . . . . . . . . . 199
listener.ora . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
tsnames.ora . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
ORA-06520 PL/SQL: Error loading external library. . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
Dependencies . . . . . . . . . . . . . . . . . . . . . . . . . 200
Using ADO. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
Example of passing large queries . . . . . . . . . . . 201
Custom Screening . . . . . . . . . . . . . . . . . . . . . . . . 202
Navigation in client programs . . . . . . . . . . . . . . 203
Explanation . . . . . . . . . . . . . . . . . . . . . . . . . . 204
Bulk loading. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
and the result: . . . . . . . . . . . . . . . . . . . . . . . . . 205
Section V: Scientific Databases . . . . 207
Subscriptions and ChemOffice Webserver Based
Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
CD Based Databases . . . . . . . . . . . . . . . . . . . . . . 207
Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . .208
Using Scientific Databases . . . . . . . . . . . . . . . . .208
ChemFinder Tips . . . . . . . . . . . . . . . . . . . . . . .208
Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .208
Online Help . . . . . . . . . . . . . . . . . . . . . . . . . . .208
ToolTips . . . . . . . . . . . . . . . . . . . . . . . . . . . . .208
Status Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . .208
Chapter 10: The Merck Index . . . . . . . . . 209
What Is It. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .209
How Is It Useful . . . . . . . . . . . . . . . . . . . . . . . . .209
Using the Merck Index CD . . . . . . . . . . . . . . . . .209
Using The Merck Index Online . . . . . . . . . . . . .210
Compound Searching. . . . . . . . . . . . . . . . . . . . .210
Organic Name Reactions . . . . . . . . . . . . . . . . . .211
Additional Tables . . . . . . . . . . . . . . . . . . . . . . . .212
Logging Off . . . . . . . . . . . . . . . . . . . . . . . . . . . .212
Chapter 11: Ashgate Drugs . . . . . . . . . . . 213
What Is It. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .213
Ashgate Databases . . . . . . . . . . . . . . . . . . . . . . . .213
Using Ashgate Drugs on CD. . . . . . . . . . . . . . . .213
Using Ashgate Drugs Online. . . . . . . . . . . . . . . .214
Compound Searching. . . . . . . . . . . . . . . . . . . . .214
Browse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .215
Chapter 12: ChemACX . . . . . . . . . . . . . . . 217
What Is It. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .217
ChemACX Database. . . . . . . . . . . . . . . . . . . . . . .217
How Is It Useful . . . . . . . . . . . . . . . . . . . . . . . . .217
Using ChemACX with ChemOffice WebServer .217
Opening ChemACX. . . . . . . . . . . . . . . . . . . . . .218
Searching ChemACX Catalogs . . . . . . . . . . . . .218
Searching Without the Plug-in . . . . . . . . . . . . .218
Creating and Editing A List of Favorite Vendors . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .219
Viewing Search Results . . . . . . . . . . . . . . . . . . .219
Viewing Search Results in List View . . . . . . . .220
Viewing Search Results in Details View . . . . . .221
Accessing MSDX Data . . . . . . . . . . . . . . . . . .222
Using the Shopping Cart . . . . . . . . . . . . . . . . . .223
Viewing Your Shopping Cart . . . . . . . . . . . . . .223
Removing Items from Your Shopping Cart . . .223
Ordering The Chemicals in the ChemACX Shopping
Cart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .223
Registering and Creating Inventory Containers 224
Registering Products in Registration System . .224
Creating Inventory Containers in Inventory for Products.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .225
Saving Hitlists and Exporting SD Files. . . . . . .226
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Logging Off . . . . . . . . . . . . . . . . . . . . . . . . . . . .226
Searching ChemACX Ultra on CD . . . . . . . . . . .226
What If My Favorite Supplier Isn’t Listed Here227
Chapter 13: ChemSCX . . . . . . . . . . . . . . . 229
What Is It. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .229
ChemACX Screening Compound Databases . . .229
How Is It Useful . . . . . . . . . . . . . . . . . . . . . . . . .229
Using ChemSCX on CD. . . . . . . . . . . . . . . . . . . .230
Chapter 14: ChemMSDX . . . . . . . . . . . . . 233
What Is It. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .233
How is it Useful. . . . . . . . . . . . . . . . . . . . . . . . . .233
Using ChemMSDX from ChemACX . . . . . . . . .233
Chapter 15: ChemINDEX . . . . . . . . . . . . 235
What Is It. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .235
How Is It Useful . . . . . . . . . . . . . . . . . . . . . . . . .235
Using ChemINDEX on CD. . . . . . . . . . . . . . . . .235
BuckyBase. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .236
Using ChemINDEX Online . . . . . . . . . . . . . . . .236
Chapter 16: ChemRXN . . . . . . . . . . . . . . 237
What Is It. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .237
How Is It Useful . . . . . . . . . . . . . . . . . . . . . . . . .237
ChemPrep . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .237
ChemSelect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .238
Selection Criteria . . . . . . . . . . . . . . . . . . . . . . . .239
Chapter 17: NCI . . . . . . . . . . . . . . . . . . . . 241
What Is It. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .241
Using NCI on CD. . . . . . . . . . . . . . . . . . . . . . . . .241
Using the NCI Forms . . . . . . . . . . . . . . . . . . . .241
Chapter 18: AIDS . . . . . . . . . . . . . . . . . . . 243
What Is It. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .243
Using AIDS on CD . . . . . . . . . . . . . . . . . . . . . . . .243
Using AIDS Online . . . . . . . . . . . . . . . . . . . . . .243
Section VI: Appendices . . . . . . . . . . . 245
Appendix A: . . Inventory Functions in Container
Details Frame . . . . . . . . . . . . . . . 247
Appendix B: Document Manager Free Text
Searching . . . . . . . . . . . . . . . . . . . . . . . . 249
Understanding Basic Text Searching . . . . . . . . .249
Exact Phrase Matching. . . . . . . . . . . . . . . . . . . .249
Wildcard Searching. . . . . . . . . . . . . . . . . . . . . . .249
Understanding Advanced Text Searching . . . . .250
ABOUT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .250
AND (&) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .251
EQUIValence (=). . . . . . . . . . . . . . . . . . . . . . . .251
Fuzzy (). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252
MINUS (-) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252
NEAR (;) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
NOT (~) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
OR (|) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
Soundex (!). . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
Stem ($) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
Appendix C: BioAssay Actions Menu Commands
. . . . . . . . . . . . . . . . . . . . . . . . . . 257
Viewing Commands . . . . . . . . . . . . . . . . . . . . . . 257
View Details . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
View Picklist . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
View Plate Format. . . . . . . . . . . . . . . . . . . . . . . 257
View (from the plates grid) . . . . . . . . . . . . . . . . 257
View (from the plate formats grid). . . . . . . . . . 257
Other Commands . . . . . . . . . . . . . . . . . . . . . . . . 257
Autofit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
AutoFit On . . . . . . . . . . . . . . . . . . . . . . . . . . . 258
AutoFit Off . . . . . . . . . . . . . . . . . . . . . . . . . . 258
Change Validity . . . . . . . . . . . . . . . . . . . . . . . . . 258
Coloring Options . . . . . . . . . . . . . . . . . . . . . . . 258
Copy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
Cut . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
Import Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
Paste. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
Recalculate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
Save Compound LIst . . . . . . . . . . . . . . . . . . . . 259
Select All . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
Show Coloring. . . . . . . . . . . . . . . . . . . . . . . . . . 259
Show Only Valid Data. . . . . . . . . . . . . . . . . . . . 259
Appendix D: BioAssay Plate Block Data
Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261
Appendix E: Oracle Cartridge Dependencies
by Operating System . . . . . . . . . . . . . . . 263
Appendix F: ChemACX Participating Vendors
. . . . . . . . . . . . . . . . . . . . . . . . . . . . 265
Appendix G: ChemSCX Participating Vendors
. . . . . . . . . . . . . . . . . . . . . . . . . . . . 271
Appendix H: Scientific Databases First
Search Tutorial . . . . . . . . . . . . . . . . . . . 275
Browsing a Chemical Database . . . . . . . . . . . . 275
Opening a Form in ChemFinder . . . . . . . . . . . 275
Switching Between Open Documents . . . . . . . 275
Browsing a Database. . . . . . . . . . . . . . . . . . . . . . 276
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The Status Bar. . . . . . . . . . . . . . . . . . . . . . . . . . 276
The Data Table . . . . . . . . . . . . . . . . . . . . . . . . . 277
Closing a Form . . . . . . . . . . . . . . . . . . . . . . . . . 278
Searching a Chemical Database . . . . . . . . . . . . 279
Performing a Text Search . . . . . . . . . . . . . . . . . . 279
Searching by Formula . . . . . . . . . . . . . . . . . . . . 279
Searching by name. . . . . . . . . . . . . . . . . . . . . . . 280
Searching by Molecular Weight . . . . . . . . . . . . .280
Performing a Structure Search . . . . . . . . . . . . . .280
Using the ChemDraw ActiveX Control . . . . . .280
Searching for the Structure in ChemFinder . . .282
Performing a Combined Search . . . . . . . . . . . . .284
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i
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viii•Contents
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ChemOffice Enterprise Workgroup &
Databases
About the Manual
The ChemOffice Enterprise Workgroup &
Databases Manual is a collection of instructions for
CambridgeSoft products not including ChemDraw,
ChemFinder, E-Notebook, and Chem3D. Because
the ChemOffice Enterprise Workgroup &
Databases Manual is a comprehensive collection,
every user may not have access to all of the
products represented.
This guide assumes familiarity with your computer’s
operating system and in some cases, a web browser.
For details about using your operating system, refer
to the user documentation provided with that
system.
For information about ChemDraw, please see the
“ChemDraw” Manual.
For information about Chem3D, ChemFinder,
and/or E-Notebook please see the “ChemOffice:
Chem3D, ChemFinder and E-Notebook” Manual.
Manual Organization
The ChemOffice Enterprise Workgroup &
Databases Manual is divided into 5sections:
• Section 1: Knowledge Management
• Section 2: Chemical Informatics
• Section 3: Biological Informatics
• Section 4: ChemOffice WebServer
• Section 5: Scientific Databases
Helpful CambridgeSoft
Links
The following table contains the addresses of
ChemDraw and ChemOffice-related web pages.
Help For ...
Technical
Support
ChemDraw
Plugin
ChemDraw for
Java
Software
Developer’s kit
Access
Installation
http://www.cambridgesoft.com/
services/
http://doc.cambridgesoft.com/
http://java.cambridgesoft.com/
http://sdk.cambridgesoft.com/
Active X control http://sdk.cambridgesoft.com/
Purchasing
CambridgeSoft
products and
chemicals
http://store.cambridgesoft.com/
Installation instructions and requirements are
contained in the “Read Me” document for each
application. Software Requirements and installation
instructions differ between applications.
ChemOffice Enterprise Workgroup & Databases 2005 ChemOffice Enterprise Workgroup & Databases • ix
About the Manual

Administrator
x•ChemOffice Enterprise Workgroup & Databases
CambridgeSoft
Installation

Section I: Knowledge
Management
This section provides information about
CambridgeSoft’s Knowledge Management
Solutions.
The following applications comprise
CambridgeSoft’s Enterprise Solutions:
• E-Notebook Enterprise (see the Chem3D,
ChemFInder, and E-Notebook manual for
more details)
• Document Manager
Research organizations thrive when information is
easily captured, well organized, and available to
those who need it. E-Notebook Enterprise
streamlines daily record keeping with rigorous
security and efficient archiving, and facilitates
searches by text and structure. Document Manager
organizes procedures and reports for archiving and
chemically-intelligent data mining. Discovery LIMS
tracks laboratory requests, and 21CFR11
Compliance implements an organization’s
regulatory compliance processes.
ChemOffice Enterprise Workgroup & Databases 2005 • 1

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2• CambridgeSoft

Chapter 1: Document Manager
Overview
The ChemOffice Document Manager utilizes the
ChemOffice WebServer to store and search
through documents.
The ChemOffice Document Manager will allow
you to:
• Create a central area, or repository, for
chemical documents in .doc, .txt, .ppt, .xls, and
.pdf formats for your entire organization, over
the web.
• Search .doc, .txt, .ppt, .xls, and .pdf*
documents in the repository. A Boolean search
can be performed over the web by chemical
structure or text.
* PDF documents can not be searched by
structure. Furthermore, full text searching is
available for PDF documents on systems with
Oracle 9i only. This is a limitation of
Intermedia (which only supports PDF files of
version 4 and below)
• Add, or submit, documents to the system over
the web. The document submitted is securely
stored in a database, indexed by both structure
and text for Document Manager users to
search and view.
• Remove documents that are no longer shared.
• Manage users as the system administrator.
Logging In
Hostname is the name of the server that the
Document Manager application is installed on.
To obtain this name, please contact your
system administrator.
2. Click on the Document Manager link.
The Log In window appears in your browser.
3. Enter a valid username and password.
4. Click Login.
The Global login page appears. Doc Manager
is in the bottom right.
5. Click on one of the links to enter Doc
Manager.
To log in to Document Manager:
1. Enter http://hostname into your web
browser.
ChemOffice Enterprise Workgroup & Databases 2005 Document Manager • 3
Overview

Administrator
Submitting Documents
Documents can be submitted through the
Document Manager web interface.
To submit a document:
1. From the Main Menu, click Submit Documents
The Submit Document page appears.
document layout in a web browser. Click Submit
This Document after you have entered your
details.
2. In the Document box, type the directory
location and file name of the document to be
submitted. The Browse button may be useful to
find the appropriate document.
• If you would like to view the document from
within your web browser, click Add
Document Details.
• The document will appear in the browser
window.
• If you would like to submit the document,
click Submit Now
• The submit documents page appears with a
message that the document was submitted
successfully.
Add Document Details
When submitting a document, you have the option
to add document details. To add details, click Add
Document Details instead of Submit Now on
the Add Document page.
The Add Document Details window allows you to
enter a title, author, and comments for the
document being submitted as well as preview the
Batch Submission
The Batch Submission tool allows administrators to
schedule the submission of documents in a
specified directory. Because batch submission often
decreases the performance of the server, it is
recommended that administrators schedule the
submission during a low use period.
To schedule a batch submission:
1. Click Batch Submission from the Doc
Manager homepage.
or click Batch Submission from the Global
Login page
4•Document Manager
CambridgeSoft
Submitting Documents

The batch submission page appears.
3. Click Show Activities.
The results appears.
2. Enter the directory which contains the
documents to be submitted.
3. Select a checkbox pertaining to a time of day
when the submission should take place.
4. Click OK.
Recent Activities
The Recent Activities tool allows administrators to
view and sort recent document submissions. To
view recent activities performed by the user:
1. Click Recent Activities.
The Recent activities page appears.
Searching for
Documents
Document Manager supports Basic and Advanced
Text searching characters and operators as well as
structure searching.
When performing a text search, type search criteria
or parameters into the search textbox. When
performing a structure search, draw a structure in
the Structure box. For more information about
drawing structures, please see “Drawing Chemical
Structures” in the ChemDraw User’s Manual.
After entering search criteria, start the search by
clicking on
Search.
For more information about Free Text Searching,
see “Document Manager Free Text Searching” on
page 249.
2. Enter sorting information.
For more information about search features, such
as Retrieve All and New Query, see the ChemOffice
WebServer User’s Guide.
ChemOffice Enterprise Workgroup & Databases 2005 Document Manager • 5
Recent Activities

Performing a Search
The Search Results form appears
Administrator
To search documents for specific information:
1. From the Main Menu page, click Search
Documents
The Search Documents page appears.
The search results form displays all documents
retrieved as a result of a search in table format. The
table includes two columns: Document
information and Download Options.
2. Enter the appropriate information. The Full
text textbox allows full text searching. Form
more information about full text searching,
please see “Document Manager Free Text
Searching” on page 249. For more information
about drawing structures, please see “Drawing
Chemical Structures” in the ChemDraw User’s
Manual.
3. Click Search
• To view one of the files in the Results form
inside your web browser, click on the title of
the appropriate document.
• To save a file to disk in order to view later, click
on the download button to the right of the
document’s information.
Manage Users and
Roles
The Document Manager application uses the global
ChemOffice WebServer User Management
interface. Please see “ChemOffice WebServer” on
page 167 for more information.
6•Document Manager
CambridgeSoft
Manage Users and Roles

Section II: Chemical Informatics
This section provides information about
CambridgeSoft’s Chemical Informatics Solutions.
The following applications comprise
CambridgeSoft’s Chemical Informatics Solutions:
• Registration System
• Formulations & Mixtures
• Inventory
• CombiChem Enterprise (see the Chem3D,
ChemFInder, and E-Notebook manual for
more details)
Managing the huge data streams of new lab
technology is a key challenge. Registration System
organizes information about new compounds
according to an organization’s business rules, while
Inventory works with Registration System and
ChemACX for complete management of chemical
inventories. CombiChem Enterprise and
Formulations & MIxtures are also important parts
of research data management.
ChemOffice Enterprise Workgroup & Databases 2005 • 7

Administrator
8• CambridgeSoft

Chapter 2: Registration System
Overview
Registration System is a powerful, web-based
registration solution, part of the ChemOffice
Enterprise suite. The system includes a robust data
model for pure compounds, batches, salt
management, automatic duplicate checking, and
unique ID assignments.
As chemicals enter a laboratory, either via synthesis
or procurement, they need to be characterized and
tracked. Since chemical names are cumbersome,
and one compound typically has many names, the
name becomes a difficult identifier. The chemical
structure, while more exact and recognizable,
cannot be verbalized, and inclusion in written
reports is difficult. The chemical registration
number, by contrast, is a simple, compact, and
unique way of identifying a chemical substance.
Registration System
Workflow
The Registration System process begins by adding a
compound to a temporary table space in the
database. This is done using the "Add Compound"
button from the main menu. The user is taken to an
"input" screen, and the ChemDraw plug-in starts
on the client. The scientist should sketch the
molecule and fill in all known information about
that compound. If this is a new batch of an existing
compound, click the "new batch" button and enter
the existing compound's registry number. If this is
a new compound, simply sketch the molecule in the
box and complete the form.
At some time, scheduled by a person designated as
a scientific administrator, the compounds are
formally "registered". Each compound or batch is
checked against a list of existing entries for
duplication. Duplicate checking is done using an
advanced structure-matching algorithm, which
checks the molecular drawing against the database.
If no match is found, a new registry number is
assigned. If a duplicate is found, the registrar is
asked how to process the duplicate.
Chemical Registry Number
Assignment
Registry numbers are drawn sequentially from a
table. If a compound is ever removed from the
database, its registry number will not be re-used.
Starting Registration
System
When Registration System is opened, you must log
in to start working.
To open and log in to Registration System:
1. Type http://hostname into your web
browser.
The main ChemOffice WebServer window
appears.
NOTE: Hostname is the name of the ChemOffice
WebServer machine. Contact your server administrator to
obtain the correct hostname.
2. Click Registration System.
ChemOffice Enterprise Workgroup & Databases 2005 Registration System • 9
Overview

The Registration System log in page appears.
Add to Temporary
Administrator
3. Type your Username and Password, and then
click Log In.
The Registration System main menu appears.
The temporary table holds all newly created
records. New records can be added to the
temporary table, or temporary database, as a
Compound or a Batch of compounds. Salts at the
Compound or Batch levels can also be added.
Adding a Compound
A compound is one of the types of records that can
be added to the temporary table. A compound
record includes information about the compound’s
physical properties as well as information about the
chemist who is recording the information.
To add a Compound record to Registration System:
1. From the Main Menu, click Add Compound.
The New Compound Submission Form
appears
From the Main Menu you can start using
Registration System.
NOTE: Your Administrator may set different privileges for
different users, so your Main Menu may not look like the
previous illustration.
The Main Menu is split into 4 major areas: “Add to
Temporary”, “Registration”, “Query & Reporting”,
and “Administration”, some of which will be
available to you, the user.
NOTE: More fields may appear in your form. These
forms are customized for your site. Please see your
system administrator for more details.
10•Registration System
CambridgeSoft
Add to Temporary

2. Enter the appropriate information into the
fields in the form..
NOTE: You may be required to complete particular fields
of a record; such information is usually surrounded by a red
box. For more information, see your system administrator.
3. Click Add Record.
The dialog box appears that confirms you have
added a record to the temporary table.
4. Click OK.
The New Compound Submission Form
reappears.
Adding a Batch/Lot
It is possible to add a Batch record to the temporary
table that contains information about a batch of a
compound. The compound is assigned a suffix to
its registration number that identifies it as part of a
Batch.
Batches of the same compound often become
available if for example, you prepare a compound,
then later repeat the preparation to make more of
the compound; or the organization purchases a
compound from two different suppliers. Batch
information is important because different batches
may contain different impurities or behave
differently in tests.
In order to add a new batch record, you must have
available the Registry Number of the compound.
The registry number is assigned to a record when
the record is registered and is included in the record
when viewed in the permanent database.
To add a Batch/Lot record to Registration System:
1. From the Main Menu, click Add Batch/Lot.
The Batch Registration Number page appears.
2. Type a Registry Number of a registered
compound and then click OK.
The New Batch Submission Form appears.
Common compound information for all the
Batches is retained, as shown in the upper gray
area of the screenshot above.
3. Enter the appropriate information into the
fields in the form.
4. Click Add Record.
A dialog box appears that confirms you have
added a record to the temporary table.
5. Click OK.
ChemOffice Enterprise Workgroup & Databases 2005 Registration System • 11
Add to Temporary

Administrator
The Batch Registration Number page
reappears.
Registration
Compounds are placed in the temporary table after
they are initially submitted. This allows the records
to be reviewed for accuracy and completeness
before being inserted into the permanent database
of registered compounds and assigned a
registration number.
When the time comes for a record to be registered,
the Registration section of the main menu is the
place to make that happen. Unlike other fields, after
a record is registred, it is possible to add certain
identifier and analytics data to a record.
Searching and Viewing
Records in the Temporary
Table
As the number of records in the temporary table
grows it becomes more difficult to locate a
particular record. For this reason, Registration
System includes a tool for searching the temporary
table.
For more information about general searching
techniques, see “Searching ChemOffice WebServer
Applications” on page 168.
To find specific records in the temporary table:
1. From the Main Menu, click Search Temporary.
The Search Temporary Structures Form
appears.
2. Take the appropriate action:
If you want to
search for records
that have specific
attributes
see all of the
records in the
temporary table
Then
a. in the Search
Temporary
Table, type or
choose the
attributes of the
records you
want to review.
b. Click Search.
click Retrieve All.
NOTE: It is also possible to access a list of records in the
Temporary Table by clicking Review/Register from the
Registration System homepage.
A list of records appears reflecting the search.
3. After locating the correct record in the search
results, click the Review/Register button
located to the left of the record summary.
The Compound Commit form appears.
Scrolling through the form allows you to view all of
the details entered for the chosen record.
12•Registration System
CambridgeSoft
Registration

The Compound Commit Form includes a number
of new operations displayed at the top of the page
in the form of buttons. The operations include:
Register, Edit, and Delete Record.
Registering Records in the
Temporary Table
When a record in the temporary table is registered,
the record is deleted from the temporary table and
moved to the permanent database. For this reason
it is important to review the record for accuracy and
completeness before registering the record. For
more information about registering a record
see“Registering a Record” on page 13.
Editing Records in the Temporary
Table
Records in the temporary table can be edited before
they are registered and inserted into the permanent
database.
NOTE: An edit operation cannot be undone.
To edit records that are in the temporary table:
1. Go to a record that you want to edit.
For more information about finding a record,
see “Searching and Viewing Records in the
Temporary Table” on page 12.
2. Click Review/ Register next to the appropriate
record.
The Compound Commit form appears.
3. Click Edit , if it is available.
The Registered Compounds Results Form
changes to allow editing.
4. Make the necessary changes to the record and
then click Update Record .
The Registered Compounds Results Form
returns to view-record mode.
Deleting Records in the Temporary
Table
Records in the temporary table can be deleted
instead of being added to the permanent database.
NOTE: A delete operation cannot be undone.
To delete a record from the temporary table:
1. From the Main Menu, choose Review/Register.
2. Go to a record you want to delete from the
temporary table.
3. Click Review/ Register.
The Compound Commit form appears.
4. Click Delete Record .
A dialog box appears before the record is
deleted to reconfirm the action.
5. Click OK.
The record is deleted from the temporary table.
Registering a Record
After a record in the temporary table is reviewed, it
can be registered. Registering a record moves it
from the temporary table to the permanent tables,
and assigns the record a unique registry number.
Anyone using Registration System can see all
records in the permanent database, unless Row
Level Security is enabled.
If the record is for a compound a registry number
is assigned and the information recorded is
assumed to be the first batch of the compound. If
the record is for a new batch of an existing
compound, the registry number is simply the
registry number assigned previously to the
compound followed by “batch”. It is possible to
ChemOffice Enterprise Workgroup & Databases 2005 Registration System • 13
Registration

Administrator
change the format of assigned registry numbers and
batch numbers. For more information about this,
please see “Defining Sequences” on page 18.
Before registering a record it is important to make
sure the record contains all of the information you
want included and the information is correct.
In addition to the initial information entered, you
can also include Identifiers and Analytics data to a
permanent record. For more information,
see“Adding Identifier Information to Records” on
page 14 and“Managing Analytics Data” on page 23
respectively.
2. Take the appropriate action:
If you want to
register
all the compounds
in the Registered
Compounds
Results List
Then
1. Click Register
All.
A window appears
asking you how
duplicates
should be
handled.
To add records to the permanent database:
1. From the Main Menu,
• If you know the record number of the
record to be reviewed, or you would like to
view a list of all compounds currently in the
temporary table: click Review/Register.
• If you would like to search for specific
records: click Search Temporary.
For more information about searching the
temporary table see “Searching and Viewing
Records in the Temporary Table” on page
12.
A list of records appears reflecting your
choices.
compounds
individually
2. Select how
duplicates
should be
handled.
3. Click OK.
1. Go to the
compound you
want to register
and then click
Register/
Review.
2. Click Register.
The Register Compounds Results Form
changes to show that you successfully
registered compounds. The Registration
Numbers and Batch numbers appear for each
record.
For more information about editing a record
before registering it, see “Editing Records in
the Temporary Table” on page 13.
Adding Identifier Information
to Records
14•Registration System
CambridgeSoft
Registration

Chemical names and synonyms can be added to
records to help identify compounds more easily.
These additional types of information are all
considered identifiers.
Before adding identifier information to records it is
necessary to obtain a Registry Number for the
record. The registry number is assigned to a record
when the record is registered and is included in the
record when viewed in the permanent database.
To add information to permanent records with
identifiers:
1. From the Main Menu, choose Add Identifiers.
The Add Records Input Form appears.
2. Type a Registry Number of a registered
compound and click OK.
The New Identifiers Submission Form
appears.
This form displays a summary about the
compound selected, and on the bottom allows
the addition of chemical names, synonyms, and
CAS numbers.
3. Take the appropriate action:
If you want to
add
a chemical name to
the record
a synonym for the
compound
Then in the
Chemical Name
box, type a
chemical name.
Synonym box,
type a synonym.
4. Click Add Record.
A dialog box appears that confirms you added
an identifier to the record.
5. Click OK.
The Add Records Input Form reappears.
Adding Analytics Data to a
Record
The Registration System software will allow you to
record analytics data linked to the correct batch of
compounds. This not only helps to identify the
record later, but also keeps all of your data together.
For more information, see “Defining New
Experiments” on page 23.
Before adding analytics data to records it is
necessary to obtain a Registry Number for the
record. The registry number is assigned to a record
when the record is registered and is included in the
record when viewed in the permanent database.
ChemOffice Enterprise Workgroup & Databases 2005 Registration System • 15
Registration

Administrator
To add analytics data to permanent records:
1. From the Main Menu, choose Add Analytics
Data.
The Add Records Input Form appears.
2. Type a Registry Number with a batch number
and click OK.
The Results Form View appears.
Query and Reporting
Records in the Registration System database are
searched using any of the fields that were entered in
the initial record. A query contains information
about fields to search under and what to search for.
Creating a query is the first step in finding the
correct record.
For more information about the different kinds of
queries you can create, see “Searching ChemOffice
WebServer Applications” on page 168.
Searching for Registered
Compounds
When a compound is registered, it is moved from
the temporary table to a permanent table.
3. From the Experiment Type menu, choose an
experiment type, and then click Add Data.
4. Add parameters and results data to the record
and click Commit Data.
The analytics data is added to the record.
To begin your search:
1. From the Main Menu, choose Search.
The Query Input form appears.
2. Enter the desired information in the
appropriate boxes and click Search.
Making your search as specific as possible is often
helpful, especially when the number of records in
the database is large. Most often, the more specific
a search is, the lower the number of records
returned will be.
If you are having trouble finding the correct record,
it may be that your search is too specific. Try
broadening your search in order to return more
records.
For more information about the different kinds of
queries you can create, see “Searching ChemOffice
WebServer Applications” on page 168.
Analytics Spreadsheets
It is possible to see records grouped by experiment
in a spreadsheet, or list, format.
16•Registration System
CambridgeSoft
Query and Reporting

To view records by experiment:
1. From the Main Menu, choose Show S/Sheet.
The Analytics Form opens.
2. Take the appropriate action:
If you want to
see
structures in the
spreadsheet
records from a
particular type of
experiment
Then
select the Show
Structures
checkbox.
choose the
experiment name in
the Select
Experiment Type
menu.
3. Click Show S/Sheet.
A spreadsheet opens with the experiment data.
Administration
All of the contents of menus, identities of users and
passwords, and definitions of types of data can be
manipulated from within Registration System. The
administration section allows for the maintenance
of Registration System and its users. This section is
often not available to regular users.
Managing Tables
The following parts of the Registration System
tables can be changed, or managed:
• Projects
• Sequence
• Structure Comments
• People
• Salts
• Solvates
To open a table to make changes:
• From the Main Menu, choose Registry Tables.
The Manage Tables page opens.
Defining Projects
A project name can be included as part of a
compound’s record. The Projects table defines the
Projects that appear when a user of the system
creates a compound record.
To open the Projects tables:
• From the Manage Table page, click Projects.
A table that defines the Projects opens.
To add a new project to the Projects table:
1. From the Projects table, click new.
A page appears allowing the definition of a new
project.
ChemOffice Enterprise Workgroup & Databases 2005 Registration System • 17
Administration

Administrator
2. Take the appropriate action:
If you want to
name the project
decide if this new
project name
should appear in
the project menu
while a user creates
a record
Then
in the Project
Name box, type a
name for the
project.
if this project
should be an
option, from the
Active menu,
choose True.
if this project
should not be an
option, from the
Active menu,
choose False.
3. Click Add Record.
The Projects table appears with the new
project.
This information appears in the Prefix menu when
records for compounds are created.
To open the Sequence tables:
• From the Manage Table page, click Sequence.
A table that defines the Sequence appears.
To add a new registration number prefix and
starting number to the Sequence table:
1. From the Sequence table, click new.
A window allowing the definition of a new
sequence appears.
2. Take the appropriate action:
If you want to
define a prefix for
compound
registration
numbers
Then
in the Prefix box,
enter a prefix.
To edit a project in the Projects table:
1. From the Projects table, click the ID number
that corresponds to the project to be edited.
A window allowing redefinition of the project
appears.
2. Follow step 2 from the previous section.
3. Click Update Record.
The Projects table is updated.
Defining Sequences
A prefix and a starting number for compound
registration numbers can be specified when a
record is created. The Sequences table defines the
compound registration numbers for each record.
18•Registration System
CambridgeSoft
Administration

If you want to
specify the number
with which to start
compound
registration
numbering
decide if this prefix
should appear in
the prefix menu
while a user creates
a record
Then
in the Next in
Sequence box,
type a number.
if this prefix should
be an option, from
the Active menu,
choose True.
if this prefix should
not be an option,
from the Active
menu, choose
False.
3. Click Add Record.
The Sequence table appears with the new
information.
To edit a sequence in the Sequence table:
2. Follow step 2 from the previous section.
3. Click Update Record.
The Sequence table is updated.
Defining Structure Comments
A comment about the structure of a compound can
be included when creating a record. The Structure
Comments table defines the structure comments
that appear when a record is created.
This information appears in the Struct Comment
menu when you create records for compounds.
To open the Structure Comments tables:
• From the Manage Table page, click Structure
Comments.
A table that defines the Structure Comments
appears.
To add a new structure comment to the Structure
Comments table:
1. From the Structure Comments table, click new.
A window allowing the definition of a new
structure comment appears.
1. From the Sequence table, click the ID number
that corresponds to the sequence you want to
edit.
A window allowing redefinition of a sequence
appears.
ChemOffice Enterprise Workgroup & Databases 2005 Registration System • 19
Administration

Administrator
2. Take the appropriate action:
If you want to
name the structure
comment
decide if this
structure comment
should appear in
the structure
comment menu
while a user creates
a record
Then
in the Structure
Comment box,
type a name for the
structure comment.
if this structure
comment should be
an option, from the
Active menu,
choose True.
if this structure
comment should
not be an option,
from the Active
menu, choose
False.
NOTE: The “no comment” structure comment
overrides the need to populate the structure field if the
structure field is a required field.
3. Click Add Record.
The Structure Comments table appears with
the new structure comment.
To edit a structure comment in the Structure
Comments table:
1. From the Structure Comments table, click the
ID number that corresponds to the structure
comment you want to edit.
A window allowing the redefinition of a new
structure comment appears.
2. Follow step 2 from the previous section.
3. Click Update Record.
The Structure Comments table is updated.
Defining Registration System People
The name of a person can be included with a
record. The People table defines the properties of
each person that appears in the People menu.
To open the People tables:
• From the Manage Table page, click People.
A table that defines the People appears.
To add a new person to the People table:
1. From the People table, click new.
A window allowing the definition of a new
person appears.
2. Take the appropriate action:
If you want to
include the code for
the person
include an unbound
user identification
include a
supervisor or
workgroup
identification
Then
in the Chemist
Code box, type a
code for the
person.
from the Unbound
User_ID menu,
select an ID.
from the
Supervisor/
Workgroup_ID
menu, select an ID.
20•Registration System
CambridgeSoft
Administration

If you want to
include the first
name of the person
include the middle
name of the person
include the last
name of the person
include a work site
for the person
include the phone
number of the
person
Then
in the First Name
box, type a name.
in the Middle
Name box, type a
name.
in the Last Name
box, type a name.
from the Site
menu, select a work
site location.
in the Telephone
box, type a phone
number.
The People table is updated.
NOTE: The default in the People Table is to display the
login name as the last name for the person. This can be
changed by adding the person, and then editing the user
information later.
Defining Salts
A salt can be included when a compound record is
created. The Salts table defines the Salts that appear
when a record is created.
To open the Salts tables:
• From the Manage Table page, click Salts.
A table that defines the Salts appears.
To add a new salt to the Salts table:
1. From the Salts table, click new.
A window allowing the definition of a new salt
appears.
include the E-mail
address of the
person
in the E-mail box,
type an E-mail
address.
2. Take the appropriate action:
decide if this
person should
appear in the
person menu while
a user creates a
record
if this person
should be an
option, from the
Active menu,
choose True.
if this person
should not be an
option, from the
Active menu,
choose False.
If you want to
enter a name for
the salt
include the
molecular weight of
the salt
Then
in the Salt Name
box, type a name
for the salt.
in the Salt MW
box, type a weight
for the salt.
3. Click Add Record.
ChemOffice Enterprise Workgroup & Databases 2005 Registration System • 21
Administration

If you want to
Then
To add a new solvate to the Solvate table:
1. From the Solvate table, click new.
Administrator
include the
molecular formula
of the salt
decide if this salt
should appear in
the salt menu while
a user creates a
record
in the Salt MF box,
type a formula for
the salt.
if this salt should be
an option, from the
Active menu,
choose True.
if this salt should
not be an option,
from the Active
menu, choose
False.
A window allowing the definition of a new
solvate appears.
2. Take the appropriate action:
If you want to
enter a name for
the solvate
Then
in the Solvate
Name box, type a
name for the
solvate.
3. Click Add Record.
The Salts table appears with the new salt.
To edit a salt in the Salts table:
1. From the Salts table, click the ID number that
corresponds to the salt to be edited.
A window allowing the redefinition of a new
salt appears.
include the
molecular weight of
the solvate
include the
molecular formula
of the solvate
in the Solvate MW
box, type a weight
for the solvate.
in the Solvate MF
box, type a formula
for the solvate.
2. Follow step 2 from the previous section.
3. Click Update Record.
The Salts table is updated.
Defining Solvates
A solvate can be included when a compound record
is created. The Solvate table defines the Solvates
that appear when a record is created.
To open the Solvates tables:
• From the Manage Table page, click Solvate.
A table that defines the Solvate appears.
decide if this
solvates should
appear in the
solvate menu while
a user creates a
record
if this solvate
should be an
option, from the
Active menu,
choose True.
if this solvate
should not be an
option, from the
Active menu,
choose False.
3. Click Add Record.
The Solvate table appears with the new solvate.
22•Registration System
CambridgeSoft
Administration

To edit a solvate in the Solvate table:
2. Take the appropriate action:
1. From the Solvate table, click the ID number that
corresponds to the solvate to be edited.
A window allowing the redefinition of a new
solvate appears.
2. Follow step 2 from the previous section.
3. Click Update Record.
The Solvate table is updated.
Managing Users and Roles
Please see “Manage Users and Roles” on page 167
for more information concerning managing users
and roles.
Defining New Experiments
Different facilities perform different tests with
compounds. For this reason, Registration System
allows you to define your own experiment. The
Experiments table is used to define the
Experiments that appear when a record is created.
To open the Experiments table:
• From the Main Menu, click New Experiment.
A table that defines the experiments appears.
To add a new experiment to the Experiments table:
If you want to
name the
experiment
include
information
describing the
experiment
include the date you
create this
experiment
include the date you
change this
experiment
include a version
identifier for this
experiment
Then
in the Name box,
type a name for the
experiment.
in the Description
box, type a
description for the
experiment.
in the Created box,
type a date.
in the Modified
box, type a date.
in the Version box,
type a way to
identify the
different version.
1. From the Experiments table, click new.
A window allowing the definition of a new
experiment appears.
3. Click Update Table.
The Experiments table appears with the new
experiment.
To edit an experiment in the Experiments table see
“Defining Experiment Type” on page 24.
Managing Analytics Data
The types of analytics data requested, such as:
• Result type
• Parameter type
can be modified in the Manage Analytics data
section.
ChemOffice Enterprise Workgroup & Databases 2005 Registration System • 23
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Administrator
Defining Result Type
A result type requested with an experiment when a
compound record is created can be modified using
the Result Types table.
To open the Result Types tables:
• From the Analytics Table page, click Result
Types.
A table that defines the Result Types appears.
To add a new result type to the Result Types table:
1. From the Result Types table, click new.
A window allowing the definition of a result
appears.
To edit a result type in the Result Types table:
1. From the Result Types table, click the ID
number that corresponds to the result type you
want to edit.
A window allowing the redefinition of a result
appears.
2. Follow step 2 from the previous section.
3. Click Update Record.
The Result Types table is updated.
Defining Experiment Type
2. Take the appropriate action:
If you want to
name the result
type
Then
in the Name box,
type a name for the
result type.
1. From the Analytics Table, click Experiment
Type.
2. Click the ID next to the Experiment you would
like to edit.
A window allowing the redefinition of an
experiment appears.
include a
description of the
result type
in the Description
box, type a
description for the
result type.
include a
description of the
units of the result
type
in the Units box,
type a description
for the units of the
result type.
3. Click Add Record.
The Result Types table is updated.
3. Edit the fields you wish to edit, and add and
delete result and parameter types. For more
information about adding result and parameter
types, see “Defining Result Type” on page 24
or “Defining Parameter Type” on page 25
respectively.
4. Click Update Record.
The Experiments table is updated.
24•Registration System
CambridgeSoft
Administration

Defining Parameter Type
A parameter type requested with an experiment
when a compound record is created can be
modified using the Parameter Types table.
To open the Parameter Types tables:
• From the Analytics Table page, click Parameter
Types.
A table that defines the Parameter Types
appears.
The Parameter Types table appears with the
new parameter type.
To edit a parameter type in the Parameter Types
table:
1. From the Parameter Types table, click the ID
number that corresponds to the parameter type
you want to edit.
A window allowing the redefinition of a
parameter appears.
To add a new parameter type to the Parameter
Types table:
1. From the Parameter Types table, click new.
A window allowing the definition of a
parameter appears.
2. Take the appropriate action:
If you want to
name the parameter
type
include a
description of the
parameter type
include a
description of the
units of the
parameter type
3. Click Add Record.
Then
in the Name box,
type a name for the
parameter type.
in the Description
box, type a
description for the
parameter type.
in the Units box,
type a description
for the units of the
parameter type.
2. Follow step 2 from the previous section.
3. Click Update Record.
The Parameter Types table is updated.
Managing Workgroups
To open the Workgroups tables:
• From the Main Menu, click Managing
Workgroups.
A table that defines the Workgroups appears.
For more information about adding workgroups,
see “Defining Registration System People” on page
20.
Importing SDFiles
SDFiles are Structure Data Files used by
ChemOffice to manage structure information and
data information in one file. If data is already stored
in SDFiles, and you would like that data imported
into Registration System, without tediously entering
it by hand, you can import the appropriate .sdf files
by importing the data into ChemFinder and then
into Registration System.
These files become records in the temporary table
or the permanent database in Registration System,
depending on the options chosen inside
ChemLoader.
ChemOffice Enterprise Workgroup & Databases 2005 Registration System • 25
Importing SDFiles

Administrator
When an .sdf file is imported into Registration
System, the following steps must be taken:
• Import an .sdf file into a ChemFinder database.
For more information, see the ChemFinder
Manual.
• Open ChemLoader on a server machine.
• Import the files.
ChemOffice must be installed somewhere on the
server machine being used in order to access
ChemFinder. For more information about
ChemFinder, see the ChemFinder Manual.
ChemOffice is installed by default with the
ChemOffice WebServer.
Steps to Import a SDFile
2. Choose Input and Output Databases
3. Match Fields in the input and output databases
chosen.
4. View the matches.
5. Import the matches into Registration System.
Choosing Input and Output
Databases
To choose input and output databases:
1. Click the Browse button to the right of the
words Input Database.
The Open dialog box appears.
To start using ChemLoader and import an SDFile
into Registration System:
1. Browse to:
\\Inetpub\wwwrootChemOffice\chem_reg\Chem
Loader_Client
and open ChemLoader.exe.
NOTE: ChemLoader can be run from client
machines. See your system administrator for a copy of
the utility.
The ChemLoader dialog box appears.
2. Choose an input database and click Open.
The database name appears in the Input
Database box found at the top of the
ChemLoader window. All of the
information, such as tables and fields,
associated with the input database appear in
the appropriate sections.
3. Click the Browse button to the right of the
words Output Database.
26•Registration System
CambridgeSoft
Importing SDFiles

The Select Server dialog box appears.
Matching Fields in the Input
and Output Databases
To match fields in the input and output databases:
1. highlight the tables containing the fields (one
under input database and one under output
database)
2. highlight the fields to be matched in the input
and output tables (one under input database
and one under output database).
The fields in the separate databases become
linked, shown by a line between them.
4. Choose a SERVER by either:
• selecting a SERVER from the list of servers
OR
• entering a server name manually into the
Server textbox.
5. Enter a username and password.
6. Indicate where the data should be imported to
by selecting the appropriate radiobutton:
• Add data to temporary table only OR
• Add data to permanent table.
7. Click OK.
The server name appears in the Output
Database box found at the top of the
ChemLoader window. All of the information,
such as tables and fields, associated with the
server appear in the appropriate sections.
3. Click Match Fields.
4. Repeat step 2 to match more fields manually.
View Matches and Import
To view the matches made and import the data into
Registration System:
1. Select the appropriate importing options:
NOTE: The following options are applied to all
imported records.
ChemOffice Enterprise Workgroup & Databases 2005 Registration System • 27
Importing SDFiles

If you want to
Then
Administrator
If you want to
include records
from the input
database that start
at a specific place in
the database
Then
enter a starting
record number in
the Start Index
textbox.
include a salt name
in the imported
files
include a batch
name in the
imported files
select a salt from
the Salt pull-down
menu.
select a batch from
the Batch pulldown
menu.
include records
from the input
database that end at
a specific place in
the database
enter an ending
record number in
the Stop Index
textbox.
2. Click Matches > View.
The Matching field list appears.
record the
importing process
in a log file
enter a logfile
location in the Log
File textbox.
3. Click OK.
include a sequence
in the imported
files
select a sequence
from the Sequence
pull-down menu.
4. To import the records into Registration System
click Import.
A progress Dialog dialog box appears.
include a project
name in the
imported files
select a project
from the Project
pull-down menu.
include a
compound name in
the imported files
include a notebook
name in the
imported files
select a compound
from the
Compound pulldown
menu.
select a notebook
from the
Notebook pulldown
menu.
When the import is complete the import dialog box
closes and the records have been imported to the
appropriate place in Registration System. No
additional steps have to be taken to use the records
normally inside the Registration System.
To abort the import:
• In the Dialog dialog box, click Cancel.
The import stops.No additional records are
added to Registration System, but records
already imported remain.
28•Registration System
CambridgeSoft
Importing SDFiles

Optional Features
There are a number of features available to
Registration System users that are not, by default, in
activated. Please see your system administrator for
more information about activating any features
described in this section.
Row Level Security (RLS)
Overview
Row Level Security is a level of security
implemented above the standard Oracle roles. The
purpose of using Roles in Registration System is to
restrict access to elements of the interface and data
to certain users. For example, User A has access to
one set of user-interface elements (such as buttons
and menus) while User B is limited to a subset of
those available to A. In addition, Roles limit what a
user can do with the data; User A can register data
and edit that data, User B can only register.
On the other hand, Roles do not distinguish which
rows a user has access to within a given table. In a
system without Row Level Security (RLS) activated,
User A sees all compounds in the registry, as does
User B. With the implementation of RLS, the rows
(records) of data are linked to projects and projects
are linked to people. Thus, User A is assigned to a
particular project, and will only be able to see
compounds that are linked to that project.
The User Interface
The number of registered compounds is displayed
on the Reg System homepage to the left of the
search buttons. With RLS implemented, this value
reflects the records a user can see, not the number
in the registry. That is, User A may see 10, while
User B sees 20.
If any screen that has a project drop-down is
viewed, that drop-down will only show projects that
the user in linked to, unlike before RLS, when all
projects were listed. Thus users will only be able to
add compounds or search compounds associated
with projects for which they have rights.
How are Projects linked to People
When a project is created in the Administration
Registry Tables, users of the system are given
permissions to those projects. If a particular project
is removed from a user, the user will no longer be
able to view records in that project. The actual data
doesn’t change, only who can see it. Users only view
records relevant to projects they are assigned to.
The Unspecified Project
Any record assigned to the unspecified project is
inserted into the Temporary Table. The
Unspecified project can be assigned to any user, but
in general probably should be limited to an
administrator. In this type of system, the
unspecified project should only be used when the
record is added from a registration attempt from
another application that doesn’t have a valid
project_id. In this case, the administrator assigned
to the unspecified project can check the temporary
table for these types of records, and assign a
relevant project to each record.
Duplicate Checking
If RLS is enabled, Registration System inspects
both the compound and the project when deciding
if a duplicate exists. If the compound being added
is a duplicate in the entire system, but not a
duplicate within a project, an end user would see no
duplicate window appear and the compound is
registered as usual. However since the same
compound is a system duplicate the record is placed
in the Duplicates Table. If a compound is a
duplicate within a project, the Duplicate Window
appears.
ChemOffice Enterprise Workgroup & Databases 2005 Registration System • 29
Optional Features

Administrator
Viewing System Duplicates
A new button is displayed on the homepage called
View Duplicates if a user has the correct privileges.
Clicking this button retrieves and displays all of the
duplicate records using the standard ChemOffice
WebServer List/Display View. The Detail button
yields - in red - the duplicate registration number.
Currently when duplicates are added they are added
twice. That is, if compound A is being registered
and Compound B is found to be a duplicate in the
system, then the entries in the Duplicates Table will
be:
• Compound A -> Compound B
• Compound B -> Compound A
Therefore, when duplicates are checked users see
both sides of the picture: A is a duplicate of B and
conversely B is a duplicate of A.
Deleting a Duplicate
If a duplicate record is deleted, it is removed from
the Duplicates Table.
Activating RLS
For details regarding the activation of the RLS
feature, please see the Registration System Admin
Guide or your system administrator.
Salt and Solvate Recognition
Both compound level records as well as batch level
records contain salt and solvate information. There
are a number of options which indicate how salt
and solvate information is recorded.
The default behavior is to automatically populate
the batch level record with salt and solvate
information from the compound record. The
options include:
• DEFAULT: Populate the batch level record
with salt and solvate information in the
compound level record, and allow the
equivalents to be changed at the batch level
• Populate the batch level record with salt and
solvate information in the compound level
record, and allow all fields to be changed at the
batch level
• The salt and solvate information is kept
completely separate in compound and batch
level records
To adjust this default, please see your system
administrator.
Customizable Fields
The Registration System has a number of fields
which are by default hidden, but are available to be
configured if none of the default Registration fields
contain necessary information. The following
customizable fields exist:
• 4 text fields
• 4 integer fields
• 4 real number fields
• 4 date fields
The name, datatype, and display type can be
adjusted for any of the above mentioned fields.
If you feel it is necessary to include an additional
field to records, please see your system
administrator. Complete details describing the field
options available are available in the Registration
System Admin Guide and the ChemOffice
WebServer Admin Guide.
Choosing Preferences
For more information, see the ChemOffice
WebServer User’s Guide.
Printing
You can print records from Registration System.
To print records:
1. Click Print.
The Print dialog box appears.
30•Registration System
CambridgeSoft
Choosing Preferences

2. Check the settings and then click OK.
A Registration System record is printed.
Logging Off
You can end your Registration System at anytime by
logging off.
To log off:
• Click Log Off.
The Registration System Log In dialog page
appears. You can log back in and continue
using Registration System, or browse to a
different site.
ChemOffice Enterprise Workgroup & Databases 2005 Registration System • 31
Logging Off

Administrator
32•Registration System
CambridgeSoft
Logging Off

Chapter 3: Formulations & Mixtures
Overview
The Formulations & Mixtures Registration
ChemOffice WebServer application makes it
possible for individuals to register mixtures in
addition to the single compound registration
offered by the Registration System application. The
application was specially designed for formulation
scientists. It can be easily integrated with other
information systems and chemical databases.
The system allows the user to register pure
compounds as well as mixtures of these
compounds. After registering the mixture, the
entries can be searched by any number of search
fields, including a structure search.
Registration
Adding a Structure
The Formulations & Mixtures Registration system
shares a structure database with the Registration
System. Therefore, structures added to the
Formulations & Mixtures Registration system can
also be viewed from the Registration System.
To register a structure from Formulations &
Mixtures:
1. From the Main Menu, click Add
Structure.
The Structure Form appears.
The Formulations & Mixtures Registration system
allows the user to register compounds, and
substances made up of multiple compounds. In
addition to this it is possible to record information
about particular samples of a substance and
analytical data gathered from that sample in the
same database. This allows an organization to keep
all of its information on a public domain, making it
easy to search through these records at a later time.
The Registration section of Mixture Registration
contains multiple web forms that aide in entering
data into the registration system. Not all users are
allowed to add records to the database. If you do
not have access to the registration section, and you
should, please see your system administrator.
2. Enter the appropriate information. For more
information about a particular field, please see
“The Result Types table is updated.” on page
43.
3. Click Add Record.
ChemOffice Enterprise Workgroup & Databases 2005 Formulations & Mixtures • 33
Overview

Adding a Product/Substance
Adding a Sample
Administrator
To register a substance in Formulations & Mixtures:
1. From the Main Menu, click Add
Substance.
The Substance Form appears.
To add a sample to a substance record in
Formulations & Mixtures:
1. From the Main Menu, click Add
Sample.
2. Select a substance registration number and
click OK.
The Substance registration number is
automatically generated when a substance
record is created. This number will be
displayed when viewing the substance record.
The Sample Form appears.
2. Enter a substance name.
3. Highlight a component under Available
Components that makes up a part of the
substance.
4. Enter the percentage of the substance that is
the highlighted component and click to
move the component to the Selected
Components list.
As components are added, they will be listed in
the right column in a tree-like interface.
5. Enter other appropriate information. For more
information about a particular field, please see
“Search Form Fields” on page 13.
6. Click Add Record.
3. Enter the appropriate information. For more
information about a particular field, please see
“Search Form Fields” on page 13.
4. Click Add Sample.
Adding Analytics Data
To register a substance in Formulations & Mixtures:
1. From the Main Menu, click Add
Analytics.
2. Select a substance registration number and
sample number and click OK.
34•Formulations & Mixtures
CambridgeSoft
Registration

The Substance registration and sample
registration numbers are automatically
generated. These numbers will be displayed
when viewing a record.
3. Select an experiment type and click
Next.
Step 2 of 3 of the Analytics Form appears.
The Query Input form appears.
4. Enter the appropriate information. For more
information about a particular field, please see
“Search Form Fields” on page 13.
5. Click Add Record.
Query and Reporting
All of the records in the Formulations & Mixtures
Registration database can be searched for using any
of the fields that were entered in the initial record.
A query contains information about fields to search
under and what to search for. Creating a query is the
first step in finding the correct record.
For more information about the different kinds of
queries you can create, see Searching in the
ChemOffice WebServer User’s Guide.
In order to begin your search:
1. From the Main Menu, choose Search.
2. Enter the desired information in the
appropriate boxes and click Search.
For more information about a particular field
in the form, please see “Record Fields” on page
311.
Making your search as specific as possible is often
helpful, especially when the number of records in
the database is large. Most often, the more specific
a search is, the lower the number of records
returned will be.
If you are having trouble finding the correct record,
it may be that your search is too specific. Try
broadening your search in order to return more
records.
For more information about the different kinds of
queries you can create, see Searching in the
ChemOffice WebServer User’s Guide.
Viewing Details of a Record
When you complete a search, records are returned
and displayed in a table format, or a list. Details of
a record can be viewed in an expanded format.
ChemOffice Enterprise Workgroup & Databases 2005 Formulations & Mixtures • 35
Query and Reporting

Administrator
To view details of a record:
1. Identify the correct record in the resulting list.
2. Click Show Details.
The record changes from Results List View to
Results Form View.
Marking Records
Records found in a Formulations & Mixtures search
can be marked in order to view again later. The list
of marked records is saved on the client and are
client-specific lists.
To mark records:
The Unmark Record button changes to Mark
Record.
Records can be unmarked so they do not appear
when marked records are retrieved. You can
unmark records individually, or unmark all of them
at once, which clears the viewing table.
To unmark, or clear all records:
• Click Clear Marked.
All previously marked records become
unmarked.
Administration
1. Perform a search. For more information, see
“Query and Reporting” on page 35.
2. Next to a record that you want to view again
later, click Mark Record.
The Mark Record button changes to Unmark
Record. The record is marked so that you can
view it later with other marked records.
Viewing Marked Records
All of the records that were marked can be viewed
later in one table.
To view marked records:
• Click Show Marked.
All the marked records appear in a new Results
List View.
Clearing Marked Records
Records can be unmarked so they do not appear
when marked records are retrieved. You can
unmark records individually, or unmark all of them
at once, which clears the viewing table.
To unmark, or clear individual records:
• Go to a record that you marked and then click
Unmark Record.
All of the contents of menus, identities of users and
passwords, and definitions of types of data can be
manipulated from within Formulations & Mixtures.
The administration section allows for the
maintenance of Formulations & Mixtures and its
users. This section is often not available to regular
users.
Managing Tables
Many fields in the Formulations & Mixtures
Registration forms are pull down menus. These pull
down menus have a limited number of options. The
options available are decided by tables which can be
populated by the administrator.
To open a table to make changes:
• From the Main Menu, choose Registry Tables.
The Manage Tables page opens.
Defining Projects
A project name can be included as part of a
compound’s record.
To open the Projects tables:
• From the Manage Table page, click Projects.
A table that defines the Projects opens.
36•Formulations & Mixtures
CambridgeSoft
Administration

To add a new project to the Projects table:
1. From the Projects table, click new.
A dialog box in which a project can be defined
appears.
To add a new registration number prefix and
starting number to the Sequence table:
1. From the Sequence table, click new.
A window allowing the definition of a new
sequence appears.
2. Enter the appropriate information. The Active
field decides if this particular project will
appear in pull down menus (True) or remain
invisible to the user (False).
3. Click Add Record.
The Projects table appears with the new
project.
To edit a project in the Projects table:
1. From the Projects table, click the ID number
that corresponds to the project to be edited.
A window allowing redefinition of the project
appears.
2. Enter the appropriate information.
3. Click Add Record.
The Projects table is updated.
Defining Prefix/Sequence
A prefix and a starting number for compound and
substance registration numbers can be specified
when a record is created. The Sequences table
defines the registration numbers for each record.
This information appears in the Prefix menu when
records are created.
To open the Sequence tables:
• From the Manage Table page, click Sequence.
A table that defines the Sequence appears.
2. Enter the appropriate information.
3. Click Add Record.
The Sequence table appears with the new
information.
To edit a sequence in the Sequence table:
1. From the Sequence table, click the ID number
that corresponds to the sequence you want to
edit.
2. Enter the appropriate information.
3. Click Add Record.
4. The Sequences table is updated.
Defining Labs
To open the Lab tables:
• From the Manage Table page, click Lab.
A table that defines the Labs opens.
To add a new lab to the Lab table:
1. From the Lab table, click new.
A dialog box in which a lab can be defined
appears.
2. Enter the appropriate information.
3. Click Add Record.
The Lab table appears with the new lab.
ChemOffice Enterprise Workgroup & Databases 2005 Formulations & Mixtures • 37
Administration

Administrator
To edit a lab in the Lab table:
1. From the Lab table, click the ID number that
corresponds to the lab to be edited.
A window allowing redefinition of the lab
appears.
2. Enter the appropriate information
3. Click Add Record.
The Lab table is updated.
Defining Safety Phrases
To open the Safety Phrase tables:
• From the Manage Table page, click Safety
Phrase.
• A table that defines Safety Phrases opens.
To add a new safety phrase to the Safety Phrase
table:
1. From the Safety Phrase table, click new.
A dialog box in which a safety phrase can be
defined appears.
2. Enter the appropriate information.
3. Click Add Record.
The Safety Phrase table appears with the new
safety phrase.
Defining Risk Phrases
To open the Risk Phrase tables:
• From the Manage Table page, click Risk
Phrase.
A table that defines Risk Phrases opens.
To add a new risk phrase to the Risk Phrase table:
1. From the Risk Phrase table, click new.
A dialog box in which a risk phrase can be
defined appears.
2. Enter the appropriate information.
3. Click Add Record.
The Risk Phrase table appears with the new
risk phrase.
To edit a risk phrase in the Risk Phrase table:
1. From the Risk Phrase table, click the ID
number that corresponds to the risk phrase to
be edited.
A window allowing redefinition of the risk
phrase appears.
2. Enter the appropriate information.
3. Click Add Record.
The Risk Phrase table is updated.
To edit a safety phrase in the Safety Phrase table:
1. From the Safety Phrase table, click the ID
number that corresponds to the safety phrase
to be edited.
A window allowing redefinition of the safety
phrase appears.
2. Enter the appropriate information
3. Click Add Record.
The Safety Phrase table is updated.
Defining Conditions
To open the Conditions tables:
• From the Manage Table page, click
Conditions.
A table that defines Conditions opens.
To add a new condition to the Conditions table:
1. From the Conditions table, click new.
A dialog box in which a condition can be
defined appears.
2. Enter the appropriate information.
3. Click Add Record.
38•Formulations & Mixtures
CambridgeSoft
Administration

The Conditions table appears with the new
condition.
To edit a condition in the Conditions table:
1. From the Conditions table, click the ID
number that corresponds to the condition to
be edited.
A window allowing redefinition of the
condition appears.
2. Enter the appropriate information
3. Click Add Record.
The Conditions table is updated.
Defining Units
To open the Units tables:
• From the Manage Table page, click Units.
A table that defines the Units opens.
To add a new unit to the Units table:
1. From the Units table, click new.
A dialog box in which a unit can be defined
appears.
2. Enter the appropriate information.
3. Click Add Record.
The Units table appears with the new unit.
To edit a unit in the Units table:
1. From the Units table, click the ID number that
corresponds to the unit to be edited.
A window allowing redefinition of the unit
appears.
2. Enter the appropriate information.
3. Click Add Record.
The Units table is updated.
Defining Business Units
To open the Business Unit tables:
• From the Manage Table page, click Business
Unit.
A table that defines Business Units opens.
To add a new business unit to the Business Unit
table:
1. From the Business Unit table, click new.
A dialog box in which a business unit can be
defined appears.
2. Enter the appropriate information.
3. Click Add Record.
The Business Unit table appears with the new
business unit.
To edit a business unit in the Business Unit table:
1. From the Business Unit table, click the ID
number that corresponds to the business unit
to be edited.
A window allowing redefinition of the business
unit appears.
2. Enter the appropriate information.
3. Click Add Record.
The Business Unit table is updated.
Defining Status
To open the Status tables:
• From the Manage Table page, click Status.
A table that defines the Status table opens.
To add a new status to the Status table:
1. From the Status table, click new.
A dialog box in which a status can be defined
appears.
2. Enter the appropriate information.
3. Click Add Record.
The Status table appears with the new status.
ChemOffice Enterprise Workgroup & Databases 2005 Formulations & Mixtures • 39
Administration

To edit a status in the Status table:
A table that defines the Physical State opens.
Administrator
1. From the Status table, click the ID number that
corresponds to the status to be edited.
A window allowing redefinition of the status
appears.
2. Enter the appropriate information.
3. Click Add Record.
The Status table is updated.
Defining Shelf Life
To open the Shelf Life tables:
• From the Manage Table page, click Shelf Life.
A table that defines the Shelf Life table opens.
To add a new shelf life to the Shelf Life table:
1. From the Shelf Life table, click new.
A dialog box in which a shelf life can be defined
appears.
2. Enter the appropriate information.
3. Click Add Record.
The Shelf Life table appears with the new shelf
life.
To edit a shelf life in the Shelf Life table:
1. From the Shelf Life table, click the ID number
that corresponds to the shelf life to be edited.
A window allowing redefinition of the shelf life
appears.
2. Enter the appropriate information.
3. Click Add Record.
The Shelf Life table is updated.
Defining Physical State
To open the Physical State tables:
• From the Manage Table page, click Physical
State.
To add a new physical state to the Physical State
table:
1. From the Physical State table, click new.
A dialog box in which a physical state can be
defined appears.
2. Enter the appropriate information.
3. Click Add Record.
The Physical State table appears with the new
physical state.
To edit a physical state in the Physical State table:
1. From the Physical State table, click the ID
number that corresponds to the physical state
to be edited.
A window allowing redefinition of the physical
state appears.
2. Enter the appropriate information.
3. Click Add Record.
The Physical State table is updated.
Managing Users & Roles
Please see “Manage Users and Roles” on page 167
for more information concerning managing users
and roles.
Defining People
The name of a person can be included with a
record. The People table defines the properties of
each person that appears in the People menu.
To open the People tables:
• From the Manage Users page, click People.
A table that defines People appears.
40•Formulations & Mixtures
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Administration

To add a person to the People table:
1. From the People table, click new.
A window allowing the definition of new
people appears.
2. Enter the appropriate information. If the
Active field is True, the person will be listed
from the application's fields allowing the
selection of a person.
3. Click Add Record.
The People table appears with the new
information.
To edit a person in the People table:
1. From the People table, click the ID number
that corresponds to the person you want to
edit.
2. Enter the appropriate information.
3. Click Update Record.
The People table is updated.
Changing Passwords
The Passwords table allows you to edit your own
password.
To open the Passwords table to make changes:
• From the Main Menu, choose Change
Password.
A window allowing the redefinition of your
password opens.
To change your password in the Passwords table:
1. Enter the appropriate information.
2. Click Update User.
The Passwords table appears with the new
password.
Managing Analytics Data
The following types of analytics data can be created
and edited from the Managing Analytics Data table:
• Experiment Type
• Parameter Type
• Result Type
To access the Managing Analytics Data table:
• From the Main Menu, click Analytics Table.
Defining Experiment Types
To open the Experiment Types tables:
• From the Analytics Table page, click
Experiment Types.
A table that defines the Experiment Types
appears.
To add a new experiment to the Experiment Types
table:
1. From the Experiment Types table, click new.
A window allowing the definition of an
experiment appears.
2. Enter the appropriate information.
3. Click Add Record.
The Experiment Types table is updated.
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To edit a experiment type in the Experiment Types
table:
To add a new parameter type to the Parameter
Types table:
Administrator
1. From the Experiment Types table, click the ID
number that corresponds to the experiment
type you want to edit.
A window allowing the redefinition of an
experiment appears.
1. From the Parameter Types table, click new.
A window allowing the definition of a
parameter appears.
2. Enter the appropriate information.
3. Click Add Record.
The Experiment Types table is updated.
Defining Parameter Types
A parameter type requested with an experiment
when a compound record is created can be
modified using the Parameter Types table.
To open the Parameter Types tables:
• From the Analytics Table page, click
Parameter Types.
A table that defines the Parameter Types
appears.
2. Enter the appropriate information.
3. Click Add Record.
The Parameter Types table is updated.
To edit a parameter in the Parameter Types table:
1. From the Parameter Types table, click the ID
number that corresponds to the parameter type
you want to edit.
A window allowing the redefinition of a
parameter appears.
2. Enter the appropriate information.
3. Click Add Record.
The Parameter Types table is updated.
Defining Result Types
A result type requested with an experiment when a
compound record is created can be modified using
the Result Types table.
To open the Result Types tables:
• From the Analytics Table page, click Result
Types.
A table that defines the Result Types appears.
To add a new result to the Result Types table:
4. From the Result Types table, click new.
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A window allowing the definition of a result
appears.
5. Enter the appropriate information.
6. Click Add Record.
The Result Types table is updated.
To edit a result type in the Result Types table:
1. From the Result Types table, click the ID
number that corresponds to the result type you
want to edit.
A window allowing the redefinition of a result
appears.
2. Enter the appropriate information.
3. Click Add Record.
The Result Types table is updated.
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44•Formulations & Mixtures
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Administration

Chapter 4: Inventory
Overview
Inventory is an application designed to manage the
chemical and reagent tracking needs of laboratories
and research centers. The system manages data
associated with both commercially procured and
internally produced chemical substances from their
procurement or initial production through their
depletion and disposal. To meet the needs of
institutions of all sizes, Inventory comes in two
Desktop editions (Pro and Ultra), a Workgroup
edition, and a ChemOffice Enterprise- based
edition.
Inventory Pro is an all-inclusive desktop product. It
includes Microsoft SQL-Server Desktop Engine ®
(MSDE), the redistributable database engine for
SQLServer 2000. No additional licensing is
required. Suitable for single-user installations, the
inventory database can accept up to five
simultaneous queries with no degradation of
performance 1 . The connection to the database is
not live except when you actually process a query, so
the only practical limit to the number of computers
connected to an Inventory MSDE database is the
probability of more than five users attempting
simultaneous queries.
1. MSDE is optimized for 5 concurrent users.
The word “optimized” is important here. With
up to 5 concurrent users, MSDE will perform
just like all other SQL Server editions. When
more users are connected, and all query the
server, MSDE will throttle the speed. If the clients
are connected, but are not active, nothing
will happen. MSDE will slow down only when
more than 5 queries arrive at the server at the
same time.
Inventory Ultra is the same MSDE-based product,
but includes the DVD version of ChemACX,
CambridgeSoft’s catalog of chemical products and
suppliers.
Inventory Workgroup is a thick-client SQLServerbased
product. Suitable for larger organizations that
don’t have the ability (or don’t want) to maintain an
Oracle server, it requires, but does not include, a
SQLServer license.
Inventory Enterprise is an Oracle-based,
ChemOffice Enterprise product. Designed for
large organizations, it has a number of features not
included in the Pro/Ultra/Workgroup versions.
This document describes all four products. Some
sections apply only to the Pro/Ultra/Workgroup
products, and some only to the Enterprise product.
This is noted in the text. In the examples that
follow, some of the illustrations are from the
Pro/Ultra version, and some from the Enterprise
version. The two versions are quite similar; users
should be able to recognize the UI components,
even if the illustration is not identical to what they
see on their screens. In some cases, both versions
are shown to avoid confusion.
This chapter introduces the terminology and the
User Interface, describes the set-up and
management of an inventory database, and
discusses the search forms used to locate
substances and containers in the inventory.
Terminology
The three primary entities in an Inventory system
are Locations, Substances, and Containers.
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Overview

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Location
An Inventory Location represents a physical location
where one or more Containers may be stored.
Locations can be nested within other locations to
produce a hierarchy. The location hierarchy is
represented as nested folders on a tree control
analogous to that found in the Windows file
explorer. Following is an example of a typical
location tree:
Substance
An Inventory Substance represents a single pure
chemical entity which can be expressed as a two
dimensional chemical structure drawing. The
system maintains its own internal chemical
structure database containing unique substances
that can be associated with Inventory Containers.
Highly advanced duplicate checking is incorporated
into the system. Only a single Substance may be
associated with each Inventory Container. Aside
from structure and name, substances can be
identified via unique registry numbers such as CAS
or ACX ID. Custom fields may also be defined.
For information on defining mixtures as
substances, see “Mixtures” on page 54.
If Inventory is integrated with the Registration
System and/or ChemACX, substances found in
either system can also be associated with an
Inventory container.
Container
An Inventory Container represents a physical
container capable of storing chemical substances.
While a Container may physically contain a
complex mixture of chemical substances, Inventory
is ideally suited for the assignment of a single
(primary) chemical substance to each Container.
Additional text fields are available to track other
chemical contents such as the solvent, or other
(secondary) chemical substances associated with
the Container. Typical containers include: bottle,
vial, tube, cylinder, box, etc...
Logging in
All versions of Inventory use a password based
login. The login screen is slightly different in the
Pro/Ultra and Enterprise versions, but the
procedure is standard. Logging in to Inventory
Enterprise brings you to the ChemOffice
Enterprise homepage.
Click the Browse link under Inventory Manager to
view the Inventory database.
NOTE: Administrative tasks relating to login, such as
adding users and changing passwords, are covered in other
sections. For Enterprise versions, see “Manage Users and
Roles” on page 167. For Pro/Ultra and Workgroup
versions, see “Managing Users and Roles” on page 78.
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Overview

Desktop/
Workgroup
Before logging in, you can review or
edit the configuration file or change your
password. Other options available from the
Setup button are described in
“Administration” on page 78.
The User Interface
The following section describes the User Interface
for all versions of Inventory. While the Inventory
Pro/Ultra and Workgroup GUIs were modeled on
the Inventory Enterprise interface, and are very
similar, they are not identical. Refer back to this
section if you have any problem locating commands
mentioned in the following procedural sections.
The User Interface (Browse mode) is divided into
three main areas or “frames”:
• Location tree.
• Container list.
• Substance details.
These areas support browsing the inventory; that is,
viewing locations, the containers present in them,
and details of the substances in the containers.
Location Tree Current Location Container Lis
Frame Frame Frame
Substance Details Frame
Location Tree Menu Bar Container List
Substance Details
The Location Tree shows all of the locations in the
inventory. It is a collapsible hierarchical tree
structure, like the Windows Explorer folders list.
The Container List displays the containers in the
selected location. Use the scroll bar to view all of
the containers in a location.
The Substance Detail section is a tabbed frame that
shows the details for the selected container. Five of
the tabs are identical in all versions:
• Summary
• Substance
• Supplier
• Quantities
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• Comments
The remaining tabs access features that are unique
to the version or the way it is set up. For example,
the Custom tab will only appear if you have defined
custom fields.
The Current Location Frame in the Enterprise version
contains links to features that are accessed by menu
commands in the Pro/Ultra and Workgroup
versions. The location text box indicates the
currently selected Inventory location. With the
exception of searches, actions performed via the
links in this frame apply to the currently selected
location. You may enter a locationID value into the
location box to rapidly access a location on the tree.
A barcode reader may be used to enter a locationID
value into this box, further expediting navigation to
a given location.
Locations
The New Location form has the same basic fields in
all versions: Parent Location, Location, Location
Name, Location Type, Location Owner, Grid
Format, and Description. In addition, the
Enterprise version allows for defining reaction plate
types. Required fields are indicated with color.
The Edit Location form is the same as New
Location, but without a Parent Location field. (You
“edit” the parent location by using the Move
Location command.)
The Location forms are accessed from the Manage
menu in Inventory Pro/Ultra/Workgroup, and
from the ... Location links in the Current Location
Frame in Inventory Enterprise.
Forms
In addition to the main Inventory GUI, there are a
number of forms for creating and editing
substances, containers, and locations, and for
searching substances and containers. These are
accessed from menus (Pro/Ultra/Workgroup) or
hyperlinks (Enterprise).
Pro/Ultra menu commands and Enterprise links
Location commands
Container commands
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Containers
New and Edit Container are tabbed forms with
many optional fields defining the container and the
substance in it. The top-most tab contains the
required fields.
Container forms are accessed from the Manage
menu in Inventory Pro/Ultra/Workgroup. In
Inventory Enterprise, the new container form is
accessed from the New Container link in the
Current Location Frame, and edit forms from the links
in the Substance Details Frame.
The Search Container form is accessed from the
Search menu in Inventory Pro/Ultra/Workgroup,
and from the New Search link in the Current
Location Frame in Inventory Enterprise. See
“Searching for Containers” on page 69 for more
information.
Substances
New substances are usually created along with new
containers. For this reason, the links to the New
Substance forms are found on the New Container
form. (In addition, Inventory Enterprise can access
the New Substance form from the Manage
Substances page by clicking the Add Mode button.)
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There are two options for inserting a substance into
a container: create from scratch, or import from an
existing database, such as ACX.
New Substance link
In Inventory Pro/Ultra/Workgroup, this is done by
selecting Substances... from the Search menu. In
Inventory Enterprise, the Manage Substances page
is accessed from the home page, or from links in
other pages.
Managing an
Inventory
NOTE: Due to the security implemented in Inventory
Enterprise, you must have the appropriate privileges to
create, move, or edit locations, substances, or containers.
Please see your system administrator for more details if you
are unable to perform a particular action.
Additional fields
Select database
Select database
Additional fields
Managing an inventory consists of creating, editing,
and organizing the locations, substances, and
containers. A particular user may have privileges to
do some, none, or all of these tasks. It also includes
tracking substance usage, disposal, and ordering.
Inventory facilitates your established procedures
for these tasks, and places all related information in
a central location.
Managing Locations
A location is defined as any “place” that a container,
plate, or another location can be stored. This
includes a laboratory, a refrigerator, or even a
particular shelf. Different facilities can decide how
best to organize locations. Inventory comes with
five special locations: Root, Disposed, Missing, On
Order, and Trash Can. You may edit the names and
other data associated with any of these locations.
You may also delete any locations that you create.
You cannot delete the special locations.
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Location Tree
The location tree control allows navigation of the
Location hierarchy. Click on the +/- symbols to
expand/contract location folders. Click on the
location name to display its contents in the
container list frame.
Desktop/
Workgroup
Right-click on a location to display a
context menu of Location commands.
NOTE: The Inventory Enterprise dialog box (shown)
above contains a field for defining plate types. Plate types
are not currently supported in the Pro/Ultra or
Workgroup versions.
Creating a New Location
To add a new location:
1. Click the New Location link or command on
the Manage menu.
The Create New Location form appears.
2. Enter the parent location (the folder that is one
level up from your new folder). If you pointed
to the parent folder before opening the dialog
box, the correct location will be entered
automatically. You may use the Browse button
for one-click entry of the correct location.
3. Enter the remaining information. Location
Name is the only required field. Inventory will
fill in the Location barcode field automatically
unless you enter your own value. (In either
case, it will assign an internal location ID
number.)
4. When you have finished entering data, click
OK.
The new location appears in the tree under the
parent, in alphabetical order.
Editing a Location
After a location is created, its properties may
change. For example, when a particular laboratory
was initially set up, a number of containers were
placed on a shelf. As the laboratory grew, it was
necessary to move the containers to a cabinet. The
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simplest way to reflect this change in Inventory is to
change the location type. Rather than create a new
location, you can edit the existing location.
To change the properties of a location:
1. Browse to the location to be edited in the
Location Tree.
2. Click the Edit Location link or menu
command.
The Edit Location form appears.
To move a location:
1. Browse to the location to be moved in the
Location Tree.
2. Click the Move Location link or menu
command.
The Move Location form appears.
3. Make sure the information listed in the window
that opens is for the correct location.
4. Enter the desired new information in the
window.
5. Click OK.
Moving a Location
After a location is created, it may be necessary to
move the location to somewhere else in the tree.
For example, a refrigerator may have been located
in a lab on the first floor, but is being moved to a
lab on the third floor. Of course all of the
containers inside the refrigerator are moved along
with it. It is easy to move a location along with all of
its contents in the Inventory system.
3. Make sure the information listed in the window
that opens is for the correct location.
4. Enter the new parent location in the Destination
Location text box.
5. Click OK.
The location and all of its sublocations and
containers is moved to the new parent location.
Deleting a Location
If a location needs to be removed from the
inventory system, you should use the delete location
tool. If the location is merely being moved, see
“Moving a Location” on page 52.
To delete a location:
1. Browse to the location to be deleted in the
Location Tree.
2. Click the Delete Location link or menu
command.
The Delete Location form appears.
NOTE: As a safety precaution, a location can only be
deleted if it is empty. You can override this precaution by
selecting the Recursively delete related locations
and containers checkbox. Use this checkbox with
caution. You cannot undo the deletion of a location.
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Enterprise
Saving a Default Location
The location tree frame allows the user to save a
default location. If a default location is chosen, each
time the user accesses the Container Management
section, the default location will be opened in the
location tree frame.
To save a default location:
1. Browse to the location to be saved as the
default in the Location Tree.
2. Click Make Default in the Location Tree
Frame.
make default
To refresh the Location Tree:
• Click the Refresh link or menu command.
Managing Substances
Substance records store the chemical structure,
formula, and molecular weight information of the
compounds in your inventory. Each record is
identified with a substance ID number, and may
also contain a CAS number and/or ACX number
for cross-reference purposes. If you are logged in as
user INVADMIN, you can also add up to five
custom fields that connecting users can
subsequently populate when defining a new
substance. You can create new substances and edit
them to correct errors.
Creating a New Substance
To create a new substance:
1. Click New Substance under the New
Container Substance Tab.
The default location window appears.
3. Click OK.
Refreshing the Location Tree
If Inventory is being used by more than one
concurrent user, the Location Tree you see may not
be the most current one. The refresh command
repopulates the tree from the most recent available
location data and returns it to its fully contracted
position. If, however, you have a location open
when you choose to refresh, that branch of the tree
is not contracted: the location will remain open for
you to work with.
Enterprise
a. Click Add Mode from the Manage
Substance form
new
substance
select
substanc
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The New Substance form appears.
Enterprise
More fields may appear in your form.
These forms are customized for your site. Please see your
system administrator for more details.
2. Fill in the fields. Substance Name is the only
required field.
NOTE: Custom fields may also be designated as
required.
3. To add a structure, click in the Structure field.
The structure field box is outlined in blue, and
the ChemDraw toolbar appears.
Enterprise
In Inventory Enterprise, the toolbar
appears as soon as you open the New Substance form.
4. When you have finished filling in the fields,
click OK.
When you create a new substance record, Inventory
searches the database for duplicates, and gives you
an opportunity to resolve any conflicts. Only if
there are no conflicts will the substance be added
automatically. If a conflict is found in the database
with any field entry, the Conflict Resolution page
appears. See “Conflict Resolution” on page 54.
Desktop/
Workgroup
Mixtures
Normally, a Substance is defined as a pure chemical
compound. However, Inventory, with some
customization, may be used to define mixtures.
Depending on the approach that makes the most
sense for your users, you could choose to use either
the custom substance fields or the custom
container fields.
For example, to define solvent mixtures commonly
used in reversed phase chromatography, each of
which contain various percentages of methanol,
acetonitrile and tetrahydrofuran, use the custom
substance fields (of which there are five available).
The Substance name would identify the mixture
(e.g. Name = “HPLC Mixture 10% Methanol”),
and the custom compound fields (defined for
example as: Mixture Component 1, Mixture
Component 2, Mixture Component 3, ...) would
identify the exact composition (e.g. Mixture
Component 1 = “10% methanol”, Mixture
Component 2 = “6% acetonitrile”, Mixture
Component 3 = “4% THF”).
This is not, however, the only way to handle
mixtures. Anything you can draw with the
ChemDraw toolbar can be stored in a structure
field—including reactions (with arrows) and labels.
While this may not be particularly useful, and might
cause problems when searching, it does give you the
flexibility to draw multiple structures and define
them as a single substance. Note that the Molecular
Weight and Chemical Formula (which are generated
automatically) will be for the total of all structures
in the field.
Conflict Resolution
Conflict Resolution flags and corrects duplicates in
the system. When creating a new substance in
Inventory, Conflict Resolution runs automatically.
You may also search for duplicates at any time.
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If a conflict is found, a page like this one appears.
The conflicting field(s) are highlighted in red.
Conflict Resolution - Select
To select one of the existing substances rather then
adding a new substance, click Select. You will be
returned to the Create New Container form with
the substance inserted.
O
Cl
Name
conflict
Select
O
Cl
Structure
conflict
In the example above, the existing substance and
the new substance share the same Substance name
and structure.
From here, the user has up to three options:
• Select an existing substance (thus cancelling the
new substance).
• Edit the conflicting substance or the existing
substance so there is no longer a conflict.
• Create a duplicate substance and resolve the
conflict later.
Enterprise
The option to select an existing
substance and abort the new substance
creation, is only available if the user is
currently creating a new container. This
option is not available from the Substance
Management area of the application.
Conflict Resolution - Edit
Create
duplicate
Edit
To edit the duplicate substance or an existing
substance:
1. Click Edit for the appropriate substance.
The substance record appears.
2. Edit the appropriate fields.
3. Click OK.
Conflict Resolution - Create Duplicate
To create the duplicate, click Create Duplicate.
You will be returned to continue creating a new
container with the substance inserted.
Creating a duplicate is not recommended. You must
have administrator permissions to delete duplicate
substances.
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Enterprise
The option to create a duplicate by
adding the new substance regardless of the
conflict, is only available if the user is
currently creating a new container. This
option is not available from the Substance
Management area of the application.
Editing a Substance
The procedure for editing substances is basically
the same in Inventory Enterprise and Pro/Ultra/
Workgroup versions, but requires slightly different
steps. In both versions, you begin by searching for
the substance, then select the substance to be edited
from a hit list.
Desktop/
Workgroup
To edit a substance:
1. Choose Substances... from the Search menu.
The Substances search form appears. For more
information on searching see “Update
Contents” on page 62.
A hit list of matching substances appears.
3. Select a substance.
The substance details appear in the lower pane.
4. Click Edit.
The Create/Edit Substance form appears.
5. Make the desired changes, and click Update.
If a duplicate for any required field is found in
the system, the conflict resolution page
appears. See “Conflict Resolution” on page 54
for more information. If there are no duplicate
fields, Inventory saves the changes to the
database.
Enterprise
To edit a substance:
1. From the homepage, select Manage
Substances.
The Manage Substances screen appears. For
more information on searching see “Update
Contents” on page 62.
2. Fill in the desired field(s) and click Search.
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2. Fill in the desired field(s) and click Search.
A hit list of matching substances appears.
6. Click OK.
If a duplicate for any required field is found
in the system, the conflict resolution page
appears. See “Conflict Resolution” on page 54
for more information. If there are no duplicate
fields, Inventory saves the changes to the
database.
Deleting a Substance
To delete a substance:
3. Click the Details tab for the chosen substance.
A page appears displaying details for the
appropriate record.
Edit Mode
button
1. From the homepage, select Manage
Substances.
2. Perform a search. Click the Details tab for the
substance you want to delete.
3. Click Delete Record in the Details window.
Delete Record
button
4. Click Edit Mode.
The record appears in Edit Mode.
A page appears asking for confirmation.
4. Click OK.
Enterprise
Synonym Management
5. Enter or edit the appropriate information.
The synonym management area of Inventory is part
of Substance Management. To access this section:
1. Perform a search from the Substance
Management area.
2. Click the Details tab for the substance you
want to edit.
A page appears displaying details for the
appropriate record.
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3. Click the Manage Synonyms link.
Manage synonym
The Synonym Management window opens.
This window allows you to add new synonyms for
a substance, edit the synonyms which are already
listed, or delete a synonym from the list.
8. Edit the name of the synonym.
9. Click OK.
To delete a synonym:
10.Click Delete next to the appropriate synonym.
11.If you want to delete this synonym from the
list, Click OK.
If you choose to delete a synonym, you will be
prompted to verify the deletion.
After accessing the Synonym Management window,
to add a new synonym:
4. Click New.
A text field allowing the addition for a
synonym appears.
Managing Containers
Containers are the main focus of Inventory. You
track your use of chemicals, ordering, reordering,
and disposal by tracking the containers.
Creating a New Container
To create a new container:
1. Click the New Container link or menu
command.
New Container
5. Enter a synonym.
6. Click OK.
To edit a synonym:
7. Click Edit next to the synonym to be edited.
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A window with multiple tabs labeled Required,
Substance, Supplier, Contents, Optional,
Owner, Comments, and Other (name may
vary) opens.
Editing a Container
To edit a container:
1. Select a container to edit.
2. Click the Edit Container link or command on
the Manage menu.
2. Enter information about the new container.
Required fields are highlighted with color.
TIP: Substance is not a required field. This allows
you to enter supplies such as glassware or disposables
into the inventory. If you don’t enter a substance, you
will get a warning when you try to create the new
container. You may safely click OK and ignore the
warning. If you don’t want to see the warning, create a
dummy Substance (such as a letter or word) for nonchemical
supplies.
3. Click OK.
Edit Container
The Edit Container form appears. This form is
identical to the Create Container form.
3. Enter new values and click OK.
Moving a Container
To move a container to another location:
1. Select a container to move.
2. Click the Move Container link or command
on the Manage menu.
3. Enter the destination location in the Move
Container form and click OK.
NOTE: Right-click on a container icon to get a context
menu of Container commands. You can also drag-and-drop
containers to move them from location to location.
Enterprise
Check-in/out, Changing
Quantities, and Other Shortcuts
Inventory Enterprise offers several shortcuts to the
full editing form. The most common operations are
checking chemicals in and out of a central
storeroom, and updating quantities as compounds
are used up. Links in the Container Details Frame
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open abbreviated edit forms that allow you to
perform these operations quickly and efficiently.
Other shortcuts available from this frame are:
• Request Container
• Copy Container
• Split Container
• Create Samples
• Move Container
• Delete Container
• History
2. Enter a value for each field. For more
information about a field, click on the image
above.
3. Click OK.
A quantity field for each new container
appears.
NOTE: In the example below, the sum of Container1
quantity and Container2 quantity must equal 24.
Enterprise
Split Container
The Split Container function splits contents of the
current container into new containers, adding the
specified number of new containers. The parent
container will be removed (the container is now
empty). Quantities in the new containers are
updated automatically. When splitting a container,
all of the contents must be used so the sum of the
quantities of the new containers must equal the
quantity of the original container.
To split a container:
1. Click Split Container.
The Split Container dialog appears.
4. Make any changes necessary.
5. Click OK.
Enterprise
Merge Containers
The Merge Containers function merges two
containers (which have the same parent ID) into
one container. If a container has no parent ID, this
function is not available.
To merge two containers (with the same parent ID):
1. Open the first container in Details view.
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2. Click Merge Containers.
NOTE: The Merge Containers function is only
available if the container has a Parent ID.
2. Enter a value for each field. For more
information about a field, click on the image
above.
3. Click OK.
The quantity remaining field is automatically
populated and a quantity field for each new
container appears.
The Merge Containers window appears.
3. Select the container to merge with the currently
selected container. Only the containers with
the same parent ID are listed.
Enterprise
Create Samples
The Create Samples function samples the current
container and creates additional containers from
that container with a specified quantity. The parent
container will remain intact with any remaining
quantity. Quantities in the new containers and the
parent container are updated automatically.
To create samples of a container:
1. Click Create Samples.
The Create Samples dialog appears.
4. Make any changes necessary.
5. Click OK.
Enterprise
Order Container
Users can enter an order for a container that has not
yet been created as part of the Inventory system by
clicking on the Order Container link. If the
container is already in the Inventory system and you
would like to reorder the same container, see
“Reorder Container” on page 62.
Order Container
Reorder Container
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The following window opens when the Order
Container link is clicked:
To reorder a container:
1. Click Reorder Container in the Container
Details Frame.
The Reorder Container window appears.
2. Enter the required information, and any other
information you wish. Click OK.
Enterprise
Update Contents
The Substance, Contents, Owner, and Comments
Tabs appear and react just as the tabs with the same
name in the New Container window react.
The Required Tab in the Order Container window
is also very similar to the New Container window.
The Order Container Required Tab does not
include all of the fields in that of the New Container
Window. Additionally, there are two location IDs:
one for the delivery location and one for the on
order location.
For more information about a particular field, click
on the field in the image above.
To order a container:
1. Click Order Container from the Current
Location Frame.
The Order Container window appears.
2. Enter the required information, and any other
information which you wish.
3. Click OK.
Enterprise
Reorder Container
Users can reorder any container in the Inventory
system, if the container is not already on order. If
the container that you would like to order is not
currently in the Inventory system, see “Order
Container” on page 61.
At times, containers are moved but not updated in
the Inventory system. Update Containers helps
users correct these errors, confirming that a
container actually is where the system thinks it is.
The Update Contents link opens a window
containing a checklist of Inventory containers in a
particular location. This tool is a casual way for
users to confirm the inventory at a particular
location. If a container is not confirmed, no action
is taken—though a correction could be performed
manually. For a tool to correct any discrepancies in
a location's contents, please see “Rectify Contents”
on page 63.
Update contents accomplishes the following:
• Confirms that containers are still where the
system thought them to be.
• Moves containers unexpectedly found at a
location to that location.
• Allows for previously unknown containers to
be created at a location.
To update the contents of a location:
1. Open a location and click Update Contents
in the Container List Frame.
The Update Contents window opens.
2. Using a barcode scanner, or by manually typing
numbers in the ID text box, enter the container
ID for each container found at the location.
NOTE: If you are entering numbers manually, follow
each entry with a TAB.
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3. If you enter an ID number that is not expected
at that location, but the container exists at
another location, a window opens asking you if
you want to move it to the current location. If
the container does not exist, you are asked if
you want to create it.
NOTE: Do not verify or reject moves until all of the
containers at the location have been entered.
4. When you have entered ID numbers for all
containers in the location, and selected or
cleared the checkboxes for unexpected
containers, click OK.
Enterprise
Rectify Contents
ID text box
unexpected
container
window
At times, containers are moved without being
updated in the inventory system. Rectifying updates
the system, confirming that a container actually is
where the system thinks it is.
The Rectify Contents link opens a window that
helps users keep the list of Inventory containers in
a particular location up to date. This tool is a formal
way to correct inventory discrepancies. That is, if a
particular container is not confirmed, that container
is moved to the Missing Location in Inventory.
Rectify Contents is meant to be used on a quarterly
or biannual basis during official inventory
reconciliation efforts. For a less formal tool which
only verifies the existence of a container in a
location, see “Update Contents” on page 62.
Rectify Contents accomplishes the following:
• Confirms that containers are still where the
system thought them to be.
• Moves containers unexpectedly found at a
location to that location.
• Allows for previously unknown containers to
be created at a location.
• Moves any containers that are not explicitly
found to a Missing location.
To rectify the contents of a location:
1. Open the location and click Rectify Contents
in the Container List Frame.
The Rectify Contents window opens.
2. Using a barcode scanner, or by manually typing
numbers in the ID text box, enter the container
ID for each container found at the location.
NOTE: If you are entering numbers manually, follow
each entry with a TAB.
3. If you enter an ID number that is not expected
at that location, but the container exists at
another location, a window opens asking you if
you want to move it to the current location. If
the container does not exist, you are asked if
you want to create it.
ID text box
unexpected
container
window
NOTE: Do not verify or reject moves until all of the
containers at the location have been entered.
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4. When you have entered ID numbers for all
containers in the location, and selected or
cleared the checkboxes for unexpected
containers, click OK.
The following message is displayed if there are
containers listed which have not been verified:
Click OK if you would like containers which have
not been verified moved to the Missing Location.
Enterprise
Multi Select
The Multi Select Link changes the container list
frame to details view and places a checkbox next to
each Container ID. This allows you to select more
than one container and perform one action on all of
those containers at once. The actions available to
Multi Select are:
• Check In
• Check Out
• Move
• Retire
• Delete
• Update
For example, if you would like to move 3 containers
to a new location:
5. Click Multi Select.
The containers are listed in the Details view
with checkboxes next to each container ID.
6. Select the checkbox next to each container you
would like to move.
7. Click Move Containers in the Container
Details Frame.
Enterprise
Managing Plates
Plates are held in locations, much like containers.
For this reason, plates are browsed in the same way
that any other container is browsed.
Plates are indicated as such in the Container List
Frame with a plate icon. When a plate is opened, the
Plate Contents Frame is displayed in the bottom
right frame.
Plates and Containers can exist in the same
location.
Creating New Plates
Inventory Manager does not contain the necessary
tools to create new plates. Plates are created
through the BioAssay HTS interface.
Please see the BioAssay HTS User's Guide for more
details.
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Searching for Plates
Plates are searched for under the plates tab on the
search page. See “Searching for Plates” on page 73
for more information about the Plate Search Tab.
Small Icons
Details
Details Frame
Rectify Contents
Print Report
After performing the search, users are given a list of
matching plates:
Viewing the Contents of a Plate
After performing a search, or navigating through
the location tree, a list of containers and/or plates
is displayed.
List Frame
The container list frame lists plates much like it
does containers. Plates are distinguished from
containers by the plate icon.
Plates are sorted in descending order by plate id, but
can be resorted by clicking any of the column
headers. The small triangle next to the column
name indicates the sorting order. Sorting affects
plates regardless of whether they are displayed on
the current page.
Click on one of the plates in the list to see the plate
details on the frame below.
The following functions are available within the List
Frame:
Multi Select
Column Chooser
All plate attributes are displayed within the Details
Frame Summary Tab. It lists all attributes for the plate,
common to all wells, including plate ID, Barcode,
Plate Type, Plate Name, Plate Format, etc...
The Plate Viewer Tab allows you to view the
contents of the plate in a grid. Click on one of the
wells to view the details for that well.
The following functions are available within the
details frame:
Create Daughter Plates Move Plate
Edit Plate
Retire Plate
Large Icons
Update Contents
Edit Well
Delete Plate
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Creating Daughter Plates
The Create Daughter Plates function allows a user
to create any number of daughter plates from a
parent as long as the parent plate contains enough
contents to fulfill the request. That is, if you would
like to create 6 daughter plates taking 10 ml of a
substance from the source plate which only
contains 10 ml, you will be denied.
To create daughter plates:
Create Daughter Plates - by Source Plate
If by Source Plate Amount was chosen, the
following screen appears:
1. Search for or browse to the source plate.
2. Open the plate in the Details Frame.
3. Click Create Daughter Plates.
The Create Daughter Plate dialog appears.
1. Select Yes if a solvent will be added to the plate
during daughtering.
2. Click Next.
• if No:
4. Select a radio button:
• by Source Plate Amount – enter parameters
based on what is taken from the source plate
• by Target Plate Concentration – enter
parameters based on the characteristics of
the daughter plates
5. Click Next.
• “Create Daughter Plates - by Source Plate”
on page 66
• “Create Daughter Plates - by Target Plate”
on page 67
• if Yes:
3. Enter the appropriate information.
4. Click Next.
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Create Daughter Plates - by Target Plate
If by Target Plate Concentration was chosen, the
following screen appears:
1. Enter the appropriate information.
Click Next.
Create Plate Map
The Create Plate Map function allows a user to
create a plate map based on the selected plate. Plate
maps are virtual representations of plates that store
the plate type, physical plate type, etc of the plate,
but most importantly the substance information for
each well. Plate maps can only be stored in special
plate map locations. New plates can be created
from a plate map.
5. Click OK.
Create a Plate Map Location
Plate Maps are stored in special plate map locations.
To create a plate map location:
1. Click New Location.
2. Enter the appropriate information.
3. Select Plate Map from the Location Type
listbox.
4. Click OK.
This new location is now ready to store plate maps
created.
Edit Plate
The Edit Plate function allows editing of plate and
well attributes. Plates are initially created in
BioAssay so any attributes which can not be
changed are greyed out (e.g. plate format).
To create a plate map:
1. Search for or browse the plate you wish to
create a plate map from.
2. Open the plate in the Details Frame.
3. Click Create Plate Map.
The Create Plate Map dialog appears.
4. Enter the location for the new plate map.
NOTE: Well attributes changed under this interface are
applied to all of the wells in the plate.
To edit a plate:
1. Search for or browse to the plate you wish to
edit.
2. Open the plate in the Details Frame.
3. Click Edit Plate.
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4. Make the appropriate edits to the given plate
and well attributes. Click on the image above
for a description of a particular field.
5. Click OK.
Move Plate
The Move Plate function allows a user to move a
plate from one location to another.
To move a plate:
1. Search for or browse to the plate you wish to
move.
2. Open the plate in the Details Frame.
3. Click Move Plate.
The Move Plate dialog appears.
The Retire Plate dialog appears.
4. Make any necessary changes.
5. Click OK to confirm you would like to retire
6. the plate.
Delete Plate
The Delete Plate function allows deleting of plate
and well attributes.
4. Enter the location you would like to move the
selected plate to.
5. Click OK.
The plate is moved to the new location.
Retire Plate
The Retire Plate function allows retiring of a plate.
Retiring is different than deleting because when a
plate is retired the data is preserved, and the plate is
placed in the Disposed location (unless specified
otherwise), while when it is deleted, the data is lost
permanently.
To retire a plate:
1. Search for or browse to the plate you wish to
retire.
2. Open the plate in the Details Frame.
3. Click Retire Plate.
To delete a plate:
1. Search for or browse to the plate you wish to
delete.
2. Open the plate in the Details Frame.
3. Click Delete Plate.
The Delete Plate dialog appears.
4. Click OK to confirm you would like to delete
the plate.
Searching Inventory
Searching is the easiest way to find particular
substances or containers in Inventory. The system
allows for combined chemical and text searches of
all attributes associated with a container or
substance. Several search forms are available to
accommodate the search preferences of different
users. For example, the Substructure Search form,
for searches based on chemical structure, substance
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name, CAS number and other attributes, is
particularly well suited for use by chemists.
Similarly, the Advanced Search form, which
exposes fields such as container and location
barcode, is particularly well suited for use by stock
room or receiving room personnel.
Catalog Number, Substance Name, Substance
Synonym, Container Name, Container Comments,
and/or Location ID.
Enterprise
The Global Search form allows you
to search over the Inventory, Registration System,
and ChemACX databases simultaneously if all three
applications are installed on the server.
Enterprise
The Plate Search form allows you to
search over fields unique to plates, such as Plate
Format and Freeze/Thaw Cycles.
Searching for Containers
To begin a search:
• Click the Search Containers link or menu
command.
This displays a tabbed search form for all search
types. Click on the tab indicating the type of search
you would like to perform, and enter your search
parameters.
Simple Search
The Simple Search option allows you to use any
combination of basic criteria, such as CAS Registry
number, Container Barcode, Location Barcode,
How to search:
1. Enter the search criteria.
2. Select the Search Sublocations checkbox if you
want to search all sublocations of the chosen
location.
3. Click Search.
NOTE: Inventory always does “substring” searches on text
queries. Thus, entering benz in Substance Name will
return Benzene, Benzyne, Bromobenzene, and so forth.
A list of containers matching your search
parameters is returned. Clicking one of the
containers will allow you to view the location of the
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container (left frame), container information (upper
right frame), and the contents of the container (lower
right frame).
information
location
contents
Advanced Search
The Advanced Search option adds a number of
categories to the basic Simple Search, such as Purity,
Concentration, Grade, Container Size, Container
Status, Unit of Measure, Quantity Remaining, and
so forth.
This search concentrates more on container
properties as opposed to substance properties.
2. Select the Search Sublocations checkbox if you
want to search all sublocations of the chosen
location.
Enterprise
3. Select the Exclude Special
Locations checkbox if you want to exclude
special locations (such as Trash Can.)
4. Click Search.
A list of containers matching your search
parameters is returned. Clicking on one of the
containers will allow you to view, the location of the
container (left frame), container information (upper
right frame), and the contents of the container
(lower right frame). See “Managing Containers” on
page 58 for more information.
Substructure Search
The Substructure search option includes most of
the criteria in the Advanced Search, in addition to
Substance Name, Molecular Formula, MolWeight
Range, and of course, Substructure.
To draw a structure, double-click in the structure
box. Use the ChemDraw toolbar to draw your
substructure. For more information about using the
ChemDraw toolbar, see Drawing Chemical
Structures in the ChemDraw User's Manual.
OH
COOH
How to search:
1. Enter the search criteria.
Custom fields, if defined, will appear on this
search form. Any additional fields have been
defined for your site. Please see you system
administrator for more details.
You may include generic atom types, such as X for
any halogen, or R for an unspecified organic group,
in your query structure. In fact, you can include any
query specifications (except those specific to
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eactions) available in ChemDraw. For more
information, see Drawing Query Structures in
the ChemDraw User's Manual.
You have a choice of how Inventory will match the
structure you draw to the structures in the
Inventory database. Select the correct type from the
Search Type drop-down menu.
Substructure
Substructure searches find structures that contain
the query, plus any additional attachments at the
open positions. Use this search type to find classes
of compounds.
Search Preferences
You can set a number of defaults that affect how
Inventory performs structure searches.
Desktop/
Workgroup
• Workgroup Click Preferences in the File
menu (or on the Search form.)
Enterprise
• In the Manage Substances Page,
click File on the toolbar, then select
Preferences.
The Search Preferences form appears.
Exact
Exact searches find structures that completely
match the query. You may get more than one hit if
there are stereo-isomers in the inventory and you
did not specify a particular one to be matched, or if
you included a generic atom type.
Identity
The Identity search type is intended for use in
compound registration, when you must know if a
perfectly identical copy of your query compound is
already present in the database. It is similar to an
exact search, except that generic atom and bond
types in the query must match corresponding atom
and bond types in the target exactly. Moreover,
stereochemistry must match precisely between
query and target.
Similarity
A Similarity search finds structures that have
structural features that generally correspond to
those in the query. Similarity searches are, by their
nature, “fuzzy”. For this reason, similarity searches
are useful if you have a general idea of the types of
compounds you are looking for, but don’t have a
precise conception of the target compound.
How to search:
1. Enter the search criteria.
2. Select the Search Sublocations checkbox if you
want to search all sublocations of the chosen
location.
Enterprise
3. Select the Exclude Special
Locations checkbox if you want to exclude
special locations.
Enterprise
4. Select the Group results by
chemical structure checkbox if you want results
grouped by chemical structure.
5. Click Search.
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A list of containers matching your search criteria is
returned.
Enterprise
If you selected the Group results by
chemical structure checkbox (the default), a list of
substances matching your search criteria is
returned. Clicking on the Details tab of one of the
substances will allow you to view all of the
inventory containers that contain that substance.
Desktop/
Workgroup
How to search for substances:
1. Select Substances from the Search menu.
The Search Substances form appears.
NOTE: The Details tab is only active if there is an
associated container.
For information about Searching for substances
and their properties, see “Searching for Substances”
on page 72.
Searching for Substances
Searching for substances is the same as the
Substructure search option for containers, except
that you begin from a different place, and fewer
fields are displayed. Perform a substance search to
edit a substance record or search for duplicates.
NOTE: Your form may not have the same number of fields,
depending on whether or not custom fields have been created.
Entering search criteria and performing the search
are exactly the same as with a Container search. See
“Substructure Search” on page 70 for details.
2. Enter search criteria and click Search. If you
are searching for duplicate substances, select
the checkbox at the top of the form. Inventory
will search for duplicates according to the fields
you enter. For more information on resolving
duplicates, see “Conflict Resolution” on page
54.
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A hit list appears.
3. Select a substance from the hit list.
A details frame opens in the lower pane.
4. Click Edit to edit the substance details. For
more information, see “Editing a Substance”
on page 56.
5. When you have finished editing, click OK.
NOTE:
Right-click on a substance
icon to delete a substance or locate its containers.
Enterprise
Desktop/
Workgroup
How to search for substances:
1. Select Manage Substances from the Home
page.
The Manage Substances page includes a search
form.
Entering search criteria and performing the search
are exactly the same as with a Container search. See
“Substructure Search” on page 70 for details.
2. Enter search criteria and click Search. If you
are searching for duplicate substances, select
Duplicate Compounds from the drop-down
menu in the Compound Type field. Inventory
will search for duplicates according to the fields
you enter. For more information on resolving
duplicates, see “Conflict Resolution” on page
54.
A hit list appears, as with a container search
when the Group results by chemical structure
checkbox is selected.
3. Click the Details tab for the substance you wish
to edit.
The substance details are displayed.
NOTE: If only one match is found, the details are
displayed directly.
Edit Mode
Delete
Search
button
Compound Type
NOTE: Your form may not have the same number of fields,
depending on your installation.
4. Click Edit Mode to edit the record. For more
information, see “Editing a Substance” on
page 56.
5. When you have finished editing, click OK.
Enterprise
Searching for Plates
The plate search option allows searching through
the use of Substructure, Substance Name, CAS
Number, ACX Number, Molecular Formula,
MolWeight Range, Purity, Concentration, Solvent,
Location ID, Plate Barcode, Plate ID (internal),
Plate Name, Plate Type, Plate Status, Unit of
Measure, Qty Remaining, Qty Initial, Molar
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Amount, Supplier Name, Supplier Shipment Code,
Supplier Shipment Number, Supplier Shipment
Date, Date Created, Plate Format, Library, Plate
Group, and Freeze/Thaw Cycles.
How to search:
1. Enter the desired information to search for.
For more information about entering search
criteria, see “Searching ChemOffice
WebServer Applications” on page 168.
2. Select the Search Sublocations checkbox if you
want to search all sublocations of the chosen
location.
3. Select the Exclude Special Locations checkbox
if you want to exclude special locations.
4. Click Search in the toolbar.
A list of plates matching your search parameters is
returned. Clicking on one of the plates will allow
you to view, the location of the plate (left frame),
plate information (upper right frame), and the
contents of the plate (lower right frame).
Enterprise
Global Search
The Global Search form allows users to search over
the Registration System, ChemACX, or both,
simultaneously with an Inventory search. When
results are returned, Inventory, Registration, and
ACX results remain separate, but the application
indicates if the retrieved substance is found in any
inventory containers.
The global search option allows searching through
the use of Substance Name, CAS number, ACX
number, Molecular Formula, MolWeight Range,
Registry Number, Registry Sequence, Reg Alternate
IDs, and Substructure.
How to search:
1. Select the checkboxes next to the applications
you would like to search over.
2. Enter the query information. For more
information about entering search criteria, see
“Searching ChemOffice WebServer
Applications” on page 168.
Additional fields may appear on this search
form. Any additional fields have been defined
for your site. Please see you system
administrator for more details.
3. Click Search.
A list of substances matching your search
parameters is returned.
4. Click on the radio button next to the
appropriate application to see results retrieved
from that application.
Viewing Results from a Global Search
Search results from a global search are split into
three lists, one for each application. To access
results from an application, select the radio button
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next to the application's name. Results are initially
listed by substance. To view the results by container,
click the Details tab for a substance.
NOTE: The Details tab is only active if there is an
associated container.
Browse Results by Container
Global Search - Registration System
Substances
Inventory result records for Registration System
substances are identified by a blue color scheme.
These substances are linked directly to the
Registration System to allow the user to retrieve
Registration data from Inventory.
Browse Results by Substance
To retrieve Registration System or ChemACX data
for a substance, click the linked Registration
number or ACX number respectively.
• Click the linked Reg# to view the record for
this substance in the Registration System
• Click Names to view a list of alternate IDs for
the substance.
• Click Details to view containers with this
substance
• Click Mark to mark the record. For more
information about marked records, please see
Marking Records.
Global Search - ChemACX Substances
Inventory result records for ChemACX substances
are identified by a a red color scheme. These
substances are linked directly to ChemACX to allow
the user to retrieve ACX data from Inventory.
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• Click the linked ACX# to view the record in
ChemACX
• Click ACX to view the record in ChemACX
• Click Inv to view containers with this
substance
• Click Mark to mark the record. For more
information about marked records, please see
Marking Records.
Printing Labels and
Reports
Inventory Pro/Ultra/Workgroup
uses the List & Label reporting utility from Combit
GmbH. Detailed information on creating
customized reports can be found in List & Label’s
Help, available from the Inventory Report dialog
box. This document describes how to use the builtin
templates to produce basic reports and barcode
labels, as well as how to design more advanced
reports.
Help
Enterprise
Custom labels and reports can be
printed from the Inventory interface. Inventory
Enterprise uses Microsoft Access reports to
accomplish this. For more information about
creating Custom Labels and Reports in Inventory
Enterprise, see your Inventory Enterprise Admin
Guide.
Desktop/
Workgroup
TIP: In the Reporting tab of the Application Configuration
dialog box, you can set the default format for Help to either
PDF or MSWord doc.
Labels
The standard Inventory Ultra/Pro/Workgroup
installation includes two sample barcode label
templates, one with compound name and barcode
number, the other with only the barcode number.
You may also design your own labels.
To print labels with a standard template:
1. Select a location.
2. Choose Labels... from the Report menu.
The Inventory Report dialog box appears, with
Label selected as the Report Type.
3. Click the Print/Preview/Export... button.
The Generating Labels window appears.
4. Select a label template and click the Open
button.
TIP: If you click Open without selecting a file, you
will activate the template Wizard to help you design a
new template.
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The Print Options dialog box appears.
Direct to
3. Proceed as with multiple labels. The only
difference is that the data for a single label only
has been passed to the print utility.
To create a new label template:
1. Select a location.
2. Choose Labels... from the Report menu.
NOTE: If there are no containers in the location you
have selected, you will get an error message.
5. Use the Direct to... drop down menu to select
Preview mode, or to send the output to a file
instead of printing.
6. When you have selected your options, click
Start.
Labels are printed for all of the containers in
the selected location.
TIP: Note the Start Position option. It allows you
utilize partially used label sheets by adjusting the start
position.
To print a label for a single container:
1. Select a container, either by browsing or
searching.
2. Click the Print Label link on the Summary tab
of the Substance Details section.
S
NH 4
N
S
Start
position
Print
label
The Inventory Report dialog box appears, with
Label selected as the Report Type.
3. Click the Design... button on the Inventory
Report dialog box.
4. Enter a new file name in the File Name text
box of the Generating Labels window.
The List & Label Project Wizard appears to
walk you through the new label creation
process.
To change the label style:
1. Select a location.
2. Choose Labels... from the Report menu.
3. Click the Design... button on the Inventory
Report dialog box.
4. Select an existing label template and click the
Open button.
The List & Label design page appears.
5. Select Page Setup from the Project menu.
6. Select the Templates tab.
7. Locate your label style on the list of Avery,
ERO, Herlitz, Herma, and Leitz standard
labels, and double-click to select it, then click
OK.
8. Adjust the label components to fit the new
label size as necessary, then close and save your
changes to the label file.
NOTE: You may want to test for the positioning of the
printed labels by printing a a sample page and adjusting
the dimensions in the designer as necessary.
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Administrator
Reports
Inventory Ultra/Pro/Workgroup can print reports
in two basic styles: with structures and without.
When you choose Location Report (include
structures), Inventory creates graphic files (*.emf)
from the structural data to import to the print
utility. This can be a time-consuming process,
especially for a large inventory. You should consider
the time factor when deciding which report
command to use.
NOTE: The names of all of the available report templates
appear when you select either report type. If you select a
template with structures, but are using the command that
does not save images of the structures, the Structure column
of the report will be blank.
Printing reports is similar to printing labels: select a
location, select the style of report to print from the
Report menu, and step through the dialog boxes. As
with printing labels, you can design your own
template rather than selecting one of the existing
ones.
TIP: The Print Preview option in the Print Options dialog
box allows you to print, save to file, or send an email of the
report in PDF, text, or graphic format.
Administration
Inventory provides an interface to some frequently
used administrative tasks. This interface is not
available to all users. If you feel you need access to
this interface, please see your system administrator.
Inventory Tasks
The following tasks are available to users with the
correct administrative privileges. If you do not have
access to something you need access to, please see
your system administrator:
• Search
• New Location
• Edit Location
• Move Location
• Delete Location
• Plate Settings
• Change Password
• Manage Users
• Manager Roles
• Manage Requests
• Manage Tables
• Reconcile Location
• Analyze Audit Trail
• Custom Reports
In Inventory Pro/Ultra/Workgroup, the tasks
specifically limited to Administrators are:
• Adding and removing Users
• Deleting substances
• Defining custom fields
• Locking/unlocking records
Regular users are not otherwise limited in
performing Inventory tasks.
Managing Users and Roles
Enterprise
Please see “Manage Users and Roles”
on page 167 for more information concerning
managing users and roles.
Desktop/
Workgroup
To manage users, you must have
SQL Server super-administrator (sa)
privileges, or local administrator privileges if
you set Trusted Connections during Setup.
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Administration

To create or delete a user account:
1. Click the arrow next to Setup on the Login
screen.
To change a password:
1. Click the arrow next to Setup on the Login
screen.
2. Select Change Password from the drop
down menu.
NOTE: Users can change their own passwords; you
do not need administrative privileges to change a
password.
2. Select Inventory User from the drop down
menu.
The User form appears.
3. Enter your administrator password, then enter
the user information and click the appropriate
button.
The user name is added to or deleted from the
list.
3. Enter the username, old password, and new
password. Click Save.
You are returned to the Login dialog box. Your
new password is now active for use.
Managing Tables
Some fields in Inventory forms are entered from
drop-down menus rather than by typing in text.
Inventory stores these pre-set field entries in tables
that can be edited by administrators. If, for example,
you want to specify a type of Container that is not
on the container type menu, the new type can be
added. You can also delete items from the tables,
provided they are not being referenced by any
records in the Inventory database.
Enterprise
To edit a table:
1. Click the Tasks link.
Tasks
The Administrative task list appears.
2. Select Manage Tables from the list.
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3. Select the table to be edited from the dropdown
menu.
The table is displayed.
New Row
3. Press the Delete key, then click Save.
Inventory stores the changes to the table.
Custom Fields
There are a limited number of custom fields built in
to the Inventory application.
To expose and use the custom fields in Inventory
Enterprise, see the Inventory Enterprise Admin
guide.
4. Select the appropriate command (Edit, Delete,
or New Row).
5. Edit the text and Close the window.
Inventory stores the changes to the table.
Desktop/
Workgroup
To edit a table:
1. Select the table to edit from the Data menu.
2. Fill in the attributes in the form that appears,
and click OK.
Inventory stores the changes to the table.
To delete a table entry:
1. In the Data menu, point to Delete and select
the table to edit.
The table is displayed.
Desktop/
Workgroup
If you have Inventory administrative
privileges, that is, if you are logged in as
“invadmin”, you can add custom fields to
compound and container records. Compounds can
have up to five custom fields. Containers can have
up to ten custom fields and five custom dates.
Custom fields and dates can be designated as
required fields. Custom compound fields can be
marked for duplicate checking.
To add custom fields:
1. From the File menu, point to Preferences and
select Custom Fields.
The Custom Fields dialog box appears.
2. Select the entire row you wish to delete.
2. The Custom Fields form has two tabs: one for
compounds and one for containers. Click the
appropriate tab, and enter the name of the new
field(s).
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The fields will appear on the blank forms when
you open them.
NOTE: The custom fields appear directly on the
Compound form. For containers, they appear on the tab
labeled “Custom”, and when applicable, on the tab
labeled “Substance”.
Record Locking
Administrators can turn record locking on or off.
When record locking is turned on (the default), a
record (that is, a container or a substance that’s
being edited) can only be accessed by one user at a
time. An administrator can unlock records to allow
immediate concurrent access. When records are
locked, a second user attempting to edit an open
record will receive a notification message that the
record is currently open, and cannot be accessed.
To adjust the column widths or change the fields
displayed in the Inventory Enterprise Container
List frame, click Column Chooser in the Container
List Frame.
Desktop/
Workgroup
• From the File menu, point to Preferences and
select Container Grid Display.
The Grid Display form appears.
If a user leaves a record open, but inactive, for more
than 10 minutes, the lock times-out, and other users
can access the record. When the original user
returns to the record, a message is displayed
warning the user to resave any changes.
You can change the Field Name, Column Order,
and Column Width. You can also select which fields
will be displayed. Clicking the name of a column in
the grid form sorts the entries by that column. This
is to facilitate rapid editing; it does not affect the
display.
The default names of custom fields in the Grid
Display is as follows:
Managing the Container list
display
Any user can adjust the display of fields in the
Container list. Changes will be viewed by all users.
Enterprise
Custom Field
Container Fields
Container Dates
Substance Fields
Field Name
Field_1 etc.
Date_1 etc.
ALT_ID_1 etc.
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Enterprise
Analyze Audit Trail
The Analyze Audit Trail tool allows users to filter
and view actions taken on containers, locations,
compounds, or links.
Standard Audit Report
The Standard Audit Report allows users to filter by
Table, User, RID, LocationID, ContianerID, Date,
Action, or CompoundID.
3. Click Filter.
To filter and display the report:
1. Click Analyze Audit Trail and make sure the
Standard Link, in the upper frame, is chosen.
2. Enter your filter criteria.
• Table – the name of table (Containers |
Locations | Compounds | Links)
• User – the user who performed the action
• RID – the action ID number (entered as a
range)
• LocationID – the location ID
• ContainerID – the container ID
• From Date – actions made after this date
• To Date – actions made before this date
• Action – type of SQL action (Update |
Delete | Insert)
• CompoundID – the compound ID
The results are displayed in the lower frame.
Aggregate Audit Report
The Aggregate Audit Report allows users to filter
by Table, User, Date, or Action. This report does
not give every step in the audit trail, like the
Standard Report, but instead provides a summary
of actions.
To filter and display the report:
1. Click Analyze Audit Trail and make sure the
Aggregate Link, in the upper frame, is chosen.
2. Enter your filter criteria.
• Table – the name of table (Containers |
Locations | Compounds | Links)
• User – the user who performed the action
• From Date – actions made after this date
• To Date – actions made before this date
• Action – type of SQL action (Update | Delete
| Insert)
3. Select Fields to display and group by selecting
the checkboxes next to Table Name, Modified
By, an Action.
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4. Indicate how date dependant data should be
grouped by selecting the appropriate radio
button next to Hour, Day, Month or Year.
5. Click Filter.
The results are displayed in the lower frame.
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Inventory Tasks

Chapter 5: Discovery LIMS
Overview
Discovery LIMS is a Web-based application
designed to manage the communication between
people who need to depend on each other to
achieve a common objective (for example between
synthetic chemists, who make compounds, and
analytical chemists, who fully characterize
compound samples). With Discovery LIMS
(DLIMS), users make requests of each other and
the software automatically tracks the history of each
request. Managers are able to assign tests to
different resources, and individuals performing
tests are able to ask questions of those who
originated requests. Users are able to search over
their requests by a range of test and result attributes.
Extensive security features are supported.
A key feature of DLIMS is its integration with
ChemOffice WebServer and the ChemOffice
Webserver Registration System. Through this
integration, DLIMS uses are able to integrate
chemical structures, including substructure search,
inside the request management environment.
DLIMS is not GMP compliant, nor is it compliant
with 21 CFR Part 11.
Searching
DLIMS provides a powerful set of searching
features allowing the user to search by materialrelated
information (e.g. by substructure), or
request and related information.
Results are listed, for any search, as a list of requests
matching the search query. For example, a structure
search will return all requests for service that
involve a material that includes the query
substructure. Requests returned are grouped by
material. Therefore, a user can view the complete
history of requests for service and related results,
for a material, from the search results.
Searches are performed using a Query Input Form,
similar to those found in other ChemOffice
WebServer applications. The user enters as many
criteria as desired in the search form, and the search
is performed using ALL criteria. For example, it is
possible to search for requests pertaining to
compounds that include a given substructure AND
that have been completed within the last year.
To navigate to the Search window:
• Click Search from the DLIMS homepage.
The Search Form appears.
To perform a search:
1. Select the radio button next to either Materials
or Requests, at the top of the page.
2. Enter search criteria.
3. Click Submit.
Search results are returned.
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Browsing
Search results are returned in a Request Tree
display. The Request Tree is the primary mechanism
for viewing requests. This display helps the user to
visualize relationships between requests and view
the entire history or workflow pertaining to a
material for which services have been requested.
Test Details
The Test Details button opens a window containing
all available information for the selected request.
To view the details of a request:
1. Highlight the appropriate request in the
Request Tree.
2. Click Test Details.
Material On/Off
Detailed information about the material to which a
request pertains is accessible by using the Material
On/Off button.
Requests are grouped by material. After a search,
materials that match the search criteria or have
requests that match the search criteria are displayed.
If the search was based on material information, the
materials may not have requests associated with
them already. In the Request Tree, a "+" sign
appears to the left of the material or request
indicating more information is available if:
• there is a request associated with the material
• a request is super ordinate to another request
• there are results associated with the request
Expand All
The Expand All button will expand all materials
and requests containing subordinated information.
Contract All
The Contract All button will contract all expanded
materials and requests containing subordinated
information.
Clicking on Material On/Off will toggle the
Material Frame on and off for the currently selected
Material ID. The Material Frame, when activated,
appears in the left of the tree frame. All available
information for the material is displayed in the
frame including:
• Structure
• Molecular Weight
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Browsing

• Molecular Formula
• Registration Date
• Structure Comment
• Chemical Name
• Synonym
• Identifiers
New Request
The New Request button brings up the New
Request window, enabling the user to enter a new
request. For more information about making new
requests, see “Creating a New Request” on page 89.
Reports
Microsoft Word and Microsoft Excel reports are
available for any search results list. To create a
report:
1. From a search results page, highlight what you
would like a report of (for a report of all results,
skip this step).
2. Click Report.
3. A page allowing you to choose a report type
appears.
New Action
The New Action button brings up the New Action
window, enabling the user to enter a new action for
the selected Request. For more information about
new actions, see “Creating a New Action” on page
89. This button is not valid for Material listings.
To enter a new action:
1. Highlight the appropriate request in the
Request Tree.
2. Click New Action.
3. Enter desired information.
4. Click Submit.
4. Select the type of report you would like.
• Metrics - Microsoft Excel report of ALL
search results.
• Test Details - Microsoft Word report for the
highlighted entry. Select the checkboxes next
to the data you would like included in the
report.
Search
The Search button returns the user to the Search
Page. For more information about searching, see
“Searching” on page 85.
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Your report appears.
NOTE: To save the report, be sure to close the browser first,
for the browser holds control of the document until it is closed.
Home
The Home button will return the user to the
DLIMS homepage.
Working with Requests
and Actions
There are two fundamental entities that the
Discovery LIMS application manages:
• Requests
• Actions
A request is a request for a service (e.g. an analytical
test of some kind). Each request has a series of
Actions associated with it that represents the
history of all steps taken to fulfill a request.
Requests are only modified by taking an Action. For
example, when a New Request is created, the
following steps are taken:
1. A Create Request action is recorded in the
database for the new request
2. When a user wants to add results for a test, the
user performs the Add Results action to add
results associated with the request.
In this way, a full audit trail is associated with each
request. One benefit of this strategy is the ability to
collate how long it takes to perform certain tasks
and to, in general, develop performance metrics
that will help improve over-all business processes.
Organizing requests is a key aspect to using DLIMS
successfully. Requests may be ordered
hierarchically. For example, you could create a
request of type "Study" and then group the
individual tests that comprise the "Study", of
whatever kind, under the "Study". Using this
feature, you can adapt DLIMS to different
workflows and track the progress of materials
through processes utilizing complex business rules.
At this time, DLIMS does not provide functionality to
enforce these business rules, so it is essential to train users
thoroughly.
All requests in DLIMS are associated with a
material on which the requested tests are
performed. Internal identifiers for each request are
generated, but these are not displayed to the users
of the software. Extensive search functionality is
provided to make it easy to find the appropriate
requests.
When a request or action is made, an email is sent
to the following individuals:
• The responder of the action
• Everyone with admin privileges
• Lab Manager
For more information about configuring your
system to use this email feature, please see “Setting
Up Email Features” on page 96.
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Working with Requests and Actions

Creating a New Request
To create a New Request:
1. Search for the material for which you would
like to make a service request. For more
information about searching, please see
“Searching” on page 85.
2. Select the appropriate object in the tree view
(either a material or another request) you would
like the request to appear directly under.
3. Click New Request.
The New Request Form appears with the
Material Identifier and Name of the material to
which the request belongs.
4. Select the Lab to which you want to assign the
New Request.
5. Select the kind of test the New Request is for.
6. Select the person who the New Request should
be assigned to.
7. Enter any comments.
8. Click Submit.
Creating a Request Short-cut
To create a top-level request (i.e. a request not
organized beneath another request), it is not
necessary to access the search page. Instead, click
New Request from the DLIMS Homepage.
To make a New Request:
1. Click New Request from the DLIMS
Homepage. A form appears allowing you to
enter a Material Number and Batch Number.
2. Enter the Material Number and Batch Number
for the compound on which you would like to
request service.
3. Click Submit.
The New Request form appears with the
Material Identifier and Name of the material to
which the request belongs.
4. Select the Lab to which you want to assign the
New Request.
5. Select the kind of test your New Request for
service is for.
6. Select the person to which you would like your
New Request for service assigned to.
7. Enter any comments.
8. Click Submit.
Creating a New Action
To create a New Action:
1. Search for the Request on which you would like
to take a New Action. For more information
about searching, please see “Searching” on
page 85.
2. Highlight the Request on which you would like
to take the New Action.
3. Click New Action.
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Administrator
The New Action form appears with the
Material Identifier, Material Name, Request
and Lab pertaining to the selected request.
4. Select the person to which you would like the
request to be assigned based on the New
Action you are taking.
5. Select the type of action you wish to take.
6. Select the Status of the request for service.
Adding and Modifying
Results
Adding results is a special type of action. To add
Results to a Request for service:
1. Search for the Request to which you would like
to add results. To navigate to the Search form,
click on the Search button in DLIMS Home.
2. Highlight the Request to which you would like
to add results.
3. Click New Action.
The New Action form appears with the
Material Identifier, Material Name, Request
and Lab pertaining to the selected request.
4. Select the person to which you would like the
request to be assigned based on the New
Action you are taking.
5. Select the Add Results action.
6. Select the Status of the request for service.
NOTE: Every time an Action is taken, the status of
the request for service is updated.
NOTE: Every time an Action is taken, the status of
the request for service is updated.
7. Enter any comments.
8. Click Submit.
NOTE: You may not be able to perform all actions. Which
actions are available depends on the user's lab and security
level.
7. Enter any comments.
8. Click Submit.
The Add Results window appears. Results
previously entered are displayed.
9. Enter or modify result values as appropriate.
10.Click Submit.
The results are added to the database and
visible in the main tree.
NOTE: You may not be able to perform all actions. Which
actions available depends on the user's lab and security level.
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Working with Requests and Actions

Viewing Request Details
To view details about a Request for service and the
history of Action taken on this Request:
1. Search for the Request on which you would like
to take a New Action. For more information
about searching, please see “Searching” on
page 85.
2. Highlight the appropriate Request.
3. Click Test Details.
The Test Details form appears.
5. Confirm that you want to delete the Request,
all child Requests and all Actions pertaining
thereto.
DATA LOSS WARNING: If a Request is deleted, all
requests grouped under the deleted request will also be deleted.
SECURITY NOTE: Only DLIMS Administrators are
able to delete Requests.
Administration and
Configuration
A key aspect to DLIMS is its configurability. Using
the Administration application, which is accessible
only to users with the required security level,
DLIMS may be configured to meet a great variety
of workflows. The following items are managed
with the Administration component:
Deleting Requests
To delete a Request for service:
1. Search for the Request on which you would like
to take a New Action. For more information
about searching, please see “Searching” on
page 85.
2. Highlight the appropriate Request.
3. Click Test Details.
The Test Details form appears.
4. Click Delete Request.
• Action Types
• Labs
• Status Types
• Test Types
• Test Attributes
• Users and Security Definitions
With DLIMS, users create Test Requests by asking
that a given Test Type be performed for them by a
certain Lab. Users may also enter Actions for each
test, such as Material Sent or Material Requested. Each
action is associated with a person who initiates the
action and a person who is responsible for the next
action. Whenever an Action is performed, the
Status of the Test Request is set. There are certain
special Actions such as Add Results. When this
Action is taken, a screen appears for users to enter
results.
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Administrator
Actions and Test are associated with security levels.
Some actions may only be performed by users in
the Lab to which the Action is assigned. Other
actions may only be performed by Lab Managers. If
users do not have access to a certain Action,
Request or Status, they do not see them.
Administrators map DLIMS to specific workflows
by adding values for the administration items using
the appropriate forms.
To access the Administration functions, click
Administer from the DLIMS Homepage.
3. Select "Yes" or "No" from the Same Lab
drop-down menu. If Yes is selected, then only
users from the same lab as the test is assigned
will be able to perform the action. For example,
if the Action is REGULATORY APPROVE
and the Yes option is selected, then only users
assigned to the Regulatory lab will see the
REGULATORY APPROVE action when they
take action on a test request.
4. Click Add.
To modify an action,
Actions
To access the Action Types form:
• Click Actions from the Administration page.
The Actions page appears.
To create a new action:
1. Scroll to the bottom of the page and enter a
name for the new action in the Action Name
column. It is recommended that you enter an
intuitive name as this value will be displayed
throughout the application.
2. Select a Role from the Required Privilege
Level drop-down. Only users with the required
privilege level or above will see this item in the
Action drop-down menus in the Create
Requests and the Create Action screens.
1. Click Edit to the left of the action you want to
edit.
The input values for this action appear in the
text boxes at the bottom of the page.
2. Scroll to the bottom of the page and edit the
values for this action as necessary.
3. Click Submit found at the top of the page to
save your changes.
To retire an action:
1. Click Retire to the left of the action you want
to retire.
2. Click OK to confirm.
Labs
To access the Labs form:
• Click Labs from the Administration page.
The Labs page appears.
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To create a new Lab:
1. Scroll to the bottom of the page and enter a
name for the new Lab in the Lab Name
column. It is recommended that you enter an
intuitive name as this value will be displayed
throughout the application.
2. Enter a Location Name in the Location
column.
3. Select a Manager from the Manager dropdown
menu.
4. Click Add.
To modify a Lab,
1. Click Edit to the left of the lab you want to
edit.
The input values for this Lab appear in the text
boxes at the bottom of the page.
2. Scroll to the bottom of the page and edit the
values for this Lab as necessary.
3. Click Submit found at the top of the page to
save your changes.
To retire a Lab:
1. Click Retire to the left of the lab you want to
retire.
2. Click OK to confirm.
Status
To access the Status form:
• Click Status from the Administration page.
The Status page appears.
To create a new Status:
1. Scroll to the bottom of the page and enter a
name for the new Status in the Status Name
column. It is recommended that you enter an
intuitive name as this value will be displayed
throughout the application.
2. Select a Role from the Required Privilege
Level drop-down. Only users with the required
privilege level or above will see this item in the
Status drop-down menus.
3. Select "Yes" or "No" from the Same Lab
drop-down menu. If Yes is selected, then only
users from the same lab as the test is assigned
will be able to perform the Status. For example,
if the Status is REGULATORY APPROVE
and the Yes option is selected, then only users
assigned to the Regulatory lab will see the
REGULATORY APPROVE Status when they
take Status on a test request.
4. Select "Yes" or "No" from the Stops Clock
drop-down menu.
5. Click Add.
To modify a Status,
1. Click Edit to the left of the status you want to
edit.
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The input values for this Status appear in the
text boxes at the bottom of the page.
2. Scroll to the bottom of the page and edit the
values for this Status as necessary.
3. Click Submit found at the top of the page to
save your changes.
To retire an Status:
1. Click Retire to the left of the status you want
to retire.
2. Click OK to confirm.
Test Types
To access the Test Types form:
• Click Tests from the Administration page.
The Test Types page appears.
2. Scroll to the bottom of the page and edit the
values for this Test as necessary.
3. Click Submit found at the top of the page to
save your changes.
To retire a Test:
1. Click Retire to the left of the test you want to
retire.
2. Click OK to confirm.
Test Attributes
To access the Test Attributes form:
• Click Attributes, on the Test Types page found
to the left of any test for which you want to edit
the attributes.
The Test Attributes page appears.
To create a new Test:
1. Scroll to the bottom of the page and enter a
name for the new Test in the Test Name
column. It is recommended that you enter an
intuitive name as this value will be displayed
throughout the application.
2. Select a Role from the Required Privilege
Level drop-down. Only users with the required
privilege level or above will see this item in the
Test drop-down menus in the Create
Requests and the Create Test screens.
3. Click Add.
For information about editing the attributes of a
test, please see “Test Attributes” on page 94.
To modify a Test,
1. Click Edit to the left of the test you want to
edit. The input values for this Test appear in
the text boxes at the bottom of the page.
To create a new attribute:
1. Scroll to the bottom of the page and enter a
name for the new Attribute. It is recommended
that you enter an intuitive name as this value
will be displayed throughout the application.
2. Select a Datatype from the Datatype dropdown
menu.
3. Click Add.
To modify an Attribute,
1. Click Edit to the left of the Attribute you want
to edit.
The input values for this Attribute appear in
the text boxes at the bottom of the page.
2. Scroll to the bottom of the page and edit the
values for this Attribute as necessary.
3. Click Submit found at the top of the page to
save your changes.
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To retire an Attribute:
1. Click Retire to the left of the Attribute you
want to retire.
2. Click OK to confirm.
3. Select a Privilege Level from the Privilege
Level drop-down menu.
Actions are secured by Privilege Level and are
hierarchically organized.
The following default privileges exist
Users and Security Level
Definitions
To access the Users form:
• Click Users from the Administration page.
The Users page appears.
Privilege
DLIMS
Browser
DLIMS
Submitter
Allows
User may see but not edit any
DLIMS information
User may submit test requests
but may not perform many
actions
To create a new User
1. Scroll to the bottom of the page. Enter
information for User Name, Password, First
Name, Last Name, etc. in the appropriate
columns.
NOTE: When the user is created, an Oracle user is
created to correspond to the DLIMS User entry. The
Oracle user will be identified with the User Name and
Password entered in the User Form. This user is also
added to the CS_Security module, so you can provide
access to DLIMS users to other CambrigeSoft
applications.
2. Enter an email address for the user. Each time
an action or request is entered, an email will be
sent to the primary email person for that action
or request. Please see “Setting Up Email
Features” on page 96 for more information.
DLIMS
Tester
DLIMS
Lab
Manager
DLIMS
Administra
tor
4. Select a Lab from the Lab drop-down menu.
5. Click Add.
User may create tests and
perform most actions
User may create tests and
perform all actions in their lab
User has full read/write
access to all DLIMS tables
To modify a User
1. Click Edit to the left of the user you want to
edit.
The input values for this user appear in the text
boxes at the bottom of the page.
2. Scroll to the bottom of the page and edit the
values for this action as necessary.
NOTE: User Names are not modifiable.
3. Click Submit found at the top of the page to
save your changes.
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Administration and Configuration

Administrator
To retire a User
1. Click Retire to the left of the user you want to
retire.
2. Click OK to confirm.
NOTE: When you retire a user in DLIMS, the Oracle
user is also removed. As such, they will not be able to login
to Oracle. If you wish to retire a user from DLIMS but
maintain their Oracle log-in privileges for other applications,
please contact your Oracle DBA. You cannot "unretire" a
user once you have retired him or her, so use caution to make
sure you intend to retire the user and you have selected the user
you want to retire before proceeding.
Setting Up Email
Features
The email feature will automatically send an email
to the specified user each time an action or request
is submitted.
To set up the email feature:
1. Open the login.asp file.
2. Make sure that the following line:
Application("MailHost") =
"exchange.cambridgesoft.com"
correctly points to a working mail host.
3. Find the line immediately following the above
line, which says either:
Session("PrimaryEmail") = "responder"
OR
Session("PrimaryEmail") = "manager"
This line indicates which email should be used
as the primary email for an action or request.
That is, if the value of the line is responder, the
responder's email address will be found in the
TO: line of the email, and all other email
address are found in the CC: line. If manager is
the value of the line, manager is found in the
TO: line and all other addresses in the CC: line.
4. Make sure email addresses are supplied for all
users in the Users Administration page.
96•Discovery LIMS
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Setting Up Email Features

Section III: Biological Informatics
This section provides information about
CambridgeSoft’s Biological Informatics Solutions.
The following applications comprise
CambridgeSoft’s BioInformatics Solutions:
• BioAssay
• BioSAR Enterprise
Finding structural determinants of biological
activity requires processing masses of biological
assay data. Scientists use BioAssay and BioSAR
Enterprise to set up biological models and visualize
information, to generate spreadsheets correlating
structure and activity, as well as to search by
chemical structure.
ChemOffice Enterprise Workgroup & Databases 2005 • 97

Administrator
98• CambridgeSoft

Chapter 6: BioAssay
Overview
BioAssay helps research biologists store, analyze,
and report on biological protocol data. It is
optimized for high-throughput screening data, but
it can also be effectively used for low-throughput
and in vivo studies.
Double-click the desktop icon.
DESKTOP and WORKGROUP: The Login
window appear:
The system allows the user to define protocols as
sets of tables holding raw data, summary data and
aggregate data. In addition to storing data, the
system also allows for curve fitting and data
manipulation.
Versions of BioAssay
BioAssay is purchased in one of three versions:
• BioAssay Enterprise
• BioAssay Workgroup
• BioAssay Desktop
ALl three versions are very similar and therefore
users of all three versions should use this chapter
for a reference in using the application. If there are
differences in the versions, it will be noted in the
chapter.
Logging in to BioAssay
To start the BioAssay client application:
1. Go to START > Programs > BioAssay >
BioAssay
OR
ENTERPRISE: The Login window appears
2. The username and password used should be a
valid BioAssay username and password. For
more information about valid usernames and
passwords, please see your system
administrator.
3. Select a connection type:
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Overview

• Direct Connection - BioAssay clients
connect directly to Oracle via Oracle client
software. Best for high-speed LANs.
If a valid username and password are entered for
the appropriate server, BioAssay opens with the
Start Page visible:
Administrator
• Oracle Service -
The Oracle service
where the
bioassayhts schema
is installed
• Schema - The
name of the
BioAssay schema -
by default
bioassayhts
• Proxy Connection - BioAssay clients use a
HTTP server to communicate with Oracle.
Fastest on lower-speed WANs, or on
machines where Oracle client software is
unavailable.
• Server - the name
of the server where
the BioAssay server
is installed
Options available from the BioAssay application
could differ from user to user depending on
permissions. If you do not see something you feel
you should have access to, please see your system
administrator.
Terminology
• HTS -High Throughput Screening - testing
thousands of compounds in a short period of
time.
• LTS - Low Throughput Screening - more indepth
screening of fewer compounds.
• Protocol - In BioAssay, a collection of
database fields and calculations that hold data
about a given biological experiment.
• Plate - A means of holding multiple samples in
an easily transportable unit.
• Plate Format - The layout of the wells on a
plate.
• Well Format - The type of contents in a well -
compound, control, empty, etc.
• Aggregate - A calculation that summarizes
multiple results in one number, e.g. Average,
Maximum, Minimum, Standard Deviation,
Curve Fits.
100•BioAssay
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Terminology

• Grouping - Used in conjunction with
aggregate calculations to summarize data.
• Primary Tables - The collection of tables that
are automatically filled and calculated.
• Summary Tables - Summary tables provide
alternate ways of summarizing primary data.
• File Import Template - A template which
indicates how to take data from a file or files
and place it into a HTS protocol
• Graph Template - Information that tells HTS
how to place data in a 2-D graph.
• Browse Table - A table allowing the user to
interact with data and perform Quality Control
tasks.
• Search Table - A table allowing the user to
search all protocol data.
• % Inhibition - A basic measure of potency
normalizing raw data to a positive and negative
control.
• IC50,EC50, LD50 - Measures of compound
potency ñ the concentration in a protocol at
which a compound is effective at the 50% level.
• Valid, Invalid, Not Validated - measures of
confidence in data. Generally, data that has less
confidence assigned is less visible.
• Curve Fitting - Using an algorithm to
determine the line that best fits a set of points.
The parameters of this equation can then be
used in further calculations.
• Direct Connection - BioAssay clients connect
directly to Oracle via Oracle client software.
Best for high-speed LANs.
• Proxy Connection - BioAssay clients use a
HTTP server to communicate with Oracle.
Fastest on lower-speed WANs, or on machines
where Oracle client software is unavailable.
• Picklist - A defined list of items a user may
pick from in a protocol.
Navigation
The user interface for BioAssay is split into two
major frames: The Navigator and the Content
Frame.
The Navigator (found in the left frame) acts much
like a tree in Microsoft Explorer. Protocols are
organized into folders in the tree. Expand folders in
the tree to find what you are looking for.
The Content Frame displays the contents of the
open folder in the Navigator. The content frame
can be used in 3 different modes: Browse, Filter,
and Edit, depending upon the table displayed. The
Actions button in the Content Frame makes data
specific tasks available to the user.
Resizing and Moving
Columns
Columns in tables in the Content Frame are resized
by the click and drag method often used in
table/spreadsheet interfaces.
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Navigation

Administrator
To resize the columns in a table in the Content
Frame:
1. Move the mouse over the border between two
columns in the table header row, until the
mouse turns into a double sided arrow.
2. Click with the mouse and hold it down while
dragging the mouse.
The column will resize as you drag the mouse.
Release the mouse when the column is the
appropriate size.
Sorting Data
Data in any table can be sorted by any of the
columns in the table. If you sort the data, the data
will be sorted accordingly the next time the table is
opened.
To sort the data by a particular column, click on the
column header.
Sorted by
Barcode
Sorted by
GroupID
In some cases (e.g. protocol data tables) the
columns can also be moved within the table. To
move a column within a table:
1. Move the mouse over the column header to be
moved and click.
2. Hold the mouse button down and drag the
column to its new location.
NOTE: A column line appears when you have
dragged the column to a new column location.
3. Release the mouse button when you have
dragged the column to the proper location.
To invert the sort, that is filter the data in
descending order instead of ascending order, click
the column header a second time.
Filtering Data
When the Filter button is available in the toolbar of
the Content Frame, the table is available in Filter
Mode. In Filter Mode, you are able to filter the data
by any criterion in the table. When data is filtered,
only the data matching the entered criteria is
displayed.
To filter the data in a table:
1. Click Filter.
A row with a green background appears at the
top of the table.
2. Enter criteria into the new row.
NOTE: This new column arrangement is saved for the
next time the table is opened.
102•BioAssay
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Navigation

Criteria can be entered using drop down lists, if
applicable, ranges for numerical columns, or
the appropriate characters for text columns.
3. Click Apply.
The data is sorted accordingly.
Refreshing the Data View
It is necessary to refresh the data view. Unless
windows in the Content Frame are closed after you
are finished, when the window is opened again, the
data will not be refreshed. To refresh the view, click
Get Data.
Tips
Searching in BioAssay is similar to searching in
other ChemOffice WebServer products:
1. Access the search form.
2. Enter search criteria.
3. Search results, made up of records matching
the entered criteria, are returned.
Numeric search criteria can be entered as a range
using > (greater then), < (less then), and - (between
one value and the next). The following table shows
some examples of range searching:
Entered
search
criteria
Really means...
3-11 Between 3 and 11 (not
including 3 or 11)
>100 Greater then 100 (not
including 100)

Administrator
Fields contained in tables are defined as simple text,
a piece of numerical data, or a calculation. After the
table structure is defined, data can be imported into
data tables from a file through the use of a user
defined file import template.
Viewing Protocols in the
Navigator
The Protocols section of the BioAssay application
allows the user to design a protocol and then import
sets of data into the system to be analyzed by that
protocol. This makes it possible to analyze different
sets of data with minimal amounts of subjectivity.
The protocols folder in the Navigator contains any
number of protocols accessed through a folder in
the Protocols folder in the Navigator.
Moving a Protocol or Project
To move a protocol or a project:
1. Right-click on the project or protocol to move.
2. Select Move Protocol (or Project)
The move project dialog appears.
3. Highlight the folder or project to move the
project or protocol to.
4. Click OK.
• Right-clicking on the projects and/or folders in
the Navigator exposes a menu which allows
users to create new
projects/folders/protocols, rename the
project/folder, or remove a project/folder.
• Right-clicking on a protocol in the Navigator
exposes a menu which allows users to create
new, or remove a protocol as well as:
• Move the Protocol
• Duplicate a Protocol
• View Protocol Properties.
Duplicating a Protocol
To duplicate a protocol:
1. Right-click on the protocol to duplicate.
2. Select Duplicate Protocol.
A copy of the selected protocol is added to the
Unclassified project. Users can rename and/or
move the protocol as desired.
Viewing a Protocol’s Properties
(Renaming)
The protocol property dialog contains a name and
description for the selected protocol along with the
date and time the protocol was created.
To view the properties of a protocol and change the
name and/or description:
1. Right-click on the protocol.
2. Select Properties.
104•BioAssay
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Protocols

The Properties dialog appears.
Protocol Data and Definitions
Protocol data and definitions are accessed by
selecting (clicking) the appropriate protocol in the
Navigator. The protocol opens in the right frame
(the Data Viewer) exposing 3 tabs:
• Tasks
• Data
• Definition
Import a Data File
This task allows users to import data into the
protocol. See “Importing Data” on page 128 for
more information.
Manage Plate Template
This tool is directly linked to Inventory. It creates
and edits plate templates according to input
parameters. Plates can be created from these
templates.
The Manage Plate Template tool allows a user to
take a plate format (from Plate Settings) and map a
compound id to each different well format. So if
you have a plate template with Compound 1,
Compound 2, Compound 3, and Compound 4, you
can create a plate template, and add compounds to
your list. For more information about creating
Compound Lists, see “Compound Lists” on page
134.
To create a plate template:
1. Click Manage Plate Templates on the Protocol
Tasks Tab.
The Manage Plate Templates dialog appears.
Tasks
The tasks tab gives users access to tools related to
the selected protocol. Those tools included
• Import a data file
• Manage plate templates
• Create plates from templates.
2. Enter a name for the template in the Plate
Templates textbox.
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Administrator
3. Click Add.
6. Drag-and-drop the compounds in the
Compound List to the plate view, and the
blocks of similarly-formatted wells will be
highlighted. Drop a compound, and it will be
assigned to those wells.
4. Select a plate format in the Based on: listbox.
5. Add compound IDs to the Available
Compounds list:
• By importing a Compound List
a. Click Open Compound List.
b. Highlight a compound list to use.
c. Select how to import the list.
• Replace Current List - replace the
current list with the new list
• Append to Current List - add the
select list to the end of the current
list.
d. Click OK.
• By adding compound IDs manually
a. Enter a compound ID in the Available
Compounds textbox.
b. Click Add.
7. Click Save.
Create Plates from Templates
This tool allows users to create plates, stored in
Inventory, but used from within BioAssay.
Plate templates are used to create plates.
To create a plate:
1. Select Create Plates from a Template.
The plates dialog appears.
2. Select the template to use when creating your
plates in the Plate Templates box.
3. Click Add.
4. Change the name of the plates to be added if
desired.
NOTE: By default, the plates are given the same
name as the templates they originate from.
106•BioAssay
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Protocols

5. Enter other data that pertains to the batch of
plates in the Other Data box.
To view your data, perform a search, or click
Retrieve All. For more information about searching
protocol data, see “Searching Data” on page 107.
Searching Data
The Protocol Search Dialog gives you the ability to
search over protocol data according to your enter
criteria. To search over the data:
1. Click the Data tab or click the Datasource
button under the Data tab if the Data tab is
already open.
The Search Dialog Appears.
6. Click OK.
Protocol Data
Stored data for a protocol is accessed by clicking on
the Data tab in the data viewer. This opens the
Data Source Search Dialog.
2. Select the table to search over by highlighting a
table under Select Data Source.
3. Enter you search criteria.
NOTE: The search fields vary depending on the data
table selected.
Primary Data tables are identified throughout the
application with the blue data table icon. Summary
tables are denoted by a similar green icon. The
tables are defined under Protocol Definitions.
4. Click Search.
Browsing Protocol Data
The data is arranged in tables, as defined by the
Protocol Definition. Double-clicking a row in a
table exposes the data related to that row in the next
table in the hierarchy. For example, your protocol
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Protocols

may contain 2 tables, a plates and a wells table.
Clicking on a row in the plates table exposes the
well data associated with the selected plate.
plate P1002, we click plate 1’s row in the Plates
table, and that information is loaded into the Wells
table.
Administrator
Tables are arranged in the data viewer by the
hierarchy defined in the assay definition. That is,
tables which are higher in the hierarchy are found at
the top of the data browser and nested tables are
displayed lower. If the number of tables displayed
exceeds 4, a button allows you to bring the hidden
tables back into view.
Changing the selection is a table higher in the
hierarchy cascades the change through the child
tables. Thus, to see data for plate P1004 instead of
NOTE: Data is only editable, and most actions are only
available, from the main grid (by default the most detailed
table open (found at the bottom of the data viewer)). To bring
a table from the top into the main grid, double click on its
title bar or click the
i icon.
Related Plate Data
If a plate icon appears in the upper right of the
data viewer, a plate view is available for the open
table.
To view that plate data:
1. Click the plate icon.
The Plate viewer appears.
2. Click on the plate barcode associated with the
plate you would like to view.
Related Graphical Data
If a graph icon appears in the upper right of the
data viewer, this indicates one or more graphs are
available from that table.
108•BioAssay
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Protocols

To view the graph:
1. Click the graph icon.
The graph viewer appears.
2. Click on the graph you would like to view.
Protocol Definitions
The Protocol Definition is accessed by clicking on
the Definition tab in the data viewer. This is where
the protocol's structure and calculations are
defined. The protocol tables must be defined
before importing data.
For more information about defining tables for a
protocol, please see “Defining Tables and Fields”
on page 113.
When a protocol Definition folder is opened, the
protocol structure is displayed in the right frame.
The tree in the protocol definition frame groups
information in four ways:
• Primary Tables
• Summary Tables
• Additional Tables
• File Import Templates
• Graph Templates
Primary Tables
Tables are arranged in levels. A table situated lower
in the tree contains rows which hold aggregate data
of one row in a higher table. For example, a plate
based protocol has at least two tables: Plates and
Wells. The Plates table is higher on the tree than the
Wells table. This makes sense because each plate
contains several wells. The Plates table defines plate
attributes such as the barcode while the Wells table
holds data associated with a particular well, such as
the well ID.
Each field falls under the appropriate table in the
tree. Clicking on a table name or field name
prompts the application to display details about the
table or field under the appropriate tab to the right
of the tree.
Parent Tables
Every primary table in a protocol, except the table
at the top of the hierarchy, has a parent. The parent
table is the table found in the next highest level in
the protocol tree. For example, in the image above,
the Summary Table is a parent of the WELLS table.
Because the Summary table is at the very top of the
hierarchy, the Summary table does not have a
parent.
In this example, and in any parent table example,
the parent table holds information summarizing the
data in tables below it. For example, the Summary
table contains a Compound ID field because all of
the data in the WELLS table have a common
Compound ID.
Child Tables
Every table in a protocol, except the table at the
bottom of the hierarchy, has a child. Child tables are
named as such because their data is summarized in
some way by its parent. For example, the WELLS
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Administrator
table in the above image is a child of the Summary
table. There are many wells which are summarized
(with various statistics) in the Summary table.
Child Tables always contain at least one field which
is identical to a field with the same name in the
Parent table. This field is the grouping field. This
field allows the user to indicate to the application
which data in the wells table belongs to the
corresponding row in the parent table (e.g. Plate
ID).
Summary Tables
Summary tables in BioAssay are used to summarize
data for a single protocol. Calculations in the
standard data tables are usually based on grouped
data. That is data for an individual plate or run.
Taking averages and standard deviations of data in
more then one plate or run helps to visualize the
overall picture.
Summary tables contain one grouping field in
addition to calculation fields. The grouping field
indicates which data should be used in a calculation.
For example, if the compound ID is used as the
grouping field, calculations are made for each
compound ID. Without the grouping field,
calculations would be based on all valid data
recorded for the protocol.
fields and these tables allow the user to enter
additional data which is mapped to the protocol but
does not belong in any other fields.
File Import Templates
BioAssay includes a wizard which aides in designing
templates called File Import Templates. These
templates define how data should be imported into
tables. The advantage of creating a template is to
indicate the format of a data file once, and not have
to enter the same information when using a file
with the same format again.
File Import Templates tell the system the format of
the file (i.e. what kind of delimiter is used, if there
are header lines in the file) as well as where to put
the data, once it is imported, in the protocol data
tables of the protocol. A File Import Template must
be defined for any file being imported.
For more information about using the File Import
Template wizard, please see “File Import
Templates” on page 125. For more information
about importing data, using a defined File Import
Template, please see“Importing Data” on page 128.
Additional Tables
Additional tables are tables which contain data
related, but not linked, to the rest of the data in the
protocol. These tables can contain any number of
Graph Templates
Graph templates are used to plot data. After a graph
template is made, you can plot data by right-clicking
on the data and choosing the graph template.
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Graph templates include information related to
both the data and the display of that data. For more
information about creating Graph Templates,
please see “Creating a Graph Template” on page
130.
Security
Change
Protocol
Definition
Description
edit, add new, and delete table
definitions, file import
templates, graph templates
and protocol security
For information about granting users permissions
to a particular protocol, please see “Defining
Security” on page 124.
Protocol Security
Protocol security is only available in BioAssay
Enterprise. The security tab does not appear in the
Ultra and Workgroup editions.
Protocol security in BioAssay is mostly centered
around permissions to view, change data related to,
and change definitions for protocols. The user who
creates a protocol is automatically given the
appropriate permissions for the protocol, but all
other users must be explicitly added to the protocol
security list.
There are three levels of protocol security for users:
Designing a New Protocol
The first step in designing a new protocol is
knowing what kind of data is going to be provided,
what the overall result should be, and finding all of
the steps necessary to move from the data to the
result.
To create a new protocol:
1. Right-click a project in the Navigator.
2. Select New Protocol.
3. Enter a name for your protocol and click OK.
The Protocol Wizard appears.
Security
Change
Data
Validate
Data
Description
edit, add new, and delete
protocol data
validate data already in
protocol data tables
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Protocols

4. Select the template you would like to use from
the Protocol Templates list.
Administrator
Protocol Template Description Plate Based Inventory
Linked
Blank
Simple 2-Tier
Blank protocol
definition
Blank protocol
definition with 2
tables
N
N
N
N
Initial Screen
one-dose, singlenumber-percompound
protocol
Y
N
Confirmation Screen
multi-dose, multiplenumber-percompound
protocol
Y
N
IC50 IC50 protocol Y N
Initial Screen
(Inventory Linked)
one-dose, singlenumber-percompound
protocol
Y
Y
Confirmation Screen
(Inventory Linked)
multi-dose, multiplenumber-percompound
protocol
Y
Y
IC50 (Inventory
Linked)
IC50 protocol Y Y
5. Click OK.
The protocol is inserted in the Navigator under
the select project.
The protocol definition must be defined, and at
least one file import template must be added before
you can import data.
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Defining Tables and Fields
How tables are arranged, depends on the data and
the desired result. Typically, raw data values are
found in a table at the lowest level. It might be
helpful to make a sketch of the table structure ahead
of time. For more information about tables and the
general table structure in BioAssay, please see
“Primary Tables” on page 109.
Any number of tables can be defined. If a table's
data depends on the data in another table, the
dependent table must be higher in the structure
than the other table. The table structure will be
defined most efficiently by, defining the lowest level
table first, and working up to the highest level table.
There are protocol templates that will help you to
get your protocol started. Please see “Designing a
New Protocol” on page 111 for more information.
To start defining tables:
1. Open the protocol and click on the Definition
tab.
The Protocol Definition appears in the right
frame.
NOTE: After importing data, the user will be limited to
adding new fields and adjusting calculation definitions.
Defining a Primary Protocol Table
If you have used a template, or if you have started
with a duplicate protocol, your table may already
exist.
Depending upon the template chosen, the
contents of the frame will differ.
2. Perform the appropriate action:
If you would like
to...
Then...
Rename the table or
edit the table
comments
Add a parent table
Click on the table and
edit the fields in the
far right frame.
Right-click on the
table name and select
Create parent table
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If you would like
to...
Then...
c. Go on to edit the field data.
• To edit the data for an existing field:
a. Click on the appropriate field in the tree.
Administrator
Add a child table
Remove a table
Right-click on the
table name and select
Create child table
Right-click on the
table name and select
Remove table
Field data appears in the right frame.
3. Click Save Changes, if necessary.
Defining Fields in a Table
If you have used a template, or if you have started
with a duplicate protocol, some fields may already
exist.
b. Edit the appropriate data in the right frame.
3. Click Save Changes, if necessary.:
NOTE: Templates do not define calculations, they only
insert a field with type calculation.
If you
would like
to...
Then...
After tables are created, the table fields must be
defined before data can populate them.
To start defining fields:
1. Open the protocol and click on the Definitions
Tab.
The Protocol Definition appears in the right
frame.
Depending upon the template chosen, the
contents of the frame will differ.
2. Do one of the following:
• To add a new field:
a. Right-click the name of the table you would
like to add a field to.
b. Select New Field.
Remove a
field
Move a field
from a higher
table to a
lower table
Right-click
on the
appropriate
field name
and select
Remove
Field
Right-click
on the
appropriate
field name
and select
Move Down
To...
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If you
would like
to...
Move a field
from a lower
table to a
higher table
Then...
Right-click
on the
appropriate
field name
and select
Move Up
To...
Field Type
Number
(Integer)
Text
Date
Yes/No
Field Options
• Display in Scientific
notation (yes if selected)
None
None
None
Move a field
up within a
table
Move a field
down within
a table
Right-click
on the
appropriate
field name
and select
Move Up
Right-click
on the
appropriate
field name
and select
Move Down
Picklist Value • Which Picklist
Calculation • Display in Scientific
notation (yes if selected)
Compound ID None
Well Index
Inventoried
Plate Barcode
• Defined calculation
None
None (only available in
BioAssay Enterprise)
Field Types
The field options available to be defined vary
according to the field type chosen. When defining a
field, after entering a name and comment, select a
field type. Enter the appropriate information.
Field Type
Field Options
Number (Real) • Display in Scientific
notation (yes if selected)
• Number of decimal places
Plate Format
Well Format
None
None
Concentration • Display in Scientific
notation (yes if selected)
Plate Identifier
None
Indexed Fields
Indexed fields have the following characteristics:
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• Fields which will be used to search data often
(searching speeds improve when a field is
indexed)
• Importing data into an indexed field is slightly
slower than importing data into a field which is
not indexed.
• Examples of fields to index:
• Compound ID
• Protocol data fields which are often search
over
Assigning a Calculation to a Field
Three different types of calculations are available to
be assigned to fields.
When a click Edit Calculation in a Calculation field
definition, the Calculations Wizard appears.
To index a field:
1. Open the field definition (click on the field in
the protocol definition tree).
2. Select the Indexed checkbox.
Key Fields
Key fields in a table accomplish two things:
• Limits the data returned to the user to only data
related to the row selected in the previous table.
• Groups data for calculations - only data with
the same value in the key field are used to
determine calculations.
NOTE: Every table must contain at least one key field.
To make a field a key field:
1. Open the field definition (click on the field in
the protocol definition tree).
2. Select the Key Field checkbox.
Required Fields
If a field is required, a value must be given to the
field before a data import is complete.
To make a field required:
1. Open the field definition (click on the field in
the protocol definition tree).
2. Select the Field Cannot be empty checkbox.
This wizard helps to define the calculation, and the
data used to compute the calculation. Three types
of calculations are available:
• Aggregate - calculations made on a rows
aggregate data found in a lower table
• Mathematical - calculations dependent upon a
user defined equation
• Curve Fit - calculations made to fit a set of data
to a particular curve
To start using the Calculation Wizard:
1. Select the tab for the appropriate calculation.
2. Highlight the calculation to be used, and click
Next.
Aggregate Calculations
Aggregate calculations are calculations performed
on a data set resulting in one figure somehow
representative of the whole group. Therefore,
aggregate calculations must be included in a table
higher then the location of the aggregated data.
The default aggregate calculations are:
• Average - takes an average of all aggregated
data
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• Standard Deviation - finds the standard
deviation of all aggregated data
• Sum - computes the sum of all aggregated data
• Maximum - returns the maximum value in the
aggregated data
• Minimum - returns the minimum value in the
aggregated data
When a user double-clicks a cell in the Calculations
column, the Calculations Wizard appears.
4. Select the field where the data that will be used
for the calculation is located, from the Values
listbox.
5. Click Next.
The Define Conditions screen appears.
If there is no calculation populating the cell, the
Aggregate Tab is shown by default.
To insert a aggregate calculation into the cell:
1. Highlight which calculation you would like
inserted into the cell.
2. Click Next.
The Input Values screen appears.
If you would like to only use data points if
certain conditions are met, add a condition:
a. Click Add.
b. Select a field where the data must fulfill the
condition.
c. Select a mathematical symbol.
d. Click in the Value column.
The condition value dialog box appears.
e. Finish the condition by entering the value
that the data must fulfill and click OK.
3. Select the table where the data that will be used
for the calculation is located, from the Table
listbox.
6. Click Next.
The Finished screen appears.
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7. Select the number of decimal places that the
result should be limited to, from the listbox.
When a user double-clicks a cell in the Calculations
column, the Calculations Wizard appears. Click on
the Mathematical Tab to access the mathematical
calculations.
8. Click Finish.
Mathematical Calculations
Mathematical calculations are any calculations
performed using a defined equation. There are
some already defined calculations which can be
used including:
• % Inhibition - returns the % inhibition (100 *
((Value - LowControlAverage) /
(HighControlAverage - LowControlAverage)))
• Log(x) - returns the log (base 10) of a value
• 10^x - returns the inverse log of a value
• Addition
• Subtraction
• Multiplication
• Division
• Percentage
• Half Life - (Time * ln(2)) / (ln(100 /
PctRemaining))
• Z' Factor - 1 - ((3*SDPosCtl + 3*SDNegCtl) /
abs(AvgPosCtl - AvgNegCtl))
There are two options in using a mathematical
calculation:
• Use a default equation
• Define a new equation
Use a Default Mathematical Calculation
To use a default calculation:
1. Click on the Mathematical Tab.
2. Highlight which calculation you would like
inserted into the cell.
3. Click Next.
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The Calculation Parameters screen appears.
Define a New Mathematical Calculation
To define a new calculation:
1. Click on the Mathematical Tab.
The equation used to compute the chosen
value is displayed.
4. Select, in the table at the bottom of the
window, what values should be used for the
variables in the equation. This involves first
selecting a Table, and then a field in that table
from listboxes.
5. Repeat step 4 for all of the variables listed in
the table.
6. Click Next.
The Finished screen appears.
2. Click New.
The Edit Custom Function window, a window
allowing the definition of a new equation,
appears.
7. Select the number of decimal places that the
result should be limited to, from the listbox.
8. Click Finish.
3. Enter a name for the calculation in Function
listbox.
4. Enter an equation for the calculation in the
Equation textarea. General information about
defining an equation is provided in the help
section of this window. Supported operators
are found under the Operators Tab and
predefined functions are listed under the
Functions Tab.
5. Click OK.
6. Highlight the function, just defined, and click
Next.
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7. Continue with step 4 in Use a Default
Mathematical Calculation.
1. Click on the Curve Fit Tab.
Administrator
Curve Fit Calculations
Curve Fit calculations are calculations obtained
from interpolating a curve to data. There are two
pre-defined calculations, which can be used
including:
• Sigmoidal dose-response
• One phase exponential decay
When a user clicks Edit Calculation, the
Calculations Wizard appears. Click on the Curve
Fit Tab to access the Curve Fit calculations.
2. Highlight the calculation you would like used.
3. Select the curve parameter to be used for the
calculation in the listbox (these options will be
limited to curve parameters which make sense
with the highlighted curve fit calculation).
There are two options in using a Curve Fit
calculation:
• Use a default equation
• Define a new equation
Use a Default Curve Fit Calculation
To use a default calculation:
NOTE: If no predicted values were defined in the
Curve Fit calculation definition, there will be no options
in the listbox (when Predicted value is selected). For
information about adding a predicted value to a Curve
Fit calculation, please see “Editing a Curve Fit
Calculation” on page 123.
4. Click Next.
The Input Values screen appears.
5. Select the table where the data that will be used
for the calculation is located, from the Table
listbox.
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6. Select the field where the data that will be used
for the x-values in the curve is located, from
the X-Values listbox.
7. Select the field where the data that will be used
for the y-values in the curve is located, from
the Y-Values listbox.
8. Click Next.
The Define Conditions screen appears.
11.Select the number of decimal places that the
result should be limited to from the listbox.
12.Click Finish.
Define a New Curve Fit Calculation
To define a new calculation:
1. Click on the Curve Fit Tab.
9. If you would like to only use data points if
certain conditions are met, add a condition:
a. Click on Add.
b. Select a field where the data must fulfill the
condition.
c. Select an equality symbol.
d. Finish the condition by entering the value
that the data must fulfill.
10.Click Next.
The Finished screen appears.
2. Click New.
The Curve Fit Template window, a window
allowing the definition of a new curve fit
calculation, appears.
For more information about creating new
models, please see “Defining a New Model” on
page 122.
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3. Enter a name for the calculation in the
Template textbox.
4. Highlight the Model to be used.
5. Enter Parameter information under the
Parameters Tab.
a. Select Variable or Constant, in the Type
column, for each parameter.
b. Enter a numerical value, or select a value
from the drop-down menu in the Value
column.
6. Enter additional calculation options under the
Advanced Tab.
b. Enter a name for the result.
c. Select which value is given (X or Y). Note:
The value not provided is the value which is
predicted.
d. Enter a value for the variable.
e. Click OK.
8. Click OK.
9. Highlight the function you have just defined
and continue with“Use a Default Curve Fit
Calculation” on page 120.
Defining a New Model
Models are, in general, equations used to calculate
curve fit parameters. New models can be defined
under the User-Defined Tab in the Curve Fit
Template dialog box.
To define a new model:
1. Click New under the User-Defined Tab in the
Curvefit Template dialog box.
The User-Defined Model dialog box appears.
7. Enter the desired predicted values for variables
under the Predicted Tab.
a. Click Add to add parameters for a predicted
value.
2. Enter a name for your model in the Name
textbox.
3. Enter an equation in the Equation textbox.
Equation definition tips and conventions can
be found in the lower half of the window.
4. Click Validate Equation to make sure the
equation entered is written in the correct
syntax.
5. Click OK.
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The new model is listed under the User-
Defined Tab.
Editing a Curve Fit Calculation
To edit a curve fit calculation:
1. Click on the Curve Fit Tab.
For more information about creating new
models, please see “Defining a New Model” on
page 122.
4. Edit the name for the calculation in the
Template textbox, if necessary.
5. Highlight the Model to be used, if it is not
selected correctly.
6. Edit Parameter information under the
Parameters Tab.
2. Highlight the calculation to be edited.
3. Click Edit.
The Curve Fit Template window, populated
with the definition of the selected calculation,
appears.
a. Select Variable or Constant, in the Type
column, for each parameter.
b. Enter a numerical value, or select a value
from the drop-down menu in the Value
column.
7. Edit additional calculation options under the
Advanced Tab.
8. Edit the desired predicted values for variables
under the Predicted Tab.
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a. Click Add to add parameters for a predicted
value.
For example, this summary table is grouped by
Compound ID:
Administrator
b. Enter a name for the result.
c. Select which value is given (X or Y). Note:
The value not provided is the value which is
predicted.
d. Enter a value for the variable.
e. Click OK.
9. Click OK.
• Compound ID -
The grouping field.
Calculations are
made according to
the grouping field.
• Count of >3 SDs
above - this
calculation counts
how many instances
are found for each
compound ID with
standard deviations
greater than 3
Summary Tables
Summary tables are treated like primary tables in
BioAssay, but they only contain a grouping field and
calculation fields. They are used to group data by a
different parameter to allow for additional analysis
(calculations).
Summary Tables include:
• One grouping field
• As many calculation fields as desired
Enterprise
Defining Security
Users, other then the creator, must be given the
appropriate permissions to access and edit
protocols. To give a user or group permissions to a
protocol:
1. Open the appropriate protocol's protocol
definition.
2. Click on the Security Tab.
The Protocol Security window opens.
3. Select either the Users or Groups radiobutton
(depending on who you would like to add to
the security).
4. Choose the appropriate action:
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• To add a user or group to the protocol's
security:
a. Highlight the user or group in the list.
b. Click Add.
c. Select the checkboxes corresponding to the
permissions you would like to give the user
or group. For more information about your
options, please see Protocol Security.
• To remove a user or group from the
protocol's security:
a. Highlight the user or group in the table
(on the right).
b. Click Remove.
5. Click OK.
Importing and Viewing Data
In order to import data, the protocol tables must
first be defined. If there are no tables listed in the
Protocol Definitions, the protocol tables have not
been defined.
The only way to import protocol data into BioAssay
is to use the File Import Wizard. The File Import
Wizard uses user defined file import templates.
Therefore, a file import template compatible with
the data being imported must also be defined
before importing data.
File Import Templates
File Import Templates are used to import data from
a file and populate user-defined tables with that
data.
To define a File Import Template:
1. Click on the Protocol Definitions folder under
the protocol that is being defined.
The protocol definition appears in the righthand
frame.
2. Right-click the File Import Templates folder
in the tree.
3. Select New Template.
The File Import Template Wizard appears.
4. Enter the a name and description for your file
import template in the Select Data File
window.
5. Click Next.
The File Format Information screen appears.
6. Select a file delimiter.
For example, with the following file name:
P1000-2004_03_18.txt
The filename delimiter could be set to "-". The
P1000 could them be set as the value of a field
in step 10 (as Use Filename Data: 1 and put the
date in Use Filename Data: 2)
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7. Select the type of file you are importing:
The Map Fields screen appears.
File Type
Description
Administrator
Columnar
(Excel-
Type)
a series of columns; each
column contains the values
for one variable.
Plate Block raw data is arranged in a
block; the block is arranged to
coincide with plate
arrangement
8. Complete the details related to your file type.
• Columnar:
• Indicate if your data file has header lines
(lines not containing actual data). If there are
header lines, enter how many in the textbox.
10.Assign values to the fields in the selected table
by:
a. Selecting what type of value to populate the
field with:
Choices depend on the type of file you have
chosen and the type of file being imported.
Data
Source
File Type
Description
• Plate Block:
• Enter the number of rows in each category
NOTE: See “BioAssay Plate Block Data Files”
on page 261 for an illustration of what part of the
data file pertains to the above nicknames.
Leave Blank
System
Assigned
Columnar
(Excel) or
Plate Block
Columnar
(Excel) or
Plate Block
No data is
imported into
this field
The
application
automatically
assigns a value
for this field
(e.g. Well
Format for a
plate linked
protocol)
9. Click Next.
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Data
Source
File Type
Description
Data
Source
File Type
Description
Data in File
Column
Number
Use
Filename
Data
Use Default
Prompt Me
Plate Block
Data
Columnar
(Excel)
Columnar
(Excel) or
Plate Block
Columnar
(Excel) or
Plate Block
Columnar
(Excel) or
Plate Block
Plate Block
Data is found
in a column in
a data file -
enter the
column
number to the
right
Data is part of
the filename -
A default
value should
be entered for
this field -
enter the
default value
to the right
During
import, the
user will be
prompted for
the value of
this field
Data is the
data found in
the plate block
File Header
Cell
Block
Header Cell
Block Footer
Cell
Block
Column Cell
Use Import
Time
Plate Block
Plate Block
Plate Block
Plate Block
Columnar
(Excel) or
Plate Block
Data is in a
particular cell
in the File
Header Block
- enter the cell
to the right
Data is in a
particular cell
in the Block
Header Cell -
enter the cell
to the right
Data is in a
particular feel
in the File
Block Footer
Cell - enter the
cell to the
right
Data is in a
particular feel
in the Block
Column Cell -
enter the cell
to the right
Uses time on
user's machine
when file is
imported
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Data
Source
File Type
Description
The File Import Wizard appears.
Administrator
Use Current
User
Columnar
(Excel) or
Plate Block
Uses
username of
user who
imports file
b. Entering the appropriate information in the
right most column, if applicable:
•for Use Default - a default value
•for Data in File Column - enter the column
number
•for Block Header Cell - enter the cell (as
entered in an application like Excel) in
the plate block header lines.
11.Repeat this for each field listed.
12.Click Finish.
The new File Import Template is defined and
ready for use.
Importing Data
If the protocol tables and a File Import Template
compatible with the data file being imported have
been defined, data can be imported through the use
of the File Import Wizard.
To import data:
4. Select an import template.
5. Click Next.
The second window appears.
6. Use the browse button to browse to the data
files you would like to import.
7. Click Next.
8. Enter the appropriate information, if the
wizard asks. This window will differ depending
on the File Import Template being used.
9. Click Next.
The Import File screen appears.
1. Open the protocol (select the protocol in the
Navigator).
2. Click on the Tasks Tab.
3. Click Import a Data File.
10.Select the checkbox if you would like to view
the data in the data tables before importing.
11.Click Finish.
The appropriate table is populated with data. If
any fields in the protocol tables are
calculations, those calculations are made.
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Searching for and Viewing Data in
Tables
See “Protocol Data” on page 107 for more
information about searching and browsing protocol
data.
4. Select the validity you would like to assign to
the highlighted data.
Validation
Option
Description
Used in
Calculations
Validating Protocol Data
When protocol data is first imported, a not
validated icon appears in the left most column in
the data table. This indicates to users that nobody
has made a decision about the validation of the data
yet. Invalid data is not used in calculations or curve
fits.
Not
Validated
Valid
no validation
decision has
been made
data is found
to be valid
Yes
Yes
To validate your data:
1. Open the data tables that contains the data to
be validated.
2. Highlight the data to be validated.
3. Select Change Validity under the Actions
Menu.
The validation dialog appers.
Invalid
Request
Review
data is found
to be invalid
data must be
reviewed
before making
a validation
decision
No
Yes
5. Select the appropriate cascading options.
• Cascade validity change to detail records -
apply the same validity decision to records
summarized by the highlighted record
• Override current invalid records - change
invalid records summarized by the
highlighted data to the new validation
6. Click OK.
Data Manipulation and Curve
Fitting
Any set of data can be plotted and fit to a curve if
desired. The only constraint is that both fields being
plotted are found in the same table.
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In order to plot your data, you must first have a
graph template designed for your protocol. Graph
templates define not only what data is plotted, but
where the graph template is accessed from, and the
physical properties of the graph.
Creating a Graph Template
Graph templates are used to plot data in a protocol.
These templates define properties such as:
• Which data is to be plotted
• Physical properties of the graph - e.g. error
bars, gridlines, graph type, data point markers
• Where the graph template can be accessed
from
To create a new graph template, right-click the
Graph Templates folder in the Protocol
Definition tree (for the appropriate protocol), and
select New Template. A new template is listed
under the folder.
To begin defining a template:
1. Click the graph template name (found in the
Graph Templates folder) in the Protocol
Definition tree.
The graph template details open in the right
frame.
2. Enter the desired information:
• Template Name - a name for the template
• Comment - additional comments for the
template.
• Available From - The table in the protocol
where this graph template can be accessed
from. That is, the place where the user can
right-click and choose to plot the data, using
this template.
• Get Data From - The table the plotted data
is taken from. This may or may not match
the Available From field.
• X-Axis - The field from which the
application should populate the X-Axis.
• Y-Axis - The field from which the
application should populate the Y-Axis.
3. Click Graph Options to define the graph
options.
The Graph Options dialog appears. Please see
“Graphing Options” on page 132 for more
information.
4. Click Save Changes.
Plotting Data using a Graph Template
Graphs are viewed using the Graph Viewer. See
“Related Graphical Data” on page 108 for more
information.
NOTE: If the opened template is new, the above frame
is populated with default information.
Fitting Data to a Curve
The graphing interface will fit any data to any curve
as long as the curve is defined in the system. Two
default curves are defined:
• Sigmoidal-dose response
• One Phase exponential decay
For more information about how to define a new
curve fit equation, please see “Define a New Curve
Fit Calculation” on page 121.
If the correct curve is already defined, do the
following to fit plotted data to a curve:
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1. After plotting data, click Curve.
2. Highlight the name of the curve in the
Available Curves box.
3. Click Graph Selected Curve.
The name of the curve appears in the Graphed
Curve box.
4. Repeat this process until all of the curves you
wanted plotted are listed in the Graphed
Curve box.
5. Click OK.
All curves listed in the Graphed Curve box are
added to the plot, fitting the equation as close
as possible to the data points.
The graph characteristics, such as the type of
scaling on the axes and how far the fitted curve
is extended from the data, are defined in the
Graph Options dialog box.
After fitting the data to a curve, the Data Tab will
display equation parameter values, and fit statistics.
Curve Fit Templates
Curve Fit Templates are listed in the Available
Curves box found in the Add or Remove Curve
window. To access this window, click Curve from
any plot. For more information about using a
template that is already listed, please see “Fitting
Data to a Curve” on page 130.
Creating a New Template
To create a new curve fit template:
1. From the Add or Remove Curve window,
click New.
The Curvefit Template window opens.
2. Enter a name for the template in the Name
textbox.
3. Highlight the Model to be used.
For more information about creating new
models, please see “Defining a New Model” on
page 122.
4. Enter Parameter information under the
Parameters Tab.
5. Select Variable or Constant, in the Type
column, for each parameter.
6. Enter a numerical value, or select a value from
the drop-down menu in the Value column.
7. Enter additional information under the
Advanced Tab.
8. Click OK.
The name or your new template will be listed in
the Available Curves box.
Editing a Template
The edit template interface behaves just like the
new template interface. If you would like to edit a
template:
• From the Add or Remove Curve window,
click Edit.
The Curvefit Template window opens with the
current template settings populating the fields in
the window. See “Creating a New Template” on
page 131 for more details.
Viewing the Plotted Data
The Data Tab found on any plot frame displays the
data plotted along with information about any
curve fits made.
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Equation
The Equation Tab displays the equation that the
data is fit to under Parameterized Equation. The
x and y variables define the x and y coordinates for
the fit curve. The values for other parameters in the
equation are assigned to fit the data the best. The
final values are recorded in the Parameter Values
table.
information found under this tab will give the user
information to determine if the data has a
meaningful fit to the curve.
Values
The Values Tab displays the actual data point
values to which the equation found under the
Equation Tab is fit.
Data Statistics
Various statistics defining the data are found under
the Data Statistics Tab. Statistics for both the X
and Y values are recorded.
Fit Statistics
The Fit Statistics Tab records statistics defining
how well the Equation, found under the Equation
Tab, fits the data found under the Values Tab. The
Invalidating Data Points
Any data point plotted can be removed from the
plot. This may be useful in removing outliers in
order to produce a better curve fit.
When viewing a plot (for more information please
see “Plotting Data using a Graph Template” on
page 130), you can exclude and include data points.
By default, active data points appear in blue,
inactive data points in red. All data points are active
by default.
To exclude an active datapoint from the fit or
include an inactive data point in the fit:
1. Find the point in the plot and right-click.
2. Select the appropriate options (Exclude from
Fit or Include in Fit).
NOTE: Points invalidated from the graphing interface are
also marked as invalid in the data tables, therefore excluding
them from calculations.
Graphing Options
There are three tabs in the Graph Options dialog:
• General - define general plotting characteristics
such as error bars, grid lines, and graph
extensions
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• Title - give the plot and its axes titles
• Plots - define display characteristics such as
data point markers and the plot type
Graph Extension =10%
To access the Graph options dialog:
1. Click Options from a plotting window OR
2. Click Graph Options from a Graph Template
definition.
Graph Options General Tab
Most of the options under the general tab will
remove and add particular parts of the plot such as
the legend, the axes labels, or the data itself.
Selecting a checkbox next to a Show option will
show that option. Unchecking the box will hide the
item.
Graph Extension = 40%
Error Bars
Error bars can be added to any plot. To add error
bars to a plot:
Graph Extension
The graph extension listbox determines how much
the fitted curve should extend from the data points.
The default is 10%. This means the fitted curve will
extend 10% more from the data points at the two
ends of the curve. Making this value larger will
extend the curve farther, as seen in the following
images:
1. Click Options.
2. Select an error bar option (found in the right
column of the Graph Options dialog box).
Only one error bar option can be chosen at one
time. Error bars can be calculated from
individual data or aggregated data.
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Administrator
Click OK.
Graph Options Title Tab
The graph options Title Tab allows you to label the
graph and its axes. To make a label:
1. Enter text in the appropriate textbox.
2. Click Font to select a font, style, and size.
3. Select a color from the drop-down box.
Compound Lists
Compound Lists are lists of compounds for use in
plate templates.
To create a new list:
1. From any data table with a Compound ID
field, select the rows containing the Compound
IDs to be saved.
2. Right-click and select Save Compound List.
Lists appear in the Navigator under the Lists
folder.
NOTE: If the list contains the same compound ID more
than once, that compound ID will only be saved once.
Graph Options Plots Tab
The graph options Plots Tab allows you to control
the display characteristics of the graph. From this
tab, select a plot type, color and point style.
Manipulating Compound
Lists
Clicking on a compound lists (found in the Lists
folder in the Navigator) opens the list in the
Content Frame. Lists can be manipulated by using
the Actions menu.
Settings
Plate settings are defined through the lists found
under the Settings heading in BioAssay. These lists
define what options are available when defining a
plate.
The following settings can be defined from
BioAssay:
• Plate Formats
• Well Formats
• Picklists
NOTE: All settings defined in BioAssay are reflected in
Inventory and vice versa.
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Compound Lists

Editing the settings tables
All of the settings tables have the same basic
interface. Data is stored in a table. By default the
table opens in Browse Mode (as seen by the active
browse button). While in Browse mode, the user
can view the settings listed, but cannot make any
changes. To make changes to a settings table, click
Edit.
When in Edit Mode, the Add, Delete, and Cancel
buttons are visible.
Adding an entry
To add an entry to a settings table:
1. While in Edit Mode, click Add.
An empty column is inserted.
2. Enter information in the appropriate columns
of the new row.
3. Click Save.
Deleting an entry
To delete an entry in a settings table:
1. While in Edit Mode, click in the row to be
deleted.
2. Click Delete.
3. Click Save.
Canceling/Discarding Changes
If you have made changes to a settings table, but
have not saved those changes, changes can be
canceled. To cancel changes:
1. While in Edit Mode (after making changes,
but before saving), click Cancel.
A dialog box appears asking if you want to
discard changes.
2. Click Yes.
Plate Formats
Plate Formats are defined as a format indicating the
layout in a plate of the general contents of each well.
For this reason, the Plate Format setting needs a
Physical Plate Type defined in order to have a
general idea of the layout and capacity of the wells
in the plate first. There are two steps in defining a
plate format.
Defining a Plate Format
The following attributes can be defined for a Plate
Format:
• Name - the name of the plate format
• Physical Plate Format - the physical plate
format to be used for the plate's layout
Defining Attributes of the Plate
After entering values for the above attributes, it is
necessary to define the general contents of each
well. This is accomplished by opening the Plate
format (by double-clicking on the appropriate row).
The plate opens with the number of wells defined
in the Physical Plate Format. The default is all wells
contain the well format compound.
The default well format options are:
• Compound - a compound can be inserted in
the well
• Empty - the well remains empty
• Positive Control - this well is reserved for a
positive control
• Negative Control - this well is reserved for a
negative control
More well formats can be defined by the user. For
more information about editing the entries in the
Plate Formats table, please see “Editing the settings
tables” on page 135.
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To define the general contents of the plate's wells:
1. Enter edit mode (by clicking Edit).
2. Highlight the appropriate wells.
3. Click on the arrow in the well to display your
options for the well format for a particular well.
4. Select a contents option.
The well label is updated.
Well Formats
Well Formats define the general contents of a well.
The well format is used when defining Plate
Formats. The default Well Formats are:
• Compound - a compound can be inserted in
the well
• Empty - the well remain empty
• Positive Control - this well is reserved for a
positive control
• Negative Control - this well is reserved for a
negative control
It is important to note that the only well that the
system recognizes as a well in which a compound
from a database can be inserted, is a well with the
Compound Well Format.
For more information about editing the entries in
the Well Formats table, please see “Editing the
settings tables” on page 135.
Protocol Picklist
Items listed in the Protocol Picklist table are items
that can be included in a protocol table, not found
in other columns in the table. For example, a default
picklist category is Scientist, an attribute that might
be important to keep with a protocol's description.
There are four picklist options defined.
Adding a Picklist to the Picklist Table
To define a new picklist:
1. In the left frame, browse to
Settings>Protocol Picklist
2. Click on Protocol Picklist.
The Protocol Picklist table appears in the right
frame.
3. Click Edit.
4. Click Add.
An empty row is inserted.
5. Enter a name for the new picklist in the empty
row.
6. Click Save.
7. Click Browse.
8. Double-click on the row with the name of the
new picklist.
A table defining the entries in the picklist
appears.
9. Click Edit.
10.Click Add.
11.Enter an entry for the picklist.
12.Click Save.
13.Repeat steps 10-12 until all of the entries you
choose to define have been entered.
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Settings

Adding Picklist Options
To edit the entries in an existing picklist:
1. In the left frame, browse to
Settings>Protocol Picklist
2. Click on Protocol Picklist.
The Protocol Picklist table appears in the right
frame.
3. Double-click on the row containing the name
of the picklist.
A table defining the entries in the picklist
appears.
4. Click Edit.
5. Do one of the following:
• Click Add.
• Double click on the entry you would like to
edit.
6. Enter the desired information.
7. Click Save.
8. Repeat steps 5-7 until all of the entries you
choose to define have been entered.
Using a Picklist
To use a picklist in a protocol's table:
1. Define a table (or choose a defined table).
2. Open the table by double clicking on its row in
the Table Definitions table.
3. Click Edit.
4. Do one of the following:
• Click Add to add a new field.
• Find the appropriate row.
5. Select a picklist name in the picklist column.
6. Click Save.
Enterprise
Administration
Publishing Tables in BioSAR
Enterprise
BioAssay exposes the data stored in the system by
means of database views. These views have
computer-generated names that do not reflect the
names of the protocols or protocol tables that have
been set up. To expose these views in BioSAR
Enterprise, contact CambridgeSoft’s Technical
Support.
Enterprise
Security
Multi-user security is only available in BioAssay
Enterprise. BioAssay Ultra and Workgroup treat all
users the same way.
BioAssay applies two levels of security. The first
level controls access to certain parts of the software,
such as plate setup, editing inventory, and user
management. The second level is more granular,
managing users' abilities to view and edit protocol
data on a protocol by protocol basis.
Managing Users
A list of ChemOffice WebServer users (including
but not limited to BioAssay users) can be found
under Settings > Users.
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BioAssay uses the ChemOffice WebServer’s global
security to add and edit the properties of users. To
access the Manage Users interface:
1. Open a browser and go to the ChemOffice
WebServer homepage (http://,
where is your server's name).
2. Click Global Login.
3. Enter a username and password and click OK.
4. From the Global Login homepage, click
Manage Users.
The Manage Users interface appears.
3. Click Add User (to add a new user) or
highlight a user name and click Update User
(to edit an existing user).
A page allowing you to enter user details
appears.
To make changes to the users in the system:
1. Select the application in which the user exists
from the View Users From drop down menu.
NOTE: Selecting All CS Applications will list all
users.
2. Click Refresh.
4. Enter user details as desired. Fields highlighted
in red are required.
5. Select the roles for the user. To select more
then one role at once, hold down the CTRL key
while highlighting.
6. Click OK.
Managing Groups
A list of BioAssay groups can be found under
Settings > Groups.
Each group contains a number of users. Applying a
role to a group applies that role to all users in the
group.
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Security

Creating New Groups
To create a new group:
1. Click Edit.
2. Click Add
A new row appears.
3. Enter the appropriate information.
4. Click Save.
Adding a User to a Group
To add a user to a group:
1. Highlight the group you would like to add a
user to, and click Actions.
2. Select View Group.
A list of the users in the group appears.
3. Click Edit.
4. Click Add
A new row appears.
5. Enter the appropriate information.
6. Click Save.
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Chapter 7: BioSAR Enterprise
Overview
The BioSAR Enterprise application allows the user
to combine data from multiple applications
including the CambridgeSoft WebServer
applications and subsequently search through, and
view that data in one screen. The application is fully
customizable allowing users to create their own
search forms and decide how data will be displayed.
Terminology
Schema
A schema details the structure of a particular
database which can be accessed from the BioSAR
Enterprise application. Each schema is made up of
several tables. Each table contains a number of
fields.
In addition to describing the contents of each table,
the schema also defines any relationships between
tables and fields in that schema. These relationships
are automatically generated for you when you
enable a schema for use in BioSAR. Relationships
that cross schemas can also be applied. For
example, if a registration id number in the REGDB
schema is the same id number included in the
CHMINVDB2 schema, these two fields can be
linked within the application.
Table
Table refers to a database table that exists in a
schema in the Oracle instance. Tables define entities
in the schema.
For example, one schema may have a table defining
a person (with fields like person id, last name and
first name) while another table might define an
order (with fields like customer id, product, and
order date).
View
View refers to a database view that exists in a
schema in the Oracle instance. Views are created by
assigning the results of a query to a new table in the
database.
For example, a view could be made from the person
and order table mentioned above (under Table).
This view could include the last name and first
name of the person as well as order date. Now, the
view can be accessed much like a table eliminating
the need for longer, more complicated SQL
statements to access the information.
In most respects, a view is dealt with in the same
way a table is dealt with in the BioSAR application.
Formgroup
Each from created with the Manage Your Forms
function actually contains 3 forms: a search form, a
list view form, and a details view form. The 3 forms
are linked. A formgroup refers to the group of 3
forms.
When creating formgroups, users are able to give
other users access. If users, other than the creator is
given access to a formgroup, the formgroup is
considered public.
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Administrator
Login to BioSAR
Enterprise
To login and start using BioSAR Enterprise:
1. Enter http:/// into your web
browser.
should be substituted for
your webserver name. To find the name of
your webserver, please see your system
administrator.
2. Click on the BioSAR Enterprise link.
The BioSAR login screen appears.
Schema Management
BioSAR Enterprise's Schema Management allows
administrators to control what is visible to users.
That is, Schema Management gives administrators
the tools to control what schemas, tables, views, and
fields can be used in forms.
Schema Management can be accessed by:
• Clicking on Schema Management from the
Global Login page OR
• Selecting Manage Schema from the BioSAR
Enterprise Admin menu.
3. Enter a username and password and click Log
in.
The ChemOffice WebServer Global Login
page appears.
4. Select the part of the application you wish to
access:
BioSAR Enterprise opens. The forms
displayed depend on the option selected. Use
the toolbar to navigate through the software.
From this page, administrators can control all
aspects of schema configurations for the
application. Any schema can be viewed from
BioSAR Enterprise. For more information, please
see the BioSAR Enterprise Admin Guide.
Refreshing Tables
Users with the appropriate privileges may see a
button called Refresh All Tables or Refresh
Table in Schema Management. Clicking on this
button will wipe out any links set up between
schemas and there is no undo operations. Please be
sure you are aware of the consequences before
refreshing a table.
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Login to BioSAR Enterprise

Add/Remove Schemas
The administrator decides which schemas are
available to users of the system. If a schema is not
visible, none of the tables or views can be seen or
used by the users of the system. Any schema which
exists on the Oracle instance of the server can be
included in the BioSAR Enterprise application.
Add a Schema
To add a schema to the list of available schemas:
1. From the main menu, click on Schema
Management.
2. Click on Add/Remove Schema.
A table containing all of the schemas which
exist on the Oracle instance appears.
4. Click Save Changes to save your changes
before returning to the previous page.
Remove a Schema
To remove a schema from the list of available
schemas:
1. From the main menu, click on Schema
Management.
2. Click Add/Remove Schema.
A table containing all of the schemas which
exist on the Oracle instance appears.
3. Select the checkbox in the Exposed column to
the right of the names of schemas you would
like to make visible.
3. Uncheck the checkbox in the Exposed
column to the right of the names of schemas
you would like to remove.
4. Click Save Changes to save your changes
before returning to the previous page.
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Edit Schema
Description/Password
To edit the description or password for a schema:
1. Select a schema from the Schema Listbox on
the Schema Management page.
Schema Display Name
The display name for the schema is the name a user
will see to identify the schema. The default display
name is the name of the schema, but it is sometimes
more convenient to enter a more descriptive name
for the schema. If you would like to change the
display name:
• Enter the new name in the textbox next to
Display Name
2. Expand the schema you would like to rename
by clicking on the arrowhead next to the
schema name in the tree control.
3. Click Edit Schema Description/Password.
The Edit Schema page appears.
Schema Password
The password for the schema is assigned when the
schema is created. For information about schema
passwords for CambridgeSoft schemas, please
contact esupport@cambridgesoft.com.
If you would like to change the password (in
BioSAR Enterprise only, it still must be the actual
schema password):
• Enter the password for the schema in the
textbox next to Schema Password
Edit Exposed Tables
Users are able to decide which tables in a schema
are visible when creating forms. To edit which
tables are visible to users creating forms:
1. Expand the schema which you would like to
edit by clicking on the arrowhead next to the
schema name in the tree control.
2. Click Edit Exposed Tables.
3. Select the checkbox in the Visible column next
to any tables you would like to see visible when
users are creating forms.
4. Click Save Changes.
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Schema Management

Edit Table Fields
The selected table's page appears.
To specify which fields in an exposed table or view
should be visible to users:
1. Select a schema from the Schema Listbox on
the Schema Management page.
2. Expand the schema which contains the table by
clicking on the arrowhead next to the schema
name in the tree control.
The following things can be defined for a table:
3. Click the Edit Table Fields arrowhead to
expand (if not yet expanded).
4. Click on the name of the table.
• Table Properties
• The display name for the table
• The primary key for the table
• Field Properties
• Which fields in the table are visible to users
• The display name and description for each
field
• A lookup table for each field
• A parent column for each field
• The Index Type
• The Content Type
After making changes to the table, be sure to click
Save Changes to save your changes.
Edit a Table's Primary Key
The primary key of a table is a column which
contains a unique value for each row. This field is
usually an ID_number of some kind. The
ChemOffice WebServer requires every table have a
primary key, even if a table doesn't have a primary
key defined in the database. Each table can only
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have one primary key, and the primary key must be
an integer field. To choose the primary key for a
table:
• Select the radio button in the primary key
column to the left of the field name.
Table Fields
Specify the Visible Fields in a Table
If you would like to make a field available to users,
select the checkbox in the Visible column, to the
left of the field name. If the checkbox is not
selected, users will not be able to use it in any forms.
Edit a Table's Default Column Order
The default column order column orders the fields
in a table. If the fields are selected to be used in a
form, the default order they will appear in the form
is indicated by the Default Column Order (the
order is chronological).
Edit the Display Name for a Field
The display name for a field is the name a user
uses to identify the field. The default display name
is the name of the field in the database. to change
the display name for the field:
• Enter the new name in the textbox in the
Display Name column.
Edit Table Display Name
The display name for the table is the name a user
uses to identify the table. The default display name
is the name of the table, but it is sometimes more
convenient to enter a more descriptive name for the
table. If you would like to change the display name:
• Enter the new name in the textbox next to
Display Name
Edit the Description for a Field
The display name for a field is the name a user will
see to identify the field. The default display name is
the name of the field, but it is sometimes more
convenient to enter a more descriptive name for the
field. If you would like to change the display name:
• Enter the new description in the textbox in the
Description column.
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Specify a Lookup Table for a Field
A lookup table for a field defines where a field's
display value can be found. Many times a lookup
table is defined for an ID field so that instead of
displaying the ID to the user when the information
is viewed, a value more useful to the user is
displayed. During installation, lookup tables are
automatically recorded for ChemOffice WebServer
schemas.
To define a lookup table for a field,
1. Click on the link in the Lookup Table column
to the right of the field name.
The Lookup Table page appears.
2. Select the schema where the lookup table exists
from the Lookup Schema listbox.
The Lookup Table listbox is populated.
3. Select the lookup table from the Lookup
Table listbox.
The Linking Column and Display Column
listboxes are populated.
4. Select the Linking Column and Display
Column.
5. Click Save Changes.
Linking Column
The linking column is the column in the lookup
table with the same value as the field whose lookup
table is being defined.
For example, there is a field called
EXPERIMENT_TYPE_ID in the
EXPERIMENTS table in the REGDB schema.
this ID, to a user, doesn't give much information,
but the EXPERIEMTNTYPE table in the
REGDB schema defines the relationship between
the ID and an experiment's name.
For this reason, the linking column for
regdb.experiments.experiment_type_id is
regdb.experimenttype.experiment_type_id.
Display Column
The display column is the value that should be used
in place of the actual field value in forms.
In our example above, we have linked two tables
together. The EXPERIEMENTS table contains a
field called EXPERIMENT_TYPE_NAME (in
addition to the EXPERIMENT_TYPE_ID). This
field contains a name for each ID. Therefore,
experimenttype.experiment_type_name is the Display
Column for regdb.experiments.experiment_type_id.
Specify a Parent Column for a Field
A parent column defines a table which is related to
many tables in the same way. As opposed to a
lookup table, which has a one to one relationship
with its related table, a parent table has a one to
many relationship.
During installation, parent columns are
automatically recorded for ChemOffice WebServer
schemas.
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To specify a parent column for a field:
• Parent Column - REG_INTERNAL_ID
Administrator
1. Click on the link in the Parent Column
column to the right of the field name.
The Parent Column page appears.
2. Select the schema where the lookup table exists
from the Parent Schema listbox.
The Parent Table listbox is populated.
3. Select the parent table from the Parent Table
listbox.
The Parent Column listbox is populated.
4. Select the Parent Column.
5. Click Save Changes.
For example, the REG_NUMBERS table is a
parent of the BATCHES table because one
compound can contain many batches. For each
REGDB.REG_NUMBERS.REG_ID, there are
one or more matching records in BATCHES.
BATCHES.REG_INTERNAL_ID contains the
same value as
REGDB.REG_NUMBERS.REG_ID. So, if we
would select the following when defining the Parent
Column for
REGDB.BATCHES.REG_INTERNAL_ID:
• Parent Schema - REGDB
• Parent Table - REG_NUMBERS
Specify an Index Type for a Field
The index type for a field is for a field containing
a LOB that is indexed. Currently the only supported
index type is the Oracle Cartridge. Most other fields
containing LOBs (such as GIFs, JPEGs, etc.) are
not indexed and should be assigned the index type
"no index".
Specify a Content Type for a Field
The content type for a field is the HTTP
MIME_TYPE for a particular LOB. The current
options are:
Type of LOB in
field
Oracle Cartridge
GIF
Content Type
ichemical/x-cdx
IMAGE/gif
Manage Your Forms
BioSAR Enterprise allows users to search through
and view data in multiple application databases all at
once. In order to accomplish this, the user must
define how information will be searched and what
will be returned. BioSAR Enterprise's Form
Management gives you the tools to create and
customize search and results forms.
Not all users are entitled to make their own forms.
If you are able to access Manage Your Forms,
please see your system administrator about gaining
the privileges to make new forms.
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Manage Your Forms

Manage Your Forms can be accessed by:
• Clicking on Manage Your Forms from the
Global Login page OR
• Selecting Manage Your Forms from the
BioSAR Enterprise Forms menu.
3. Click Save Changes.
NOTE: To continue defining the form, select the new
form from the listbox and click Edit.
Selecting a Base Table
The base table is the table which your form is built
around. Not only is it the first table in any form, all
additional tables included must be linked to the base
table in some way.
The base table for a form can be any of the tables
contained in the visible schemas on the system.
Only one base table can be chosen, and the list of
child tables to choose from will change depending
on the base table chosen.
To select a base table:
1. Click on [Select Base Table].
A page allowing you to select a table appears.
Create a New Form
To create a new form:
1. From the Manage Your Forms page, click
Create New Form.
A page allowing the definition of a new form
appears.
2. Select a schema from the Schema listbox.
The Base Table listbox is populated.
3. Select the base table from the Base Table
listbox.
4. Click Save Changes.
You are returned to the Edit Form page and
the name of the table chosen will be listed
under Base Table.
2. Enter a name and description for the new form
is the appropriate textboxes.
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Selecting Fields in a Table
After selecting a base or child table, it is necessary
to indicate which fields should be visible to the
form user, and when. To do this:
1. Click Edit in the Fields column.
A page listing all fields available in the table is
listed.
How Fields are Displayed in Forms
It is also possible to indicate how fields should be
displayed in a form. To do this:
1. Click Edit in the Field Options column.
A list of all available fields appears.
2. Three columns are shown to the right of field
names and descriptions in the table,
representing different views, entitled
• Query - visible in the query form used to
search
• List - visible in the results list form (multiple
records viewed at one time)
• Detail - visible when one record is viewed
alone
Select the checkboxes in the appropriate
columns to indicate the field should be visible
in that view.
3. Click Save Changes.
2. Select a format for the field to be displayed in,
for each view, from the Format drop down
menu.
For more information about the field formats,
see the table below.
NOTE: Note: Some fields have only one way of being
displayed. In this case, there is no choice given.
3. Enter the desired dimensions of each field in
each view.
4. Select the Show checkbox if you would like
that field to be visible to users in the specified
view.
5. Click Save Changes.
Display
Type
Description
Option
in which
View
Structure
A structure
window appears
Search
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Display
Type
Description
Option
in which
View
Display
Type
Description
Option
in which
View
ChemDraw
PlugIn
Graphic
A CDX file is
displayed (can be
edited with
ChemDraw
toolbar).
A graphic is
displayed. IN-
LINE means the
graphic appears in
the current
window, NEW
WINDOW means
a link to the
graphic will be
displayed and
clicking on the link
will open the
graphic in a new
window.
List,
Detail
List,
Detail
TextArea
TextBoxAllow
List
A larger area
allowing multiple
lines of text to be
entered.
Allows users to:
1. Browse to a list
of files and use
that as the entry
OR
2. Enter multiple
values delimited
by commas,
tabs, or
linefeeds. These
values can be
pasted from
Excel, or a text
file.
Search
Search
Static GIF
A GIF (showing
an image of the
structure) is
displayed. Cannot
be edited.
List,
Detail
DatePicker
Validated as a text
field, includes a
calendar icon
allowing easier
input of dates.
Search
TextBox A textbox. Search
Date
Validated as a date. Search
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Display Order of Fields
A user can also decide the order in which fields are
shown in a form. To do this:
1. Click the appropriate view name in the Field
Order column.
A page listing all chosen fields are listed.
5. Indicate the order you would like the tables to
be displayed in the form by clicking on the
arrows in the Table Order column.
6. Click Save Changes.
Form Roles and Users
Some users are given the option to choose specific
roles or users that should have access to a form. If
this is the case, a table like the one below will be
visible:
2. Click on the arrows to the right of a field name
to move a field higher or lower on the form.
3. Click Save Changes.
Selecting Child Tables
Child table options for a form will change
depending on the base table chosen.
To select a child table:
1. Click on [Select Child Tables].
A page listing all child tables, compatible with
the chosen base table, appears.
2. Select the checkbox next to any table you
would like visible on the form.
3. Click Save Changes.
You are returned to the New Form page and
the names of the tables chosen are listed under
Child Tables.
4. Select the appropriate fields for each table.
Fields are selected in the same way as for the
base table.
To add users or roles for the form, highlight the
appropriate listing in the listbox below All Users
and Roles and click Add. This will move the listing
into the Permitted Users and Roles listbox to the
right.
To remove a listing from the Permitted Users and
Roles listbox, highlight the appropriate listing in
the listbox below Permitted Users and Roles and
click Remove.
If roles or users are chosen, even if an individual
user is missing a role (for example, one to view a
specific table in the form), this role is granted to the
user for the use of the form automatically.
Editing a Form
After a form has been created, the information can
be edited at anytime as long as you are logged in as
the user who made the form in the first place, or
you are assigned the appropriate privileges to edit
other user’s forms.
To edit a form:
1. From the Manage Your Forms page, select
the form from the listbox.
2. Click Edit.
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A page allowing the definition of a form
appears.
A page allowing you to rename the form
appears.
3. Edit the name and description in the textboxes.
4. Click Save Changes.
3. Enter/Select the appropriate information.
There are four parts of a form's setup:
• Edit the name and description for the form
(cannot be changed from this page).
• Select users and roles entitling access.
• Select a Base Table for the form and define
which fields will be visible to the user.
• Select Child Tables for the form and define
which fields will be visible to the user.
4. Click Save Changes.
Renaming a Form
The name and description of a form are used to
identify the form when it is restored to search.
Duplicating a Form
Duplicating a form is often useful if there is a form,
that already exists, which has many of the properties
that you would like in a new form. For example, if
you are creating a new form with the same base
table and field properties of an old form,
duplicating a form can save time in defining the new
form.
To duplicate a form:
1. From the Form Management page, select the
form to be duplicated from the listbox.
2. Click Duplicate.
The form is duplicated and can now be
accessed from the listbox. The name of the
new form is the name of the old form preceded
by "Copy of".
To rename or change the description of a form:
1. From the Form Management page, select the
form from the listbox.
2. Click Rename.
Delete an Existing Form
To delete a form listed on the Manage Your
Forms page:
1. From the Form Management page, select the
form from the listbox.
2. Click Delete.
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The following warning appears:
The search form you chose appears.
3. Click the appropriate link.
Administrator
Opening a Form/Searching
Using a Form
One way to retrieve search results is to perform a
search with the use of a search form. For more
information about defining search forms, please see
“Manage Your Forms” on page 148. To search
using a search form:
1. Select Open Forms from the Forms Menu.
2. Select a search form to use, from the list of
forms.
The form you see will depend on the form
group chosen and will most likely not have all
of the same fields as the above form.
3. Enter the desired information in the form.
4. Select a Sort by field, from the Search Sort By
drop down menu, if desired.
5. Select one of the following radiobuttson:
• Show All Child Data - show all child data for
matching records (if one set of child data
matches the entered criteria, but another set
for the same base record doesn’t, this option
allows you to view all data)
• Show Only Child Data Matching Entered
Criteria - show only the child data which
matches the entered criteria
6. Click Search.
Your search results are displayed.
For tips in using ChemOffice WebServer search
forms, please see Performing Searches in the
ChemOffice WebServer Chapter.
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Searching
There are three different ways to retrieve search
results from the main menu under the heading
Search Using:
• Using a Form Group
• Retrieving a Saved Query
• Retrieving a Query in the History
After performing a search, search results are always
displayed in the same format. For more
information about viewing search results, please see
“Viewing Search Results” on page 156.
Search Using a Saved Query
It is possible to save a query after it has been
entered. Saving queries might be helpful if it is
necessary to repeat a query a number of times. With
this feature, it would, for example, allow you to save
a query which searches for batch information for a
particular compound. Since batches are not all
made at once, one day the results may be one set,
but the next day (after another batch was made),
more results would be retrieved.
To save a query:
• Select Save from the Queries menu.
To use a saved query:
1. Select Restore from the Queries menu.
2. Select either Saved or Last depending on the
query you wish to restore. If you select Saved,
a dialog box opens.
3. Select the appropriate form, and the query
associated with that form.
4. Click Restore.
5. Add more information, if desired, and click
Search.
For tips in using ChemOffice WebServer search
forms, please see Performing Searches in the
ChemOffice WebServer User's Guide.
Searching Using the History
A history of searches performed is automatically
saved for each session. Once a session is ended, the
history is erased. If you would like to save a query
after an individual session with BioSAR Enterprise
ends, please see “Search Using a Saved Query” on
page 155.
Queries saved in the history are saved under names
of the following format:
HISTORY-
• where is the date the query was
entered and is the time at which the
query was entered
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Administrator
To access a query in the history:
1. Select Queries from the History menu.
The history dialog box opens.
To show all retrieved information for a particular
record, click on Show Details.
What information is displayed at the different view
levels is defined when creating a new form. For
more information about manipulating search
results, please see Search Results in the ChemOffice
WebServer User's Guide.
After clicking on Show Details, the Results Form
View appears. Here, it is possible to view your
results in different formats. The information
displayed in each of the formats is the same and the
screen differs only in its layout.
2. Select the appropriate search from the listbox.
3. Add more information, if desired, and click
Search.
For tips in using ChemOffice WebServer search
forms, please see Performing Searches in the
ChemOffice WebServer User's Guide.
Viewing Search Results
After a search is performed, the results are
displayed in a list form allowing the user to view
some of the contents from each record retrieved.
Sorting Results
Search results can be sorted by clicking on the table
header of one of the columns.
Dynamically Editing a Form
Often, once a form is opened, a user would like to
edit the layout or content. To edit the form which is
currently open:
1. Select Edit this Form from the Forms menu.
2. Make your changes.
3. Click Save Changes.
You are returned to the open form, reflecting
the changes made.
List View Options
List view allows two layout options:
• Columns Down - arranges fields in columns
spaced horizontally.
• Columns Across - arranges fields in columns
spaced vertically.
Click Toggle Layout to switch between the two
views.
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Columns Down
Tab View
In Tab View, each table's or view's data is separated
into tabs. Click on the tab to access the appropriate
information.
Columns Across
Report View
In the Report View, all data is displayed on one
page, in one frame. Base table data is displayed at
the top, and child table data appears below.
Details View Options
Frame View
Frame View is the default search results details view.
This view shows data in two frames, the base table
in the left frame and the child tables in the right
frame.
Generating Reports
BioSAR Enterprise allows users to generate reports
for any publicly defined formgroup. After
performing a search using a public formgroup, a
Generate Report link is found at the top of the
page.
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Administrator
To generate a report:
1. Perform a search using a public form group.
2. Select Generate Report from the Reports
menu.
The Report window appears.
3. Select the appropriate options for your report.
Report
Setting
Data View
Description
The data view is
the cross-section
of data you
would like to see.
When creating
your forms, you
defined a List
and Details view.
Usually the
Details view has
more
information
about each
record in the list
view. Select the
data you would
like the create the
report for.
Table Layout Tables can be
placed across
(arranged
horizontally next
to each other) or
down (arranged
vertically).
Options
• List
• Details
• Tables
Across
• Tables
Down
Report
Setting
Settings
profile for
the report
Page
Orientation
Description
Profiles define
the display
settings for a
report. This
includes font
size, color, and
style as well as
the inclusion or
exclusion of
logos. Use the
links to the right
of the listbox to
view, edit, or
delete the
selected profile
before creating
the report.
Reports can be
forced to be
created to fit a
portrait of
landscape
format. If Auto
is selected, the
appropriate size
(in the attempt to
display as much
information as
possible) is
chosen and
implemented.
Options
List of all
available
profiles.
Profiles can
be made
public.
• Auto
• Portrait
• Landscape
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Report
Setting
Page Size
Description
The page size is
implemented
when the report
is created to fit
on the page you
are using.
Options
• Letter
(8.5 x 11
in.)
• Legal (8.5
x 14 in.)
• A3 (297 x
197 mm)
4. Click Run Report.
NOTE: If structures are not appearing in your reports, the
schema may not be configured correctly. Please see your system
administrator.
Create a New Profile
A Report Profile controls the font color, style, and
size as well as the inclusion or exclusion of logos
and header lines.
To create a new profile:
• A4 (210 x
297 mm)
1. Click the New link to the right of the profile
listbox.
• B4 (250 x
354mm)
• B5 (182 x
257mm)
The Profile window appears.
The defaults are the values in the default
profile.
• Tabloid (
11 x17in.)
New page
for each
record
If you would like
a page break to
be inserted after
each record, use
this setting by
selecting Yes.
• No
• Yes
Report
Format
Select the format
you would like
the report
displayed in
• SNP
(Microsof
t Access
reporting
format)
• PDF
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Administrator
2. Enter the appropriate settings:
If you
would
like to ...
Give the
profile a
name
(*required)
Then ...
Enter a name for your profile
in the Profile Name textbox.
This name is used as an
identifier and is listed in the
profile listbox in the Report
window.
If you
would
like to ...
Adjust the
font type,
style, size,
weight, or
color of a
particular
part of your
report
Then ...
Select the appropriate options
from the listboxes to the right
of the appropriate text block
name.
write a brief
description
of the
profile.
Make the
profile
public
Set the
margin
width
Set the
color of the
header,
footer, or
detail in the
report
Enter a description in the
Description textbox.
Select Yes in the Public
listbox. Note: Making a
profile public makes it
available to other user's use
when generating reports.
Only the owner of a profile
can edit or delete a profile.
Select the appropriate margin
size in the margin listboxes.
Select the color in the
appropriate listboxes
Insert
header lines
to the top
of the
report
Include a
logo
3. Click OK.
Adding Logos
Enter text into the header line
textboxes.
Select the logo to include
from the Logo listbox, or
click Add to add a new logo.
Logos can be used at the top of reports. To add a
logo to the list of options:
1. Click the Add link to the right of the Logo
listbox.
The Add window appears.
2. Click Browse and browse to the file. Logos
must be of one of the following file types:
• GIF (.gif)
• JPEG (.jpg)
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• PNG (.png)
3. Click Add Logo when the file name appears in
the textbox.
Edit a Profile
Profiles can only be edited by the user who created
them, even if the profile is public.
To edit an existing profile:
1. Select the profile to be edited from the listbox.
2. Click Edit.
The Profile window appears with the selected
profile's values populating the fields.
If you
would
like to ...
write a brief
description
of the
profile.
Make the
profile
public
Then ...
Enter a description in the
Description textbox.
Select Yes in the Public
listbox. Note: Making a
profile public makes it
available to other user's use
when generating reports.
Only the owner of a profile
can edit or delete a profile.
Set the
margin
width
Select the appropriate margin
size in the margin listboxes.
3. Change the appropriate settings:
Set the
color of the
header,
footer, or
detail in the
report
Select the color in the
appropriate listboxes
If you
would
like to ...
Give the
profile a
name
(*required)
Then ...
Enter a name for your profile
in the Profile Name textbox.
This name is used as an
identifier and is listed in the
profile listbox in the Report
window.
Adjust the
font type,
style, size,
weight, or
color of a
particular
part of your
report
Select the appropriate options
from the listboxes to the right
of the appropriate text block
name.
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If you
would
like to ...
Then ...
The profile appears.
Administrator
Insert
header lines
to the top
of the
report
Enter text into the header line
textboxes.
Include a
logo
Select the logo to include
from the Logo listbox, or
click Add to add a new logo.
4. Click OK.
View a Profile
BioSAR Enterprise allows users to generate reports
for any publicly defined formgroup. After
performing a search using a public formgroup, a
Generate Report link is found at the top of the
page.
To view an existing profile:
1. Select the profile to be viewed from the listbox.
2. Click View.
NOTE: Profiles can be edited, only by the creator of the
profile. Select Duplicate to create a new profile using another
profile's settings.
Delete a Profile
Profiles can only be deleted by the user who created
them, even if the profile is public. The default
profile can not be deleted.
To delete an existing profile:
1. Select the profile to be deleted from the listbox.
2. Click Delete.
A confirmation message appears.
3. Click OK.
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Ordering Fields and Changing Label
Sizes in Reports
The order and size of fields in reports are a direct
result of the form the report is generated from.
Therefore, to change the order of fields, or the size
of field labels in a report, you need to change the
size of the field specified in the form.
3. Click on the name of the form you would like
to adjust.
4. Select the link for the appropriate table under
Field Options.
5. Scroll to the appropriate field and set the width
to the width you would like to see in your
report.
To change the order of fields:
1. Return to the Main Menu.
2. Click Mange Your Forms.
3. Click on the name of the form you would like
to adjust.
4. Click on the link in the Field Order column.
5. Use the Arrow buttons to move fields up and
down.
6. Click Save Changes.
To change the field label size:
1. Return to the Main Menu.
2. Click Mange Your Forms.
6. Click Save Changes and return to your form.
7. Generate the report again.
Your new width will be reflected.
Manage Users and
Roles
The BioSAR Enterprise application uses the global
ChemOffice WebServer User Management
interface. Please see Managing Users and Roles in
the ChemOffice WebServer User's Guide for more
information.
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Administrator
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Section IV: ChemOffice
WebServer
This section provides information about
CambridgeSoft’s ChemOffice WebServer and
Oracle Cartridge, the core structure for all other
enterprise solutions.
ChemOffice WebServer
Sharing information within a company has become
easier with the use of the internet, and companywide
intranets. The CambridgeSoft ChemOffice
WebServer makes it possible for pharmaceutical
companies, and laboratories to use this technology
to store, manipulate and share chemical structure
data, inventory information, and assay data by
delivering customized information directly to each
user’s desktop.
The ChemOffice WebServer includes applications
addressing Knowledge Management, Research &
Discovery, and Biological Informatics concerns of
any cooperation struggling with ways to organize
and distribute chemical and biological data.
The real strength of the package is revealed when
multiple applications are integrated together
allowing an individual, for example, to track the
amount of a particular registered compound, which
is available in a storage plate, being used for assay
testing in a different facility. Such a process utilizes
Inventory, Registration System, and BioAssay.
Entering information in one of these 3 applications
is reflected in the rest, simplifying the effort by
users, and limiting the risk for error.
The ChemOffice WebServer is installed on a server
to be accessed by any number of client machines on
the network. All WebServer applications are
accessed through the user’s favorite web browser. A
familiar looking interface, the WebServer
applications use multiple web input forms to
receive, retrieve, and display data.
CS Oracle Cartridge
The CambridgeSoft Oracle Cartridge introduces a
new way of dealing with chemical structure and
reaction data in an Oracle database, improving
portability and consistency in applications. Since the
CS Cartridge is accessed through Oracle, this opens
the door for programmers interested in manipulating
chemical structure data directly from their code
without learning a new language. Using the CS
Cartridge is as easy as using a few simple SQL
commands. The CambridgeSoft Oracle Cartridge
supports CDX, CDXML, MolFile, RXN, and
SMILES formats making it flexible enough to be
included with both new and legacy data, without the
need for conversion.
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Chapter 8: ChemOffice WebServer
About ChemOffice
WebServer
ChemOffice WebServer is a World Wide Web (web)
chemical information server. Through a web
browser, you can use the ChemOffice WebServer
web applications to search databases for chemical
and biological information.
ChemOffice WebServer is the basis for
CambridgeSoft’s enterprise applications.
Installation and
Administration
Installation instructions, configuration options, and
other administration tips can be found in the
Admin guide for the ChemOffice Webserver and
each of its applications.
Please see the application’s readme file and
Administrator’s Guide (if applicable) for more
information.
Global Login and
Security
The ChemOffice WebServer uses a global login
interface to manage user information for most
applications (Sample not included). After logging in
once with your user name and password, users have
access to all WebServer applications that they have
permissions to, without having to login to each
application separately.
After logging in, a cookie is written to the client
machine, holding login information. The cookie
expires after 25 minutes of inactivity. Therefore,
login information is recognized even after a
browser is closed.
Logging In
To login to the ChemOffice WebServer suite of
products:
1. Access the ChemOffice WebServer homepage
and click on the Global Login link.
A login box appears.
2. Login with a valid username and password and
click OK.
The Global Login page appears.
NOTE: The links visible on this page depend on the
permissions of the user who is logged in.
This page includes links to all of the
applications the logged in user has access to.
3. Click on a link to enter a particular application.
Manage Users and Roles
Users and Roles are managed universally for all
ChemOffice WebServer applications. Links to User
Management is available from each application as
well as from the main global login page, if the user
has the correct privileges.
Users
To access the Manage Users interface:
• From the Global Login homepage, click
Manage Users.
The Manage Users interface appears.
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Administrator
To make changes to the users in the system:
1. Select the application in which the user exists
from the View Users From drop down menu.
NOTE: Selecting All CS Applications will list all
users.
2. Click Refresh.
3. Click Add User (to add a new user) or
highlight a user name and click Update User
(to edit an existing user).
A page allowing you to enter user details
appears.
4. Enter user details as desired. Fields highlighted
in red are required.
5. Select the roles for the user. To select more
then one role at once, hold down the CTRL key
while highlighting.
6. Click OK.
Roles
To access the Manage Roles interface:
• From the Global Login homepage, click
Manage Roles.
The Manage Roles interface appears.
To make changes to the roles in the system:
1. Select the application in which the role exists
from the View Roles From drop down menu.
NOTE: Selecting All CS Applications will list all
roles.
2. Click Refresh.
3. Click Add Role (to add a new role) or highlight
a role name and click Update Role (to edit an
existing role).
A page allowing you to enter role details
appears.
4. Enter role details as desired. Fields highlighted
in red are required.
5. Select the roles for the role. To select more
then one role at once, hold down the CTRL key
while highlighting.
6. Click OK.
Searching ChemOffice
WebServer
Applications
ChemOffice WebServer applications are accessible
from any remote computer that has access to the
server machine with the ChemOffice WebServer
and its applications installed.
ChemInfo is a collection of databases which can be
used with the ChemOffice WebServer. For more
information about the ChemInfo Databases, please
see “Scientific Databases” on page 207.
All of the ChemOffice WebServer applications
incorporate a system of forms which allow the user
to search a database of information. Searches are
performed by entering information in fields on a
search form. The information entered makes up a
search query.
Before beginning a search you must take the
following steps:
1. Login to and open a WebServer application.
2. Choose the appropriate search form.
3. Enter your search criteria and click Search.
Due to the similarities between applications, in this
chapter, the Sample application is used to illustrate
the basic functionality of the available WebServer
applications. For more detailed information about a
particular application, please see, its chapter in this
section.
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Accessing a ChemOffice
WebServer Application
To access a ChemOffice WebServer application:
1. Access the following URL:
http://servername/chemoffice.asp where
servername is the name of the server where
ChemOffice WebServer 2003 is installed.
Contact your server administrator for this
name.
2. Click the ChemOffice WebServer application
link you want to search. For this example, click
Sample.
The Query Input Form appears. Click on the
image below for more information about its
function.
The Query Input Form User
Interface
The Navigation Toolbar
The navigation toolbar appears at the top of most
search forms in the ChemOffice WebServer. It
consists of a menubar and a series of buttons. The
actions available in the Sample application are
listed:
Feature
Description
Total Records
The number next to this
image indicates the total
number of records in the
database being searched.
File Menu
Preferences - Accesses the
Preferences dialog box,
where you can set search
preferences for the session
you are currently in. For
more information, see
“Setting Your Display and
Search Preferences” on
page 184.
Print - Prints the current
window (equivalent to
using the browser's print
button).
Export Hits - Exports hits
to a SD or RD File.
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Feature
Description
Feature
Description
Administrator
History Menu
Queries - Allows users to
retrieve a query which was
executed in the current
session (does not require
having saved the query).
Hit lists - Allows users to
retrieve a hit list which was
created in the current
session (does not require
having saved the hit list).
Queries Menu
Restore - Displays the last
query entered in the Query
Input Form, or one of the
saved queries.
Save - Saves the current
query.
Manage - Allows users to
manipulate (restore, edit,
and delete) saved queries
and queries in the current
history.
Hit Lists Menu
Restore - Displays the last hit
list created, or one of the
saved hit lists.
Save - Saves the current hit
list.
Manage - Allows users to
manipulate (restore, edit,
and delete) saved hit lists
and hit lists in the current
history.
Marked Hits Menu
Show Marked - Displays all
marked records.
Clear Marked - Clears the
marked hits.
Help Menu
Contents - Accesses the
online Help.
About - Provides
information about the
version of the ChemOffice
WebServer software and
the database being
searched.
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Feature
Description
LogOff Menu
Ends the current session
and clears any resources
used by the user.
Search Button
Starts a search.
Clear Form
Deletes all information in
the input form.
Add Mode
Switches to Add Mode
which gives users the ability
to add records to the
database.
Retrieve All
Performs a search that
retrieves all records in the
database.
Search Input Form
The following is a list of fields found in the Sample
application. For more information about a field in
another WebServer application, please see the
application’s chapter in the “ChemOffice Desktop
to Enterprise Solutions” Manual.
Search Field
Search Type pulldown
menu.
Structure box and
ChemDraw Tools
toolbar
Action
Select the type of
structure search for
your query:
Substructure, Exact
Structure, Identity
Search, or Tanimoto
Similarity. For more
information about
structure types, see
“Searching With
Structures” on page
173.
Draw a structure. For
more information
about drawing
structures, see the
ChemDraw User’s
Guide.
Molecule Name
Synonym
Enter a molecular
name or a portion of a
molecular name.
Enter a synonym for a
molecular name.
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Search Field
Action
The Results List View window appears.
Administrator
Molecular Weight
Enter a molecular
weight or a range of
molecular weights. For
more information, see
“Searching With
Numerical Ranges” on
page 175.
Formula
Enter a molecular
formula. For more
information, see
“Searching With
Molecular Formulas”
on page 174.
Performing a Simple Search
Queries are used to search for information in
databases. Queries can contain different types of
information and can be simple or complex,
depending on the database you want to search. This
example shows how to create a simple text query
for searching the Sample database.
To create a simple text query:
ChemOffice WebServer finds 30 records that
match your query. These results can also be
called hits.
For more information about:
This subject
See
1. In the Molecule Name box, type benz.
2. Click Search.
changing the way
results appear.
“Setting Your Display
and Search
Preferences” on page
184.
using results for other
searches.
“Search Results” on
page 176.
searching with other
types of queries.
“Searching by
Different Query
Methods” on page
173.
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Searching by Different Query
Methods
The following is a list of the basic types of searches
or query methods utilized in ChemOffice
WebServer applications:
• Text
• Structure
• Molecular Formula
• Numeric (e.g. Molecular Weight)
• Combination (a combination of the above
types)
Each of the above methods include distinct features
which, when used correctly, can help to manipulate
a search.
In addition, search preferences can be modified to
allow valence modifications. For more information
on setting preferences, see “Setting Your Display
and Search Preferences” on page 184.
Searching With Text
One example of a text field, in the Sample
Application, both Molecule Name and Synonym
are text fields.
When entering search criteria into a text field, use
the following rules:
• Use wildcard characters (*) to broaden search
results.
• Use equals (=) to narrow search results.
• A regular text field is not a free text search so
do not use AND, OR, or NOT for queries.
For example, the following searches actually mean:
Text entered
ben
*ben
=Benzene
Ben*chl
Search Results include
Records that start with
“ben,” with any combination
of characters following.
Matches include benzene
and benzofuran, but not
bromobenzene.
Records that include “ben”
anywhere within the field.
Other characters can be
found before or after “ben”.
Matches include benzene,
benzofuran, and
bromobenzene.
Records that include
“Benzene” with no other
characters in the field’s entry.
Records that have “ben” as
the first three letters of the
entry, followed by any
number of characters,
followed by “chl” and any
number of characters to end
the entry. A match would
include Benzyl chloride but
not Benzene.
Searching With Structures
Searching by chemical structure is greatly simplified
by using a ChemOffice WebServer structure search.
There are four types of structure searches. The type
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of search is indicated by the choice made in the
structure pull-down menu found above the
structure box.
The following is a list of types of structure
searching found in the Structure pull-down menu:
• Substructure - identical to the structure drawn
in addition to any records with other
attachments at open positions of the structure
• Exact Structure - identical to the structure
drawn (hits isotopes)
• Identity - identical to the structure drawn (does
not find isotopes) including equivalent
stereochemistry
• Tanimoto Searching - similar to the structure
drawn
Drawing a structure in the box provided is
facilitated by the ChemDraw toolbar. The
ChemDraw toolbar makes particular pieces of a
structure available with one mouse click. For more
information about using the ChemDraw toolbar,
please see “Drawing Chemical Structures” in the
ChemDraw Manual.
If the ChemDraw toolbar is not visible when you
are ready to start drawing:
1. Right click anywhere inside the structure box.
2. Go to View>Main Tools.
The ChemDraw Toolbar appears
Similarity (Tanimoto) Searching
The Tanimoto Similarity option finds structures
that have structural features that generally
correspond to those in the query. Similarity
searches are usually indistinct. In a full structure
similarity search, the results are guaranteed to
include all those you would obtain from a
substructure search with the same query and usually
some additional hits. Similarity searches are useful if
you have a general idea of the types of compounds
you are looking for, but do not know the precise
target compound. Similarity searching matches
general structural features and not specific atoms
and bonds.
The application uses a Tanimoto calculation to
determine if compounds are similar. How similar
the results should be can be specified in the
Preferences dialog box. For more information on
setting preferences, see “Setting Your Display and
Search Preferences” on page 184.
Searching With Molecular Formulas
Searching for molecular stoichiometry is
accomplished with the inclusion of a formula query
method. Formula queries consist of element
symbols and element counts or ranges.
When searching by formula, use the following rules:
• Capitalize the symbols properly.
• Use symbols that are one or two letters, and
upper or lower case.
• Use element counts that are single integers or
ranges (two integers separated by a hyphen). If
a count is omitted, it is assumed to be 1.
• Note that formula searches are completely
non-structural. The formula CH3CH2OH
matches dimethyl ether and ethyl alcohol
because both compounds have the same
molecular formula: C2H6O.
For example, the following searches really mean:
Formula
Results
C6H6* Entries with 6 carbons and 6
hydrogens, plus any number of
other elements in the formula
field. Matches include C6H6,
C6H6N2O.
CH3CH3 2 carbons and 6 hydrogens.
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Formula
Results
For example, the following searches really mean:
(CH2)3
3 carbons and 6 hydrogens.
C6* 6 carbons plus any number of
other elements.
Molecular Weight Results
78.15 78.145 to 78.155.
78 77.5 to 78.5.
C6 N1-3*
6 carbons and between one and
three nitrogens, plus any number
of other elements. Matches
include C6H7N and C6H5NO2.
89.5–90.5 89.5 to 90.5.
90.05–91.05 90.05 to 91.05.
Searching With Numerical Ranges
All numeric fields allow the inclusion of one
particular number or a range of numbers. The
Molecular Weight field is an example of a numeric
range field found in the Sample Application.
If a numeric search is performed with one number,
the application will interpret the number as a range.
For example, if 78 is entered, the range used spans
.5 above and .5 below the number (77.5-78.5).
When searching by molecular weight, use the
following rules:
• To search over a range of weights, use a hyphen
between the values at either end of the range.
Ranges may also be indicated using inequality
operators () together with the AND
operator.
• Note that the number of significant digits
determines the precision of the search. A hit is
any value that rounds off to the query.
90–100 90 to 100.
>=90 and 90 and

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The ChemOffice WebServer finds 1 record
that matches your query.
Notice that if the molecular weight range (for
example) was not included, more results would
have been returned.
Search Results
Viewing Results in List View
The List View allows the user to view information
about multiple records at once. In general, List
View does not display all the fields available for a
record.
Use the browse buttons to view additional hits.
To change from Form View to List View:
• In a Results Form View window, click Return to
List.
The record you want to see appears in the
Results List View window, along with the other
search results.
Performing a search within an application results in
a list of items matching your query. All result forms
in the WebServer applications have similar formats,
but vary according to what you are searching for,
and what is returned.
This section describes the results obtained when
searching the Sample Database. In order to follow
along, login to the Sample Database and perform
the search described in Performing a Simple Search.
Viewing Search Results
There are two result formats available:
• List View
• Form View
The appearance of search results can be changed in
the Display Preferences. For more information
about Preferences, see “Setting Your Display and
Search Preferences” on page 184.
Viewing Results in Form View
Form View allows the user to view all of the
information available in one record.
To change from List View to Form View:
1. In a Results List View window, go to the record
you want to see in Form View.
2. Click Show Details.
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The record you want to see appears in the
Results Form View window.
The following buttons are available at the top of the
results form to allow the user to view additional
records:
If you want to
see
Then click
the next group of
records.
Next Record
the last record of all
the records returned
from the search.
Last Record
Browsing Other Records
After the ChemOffice WebServer completes a
search, the results appear in a Results window.
Sometimes, not all the records returned from the
search appear in the Results window.
For example, if a search was performed in the
Sample application to find the molecule named
“benz”, although the application returns 13
records, only one through five of the 13 appear in
the current Results List View window.
NOTE: The maximum number of records displayed on one
page in Results List View is set in the Preferences box. The
default is five records. For more information, see “Setting
Your Display and Search Preferences” on page 184.
the group of records
you saw most
recently.
the first record of all
the records returned
from the search.
a specific record.
Previous Record
First Record
Record Number
Type a number in the
box, within the given
range.
Click OK.
Viewing All Records
ChemOffice WebServer retrieves a set number of
records at a time, and these records are displayed
several at a time in the Results View window (the
number of records displayed depends on user
preferences). The number of records retrieved
depends on a setting in the application’s INI file.
For information about the maximum number of
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hits retrieved for your application, please see your
system administrator. The default number of
maximum hits for Sample is 100.
To retrieve the first 100 records of a database:
1. From the Query Input Form, click Retrieve All.
The Results List View appears, showing
records 1–5 of 100 hits.
To see the next 100 records:
• In a Results Form View window, click Get More
Hits.
The Results List View changes, showing
records 101–105 of 200 hits.
Marking and Unmarking Records
Records retrieved from a search can be marked to
allow viewing later without repeating the search.
To mark a record to view again later:
1. From the Query Input Form, in the Molecule
Name box, type benz.
2. From the Search Type menu, choose
Substructure.
3. Click Search.
The Results List View window appears.
The Sample Application finds 13 records that
match your query.
4. Click Mark Record for records #1 and #3.
The Mark Record button changes to the
Unmark Record button for records #1 and #3
only.
The Show Marked and Clear Marked buttons
appear on the left side of the window.
To see the records marked in a List View:
• From the Results Form View or the Results List
View, click Show Marked.
Records 1–2 of 2 hits appear in the Results List
View window.
The Show Last List button appears on the left
side of the window, below the Clear Marked
button.
To see the most recent Results List View:
• From the Results List View, click Show Last List.
The most recent Results List View appears.
To remove a record from the marked records list:
• From the Results Form View or the Results List
View, click Unmark Record.
The Unmark Record button changes to the
Mark Record button for the records you
unmarked.
To remove all of the marked records from the
marked records list:
• From the Results Form View or the Results List
View, click Clear Records.
The Unmark Record button changes to the
Mark Record button. No records remain
marked.
Manipulating Queries
The Queries menu gives users access to tools,
which allow you to restore, save, and manage
queries which have been performed. This is
especially useful to users interested in using a
particular query more than once without going
through the process of entering the parameters
each time.
Restoring Queries
Restore Query allows the user to restore previously
entered search criteria to an input form.
There are two options when restoring a query:
• Restore the last query entered
• Restore a saved query
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To Restore the Last Query:
The query input form appears:
1. Select Restore > Last from the Queries
Menu.
The query input form appears:
4. Edit your criteria and click Search.
2. Edit your criteria and click Search.
To Restore a Saved Query:
1. Select Restore > Saved from the Queries
Menu.
Saving Queries
Users can save a query to be recalled at a later time.
This is often useful when you expect to run the
same search more than once.
To Save a Query:
1. After performing a search, select Save from
the Queries Menu.
2. Select the appropriate query from the listbox.
3. Click Restore.
2. Enter a name and description for the query.
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3. Select the Make Public checkbox if you would
like other users to be able to access the query.
4. Click OK.
Your query is saved. For information about
retrieving this query, please see “Restoring
Queries” on page 178.
Managing Queries
The Manage Queries dialog box allows users to
restore, edit, and delete queries in the current
history and saved queries. Saved queries are user
specific.
To start managing your queries, select Manage
from the Queries menu.
The Manage Queries dialog appears.
Editing Queries
Edit Query allows the user to enter new identifier
information for the query, such as a new name and
description, or make the query public. Making a
query public makes your query accessible by any
other user of the system.
To edit a query:
1. Select the appropriate query from the listbox.
2. Click Edit.
The edit query window appears:
Restoring Queries
For information about restoring queries, please see
“Restoring Queries” on page 178.
To Restore a Query from the Manage Queries
dialog:
1. Select the appropriate query from the listbox.
2. Click Restore.
The query input form appears.
3. Enter the appropriate information and click
OK.
The query information has been edited and
you are returned to the Manage Query window.
Delete Queries
Only saved queries can be deleted. History queries
remain in the query list until the history is cleared.
To change when the history is cleared, please see
your system administrator.
To delete a query:
1. Select the appropriate saved query from the
listbox.
2. Click Delete.
The query is deleted from the list.
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Manipulating Hit Lists
The Hit Lists menu gives users access to tools,
which allow you to restore, save, and manage hit
lists which have been generated by the current user.
Restoring Hit Lists
Restore Hit List allows the user to restore a hit list
which was previously generated.
There are two options when restoring a hit list:
• Restore the last hit list generated
• Restore one of the saved hit lists
Managing HIt Lists
The Manage Hit Lists dialog box allows users to
restore, edit, and delete hit lists in the current
history and saved hit lists. Saved hit lists are user
specific.
To start managing your hit lists, select Manage
from the Hit Lists Menu.
The Manage Hit Lists dialog appears.
To Restore the Last Hit List generated:
• Select Restore > Last from the Hit Lists
Menu.
The hit list is displayed in list form.
To Restore a Saved Hit List:
3. Select Restore > Saved from the Hit Lists
Menu.
4. Select the appropriate hit list from the listbox.
5. Click Restore.
The hit list is displayed in list form.
Saving Hit Lists
Restoring a Hit List
When restoring a hit list from the Manage Hit Lists
dialog box, saved hit lists can be merged in specified
ways to generate a new hit list. The options when
restoring a hit list are:
Save Hit List allows a user to save a hit list and recall
it at a later time.
To Save a Hit List:
1. After performing a search, select Save from
the Hit Lists Menu.
2. Enter a name and description for the hit list.
3. Click OK.
Your hit list is saved. For information about
retrieving this hit lists, please see “Restoring
Hit Lists” on page 181.
Restore
Option
Replace
Current
List
Intersect
with
Current
List
Result
The saved list is displayed in
list view as it was saved.
A hit list is displayed which
contains only the hits found
in both the saved list and the
current list.
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Restore
Option
Subtract
from
Current
List
Union with
Current
List
Result
To restore a hit list:
A hit list is displayed which
contains all of the hits in the
current list, not including any
hits also found in the saved
list.
A hit list is displayed which
contains all of the hits in the
saved list as well as those in
the current list.
1. Select the appropriate hit list from the listbox.
2. Select the appropriate radio button (to indicate
how you would like the list restored).
3. Click Restore.
The hit list is displayed in list view.
Editing a Hit List
Edit Hit List allows the user to enter new identifier
information for the query, such as a new name and
description, or make the query public. Making a
query public makes your query accessible by any
other user of the system.
The hit list information has been edited.
Delete a Hit List
Only saved hit lists can be deleted. Hit lists in the
history remain in the hit list until the history is
cleared. To change when the history is cleared,
please see your system administrator.
To delete a hit list:
1. Select the appropriate saved hit list from the
listbox.
2. Click Delete.
The hit list is deleted from the list.
Refining Search Results
A query can be changed to narrow search results.
This can be accomplished by either editing the
current query and searching over the records that
have already been retrieved, or by editing the
current query and searching over the whole
database again.
To refine a search over the current records:
1. Create a query.
2. Click Search.
The Results View window appears.
3. Click Refine.
The Refine Query box appears.
To edit a query:
Edit Hit List allows the user to enter new identifier
information for the hit list, such as a new name and
description.
1. To edit a hit list:
2. Select the appropriate hit list from the listbox.
3. Click Edit.
The edit hit list window appears:
4. Enter the appropriate information and click
OK.
4. Click Refine over current records found.
5. Click OK.
The Refine Query Input Form appears.
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6. Change the query.
7. Click Apply.
The Results View window appears.
Refining Over Current Records Found
In a large dataset, you may want to modify your
search criteria to search over the current result set
rather than the entire database.
To export search results:
1. After marking his, from a Results View, click
Export Hits.
The Export Hits dialog box appears.
To refine over the current records:
1. In the Refine Query Input Form, enter your
query.
• For example, if you want to refine the search to
only compounds that have a hydroxyl attached:
a. Draw methanol.
b. From the Search Type list, choose
Substructure.
2. Click Apply.
Results from the example refined search
(above), contain all of the compounds in the
dataset which include the hydroxyl group.
Records in the database which were not hit in
the original search will likewise, not be part of
the refined search.
Undoing a Refined Search
To return to results obtained previous to a refined
search:
• Click Undo Refine.
The results from the previous search appear.
Exporting Search Results
The results of a search can be saved as a .sdf file. A
.sdf file can be exported to ChemFinder and other
ChemOffice applications. Information such as
structure, molecular weight, and formula are
automatically exported in the file. Additional
information can be selected to be included in the
file.
2. Select the information you want to include in
the file.
3. Click OK.
4. Click to Download.
The Save As dialog box appears, containing a
numerical name for the sdf file, based on the
date and time.
5. Select a download location and click Save.
Histories
The application history can be used to retrieve
queries and hit lists which had been executed earlier,
but were not necessarily saved. The history is
cleared periodically, according to how the
application is configured. Please see your system
administrator for more information about when the
history is cleared.
Use the History menu to restore a query or hit list
in your history:
1. Select Queries or Hit Lists from the History
Menu.
2. Select the appropriate query or hit list from the
list box.
3. Click Restore.
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Setting Your Display
and Search
Preferences
Display and search preferences are set in the
ChemOffice WebServer Preferences dialog box.
To set display preferences:
1. From a page in a ChemOffice WebServer
application, click Preferences.
The Preferences dialog box appears.
If you want to
specify the number
of records you see in
List View.
Action
From the Number
Displayed in List
View, type a number
in the Number box.
3. Click Apply.
The new preferences are applied to your next
search.
To set search preferences:
1. Click Preferences.
The Preferences dialog box appears.
2. Take the appropriate action:
If you want your
search to
Then, in the
Search
Preferences
section
match the charges or
radicals to the
heteroatom in your
query structure.
Click Hit any
charge on
heteroatom.
2. Take the appropriate action:
match the reaction
centers in your query
structure.
Click Reaction
query must hit
reaction center.
If you want to
see search results one
record at a time.
Action
From Results
Display, click Form.
match the charges or
radicals to the carbon
in your query
structure.
Click Hit any
charge on carbon.
see search results
several records at a
time.
From Results
Display, click List.
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Setting Your Display and Search Preferences

If you want your
search to
Then, in the
Search
Preferences
section
If you want your
search to
Then, in the
Search
Preferences
section
require that the
reaction centers in
the query overlap the
reaction centers in
the target
specify exact
structure searching
options
Click Reaction
Query Hit
Reaction Center.
Select the
appropriate
checkbox next to
Permit Extraneous
Fragments in Full
Structure or Reaction
searches.
match the tetrahedral
chirality to your
query structure.
match the cis/trans
double bond
geometry to your
query structure.
make thick bonds
represent relative
stereochemistry
Click Match
tetrahedral stereo.
Click Match double
bond stereo.
Click Thick Bonds
Represent Relative
Stereochemistry
match the similarity
of your query
structure by a
specific percentage.
If Permit Extraneous
Fragments (for
structure or reaction
searching) is selected,
the search wil allow
hits to contain
molecular fragments
in addition to that
which was hit by the
query.
From the Similarity
search box, type a
number between 0
and 100.
A lower value
requires the target to
be less similar than
your query structure.
require absolute
relative
stereochemistry
Click Absolute
Relative Chemistry
3. Click Apply.
ChemOffice WebServer applies your
preferences to your next search.
Server Information
You can retrieve information about the server
software currently in use and the database being
searched from the application window.
To get Server information:
• Click the About button in the ChemOffice
WebServer navigation bar.
To return to the previous page:
• Click OK.
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Logging Off
When you first access a ChemOffice web
application, you start a user session with the server.
Although the server times out after a period
specified by your administrator, you can log off
when you are finished with the session.
To log off:
• Click Log Off.
You are logged off and the server resources
that you use are released.
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Logging Off

Chapter 9: CS Oracle Cartridge
Overview
The CambridgeSoft Oracle Cartridge allows the
storage of chemical structures, and performing fast
substructure searches in an Oracle database.
There is minimal overhead for the programmer,
and all relevant pieces of data are stored inside the
database. Therefore, every service, like transaction
processing and backup procedures, apply
transparently to the cartridge with no special action
required from the database administrator.
Installation
Minimum Requirements
• Oracle 8.1.0
• ChemOffice 7.0 or later
or higher.
• Users planning to index their tables with the
cartridge must have the following privileges
granted:
• CREATE TABLE
• CREATE ANY INDEXTYPE
Installation
Please take the following steps to install the Oracle
Cartridge (for the first time):
1. Double-click the SetupCartridge.exe
Windows program. The following dialog
appears:
Supported Platforms
• Windows 2000
• 32 and 64 bit Sun Solaris
• HPUX
• Linux Red Hat
• Red Hat Linux Enterprise
NOTE: See the Oracle Cartridge readme for a complete list
of supported platforms.
Before installation
Before attempting to install the Oracle Cartridge,
please take the following steps:
• The file init.ora must contain the following
line:
COMPATIBLE=8.1.0
2. Fill in the required fields for the required
platform, then hit OK.
The installation program checks if Oracle is
configured correctly to be able to run the
extproc agent. Without the correct
configuration, the cartridge can not be used.
See “What to do if creating an index fails” on
page 198.
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During the installation the installer executes a sql
script, and copies files to the server.
• In Windows installations the installer must run
on the server.
• In Unix installations, the server must run ftp
service. If the server does not run an ftp
service, or using it is not allowed for security
reasons, the Unix system access must be left
empty. In this case the files to be copied to the
${ORACLE_HOME}/lib are copied to the
users temporary directory, usually
Documents and settings\user_name\Local
Settings\Temp
and it is the DBA’s responsibility to copy them to
the target directory. See “Oracle Cartridge
Dependencies by Operating System” on page 263
for more information.
Un-installation
To uninstall the Oracle Cartridge, please do the
following:
1. Remove the following file:
• On Windows: CsCartridge.dll from
${ORACLE_HOME}/bin
• On UNIX: CsCartridge.so from
${ORACLE_HOME}/lib
2. Execute the DROP USER CsCartridge
command while connected to Oracle as a
system administrator.
Re-installation
Re-installing the Oracle Cartridge can be
accomplished by following the same steps as
“Installation” on page 187
It must be noted, that the indexes created with the
optional PARAMETERS clause will be re-created.
That is, as soon as the re-installation is finished,
those indexes are immediately ready for use. The
remaining indexes need to be manually created by
executing DROP INDEX and CREATE
INDEX statements.
Only users with CREATE TABLE and CREATE
ANY INDEXTYPE privileges can index tables
with the cartridge.
Security
The CsCartridge.sql script creates a new user with
the name of CsCartridge and password also set to
CsCartridge. The following system privileges are
granted to CsCartridge:
• GRANT CREATE SESSION TO
CsCartridge
• CREATE TABLE
• CREATE LIBRARY
• CREATE PROCEDURE
• CREATE OPERATOR
• CREATE INDEXTYPE
• CREATE TYPE
• SELECT ANY TABLE
• UNLIMITED TABLESPACE.
The CsCartridge user in turn grants EXECUTE
privileges to PUBLIC on all the function, operators,
and types designed to be accessible from external
accounts. It also grants all privileges on tables it
creates in its schema to the response of a user
request to index a table.
DDL Considerations
DDL (Data Definition Language) statements
include statements used to create and manipulate
data. Examples include (but are not limited to)
CREATE, and DROP.
Chemical structures must be stored in either BLOB
(binary large object) or CLOB (character large
object) data type fields.
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Security

BLOB fields must contain CDX documents. CDX
documents are created by the ChemDraw
application, or by the ChemDraw ActiveX control.
CLOB fields can contain base64CDX or CDXML
encoded CDX documents, to SMILES strings or
MolFiles. A SMILES string is a way to describe a
chemical structure in a line of text. MolFiles are
ASCII files containing atom and bond property
information. When MolFiles are used as input,
carriage return/linefeed characters must be
replaced by a single back-slash (\) character.
NOTE: For more information about CDX and MolFile
formats, please see “Exporting and Importing Using File
Formats” in the ChemDraw User’s Guide. For additional
help in creating SMILES strings, please see “SMILES and
SMIRKS Strings” in the ChemDraw User’s Guide.
The ChemDraw ActiveX control as well as a
number of other applications, can save documents
in any of the above formats.
Fast Substructure Search
To enable the fast substructure search feature of the
cartridge, the field containing structure information
must be indexed as follows:
CREATE INDEX ix ON tab(fld) INDEXTYPE
IS CsCartridge.MoleculeIndexType
[PARAMETERS('CsCartridge')];
where:
ix - is an arbitrary name. This name should be
short, because the cartridge concatenates it
with the user name to create different tables,
and the length of table names is restricted to 20
characters.
tab - is the name of the table containing a field
designated to store chemical structure
information.
fld - is the name of the field designed to store
chemical structure information.
The PARAMETERS clause is optional.
• TABLESPACE=tablespace_name
If present, then the the tables created by the
cartridge will not be created in the default
T_CsCartridge tablespace, but rather in the
tablespace_name tablespace provided by the
user. The creator of the tablespace must have
already allocated a reasonable quota to the
CsCartridge user on that tablespace.
• SKIP_POPULATING=[YES|NO]
If present, the indexes will be created normally,
but data stored in the table will not be used to
populate the tables created by the cartridge.
The user has to do it manually. This option
should be used only for troubleshooting. That
is, use this option only if an earlier attempt to
create an index failed for some reason. The
cartridge tables can then be populated by one
or more UPDATE statements following the
pattern below:
• UPDATE tab SET fld = fld;
• One table can contain any number of fields
designed to store chemical structure
information, and some or all of them can be
indexed by the cartridge. If indexing of the
structure field is not desired, use the
following:
• DROP INDEX ix
• This will disable the cartridge, and remove
all data, created in conjunction with the
working of the cartridge, from the database.
Example
CREATE TABLE moltable(mol CLOB);
CREATE INDEX mx ON moltable(mol)
INDEXTYPE IS
CsCartridge.MoleculeIndexTypeaAM
ETERS(‘tablespace=T_chemdat’)];
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It is important to remember, when creating an
index in a different schema, then the logged-on
user, both the index name and the table name must
be qualified by the schema name. Otherwise, the
cartridge will not connect its tables to the original
table.
For example:
CREATE INDEX mx ON
USER1.moltable(mol)...
is incorrect. The correct format is:
CREATE INDEX USER1.mx ON
USER1.moltable(mol)...
NOTE: Creating an index may be time consuming if the
table already contains lots of records when the index is
created.
DML Considerations
DML (Data Manipulation Language) statements
include statements used to manipulate data.
Examples include (but are not limited to) SELECT,
INSERT, DELETE, and UPDATE.
Data maintenance related to the cartridge is for the
most part automatic, and no extra work is required.
Every time a record is inserted into a table
containing an indexed field, the cartridge is
automatically invoked by the Oracle server. The
cartridge is also invoked if a record is deleted, or if
an indexed field storing a chemical structure is
updated.
Fast Substructure Search
Fast substructure search can be invoked by the
MoleculeContains operator in a SELECT
statement as follows:
SELECT ... FROM tab WHERE
CsCartridge.MoleculeContains(fld
, query4000, query8000,
options)=1
where:
tab - is the name of the table to be retrieved
fld - is the name of the field indexed by the
cartridge
query4000 - is the first 4000 characters of the
query string. The query string can be an
encoded CDX document, a SMILES string, or
a MolFile. For more information about these
formats, please see “DDL Considerations” on
page 188. The Oracle server limits the size of
string literals to 4000 characters.
query8000 - is the second 4000 characters of
the query string. Queries exceeding the 8000
character limits will fail. Since CDX documents
can be voluminous, this limitation may become
important. However even in this case, an 8000
byte limit should not impose too much of a
restriction.
options - is a string containing keyword=value
pairs separated by commas. The interpreted
keywords are:
ABSOLUTEHITSREL=[YES | NO] -
Default is NO
COMPLETE= - to limit the
number of hits tested against atom by atom
matching
DOUBLEBONDSTEREO=[YES|NO] -
double bond stereo matching. Default is
YES.
FRAGMENTSOVERLAP=[YES|NO] -
fragments can overlap. Default is NO.
FULL=[YES|NO] - to specify full
structure search. Default is substructure
search
HITANYCHARGECARBON=[YES|NO] -
hit any charged carbon. Default is YES.
HITANYCHARGEHETERO=[YES|NO] -
hit any charged hetero atom option. Default
is YES.
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IDENTITY=[YES | NO] - Default is
NO
MASSMIN= - to prescribe
minimum molecular mass to matching
records
MASSMAX=- to prescribe
maximum molecular mass to matching
records
PERMITEXTRANEOUSFRAGMENTS=[YES
|NO] - permit extraneous fragments.
Default is NO.
REACTIONCENTER=[YES|NO] - to
specify if reaction search can match only
reaction centers. Default is YES.
RELATIVETETSTEREO=[YES |
NO] - Default is NO
SIMILAR=[YES|NO] - similarity search.
Default is NO.
SIMTHRESHOLD= - to set
the similarity percentage when
SIMILAR=YES is set as well. Otherwise
disregarded. Default value is 90 percent.
TETRAHEDRALSTEREO=[YES|NO] -
tetra hedral stereo matching. Default is YES.
There is no restriction for SELECT statements
when used with the cartridge. Tables can be joined
by other tables, and the WHERE clause can be
formed by using all the options of Oracle.
The COMPLETE option can be used by client
programs, which expect huge databases and
substructure searches resulting in large hit lists. The
cartridge will apply the atom by atom matching only
until the value specified in the COMPLETE option is
satisfied. After this value is satisfied, everything
which passes the screening process will be returned
to the client program as a hit. It is the responsibility
of the client program to call the
CsCartridge.ContainsCDX.MolContains
function to apply atom-by-atom matching test. This
function has the same syntax as the
MoleculeContains operator.
A major advantage of this approach is, the hit list
will be returned at least ten times faster. The
disadvantage is, atom by atom matching must be
invoked for every item in the hit list before the first
number of records indicated by the COMPLETE
option. Therefore, the number of hits will not be
accurate. The use of this option is recommended,
when the result is presented to the user in segments
and the user is not expected to browse through a
huge list.
Simple Example
SELECT mol FROM moltable WHERE
CsCartridge.MoleculeContains(mol
, 'c1ccccc1', '', 'MASSMIN=200,
MASSMAX=500')=1;
selects all records from the table moltable
where the mol field contains benzene as a
substructure (c1ccccc1), and the molecular
mass is between 200 and 500.
Querying large structures
If a query exceeds 8000 bytes, another format of the
MoleculeContains operator can be used to pass
queries up to a length of 4 million bytes. In this
form a maximum of 1000 segments each with a
maximum size of 4000 characters can be passed to
the cartridge in the place of the second parameter.
However, even this form fails when using ADO if
the query structure is passed as a list of literals. This
strategy can be used only if the query is specified as
a list of parameters and the parameters are passed
separately.
The Select statement would look like this:
SELECT ... FROM tab WHERE
CsCartridge.MoleculeContains(fld
, CsCartridge.XArray(:xpar0,
:xpar1, :xpar2,...), options)=1
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where each parameter (xpar) represents a string up
to 4000 characters in size. For more information
about the other variables in the above statement,
please see “Fast Substructure Search” on page 190.
The programming required to pass the parameters
to the Oracle Server depends on the environment
used to develop the client application. For an
example program please see “Navigation in client
programs” on page 203.
Safe querying of large structures
Unfortunately the above approach does not work
on all platforms. According to test results, on some
systems, where the server and client systems'
character set is different, the ORA-01460
unimplemented or unreasonable conversion
requested exception is raised by the server. The root
of this problem is still under investigation. To
bypass the possibility of this problem:
• The client program may pass the text of a
SELECT statement to the MoleculeContains
operator as its second parameter in the first
form of MoleculeContains.
• The third parameter should be left blank.
• The first element of the SELECT statement's
select list must be a CLOB field, and the
execution of the SELECT statement should
result in one output record. This data will be
used by the cartridge as the query structure.
• The application program has to store the query
structure before using the MoleculeContains
operator.
• The CsCartridge user must have access to the
table or tables referenced in its parameter. The
programmer can use the Queries table in the
CsCartridge schema to store query structures.
The Queries table has three fields:
• ID - a numerical identifier
• primary key
• NOTE - text field to add some meaningful
explanation to the query, and the QUERY
field itself.
Also available is the QuerySequence SEQUENCE
to ensure unique identification.
A simple example to illustrate the programming
required for the usage of this feature:
INSERT INTO
CsCartridge.Queries(id, note,
query) VALUES(1234, 'benzene
query', 'c1ccccc1');
SELECT mol FROM moltable WHERE
CsCartridge.MoleculeContains(mol
, 'SELECT query FROM
CsCartridge.Queries WHERE id =
1234', '', '')=1;
Formula query
A subset of a table can be selected by setting
constraints on the formula of a structure by using
the FormulaContains operator. This operator can
be used in a SELECT statement as follows:
SELECT ... FROM tab WHERE
CsCartridge.FormulaContains(fld,
formula, options)=1
where:
tab - is the name of the table to be retrieved
fld - is the name of the field indexed by the
cartridge
formula - is a list of atom symbols followed
by a number or a range of numbers (i.e. 3-6)
options - can be an empty string or the
string 'FULL=YES' or 'FULL=NO'
The FormulaContains operator will select records
from the database, where the counts of the
specified atoms are in the prescribed limits. If the
options field specified full match, then no other
kinds of atoms are allowed in the formula.
For example:
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SELECT mol FROM moltable WHERE
CsCartridge.FormulaContains(mol,
'C6Br2-3N', '')=1;
MolWeight query
The cartridge allows quick search by molecular
weight by the MolWeightContains operator. This
operator can be used in the WHERE clause of a
SELECT statement as follows:
SELECT ... FROM tab WHERE
CsCartridge.MolWeightContains(fld, massMin,
massMax, options)=1
where
tab - is the name of the table to be retrieved
fld - is the name of the field indexed by the
cartridge
massMin - is a numeric value setting the
minimal molecular mass retrieved
massMax - is a numeric value setting the
maximal molecular mass retrieved
options - in this version the options field is
not used
For Example:
SELECT mol FROM moltable WHERE
CsCartridge.MolWeightContains(mo
l, 70.0, 70.1, '')=1;
Migration
Recommendations
An existing table with a field containing chemical
structure information in any form supported by the
cartridge can be indexed for fast substructure
retrieval. If the chemical structure information is
stored in a different format, or the same format but
a different data type, then some programming is
required.
Support functions
The cartridge supports the retrieval of chemical
structure information in different formats beyond
the default CDX format. At the present SMILES,
RXN and Molfile formats are allowed.
Conversion functions are available. They are
grouped together into the ConvertCDX package.
The functions are:
CDXToMolFile(fld, i)
CDXToRxnFile(fld, i)
CDXToSmiles(fld, i)
CDXToMolWeight(fld)
CDXToFormula(fld, option)
CDXToB64(fld, i)
CDXToCDXML(fld, i)
CDXToCanonical(fld)
CDXToName(fld)
CDXToScreen(fld)
where:
fld - is the name of a BLOB or CLOB field
storing chemical structure information in any
form supported by the cartridge, but not
necessarily maintained by the cartridge.
i - is an index beginning with 1 referring 4000
character long chunks of the resulting text.
This is necessary, because ORACLE limits the
size of string results in 4000 characters.
option - is a field that is either empty or:
SORTABLE=YES
to generate formula strings where the elements
are two characters wide, and the numbers are
three characters wide with leading zeros. The
field does not have to be indexed; only the
content must match the supported content
kinds of the cartridge. They can appear in a
SELECT list, but there is no restriction on
their usage.
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Those conversion functions, which take i as the
second parameters must be called with the actual
value increased by one as long as the result is not an
empty string. The index value 1 asks for the first
4000 bytes of the result, the index value 2 points to
the second 4000 bytes of the result, and so on. The
4000 byte chunks of the results must be
concatenated to really get the desired output. This
by no way an effective way of retrieving those
converted formats, that hopefully will be improved
in later versions of the cartridge.
For example:
SELECT
CsCartridge.ConvertCDX.CDXToMolF
ile(mol) from .....
The functional implementations of the
MoleculeContains operator can also be used to
perform atom-by-atom matching on fields. It can
be used if the field is not indexed, and the result set
will be the same, but the execution will be slow. This
is because Oracle will sequentially read in the whole
table, and select those records which pass the atomby-atom
matching. There are two functions:
• MoleculeContainsFunction operates on
CLOB fields
• MoleculeContainsBLOBFunction operates
on BLOB fields.
The remaining three parameters are the same as for
the MoleculeContains operator.
Example:
SELECT mol FROM tab WHERE
CsCartridge.MoleculeContainsFunction(mol,
'c1ccccc1','','')=1;
The cartridge also provides an opportunity to check
data integrity by retrieving an md5 checksum for
any CLOB or BLOB field. That feature can be
invoked in a select statement with the following
format:
SELECT
CsCartridge.CheckSum.Calculate(f
ld) FROM ...
A more advanced way of retrieving the molecular
weight or the formula is using the MolWeight,
Formula and Canonical operators. They can be
used as normal functions, but they are implemented
in a way to take advantage of the data calculated by
the cartridge when records are stored. If the field
name parameter passed to these operators refers to
a field indexed by the cartridge, instead of
processing the input data, the operators use data
stored by the cartridge, thus improving the
processing speed. However, these operators can not
be used for search effectively, because they never
trigger index scan.
Usage example:
SELECT
CsCartridge.MolWeight(mol),
CsCartridge.Formula(mol, ''),
CsCartridge.Canonical(mol) FROM
moltable;
Using data
maintained by the
cartridge
Instead of using the support functions it is also
possible to use the tables maintained by the
cartridge to retrieve calculated data. Using these
tables are much more effective, than using the
support functions because no calculation has to be
performed, but calculated and indexed data can be
used. The disadvantage of using these tables is that,
using them is not transparent, the names of the
tables and fields can be changed in later versions, so
client programs may become incompatible with
different cartridge versions. To provide full
compatibility with cartridge versions client
programs have to check the cartridge version, and
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act accordingly. A full list of the tables and fields
maintained by the cartridge can be found in the
heading Data Structures.
The AUX package of the cartridge can be used to
avoid compatibility problems with later versions.
The AUX package contains trivial functions, which
return the names of the tables and fields to be used
to access the tables in the cartridge schema. With
this extra care, future incompatibility can be
avoided. The functions in that package will be
explained later in the chapter. Generally, using these
functions is more complicated than using operators
returning the same value.
The best way to use data stored by the cartridge is
to create synonyms for the tables stored in the
CsCartridge schema.
CREATE SYNONYM MyWeight FOR
CsCartridge.sch_ix_W; for accessing
molecular weight
CREATE SYNONYM MyCode FOR
CsCartridge.sch_ix_A; for accessing
formula and canonical code
This way, the fields of MyMol and MyCode tables
can be used simply as if they were defined in the
user's schema. Both of these tables have a field
called RID. It contains the ROWID of the original
table. The original table and the table maintained by
the cartridge can be joined by an inner join by an
original_table.ROWID = MyCode.rid condition in
the WHERE clause. When the tables are joined, the
data fields maintained can be used. Among them
are:
• MyMol.MolWeight which stores the molecular
weight of the structure.
• MyCode.Formula contains the formula of the
structure
• MyCode.CText contains the canonical code of
the structure
These fields are indexed, so using them in the
WHERE clause of a SELECT statement may yield
enormous speed improvement compared to nonindexed
fields.
Example:
CREATE TABLE mx(id, NUMBER, m CLOB);
CREATE INDEX mxix ON mx(m) INDEXTYPE IS
CsCartridge.MoleculeIndexType;
CREATE SYNONYM MxWeight FOR
CsCartridge.schemaname_mxix_W; -
- replace schemaname with the name of your
schema
CREATE SYNONYM MxCode FOR
CsCartridge.schemaname_mxix_A; --
replace schemaname with the name of your
schema
SELECT mx.id, MxWeight.MolWeight FROM
mx, MxWeight WHERE mx.rowid =
MxWeight.rid; -- to list the identifiers and
molweights for the table
SELECT mx.id, MxCode.CText FROM mx,
MxCode WHERE mx.rowid = MxCode.rid; -
- to list the identifiers and canonical codes for the
table
SELECT mx.id, MxCode.Formula FROM mx,
MxCode WHERE mx.rowid = MxCode.rod; --
to list the identifiers and formula for the table
If two tables are to be joined by chemical identity,
then there is no better way to join them than the
CText field maintained by the cartridge. The CText
field is an index field, join by that this field saves one
table scan.
The functions of the AUX package:
• MWTabName(SchemaName VARCHAR2,
IndexName VARCHAR2)
• MWRidNameMWFldName
• FMTabName(SchemaName VARCHAR2,
IndexName VARCHAR2)
• FMRidName
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• FMFldName
• CNTabName(SchemaName VARCHAR2,
IndexName VARCHAR2)
• CNRidName
• CNFldName
• XXTabName(SchemaName VARCHAR2,
IndexName VARCHAR2) returns the name of
the table the data is stored in
• XXRidName returns the name of the field
which stores the rowid of the original record
• XXFldName returns the name of the field
which stores the data desired
The MW functions must be used for MolWeight,
the FM functions for formula, and the CN
functions for canonical code.
The following VB example code follows to
illustrate how to retrieve the rowids of two different
tables joined by their canonical codes. This
SELECT statement will retrieve only those records
that are chemically identical in both tables. Here the
table names do not appear, the index names are
used instead, to specify the tables.
Dim CNTab1, CNTab2, CNRidName,
CNFldName As String
Set c = New ADODB.Connection
Dim r As ADODB.Recordset
c.Open
ConnectionString:="Provider=OraOLEDB.O
racle.1;Persist Security
Info=False;Data Source=" + "myserver",
UserId:="myschema",
Password:="mypassword"
sql = "SELECT
CsCartridge.Aux.CNTabName('myschema',
'my1index') FROM DUAL"
Set r = c.Execute(sql)
If Not r.EOF Then CNTab1 = r.Fields(0)
sql = "SELECT
CsCartridge.Aux.CNTabName('myschema',
'my2index') FROM DUAL"
Set r = c.Execute(sql)
If Not r.EOF Then CNTab2 = r.Fields(0)
sql = "SELECT CsCartridge.Aux.CNRidName
FROM DUAL"
Set r = c.Execute(sql)
If Not r.EOF Then CNRidName =
r.Fields(0)
sql = "SELECT CsCartridge.Aux.CNFldName
FROM DUAL"
Set r = c.Execute(sql)
If Not r.EOF Then CNFldName =
r.Fields(0)
sql = "SELECT " + CNTab1 + "." +
CNRidName + ", " + CNTab2 + "." +
CNRidName + " FROM " + _
CNTab1 + ", " + CNTab2 + " WHERE " +
CNTab1 + "." + CNFldName + " = " +
CNTab2 + "." + CNFldName
Set r = c.Execute(sql)
Error Handling
The cartridge can not communicate with the user.
It can communicate erroneous situations only
through either raising an exception or storing
information related to the erroneous situation into
a table.
If the cartridge raises and exception, then the client
program is terminated. The default action of the
cartridge is to continue the program and store
information about the failed chemical data into the
database.
This behavior can be changed by executing the
following SQL statement:
UPDATE CsCartridge.__O
SET
Raise_on_error = 'YES'
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If the Cartridge does not raise an exception, then
the CsCartridge.__E
table will
contain the rowid-s of those records containing
invalid chemical data in their indexed fields.
The rid field of this table contains the rowid of the
indexed record, and the text field may contain
additional information. A SQL statement, which
joins this table with the indexed table lists the
erroneous records.
For example, if the following is true:
• the user's schema is ‘cs_notebook’
• the indexed table name is ‘eln_structures’
• the name of the index used by the cartridge is
'sx'
• the 'key' field is a good way of identify a record,
then:
SELECT eln_structures.key from
eln_structures,
CsCartridge.CS_NOTEBOOK_SX_E
where eln_structures.rowid =
CsCartridge.CS_NOTEBOOK_SX_E .rid
will retrieve the identifying fields of those records,
which are not indexed because of an error.
Performance
The MoleculeContains operator is implemented
both as an index scan, and as a function. The query
optimizer decides which implementation to use.
If the WHERE condition contains more selective
elements then the MoleculeContains operator,
like a reference to a unique key, then Oracle will
retrieve the only matching record, and then apply
the function implementation, which will perform
an atom-by-atom matching. When the index scan is
executed, the cartridge creates a complicated query
accessing different tables. The performance of that
query can be dramatically improved by occasionally
executing an ANALYZE INDEX statement on the
INDEX created by the cartridge:
ANALYZE INDEX mx;
Executing this statement will calculate statistics on
the tables created and maintained by the cartridge,
and these statistics are used by the Oracle query
optimizer. This command should be executed
periodically depending on the frequency of the
update of the table.
Troubleshooting
If there is a serious problem with the cartridge, it is
sometimes appropriate to rerun the
CsCartridge.sql script, which will re-install the
cartridge software. After running the script every
indexed table the cartridge index should be
dropped, and re-created again. In addition, update
every record in the table by executing the following
SQL statement:
UPDATE tab SET fld=fld;
COMMIT;
This is necessary for only those tables where the
index was created without the
PARAMETERS('CsCartridge') clause.
If the problem persists, then the problem should be
reported to CambridgeSoft.
Checking the presence of the
cartridge
If the following query returns no result, then the
cartridge is not present in the Oracle database.
SELECT username from all_users
where username = 'CSCARTRIDGE'
Checking the version of the
cartridge
This following statement yields a string containing
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the actual version of the CambridgeSoft Oracle Cartridge
software.
• select * from
cscartridge.globals;
returns the whole table of cartridge
infromation
• select value from
cscartridge.globals where id =
'VERSION'
reyurns only the version of the cartridge
Checking for fields indexed
by the cartridge
The cartridge maintains the all_csc_indexes table in
its own schema or in the tablespacedesignated in
PARAMETERS when creating the index. The
columns of this table are:
• OWNER
• INDEX_NAME
• TABLE_NAME
• COLUMN_NAME
• COLUMN_TYPE
All of the fields are defined as VARCHAR2(30)
columns. Every index created by the cartridge has
an entry in this table. The content of this table can
be retrieved by the public. By retrieving the content
the client program can know if a column is
supposed to contain chemical structures.
For Example:
select * from
cscartridge.all_csc_indexes where
owner = 'me' and
table_name = 'my_table' and
column_name = 'my_column'
What to do if creating
an index fails
When the user executes a CREATE INDEX
command, the cartridge reads all the rows from the
table, and creates its own tables for fast
substructure search.
There are three different outcomes of the execution
of the CREATE INDEX command
1. Success indicated by an "index created"
message usually displayed by the client
program
2. Invalid data in one or more records indicated
by an "ORA-29863: warning in the execution
of ODCIINDEXCREATE routine" message.
In this case the user should check the content
of the CsCartridge.Index_name_E table for
the unhandled records, which are logged by the
cartridge. The index is usable as it is, the noninterpreted
records should be manually
reviewed and corrected. The
CsCartridge.Index_name_E table contains the
rowid-s of the failed rows, and an error
message, The user has to locate the failed rows
by the rowid, and correct the errors.
3. If an exception is thrown by ORACLE, which
is not handled by the cartridge, then the index
creation results in an ORA-xxxxx message, and
a call stack. If this happens, then the index is
marked by Oracle as
LOADING/FAILED/UNUSABLE, and the
only command a user can execute regarding the
index is the ALTER INDEX REBUILD
command. The following:
ALTER INDEX ixname REBUILD
PARAMETERS('CONTINUE_POPULATIN
G');
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will attempt to continue processing the input
data. If this process fails repeatedly, it is
recommended to call support at
CambridgeSoft.
It may also be worth trying the following
alternative:
NOTE: The following must be accomplished for
Oracle versions 9.2.0.2, 9.2.0.3, or 9.2.0.4 due to an
Oracle bug. See the Oracle Cartridge readme for
another known issues.
DROP INDEX ixname FORCE; -- to
remove the index even if it is in
LOADING/FAILED/UNUSABLE state
CREATE INDEX ixname ON tab(fld)
INDEXTYPE IS
CsCartridge.MoleculeIndexType
PARAMETERS('SKIP_POPULATING');
UPDATE tab SET fld=fld;
COMMIT;
If the UPDATE fails, then the
CsCartridge.schema_name_ixname_O.current_ro
wid points to the record which failed. The failed
record should be deleted or corrected. After
accomplishing this, the UPDATE and COMMIT
commands must be executed again.
Setup problems
ORA-28575 unable to open
RPC connection to external
procedure agent
When using the cartridge for the first time some
users may experience the above error message.
This message is the consequence of some mistake
in the ORACLE server's setup. It is issued by the
Oracle server, when it tries to load the extproc
program, an agent which in turn loads the
CsCartridge.dll (Windows) or the CsCartridge.so
(Unix) program into memory.
Oracle uses the extproc program (called external
procedure agent) to load external binaries into
memory because, the binary executables written by
independent developers are not trustworthy
enough to be loaded into Oracle's main address
space. The executables can crash, thus shutting
down the whole service. Loading into the address
space of the extproc agent, is optimal because even
if it crashes, it just crashes the client program which
triggered its use, leaving the server intact. To find
the extproc program in the Oracle installation,
Oracle uses two configuration files:
• listener.ora
• tnsnames.ora
If those files are missing, or are not set up correctly,
or if the extproc program is missing, then Oracle
can not load the extproc program, and issues the
ORA-28575 error message.
The listener.ora and the tnsnames.ora files are
located in the
$ORACLE_HOME/network/admin directory.
The listener.ora file is used, whenever the listener
service is restarted. On Windows computers it is
started usually when the computer starts up, and
can be stopped/started using the "services" list
from the Control Panel. On Unix computers they
are controlled by the
$ORACLE_HOME/bin/lsnrctl command.
listener.ora
The listener.ora file must have the following lines
LISTENER =
(DESCRIPTION_LIST =
(DESCRIPTION =
(ADDRESS_LIST =
(ADDRESS = (PROTOCOL = IPC)(KEY =
EXTPROC))
)
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)
)
SID_LIST_LISTENER =
(SID_LIST =
(SID_DESC =
(SID_NAME = PLSExtProc)
(ORACLE_HOME = C:\oracle\ora81)
(PROGRAM = extproc)
)
)
where the value of the KEY symbol may be
different than EXTPROC, but must be the same as
the value of the KEY symbol in the tnsnames.ora
file. The same is true for the value of the
SID_NAME symbol, but that it is always
PLSExtProc.
If this text file is changed, then the listener service
must be restarted. Oracle 8 and 9 do not seem to
use the ORACLE_HOME entry. Instead, Oracle
uses the ORACLE_HOME entry in the Windows
registry, and the ORACLE_HOME environment
variable on UNIX systems. So, when the listener is
started, then the ORACLE_HOME must point to
the directory, where the Oracle server is installed.
That usually reads, like
/mount-directory/app/oracle/product/version
If in doubt:
1. Execute the statements in the same
environment, where the listener is started:
ORACLE_HOME = /mountdirectory/app/oracle/product/ver
sion
export ORACLE_HOME
2. Start the listener with the command
$ORACLE_HOME/bin/lsnrctl
3. Check status, and stop/start it according to its
status.
tsnames.ora
The tnsnames.ora file must have lines as follows:
EXTPROC_CONNECTION_DATA.CAMSOFT.
COM =
(DESCRIPTION =
(ADDRESS_LIST =
(ADDRESS = (PROTOCOL = IPC)(KEY =
EXTPROC))
)
(CONNECT_DATA =
(SID = PLSExtProc)
(PRESENTATION = RO)
)
)
The value of KEY must be the same as the value of
KEY in the listener.ora file, and the value of SID
must be the same as the value of SID_NAME in the
listener.ora file.
ORA-06520 PL/SQL: Error
loading external library
If the communication with the extproc agent is
operable the user still can be faced with the above
error message.
This happens if the extproc agent can not load the
CsCartridge.dll or the CsCartridge.so into memory.
The reason is either:
• the CsCartridge library does not exist OR
• some libraries it depends on do not exist.
Dependencies
The CsCartridge library depends on every platform
on the existence of
• OCI library. (extension may be .dll, .so, .sl)
For a list of additional dependencies for specific
operating systems, please see “” on page 263.
200•CS Oracle Cartridge
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Setup problems

In addition to the file requirements, the
environment must be set up so that the system can
find them. These issues are explained in detail in the
system manuals of the actual platform.
Using ADO
Microsoft's ADO is a convenient way to write client
programs utilizing the cartridge.
To create an Oracle service on any client computer,
the Oracle client tools must be installed, and the
Net8 assistant program must be used to create a
service by entering the following information:
Net Service Name: any valid string would do
(this string must be used in ADO)
Protocol: TCP/IP
Host Name: a computer running the Oracle
server
Port Number: 1521
(Oracle 8i) Service Name: the service name
on the server.
DIM c as ADODB.Connection
set c = new ADODB.Connection
ServiceName = "" Rem the name of Oracle
service
UserName = "" Rem user name
Password = "" Rem password
s =
"Provider=OraOLEDB.Oracle.1;Persist
Security_ Info=False;Data Source=" +
ServiceName + ";"
s = s + "User ID=" + UserName + ";"
s = s + "Password=" + Password
c.Open s
Dim r as ADODB.Recordset
Set r = c.Execute("SELECT * FROM
moltable WHERE_
CsCartridge.MoleculeContains(mol,
'c1ccccc1','', '')=1");
Rem process the recordset
c.Close
NOTE: When using Microsoft ADO data controls to
access the cartridge, the CursorLocation property must be set
to adUseServer. Otherwise data updates will fail, if the
structure field is larger, then 4000 bytes.
Example of passing large
queries
NOTE: Comments are in bold.
Dim r As ADODB.Recordset
ChemDrawCtl1.DataEncoded = True '
b64 encoded cdx is required
Dim s As String
s = ChemDrawCtl1.Data("cdx") '
get the cdx document from the ChemDraw
ActiveX control
Dim com As ADODB.Command '
create a new ADODB.command
Set com = New ADODB.Command
Rem now build the sql string step by
step, and create the corresponding
parameters as well
Rem the query data will be passed as an
array defined in CsCartridge
Rem
sql = "Select " + idSelect '
idSelect contains the column name to be
selected
sql = sql + " from " + TableName ' from
table
sql = sql + " where
CsCartridge.MoleculeContains(" +
StructName '
first param is column name of the
chemical structure
sql = sql + ", CsCartridge.Xarray(" '
second param is an array of string
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literals
n = Len(s) ' number of characters in the
query structure
pos = 1 ' starting position
i = 0 ' starting index
segmentLength = 4000 ' the length of a
segment of the query string
While pos < n ' there is remaining part
of a query string to be passed
si = Mid(s, pos, segmentLength) '
get one 4000 character chunk of the
query
Dim v As Variant
v = si '
create parameter expects the value as
variant
parname = ":xpar" + CStr(i) '
parameter name as a stem and running
index
Dim par As ADODB.Parameter '
create the parameter
Set par = com.CreateParameter(parname,
adLongVarChar, adParamInput, Len(si),
v)
com.Parameters.Append par '
append it to the parameters
accompanying the command
sql = sql + parname '
the sql command will have a new
parameter
pos = pos + segmentLength ' move the
position
If pos < n Then '
if there is data still to be processed
sql = sql + "," '
add a comma to separate the parameters
End If
i = i + 1
Wend
sql = sql + "),'FULL=NO')=1" ' finish
up the sql text
com.CommandType = adCmdText
com.ActiveConnection = c
com.CommandText = sql '
set the CommandText field of the
command object
Set r = com.Execute '
and now the command is ready to be
executed
Custom Screening
Custom screening is a tool for a database
administrator to affect the processing of a SELECT
statement. The database administrator can define
any structure to screen the database when
processing a substructure search. If a screen
structure is a substructure of a query structure, then
the processing of that particular query will be faster.
There is no recommendation on how to choose
custom screens. Choosing them should be based on
the particulars of the database and expected interest
of the users.
Custom screen can be defined by calling the
MolScreen procedure.
CALL
CsCartridge.MolScreen('schema_na
me', 'table_name', 'field_name',
'index_name',
'smiles_or_encoded_cdx',
'second_part');
where
• schema_name - is the schema the table is
owned by
• table_name - is the name of the table to be
custom indexed
• field_name - is the name of the field
containing chemical information
202•CS Oracle Cartridge
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Custom Screening

• field_name - is the name of the index used
to index the chemical information
• smiles_or_encoded_cdx - is the
substructure depicted by a smiles string or an
encoded CDX document.
• second_part - is the second 4000 bytes of
an encoded CDX document.
All of the names must be enclosed by single quotes.
The strings are not processed by Oracle, but rather
the MolScreen procedure.
For example:
CALL
CsCartridge.MolScreen('MySchema'
, 'molecule', 'mol', 'mx',
'Oc1ccccc1', '');
This will improve the speed of the substructuresearch
of phenol derivatives.
Navigation in client
programs
The client program usually provides navigation
buttons or commands to browse through the
recordset, when the result of a query is displayed, or
when a full table is presented to the user.
Commands usually allow moving to the next or
previous, first or last record, and some kind of
direct positioning is provided as well.
When the result of a query is presented, the client
program usually maintains a hit list, and allows
navigation by this list in any direction.
After executing a DML statement it is not
immediately clear if a next or previous record exists,
and if those commands or buttons should be
enabled. The cartridge maintains information to
help the client program in solving this problem.
The client program has to retrieve this information
as it is demonstrated with the following BASIC
program.
Dim c as ADODB.Connection 'must be
an open connection
Dim userName as String 'must
contain the connected user's name
Dim tableName as String 'must
contain the table name processed
Private Function GetIndexName()
As String
Dim s As String
Dim r As ADODB.Recordset
s = "SELECT INDEX_NAME FROM
ALL_INDEXES WHERE TABLE_OWNER =
'" + UCase(UserName) + "' AND
TABLE_NAME = '" +
UCase(tablename) + "' AND
ITYP_OWNER = 'CSCARTRIDGE' AND
ITYP_NAME = 'MOLECULEINDEXTYPE'"
Set r = c.Execute(s)
GetIndexName =
r.Fields("INDEX_NAME").Value
End Function
Private Sub CheckEOFBOF()
Dim s As String
Dim indexName As String
indexName = GetIndexName
s = "CALL
CsCartridge.UpdateEOFBOF('" +
UserName + "', '" + tablename +
"', '" + indexName + "')"
c.Execute (s)
Dim r As ADODB.Recordset
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Set r = c.Execute("SELECT * FROM
CsCartridge." + UserName + "_" +
indexName + "_O")
Dim isEOF, isBOF As Boolean
Dim rowid As String
isEOF = r.Fields("EOF").Value =
"YES"
isBOF = r.Fields("BOF").Value =
"YES"
rowid =
r.Fields("CURRENT_ROWID").Value
End Sub
Explanation
The client program has an active connection, which
requires the knowledge of the user's name. It also
decides what table to present. The cartridge needs
the index-name associated with the table. The
GetIndexName function returns the index_name
created by the cartridge.
Next, the client program must make a call to the
CsCartridge.UpdateEOFBOF stored
procedure and has to pass the username and the
index_name in the call. This procedure can be
called at any time, but it should be called after a
DML is executed. After that, the client program has
to query the table, where the results of the
UpdateEOFBOF procedure are stored. The table
has one record and includes fields storing the rowid
of the recommended rowid if it exists, and flags
showing whether end-of-file and/or beginning-offile
conditions are set.
Bulk loading
The speed of importing large amounts of data into
the cartridge can be improved by temporarily
suspending the maintenance of the tables the
cartridge uses to achieve high speed substructure
searching.
The
ALTER INDEX index_name
PARAMETERS('SUSPEND')
and the
ALTER INDEX index_name
PARAMETERS('RESUME')
statements suspend and resume the maintenance of
the tables used by the cartridge, respectively. When
the maintenance is suspended, then the cartridge
bypasses the most time consuming tasks, and
remarks that jobs will be due when the maintenance
is resumed. When the maintenance is resumed, all
deferred jobs are executed at once. The advantage
of this approach is an increase in the speed of
loading by a factor of 2.
This approach can also be used to speed up
maintenance with some consideration. If the index
is in suspended mode (i.e. the user executed an
ALTER INDEX command), then updates of the
table will be faster, however data entered after
indexing was suspended, will not appear as a result
in substructure search. The cartridge only notes
that the indexing has to be done later, and finishes
processing. When the indexing is resumed, all of
this saved data is processed at one step (much faster
when processed individually), and the index
becomes fully usable again.
Also related to bulk loading, the client program can
change the way the cartridge handles exceptions.
Normally the cartridge raises an oracle exception if
a procedure can not be executed because of a data
error, or any other kinds of errors. This can be
suppressed by the
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Bulk loading

ALTER INDEX index_name
PARAMETERS('RAISE_ERROR=NO')
statement, and the default behavior can be restored
by the
ALTER INDEX index_name
PARAMETERS('RAISE_ERROR=YES')
statement. If the alter index statement was called
with 'RAISE_ERROR=YES' parameter, then any
erroneous input data will be rejected, and an
exception will be thrown. Otherwise, the data will
be stored, no error message will be generated, but
an entry will be added to the
schema_name.index_name_E table.
The following sql script illustrates this process:
truncate table mx;
alter index mxix
parameters('RAISE_ERROR=YES');
insert into mx values(1, 'CCj');
select * from mx;
alter index mxix
parameters('RAISE_ERROR=NO');
insert into mx values(1, 'CCj');
select * from mx;
and the result:
Table truncated.
Index altered.
insert into mx values(1, 'CCj')
*
ERROR at line 1:
ORA-29875: failed in the
execution of the ODCIINDEXINSERT
routine
ORA-29400: data cartridge error
ORA-29400: no chemical data in the
document, can not be indexed
ORA-06512: at
"CSCARTRIDGE.MOLECULEINDEXMETHOD
S", line 28
ORA-06512: at line 1
no rows selected
Index altered.
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1 row created.
ID
M
--------------------------------
------------------------------
1 CCj
206•CS Oracle Cartridge
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Bulk loading

Section V: Scientific Databases
CambridgeSoft offers a library of chemical
information databases, containing compounds and
chemical reactions. Users may search over the
databases with tools provided in the ChemOffice
software suite.
The Scientific Databases bring a wealth of chemical
information to your desktop. Searching through
these databases by chemical names, structures,
physical data, suppliers, safety data, and literature
references becomes as easy as clicking a mouse.
All of the databases are available to the user on CD,
for individual use.
Subscriptions and
ChemOffice Webserver
Based Databases
The following databases are available as a
ChemOffice WebServer application and/or webbased
subscription as well as on CD:
• The Merck Index
• Ashgate Drugs
• ChemACX
• ChemINDEX
• NCI
• AIDS
The databases available through a subscription or
the ChemOffice WebServer applications use the
same conventions as other WebServer applications.
For more information about general ChemOffice
Webserver application concepts, please see
“ChemOffice WebServer” on page 3.
CD Based Databases
The following chemical databases, available on CD,
are described in this section:
• The Merck Index
• Ashgate Drugs
• ChemACX
• ChemSCX
• ChemMSDX
• ChemINDEX
• ChemRXN
• NCI
• AIDS
The chemical Databases work with ChemOffice, an
integrated suite of software tools for chemists with
personal computers. The ChemOffice applications,
ChemFinder, ChemDraw, and Chem3D, help
ChemInfo deliver information.
ChemOffice includes the following:
ChemFinder—The primary application used by
ChemInfo. It provides the engine for searching the
data the forms and tables for viewing it. Relational
databases are supported by ChemFinder.
ChemDraw—The chemical drawing standard
allows structures to be drawn and edited in
ChemFinder. It can represent individual structures
or chemical reactions, complete with atom-to-atom
mapping and absolute or relative stereochemistry,
for detailed structure-based queries.
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Administrator
Chem3D—A molecular modeling and
computations application offers molecular
mechanical and quantum mechanical computational
capability. Featuring an intuitive graphical user
interface, it displays molecules as three-dimensional
models that you can rotate and translate to reveal
details of a structure not evident in two dimensions.
Installation
The databases do not have to be installed; they can
be accessed directly from the CDs. If the databases
are accessed from a CD, they are Read-only. If you
have sufficient hard disk space, you can copy the
databases from the CDs. This not only makes
searching faster but allows you to edit the databases,
except ChemACX, ChemSCX, The Merck Index,
and Ashgate Drugs..
Using Scientific Databases
The CD based databases use ChemFinder to deliver
data to the user. “ChemOffice WebServer” on page
3 contains a tutorial that gives an overview of using
ChemFinder with CambridgeSoft’s Scientific
Databases.
ChemFinder Tips
Some databases are provided with customized
applications. If the database you are using does not
include such an application:
the Windows Explorer and open ChemFinder by
double-clicking one of the ChemFinder form icons.
Help
Additional sources of help for using ChemInfo
include the following:
• Quick Reference Card
• ChemFinder and ChemDraw online help
• ToolTips
• Status Bar
• CambridgeSoft Technical Support
Online Help
Access to online help is provided from the
ChemFinder and ChemDraw help menus.
To learn about using the online Help:
• From the Help menu, choose How to Use Help.
To access online Help:
• From the Help menu, choose Contents.
ToolTips
ChemFinder and ChemDraw provide ToolTips as an
additional form of online Help. Rest your pointer on
a tool to display a message box with a brief
description of the tool.
1. Insert one of the ChemInfo CD-ROMs into
your CD drive.
2. Start ChemFinder.
3. From the File menu, select Open and select a
form for one of the databases.
Alternatively, you can explore the CD-ROM with
Status Bar
The bottom left corner of the ChemFinder and
ChemDraw Status Bars display a slightly more
detailed description of the tool icons.
208• CambridgeSoft
CD Based Databases

Chapter 10: The Merck Index
What Is It
The Merck Index is a one-volume encyclopedia of
chemicals, drugs and biologicals that contains more
than 10,000 monographs. The entries are not a
listing of Merck & Co., Inc. products, but rather
cover a wide range of compounds that have been
selected by the editors on the basis of present or
historic importance and interest. Since the
publication of its Twelfth Edition in 1996, over
5,000 monographs have been significantly revised
and updated. Each monograph is a concise
description of a single substance or a small group of
closely related compounds. The information
provided includes chemical, common and generic
names, trademarks and their associated companies,
Chemical Abstracts Service (CAS) Registry
Numbers, molecular formulas and weights, physical
and toxicity data, therapeutic and commercial uses,
citations to the chemical, biomedical and patent
literature, and chemical structures.
How Is It Useful
For more than 100 years, the printed edition of The
Merck Index has been the premier reference for
validated data about many compounds of general
interest. The subjects covered include human and
veterinary drugs, biologicals and natural products,
agricultural chemicals, industrial and laboratory
chemicals, and environmentally significant
compounds. The electronic version includes all of
the information in the printed edition, and
enhances it by allowing direct and rapid searching
over all data fields. Where the printed edition offers
indexes of names and CAS Registry Numbers, the
electronic version allows the user to enter them as
search terms, and takes you directly to the relevant
monographs without having to flip through a bulky
printed volume. Physical properties as well as many
other attributes can also be used in the search. As
with the other ChemInfo databases, The Merck
Index also allows searching by structure,
substructure, and similarity, all of which are virtually
impossible when using the printed edition alone.
Organic Name Reactions, and Additional Tables
are also available to search through.
Using the Merck Index
CD
Directory: The Merck Index CD-ROM
Filenames: The Merck Index.cfw
Number of Compounds: 10,890
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Administrator
Using The Merck Index
Online
The Merck Index is split into 5 tabs:
• Introduction
• Compound Searching
• Organic Name Reactions
• Additional Tables
• System Requirements
.
applications. For more information about
searching, please see “ChemOffice WebServer” on
page 167.
To access the Compound Searching section:
Click on the Compound Search Tab found at
the top of the page.
The Compound Search Form appears
The Introduction and System Requirements tabs
deliver important information about The Merck
Index, compatibilities, and how to navigate the site.
Each of the other tabs allow the user to access three
major sections of The Merck Index: Compounds,
Organic Name Reactions, and Additional Tables.
Compound Searching
The Compound Searching section allows searching
for compounds by physical properties, compound
attributes, and structure. The Merck Index’s
compound searching form acts much like the other
search forms found in ChemOffice WebServer
To search for compounds:
1. Enter the desired information into the fields
provided in the Compound Searching Form.
To search without using the structure search,
click on the Click Here for Non-Plugin
Searching link.
2. Click Search.
A list of search results appears
210•The Merck Index
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Using The Merck Index Online

To view the contents of a particular record in the
list, click
Show Details.
The complete contents of the chosen record is
displayed.
• cross references to other ONR based on
commonalities.
Useful abbreviations can be found on the mainpage
of this section. To access the Organic Name
Reactions section:
Click on the Organic Name Reactions Tab
found at the top of the page.
The Organic Name Reactions homepage
appears.
Organic Name Reactions
The Organic Name Reactions (ONR) section
contains a list of reactions which have come to be
recognized and referred to by name within the
chemistry community. The reaction descriptions
are meant to be informative, but not
comprehensive. The descriptions are composed of
the following:
• name(s) associated with the reaction
• the original and/or primary contributor(s)
connected with the discovery and/or
development of the reaction
• a concise description of the transformation
• a reaction scheme
• key references
The left frame of the homepage contains 2 tabs:
Browse and Search.
The Browse Tab lists all reaction names included in
the Merck Index. To view the contents of a record,
scroll to the appropriate reaction and click on the
link.
The Reaction details appear in the right frame
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Administrator
The Search Tab allows the user to enter a free text
search for the appropriate reaction. To search for a
reaction:
3. Enter keywords into the text box available.
4. Click Search.
A list of matches is returned.
5. Click on the link for the appropriate reaction.
The Reaction details appear in the right frame.
For tips about entering a free text search, click on
the Tips for Searching link found below the free
text search textbox under the Search Tab.
Additional Tables
The Additional Tables section lists multiple tables
available to view by the user in PDF format.
To access the Additional Tables section:
Click on the Additional Tables Tab found at
the top of the page.
The Additional Tables homepage appears.
To view a particular table, click on the link
provided. All tables are available in PDF format and
therefore require the Adobe Acrobat Reader to
view. If you do not have the Adobe Acrobat Reader
installed, click on the link provided to obtain a free
copy.
Logging Off
You can end your session with The Merck Index at
anytime by logging off.
To log off:
• Click Log Off.
212•The Merck Index
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Using The Merck Index Online

Chapter 11: Ashgate Drugs
What Is It
Ashgate Drugs is fully searchable database created
from the popular book, Drugs: Synonyms and
Properties, published by Ashgate
The online database has 7,922 drugs which are
currently in common use worldwide. It includes all
drugs approved by FDA prior to 2004. These drugs
all have recognized applications, and are classified
into one or more of 201 therapeutic categories.
Each entry is accompanied by:
• The CAS Registry Number and, as available,
• The Merck Index (13th Edition) monograph
number
• The European Inventory of Existing
commercial Chemical Substances (EINECS)
number
Each field is fully searchable. Thus an entry may be
located on the basis of structure or substructure,
synonyms, biological activity, physical properties or
manufacturer.
This reference will be invaluable to research
chemists, biologists, and physicians and to anyone
interested in drugs who, starting with a single
synonym for a drug, will be able to quickly find a
thumbnail sketch of the essential information
concerning that agent.
Ashgate Databases
• CAS Number
• The Merck Index (13th edition) Monograph
Number
• EINECS Number
• Chemical name
• Molecular formula
• Synonyms, including tradenames
• Medical application
• Manufacturer
• Physical Properties
Using Ashgate Drugs
on CD
Directory: Ashgate Drugs
Filenames: Ashgate Drugs.cfw
Number of Compounds: 7,922
Number of Record: 7,922
Key Fields:
• Chemical Structure
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What Is It

Using Ashgate Drugs
Online
Click on the Compound Search Tab found at
the top of the page.
The Compound Search Form appears
Administrator
Ashgate Drugs is split into 4 tabs:
• Introduction
• Compound Searching
• Browse
• System Requirements
.
The Introduction and System Requirements tabs
deliver important information about Ashgate
Drugs, compatibilities, and how to navigate the site.
The Compound Searching and Browse tabs bring
the Ashgate Drugs data to the user.
To search for compounds:
1. Enter the desired information into the fields
provided in the Compound Searching Form.
for more information about a particular field.
To search without using the structure search,
click on the Click Here for Non-Plugin
Searching link.
2. Click Search.
A list of search results appears
Compound Searching
The Compound Searching section allows searching
for compounds by physical properties, compound
attributes, and structure. The Ashgate Drugs
compound searching form acts much like the other
search forms found in ChemOffice WebServer
applications.
To access the Compound Searching section:
To view the contents of a particular record in the
list, click
Show Details.
214•Ashgate Drugs
CambridgeSoft
Using Ashgate Drugs Online

The complete contents of the chosen record is
displayed.
Browse
The Browse Tab lists therapeutic categories in
alphabetical order. Click on a link to view the record
for compounds with the listed therapeutic category.
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216•Ashgate Drugs
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Using Ashgate Drugs Online

Chapter 12: ChemACX
What Is It
ChemACX (Available Chemicals Exchange) is a
class of databases available from chemical
manufacturers and distributors, featuring complete
catalogs of major world suppliers of fine research,
specialty, and industrial chemicals. ChemACX is a
read-only database.
ChemACX Database
Directory: ChemACX
Filenames: Acx2004Index.cfw, Acx2004Prod.cfw,
Acx2004Supplier.cfw
Number of Catalogs: 346
Number of Unique Chemical Entities: >305,
000
Number of Chemical Products: >595, 000
Key Fields:
• Structure
• Formula
• ACX Number
• Product Name
• Molecular Weight
• CAS Registry Number
• Synonym
• Product ID
• Catalog Number
• Supplier ID
• Property
• Supplier Name
How Is It Useful
ChemACX is your guide to commercially available
chemicals worldwide. Whether you are planning a
bench synthesis, scale-up, or a commercial process,
you can search these databases to determine the
availability and sources for the chemicals you need.
You can search ChemACX by any of the following:
• Chemical structure
• Chemical substructure
• Compound name
• Molecular formula
• CAS Registry Number
• Molecular weight range
• Combinations of the above criteria
For information about searching, see the
ChemFinder section in the purple ChemOffice
manual.
Using ChemACX with
ChemOffice WebServer
ChemACX allows the user to search for particular
chemicals, view a list of vendors providing what was
searched for, and save the products desired to a
Shopping Cart.
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What Is It

Administrator
Opening ChemACX
To open ChemACX:
Type http://servername into your web browser.
NOTE: Servername is the name of the ChemOffice
WebServer machine. For more information about your server,
please contact your system administrator.
The main ChemOffice WebServer window
appears.
• Click ChemACX.
The ChemACX Query Input Form appears.
• MW Range (molecular weight search)
• Catalog Number
To search for information from ChemACX
vendors:
1. Open ChemACX.
2. Enter search criteria.
3. Select the appropriate Search:
• If you would like to search over all of the
vendors in ChemACX, select Search all
vendors.
• If you would like to search over a previously
generated list of favorite vendors, select
Search your favorite vendors.
4. Click Search.
The Search Results page appears. The
following illustration shows part of the results
from a substructure search for cyclohexane.
Searching ChemACX Catalogs
Searching ChemACX is similar to searching all
other ChemOffice WebServer applications. For tips
regarding searching ChemOffice WebServer
applications, please see “ChemOffice WebServer”
on page 167.
Searches for chemicals in ChemACX can include a
combination of any of the following fields:
• Substance Name (text search)
• CAS Registry Number
• ACX Number
• Mol. Formula (formula search)
Searching Without the Plug-in
A ChemDraw plug-in is available from the
ChemACX Query Input Form. This plug-in aides
in the process of searching by substructure. If
searching by substructure is not necessary,
searching without the plug-in may be appropriate.
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Searching without the plug-in allows the user to
simplify the search to a chemical name or a CAS
number only.
To search without the plug-in:
1. From the ChemACX query input form, click
Click for Non-Plugin
Search.
The Non-Plug-in Search page appears.
To create or edit a list of favorite vendors available
to search under:
1. From the ChemACX Query input form, click
Edit Favorite Vendors List.
The Vendor Selector box appears.
2. Take the appropriate action:
If you want to
search
by chemical name
by CAS number
Then
in the text box, enter
a chemical name.
in the text box, enter
a CAS number.
2. Select the checkbox next to any vendor that
should be included in the favorite list. To
remove a vendor, deselect the checkbox.
3. Click Save as Preferred List.
A list of favorite vendors is saved and the
Vendor Selector box closes.
with the full query
page, including
structures and other
criteria
3. Click Search.
The Search Results page appears.
click Advanced
Query with Plugin.
Creating and Editing A List of Favorite
Vendors
It is possible for the user to search for substances
under a shorter list of preferred vendors. This
shorted list helps to limit search results to include
products from only your “favorite vendors”.
Viewing Search Results
Similar to other ChemOffice WebServer
applications, search results can be viewed in two
major formats: List View and Details View.
• List View - lists all results in a compact manner,
giving only summary information for each
result. You are able to register and lookup
MSDX data from this view.
• Details view allows users to view all
information in the selected record. You are
able to register and lookup MSDX data from
this view as well as add items to your shopping
cart from this view.
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To view a record's entry:
1. Search for a chemical on ChemACX. For more
information about searching in ChemACX, see
“Searching ChemACX Catalogs” on page 218.
2. To view vendors for a specific record, click
Details.
The detailed view appears
The order is added to your Shopping Cart.
7. To view the full catalog listing, click Catalog
Details, and a new window will appear
displaying catalog information.
8. In the list, select the checkbox next to Add to
Cart and enter a quantity. The order is added to
your Shopping Cart.
Viewing Search Results in List View
Results of a search are returned in list view by
default. The maximum total number of records
returned and the number of records returned on
each page is controlled by user preferences.
3. Select one of the tabs: Online Vendors, Your
Favorite Vendors, or Other Vendors.
4. Highlighting a vendor name in the list found in
the tabs will display a catalog listing to the right.
To compare more then one vendor, hold down
CTRL when highlighting vendor names.
5. Clicking Catalog View or Compact View will
toggle between the two viewing options. Select
whichever view you are most comfortable with.
6. In the list, select the checkbox next to Add to
Cart and enter a quantity.
The following functions can be performed from
this view:
• Zoom in on the structure.
• List all Synonyms for the substance.
• Access the record in details view.
• Mark the record.
• Register the compound in Registration System.
• Access the MSDX data for the compound.
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To view results in list view, perform a search. Use
the browsing buttons to browse through the pages
of result.
• Add products to your shopping cart.
Viewing Search Results in Details
View
Clicking on the Details button for a record in List
View brings you to details view for that record.
Details view makes available all of the tools to
browse through vendor catalogs and add products
to your shopping cart.
The following functions can be performed from
this view:
• Zoom in on the structure.
• List all Synonyms for the substance.
• Return the List View.
• Mark the record.
• Register the compound in Registration System.
• Access the MSDX data for the compound.
• Browse Vendor information.
Browsing Vendor Information
Records in details view are displayed with both
structure and vendor information.
To find the vendor catalog you are looking for:
1. Select one of the tabs: Online Vendors, Your
Favorite Vendors, or Other Vendors
depending on your preference.
2. Highlighting a vendor name in the list found in
the tabs will display a catalog listing to the right.
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Note: To compare more then one vendor, hold
down CTRL when highlighting vendor names.
3. Select the appropriate viewing option by
clicking on one of the following buttons:
Catalog View
• For details about using the shopping cart,
please see “Using the Shopping Cart” on
page 223.
Accessing MSDX Data
MSDX Data, when available, can be accessed from
the MSDX link found in list and details view on a
substance's record. MSDX data is not available for
all substances. By default, when the data is not
available, the MSDX link will appear greyed out.
To access a substance's MSDX data, click the
MSDX link in list or details view.
• To view the full catalog listing, click Catalog
Details, and a new window will appear
displaying catalog information.
Compact View
• If there is more then one data sheet for the
substance, an option window appears.
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• If there is only one data sheet available, or as a
result of selecting one of the options, the
datasheet appears in PDF format.
Viewing Your Shopping Cart
Your Shopping Cart list can be retrieved from the
ChemACX Query Input form or the Search Results
page.
To view your Shopping Cart, click either
• OR
•
Your Shopping Cart list appears.
Using the Shopping Cart
The Shopping Cart is a convenient way to save a list
of chemicals to be ordered. For more information,
about ordering the chemicals in your shopping cart,
see “Ordering The Chemicals in the ChemACX
Shopping Cart” on page 223.
You can add items in the shopping cart from details
view of any record.
To view a record's entry:
1. Search for and access a record in details view.
2. Browse to the product you would like to add to
your shopping cart.
3. In the list, select the checkbox next to Add to
Cart and enter a quantity.
The order is added to your Shopping Cart.
Removing Items from Your Shopping
Cart
To remove an item from your Shopping Cart:
• On the Shopping Cart page, click
Remove.
To remove all items from your Shopping Cart:
• On the Shopping Cart page, click
Remove all.
Ordering The Chemicals in the
ChemACX Shopping Cart
There are three options in saving the ChemACX
shopping cart information gathered during a
session: Print, Export to Excel, or Export to
Word.
To print your shopping cart, click on
Print.
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To export shopping cart data to Excel or Word:
1. Click Export to
Excel (or Export to Word).
NOTE: Exporting to MS Excel or MS Word
are options configured by your system
administrator. See your system administrator
for more details.
The Requisitioner Information Form appears.
Send Hits to Inventory button (on the shopping
cart page) are visible. Otherwise, these tools will not
be available.
For more information about configuring your
system to link to Registration System and/or
Inventory, please see your system administrator.
Registering Products in Registration
System
.When this feature is available, a Register link
appears in List View.
To register the compound:
1. Click the Register link.
A registration window appears.
2. Enter appropriate information in the space
provided.
3. Click Export to
Excel (or Export to Word).
Your shopping Cart information is saved to an
Excel workbook or Word Document with one
sheet for each vendor.
Registering and Creating
Inventory Containers
ChemACX can be integrated with Registration
System and Inventory if they are installed. If the
system is configured to utilize these features, the
Register link (on search results pages) and the
2. Adjust the information as desired.
• Change the CAS number in the CAS
textbox.
• Select a name from the Chemical Name
listbox. The names listed are all names
associated with the record in ChemACX.
3. Click OK.
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The compound is added to the Temporary
Table in Registration System by default.
3. Click OK.
Creating Inventory Containers in
Inventory for Products
When this feature is available, a Send Hits to
Inventory button is found on the shopping cart
page.
4. From this screen, you are able to commit the
information you have entered or test the
commit process before actually committing the
data.
• To test the data before committing, click
Test.
To Send the contents of your Shopping Cart to
Inventory and make containers for them:
1. Click Send Hits to Inventory.
An Inventory window appears.
• To commit the data to Inventory, click
Commit Click View to view your new
containers in Inventory.
2. Enter the appropriate information about the
containers being created for each ChemACX
product.
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Saving Hitlists and Exporting
SD Files
ChemACX, being a ChemOffice WebServer
application, uses the hitlist management and SD
File Export Features of the ChemOffice
WebServer. See “Manipulating Hit Lists” on page
181 and “Exporting Search Results” on page 183
for more information.
Logging Off
You can end your session with ChemACX at
anytime by logging off.
To log off:
If you start your search with the Index form and
find some matching compounds:
• A list of synonyms in the Synonyms subform
appears.
• A list of suppliers in the Products subform
appears.
• Search MSDX by clicking the MSDX button.
To view product information:
• On the Index form, click a product name.
The Product form appears.
• Click Log Off.
Searching ChemACX
Ultra on CD
If you want to search over the entire database for a
chemical, start with the Index form.
To return to the Index form:
• Click Index Form.
To view information about the supplier of the
chemical:
226•ChemACX
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• Click Supplier Info Form.
The Supplier form appears.
What If My Favorite
Supplier Isn’t Listed
Here
A list of participating vendors can be found in
“ChemACX Participating Vendors” on page 265.
CambridgeSoft is always adding new companies to
ChemACX. The one you want might be in the next
release of ChemInfo, or it might already be
CambridgeSoft’s WWW subscription service,
ChemInfo Pro.
To display a list of products for the displayed
supplier:
• Click Products.
The Products form appears.
Contact your supplier and ask them to participate in
ChemACX. To participate, your supplier sends
CambridgeSoft its product list. The preferred
format for submission is a ChemFinder database
with structures. They can also use other electronic
formats such as Access databases or Excel
spreadsheets. They can use a brochure for short
product lists. Send the information to one of the
following:
• csinfo@camsoft.com
• ChemACX Data, CambridgeSoft Corporation,
100 CambridgePark Drive, Cambridge, MA
02140 (USA)
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What If My Favorite Supplier Isn’t Listed Here

Chapter 13: ChemSCX
What Is It
ChemSCX is designed to complement ChemACX
with structures from high-throughput screening
sample providers. ChemACX is a collection of fully
structure-searchable catalogs from leading
screening compound suppliers. ChemSCX is a
read-only database.
ChemACX Screening
Compound Databases
Directory: ChemACX_SC
Filenames: AcxSC2004Index.cfw,
AcxSC2004Prod.cfw, AcxSC2004Supplier.cfw
Number of Suppliers: 15
Number of Compounds: >500, 000
Key Fields:
• Structure
• Formula
• ACX Number
• SC Number
• Molecular Weight
• Supplier
• Catalog
How Is It Useful
ChemSCX allows you to locate and order
compounds used for high-throughput screening
programs. The database provides consolidated
supplier data to enable you to quickly and easily
search and compare compounds. Using the
database, you can easily choose the most useful and
interesting compounds for screening.
ChemSCX can be searched by any of the following:
• Chemical structure
• Chemical substructure
• Compound name
• Molecular formula
• CAS Registry Number
• Molecular weight range
• Combinations of the above criteria
For information about searching, see the
ChemOffice WebServer User’s Guide
documentation.
ChemSCX has three linked forms:
• Index form
• Product form
• Supplier form
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Using ChemSCX on CD
To search over the entire database for a chemical,
access the Index form.
To return to the Index form:
• Click Index Form.
To view information about the supplier of the
chemical:
• Click Supplier Info Form.
The Supplier form appears.
To view product information:
• From the Index form, click a product name.
The Product form appears.
To display a list of products for the displayed
supplier:
• Click Products Form.
The Products form appears.
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Chapter 14: ChemMSDX
What Is It
CS ChemMSDX is a collection of over 21,000
Material Safety Sheets presented through
ChemACX in PDF format.
How is it Useful
ChemMSDX provides rapid access to
comprehensive health and safety information to aid
in the safe handling, storage, and transportation of
materials, and provides precautionary and
emergency medical information.
Directory: ChemACX/
Filenames: *.pdf
Number of Compounds: > 21,000
Using ChemMSDX
from ChemACX
Access MSDX data from ChemACX by clicking the
MSDS Database button in the record’s form.
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Using ChemMSDX from ChemACX

Chapter 15: ChemINDEX
What Is It
ChemINDEX is a class of chemical reference
databases composed of the BuckyBase,
ChemINDEX Net, and NCI databases. Its
databases are found in the ChemINDEX CD-
ROM.
How Is It Useful
• Name
• Vapor Pressure
• Synonym
• CAS Registry Number
• Boiling Point
• Melting Point
• Site ID
This class of databases serves as an extensive
chemical reference for finding general information
about commonly used compounds, such as
structure, name, molecular weight, CAS Registry
Number, synonyms, and physical data (melting
point, boiling point, vapor pressure, etc.).
ChemINDEX Net contains active hyperlinks to
WWW sites with further information about the
compounds.
Using ChemINDEX on
CD
Directory: IndexChem
Filename: Indexnet.cfw
Number of compounds: >78, 000
Key Fields:
• Structure
• Formula
• ACX Number
• SC Number
• Molecular Weight
• Supplier
• Catalog
Each data field on this form is labeled. Melting
points and boiling points are presented as three
fields:
• If only a single value is available, it is placed in
the first field.
• If a range is available, the low and high limits of
the range are placed in the first two fields.
• The third field is for a note, such as (dec) for
decomposes.
Synonyms and hyperlinks are displayed in the
subforms on the right side of the form. You must
have an internet connection to use the hyperlink
features. If you are connected to the internet, the
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GO button at the upper right connects to
CambridgeSoft’s WWW server for this database.
Click the button or one of the hyperlinks, and
ChemInfo attempts to start your system’s default
web browser and direct it to the appropriate URL.
BuckyBase
The subfolder BUCKYBSE within ChemINDEX
contains two databases. BUCKBALL is a file of 132
buckminsterfullerenes, and BUILDING is a file of
99 building blocks which can be joined together to
make new or existing buckminsterfullerenes.
Directories: buckybse, balls, building
Filenames: Buckball.cfw, Building.cfw
Number of compounds: 132 buckyballs; 99
building blocks
Key Fields:
• Structure
• Formula
• Molecular Weight
• Name
To view any of the buckyballs or building blocks as
a 3-dimensional model using Chem3D:
• Right-click the structure and select View Model.
Chem3D starts and displays the molecule.
The webserver at www.chemfinder.com, is one of
the most heavily used public-access chemical
information site on the Internet. ChemINDEX is
the ChemFinder database of small molecule
information presented at this site. Many of the
individual compound records also contain lists of
hyperlinks (URLs) to other sites containing
additional information about the compound. To go
to a site, click its link. The default web browser on
your system will be activated and directed to the
target URL.
Using ChemINDEX
Online
ChemINDEX, available online through a
Subscription uses the same conventions as other
webserver applications. For more information about
general ChemOffice Webserver application
concepts, please see “ChemOffice WebServer” on
page 3.
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BuckyBase

Chapter 16: ChemRXN
What Is It
ChemRXN is a class of databases of chemical
reactions which include literature citations,
products, reactants, solvent and catalyst data, yields,
and reaction conditions. ChemRXN consists of
ChemPrep and ChemSelect.
How Is It Useful
ChemRXN provides ready access to information
useful in planning a chemical synthesis. A reaction
query can search for all reactions that:
• Yield a particular product
• Use a particular catalyst or solvent
• Consume a particular reactant
• Have been published by a certain author
For example, you can search for reactions which
produce benzofurans in greater than 90% yield.
ChemPrep
ChemPrep is a carefully prepared chemical reaction
database from the Institute for Scientific
Information (ISI). ISI is one of the largest and most
reputable providers of scientific information, and
has a number of scientific databases available
including exhaustive reaction and molecular
literature databases.
Directory: ChemPrep
Filenames: Chemprep.cfw, Catalyst.cfw,
Reaction.cfw, Solvent.cfw
Number of Reactions: 16,761
Key Fields:
• Structure (reaction)
• Reaction Formula
• Abstract
• Molecular Weight (components)
• Atmosphere
• Reaction text
• Time
• Key phrases
• Pressure
• Reflux
ChemPrep has a principal form or main screen,
Chemprep.cfw, and three associated forms:
• Reaction.cfw
• Solvent.cfw
• Catalyst.cfw
Reaction.cfw shows the reaction diagram in a larger
window. It is useful in case the reaction is
complicated or has large molecules or many
components. Reaction.cfw is called from the main
screen by clicking the zoom Reaction button. The
“view Solvents” and “view Catalysts” buttons
provide larger views of the solvent (form
Solvent.cfw) and catalyst (form Catalyst.cfw)
molecules which appear in the scrolling lists on the
right of the main screen. Each of these associated
forms has a button to return to the main screen.
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The reactions in ChemPrep were selected by ISI
from their larger reaction databases and were
provided with full literature references. The
reaction centers and atomic transformation
matrices were computed with ChemFinder.
ChemSelect
ChemSelect is a collection of the most commonly
cited reactions from the literature, selected by
InfoChem GmbH of Germany. The ChemSelect
data is taken from the VINITI project of the
former Soviet Union, in which over 2 million
chemical reactions were compiled. The 13,037
reactions of ChemSelect were obtained using a
defined statistical methodology which selects the
most representative reactions from the database.
All reactions contain full literature citations.
Directory: ChemSelect
Filenames: ChemSelect.cfw, Catalyst.cfw,
Reaction.cfw, Solvent.cfw
Number of reactions: 13,037
Key Fields:
• Structure (reaction)
• Reaction Formula
• Year
• Molecular Weight (components)
• PageNumber
• Journal
• Yield
• Reaction Text
• Pressure
• Reflux
• Literature text
• Author
• Type
• Title
• Language
• Volume
ChemSelect has a main form, ChemSelect.cfw, and
three associated forms:
• Reaction.cfw
• Solvent.cfw
• Catalyst.cfw
The associated forms show the data in a larger
window.
To access Reaction.cfw:
• From the main screen, click Zoom Reaction.
To display larger views of Solvent.cfw and
Catalyst.cfw molecules:
• Click Zoom Solvent(s) or Zoom Catalyst(s).
To return to the main screen:
• Click Return or Return to main screen.
InfoChem is a major provider of scientific
information, and has also created selections called
ChemReact41 (41,000 reactions), ChemSynth
(100,000 reactions), and ChemReact (400,000
reactions). These will also be available as
ChemFinder databases. For further information,
contact CambridgeSoft or InfoChem GmbH.
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Selection Criteria
For inclusion in ChemSelect, each reaction must
typify at least five different reactions. Two reactions
are considered to be of the same type if the reaction
centers and the groups around the reaction centers
are identical. Each reaction in ChemSelect has been
cited in at least five different journal articles, has a
yield of at least 50%, and has been published in a
generally available journal.
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ChemSelect

Chapter 17: NCI
What Is It
NCI (National Cancer Institute) is a database of
potential screening compounds provided by the
National Cancer Institute.
The NCI database is provided with CambridgeSoftgenerated
2-dimensional structures.
Using NCI on CD
Directory: nci
Filenames: NCI2004.cfw
Number of compounds: >223,000
1. Basic Chemical Information
searchable by:
• Chemical Structure
• Molecular Formula
• Molecular Weight
• NSC Number
• CAS Number
• Synonym
•
2. Human Tumor Cell Line
NOTE: The National Cancer Institute’s AIDS database
can be accessed through the NCI database. Please see“” on
page 243 for more information.
Using the NCI Forms
The NCI Database ChemFinder form consists of
three tabs:
• A box appears under the Basic Chemical
Information tab if data is available.
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3. AIDS Antiviral Screen (Please see“” on page 243
for more information)
• A box appears under the Basic Chemical
Information tab if data is available.
Using NCI Online
ChemINDEX, available online through a
Subscription uses the same conventions as other
ChemOffice WebServer applications. For more
information about general ChemOffice WebServer
application concepts, please see “ChemOffice
WebServer” on page 3.
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Chapter 18: AIDS
What Is It
AIDS (The National Cancer Institute’s AIDS
database) is a library of potential HIV screening
compounds provided by the National Cancer
Institute.
The AIDS database is provided with
CambridgeSoft-generated 2-dimensional
structures.
Using AIDS on CD
The AIDS database is available through the NCI
search forms. Please see “NCI” on page 241 for
more information. If AIDS information is available
for the substance retrieved, a box appears under the
Basic Chemical Information tab.
Using AIDS Online
The AIDS database is available through the NCI
search forms online.Please see “NCI” on page 241
for more information.
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Section VI: Appendices
This section contains appendices in the following
order:
• Appendix A: Inventory Functions in
Container Details Frame - Gives an
overview of functions available in the
Container Details Frame of Inventory’s
Container Management.
• Appendix B: Document Manager Free
Text Searching - Describes the use of key
words and symbols in Free Text Searching
• Appendix C: BioAssay Actions Menu
Commands - Describes the actions
available form the Actions button within
BioAssay.
• Appendix D: BioAssay Plate Block Data
Files - Indicates how to indicate to
BioAssay’s FIle Import Template Wizard
how your plate block data file is formatted.
• Appendix E: Oracle Cartridge
Dependencies by Operating System -
lists the libraries neccessary for the Oracle
Cartridge
• Appendix F: ChemACX Participating
Vendors - A list of vendors in the
ChemACX database
• Appendix G: ChemSCX Participating
Vendors - A list of vendors in the
ChemSCX database
• Appendix H: Scientific Databases First
Search Tutorial - A tutorial for using the
CD based Scientific Databases with
ChemFinder.
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Appendix A: Inventory Functions in
Container Details Frame
The following functions can be available from the
Container Details Frame.
Function Name
Change Qty
Check Out
Check In
Copy Container
Reorder Container
Description
The Change Qty function allows the modification of the quantity
of material remaining in the container. Quantities are measured in
the predefined unit of measure associated with the container.
The Check Out function is typically used when a user removes a
container from a central storage location for subsequent use at a
different location. The act of checking involves a change in
container location plus a change in the current user responsible for
the container.
The Check In function performs the reverse of the check out
process. It is typically performed when a user returns a chemical
container to its central storage location. The system remembers the
location and user under which the container was created and uses
them as the default values during the check in process.
The Copy Container function allows you to create one or more
containers using a preexisting container as a starting template.
Typically attributes such as lot number, container cost of expiration
dates may need to be modified before the new container/s are
created.
The Reorder Container function places an order for the selected
container, meaning a new container with the same attributes is
created and placed in the On Order location.
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Function Name
Description
Administrator
Edit Container
Move Container
The Edit Container function allows editing of all container
attributes. You may switch between the various tabs to access all
container attributes. Changes to the container are only committed
to the database once the Update Container button is clicked.
The Move Container function moves the currently selected
container to a new location. The destination location id can be
directly entered or scanned into the text box in the dialog, or the
browse link can be used to select a location from the tree.
Delete Container
Retire Container
The Delete Container function deletes the currently selected
container. The container is permanently removed from the system.
The Retire Container function retires the currently selected
container. When a container is retired, it is not deleted, but is no
longer in use.
Split Container See “Split Container” on page 60
Merge Containers See “Merge Containers” on page 60
Create Samples See “Create Samples” on page 61
History
Print Label
The Container History link uses the Audit Report window to
display a container's history. Clicking on the History link will bring
up the audit window and filters information to show any activity
involving the current container.
Prints a barcode label for the container.
248•Inventory Functions in Container Details Frame
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Appendix B: Document Manager
Free Text Searching
Understanding Basic
Text Searching
You can use basic text searching, or querying, to
find information in documents within
Documentation Manager. There are a number of
special characters used in basic text searching which
will help narrow or increase search results.
Normally, the more narrow a search, the less
ambiguous and more precise search results become,
making it easier to find the correct information. As
a search gets broader, the longer the search results
list becomes.
Different types of basic text searching are available,
depending on the needs of the search.
Exact Phrase Matching
If a search is meant to find only exact matches for
the text entered, exact word or phrase matching
should be used. This is the most simple search, or
query, which returns exactly the information
requested.
For example, the following searches really mean:
Searching for
thymidine synthesis
cyclohexane
Wildcard Searching
Returns
documents with
the words thymidine
synthesis in that order,
with no words between
in a document’s text.
the word cyclohexane in
a document’s text.
If a prefix or a suffix for a word is either unknown
or variable, wildcard characters become useful in a
free text search to return all words with the same
word root. Wildcard characters can be used in a
basic text search when searching for all documents
that contain a part of a word. This kind of search
typically returns more matches to search criteria
than the exact phrase search.
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Understanding Basic Text Searching

Administrator
For example, the following searches really mean:
Searching for
synth*
*ethane
Returns
documents with
any word with synth as
the first 5 letters in a
document’s text.
Matches include
synthesis, synthetic, and
syntheses.
any word with ethane as
the last 6 letters in a
document’s text.
Matches include ethane,
and methane.
• NOT (~)
• OR (|)
• soundex (!)
• stem ($)
ABOUT
The ABOUT operator, when used in an advanced
text search, or query, retrieves documents that
contain information related to a word or phrase.
The ABOUT operator is used, by entering the word
ABOUT in all capital letters followed by the word
or phrase on which to search in parentheses.
ABOUT searches are always case-sensitive. The
text string inside the parentheses is interpreted with
respect to case.
For example, the following searches really mean:
Understanding
Advanced Text
Searching
Advanced text searching, or querying, is also
available for document searching from within
Documentation Manager. Using specific operators
in an advanced search allows the user to narrow
search parameters dramatically.
The following is a list of some of the special
operators used in advanced searching:
• ABOUT
• AND (&)
• EQUIValence (=)
• fuzzy ()
• MINUS (-)
• NEAR
Searching for
ABOUT (carbon)
ABOUT (carbon biproducts
from
syntheses at 25 degrees
Celcius)
Returns
documents with
any word with words
related to carbon in the
document’s text.
Matches include coal
and diamond.
any word with words
related to carbon biproducts
from syntheses at
25 degrees Celcius in the
document’s text.
Matches include coal
and diamond
The ABOUT operator becomes very powerful
when coupled with other operators, such as AND
or NOT.
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Understanding Advanced Text Searching

For example, the following searches really mean:
For example, the following searches really mean:
Searching for
Returns
documents with
Searching for
Returns
documents with
ABOUT (carbon)
AND diamond
any word with words
related to carbon as well
as the word diamond in
the document’s text.
carbon AND diamond both the words carbon,
and diamond, found
anywhere within a
document’s text.
ABOUT (carbon)
NOT ABOUT
(diamond)
NOTE: For advanced Oracle users: The word or phrase
specified in an ABOUT query does not have to exactly
match the themes stored in the index. Oracle automatically
normalizes the word or phrase before performing lookup in
the Text index.
AND (&)
any word with words
related to carbon but
excluding the word
diamond in the
document’s text.
The AND operator used in an advanced text search
or query, finds documents that contain more than
one word or phrase. The AND operator is used to
search for documents that contain at least one
occurrence of each of the query terms.
The AND operator, is used by entering the first
term, then the word AND in all capital letters (or
entering the ampersand (& symbol)), followed by
another word or phrase on which to perform a
search.
carbon & diamond
carbon & diamond &
graphite
thymidine synthesis
AND carbon dioxide
EQUIValence (=)
both the words carbon,
and diamond, found
anywhere within a
document’s text.
all the words carbon,
diamond, and graphite,
found anywhere within
a document’s text.
both the phrases
thymidine synthesis, and
carbon dioxide, found
anywhere within a
document’s text.
The EQUIValence operator used in an advanced
text search, or query, will allow the user to find
documents that contain information about words
that can be used in place of each other, alone or in
a phrase. The EQUIValence operator is used to
specify an acceptable substitution for a word in a
query.
The EQUIValence operator is used by, entering
EQUIV in all capital letters (or enter the equal sign
(=)), followed by the phrase on which the search is
to be performed.
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Understanding Advanced Text Searching

For example, the following searches really mean:
For example, the following searches really mean:
Administrator
Searching for
graphite EQUIV
diamond
graphite = diamond
carbon
dioxide=monoxide
NOTE: The EQUIValent operator has higher precedence
than all other operators except the expansion operators
(fuzzy, soundex, stem).
Fuzzy ()
Returns
documents with
the words graphite or
diamond found
anywhere within a
document’s text.
the words graphite or
diamond found
anywhere within a
document’s text.
the words carbon
dioxide, carbon monoxide,
or both terms found
anywhere within a
document’s text.
The fuzzy operator used in an advanced text search,
or query, will find documents that contain words
similar to the word used in a search. For example,
the fuzzy operator can be used to expand queries to
include words that are spelled similarly to the
specified term. This type of expansion is helpful for
finding more accurate results when there are
frequent misspellings, or alternate spellings in the
documents in the database.
The fuzzy operator is used by, entering a question
mark (), followed by the word on which to perform
a search.
Searching for
boron
read
chemist
MINUS (-)
Returns
documents with
any word spelled
similarly to boron found
anywhere within a
document’s text.
Matches include baron.
any words spelled
similarly to read found
anywhere within a
document’s text.
Matches include read,
lead, and real.
any words spelled
similarly to chemist
found anywhere within
a document’s text.
Matches include
chemists and chemistry
The MINUS operator can be used in an advanced
text search, or query, to find documents that
contain two phrases, with the first phrase taking
precedence. The MINUS operator is used to search
for documents that contain two query terms, but
documents containing the second term are ranked
lower than documents without the second term.
The MINUS operator is useful for lowering the
score of documents that contain a certain term,
without eliminating those documents.
The MINUS operator is used, by entering the first
term, then MINUS in all capital letters (or enter the
minus sign or hyphen (-)), followed by another term
on which to perform a search.
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Understanding Advanced Text Searching

For example, the following searches really mean:
Searching for
carbon - diamond
carbon MINUS
diamond
diamond - carbon
NEAR (;)
Returns
documents with
the words carbon and
diamond in them, but
documents with
diamond are listed last.
the words carbon and
diamond in them, but
documents with
diamond are listed last.
the words diamond and
carbon in them, but
documents with carbon
are listed last.
The NEAR operator is used in an advanced text
search, or query, to find documents that contain
two phrases that are close together. The maximum
distance between the two terms can be specified.
The NEAR operator is used by, entering the first
term, followed by NEAR in all capital letters (or
enter a semicolon (;)), followed by the second term
on which the search is to be performed.
Use the NEAR operator to return documents
based on the proximity of two or more query terms.
NOTE: NEAR cannot be used in ABOUT queries.
For example, the following searches really mean:
Searching for
carbon NEAR
diamond
NEAR uses the following defaults:
Returns
documents with
the words carbon and
diamond in them, but
only when they appear
less than 100 words
apart and in no specific
order.
• Search terms are found if they are 100 words
apart or less, unless specified otherwise. Use
whole numbers between 1 and 100.
• Search terms are found in any order, specified
otherwise. Use TRUE or FALSE.
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Understanding Advanced Text Searching

Administrator
The NEAR operator can be used with other
operators, such as AND, OR, and EQUIValence.
For example, the following searches really mean:
Searching for
NEAR ((carbon,
diamond), 20, FALSE)
NEAR ((carbon,
diamond), 20, TRUE)
NEAR ((carbon,
diamond), 10) AND
benzene
Returns
documents with
the words carbon and
diamond in them, less
than 20 words apart, in
no specific order.
the words carbon and
diamond in them, less
than 20 words apart, in
this specific order.
the words carbon,
diamond, and benzene in
them, but only when
carbon and diamond
appear less than 10
words apart and in no
specific order.
by, entering the term to be found, followed by the
word NOT in all capital letters (or enter a tilde (~)),
followed by the term to be excluded in the search.
Use the NOT operator to search for documents
that contain one query term and not another.
For example, the following searches really mean:
Searching for
Returns
documents with
carbon NOT diamond the word carbon, but
not the word diamond
anywhere in the
document’s text.
carbon ~ diamond
carbon NOT
(diamond OR
graphite)
the word carbon, but
not the word diamond
anywhere in the
document’s text.
the word carbon, but
not the word diamond
or graphite anywhere in
the document’s text.
NEAR ((carbon,
diamond = graphite),
10)
NOT (~)
the words carbon,
diamond, and graphite in
them, but only when
carbon and diamond or
carbon and graphite
appear less than 10
words apart and in no
specific order.
The NOT operator can be used in an advanced text
search, or query, to find documents that contain a
word or phrase, but only when it appears without a
second word or phrase. The NOT operator is used
NOTE: The NOT operator does not affect other logical
operators.
OR (|)
The OR operator can be used in an advanced text
search, or query, to find documents that contain
information about any words in the query, but not
necessarily all words in the query. The OR operator
is used by, entering the first term, followed by the
word OR in all capital letters (or enter the pipe (|)),
followed by another term on which the search is to
be performed.
254•Document Manager Free Text Searching
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Understanding Advanced Text Searching

Use the OR operator to search for documents that
contain at least one occurrence of any of the query
terms.
For example, the following searches really mean:
Searching for
carbon OR diamond
carbon | diamond
carbon OR diamond
OR graphite
thymidine synthesis
OR carbon dioxide
Soundex (!)
Returns
documents with
the words carbon,
diamond, or both
anywhere in the
document’s text.
the words carbon,
diamond, or both
anywhere in the
document’s text.
the words carbon,
diamond, graphite, or any
combination of the
terms anywhere in the
document’s text.
the words thymidine
synthesis, carbon dioxide,
or both terms
anywhere in the
document’s text.
The soundex operator is used in an advanced text
search, or query, to find documents that contain
words that sound like the word used in a search.
The soundex operator is used by, entering an
exclamation point (!), followed by the word on
which to perform a search.
Use the soundex (!) operator to expand queries to
include words that have similar sounds; that is,
words that sound like other words. This function
allows comparison of words that are spelled
differently, but sound alike in English.
For example, the following searches really mean:
Searching for
!carben
!read
Stem ($)
Returns
documents with
any words that sound
like the word carben in
a document’s text.
Matches include carbon
and carboxcylic.
any words that sound
like the word read in a
document’s text.
Matches include read
and lead.
The stem operator is used in an advanced text
search, or query, to find documents that contain
words similar to the word used in a search. When
the stem operator is used, enter a dollar sign ($),
followed by the word on which to perform a search.
Use the stem operator to search for terms that have
the same linguistic root as the query term. Stem
expands a query to include all terms with the same
stem or root word as the search term.
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Understanding Advanced Text Searching

For example, the following searches really mean:
Administrator
Searching for
$commit
Returns
documents with
any words with the
root commit found in
the document’s text.
Matches include
commits, committing,
committee, and committed.
$chemist
any words with the
root chemist found in
the document’s text.
Matches include
chemist, chemistry, and
chemists in them.
256•Document Manager Free Text Searching
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Understanding Advanced Text Searching

Appendix C: BioAssay Actions Menu
Commands
All of the following commands are available from
the Actions menu of BioAssay. The commands are
only available from the menu when they are
relevant.
Viewing Commands
View Details
The View Details action can be accessed from any
Protocol Data table, except from a table found at
the bottom of the hierarchy. The View Details
action brings about the same result as doubleclicking
on a row in the table: the data table holding
aggregate data for the current table, is opened. This
result makes sense because the data that makes up a
particular row in one table is formed by the data
calculated in the next lowest table.
View Picklist
The View Picklist action is available from the table
containing protocol picklist definitions. This action
will open a table defining the options available in
the chosen picklist.
To view a picklist's table:
1. Select the row defining the picklist to be
viewed.
2. Select View Picklist from the Actions menu.
View Plate Format
The View Plate Formats action is available from the
plate formats table. This action will open a table
defining the chosen plate format.
To view a plate format:
1. Select the row defining the plate format to be
viewed.
2. Select View Plate Formats from the Actions
menu.
View (from the plates grid)
The View action will populate the cells in the grid
with the indicated data. For example, selecting
View>Well Contents will populate the cells in the
grid with the contents of the well (assigned when
defining the plate's format).
View (from the plate formats
grid)
The View action will populate the cells in the grid
with the indicated data. For example, selecting
View>Well Contents will populate the cells in the
grid with the assigned contents (e.g. Empty, or
Compound).
The following options are available from the View
action on the plate formats grid:
• Well Contents
• Well Name
Other Commands
Autofit
The AutoFit action is available from any grid view.
If AutoFit is turned on, the grid will automatically
resize to fit in the current window. If the window is
then resized, the grid will resize accordingly.
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Viewing Commands

AutoFit On
The Change Validity window appears.
Administrator
AutoFit Off
Change Validity
The Change Validity action is available from any
Protocol Data table. By default, all data is assumed
to be Not Validated unless otherwise specified.
Data which is Not Validated is noted by in the
leftmost column of the data table. After adjusting
the validity of data, it is possible to view only valid
data in the tables.
Calculations are based on data which is marked with
any validity except Invalid.
4. Select the appropriate validity.
• Not Validated
• Valid
• Invalid
• Request Review
If you are validating data in a summary table, you
can also choose to cascade the validity change to the
summary data. Select this box if you would like to
apply the new validity to the summarized data.
Coloring Options
The coloring options are used to implement heat
maps. The Coloring Options Dialog box will allow
the user to select a parameter to base a heat map on,
and select what values for that parameter will
appear in which colors.
To set coloring options:
1. Select Coloring Options from the Actions
Menu.
The Coloring Options dialog box appears.
To change the validity of data in certain rows in the
table:
1. Browse to the table holding the appropriate
data.
2. Highlight the rows holding the data.
3. Select Change Validity from the Actions
Menu.
258•BioAssay Actions Menu Commands
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Other Commands

2. Select a parameter to base the heat map on
from the Color based on listbox.
3. Enter maximum and minimum values along
with colors that correspond to each.
4. Click OK.
Copy
The Copy action is only used in Edit mode. The
action will copy any highlighted information.
Cut
The Cut action is only used in Edit mode. The
action will cut any highlighted information.
Import Data
The Import Data Action is available from any
Protocol Data table. This action will bring up the
File Import Wizard. The wizard assists in importing
data through the use of a defined File Import
Template.
Paste
The Paste action is only available in Edit Mode.
This action pastes whatever is on the clipboard to
the selected area.
Recalculate
The Recalculate action will run all calculations
defined in the chosen table again. This is useful if
the user changes a key piece of data and is interested
to see how the calculations will be effected by the
change.
Save Compound LIst
The Save Compound List action, available from a
data table or search data table, allows the user to
save the currently selected rows to a list
Select All
The Select All action will select all of the rows in a
table. This is often helpful when applying a
different action to all of the rows in a table.
Show Coloring
This action shows the heat map coloring. When this
action is selected, each cell in the grid will be filled
with a color representing a value defined in the
coloring options. This is available from all views.
Show Only Valid Data
The Show Only Valid Data will display in any
Protocol Data table only the data.
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Other Commands

Administrator
260•BioAssay Actions Menu Commands
CambridgeSoft
Other Commands

Appendix D: BioAssay Plate Block
Data Files
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Administrator
262•BioAssay Plate Block Data Files
CambridgeSoft

Appendix E: Oracle Cartridge
Dependencies by Operating System
In addition to the OCI library. (extension may be
.dll, .so, .sl), the following files are a requirement on
the specified Operating Systems.
Windows Linux Solaris HP/UX AIX
• MSVCRT.dll
• libstdc++.so
• libclntsh.so
• libclntsh.sl
• libclntsh.a
• MSVCP70.dll
• libclntsh.so
• libCstd.so
• libstd_v2.sl
• libpthreads.a
• MSVCR70.dll
• libgcc_s.so
• libpthread.so
• libCsup_v2.sl
• libC.a libc.a
• libpthread.so
• libdl.so
• libcl.sl libdl.sl
• libc_r.a libdl.a
• libdl.so
• libpthread.sl
• libodm.a
• libcrypt.a
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Administrator
264•Oracle Cartridge Dependencies by Operating System
CambridgeSoft

Appendix F: ChemACX Participating
Vendors
A.G. Scientific Abbey Color Abbott Laboratories
Chemical Division
AccuStandard Aceto Corporation Acros Organics -
International
Advanced Aromatics, L.P. Advanced ChemTech Air Products & Chemicals,
Inc.
ABCR GmbH & Co. KG
Acros Organics - USA
Ajinomoto - Amino Acid
Department
Albemarle Corporation
Albright & Wilson
Americas
Alchem International
Limited
Alchymars SpA
Aldrich Alfa Aesar AlliedSignal Inc. Specialty
Chemicals
American Advanced
Organics
American Radiolabeled
Chemicals, Inc.
Amresco Inc. Angelini Fine Chemicals Angus Chemical Company
Antibiotics SPA AppliChem Array BioPharma, Inc. Asahi Glass Company -
Fluorochemicals Division
Ashwood Chemicals Ltd. Asymchem Aviabor Fine Boron
compounds
BACHEM AG
BASF Chemical
Intermediates
Bayer Corporation Bayer Inorganics Bedoukian Research, Inc.
Beta Pharma, Inc. Biddle Sawyer Corporation Biochemie GmbH Biomol
BioQuadrant Inc. Biosynth International, Inc. Biotium, Inc. BIOTRENSD Chemikalien
GmbH - Neurochemicals
BIOTRENSD
Chemikalien GmbH -
Radiochemicals
Boulder Scientific
Company
BioVision, Inc. Boehringer Ingelheim KG Borregaard Synthesis
Bright Evergreen Burdick & Jackson, Inc. Bush Boake Allen Inc.
Calaire Chimie s.a. Callery Chemical Company Cambrex Corporation Carbomer
ChemOffice Enterprise Workgroup & Databases 2005 ChemACX Participating Vendors • 265

Cayman Chemical
Company
Celanese, Ltd.
Central Glass Co. Ltd.- Fine
Chemical Department
Charkit Chemical
Corporation
Administrator
Chattem Chemicals, Inc. Chemada Chematek S.p.A. ChemDesign Corp. (A
Bayer Company)
Chemetall GmbH,
Lithium Division
CHEMI S.p.A. Chemicrea Inc. Chem-Impex International,
Inc.
Chemisphere Limited ChemPacific Corporation ChemService, Inc. Chemtec Leuna - Specialty
Chemicals and Fine
Chemicals
China National Chemical
Construction Corporation
Chiragene Corporation ChiRex Ltd. ChiroTech Technology
Limited
Chugai Kasei Co., Ltd. Cilag AG Clariant Corporation Classic Flavors &
Fragrances
CMS Chemicals Ltd --
Carbohydrates
CMS Chemicals Ltd --
Organics
Coalite Chemicals
CreaNova, Inc. (Formerly
Hüls America, Inc.)
CU Chemie Uetikon D&O Chemicals, Inc. D.F. Goldsmith Chemicals
& Metals Co.
Daicel Chemical Industries,
Ltd.
Daikin Industries Ltd Daiso Co., Ltd. Dannier Chemical, Inc. Davos Chemical Corp.
De Voit Associates Deepak Chemicals Group Deepwater Chemicals Degussa Corp.
Diagnostic Chemicals
Limited
Diaz Chemical Corporation
Digital Specialty Chemicals,
Inc.
Dinamite Dipharma SpA
Diosynth b.v. Dishman USA Dixie Chemical Company,
Inc.
DSM Fine Chemicals Inc.
Dynamit Nobel GmbH
Eastman Chemical
Company
Elan Chemical Company,
Inc.
Electron Microscopy
Services
Eastman Chemical
Company
Elan Chemical Company,
Inc.
Electron Microscopy
Services
Elpar International Inc.
EMS Dottikon AG Ernesto Ventos S.A. ERREGIERRE Industria
Chimica S.p.A
Esprit Chemical Company
Eurolabs Limited Exchem Organics Expansia S.A F2 Chemicals Ltd.
.Fabbrica Italiana Sintetici FAR Research Farchemia Division of
Tessenderlo Chemie
Farmak, a.s.
266•ChemACX Participating Vendors
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Fine & Performance
Chemicals Ltd.
Fine Chemicals
Corporation (PTY) Ltd.
Fine Organics Ltd., Seal
Sands
First Chemical Corp.
Fisher Scientific Fluka Fluorochem USA Fluorous Technologies, Inc.
Frinton Laboratories Frontier Scientific, Inc. FrutArom (laboratory
chemicals)
FrutArom Ltd (aroma
chemicals)
FTech, Inc.
Fuji Hunt Specialty
Products
G.J. Chemical Company,
Inc.
Ganes Chemicals Inc.
Gaylord Chemical
Corporation
Gelest Inc. Generichem Corp. Genosys (a Sigma Aldrich
Brand)
Genzyme Pharmaceuticals George Uhe Company, Inc. GFS GNI Chemicals
Corporation
Great Lakes Chemical
Corp.
H&S Chemical Co. Inc. Halocarbon Products Corp. Hokko Chemical Industry
Co., Ltd. - Fine Chemicals
Division
Hovione Group
ICN Biomedical Research
Products
Ihara Chemical Industry
Co., Ltd.
Ihara Nikkei Chemical
Industry Co., Ltd.
Inabata America Corp.
INDOFINE Chemical
Company, Inc.
Industria Chimica Milanese
S.p.A.
Interchem Corp.
ISOCHEM, Groupe
SNPE
Isotec Inc.
ISP Fine Chemicals
(formerly GAF)
J.T. Baker
Jiangsu Institute of
Ecomones
Jost Chemical Jupiter Chemicals, Inc. Jupiter Orga Limited
K-I Chemical Industry
Co., Ltd.
Kaden Biochemicals
GmbH
Kaneka Corporation - Fine
Chemicals Division
Kanto Chemical Co., Inc.
Katwijk Chemie bv Kemira Fine Chemicals Key Organics Limited,
Bionet Research Division
KingChem
Klaus F. Meyer GmbH
KOEI Chemical Company,
Ltd
Kyowa Hakko Kogyo Co.,
Ltd.
Laboratori MAG spa
Lancaster Synthesis Inc.
Laporte Performance
Chemicals (Formerly
Inspec Group)
LC Laboratories, a Div. of
Procyon Pharmaceuticals,
Inc.
Lonza Ltd.
Lumac*LSC B.V.
Lyondell Chemical
Company (formerly ARCO
Chemical Company)
MacFarlan Smith
Mallinckrodt Laboratory
Chemicals
ChemOffice Enterprise Workgroup & Databases 2005 ChemACX Participating Vendors • 267

Marker Gene
Technologies, Inc.
Marshallton Research
Laboratories, Inc.
Matrix Scientific
Maybridge Chemical
Company, Ltd.
Administrator
Menai Organics -
Intermediates
Metall-Chemie Goerrig
GmbH & Co. KG
MillionLink (Tianjin)
International Trade Co.,
Ltd.
Mitchell Cotts Chemicals
Miteni SpA Mitsubishi Rayon Co., Ltd. Mitsui Chemicals, Inc. Molecular BioSciences
Molecular Probes, Inc. Moravek Biochemicals MORFLEX, Inc. Morre-Tec Industries, Inc.
Morton International, Inc. MV Laboratories, Inc. Nanjing Redline Ltd. Neosyn Laboratories Inc.
Nichimen America Inc. NIGU Chemie GmbH Nihon Nohyaku Co., Ltd. NIPA Hardwicke Inc.
Nippoh Chemicals Co.,
Ltd.
Norquay Technology Inc.
USA
Nippon Shokubai Co. Ltd. Nippon Zeon Co., Ltd. Norchim S.A.
NSC Technologies Oakwood Products, Inc. Occidental Petroleum
Corporation
Omega Chemical Co., Inc.
Optima Chemical Group
LLC
ORGANICA Feinchemie
GmbH Wolfen
Organix, Inc.
Orgasynth
Orion Corporation
Fermion
Osaka Organic Chemical
Industry, Ltd.
Palindent Organic
Intermediates
Parish Chemical Company PCAS Peakdale Fine Chemicals
Limited
PepTech Corporation Pfaltz & Bauer, Inc. Pfanstiehl Laboratories,
Inc.
Penn Specialty Chemicals,
Inc.
Pharmaceutical Works
POLPHARMA S.A.
Pharmacia & Upjohn
Company
POLI Industria Chimica
S.P.A.
Pharmco Products Inc. Phoenix Chemicals PNK United, Inc.
PolyCarbon Inds., Inc. PPG-SIPSY Precision Biochemicals,
Inc.
Precursor Chemicals, Inc. Prodotti Chimici e
Alimentari SPA
Quanta Biodesign, Ltd.
Queen's University of
Belfast
R.I. Chemical, Inc. Raschig AG RCA KG (Reuter
Chemische Apparatebau
KG)
Reilly Industries, Inc. RELAX Ltd Reliable Biopharmaceutical
Corporation
Regis Technologies, Inc.
Research Organics
268•ChemACX Participating Vendors
CambridgeSoft

Rhodia Fine Organics Richman Chemical Inc. Riedel-de Haën Robinson Brothers Limited
Rohner Ltd. ROMIL Ltd RSP Amino Acid
Analogues, Inc.
Ruetgers-Nease
Corporation
Ryscor Science, Inc. S.I.M.S. s.r.l. S.K. Chemical Industries Salford Ultrafine Chemicals
& Research Ltd.
Samchully Pharmacy
Company, Ltd.
Sanfur USA, Inc.
Sanochemia Pharmazeutika
AG
Saudi Basic Industries
Corporation
Säurefabrik Schweizerhall Schering AG SEAC Senn Chemicals
Shell Chemical LP Sigma Sigma Aldrich Library of
Rare Chemicals
Sigma Diagnostics (a Sigma
Aldrich Brand)
Silar Laboratories - A
Division of Wright
Corporation
Simafex
Sinochem Hebei Tianjin
Import - Export
Corporation
SK Energy and Chemical,
Inc.
SKW Chemicals
SNPE Chemicals, Groups
SNPE
Soltec Ventures, Inc.
Spectrum Quality Products,
Inc.
Spherotech, Inc.
Stanford
MaterialsCompany
Strem Chemicals, Inc.
Sumikin Chemical Co. Ltd.
Sumitomo Seika
Chemcials Co., Ltd.
Sunoco Chemicals
Supelco (a Sigma Aldrich
Brand)
Supriya Chemicals
SYNCHEM
Laborgemeinschaft OHG
SynChem, Inc. SynQuest Laboratories, Inc. Syntai Chemicals &
Pharmaceuticals, Ltd.
Syntesia Chemie GmbH Synthetech .Synthon Chiragenics
Corporation
Taizhou Kangduo Sea
Biochemical &
Pharmaceutical Co. Ltd.
Takasago International
Corp.
The Shepherd Chemical
Company
Taoka Chemical Co., Ltd. TCI Teva Group API Division
Tocris Cookson Ltd. Tokuyama Corporation Tomah Products, Inc.
Toray Industries, Inc.
Toronto Research
Chemicals, Inc.
Tosoh Corporation
Trans World Chemicals Inc.
Tyger Scientific Inc.
UBE Industries, Ltd. - Fine
Chemicals Division
Ubichem plc
VanDeMark Group
ChemOffice Enterprise Workgroup & Databases 2005 ChemACX Participating Vendors • 269

Varsal Instruments, Inc. VIS Farmaceutici SpA Wacker Chemicals (USA) Wako Pure Chemical
Industries, Ltd.
Administrator
Whyte Chemicals Limited William Blythe Ltd Wilshire Chemical Co., Inc. Wujin Linchuan Chemical
Factory
WYCHEM Limited Yamakawa Chemical Yuhan Corporation Zambon Group
ZENECA Specialties
Zhejiang Kangyu
Pharmaceutical Co., Ltd.
270•ChemACX Participating Vendors
CambridgeSoft

Appendix G: ChemSCX Participating
Vendors
ChemSCX suppliers are listed below:
AsInEx
BIONET Research
Ltd.
Butt Park Ltd
ChemBridge
Corporation
ChemStar, Ltd.
Contact Service
Company -
ReFine(TM)
Collection
Florida Center for
Heterocyclic
Chemistry
G&J Research
Chemicals Ltd
Maybridge Chemical
Company, Ltd.
Menai Organics
Limited
Molecular Diversity
Preservation Intl.
OAK Samples
Trading, Ltd.
Orion Research Ltd. Sherk Chemicals sas Sigma Aldrich Library
of Rare Chemicals
ChemOffice Enterprise Workgroup & Databases 2005 ChemSCX Participating Vendors • 271

Administrator
272•ChemSCX Participating Vendors
CambridgeSoft

ChemOffice Enterprise Workgroup & Databases 2005 ChemSCX Participating Vendors • 273

Administrator
274•ChemSCX Participating Vendors
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Appendix H: Scientific Databases
First Search Tutorial
Browsing a Chemical Database
Browsing a database with ChemFinder is intuitive
and simple. It requires only two basic steps:
1. Opening a Form (which can be thought of as a
viewer for the database)
2. Browsing the database.
Opening a Form in
ChemFinder
First, start the ChemFinder application:
• From your Windows START menu, select
Program Files >ChemOffice2004 >
ChemFinder Net 8.0
ChemFinder launches and an empty form
appears.
5. Click Open.
The CS_demo database opens in ChemFinder
with the first record displayed.
To open a database (e.g. CS_demo):
3. Select Open from the File menu or click the
Open tool.
The open dialog box appears
4. Navigate to …\ChemFinder\samples and
highlight CS_demo.cfw.
Switching Between Open
Documents
Each time you open a form, a form window
appears. If you open more than one form, the form
windows are stacked. The front-most form is the
active window. All open forms are listed in the
Window menu.
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There are several ways to make another open form
the active window:
Administrator
• Select the form from the Window menu.
• Click any exposed area of the window you want
to be active.
• Press CTRL+Tab to switch among the currently
open form windows.
Browsing a Database
One option in viewing a ChemFinder database is to
browse through the database one record at a time,
just as you would turn the pages in a book.
The Record Toolbar contains intuitive tools for
browsing through the database. Try it!
First record
Previous record
Go to record
Next record
Last Record
In addition to browsing through the records, you
can also go directly to a specific record by using the
Go To Record command found in the Record
menu.
1. Select Go To Record from the Record menu,
or click the Go To Record Tool.
The record Number dialog box appears.
By default, the toolbar is docked. If you wish,
however, you can grab it with the mouse and drag it
anywhere on the screen that is convenient.
Alternatively, you can select the corresponding
commands from the Record menu, instead of
using the toolbar.
2. In the Record Number dialog, enter the record
number (within the current list) you want to
display.
3. Click OK.
The specified record is displayed.
The Status Bar
As you browse through records, counters in the
lower right corner of the ChemFinder window
change to indicate the current record, the current
list size, and the total number of records in the
database. The lower left corner of the same window
displays help for menu items and other
information.
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Browsing a Database

When a form is first opened, the current list size
will equal the total database record count. If you do
a search (see : “Scientific Databases First Search
Tutorial”) to find a subset of the entries in the
database, the current list size will change to indicate
the number of hits in the search.
A list window, containing the fields and records
in the form, appears.
To the left of these counters are three other
indicators that show the general status of the
database. The first will display the word READ
when you are using. The second indicator will
display the word ADD when you are entering a new
record. The third will display QRY when you are
entering a query.
NOTE: The ADD indicator is not applicable to CD-
ROM-resident or Read-only databases.
To display a particular record in the form:
• Click the record’s entry in the list window.
To resize the column widths in the Data Table:
4. Place the cursor on the dividers in the top
header.
The cursor changes.
5. Click and drag to adjust the column width.
To hide/show the Status Bar:
• Uncheck Status Bar in the View menu.
The Data Table
Sometimes browsing through a data record set is
more convenient if the data are presented in tabular
format.
To display data in a table:
• Select Data Table from the View menu. You
can change the current window or open a new
one.
To resize the row heights in the Data Table:
6. Place the cursor on the dividers in the left
header.
The cursor changes.
7. Click and drag to adjust the row height.
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Browsing a Database

Administrator
By default, the fields in the data table are displayed
in the order they were created.
To reorder the columns in the Data Table:
8. Click one of the column headers to select the
column.
9. Drag that header to a new position.
12.Select Tile from the Window menu.
The form selected in step 2 appears in the
upper half of the ChemFinder window, and the
data table is in the lower half.
Another convenient method of viewing data is by
displaying a form and data table simultaneously in
Tile layout.
10.If you haven’t done so, open a Data Table view
in a separate window.
11.Click on the Form view to activate it.
NOTE: If the Data Table view window is active (i.e. its
title bar is highlighted), some menu options are not available.
To access these options, first click on the Form view window.
Closing a Form
To close the form you have opened, select Close
from the File menu.
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Browsing a Database

Searching a Chemical Database
Browsing is often a less efficient way to locate
specific information when databases become large.
In such cases it is better to search the database for a
record or data item.
Searching a database is like using the index of a
book. It is easy to quickly focus on the few pages
you are interested in when using an index. Similarly,
when searching a database, you enter search
parameters and only those records that match that
criteria are returned. Once you have this smaller
collection (often called a hit list with each record
found termed a hit), you can browse it much more
efficiently than you could the whole database.
In this tutorial you will learn how to perform the two
basic types of searches:
• Text search
• Structure search
You will also do a combined search.
Performing a Text
Search
Searching by Formula
For our first text example, we’re going to perform a
Formula search:
1. To clear your query form select Enter Query
from the Search menu or click on the
Enter Query tool on the Search toolbar.
The form is cleared to allow you to enter your
search terms. The status indicator in the status
bar is changed to show you have switched to
query mode.
2. Click in the Mol Formula data box, and enter
the query “C6N1-2”, without the quotation
marks, in the Formula box.
This entry specifies a molecular formula having
6 carbon atoms and 1 or 2 nitrogen atoms.
3. Click the Find tool or the Search button.
ChemFinder begins searching.
The progress of the search is indicated by counters
in the status bar at the bottom of the window. When
the search is complete, the number of hits is
displayed in the Current List Size window of the
Status Bar, and the form displays the first hit.
NOTE: If a search returns no hits, an alert appears.
After the alert is cleared, the screen is left in query
mode with the last query shown to allow you to
modify it and try again.
4. Select Data Table from the View menu to
display the hits and verify that the formulas are
correct.
Find
Enter Query
Find current molecule
Save list Over current list
Find list
Retrieve all
Previous query
Restore list
Restore previous list
ChemOffice Enterprise Workgroup & Databases 2005 Scientific Databases First Search Tutorial • 279
Performing a Text Search

Administrator
Searching by name
For our next example, we’ll perform a text search to
find all compounds with molecular names starting
with “benz”.
To perform this text search:
1. Click in your form to activate it.
2. Click the Enter Query button to clear the
query form.
3. Click in the Product Name data box, and enter
the query “benz”, without quotation marks, in
the data box.
4. Click the Find icon or the Search button.
5. Select Data Table from the View menu to
display the hits and verify the molecular names
are correct.
NOTE: Notice that this search returned benzene
but not bromobenzene. The query entered is an
anchored substring and thus will only return strings
starting with the indicated substring. For more
information regarding how to specify text queries,
see “Text Searching” in ChemFinder Help (press
the F1 key).
Searching by Molecular Weight
When performing a numerical search, you can use
exact values or ranges of values to target desired
information. This exercise searches for compounds
whose molecular weights fall within a specified
range.
To search for compounds with molecular weights
between 90 and 100:
1. Click in the form to make it active.
2. Click the Enter Query button to clear the
form.
3. Click the Mol Weight box and enter the query
“90-100” without the quotation marks.
4. Click the Find icon or the Search button.
5. Verify that the molecular weights are correct by
checking the Data Table.
Performing a Structure
Search
To perform a structure search of a ChemFinder
database, a query is entered by drawing the target
structure using the ChemDraw ActiveX ® control.
Structure searches may be used to find compounds
which:
• contain the drawn structure as a substructure
(the default setting)
• are identical to the drawn structure
• are similar to the drawn structure
In this tutorial you will search to find all molecules
containing the propane-2-one (acetone) skeleton as
a substructure.
Using the ChemDraw ActiveX
Control
The first step in performing this substructure search
is to draw a structure query using the ChemDraw
ActiveX control.
Begin as you did for the text search
• To clear your form: select Enter Query from the
Search menu or click on the Enter Query
tool on the Search toolbar.
Now that the form has been cleared:
• Double-click in the Structure/Substructure
box.
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Performing a Structure Search

A blue outline appears around the structure box,
and the ChemDraw ActiveX control appears.
NOTE: If the ActiveX control does not appear, or if
you should accidentally close it, right-click in the
structure box and select View > Show Main Tools.
3. Drag the mouse diagonally upwards to the right
at an angle of about 30 degrees (a message in
the lower left corner of the document window
shows the angle) and release the mouse button
when you have extended the bond to its fixed
length.
2. point 3. drag
NOTE: Right-click in the structure box and select
the Object menu. Fixed Lengths and Fixed Angles
should be checked, as shown below. If either is not
checked, select it in the menu to place a check beside
it.
Next, draw acetone in the Structure window.
1. Click on the solid bond tool in the toolbar.
Next, add a bond:
4. Point to the right atom of the bond.
5. Click the atom to add a bond.
A second bond is automatically deposited at a
120-degree angle between the bonds.
2. Position the pointer (which appears as a cross
when a bond tool is selected) anywhere in the
empty Structure/Substructure window and
hold down the mouse button.
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Performing a Structure Search

4. point 5. click
11.Double-click the atom.
Next, add a second bond:
Administrator
6. Continue pointing to atom C2.
7. Click the atom to add a bond.
10.point
11.double-click
6. point 7. click
Now, change the single bond into a double bond:
12.Type a capital O in the textbox that appears.
To close the textbox, click in an empty area of
the window, press Enter, or click the ActiveX
control to select another tool.
8. Point to C2 and hold the mouse button down.
9. Drag from C2 to C4 over the existing single
bond.
Release the mouse button.
12. type
8. point 9. drag
Next, add labels to the structure. Atom labels can be
added in several ways. One way is illustrated below.
10.Point to the atom shown below.
13.Click outside the Structure box to complete the
structure drawing.
Now that you have drawn acetone in the structure
box, you are ready to perform a search.
NOTE: See the Tutorials in the ChemDraw User’s
Guide for more information on drawing in
ChemDraw.
Searching for the Structure in
ChemFinder
The Search menu offers a number of options. Since
you would like to view all records in the database
containing molecules that have a propane
substructure, you should make sure that the
Substructure option is selected in the Search menu,
and the Similarity option is not selected. These
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Performing a Structure Search

menu items are toggles; each time they are selected
them, the check mark is removed if it was there
already, or added if it wasn’t previously visible.
So, before you commence the search:
1. Enable Substructure from the Search menu.
2. Disable Similarity form the Search menu.
You can also conveniently view the database in
tabular form.
• Select Data Table from the View menu. Open a
Data Table in a separate window.
The Data Table appears and displays all records
in the current list in tabular form.
NOTE: See “Similarity Searching” in
ChemFinder Help (press the F1 key) for more
information.
The Search menu should now look like this:
Click a record in the Data Table to display its records
in your form window.
It is possible to sort records on any field.
To search for structures containing propane:
• Select Find from the Search menu, or click
the Find tool.
In the case of a substructure search, the matched
portion of each molecule is highlighted in red. All
hits are structures that contain a acetone
substructure.
Now, you can browse through these hits.
• Use the Record menu or the Record toolbar to
browse the hitlist (see “Browsing a Chemical
Database” on page 275).
To sort on the ItemNumber field:
• Double-click on the ItemNumber table header
in the Data Table.
After a short pause, the table is sorted by
number.
Close the Data Table by selecting Close from the
File menu.
You can return to the full database at any time. To
retrieve all the records in your database:
• Select Retrieve All from the Search menu or
click the Retrieve All tool.
NOTE: After a search, you do not need to retrieve
all your records before conducting another search;
you can perform another search at any time. Each
search will search over all records in the database.
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Performing a Structure Search

Administrator
Performing a Combined
Search
In some cases, you may wish to combine more than
one type of search to find a specific class of
compounds. For example, you may want to find all
compounds in the database that have a benzene
substructure and that have a molecular weight
greater than 400.
The procedure for this search is similar to the ones
performed previously:
1. With the database open, click in your form to
activate it, then click the Enter Query button.
2. Double-click on the Structure/Substructure
databox.
3. Draw benzene in the window by doing the
following:
a. Click on the Benzene Ring tool.
b. Click in the Structure/Substructure box.
4. Click in the query form somewhere outside the
Structure/Substructure box to complete the
structure.
5. Click the Mol Weight databox and type “>400”
without the quotation marks.
6. Click the Find icon or the Search button.
7. Browse your hit list to verify your hits.
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Performing a Combined Search

i
Index
A
About button
definition 170
server information 185
About, ChemOffice WebServer 2001 167,
187
Administration 78
Audit report, aggregate 82
Audit report, standard 82
Audit trail, analyzing 82
Avery labels, selecting 77
B
Browsing search records 177
Buckminsterfullerenes 236
BuckyBase 236
C
CAS registry number 235
Changing
password for Documentation Manager
6
Changing, results views 176
Check-in/out, Changing Quantities, and
Other Shortcuts 59
ChemACX 213, 217, 229
opening 218
ordering chemicals 223
removing from shopping cart 223
saving search results 219
searching 218
using 217, 227
viewing search results 223
ChemACX-SC 213, 229
Chemical Registration
adding a batch 11
adding a compound 10
defining password 23, 40
deleting a record 13
editing a record 13
identifiers 14, 15
importing sdfiles 25
Log in 10
Log off 31
MatchDatabase 25
new experiments 23
notebooks 18
opening 9
Overview 9
parameter type 25
people 20
printing records 30
projects 17
registering records 13
result type 24
reviewing a record 12
salts 21
searching records 16
sites 21
structure comments 18
temporary table 10
vewing experiment spreadsheets 16
Chemical registration
defining passwords 78
Chemical synthesis database 237, 243
Chemicals database 213, 217, 229
ChemIndex 235
ChemInfo 208
ChemMSDX 233
ChemOffice 208
ChemPrep 237, 238
ChemRXN 237, 243
ChemSelect 238
Clear Form button 170, 171

Administrator
Clearing marked records 178
Client requirements 167, 187
Combination searching 175
Commonly cited reactions 238
Conflict resolution 54
create duplicate 55
edit 55
select 55
Container grid 81
Containers 46, 49
definition 46
editing 49
merging 60
new 49
ordering 61
reordering 62
splitting 60
Creating
a plate map location 67
daughter plates 66
daughter plates by target plate 67
daughter platesby source plate 66
new containers 58
new locations 51
new plates 64
new substances 53
new user accounts 78
plate maps 67
samples 61
Custom fields 80
D
Deleting
locations 52
plates 68
substances 57
Details frame 65
Display preferences settings 169
Documentation Manager
overview 3
password 6
submitting documents 4
Drag-and-drop of containers 59
E
Editing
containers 59
favorite vendors list 219
locations 51
plates 67
substances 56
Element counts 174
Exiting web applications 186
Exporting
search results 183
F
Form view, results 176
Form, see Query Input Form
Forms 48
Formula searching 174
Frame
details 65
list 65
G
Global searches see Searches, global
H
Hits, exporting 183
I
Importing sdfiles into Chemical Registration 25
Index form
ChemACX 226
ChemACX-SC 230
Input form, see Query Input Form
Installation ix, 208
Installation requirements 167, 187
Inventory terminology 45
Inventory, non-chemical 59
L
Labels, printing 76
List frame 65
List View, results 176
Location
definition 46
Location tree 51
Locations 48
editing 48
new 48
updating 62
Locking records 81
ii•Index
CambridgeSoft

Log off
button 170
web applications 186
Logging in 46
M
Macintosh system requirements 167, 187
Managing
an inventory 50
containers 58
locations 50
plates 64
substances 53
the container list display 81
users and roles 78
Marking records 178
MatchDatabase 25
Merge containers 60
Molecular weight searching 175
Moving
locations 52
plates 68
Moving containers 59
Moving containers, with drag-and-drop 59
MSDS database 233
Multi-select 64
N
National Cancer Institute database 241
O
Online help 208
Opening
ChemACX 218
server information 185
Ordering chemicals through ChemACX 223
Overview
Chemical Registration 9
Documentation Manager 3
P
Plates
retiring 68
viewing contents 65
Preferences
button 169
display 184
search 184
Printing 76
labels 76
reports 78
template Wizard 76
Product form
ChemACX 226
ChemACX-SC 230
Q
Query
see also Searching
combination 175
different methods 173
formula 174
molecular weight 175
structure 173
text 173
Query Input form
accessing 218, 249
components 169
opening 218, 249
search preferences 184
using 169
Quitting web applications 186
R
RAM ix
Reaction 184
Record locking 81
Records
clearing marked 178
marking 178
unmarking 178
viewing
all 177
marked 178
Rectifying contents 63
Refining
search results over current records 182
Refreshing the location tree 53
Removing
ChemACX shopping cart 223
Reports, printing 76, 78
Requirements
RAM ix
system ix
ChemOffice Enterprise Workgroup & Databases 2005 Index • iii

Administrator
Requirements, installation 167, 187
Results
changing views 176
exporting 183
form view 176
list view 176
S
Saving
ChemACX search results 219
to Shopping cart 219
Saving a default location 53
sdf file 183
Search button 170
Search Type list 171
Searches
global 74
global, ChemACX substances 75
global, registration system substances 75
global, viewing results 74
simple 69
Searching 68
advanced techniques 70
ChemACX 218
combination search 175
for containers 69
for plates 65, 73
for substances 72
formula search 174
molecular weight search 175
preferences 71
query methods 173
similarity 174
structure search 173
text search 173
using query input form 169
viewing
all records 177
more records 177
results 176
Selecting multiple containers 64
Server information 185
Settings
display preferences 184
search preferences 184
Shopping cart
removing entries 223
saving to 219
viewing 223
Similarity searching 174
Structure searches
exact 71
identity 71
similarity 71
substructure 71
Structure searching 173
Submitting documents 4
Substance
definition 46
Substances 46, 49
new, form 49
select, form 49
Substructure Search see Structure searches
Supplier form
ChemACX 227
ChemACX-SC 230
Supplier Information Form 219
Suppliers
ChemACX-SC 271
Suppliers, adding to ChemACX 227
Synonym management 57
Synthesis database 237, 243
System requirements ix, 167, 187
T
Table view, search results 176
Text Searching 173
ToolTips ix, 208
U
Unmarking records 178
Using
ChemACX 217, 227
query input form 169
Shopping cart 219
V
Version information 185
Viewing
all search records 177
ChemACX shopping cart 223
marked records 178
iv•Index
CambridgeSoft

more search records 177
search results 176
Views, changing 176
W
Web application
logging off 186
quitting 186
Windows system requirements 167, 187
ChemOffice Enterprise Workgroup & Databases 2005 Index • v

Administrator
vi•Index
CambridgeSoft

Desktop Software
Enterprise Solutions
Research & Discovery
Applied BioInformatics
Knowledge Management
Chemical Databases

CAMBRIDGESOFT
ChemOffice Desktop to
KNOWLEDGE
MANAGEMENT
RESEARCH &
DISCOVERY
Desktop
E-Notebook
Enterprise
Discovery
LIMS
Registration
System
Inventory
Manager
Document
Manager
21CFR11
Compliance
Formulations
& Mixtures
Enterprise
WebServer
DESKTOP SOFTWARE
ChemOffice
E-Notebook
ChemDraw
Chem3D
ChemFinder
ChemInfo
ChemOffice WebServer
Oracle Cartridge
Success begins at the desktop, where scientists use ChemDraw and ChemOffice to
pursue their ideas and communicate with colleagues using the natural language of
chemical structures, models, and information. In the lab, scientists capture their
results by organizing chemical information, documents, and data with E-Notebook.
Chem3D modeling and ChemFinder information retrieval integrate smoothly with
ChemOffice and Microsoft Office to speed day-to-day research tasks.
ENTERPRISE SOLUTIONS
Just as ChemOffice supports the daily work of the individual scientist,
enterprise solutions and databases, built on ChemOffice WebServer, and Oracle
Cartridge help organizations collaborate and share information.
KNOWLEDGE MANAGEMENT
E-Notebook Enterprise
Document Manager
Discovery LIMS
21CFR11 Compliance
Research organizations thrive when information is easily captured, well organized,
and available to others who need it. E-Notebook Enterprise streamlines daily record
keeping with rigorous security and efficient archiving, and facilitates searches by text
and structure. Document Manager organizes procedures and reports for archiving
and chemically-intelligent data mining. Discovery LIMS tracks laboratory requests, and
21CFR11 Compliance implements an organization’s regulatory compliance processes.

SOLUTIONS
Enterprise Solutions
APPLIED
BIOINFORMATICS
CHEMICAL
DATABASES
CombiChem
Enterprise
BioAssay
HTS
ChemACX
Database
The Merck
Index
Oracle Cartridge
or SQL DB
BioSAR
Browser
ChemSAR
Properties
Chemical
Databases
RESEARCH & DISCOVERY
Registration System
Formulations & Mixtures
Inventory Manager
CombiChem Enterprise
BioAssay HTS
BioSAR Browser
Managing the huge data streams of new lab technology is a key challenge.
Registration System organizes information about new compounds according to an
organization's business rules, while Inventory Manager works with Registration System
and chemical databases for complete management of chemical inventories.
CombiChem Enterprise and Formulations & Mixtures are also important parts of
research data management.
APPLIED BIOINFORMATICS
Finding structural determinants of biological activity requires processing masses of
biological assay data. Scientists use BioAssay HTS and BioSAR Browser to set up
biological models and visualize information, to generate spreadsheets correlating
structure and activity, and to search by structure.
CHEMICAL DATABASES
ChemACX Database
ChemSAR Properties
The Merck Index
Chemical Databases
Consulting Development
Support & Training
Good research depends on reference information, starting with the structure-searchable
ChemACX Database of commercially available chemicals. The Merck Index 13th
Edition and other databases provide necessary background about chemicals, their
properties, and reactions.
CONSULTING & SERVICES
CambridgeSoft's scientific staff has the industry experience, and chemical and
biological knowledge to maximize the effectiveness of your information systems.

CS ChemOffice
Software Suites
ChemOffice Ultra
ChemDraw Ultra
ChemOffice Pro
ChemDraw Pro
ChemDraw Std
E-Notebook Ultra
Chem3D Ultra
Software
Includes
*ChemDraw Ultra
*ChemDraw Pro
*ChemDraw Std
*ChemDraw Plugin Pro
*Chem3D Ultra
*Chem3D Pro
Chem3D Std
*Chem3D Plugin Pro
*E-Notebook Ultra
ChemFinder Pro
ChemFinder Std
Win/Mac
Win/Mac
Win/Mac
Win/Mac
Win
Win
Win
Win
Win
Win
Win
Applications & Features
ChemDraw/Spotfire
*BioAssay Pro
Purchase/Excel
CombiChem/Excel
ChemFinder/Office
ChemDraw/Excel
Name=Struct
Struct=Name
ChemNMR
CLogP/ChemDraw
BioArt
Structure Clean Up
Polymer Draw
LabArt
ChemSAR/Excel
3D Query
MOPAC/Chem3D
GAMESS Client
Gaussian Client
Tinker/Chem3D
*CAMEO/ChemDraw
Win
Win
Win
Win
Win
Win
Win/Mac
Win/Mac
Win/Mac
Win/Mac
Win/Mac
Win/Mac
Win/Mac
Win/Mac
Win
Win
Win
Win
Win
Win
Win
Databases
*The Merck Index
*ChemACX Ultra
ChemSCX
ChemMSDX
*ChemINDEX Ultra
ChemRXN
NCI & AIDS
*Available Separately
Win
Win
Win
Win
Win
Win
Win

Desktop to Enterprise Solutions
ChemOffice Ultra includes it all, providing
ChemDraw Ultra, Chem3D Ultra, E-Notebook
Ultra, ChemFinder, CombiChem, BioAssay and
The Merck Index, for a seamlessly integrated suite
for chemists.Use ChemDraw/Excel and ChemFinder/
Word for Microsoft Office integration. Predict spectra,
use Name=Struct, and visualize 3D molecular surfaces
and orbitals with MOPAC. Use the ChemDraw and
Chem3D Plugins to publish your work or to query
databases on the web.
ChemOffice WebServer enterprise solutions and databases help
organizations collaborate on shared information with ChemDraw webbased
interface and Oracle Cartridge security.
Knowledge Management with E-Notebook Enterprise streamlines
daily record-keeping with rigorous security and efficient archiving.
Document Manager indexes chemical structure content of documents
and folders.
Research & Discovery efforts are improved with Registration System
by organizing new compound information, while Inventory Manager
works with chemical databases for complete management of chemical
inventories.
Applied BioInformatics scientists use BioAssay HTS and BioSAR
Browser to set up biological models and visualize information, to generate
spreadsheets correlating structure and activity, and to search by structure.
Chemical Databases include the ChemACX Database of commercially
available chemicals, The Merck Index 13th edition, and other databases.
Consulting & Services includes consulting development, technical
support, and education training for pharmaceutical, biotechnology, and
chemical customers, including government and education, by
CambridgeSoft’s experienced staff.
ChemOffice WebServer
Enterprise Solutions & Databases
• Oracle Cartridge & Database Webserver
Knowledge Management
• E-Notebook Enterprise, Document Mgr,
Discovery LIMS & 21CFR11 Compliance
Research & Discovery
• Registration System, Formulations & Mixtures,
Inventory Manager & CombiChem Enterprise
Applied BioInformatics
• BioAssay HTS & BioSAR Browser
Chemical Databases
• The Merck Index, ChemACX & ChemSAR Properties
ChemOffice Ultra
Ultimate Drawing, Modeling & Information
• Adds The Merck Index, E-Notebook, CombiChem,
MOPAC, BioAssay & ChemACX to Office Pro
ChemOffice Pro
Premier Drawing, Modeling & Information
• Includes ChemDraw Ultra, Chem3D Pro,
ChemSAR/Excel, ChemFinder Pro,
ChemINDEX & ChemRXN databases
Also Available Separately…
ChemDraw Ultra
Ultimate Drawing, Query & Analysis
• Adds ChemDraw/Excel, ChemNMR, Name=Struct,
AutoNom & ChemFinder /Word to ChemDraw Pro
• ChemNMR, Stereochemistry, Polymers & BioArt
ChemDraw Pro
Premier Drawing & Database Query
• Define complex database queries
• ISIS/Draw & Base compatible via copy/paste
• Structure CleanUp and Chemical Intelligence
Chem3D Ultra
Ultimate Modeling, Visualization & Analysis
• Adds MOPAC, CLogP, Tinker, ChemProp,
ChemSAR & Chem3D Plugin to Chem3D Pro
• Advanced modeling & molecular analysis tool
E-Notebook Ultra
Ultimate Journaling & Information
• E-Notebook, ChemDraw Std, Chem3D Std,
ChemDraw/Excel & CombiChem/Excel
• Includes ChemFinder, ChemFinder/Word,
ChemINDEX & ChemRXN databases
Some features are Windows only.
All specifications subject to change without notice.

DESKTOP
CS E-Notebook
Electronic Journal J
and Information
E-Notebook Ultra streamlines daily record keeping tasks of research scientists, maintains live chemical
structures and data, and saves time documenting work and retrieving chemical information. E-Notebook combines
all of your notebooks into one and sets up as many project notebooks as you need, organized the way you
work. Notebook pages include ChemDraw documents, Excel spreadsheets, Word documents and spectral data.
E-Notebook automatically performs stoichiometry calculations on ChemDraw reaction pages. Search by structure,
keyword, dates and other types of data. Maintain required hardcopy archives by printing out pages.
Information cannot be accidentally modified. Spectral controls from Thermo Galactic are available.
CombiChem/Excel builds combinatorial libraries with embedded ChemDraw structures using
ChemDraw/Excel for Windows. Find reagents with ChemFinder and design experiments.
BioAssay Pro, available in ChemOffice Ultra, allows for flexible storage and retrieval of biological data. It
is designed for complex lead optimization experiments and supports almost any biological model.
Automatic
Stoichiometric
Calculations
Scanned Images in
Notebook Pages

SOFTWARE
E-Notebook Ultra
Ultimate Journaling & Information
• Advanced search and structure query features
• Stores structures and models for easy retrieval
• Stores physical and calculated data
• Search by substructure, including stereochemistry,
using ChemDraw
• Search and store chemical reaction data
• CombiChem/Excel combinatorial libraries
• Integration with ChemDraw and Chem3D
• Import/export MDL SD & RD files
CombiChem/Excel
Combinatorial Chemistry in Excel
• Generate combinatorial libraries
•Choose starting materials & reaction schemes
•View structures & track plate/well assignments
ChemFinder Pro
Premier Searching & Information
• Advanced search & structure query features
• Stores structures & reactions along with calculated data & associated information
• Search by substructure including stereochemistry using ChemDraw
• Integration with ChemDraw & Chem3D
•Import/export MDL SD & RD files
ChemInfo Std
Reference & Reaction Searching
• ChemINDEX for small molecule information
• ChemRXN for reaction databases
BioAssay Pro
Biological Assay Structure Activity
• Set up biological models & visualize information
• Search data by structure to isolate key structural determinants of biological activity
•Tabulate & analyze structure-activity relationships with spreadsheet templates
•Available in ChemOffice Ultra
SYSTEMS & LANGUAGES
English & Japanese
Windows: 95, 98, Me, NT, 2000, XP
This software is Windows only.
All specifications subject to change without notice.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

DESKTOP
CS ChemDraw
Chemical Structure Drawing Standard
ChemDraw Ultra adds ChemDraw/Excel, ChemNMR, Name=Struct, Beilstein’s AutoNom, CLogP and
ChemFinder/Word to ChemDraw Pro. With rich polymer notation, atom numbering, BioArt templates, and
modern user interface, ChemDraw is more powerful than ever before. Create tables of structures, identify and
label stereochemistry, estimate NMR spectra from a ChemDraw structure with structure-to-spectrum
correlation, obtain structures from chemical names, assign names from structures, and create multi-page
documents and posters.
ChemDraw Pro will boost your productivity more than ever. Draw publication-quality structures and
reactions. Publish on the web using the ChemDraw Plugin. Create precise database queries by specifying atom
and bond properties and include stereochemistry. Display spectra, structures, and annotations on the same
page. Use the Online Menu to query ChemACX.Com by structure, identify available vendors, and order online.
Stereochemistry
Structure-to-Spectrum
NMR Correlation

SOFTWARE
ChemDraw Ultra
Ultimate Drawing, Query & Analysis
• Adds ChemDraw/Excel, ChemNMR, Name=Struct,
AutoNom & ChemFinder/Word to ChemDraw Pro
• Name=Struct/AutoNom creates structures from
names & vice versa
• ChemNMR predicts 1 H & 13 C NMR line spectra
with peak-to-structure correlation
• Polymer notation based on IUPAC standards
• ChemDraw/Excel brings chemistry to Excel
ChemDraw Pro
Premier Drawing & Information Query
• Query databases precisely by specifying atom & bond properties, reaction centers,
substituent counts, R-groups & substructure
• Read ISIS files with Macintosh/Windows cross-platform compatibility
• Structure Clean Up improves poor drawings
• Display spectra from SPC and JCAMP files
• Chemical intelligence includes valence, bonding & atom numbering
• Right-button menus speed access to features
ChemDraw Std
Publication Quality Structure Drawing
• Draw and print structures & reactions in color,
and save as PostScript, EPS, GIF, SMILES & more
• Collections of pre-defined structure templates
• Large choice of bonds, arrows, brackets, orbitals, reaction symbols & LabArt
• Style templates for most chemical journals
• Compatible with Chem3D, ChemFinder, ChemInfo, E-Notebook & Microsoft Office
ChemDraw Plugin
Advanced WWW Structure Client
• Embed live ChemDraw documents in WWW pages
•Works with Netscape & Internet Explorer
• Included with ChemDraw Ultra & Pro
SYSTEMS & LANGUAGES
Windows & Macintosh English, Japanese, French, German
Windows: 95, 98, Me, NT, 2000, XP
Macintosh: MacOS 8.6-10.1
Some features are Windows only.
All specifications subject to change without notice.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

DESKTOP
CS Chem3D
Molecular Modeling and Analysis
Chem3D Ultra includes MOPAC, Tinker and set-up/control interfaces for optional use of GAMESS and
Gaussian. Estimate advanced physical properties with CLogP and ChemProp, and create SAR tables using
property servers to generate data for lists of compounds. Use ChemSAR/Excel to explore structure activity
relationships and use add-on Conformer for conformational searching. Publish and view models on the web
using the Chem3D Plugin.
Chem3D Pro brings workstation quality molecular visualization and display to your desktop. Convert
ChemDraw and ISIS/Draw sketches into 3D models. View molecular surfaces, orbitals, electrostatic potentials,
charge densities and spin densities. Use built-in extended Hückel to compute partial atomic charges. Use MM2
to perform rapid energy minimizations and molecular dynamics simulations. ChemProp estimates physical
properties such as logP, boiling point, melting point and more. Visualize Connolly surface areas and
molecular volumes.
Molecular Modeling & Analysis
Large Molecular
Visualization

SOFTWARE
Chem3D Ultra
Ultimate Modeling, Visualization & Analysis
• Adds MOPAC, CLogP, Tinker, ChemProp,ChemSAR
& Chem3D Plugin to Chem3D Pro
•Includes GAMESS & Gaussian client interfaces
• ChemSAR/Excel builds SAR tables
Chem3D Pro
Premier Modeling, Visualization & Analysis
•Create 3D models from ChemDraw or ISIS Draw, accepts output from other modeling packages
• Model types: space filling CPK, ball & stick, stick, ribbons, VDW dot surfaces & wire frame
• Compute & visualize partial charges, 3D
surface properties & orbital mapping
• Polypeptide builder with residue recognition
• ChemProp—Basic property predictions with Connolly volumes & surface areas
• MM2 minimization & molecular dynamics, extended Hückel MO calculations
• Supports: PDB, MDL Molfile, Beilstein ROSDAL, Tripos SYBYL MOL, EPS, PICT, GIF, 3DMF, TIFF, PNG & more
MOPAC/Chem3D
Advanced Semi-Empirical Computation
• Calculate ∆H f , solvation energy, dipoles, charges, UHF & RHF spin densities, MEP, charge densities & more
• Optimize transition state geometries
• AM1, PM3, MNDO & MINDO/3 methods
CAMEO/ChemDraw
Synthetic Reaction Prediction
• Expert system predicts and displays products
• ChemDraw creates starting materials when you choose reaction conditions; sold separately
Chem3D Plugin
Advanced WWW Model Client
•Works with Microsoft Internet Explorer
•Visualize 3D molecules on ChemFinder.Com
SYSTEMS & LANGUAGES
Windows & Macintosh English & Japanese
Windows: 95, 98, Me, NT, 2000, XP
Macintosh: MacOS 8.6-9.2.X
Some features are Windows only.
All specifications subject to change without notice.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

DESKTOP
CS ChemFinder
Searching and Information Integration
ChemFinder Pro is a fast, chemically intelligent, relational database search engine for personal, group or
enterprise use. Extended integration with Microsoft Excel and Word adds chemical searching and database
capability to spreadsheets and documents.
An ever-increasing number of chemical databases are available in ChemFinder format. Compatibility with MDL
ISIS databases is provided by SDfile and RDfile import/export. ChemFinder provides network server workgroup
functionality when used with ChemOffice WebServer.
ChemFinder/Word is an extension of Microsoft Excel and Word for Windows. Create structure searchable
spreadsheets and index documents with embedded ChemDraw structures.
ChemDraw/Excel adds chemical intelligence to Microsoft Excel for Windows. Show structures in spreadsheet
cells, tabulate chemical calculations and analyze data with Excel functions and graphs.
Purchase/Excel uses ChemDraw/Excel to manage reagent lists and track purchasing information.
CombiChem/Excel builds combinatorial libraries with embedded ChemDraw structures using
ChemDraw/Excel for Windows. Find reagents with ChemFinder and design experiments.
ChemDraw/Excel
Search Chemical
Databases

SOFTWARE
ChemFinder/Word
• Search structures in documents & folders
ChemDraw/Excel
• Add chemical intelligence to spreadsheets
Purchase/Excel
•Organize chemical purchasing information
ChemFinder Pro
Premier Searching & Information
• Advanced search and structure query features
• Stores structures and reactions along with calculated data and associated information
• Search by substructure including stereochemistry using ChemDraw
• Import/export MDL SD and RD files
• Integration with ChemDraw and Chem3D
ChemFinder/Word
Searching Word, Excel & More
• Searches documents for embedded structures
• Indexes structures and source locations
• Searches specified folders and whole hard drives
ChemDraw/Excel
Searching & Calculating in Excel
• Displays ChemDraw structures in spreadsheet cells
• Adds chemical calculations to Excel functions
• Useful for graphing and analyzing chemical data
Purchase/Excel
High Throughput Purchasing
• Finds vendor and price information from ChemACX Database or ChemACX.Com
• Search for suppliers and purchase online
• Maintains lists of compounds
CombiChem/Excel
Combinatorial Chemistry in Excel
• Generate combinatorial libraries
•Choose starting materials and reaction schemes
•View structures and track plate/well assignments
SYSTEMS & LANGUAGES
English & Japanese
Windows: 95, 98, Me, NT, 2000, XP
This software is Windows only.
All specifications subject to change without notice.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

DESKTOP
CS ChemInfo
Reference and Chemical Databases
The Merck Index is an encyclopedia of chemicals, drugs, and biologicals, with over 10,000 monographs
covering names, synonyms, physical properties, preparations, patents, literature references, therapeutic uses
and more.
ChemACX Pro includes 500,000 chemical products from 300 supplier catalogs, searchable with a single
query by structure, substructure, name, synonym, partial name, and other text and numeric criteria.
ChemACX-SC is a compilation of searchable catalogs from leading screening compound suppliers.
ChemACX.Com is the ChemACX web site with full search capabilities and convenient online ordering
from major suppliers.
ChemINDEX includes 100,000 chemicals, public NCI compounds, and more.
ChemRXN is a collection of 30,000 fully atom-mapped reactions selected and refined from the chemical
literature. It includes reactions from InfoChem’s ChemSelect database and ISI’s ChemPrep database.
ChemMSDX provides material safety data sheets for 7,000 pure compounds.
ChemFinder.Com is the award-winning web site with information and WWW links for over 100,000
chemicals. Search by name or partial name, view structure drawings, or use the ChemDraw Plugin for structure
and substructure searches. View live ChemDraw files on Windows and Macintosh clients.
ChemRXN database
on CD-ROM
ChemINDEX database on
ChemFinder.Com

SOFTWARE
The Merck Index
• Encyclopedic chemical reference
ChemACX Pro
• Chemical searching & buying
The Merck Index
Chemistry’s Constant Companion
• Over 10,000 monographs of chemicals, drugs & biologicals
ChemACX Pro
Chemical Searching & Buying
• Database of commercially available chemicals: 300 catalogs with 500,000 chemical products
• ChemACX-SC database with 500,000 structures from leading screening compound suppliers
ChemACX.Com
WWW Chemical Searching & Buying
• Search by text, structure or substructure and order online from major catalogs
ChemINDEX
Reference Searching & Information
• NCI database of over 200,000 molecules, with anti-HIV & anti-cancer assay data
ChemRXN
Reaction Searching & Information
•Includes ChemSelect with reactions from InfoChem GmbH & ISI’s ChemPrep
ChemMSDX
Safety Data Searching & Information
•Provides full Material Safety Data Sheets for over 7,000 pure compounds
ChemFinder.Com
WWW Reference Searching & Info
• WWW links for over 100,000 compounds
• Enter text queries or use ChemDraw Plugin for structure & substructure searching
•Works with Netscape & MS Internet Explorer
SYSTEMS & LANGUAGES
English & Japanese
Windows: 95, 98, Me, NT, 2000, XP
CD-ROM software is Windows only.
All specifications subject to change without notice.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

ENTERPRISE
ChemOffice WebServer
Enterprise Solutions, Applications and Databases
ChemOffice WebServer
ChemOffice WebServer is the leading solution platform for enterprise, corporate intranet, and Internet scientific
information applications. Compatible with major databases including Oracle, SQL Server, and Microsoft
Access, ChemOffice WebServer is the development and deployment platform for custom applications and those
listed below.
ChemOffice Browser
ChemOffice Browser, including ChemDraw Java, ActiveX, and the ChemDraw and Chem3D Plugins, brings the
power and chemical intelligence of ChemOffice to Internet and intranet applications.
User Friendly & IT Ready
User-friendly and IT ready ChemOffice WebServer and Browser enterprise solutions, applications and databases
are easier and faster for users to learn and the IT staff to deploy. Using ChemOffice WebServer technology,
along with familiar browser technology, overall costs are lowered and less time is required for implementation.
Enterprise Solutions
Enterprise solutions built upon ChemOffice WebServer, including Oracle Cartridge, help workgroups and
organizations collaborate and share information, just as ChemOffice supports the daily work of the scientist.
Browse Detailed
Compound Information
Easy Management
of Search Results

SOLUTIONS
•Development and deployment platform for workgroup
and enterprise chemical information applications
•Webserver and browser components facilitate
application deployment to desktops with minimal
impact and training
• Enterprise Solution applications address areas of
Knowledge Management, Research & Discovery,
Applied BioInformatics and Chemical Databases
Knowledge Management
Knowledge Management applications organize and distribute chemical information. E-Notebook Enterprise
streamlines daily record keeping with rigorous security and efficient archiving, and facilitates information
retrieval by structure and text searching. Document Manager indexes the chemical structure content of documents,
Discovery LIMS tracks laboratory requests, and 21CFR11 Compliance implements an organization’s regulatory
compliance processes.
Research & Discovery
Research and discovery applications include Registration System for managing proprietary compound information,
Inventory Manager for reagent tracking needs, and chemical databases for complete management of chemical
inventories. Formulations & Mixtures and CombiChem Enterprise also provide tailored approaches to managing
chemical data.
Applied BioInformatics
BioAssay HTS and BioSAR Browser applications process biological assay data to pinpoint the structural determinants
of biological activity. BioAssay HTS supports low, high, and ultra-high throughput workflow, including
sample and plate management, while BioSAR Browser probes structural details within assay data.
Chemical Databases
The Merck Index and ChemACX Database provide reference information, property estimations, and searchable
compilations of commercially available chemicals.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

ENTERPRISE
Oracle Cartridge
Enterprise Infrastructure for Database Security
WebServer Oracle Cartridge
In scientific applications, the ability to store and manipulate chemical information is essential. By using
CambridgeSoft’s Oracle Cartridge, you add chemical knowledge to your Oracle platform and automatically
take advantage of Oracle’s security, scalability, and replication without any other external software or programs.
You can search the chemical data by structure, substructure, and similarity, including options for stereo-selectivity,
all through extensions to Oracle’s native SQL language. Tools like PowerBuilder, Visual Basic and Visual
C++ readily lend themselves as database clients. With the addition of the ChemDraw ActiveX control in the client,
your end users can be structure-searching in no time.
Chemical Data Formats
CambridgeSoft recognizes that there is an enormous amount of legacy data out there in a myriad of formats,
and most users have no desire to make wholesale changes to their chemical data generation or storage. To this
end, Oracle Cartridge supports all major data types without translation or modification. In addition to CDX,
it supports CDXML, MolFile, Rxn, and SMILES formats. Moreover, there are built-in extensions to SQL that
allow you to extract data in all supported formats. Due to the variety of data formats supported, Oracle
Cartridge is easily deployed even within existing applications. Since no manipulation of the data is needed, new
records are automatically added to the index for searching.
Simple Client-Server
Architecture
Web Based
Architecture

SOLUTIONS
•Adds chemical data types to Oracle, linking chemical
applications to enterprise software systems without
special programming
• Confers Oracle’s security and scalability, simplifying
large-systems’ architectural considerations
•Makes legacy chemical data, such as MDL ISIS,
accessible to ChemOffice WebServer applications
WebServer Enterprise Solutions
Even if you’re not developing your own applications, or interested in the advanced data portability aspects of
the Oracle Cartridge, CambridgeSoft’s strategy will have a positive benefit for your IT infrastructure.
CambridgeSoft’s enterprise solutions are available in Oracle Cartridge versions, including E-Notebook Enterprise,
Document Manager, Registration System, Inventory Manager, and BioAssay HTS. By utilizing Oracle Cartridge,
you can deal with issues such as scalability and security entirely through the database layer, simplifying largesystems’
architectural considerations. Oracle Cartridge has the side benefit of providing a database-level interface
to key applications, so developers can integrate CambridgeSoft’s solution platform with in-house IT solutions
without tinkering with the business tier. Communicating with Oracle Cartridge is as simple as learning a few
extensions to SQL.
Systems & Support
Support extends to include a variety of UNIX operating systems in addition to Windows servers. Oracle
Cartridge has been deployed by large pharmaceutical companies with Oracle 8i and 9i.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

KNOWLEDGE
E-Notebook Enterprise
Desktop to Enterprise Knowledge Management
E-Notebook
E-Notebook provides a smooth web-based interface designed to replace paper laboratory notebooks, with a fully
configurable, secure system for organizing the flow of information generated by your organization. You can enter
reactions, Microsoft Word documents, spectra and other types of data, and then search this data by text, substructure
or meta-data. You can organize your electronic pages by projects, experiments or any other classification
that conforms to your workflow.
Desktop to Enterprise
E-Notebook allows organization of notebook pages at either the personal or enterprise level. Enterprise groups can
organize and store notebook pages in a central data repository, allowing colleagues to take advantage of each
other’s work. All access to data is subject to granular security. E-Notebook works with Oracle Cartridge and SQL
Server, for departments or entire enterprises, and Microsoft Access, for individuals or small groups.
ChemDraw & Stoichiometry Calculations
While not quantum theory, stoichiometric calculations remain long and tedious. E-Notebook tackles this troublesome
problem. First, draw your reaction directly in the page. Then, simply enter the mass, volume and den-
Automatic Stoichiometric Calculations
Scanned Images in
Notebook Pages

MANAGEMENT
•Custom organization of notebook pages at personal
or enterprise levels with links to chemical registration
•Notebook pages include ChemDraw reaction schemes,
Microsoft Word and Excel documents, and spectral
data using the Galactic Spectral Control
• Oracle Cartridge provides detailed security and data
integrity; SQL Server also available
sity, volume and molarity, and other factors of the limiting reagent and specify the number of equivalents of the
other reactants. The notebook will do everything except calculate the experimental yield. To do that, you still
have to run the experiment!
Microsoft Office & Galactic Spectra
E-Notebook manages all the other kinds of data chemists store in their notebooks. For free-form data, you can
include Microsoft Word or Excel documents. For spectral data, you can take advantage of the Galactic Spectral
Control embedded in the notebook that allows for analysis and storage of hundreds of kinds of spectra files.
Inventory Manager
E-Notebook includes an inventory of common reactants and reagents. If you have one of these common components
loaded into the inventory application, all you have to do is click the Add Reactant button in
E-Notebook. From here, you navigate to the desired compound and include it in your stoichiometry calculations.
The enterprise edition of E-Notebook integrates with procurement and inventory management systems.
Not only does this provide a useful way to know what compounds you have in stock and where they are located,
it also saves time entering data.
Registration System
E-Notebook can be integrated into the entire chemical workflow of enterprise organizations. For example, once
you record a reaction in your notebook, you can click a button to forward the products of the reaction to your
compound registration system. These kinds of workflow enhancements increase productivity for the entire
organization.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

KNOWLEDGE
Document Manager
Desktop to Enterprise Document Searching
Document Manager
Everyone produces reports electronically, but searching information located in these reports has always been
difficult. Thousands of Microsoft Word, Excel, PowerPoint, and other documents reside on file servers or individual
computers, with no way to globally search them for information. Certainly, no easy way exists to search
for the chemistry contained in these documents. Document Manager solves this problem, and requires no
change in how you write and distribute reports.
Easy to Use
Document Manager manages a repository of new documents. These can be Microsoft Word, Excel, PowerPoint,
or many other document types. When a new document is added, Document Manager automatically builds a
free-text index of the document, and automatically extracts the chemical information into a chemically-aware,
substructure searchable database. Chemical information can be both ChemDraw and ISIS/Draw. Finding information
in reports is now as simple as entering a query through your web browser.
Unattended Data Indexing
As new documents are added they are automatically indexed and chemical information is extracted. Similarly, if
a document is modified, it is re-indexed. No administration of the server is necessary other than routine back-up.
Unattended Data
Repository Indexing
Search Documents
by Structure

MANAGEMENT
• Indexes chemical structure information in documents and
compiles a structure-searchable database
• Monitors designated folders or drives and automatically
indexes new documents as they appear
• Documents are searchable by structure and free text
Free Text Searching
Documents are searchable by free text, including Boolean expressions, proximity operators, or simple queries.
For example “author near Saunders” finds all Word documents where the word “author” appears near the word
“Saunders”.
Advanced Chemical Searching
Since the chemical information is automatically extracted, documents can be queried by structure, substructure,
similarity, molecular weight and formula. Chemical queries also support atom lists, Boolean operations
on structures, superatoms, functional groups and many others. Queries can also be refined after an initial
search, extending the power of the query language.
Structured Document Support
Structured documents, including documents created with Word templates or XML, are also supported.
Information in structured documents is extracted and stored in specific fields of the database for more precise
searching.
ChemFinder/Word
ChemFinder/Word, the desktop version, searches Word documents, Excel spreadsheets, ChemDraw files,
ChemFinder databases, SD files, MDL molfiles, and more. Unlike other Microsoft Find facilities,
ChemFinder/Word lets you work with the results you’ve located. Once you have a hit list, you can browse,
search, refine, or export it to any destination.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

KNOWLEDGE
21CFR11 Compliance
Electronic Records and Signatures Regulations
The Challenge
Large and growing enterprises are facing a challenge to their core missions of developing and producing new
products including food, therapeutic pharmaceuticals, medical devices, cosmetics or other health enhancing
items. The complexity lies in complying with government regulations designed to protect public health and
safety. The most notable of these is Title 21 of the Code of Federal Regulations governing Electronic Records
and Signatures (21CFR11). Although 21CFR11 has been in the draft stage for almost a decade, final regulations
have recently been created. Enforcement of these regulations is beginning to take place and enterprises are
responding with a wide variety of initiatives, both within individual organizations and across industry sectors.
Integrated Software
CambridgeSoft applications, such as E-Notebook Enterprise and Document Manager, are at the leading edge of
the integration of corporate knowledge management with 21CFR11 Compliance. These products are designed so
that as your organization reviews its internal processes for 21CFR11 Compliance, the software can be configured
to support these internal processes. Major requirements of 21CFR11, such as electronic signatures, audit trails,
and long-term archiving, are incorporated within the routine workflow to generate the critical information
required by research, development and production. In addition, E-Notebook Enterprise and Document Manager
can be integrated with existing critical data systems.
Document and
Record Management
E-Notebook Data Capture

MANAGEMENT
• E-Notebook Enterprise and Document Manager
integrate corporate knowledge with regulatory
compliance
• Consulting teams analyze and adapt existing
procedures to comply with new regulations
• Systems include authentication and digital signatures
and adapt to changing regulations and demands
Analysis
As your enterprise develops the operating procedures that you will need to adopt for 21CFR11 Compliance,
CambridgeSoft’s consulting team can provide invaluable assistance in analyzing your current operating procedures,
adapting your existing procedures to comply with new regulations, and validating the software and the
operating procedures that you will use. CambridgeSoft’s consulting teams consist of individuals who have
extended experience in deploying systems used by large pharmaceutical companies, emerging biotechs, and
major enterprises worldwide.
Implementation
Once you have determined how your enterprise will comply with these new regulations, implementing those
decisions needs to be done quickly, efficiently and with the understanding that the rules for compliance are in
flux. In order to succeed, you must be able to respond to change. CambridgeSoft’s 21CFR11 Compliance consulting
has both the tools and the expertise to provide complete solutions, carry out integration with your existing
systems, and help you execute the process as quickly as your organization demands. Since ongoing monitoring
is a part of business for regulated industries, you can be confident that, as regulations evolve and your
requirements change, your systems can adapt. With CambridgeSoft, you can take advantage of the knowledge
that has helped dozens of businesses, large and small, gain control over their business processes, their
intellectual capital, and their material resources.
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ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

RESEARCH
&
Registration System
Chemical and Biological Registration
Registration System
Registration System includes a robust data model for pure compounds, batches, salt management, automatic
duplicate checking and unique ID assignments. Compounds may be entered individually or with SD files. The
data model resides entirely in Oracle and uses Oracle’s security and transaction framework. For companies
intending to modify or construct their own registration system, ChemOffice WebServer includes a powerful
Software Developer’s Kit (SDK) to add custom functionality. Instead of inventing a proprietary language,
ChemOffice WebServer SDK extends the Microsoft and Oracle platforms, allowing information scientists to use
the industry’s most powerful development tools.
ChemDraw Plugin & WebServer
Registration System is easily adapted in almost any work environment. Its web-based, industry standard
ChemDraw interface, makes ChemOffice WebServer the best choice for your corporate scientific information.
User Friendly Chemical Registration
New compounds are entered through a web form, and chemical, along with non-chemical, data is kept in a
temporary storage area. When the compound is registered, it is compared for uniqueness via a configurable,
stereoselective duplicate check, and assigned a registry number. All information about the compound, including
its test data and other syntheses, is tracked by the registry number.
Display & Format Results
Search for a Compound

DISCOVERY
• Accessed through your favorite web browser, the
system uses Oracle with robust data model to manage
chemical products and their properties
• Checks for uniqueness during registration and optionally
registers duplicates as batches of existing substance
• User administration and data entry are done through
simple, easy-to-learn web forms; highly configurable
system avoids tedious and expensive customization
Duplicate Checking with Override
When compounds are registered, the structure is checked for novelty. If a duplicate already exists in the database,
the user can elect to register the information as a new batch of the existing compound, or assign it a
unique registry number.
Oracle Cartridge
Registration System is the only true n-tiered application of its kind that is designed around thin clients and thin
servers. This translates into ultimate flexibility on both the client and server side. Oracle is supported as a host,
both with native security, on a variety of platforms and operating systems. The chemical information is directly
stored in the Oracle tables.
Web Based User Interface
While the business logic of Registration System is complex, its user interface is clean and simple. Web browser
support for Netscape Navigator and Internet Explorer, plus a choice of ChemDraw Plugin, ActiveX or Java
client tools are provided. This significantly reduces training time and cost of client maintenance.
Advanced Chemistry Features
Duplicate checking is stereochemically aware. Batch data is maintained separately from compound data.
Registration numbers support multiple sequences, including one for synthesized and one for procured.
Compounds can be tracked by project and notebook reference, and registered in batches from SD files or other
sources of molecular information.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

RESEARCH
&
Inventory Manager
Chemical and Biological Inventory Integration
Database Technology
Inventory Manager is a ChemOffice WebServer based application designed to manage the reagent tracking needs of
chemical and pharmaceutical research centers. The system manages data associated with both commercially
and internally produced chemical substances. Although Inventory Manager is a stand-alone application, it can
be tightly integrated with CambridgeSoft’s Registration System and chemical procurement ChemACX Database.
Inventory Manager is designed for a range of sizes from large workgroups to enterprises, and captures both
stockroom and reagent needs as well as high-throughput discovery.
Cascading Location Model
Inventory Manager has a fully cascading location model. This means that laboratories can decide for themselves
the granularity of their locations. Some labs may define locations as wells on plates residing on shelves inside
refrigerators, which, in turn, are found in laboratories. Another lab may decide to track reagents at the bench
or cabinet level. Still, in other settings, it may suffice to track chemicals on a lab-by-lab basis. The moving of
chemical inventories is greatly helped by this model. For example, if an entire refrigerator is relocated, all of its
containers move along with it. There is no need to re-catalog or reconcile, which saves a great deal of time.
Substructure Search
Form
Viewing Information
by Container

DISCOVERY
• Integrated with Registration System and ChemACX
for procurement and life cycle chemical tracking
• Cascading location model allows different labs to track
reagents at different levels (stockroom, refrigerators)
• Designed for tracking reagents, high-throughput
discovery libraries, and true HTS plate management
at multiple levels
Discovery, Reagents & Stockroom
Inventory Manager integrates fully with CambridgeSoft’s ChemACX Database of available chemicals and
Registration System. It also functions completely as a stand-alone application. Through this architecture,
CambridgeSoft’s enterprise solutions are truly plug-and-play. There are no added system integration costs, and
the applications can live on different servers in different parts of the world.
Flexibility
The flexibility of the location model allows Inventory Manager to accommodate both reagent and discovery
inventories in the same system. Each container in the system can be configured to track quantities in increasingly
small values. A reagent bottle, for instance, can be measured as “full” or “empty”, while wells in a 96-well
plate can be measured in microliters. By moving such settings and preferences down to the container level,
rather than system-wide or custom programming, Inventory Manager can accommodate both worlds in a
single instance.
Integration with Purchasing & Registration
Inventory records are created directly from ChemACX Database of available chemicals, as well as from
Registration System. For substances that do not exist in either database, Inventory Manager has its own chemically
aware user interface. By tightly coupling with ChemACX Database and Registration System, the need for
duplicate data entry is virtually eliminated. Once a product is ordered, its chemical information is stored and
it is given an “on order” status, reducing duplicate ordering of popular reagents.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

RESEARCH
&
CombiChem Enterprise
Desktop to Enterprise Combinatorial Chemistry
Benefits of Combinatorial Chemistry
Combinatorial chemistry, in particular the technique of parallel synthesis, has become an essential element of
the drug discovery process. This is true both at the point of finding new leads as well as optimizing a promising
lead. By using parallel synthesis techniques, chemists are able to multiply their productivity by a factor of
between 5 and 100. This increase in productivity creates data management challenges. CombiChem Enterprise
has been developed to provide the software tools required by the combinatorial chemist to manage and
document parallel synthesis experiments. The software models real-world workflow as much as possible.
Starting Out
To start, the user simply draws a generic reaction step in a ChemDraw ActiveX control directly embedded in
the notebook environment. Multiple reactants and products are supported. Points of variability on the molecules
are indicated by the traditional “R” designation. Furthermore, query features can be used to precisely define
the intended molecules. After drawing the reaction, the software analyzes the generic
reaction, determines the role of each molecule, and creates pages for managing the lists of real reagents to be
used in the actual parallel synthesis experiment.
Reaction Based
Library Generation
Library in
Spreadsheet View

DISCOVERY
• Reagent lists can be drawn from varied sources
• Reaction based library generation allows for
evaluation by product or reagent
• Data management is simplified and library
specifications are available to others on the network
Finding Reagents
Flexibility is the key when dealing with databases of chemical compounds. CombiChem Enterprise can use
reagent lists from a variety of different sources: SD files, ChemFinder databases, ChemFinder hit lists, ChemOffice
WebServer hit lists, ChemACX Database, or directly from the user via ChemDraw. Regardless of the source,
CombiChem Enterprise produces a list of reagents which match a particular generic reactant. The chemist then
chooses which of the compounds to use for generating products.
Getting Results
Once the chemist has given CombiChem Enterprise a set of reagents for each of the generic reactants in the
reaction scheme, the software generates the set of products which would result from running the experiment.
CombiChem Enterprise evaluates the products using several in silico methods, and the chemist can then choose
which compounds to keep and which ones to reject. After the products have been generated, the software
provides product information for each of the reagents. The chemist can use that information, for example, to
trim away reagents having few or no products which pass the Lipinski Rule of Five test. Finally, the products
are laid out on plates based on user-definable plate layouts.
Integration with E-Notebook
Keeping track of compound library data can be a challenge: which reagents led to this product, which
product goes with that spectrum, what was in the mixture used in this thin layer chromatography CombiChem
Enterprise provides ways to organize the data and navigation is simple. When used with E-Notebook Enterprise,
the data for a library of shared compounds, and the entire experiment, is automatically documented and made
available to the entire organization.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

RESEARCH
&
BioAssay HTS
Biological Assay and High Throughput Screening
BioAssay HTS
BioAssay HTS provides scientists with an effective way of managing test results for biological and other kinds
of experiments intended to assess the efficacy of compounds. Suitable for both plate-based high throughput
screening assays and smaller-scale lead optimization experiments, BioAssay HTS provides researchers with
simple tools for setting up their models in a database, uploading data, automating calculations and reporting
on their findings.
User Friendly Assay Management
Even for the most basic protein assays, the independent and dependent variables used by the biologist to quantify
efficacy can vary substantially from assay to assay. The underlying requirement that follows from this variability
is for a flexible data management system that can adapt quickly to different assays and biological models.
With BioAssay HTS, researchers or IT support staff simply define the observables and calculations that
make up the assay. The database does the rest. Users can set up unlimited levels of drill-down. This allows users,
for example, to click an IC50 and see a graph of percent inhibition versus concentration. Click again, and the
software displays the original triplicate results, with outliers marked. The software even supports complex in
vivo models.
Automated Curve
Fitting & Data Analysis
Flexible Assay
Definition Tools

DISCOVERY
•Effectively manages data from complex biological
assays involved with lead optimization
• Adapts quickly and flexibly to different assays and
biological models
• Closely integrated with Microsoft Excel, ChemOffice
and ChemDraw
Easily Manage Large Volumes of Data
BioAssay HTS offers an easy way to capture large volumes of data from automated laboratory equipment and
store it securely in Oracle. Scheduled data import means you can set up an import template once, and all future
data will appear in the system as it is gathered. BioAssay HTS contains a complete plate inventory system that tracks
plates and compound groups across plates. It easily manages daughter plate creation, barcoding, and freeze/thaw
cycle tracking. Since it is integrated with your assay data, you can instantly view compound information and
visualize results plate-wise to detect anomalies before they become a problem.
Automated Calculations & Curve Fitting
Once the database is configured for an assay, calculations are performed automatically whenever new data is
entered or imported. Calculations can be quite complex, built from multi-step procedures. For an IC50 assay in
triplicate, the software can average your triplicate results, take control values into account, and perform a
sigmoidal dose-response curve fit according to your specifications. It is now as easy to do for 10,000
compounds as it is for ten.
Find Structure-Activity Relationships
Users can visualize data for multiple assays with BioSAR Browser, which is specifically designed for viewing
structures and alphanumerics side-by-side. Other components of the ChemOffice product line provide
additional ways to analyze structural and biological data and perform structure searches. Both ChemFinder and
ChemOffice WebServer make it easy to create customized forms for viewing data. Users can export data to Excel
or Spotfire for further analysis and reporting.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

RESEARCH
&
BioSAR Browser
Biological and Chemical Meta Data Catalog
BioSAR Browser
BioSAR Browser, a strategic must for any discovery organization interested in serious data mining, is a data-dictionary
driven structure-activity analysis program. Users may choose among assays registered in the dictionary or
search for assays of interest.
Providing Catalog Capabilities
The power of BioSAR Browser lies in the researcher’s freedom from dependence on IT support. Once an assay
is registered into the data-dictionary it is automatically included in the powerful analysis framework. By reducing
the time between question and answer, BioSAR Browser gives researchers the freedom to explore new
ideas—the bottom line for discovery information systems. Systems that provide answers after questions have
become irrelevant are of no use. BioSAR Browser avoids this by placing application development in the
researcher’s control.
Forms & Tables in a Unified Interface
While most SAR tools provide only a table-based interface, BioSAR Browser provides a forms-based interface in
addition to a tabular view. Researchers have demonstrated that both form and tabular views are essential. Forms
provide highly detailed information about one compound, whereas tabular views make comparisons between
Form and Table Views
Data Dictionary
Organizes Reports

DISCOVERY
• Catalog driven data mining and analysis operation
• Both form and table views available within simple
web interface; ChemDraw for Spotfire
• Role based security specifies operations allowed for
administrators, publishers and browsers
compounds more feasible. There is often a tradeoff between power and simplicity, and most SAR tools opt for
the former at the expense of the latter. BioSAR Browser, however, merges the sophistication of a powerful data
catalog technique with knowledge gained through years of working closely with users. The result is a SAR
application that is as intuitive as it is powerful.
Security & Convenience
Security within BioSAR Browser is highly granular. Different roles exist for administrators, publishers, and
browsers. Administrators may add assays to the data catalog engine, publishers may create reports and publish
them, and browsers may use data query and analysis. Most data mining tools provide a mechanism to store
queries, but the interface for creating queries is too complex. With BioSAR Browser, each set of assays is a complete
report with a query form, a view form, and a table view, combining the convenience of a ChemFinder or
ISIS application with the power and flexibility of a data catalog-driven mining program.
ChemDraw for Spotfire
ChemDraw for Spotfire is a powerful add-in for the Spotfire DecisionSite software. Spotfire makes industry
standard applications for high-dimensional visual data analysis, and is used to explore large biological datasets.
ChemDraw for Spotfire adds chemistry to DecisionSite, providing structure visualization and searching services.
Highlight a spot in Spotfire’s DecisionSite, and a structure is displayed directly in the window. If you draw
a structure and click Search, the matching records are displayed right in the Spotfire window. The structures
are retrieved from a chemical database such as Registration System, ChemFinder, or Oracle Cartridge, and are
returned directly over the network. In this way, structures can be linked by registry number, CAS number, or
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
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ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

CHEMICAL
ChemACX Database
Available Chemicals and Screening Compounds
ChemACX Database
Sifting through chemical catalogs is a poor use of time for any researcher. The Available Chemicals Xchange
database, ChemACX Database, provides a complete tool for research chemical sourcing and purchasing. The
database can be accessed from both desktop and enterprise environments and boasts an impressive list of major
suppliers, from Alfa Aesar and Aldrich, to TCI and Zeneca with hundreds in between. The enterprise procurement
solution for ChemACX saves time by streamlining the entire purchasing process. Use ChemACX to
build an internal requisition, print the form on your company template, fill it out and submit it to purchasing.
ChemACX-SC
ChemACX-SC is an additional fully structure searchable database containing the catalogs of leading screening
compound suppliers, including ChemBridge, Maybridge, Sigma-Aldrich’s Rare Chemical Library and others.
Data Quality
Over 500,000 products from 300 research chemical and biological catalogs have been selected to have their
product catalogs prepared for electronic delivery. The data provided by the suppliers is enriched by editors who
add searchable chemical structures, physical and chemical properties, and incorporate a comprehensive
chemical synonym dictionary. All substances and supplier catalog numbers are cross-referenced, making it easy
to locate alternate sources for back ordered or discontinued items.
ChemACX on the Web
ChemACX on CD-ROM

DATABASES
• Fully structure-searchable database of 500,000 products
from 300 chemical catalogs; separate ChemACX-SC
database contains screening compounds
• Search by name, synonym, partial name, formula, and
other criteria, as well as structure and substructure
• Shopping cart system works with requisition forms
and purchasing systems, such as SAP, Ariba and
Commerce1, to streamline chemical purchasing
Data Currency
A premium is placed on the accuracy and currency of the ChemACX Database. Many suppliers listed in the
database are also currently selling their products online through the ChemACX.Com web site, and therefore
have a vested interest in ensuring that their data remains complete, accurate and up-to-date. You won’t find a
sourcing database with more frequently updated content and current pricing than ChemACX.
Data Accessibility
The same way that Internet users can publicly access ChemACX.Com, enterprise users can access their private
ChemACX Database via a standard web browser. There is no need to configure or install any additional software.
ChemDraw users can either use the ChemDraw Plugin to draw chemical structures directly in the browser’s
search page, or alternatively submit queries to the database server directly from ChemDraw. ChemFinder
users can access their own copy of the database right from their local hard drive.
Electronic Requisitions
Traditional sourcing databases were conceived merely as reference tools. ChemACX Database, however, goes
one step further by including the ability to collect products into an electronic shopping cart and export its contents
into electronic requisition forms or purchasing systems. This time-saving feature has proven to be one of
the most popular advantages of ChemACX among scientists and purchasing agents alike. Users can readily
export data from the shopping cart into Excel and Word templates used as departmental requisition forms.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
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ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

CHEMICAL
The Merck Index
Chemistry’s Constant Companion
Industry Standard
Among printed chemical reference works, one that stands out for its integrity, detail and longevity is The Merck
Index. This encyclopedia of chemicals, drugs and biologicals has 10,250 monographs, 446 named reactions and
23 additional tables. Merck & Co., Inc., the publisher of The Merck Index, has chosen CambridgeSoft to produce
the complete contents of the 13th edition in a fully searchable ChemOffice format.
Detailed Monographs
The subjects covered include human and veterinary drugs, biologicals and natural products, agricultural chemicals,
industrial and laboratory chemicals, and environmentally significant compounds. What makes The
Merck Index so valuable is its extensive coverage. The information provided includes chemical, common and
generic names, trademarks, CAS registry numbers, molecular formulas and weights, physical and toxicity data,
therapeutic and commercial uses, and literature citations. In addition to the standard searches, compound
monographs can now be searched by ChemDraw structure as well as substructure. Moving this information to
the fully searchable ChemOffice format makes it easier and faster to search and get results. Instead of consulting
the auxiliary indices and then turning to the actual monograph, all searching can be done from a single form.
Organic Name Reactions
Query Search Form

DATABASES
• Encyclopedic reference for over 10,000 chemicals,
drugs, and biologicals
• Fully searchable by ChemDraw structure, substructure,
names, partial names, synonyms and other data fields
• Available in desktop, enterprise and online formats
Integrated Information
Having The Merck Index in ChemOffice format confers another valuable benefit: integration with other information
sources. For example, after locating a substance in The Merck Index, it is a simple matter to copy the
name, structure or other data elements to search ChemACX Database to find out whether there are commercial
suppliers of the substance. The structures could also be used as input to Chem3D to obtain three-dimensional
models and to perform electronic structure and physical property calculations. Information can also be brought
into any ChemOffice desktop or enterprise solution, including ChemDraw/Excel, ChemFinder/Word, E-Notebook
and Registration System.
ChemOffice Formats
The Merck Index is available in two ChemOffice compatible formats. The desktop edition is a CD-ROM in a
ChemFinder database format, for use by an individual researcher. The enterprise edition, designed for workgroups
and larger user communities, is served by ChemOffice WebServer to connected users. The Merck Index thus adds
to the growing set of reference databases served by ChemOffice WebServer. Just as ChemOffice integrates the
desktop edition of The Merck Index with the scientist’s everyday activities, the enterprise edition becomes an integral
part of the applications deployed on ChemOffice WebServer.
Web Versions
The complete contents of The Merck Index are also available online through your favorite web browser. To
meet your specific needs, single user subscriptions, corporate extranet subscriptions and intranet webservers are
all available.
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TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

CHEMICAL
Chemical Databases
Reference, Chemicals, Reactions, Patents P
and MSDS
Databases
ChemOffice WebServer provides a full range of compound and reaction databases essential for research.
Databases are available at ChemFinder.Com, or over corporate intranets.
Reference
The Merck Index contains encyclopedic references for over 10,000 chemicals, drugs and biologicals.
ChemINDEX includes 100,000 chemicals, public NCI compounds and others.
World Drug Index (WDI) from Derwent contains over 58,000 compounds with known biological activity.
WDI classifies compounds according to type of biological activity, mechanism, synonyms, trade names,
references and more.
Chemicals
ChemACX and ChemACX-SC, Available Chemicals Xchange, is a large and growing source for information
on compound availability. It lists compounds from Alfa Aesar and Aldrich to TCI and Zeneca with hundreds
in between, including 500,000 products from 300 catalogs. ChemACX-SC is a library of screening compounds.
ISI Reactions
Derwent Patents

DATABASES
• Extensive collection of chemical reference information
in fully searchable database format
• Includes information on commercial availability;
properties; biological activity; organic reactions; material
safety data sheets; and patent or development status
• Developed by CambridgeSoft in partnership with the
leading chemical database publishers
Reactions
Organic Syntheses is the electronic version of the annual and collective volumes of trusted, peer reviewed synthesis
procedures published since 1921 by Organic Syntheses.
Current Chemical Reactions (CCR) from ISI is both a current awareness and a data mining application used to
design chemical syntheses. Renowned for its quality, CCR contains information from over 300,000 articles
reporting the complete synthesis of molecules. Updated daily, CCR is an excellent way to stay on top of recent
developments.
ChemReact and ChemSynth from InfoChem are carefully selected from a database of over 2.5 million reactions
through an automated process of reaction classification. With over 390,000 reaction types, ChemReact is for
expert synthetic chemists designing novel syntheses. Entries in ChemSynth are further refined to those with over
50% yield and at least two literature references.
ChemRXN is a refined selection of over 29,000 fully atom-mapped reactions. Including carefully selected reactions
from InfoChem’s ChemSelect database and ISI’s ChemPrep database, ChemRXN is a terrific combination of utility.
Patents
World Drug Alerts (WDA) from Derwent is a current awareness application providing information on patents,
new biologically active compounds, new methods for synthesizing drugs, and other data. It is a requirement for
effective decision making in all stages of drug design.
Investigational Drugs Database (ID db) from Current Drugs is the world’s leading competitor intelligence
service on drug R&D. Updated weekly, it covers all aspects of drug development world wide, from first patent to
launch or discontinuation.
Safety MSDS
ChemMSDX provides over 7,000 material safety datasheets.
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TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
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All other trademarks are the property of their respective holders. All specifications subject to change without notice.

CONSULTING &
Consulting & Services
Development, Installation & Training T
Services
Managing Information
Today’s businesses are facing many complex issues. Among them are the overloads of disparate types of information,
unmanaged proliferation of valuable research data, virtual projects in many locations, uncontrolled
research data, compliance, certification and regulation. Technological solutions to these issues require careful
planning and management. CambridgeSoft now offers the following professional services to assist businesses
in fully utilizing the power of technology.
Decision Making
CambridgeSoft believes that successful technology utilization begins with the assessment and decision making
process. Our experts can assist clients with:
· Readiness Assessment: Identify the scope, requirements, and deliverables for your project. Assure critical IP
is incorporated. Allow end-users to capitalize on existing scientific and technology resources.
· Strategic Planning: Conduct formal analysis of scientific, technical, operational, and process environments
to determine the necessary approach to customization and deployment.
· Prototypes and Proof of Concept: Prototypes allow you to test the technical feasibility of solutions. This
activity can provide a baseline for the future roll-out of the solution, and can also gather user feedback so
requirements can be refined.
DECISION
MAKING
CUSTOM
DEVELOPMENT
DEPLOYMENT &
TRAINING
MANAGE
THE PROCESS
Readiness
Assessment
Strategic
Planning
Prototype or
Proof of Concept
Business Case
Development
Custom
Application
Development
Data
Integration
Installation &
Customization
of Applications
Application
Development
Beta &
Pre-Release
Programs
Controlled
Pilots
Training

SERVICES
· Business Case Development: Business cases help define a clear and purposeful solution based on well-defined
and documented business needs. Having a business case helps to justify good projects, stop bad projects
before they are started, and provides the basis for ongoing measurements after project completion to make
sure that the business is getting the results they wanted.
· Operational Planning: In order to effect change on complex environments, it is necessary for organizations
to develop operational plans. These plans minimize the risks associated with large technology deployments.
Plans may incorporate key business processes and workflows, and help to identify any operational constraints.
Custom Development
Your organization requires solutions that meet you unique needs. CambridgeSoft consultants can assist with:
· Custom Application Development: Assess business needs, document specifications, and create custom webbased
solutions for your enterprise.
· Data Integration: Create interfaces with other data management systems to incorporate your data into an
enterprise system.
· Installation and Customization: Customize your solution to your specifications. Make certain that all technical
and logistical installation processes are managed.
Deployment & Training
Develop a comprehensive road map for deployment of technology solutions across the enterprise. Our experts
help you plan and deploy your solutions by:
· Application Deployment: Document, define and execute all of the actions required to support end user
acceptance. Manage the deployment process to assure a smooth roll-out to the end-users
· Beta and Pre-Release Programs: Beta and pre-release programs involve a limited deployment to a small set
of users in order to identify deployment readiness or logistical issues that must be addressed prior to a largescale
deployment. When early release programs are employed, the success rate of large scale deployments
is greatly increased and end users are more likely to adopt the new technology.
· Controlled Pilots: Controlled pilots involve deploying a pre-production system to a small group of users to
evaluate it's functional, usability, technical, and operational characteristics in a real-world environment
prior to the completion of final system development. A controlled pilot helps identify and correct showstopper
technology or operational issues before a final roll out program is implemented.
· Training: Develop customized training materials for users, system administrators, and help desk personnel.
If you choose to outsource training management, CambridgeSoft can schedule and conduct training for
all users and stakeholders.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

CS Software Problem Report
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FAX 1 617 588–9360
MAIL CambridgeSoft, 100 CambridgePark Dr.
Cambridge, MA 02140 USA
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US 1 617 588-9300 FAX 1 617 588–9390 WWW www.cambridgesoft.com
EU 00 800 875 20000 FAX +44 1223 464990 EMAIL info@cambridgesoft.com
MAIL 100 CambridgePark Drive Cambridge, MA 02140 USA

CS ChemOffice
®
Desktop to Enterprise Solutions
ChemOffice Ultra, desktop
edition, includes it all, with
ChemDraw Ultra, Chem3D Ultra,
BioOffice Ultra, Inventory Ultra,
E-Notebook Ultra and ChemInfo Ultra for
a seamlessly integrated suite. Draw reaction
mechanisms for publication and visualize
3D molecular surfaces, orbitals and
molecular properties. Features include
The Merck Index, ChemACX Database,
CombiChem/Excel, ChemDraw/Excel, and BioViz.
Bring your work to the web or query online
databases with the ChemDraw ActiveX/Plugin.
ChemOffice Enterprise is a comprehensive
knowledge management and informatics solution,
covering elextronic notebooks, biological screening,
chemical registration and more over your intranet.
Enterprise Ultra includes E-Notebook for record
keeping, BioAssay for low and high-throughput
screening, integrated plate inventory, Inventory for
reagents, BioSAR for SAR reports, Registration
system and ChemACX Database of available chemicals.
Technologies include ChemDraw ActiveX and Oracle Cartridge.
US 1 617 588-9300 FAX 1 617 588–9390 WWW www.cambridgesoft.com
EU 00 800 875 20000 FAX +44 1223 464990 EMAIL info@cambridgesoft.com
MAIL 100 CambridgePark Drive Cambridge, MA 02140 USA
MAE 04980 0408