uploading resources to the marine geospatial bibliography ... - IPIECA

UPLOADING RESOURCES TO THE MARINE
GEOSPATIAL BIBLIOGRAPHY (MGB)
CONTENTS
Introduction ............................................................................................................................................................ 2
Submitting reference information to the MGB .................................................................................................. 2
Direct input of references into the MGB ................................................................................................................ 2
Import a RIS format file containing one or more references ................................................................................. 3
Overview of typical process for reference management and multi-resource upload to MGB .......................... 3
Local reference management ............................................................................................................................ 3
Reference management software ................................................................................................................. 3
Obtaining and using Endnote ......................................................................................................................... 3
Input of reference information in Endnote ................................................................................................... 3
Export of RIS file from Endnote ..................................................................................................................... 5
Import of references to the MGB ....................................................................................................................... 6
Handling upload errors .................................................................................................................................. 9
Appendices ........................................................................................................................................................... 10
What is RIS? ...................................................................................................................................................... 10
Structure of RIS file........................................................................................................................................... 10
Mapping between RIS format and MGB categories ......................................................................................... 11
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INTRODUCTION
Welcome to IPIECA's Marine Geospatial Bibliography. The MGB is a knowledge sharing platform collecting and
making available information on oil, gas and the environment for industry, science and the public. This
document explains how you can add references to the MGB using both manual and automatic processes. It
also suggests an approach for reference management and provides detailed technical information on the
automated import process.
Please check whether a reference is already in the MGB before uploading a duplicate.
SUBMITTING REFERENCE INFORMATION TO THE MGB
There are two main ways to upload references to the MGB:
1. Type it in directly
2. Import a RIS format file containing one or more references
The steps required for all of these processes are outlined below.
DIRECT INPUT OF REFERENCES INTO THE MGB
1. Open the MGB in an internet browser: http://mgb.ipieca.org
2. If you have not previously registered, click ‘Register’ and fill out your details
3. Log on to the MGB
4. Click ‘Submit’
5. Fill out fields as thoroughly and accurately as possible.
6. Click ‘Create’. If the update has been successful the reference will go into the approval pool.
7. Approval
a. References meet all the criteria for the MGB and will be held in an approval pool after
upload.
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. If you are an admin on the MGB website, you can access the approval pool by clicking on
‘Admin’ then ‘Approve’. If you are not an admin, the uploads will be approved by a site
admin. Please contact IPIECA if you wish to be added as a site admin.
IMPORT A RIS FORMAT FILE CONTAINING ONE OR MORE REFERENCES
It is possible to import one or more references into the MGB from a file in the .RIS format. RIS files can be
obtained in many ways, such as direct output from an online reference repository e.g. Science Direct or from a
local reference manager. A single .RIS file can contain one or more references (more details on the .RIS format
are in the appendices).
OVERVIEW OF TYPICAL PROCESS FOR REFERENCE MANAGEMENT AND MULTI-RESOURCE
UPLOAD TO MGB
For a small number of references it may be practical to upload RIS files for individual references created by an
online journal or reference repository e.g. ScienceDirect. However, for larger uploads and full control we
would recommend collection and curation of references is done using reference management software that is
local to your computer (i.e. stored on your hard drive). This enables you to collect, carry out quality control
assurance, check for duplicates and assign appropriate keywords and further relevant material to references
quickly and consistently. Once you are happy with your local reference database you can export it using the RIS
format and import the file to the MGB.
LOCAL REFERENCE MANAGEMENT
REFERENCE MANAGEMENT SOFTWARE
There are a series of software packages for management and databasing of bibliographic information. We
have used Endnote (version X4) in the examples, but other packages and versions of Endnote are similar.
Reference management software packages are designed to integrate seamlessly with many online reference
repositories, such as library catalogues, and digital libraries, such as Web of Science and ScienceDirect,
allowing searches and reference downloads to be made within the reference management software
environment. Reference management software also allows storage of associated information, full text files,
figure files etc. alongside each reference. Finally they provide a mechanism for using the reference
information in documents, integrating with word processors (such as Microsoft Word) to automatically ensure
consistency in reference style and to automate creation of reference lists and bibliographies.
OBTAINING AND USING ENDNOTE
Instructions for obtaining and use of the latest version of Endnote software can be found on their website
www.endnote.com .
INPUT OF REFERENCE INFORMATION IN ENDNOTE
References can be inputted into Endnote in two ways: automatic import and manual entry.
Automatic import: Most of the digital repositories support RIS or Endnote specific export formats (e.g. .enw).
Once you select the references of interest on an online reference repository you select the export option and
in some cases decide which additional information is transferred (e.g. abstract, references). This will download
a file (.ris or .enw) to your computer which will generally automatically import into Endnote. If you are asked
to pick an import filter at this stage choose Endnote or RIS (most of the repositories will mention Endnote by
name in the appropriate import filters).
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Manual entry: This is a fully flexible, but more time consuming, method of entering data into Endnote. It is
likely that most of the data of interest to the MGB will be inputted using this method.
1. Open Endnote
2. Select References, new reference
3. You are then presented with the input screen. The first thing to do is to set the reference type. This
automatically places the most applicable fields at the top of the screen.
4. Fill out the fields
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5. When you are finished you just click the smaller (not red) cross at the top right of the screen. Endnote
will automatically save the reference (it occasionally asks if you want to save automatically – click
‘yes’). You will be taken back to the main reference screen and your new reference will be shown.
6. Repeat until all the references you want to include are in your Endnote database.
EXPORT OF RIS FILE FROM ENDNOTE
Using Endnote as an example of common reference management software, RIS export is straightforward.
1. Select references to export in Endnote
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2. File -> export

3. Type file name, select save location and set the export style as “RefMan (RIS) export”
4. Optionally you can change the file extension to ‘.RIS’. However the MGB will also accept files with the
extension ‘.txt’.
a. If you can’t see the file extension (i.e. Filename.txt) then you have to change your windows
settings. To do this, open control panel, then select folder options. Under the 'view' tab,
uncheck the 'Hide extensions for known file types' box, then click on 'OK'
b. Change name in windows explorer to filename.RIS
IMPORT OF REFERENCES TO THE MGB
1. Open the MGB in an internet browser: http://mgb.ipieca.org
2. If you have not previously registered, click ‘Register’ and fill out your details
3. Log on
4. Go to ‘Admin’ then select ‘Import file’
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5. Click on ‘Choose file’ or ‘Browse’
6. Select RIS file using the file manager
7. Click on ‘Save’
8. The MGB will then import the files in your RIS file. If there are any problems and you get an error
message see the section on handling upload errors.
9. If the import is successful, references will be assigned to either fully imported or partially imported.
10. Partially imported references
a. A summary showing partially imported references will be shown
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. Click on the pen (edit) symbol for each reference in turn
c. The guidelines will let you know what has to be filled out. The reference will be assigned as
partially imported because one of the necessary fields is not filled out (usually region/map
coordinates). Fill out the required fields.
d. Click ‘Save’ at the bottom of the page. If the update has been successful the reference will go
into the approval pool.
11. Imported references
e. These references meet all the criteria for the MGB and will be held in an approval pool after
upload.
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f. If you are an admin on the MGB website, you can access the approval pool by clicking on
‘Admin’ then ‘Approve’. If you are not an admin, the uploads will be approved by a site
admin. Please contact IPIECA if you wish to be added as a site admin.
HANDLING UPLOAD ERRORS
Errors can occur in upload for a variety of reasons. The most common reason is that there is a missing or
incorrectly filled out RIS field. The error message will identify which part of the reference has an error.
If you have a large RIS file and an error occurs in upload, the references before the upload will appear in the
MGB. It is considerably easier to adapt the RIS file than to delete the uploaded references in the MGB. The
easiest way to do this is:
1. Note the reference title of the reference with an error
2. Open the RIS file in a text editor (e.g. Notepad)
3. Search for the problematic reference (using the ‘Find’ option)
4. Fix the error manually in the text editor
a. There is usually an obvious problem in the reference that is identified in the error message
b. Other common errors are:
i. Missing region keywords (fix by adding keywords)
ii. Punctuation at the start of a field (fix by removing)
iii. Incorrect URL (fix by correcting or deleting)
iv. Fields too long (fix by removing characters)
5. Delete all preceding references
6. Save the text file
7. Repeat upload.
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APPENDICES
WHAT IS RIS?
RIS is a standardized tag format for bibliographic citations developed by Research Information Systems
Incorporated (the format name refers to the company) to enable citation programs to exchange data. It is
supported by a number of reference management software packages such as Endnote (www.endnote.com)
and RefMan (www.refman.com). RIS is a common and flexible format that has been adopted by IPIECA for
upload of multiple resources to the MGB. It is also used as an export option by many digital libraries, such as
Web of Science (wok.mimas.ac.uk) and ScienceDirect (www.sciencedirect.com).
STRUCTURE OF RIS FILE
An RIS file is a simple text file with a file extension ‘.ris’. It is a tagged format that stores bibliographic
information. A file can store multiple references. Each reference is coded by multiple lines of text (ending in
the ASCII carriage return and line feed characters in Microsoft Windows). Each line starts with two letters, two
spaces, a dash (-) and two spaces.
There are many letter codes in use to describe the bibliographic information available. The most up-to-date list
of codes and their meanings can be accessed on the Wikipedia article on RIS
http://en.wikipedia.org/wiki/RIS_(file_format).
Each reference has to start with the TY - field (which stands for reference type e.g. TY - JOUR for journal). This
is followed by a series of other fields describing the reference. The reference ends in ER - (which stands for
end reference). Other references are added sequentially. As an example of how the article " Jones, D. O. B.,
Gates, A. R. and Lausen, B. (2012) Recovery of deep-water megafaunal assemblages from hydrocarbon drilling
disturbance in the Faroe-Shetland Channel. Marine Ecology Progress Series. 461:71-82." would be expressed in
the RIS file format:
TY - JOUR
AU - Jones, D. O. B.
AU - Gates, A. R.
AU - Lausen, B.
PY - 2012
TI - Recovery of deep-water megafaunal assemblages from hydrocarbon drilling disturbance in the Faroe-
Shetland Channel
JO - Marine Ecology Progress Series
SP - 71
EP - 82
VL - 461
ER -
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MAPPING BETWEEN RIS FORMAT AND MGB CATEGORIES
The table below shows how RIS prefixes are recognised by the MGB
RIS prefix MGB Category Details
TY Type Three possibilities:
JOUR (Journal article / paper)
BOOK (Book)
RPRT (Report)
You just use the four letter acronym in the RIS field.
T1, TI, CT, BT Title Max length: 256 characters The first field found is stored the rest
are ignored.
AB, N1 Description First field found is stored the rest ignored. No character limit.
AU Author Max length: 256 characters per author. No maximum number of
authors.
PY, Y1, DA Date Published First field found is stored the rest ignored.
SN
ISBN/ISSN
T2
Journal Name
VL
Journal Volume
IS
Journal Issue
SP Journal Pages Start page
EP Journal Pages End page
CY
Place Published
PB
Publisher
Not available in Files
Have to upload separately after in MGB
multiple upload
UR URL First field found is stored the rest ignored.
M3, DO DOI First field found is stored the rest ignored. (M3 is used by
ScienceDirect instead of DO for the DOI).
Max length: 256 characters
DOI = Digital Object Identifier
KW Keywords ,
Additional
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Each field is stored in the “Keywords”, “Region” field if an exact
match is found with the keywords are in the MGB table. Multiple

Keywords,
Region
KW Latitude /
Longitude
RN
Acknowledgements
Date Created
Date Edited
keywords and regions can be used. If the keyword present in the
RIS file is not found in the MGB table it is put into “Additional
Keywords” field of the MGB.
If a string in the following format is found in the keywords field it
gets stored as the lat/long:
60.9453333N, 02.8913333W
This is a position in decimal degrees (WGS ’84)
Automatically created at import
Automatically created on editing
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