DATA MANAGEMENT: KEEPING A RESEARCH NOTEBOOK, FILES AND RELATED ISSUES

PERCSS
Program for the Ethical and Responsible Conduct of Science and
Scholarship
DATA
MANAGEMENT: KEEPING A
RESEARCH NOTEBOOK, FILES
AND RELATED ISSUES
Steven Brody, MD
Department p of Internal Medicine
Washington University School of Medicine
1

Good record keeping promotes
accountability t bilit and d integrity i t it iin researchh
Necessary for data analysis, publication,
collaboration, peer review among
others.
Necessary ecessa y to suppo support t intellectual te ectua
property claims.
Can defend you against false allegations
of research misconduct.
2

Good record keeping,
contin continued… ed
Important for the care of human
subjects.
necessary for members of your group
or o any a y ot other e researcher esea c e to be ab able e to
duplicate your work, when needed.
Required by NIH and other granting
institutions to meet policies and
standards for the conduct of good
science
3

The lab notebook notebook: Overview O e ie
It is a record of both physical and
mental activity.
Good records are complete, accurate
and a d understandable u de sta dab e to ot others. e s
Each member of the research team is
responsible for his/her records records.
The PI has the final responsibility for
the laboratory records. records
4

CCurie’s ie’s Notebook
Ca. 1900
5

PProf. of X’s Notebook
Ca. 2000
6

Wh What t iis a LLab b NNotebook? t b k?
Complete record of procedures,
reagents, data, and thoughts to pass
on t to other th researchers h
Why experiments were initiated, how performed,
and results, results comments
Place to compile data/charts/photos/ideas
Place of clues, , to troubleshoot problems p
Place to observe whole picture and think
Legal document, to prove patents
Defense against accusations of fraud or lawsuits
7

TpeandFomat
Type and Format…
Ultimately dictated by your PI
Type yp Advantages g Drawbacks
Bound book
(stitched)
No lost sheets
Proof against Fraud
Entered as done
No logical order
Duplicate “Bound” Double record. Easy Diff. To Read.
Book (yellow sheets) copies
Not true duplicate
Loose Leaf
Order by expts Lost sheets
(folders/notebooks) Easy recording Authenticity prob.
Computer p
Easy y to read Lost data
(ELN)
Easy calculations Authenticity prob
8

Physical Characteristics of a
Good Notebook Notebook…
Large >= 8.5x11 at least
Bound (stitched) pages to ensure integrity
Numbered pages
Number the book
White gridded
Acid free paper p p (30 ( years) y )
Name
Dates
PI
Book No.
Duplicate pages (differing opinions)
Written in Pen (gel pens are good). good) Felt tip is bad. bad
9

What pen is best? Roller tip in this test:
http://www.swarthmore.edu/NatSci/cpurrin1/images/penexp2.jpg10

PPreparing epa ing a Ne New Lab Notebook
Create a table of contents in the first 2
pages
List experiments by:
Title
Date
Lab Book Number/Page Number
11

For Every Experiment, Record:
Start Date: on all pages
Title
Why: Brief statement of purpose, rationale
How: Description/protocol with ref to origin
Calculations, concentrations, dilutions, etc.,
Include sketches, diagrams
What Happened:
All (protocol changes; on floor, kicked)
Taped/stabled in Information
Data
Associated information: Samples, storage
llocation, ti DData t Files, Fil Disks, Di k Images I
What It means: Interpretation (and comments)
What’s Next
12

Attaching mate materials ials
Computer generated data
Photographic data
Printed graphs (make as you go)
Datasheet templates
Product labels
Who provided plasmids, etc.
Notes (or pasted copies) of discussions, conversations,
emails, readings related to exp’t design or goals
Archive locations of plasmids, plasmids probes, probes etc. etc
X-rays and other large items may be kept in a
separate folder if they don’t fit in the lab notebook.
13

Referencing attached data and
samples
Name
Expt/Dates
Book#/page#
Name
Expt/Dates
Book#/page#
Name
Expt/Datees
Book#/pagge#
Label Notebooks, Boxes with Lab Book Book#/Page#
14

Also record… eco d
Discussions with others (time, names,
issues). Good for future credit.
Correspondence with colleagues (phone
calls calls, ee-mails) mails).
Names of individuals who have played
any role in your research. research Technicians
in core laboratories are also important
15

Date
Title
Times
Data
Calculations
Interpretation
Future studies
Correction
16
Taken from the online Linus Pauling Research Notebooks, http://osulibrary.orst.edu/specialcollections/rnb/index.html

FFrequently eq entl Fo Forgotten gotten Info Info…
Serum lot number
Antibody titer
Oth Other people l involved i l d
Centrifuge model,
speed, temp
Incubation time
# washes
Tube size and type
Unexpected delays
Growth medium used
Buffer pH
CCalculations l l ti
Initial # cells
Age/passage culture
% Gel
Growth stage g Bact.
Condition of cells used
17

The impo importance tance of timing timing…
Always record, update, review…
Record as you go
Input paper towel and post-it info ASAP!
At the LATEST, insert data the next day!
Do a weekly checkup
1 hour to review
Make sure everything is attached securely, all
summaries written written, future directions written written,
record in table of contents
Retractions have been associated with untimely
record keeping
18

If you o make a mistake mistake…
They should be marked through with a
single line and a full explanation of the
error provided.
Never e e ob obliterate te ate mistakes sta es with t ink oor
cover them with corrective fluid.
To a casual observer these actions may
suggest improper reasons.
19

Characteristics Helpful for Filing a
PPatent t t
Patents on intellectual property p p y are awarded not by y the first to
file, but “first to invent” – first to record!
Sign and date each entry
HHave an iindependent d d witness i sign i and d ddate each h entry
Witness cannot be co-inventor and must understand data
Do not change entries (make a new entry and cross-reference
tto prior i entry) t )
Use past tense
Never remove original pages or attachments
RRecord d all ll di discussions/meetings/ideas i / ti /id relevant l t tto th the project j t
Record as much detail as possible
http://www.invention-protection.com/ip/publications/docs/A_Primer_On_Lab_Notebooks.html
http://www http://www.uspto.gov/web/offices/pac/doc/general/
uspto gov/web/offices/pac/doc/general/
20

Paper vs. Electronic Lab
Notebook:
Paper notebooks have limited capacity
Raw data is massive
Data capture is archaic
RRaw printouts i t t can no llonger be b stored t d
Data formats are restricted
2-D gels, photomicrographs
RRecord-keeping d k i is i tedious t di
Repetitive protocols lost, require manual entries
Searching is difficult
Context of work is often lost
No connection to other people, projects, labs
Paper records no longer legally required
p g g y q
Electronic records are legal
21

Data Flow in the Laboratory
Lab Automation
& Robotics
Equipment
Interfacing
Chromatography
Data Systems
DData t
Analysis
Data
Warehousing
Laboratory
Laboratory Information
Management
Data
IInstruments t t
SSystems t (LIMS) Mi Mining i
Electronic
Laboratory
Notebooks
Data Acquisition q Information Processingg Knowledge g Management g
22

Collabo Collaborative ati e ELN
scientist
writer
clinician
statistician
research
specialist
lab
manager
nurse
data
encoder
lab
technician
23

Demands for ELN:
21 CFR part pa t 11*
FDA rule initiated August 1997
Sets standards for electronic submission
Electronic records
Thoroughly validated
Automatic audit trails
Results can be recreated
Electronic signatures
Unique identity
Linked to e-record
No grandfather clause
*Code of Federal regulations Title 21, Part 11, Electronic Signatures
http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?cfrpart=11
24

Software for ELN
25

How long to keep notebooks
and records? eco ds?
NIH policy mandates 3 years after the
end of the project p j (grant (g funding g period) p )
FDA policy mandates 10 years after use
P Patent t t policy li mandates d t 23 years after ft
issue of the patent.
The organization with the longest policy
has priority p y
26

Who owns notebooks and
data?
When NIH awards a research grant to a
university, any and all data collected as
part of that funded project are owned
by the grantee institution.
Data books of all investigators (PI,
postdocs, grad g ad students, stude ts, technicians)
tec c a s)
are the property of the institution.
27

Who owns notebooks and
data?
The principal investigator is the
steward.
If the PI resigns or moves to another
institution: st tut o
Equipment and all data belong to the initial
institution.
Permission can be obtained to transfer the
award, equipment q p and data.
28

Resea Research ch data do not incl include: de
Preliminary analyses
Drafts of papers
Plans for future research
Peer reviews
Physical objects (samples, tapes)
Trade secrets or commercial
information
29

Applicabilit Applicability of rules les
Data produced with Federal support that are
cited publicly and officially.
Data collected by institutions of higher education,
hospitals, and non-profit institutions
Does not apply l to state and d local l l govt
Does not apply to commercial organizations
Applies to new and competing awards made after
the effective date of the amendment (11/8/1999)
30

PPublic blic Access to Data
The Office of Management and Budget
(OMB) revised the regulations regarding
public access to experimental data in
1999
The public can obtain access to
experimental data through the Freedom
of Information Act (FOIA)
31

What happens if the PI
refuses ef ses to compl comply? ?
This is view as a material failure to
comply with the terms of the award
NIH would initiate appropriate
enforcement e o ce e t acto action
This could include withholding future
support to the institution
32

Consequences of Research
Mi Misconduct d t
Debarment from eligibility to receive Federal
ffunds d
Prohibition from service on advisory
committees, peer review committees, or as
consultants
Certification of information sources that is
forwarded by the institution
Certification of data by the institution
Supervision by the institution
Submission of a correction or retraction of a
published article
http://ori.dhhs.gov/html/misconduct/administrative_actions.asp
33

Best practice principles for
leade leaders s of research esea ch ggroups: o ps
Set standards and provide examples of
good record keeping practices for the
group
Provide o de too tools s for o good record eco d keeping eep g
Provide training for the group and
review records
Clarify data and research ownership and
access rights
34

Institutional Best Practice
PPrinciples: inciples WUSTL
“It is the policy of WUSTL to publish
research results and to foster the use of
University inventions, discoveries and and
other works for the common good good. ”
Intellectual Property Policy
http://www.wustl.edu/policies/intelprop.html
35

With care and attention to our
work o k we e sho should ld avoid… a oid
RETRACTION
“We wish to retract our report (Science 2004;
303 303, 371) iin which hi h we reported d that h ββ-N N
acetylglucosamine-serine can be
bi biosynthetically th ti ll incorporated i t d at t a defined d fi d site it in i
myoglobin in E. coli. …
36

RETRACTION
RETRACTION…
Regrettably Regrettably, through no fault of the authors, authors
the lab notebooks are no longer available to
replicate the original experimental conditions, conditions
and we are unable to introduce this amino acid
into myoglobin with the information and
reagents currently in hand…”
ZZ. Zhang et al al., UT at Austin Austin.
Science 2009; 326, 326 1187. 1187
37

Notebook Ethics
"Many people say that it is the intellect
which makes a great scientist. They are
wrong: it is character." -- Albert
Einstein
38

Resea Research ch Integ Integrity it
The h NIH Office Off of f Research h Integrity defines d f
misconduct in science as:
“Fabrication, ab cat o , falsification, a s cat o , pplagiarism, ag a s , oor ot other e
practices that seriously deviate from those that
are commonly accepted within the scientific
community. This does not include honest error or
hhonest t diff differences iin interpretations i t t ti or jjudgments d t
of data.” (Federal Register 54:32446-32451, Aug
8, 1989)
“Th “The iintegrity t it of f research h ddepends d on
accurate, detailed, organized, complete, and
accessible data” Office of Research Integrity
39

Tips to PPreserve ese e Data Integ Integrity it
Never, e e , eever, e , remove e o e a page
Fill consecutive pages
Cross out unused parts p of pages p g
Record all info as accurately as possible.
Do NOT omit any result, no matter how odd.
Cross out mistakes lightly (might need to
recover)
Write llegibly bl
Put a full date (international date problems…)
with month spelled out out.
40

Mo More e Helpf Helpful l Tips
The institution owns “your” your notebook
Do NOT remove your notebook from the lab
( (unless l this thi is i an acceptable t bl lab l b practice) ti )
You may get permission to take copies at
graduation graduation, but do not take original pages
Do NOT read another person’s notebook
without permission (even the PI won won’tt look at
advanced researcher’s notebooks secretly).
Should be kept for at least 5 years
41

Data manipulation
manip lation
“Data may be excluded from the
experimental i l results l only l if if you have h
a sound reason to do so!”
Mother Nature
42

misleading presentation of
ddata t ffrom ddata t management t
errors
Number of animals vs. number of
determinations
Non-standard normalization
Not showing entire gel
Varying Varying exposures of images
INSIST ON VIEWING THE RAW DATA!
43

As photographed
Brightness Brightness-
Contrast
Adjustment
44

As photographed
Erasing
45

The The Journal Journal of of Cell Cell Biology:
Biology:
• revokes the acceptance of about 1% of its
papers due to inappropriate image
image
manipulation
• 25% of accepted accepted p papers p p have at least 1 figure g
with undocumented manipulation
“If you misrepresent your data you are deceiving
people.”
Rossner, M. (2006). The Scientist 20:24 20:24-25.
25.
46

What can I do?
Nature, instructions to authors (2006)
• List all image acquisition and processing tools and
software
•Document key y image-gathering g g g setting g and
manipulations in the Supplemental materials
• Clearly demarcate borders between images collected at
different times
• Avoid use of touch up tools or deliberately obscuring
parts of an image
• Processing is acceptable bl only l if f applied l d across the h
entire image
•Be prepared p p to deliver the original, g , unprocessed p images g
to the editor
48

Slide sources: so ces
•Gail Gail P. P Taylor PhD and Angelina
Hoefle, UT San Antonio
•Carmen S. S Dence MS, MS Washington
University
•Edward Ed Edward d Krug K PhD PhD Medical M di l College C ll
of South Carolina
•Douglas Perry PhD,
IU School of Informatics
49

Acknowledgements and
Refe References ences
Kathy Barker, At the Bench: A laboratory Navigator. Cold Spring
Harbor Laboratory yppress.
1998.
Guidelines for Keeping a Laboratory Record. David Caprette, Rice
University. http://www.ruf.rice.edu/~bioslabs/tools/notebook/notebook.html
Guidelines for Keeping a Laboratory Notebook. Colin Purrington,
Swarthmore Univ Univ.
http://www.swarthmore.edu/NatSci/cpurrin1/notebookadvice.htm
Laboratory Record Keeping. Todd E. Garabedian, Nature
Biotechnology v. 15 (August 1997) pp.799-800
http://biotech http://biotech.about.com/gi/dynamic/offsite.htm
about com/gi/dynamic/offsite htm
Office of Research Integrity, U.S. Dept. of Health and Human
Services http://www.unh.edu/rcr/
Responsible Conduct of Research Online Study Guide. Julie
Si Simpson, UUniversity i it of f New N Hampshire H hi http://www.unh.edu/rcr/
Francis L. Macrina, Scientific Integrity: An Introductory Text with
Cases. ASM Press. 2000.
Academic Research Record Record-keeping: keeping: Best Practices for Individuals Individuals,
Group Leaders and Institutions. Academic Med. 81, 42-47; 2006,
50

QQuestions estions
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