DATA MANAGEMENT: KEEPINGA MANAGEMENT: KEEPING A ...

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RESEARCH NOTEBOOK, FILES ... What is a Lab Notebook? ... in Pen (gel pens are good) Felt tip is bad. Written in Pen (gel
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 t bilit and d integrity i t it iin research h accountability Necessary for data analysis, publication, collaboration, peer review among others. Necessary ecessa y to suppo supportt intellectual te ectua property claims. Can defend you against false allegations of research misconduct. 2

Good record keeping, contin ed continued… Important for the care of human subjects. necessary for members of your group or any o 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

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The lab notebook O e ie notebook: Overview 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. es 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

C ie’s Notebook Curie’s Ca. 1900

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P of X’s Notebook Prof. Ca. 2000

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Wh bN t b k? Whatt iis a LLab Notebook? Complete record of procedures, reagents, data, and thoughts to pass on to t 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

T pe and Format… Type Fo mat 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” Book (yellow sheets)

Double record. Easy copies

Diff. To Read. Not true duplicate

Loose Leaf (folders/notebooks)

Order by expts Easy recording

Lost sheets Authenticity prob.

p Computer (ELN)

Easyy to read Easy calculations

Lost data 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

Name Dates PI Book No.

Acid free p paper p (30 ( years) y ) 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

P epa ing a Ne Preparing New Lab Notebook Create a table of contents in the first 2 pages List experiments by:   

Title Date Lab Book Number/Page Number

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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 l location, ti D Data t Files, Fil Disks, Di k Images I What It means: Interpretation (and comments) What’s Next 12

Attaching mate ials materials 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/Date es Book#/pag ge#

Name Expt/Dates Book#/page#

Label Notebooks, Boxes with Lab Book Book#/Page#

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Also record… eco d Discussions with others (time, names, issues). Good for future credit. Correspondence with colleagues (phone calls e calls, e-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

F eq entl Fo gotten Info Frequently Forgotten Info… Serum lot number Antibody titer Oth people Other l involved i l d Centrifuge model, speed, temp Incubation time # washes Tube size and type Unexpected delays

Growth medium used Buffer pH C l l ti Calculations Initial # cells Age/passage culture % Gel Growth stage g Bact. Condition of cells used

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The impo tance of timing importance 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 o or cover them with corrective fluid. To a casual observer these actions may suggest improper reasons. 19

Characteristics Helpful for Filing a P t t Patent  Patents on intellectual p property p y are awarded not by y the first to file, but “first to invent” – first to record! Sign and date each entry H Have an iindependent d d witness i sign i and dd date each h entry Witness cannot be co-inventor and must understand data Do not change entries (make a new entry and cross-reference t prior to i entry) t ) Use past tense Never remove original pages or attachments R Record d allll 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 uspto gov/web/offices/pac/doc/general/ http://www.uspto.gov/web/offices/pac/doc/general/

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Paper vs. Electronic Lab Notebook: Paper notebooks have limited capacity 

Raw data is massive

Data capture is archaic 

R Raw printouts i t t can no llonger be b stored t d

Data formats are restricted 

2-D gels, photomicrographs

R Record-keeping dk 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 p records no longer g legally g y required q 

Electronic records are legal

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Data Flow in the Laboratoryy Lab Automation & Robotics

Chromatography Data Systems

Data Warehousing

Equipment Interfacing

Laboratory I t Instruments t

Data Acquisition q

Data D t Analysis

Laboratory Information Management S t Systems (LIMS)

Information Processing g

Electronic Laboratory Notebooks

Data Mi i Mining

Knowledge g Management g

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Collabo ati e ELN Collaborative research specialist clinician

nurse

data encoder scientist

lab technician

writer statistician

lab manager

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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

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How long to keep notebooks and records? eco ds? NIH policy mandates 3 years after the

end of the p project j (grant (g funding g period) p ) FDA policy mandates 10 years after use Patent P 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 ch data do not incl de Research include: Preliminary analyses Drafts of papers Plans for future research Peer reviews Physical objects (samples, tapes) Trade secrets or commercial information 29

Applicabilit les Applicability of rules 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

P blic Access to Data Public 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 ef ses to compl refuses 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 act action o This could include withholding future support to the institution

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Consequences of Research Mi d t Misconduct Debarment from eligibility to receive Federal f d funds 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 esea ch g o ps leaderss of research groups: Set standards and provide examples of good record keeping practices for the group Provide o de too toolss 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 P inciples WUSTL Principles: “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

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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; 303 371) iin which 303, hi h we reportedd that h β-NβN acetylglucosamine-serine can be bi biosynthetically th ti ll incorporated i t d att a defined d fi d site it in i myoglobin in E. coli. … 36

RETRACTION… RETRACTION Regrettably, through no fault of the authors, Regrettably 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…” Z Zhang et al Z. 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

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Resea ch Integ it Research Integrity The h NIH Office Off off Research h Integrity defines d f misconduct in science as: 

“Fabrication, ab cat o , falsification, a s cat o , p plagiarism, ag a s , o or ot other e practices that seriously deviate from those that are commonly accepted within the scientific community. This does not include honest error or h honest t diff differences iin interpretations i t t ti or jjudgments d t of data.” (Federal Register 54:32446-32451, Aug 8, 1989)

“The iintegrity “Th t it off research hd depends d on accurate, detailed, organized, complete, and accessible data” Office of Research Integrity

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Tips to P ese e Data Integ it Preserve Integrity Never, e e,e ever, e , remove e o e a page Fill consecutive pages Cross out unused p parts 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 legibly l bl Put a full date (international date problems…) with month spelled out out. 40

Mo e Helpf More Helpfull Tips  The institution owns “your” your notebook Do NOT remove your notebook from the lab ( l (unless this thi is i an acceptable t bl lab l b practice) ti ) You may get permission to take copies at graduation but do not take original pages graduation, 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 you have h a sound reason to do so!” Mother Nature

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misleading presentation of d t ffrom d data data t managementt errors Number of animals vs. number of determinations Non-standard normalization Not showing entire gel Varying exposures of images

INSIST ON VIEWING THE RAW DATA! 43

As photographed

BrightnessBrightnessContrast Adjustment

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As photographed

Erasing

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The Journal of Cell Biology: • revokes the acceptance of about 1% of its papers due to inappropriate image manipulation • 25% of 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. 46

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What can I do? Nature, instructions to authors (2006) • List all image acquisition and processing tools and software • Document keyy 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 iff applied l d across the h entire image prepared p to deliver the original, g , unprocessed p images g • Be p to the editor 48

Slide sources: so ces •Gail P. P Taylor PhD and Angelina

Hoefle, UT San Antonio •Carmen S. S Dence MS, MS Washington University •Edward Ed d Krug K PhD Medical M di l College C ll of South Carolina •Douglas Perry PhD, IU School of Informatics 49

Acknowledgements and Refe ences References Kathy Barker, At the Bench: A laboratory Navigator. Cold Spring press. 1998. Harbor Laboratoryy p 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 about com/gi/dynamic/offsite htm http://biotech.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, U University i it off 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

Q estions Questions

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