NEDCC 2010 Piwowar Leaders and Laggards

Leaders and Laggardsin the preservation of

raw biomedical research data

Heather Piwowar

Department of Biomedical InformaticsUniversity of Pittsburgh

Soon‐to‐be Postdoctoral Associate with Data Observation Network for Earth (DataONE)

http://www.metmuseum.org/toah/ho/09/euwf/ho_24.45.1.htm

http://www.flickr.com/photos/jsmjr/62443357/

http://www.flickr.com/photos/camilleharrington/3587294608/

http://www.flickr.com/photos/rkuhnau/3318245976/

http://www.flickr.com/photos/conformpdx/1796399674/

http://www.flickr.com/photos/rkuhnau/3317418699/

http://www.flickr.com/photos/zemlinki/261617721/

http://www.flickr.com/photos/tracenmatt/3020786491/

http://www.flickr.com/photos/the-o/2078239333/

Researchers have a choice

http://upload.wikimedia.org/wikipedia/commons/7/76/PeptideMSMS.jpg; http://en.wikipedia.org/wiki/Image:Helices.png; http://en.wikipedia.org/wiki/Image:Heatmap.png; http://en.wikipedia.org/wiki/Image:Microarray2.gif; http://zellig.cpmc.columbia.edu/medlee/demo/; htp://www.plosone.org/article/fetchArticle.action?articleURI=info:doi/10.1371/journal.pone.0000441

http://upload.wikimedia.org/wikipedia/commons/7/76/PeptideMSMS.jpg


http://en.wikipedia.org/wiki/Image:Helices.png


http://en.wikipedia.org/wiki/Image:Heatmap.png




http://en.wikipedia.org/wiki/Image:Microarray2.gif


http://zellig.cpmc.columbia.edu/medlee/demo/


http://www.plosone.org/article/fetchArticle.action?articleURI=info:doi/10.1371/journal.pone.0000441



















PAST MEDICAL HISTORY:

Past medical history showed she had

superficial phlebitis times two in the past, had non-insulin dependent diabetes mellitus for

four years.

She had been hypothyroid for three years.

HISTORY OF PRESENT ILLNESS:

The patient is a 58-year-old female, …




















four years.























four years.























four years.



















Shared data benefits science

VerifyUnderstandExtendExploreCombineSynergizeTrainReduce

But... costly for authorsFindOrganizeDocumentDeidentifyFormatDecideAskSubmit

Answer questionsWorry about mistakes being foundWorry about data being misinterpretedWorry about being scoopedForgo money and IP and prestige???

http://www.flickr.com/photos/75166820@N00/5318468/

As a result, policy makers have spent lots of time and money ....

http://www.flickr.com/photos/tonivc/2283676770/

http://www.flickr.com/photos/johnnyvulkan/381941233/





... on initiatives, requests, requirements, and tools

• Funder requirements• Journal requirements

• Public databases• Data sharing grids

• Data formatting standards

• Peer encouragement in editorials, letters to the editor...

Does it work?

http://www.flickr.com/photos/archeon/2941655917/



lots of data sharing!

http://www.genome.jp/en/db_growth.html

but how much isn’t shared?

what isn’t shared?

who isn’t sharing it?why not?

what can we do about it?

how much does it matter?

http://www.flickr.com/photos/paulhami/1020538523//



who

what

when

where

why

how

http://www.flickr.com/photos/ryanr/142455033/



Who to share data with?

• everyone on the internet

• “qualified” researchers for “qualified” research projects

• friends

• your lab

What data is shared?

• everything

• all the datapoints

• all the research notes

• code

• just what is needed to reproduce the results in the paper

• raw? cleaned? every processing step?

When is the data shared?

• upon collection

• upon submission for publication

• upon publication

• time-embargo after publication

• upon retirement or death

Where is it deposited?

• centralized datatype specific repositories

• journal supplementary information

• institutional repositories

• disciplinary repositories

Why share it?

How to share it?

• massive datasets

• syntactic format

• semantic format

• sensitive data (privacy, endangered species locations, security-related, ...)

• what license or community norm








• biomedical data

• few privacy concerns raw data (not images or processed)

• openly on the internet

• upon publication

• datasets are large but manageable

• datatypes with mature standards for semantics, syntax, locations













Data sharing frequency depends on how you ask

Campbell et al. JAMA. 2002.Kyzas et al. J Natl Cancer Inst. 2005.

Vogeli et al. Acad Med. 2006.Reidpath et al. Bioethics 2001.

10%

25-40%

Noor et al. PLoS Biology 2006.Ochsner et al. Nature Methods 2008.

Piwowar et al. PLoS ONE 2007.Editorial. Nature Biotech 2007.

DNA sequences

gene expression microarrays

proteomics spectra

0% 25% 50% 75% 100%

Data sharing frequency depends on datatype

Data sharing frequency depends on when the data was published

0%

10%

20%

30%

40%

2000 01 02 03 04 05 06 07 08 2009

lots of data sharing!

http://www.genome.jp/en/db_growth.html


0%

10%

20%

30%

40%

2000 01 02 03 04 05 06 07 08 2009






microarray data

http://en.wikipedia.org/wiki/DNA_microarray


http://commons.wikimedia.org/wiki/File:DNA_double_helix_vertikal.PNG

How often was research data shared upon

publication?

Funder Journal Investigator Institution Study

Number of studies that share their data= _____________________________________Number of studies that create data


publication?



publication?

http://www.flickr.com/photos/lofaesofa/248546821/



Look for wetlab methods in full text:

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1522022&tool=pmcentrezhttp://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1590031&tool=pmcentrez

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1482311&tool=pmcentrez#id331936http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2082469&tool=pmcentrez

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=126870&tool=pmcentrez#id442745

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1522022&tool=pmcentrez










Query the full text of published articles:

("gene expression" AND microarray AND cell AND rna) AND (rneasy OR trizol OR "real-time pcr") NOT (“tissue microarray*” OR “cpg island*”)



publication?

Querying databases for citation links to data creation studies



publication?

11,603 studies that create data

we found shared datasets for 25%

results


0%

10%

20%

30%

40%

2000 01 02 03 04 05 06 07 08 2009


funded by NIH?

size of grant

sharing plan req’d?

funded by non-NIH?

impact factor

strength of policy

open access?

number of microarray studies published

years since first paper

# pubs

# citations

previously shared?

previously reused?

gender

sector

size

impact rank

country

humans?

mice?

plants?

cancer?

clinical trial?

number of authors

year


study type

Author publication history:

Citation counts:

Author-ity web serviceTorvik & Smalheiser. (2009). Author Name Disambiguation in MEDLINE. ACM Transactions on Knowledge Discovery from Data, 3(3):11.

Author name disambiguation:

author “experience”

author gender

institution rank

Yu et al. BMC medical informatics and decision making (2007) vol. 7 pp. 17

funding level

PubMed grant lists + NIH grant details

funder mandates

Requires a data sharing planfor studies funded after October 2003

that receive more than $500 000 in direct funding per year

“An inherent principle of publication is that others should be able to replicate and build upon the authors' published claims. Therefore, a condition of publication in a Nature journal is that authors are required to make materials, data and associated protocols available in a publicly accessible database …”

http://www.nature.com/authors/editorial_policies/availability.html

http://www.nature.com/nature/journal/v453/n7197/index.html

journal mandates

and so on...

124 variables

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0.25 0.50 1.00 2.00 4.00 8.00

Has journal policy0.95Count of R01 & other NIH grants

Authors prev GEOAE sharing & OA & microarray creation

NO K funding or P funding

Institution high citations & collaboration

Journal impact

Journal policy consequences & long halflife

NOT animals or mice

Instititution is government & NOT higher ed

Last author num prev pubs & first year pub

Large NIH grant

Humans & cancer

NO geo reuse + YES high institution output

First author num prev pubs & first year pub

Multivariate nonlinear regressions with interactions

Odds Ratio

0.25 0.50 1.00 2.00 4.00 8.00

Has journal policy0.95Count of R01 & other NIH grants

Authors prev GEOAE sharing & OA & microarray creation

NO K funding or P funding

Journal impact

Journal policy consequences & long halflife

Institution high citations & collaboration

NOT animals or mice

Instititution is government & NOT higher ed

Last author num prev pubs & first year pub

Large NIH grant

Humans & cancer

NO geo reuse + YES high institution output

First author num prev pubs & first year pub

Multivariate nonlinear regressions with interactions

Odds Ratio

0.25 0.50 1.00 2.00 4.00

OA journal & previous GEO-AE sharing

0.95Amount of NIH funding

Journal impact factor and policy

Higher Ed in USA

Cancer & humans

��

• association not causation

• lots of assumptions

• don’t know how generalizable it is

• hypothesis-generating

http://www.flickr.com/photos/vlastula/300102949/



• those studying cancer

• on human patient data

• in journals with few data sharing policies (clincal journals)

• labs with fewer funding sources

• ...


who isn’t sharing it?

• investigators who have shared before

• investigators who publish in open access journals

• from Stanford

• in Physiological Genomics

• ...

(what is shared?who is sharing it?)

• current data repositories are not representative of all data generated

• they are missing some of the good stuff

• Good news: actionable to learn from the leaders and focus on the laggards

Take home






http://www.flickr.com/photos/jima/606588905/



Blumenthal et al. Acad Med. 2006

industry involvement

perceived competitiveness of field

0 1 2 3

Withholding is associated with industry links, competitiveness

40% of surveyed scientists said data sharing was discouraged during their training!

Campbell et al. JAMA 2002.

sharing is too much effort

want student or jr faculty to publish more

they themselves want to publish more

cost

industrial sponsor

confidentiality

commercial value of results0% 20% 40% 60% 80%

Withhold because too much effort, desire for continued publishing

Comments show desire for control`Before I send you the data could I ask what you want it for?'

`Can you be more explicit, please, about the analyses you have in mind and what you plan to do with them?'

`We'll have to discuss your request with the other coauthors. Before we do that, I'd like to know your proposed analysis plan.'

`We are not finished using the data, but when we are finished with it, we would be open to requests for the data.'

`Any use of the data other than for the specific purpose laid down in the contract of collaboration is effectively ruled out.'

Reidpath et al. Bioethics 2001.






Estimating societal benefit‐ assume each database hit saves $0.10, or a fraction of data collection costs

‐ assume the value is approximated by the (idealized) funding target for data maintenance: 20‐25% the cost of generating the data

Remembering, moreover, the indirect benefits are much higher than the direct ones.

Ball et al. Nature Biotechol. 2004.

Foster et al. Share and share alike: deciding how to distribute the scientific and social benefits of genomic data.Nature Reviews Genetics 8, 633-639

Number of stakeholders

Survey of doctoral students and postdocs:

23.0% been denied access to information, data, materials, or programming associated with published research

28-50% reported withholding caused negative effects on these aspects of their training:•progress of their research, •rate of discovery in their lab/research group, •quality of their relationships with academic scientists, •quality of their education, •level of communication in their lab/research group.

Vogeli et al. Acad Med. 2006 Feb; 81(2):128-36

Impact on training

More research needs to be done!






Look to the leaders and laggards

• Stanford

• Physiological Genomics

• cancer data

• human data

• those who haven’t shared before

http://www.flickr.com/photos/sunrise/35819369/



Gleditsch et al. Int Studies Perspectives. 2003.Piwowar et al. PLoS ONE. 2007.

Measuring personal benefit: increased citations

70% more citations

Piwowar et al. PLoS ONE. 2007.

Hedstrom et al. IASSIST 2006.

What would make it easier? help and straightforward guidelines

more funder time and moneyhelp with confidentiality issues

on-site helpmore training

better guidelinesbetter tools

simpler requirementsless staff turn-over

0% 25% 50% 75%







0% 25% 50% 75%







0% 25% 50% 75%

Hedstrom. Society of Am Archivists Ann Meeting. 2008.

if I thought it would really benefit othersif required for future funding

if required for publicationif deposits counted as a publication

if citations to data were valuedif monetary compensation

0% 25% 50% 75%

Incentives to share: perceived value, mandates, recognition as publication

Hedstrom. Society of Am Archivists Ann Meeting. 2008.

if I thought it would really benefit othersif required for future funding

if required for publicationif deposits counted as a publication

if citations to data were valuedif monetary compensation

0% 25% 50% 75%

Incentives to share: perceived value, mandates, recognition as publication

http://www.flickr.com/photos/gatewaystreets/3838452287/

• #oa.data

• Science Commons

• DataCite

• Dataverse

• MGED

• Open Notebook Science

• Friendfeed

• Nature editorials

• many others...

NSF-funded distributed framework and cyberinfrastructure for environmental science.

Dryad is a repository of data underlying scientific publications, with an initial focus on evolution, ecology, and related fields.

The National Evolutionary Synthesis Center, NSF-funded:

• Duke University,• UNC at Chapel Hill• North Carolina State University

http://www.flickr.com/photos/g_kat26/4255119413/

Begin to investigate reuse

http://www.flickr.com/photos/boitabulle/3668162701/

who reuses data?

when?

why aren’t they?

which datasets are most likely to be reused?


how many datasets could be reused but aren’t?

why?

who doesn’t?

what should we do about it?

I share my code and data at http://www.researchremix.org

Sharing data is not easy.Some is better than none.Be the change you want to see.

http://www.flickr.com/photos/myklroventine/892446624/



thank you

Dept of Biomedical Informatics at U of Pittsburgh

NLM for training grant funding

Open science online community and those who release their articles, datasets and photos openly

NEDCC

Once shared, always there?

Data contacts and storage decay with time

URL decay: email decay:

Supplementary information: in 6 top journals: 5% unavailable after 2 years, 10% unavail after 5 years

Evangelou et al. FASEB J. 2006.Wren. Bioinformatics 2008.Wren et al. EMBO Rep 2006.


saves other people effort

for the public good

will be cited and enhance my reputation

saves me effort in answering questions

saves me effort in managing my data0% 20% 40% 60% 80%

Benefits both societal and personal

http://www.flickr.com/photos/sunrise/35819369/http://www.flickr.com/photos/fboyd/2156630044/



http://www.flickr.com/photos/fboyd/2156630044/

http://www.flickr.com/photos/fboyd/2156630044/

http://www.flickr.com/photos/jep42/3017149415/in/set-72157608797298056/

Health & Medicine

NEDCC 2010 Piwowar Leaders and Laggards