1. Towards Data Attribution & Citation in the Life Sciences Philip E. Bourne UCSD pbourne@ucsd.edu 8/22/11Data Attribution and Citation

2. Life Science Data Repositories  NLM is the elephant in the room.. However..  There are thousands on community maintained efforts – all want an NAR publication  The ability to cite and attribute the data are highly variable: –DOIs assigned in some cases, but not used –Attribution is through the metadata in most cases –Citation is typically by the associated literature reference if it exists, and/or a database identifier –The use of data repositories such as Dryad is compelling for the long tail problem –Data journals are on the horizon 8/22/11Data Attribution and Citation

3. Consider the PDB as a Use Case  Oldest data resource in biology?  A resource used by ~ 200,000 individuals per month – increasing number of school kids!  A resource distributing worldwide the equivalent to ¼ the National Library of Congress each month  A bicoastal/worldwide resource  1TB 8/22/11Data Attribution and Citation

4. Number of released entries Year PDB Typical Growth Curve – But the Complexity! 8/22/11

5. People are doing more with the data  Number of visits and page views is growing faster than number of unique visitors

6. The Data May Save Lives? * http://www.cdc.gov/h1n1flu/estimates/April_March_13.htm Jan. 2008Jan. 2009Jan. 2010Jul. 2009Jul. 2008Jul. 2010 1RUZ: 1918 H1 Hemagglutinin Structure Summary page activity for H1N1 Influenza related structures * 3B7E: Neuraminidase of A/Brevig Mission/1/1918 H1N1 strain in complex with zanamivir

7. PDB Data Attribution and Citation  About 25% of our budget has been spent on data remediation – multiple versions supported – the copy of record (as defined by the publication) is always available  Cant publish unless data are deposited – motivated by the community - very good data to publication correspondence  Data objects are discreet and we assign DOIs – but they are not used – database identifiers preferred 8/22/11Data Attribution and Citation

8. Ah yes.. But the CD4 Story…

9. 1. A link brings up figures from the paper 0. Full text of PLoS papers stored in a database 2. Clicking the paper figure retrieves data from the PDB which is analyzed 3. A composite view of journal and database content results Literature/Data Integration 1.User clicks on content 2.Metadata and webservices to data provide an interactive view that can be annotated 3.Selecting features provides a data/knowledge mashup 4.Analysis leads to new content I can share 4. The composite view has links to pertinent blocks of literature text and back to the PDB 1. 2. 3. 4. The Knowledge and Data Cycle PLoS Comp. Biol. 2005 1(3) e34 8/22/11

10. www.rcsb.org/pdb/explore/literature.do?structureId=1TIM Example of Interoperability: The Database View BMC Bioinformatics 2010 11:220

11. Example of Interoperability – The Literature View From Anita de Waard, Elsevier

12. Acknowledgements Funding Agencies: NSF, NIGMS, DOE, NLM, NCI, NCRR, NIBIB, NINDS, NIDDK 128/22/11Data Attribution and Citation