BRIF workshop Toulouse 2012 Digital IDs subgroup
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BRIF workshop Toulouse 2012 Digital IDs subgroup

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  • 1. BRIF Digital identifiers subgroup Gudmundur A. Thorisson <gt50@leicester.ac.uk> GEN2PHEN / University of Leicester Pierre-Antoine Gourraud <pierreantoine.gourraud@ucsf.edu> UCSF -- Overview -- ‣Brief backgrounder on identification & digital identifiers ‣Use cases for bio-resource identification in BRIF ‣Digital resources: datasets, databases (Mummi) ‣Non-digital resources: projects, studies, cohorts [...] (Pierre) ‣Conclusions and next steps This work is published under the Creative Commons Attribution license (CC BY: http://creativecommons.org/licenses/by/3.0/) which means that it can be freely copied, redistributed and adapted, as long as proper attribution is given.Monday, 22 October 12
  • 2. BRIF and bio-resource identification • The identification requirement: need to identify resources in order to – track use/reuse and impact – credit those who contribute to them • Biobanking projects have relied on: – Project/study/cohort names • Example: the GAZEL study in France >20 years http://www.gazel.inserm.fr • Challenges: - ad hoc agreements with research groups who reuse samples or data - painstaking manual searching through literature for mentions of ‘GAZEL‘ - project names are often ambiguous in global context BRIF workshop, Toulouse Oct 22 2012Monday, 22 October 12
  • 3. Monday, 22 October 12
  • 4. BRIF and bio-resource identification • The identification requirement: need to identify resources in order to – track use/reuse and impact – credit those who contribute to them • Example: biobanking projects frequently rely on... – Project/study/cohort names • Example: the GAZEL study in France >20 years http://www.gazel.inserm.fr • Challenges: - ad hoc agreements with research groups who reuse samples or data - painstaking manual searching through literature for mentions of ‘GAZEL‘ - project names are often ambiguous in global context – Citations to journal publications • Which paper to cite? Tricky to keep track of which citations are relevant to impact • Also troublesome if there is no paper to cite (e.g. for a new study) BRIF workshop, Toulouse Oct 22 2012Monday, 22 October 12
  • 5. Digital identifiers - some background • Definition: a digital identifier is a character string used to uniquely identify i) a digital object in a computer system, or ii) a record in a computer system which describes a non-digital object • Persistence - once assigned, identifier MUST NOT change • Uniqueness - global scope vs local scope – Most ID schemes require tacid knowledge of the type of identifier to interpret • Example: EC grant identifiers in acknowledgement statements BRIF workshop, Toulouse Oct 22 2012Monday, 22 October 12
  • 6. This work has received funding from the European Communitys Seventh Framework Programme (FP7/2007-2013) under grant agreement number 200754 - the GEN2PHEN project. BRIF workshop, Toulouse Oct 22 2012Monday, 22 October 12
  • 7. This work has received funding under grant agreement number 200754 BRIF workshop, Toulouse Oct 22 2012Monday, 22 October 12
  • 8. Digital identifiers - some background • Definition: a digital identifier is a character string used to uniquely identify i) a digital object in a computer system, or ii) a record in a computer system which describes a non-digital object • Persistence - once assigned, identifier MUST NOT change • Uniqueness - global scope vs local scope – Most ID schemes require tacid knowledge of the type of identifier to interpret • Example: EC grant identifiers • Some problem domains require for globally unique IDs – Example: ISBN numbers to identify books, e.g. for copyright purposes • Some problem domains require resolvable IDs – Resolve = retrieve out information about the thing being identified, including where to access it (for a digital object, its location on the Internet) – Digital Object IDs best known, but several other systems exist BRIF workshop, Toulouse Oct 22 2012Monday, 22 October 12
  • 9. Monday, 22 October 12
  • 10. Identifier use cases in BRIF • 3x broad categories of “stuff” to identify i) Digital resources Resources that actually “lives” in computers (born-digital or digitized content): datasets and databases ii) Physical resources Resources corresponding to actual physical things: samples, groups of samples, experimental instruments, etc. iii) Project-level and other “meta” resources Higher-level aggregates of things, projects, organizations, consortia etc. NB in many cases identifiers already exist for these things, but they are not exposed to the outside world in a usable form (i.e. made resolvable, citable, globally-unique). BRIF workshop, Toulouse Oct 22 2012Monday, 22 October 12
  • 11. Datasets • Definition: a data set (or dataset) is a collection of data, often presented in tabular form but in the bio-sciences also frequently in a multitude of domain-specific formats, such as FASTA for biological sequences • Data publication and data citation is a hot topic - lots of research and infrastructure-building activity in recent years • Emerging best practices for data citation & attribution • Identifiers for dataset - persistent data DOIs issued via DataCite • Little new for BRIF to add here, except issue recommendations – KEY POINT: infrastructure for data preservation and access is a prerequisite for any sort of persistent bio-dataset identification scheme. Many projects don’t have this! BRIF workshop, Toulouse Oct 22 2012Monday, 22 October 12
  • 12. Data DOI scenario (simplified) 1. Research group registers a dataset and metadata in a suitable domain repository (or their own repository) 2. Repository archives dataset and and assigns a DOI name to it 3. Unique DOI name is used by article authors (and others) to indicate resource reuse (ideally via formal data citation) 4. Journal article reference listings & full-text and other sources are mined to identify references to dataset and/or downloads 5. Dataset-level metrics calculated from collected data e.g. - total no. citations in scholarly articles - no. secondary citations (citations to papers which cited the original dataset) - no. downloads in the last 2 years BRIF workshop, Toulouse Oct 22 2012Monday, 22 October 12
  • 13. ORCID and DataCite Interoperability Network • Persistent identifiers for connecting people and dataset • 2y EC-funded project, 7 partners in Europe + USA • Two main proof-of-concept pilots – Social Science data - use and citation of British Birth Cohort Studies • historical data, decades old, steadily being curated by lots of different people • high rate of reuse, often cited in papers – High-energy physics - attribution challenges • dealing with large no. authors on HEP papers - ‘dilution’ of the term authorship • Linking HEP papers to supporting datasets http://odin-project.eu/ BRIF workshop, Toulouse Oct 22 2012Monday, 22 October 12
  • 14. Databases • Definition: an online database can be regarded as a collection of data, but made accessible in such a way that facilitates using the data to answer scientific question, via  structured querying and/or free-text searching of the data over the Internet • Broad range, from large-scale DNA and protein sequence repositories to small locus-specific databaess – E.g. GenBank, UniProt, GWAS Central, Ehlers-Danlos Syndrome Variant Database • Challenges in assessing impact & attributing curators – Reliance citations to database paper, if there is one (sometimes many) • Analyzing website traffic is another indicator - highly-accessed database =~ important – Database URLs sometimes change – Database name + URL often only mentioned only in materials&methods, no citation – Credit via authorship impossible if there is no database journal paper BRIF workshop, Toulouse Oct 22 2012Monday, 22 October 12
  • 15. BioDBCore - global catalogue of bio-db’s • BioDBCore aims – annotation - organize the bio-database ‘resourceome’ – discovery - e.g. which protein sequence databases are available? • Who’s behind it? – International Society for Biocuration – Resource catalogues: Bioinformatics Links, BioSiteMaps, NAR db-issue etc – Working group includes reps from NAR and DATABASE journals, MIBBI, Model organism db’s, others • Catalogue will have persistent identifiers for each db entry http://www.biosharing.org/biodbcore BRIF workshop, Toulouse Oct 22 2012Monday, 22 October 12
  • 16. Monday, 22 October 12
  • 17. •[slot in Pierre] BRIF workshop, Toulouse Oct 22 2012Monday, 22 October 12
  • 18. From  Pa(ents  to  BioBanks  and  back… • Persistent  IDs  for  datasets  &  other  digital  resources – Absolute  need • From  BioresourceResearchIF  to  BioresourceXIF – More  than  an  IP  address  ?   • Increase  need  of  iden<fica<on  for  source  of  informa<on   in  general   –  Not  only  research  purpose… – “Big  data”   – Quan<fied  self. • Blurring  the  border  between  :  Research,  data  (Non-­‐CLIA),     Clinically  approved  ,  consumer  centered  dataMonday, 22 October 12
  • 19. Database  Gateway    &  Computa1ons User  data Imaging Reference   Front-­‐end   Individual  data groups  of  pa.ents tablet   Applica1onCopyright  ©  2012  The  Regents  of  University  California,  USA  -­‐  All  right  reserved.  Monday, 22 October 12
  • 20. Conclusions / next steps • Complex landscape, lots of problems to tackle • Key challenge will be to get authors to use the right identifiers – education, awareness, best practices, journal guidelines etc. – build support into tools that researchers use • Potential outputs from BRIF subgroup, by end of GEN2PHEN – Continue work on whitepaper on identifiers (partial drafted earlier in the year) – Compile recommendations for authors & biobankers, for use cases where workable solutions exist or are emerging (data DOIs, BioDBCore) • Need some biobanker-expert help in ID subgroup! – Esp. to look in-depth into study catalogues with established identifier schemes • International Clinical Trials Registry Platform • ClinicalTrials.gov • P3G study catalogue BRIF workshop, Toulouse Oct 22 2012Monday, 22 October 12
  • 21. Acknowledgements GEN2PHEN Consortium This work has received funding from the http://www.gen2phen.org/about-gen2phen/partners European Communitys Seventh Framework Programme (FP7/2007-2013) under grant agreement number 200754 - Prof Anthony J. Brookes Bioinformatics Group, Leicester the GEN2PHEN project. Contact me! <gt50@le.ac.uk> |<gthorisson@gmail.com> http://www.linkedin.com/in/mummi http://www.twitter.com/gthorisson Published under the CC BY license (http:// http://www.gthorisson.name creativecommons.org/licenses/by/3.0/) BRIF workshop, Toulouse Oct 22 2012Monday, 22 October 12