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Life science odin-oct2013-sa-sansone
The document discusses challenges in data standards, sharing, and publication in life sciences. It notes there are many reporting standards to describe experiments but issues in identifying, tracking usage, and assessing impact of standards. It proposes creating a registry of standards that is searchable and associates standards with data policies, databases, and metrics to evaluate use. This would help stakeholders identify appropriate standards and credit contributors to maintaining open standards.
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Life science odin-oct2013-sa-sansone
- 1. ODIN “Big Bang”event, CERN, Thursday, 17 October 2013 www.slideshare.net/SusannaSansone Data standards, sharing and publication in the life sciences Susanna-Assunta Sansone, PhD Data Consultant, Associate Director, Honorary Academic Editor Principal Investigator Board of Directors
- 2. ODIN mission Outline ofmy talk Problem: Identification of datasets in pivotal. But meaningful sharing and (re)use also depend on how well described the datasets are. Status quo: In the life sciences there is a wealth of „reporting standards‟ set to enhance and facilitate the experimental descriptions. Challenges: Identify „reporting standards‟ and their organizations, track their use, usability and impact (e.g. linking them to datasets), credit their developers, users (e.g. curators)...
- 3. My team‟s activitiesand groups we work with data management, biocuration and publication, collaborative development of software, database, standards and ontology • • • • • environmental genomics metabolomics metagenomics nanotechnology proteomics • • • • • stem cell discovery system biology transcriptomics toxicogenomics environmental health env agro tox/pharma health
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- 6. Growing movement forreproducible research Researchers and bioinformaticians in both academic and commercial arenas, along with funding agencies and publishers, embrace the concept that to be comprehensible, interoperable and reusable shared datasets we should have richly described: • entities of interest e.g., genes, metabolites, phenotypes, computational models, diseases ... • experimental steps e.g., provenance of study materials, technology and measurement types, experimentalists and curators ...
- 7. The necessity forwell-annotated data and unambiguous experimental metadata was especially apparent • during cross-study comparisons and data analysis • in preparation for reformatting the datasets for submission to the different EBI repositories, requiring different level of information experimental design sample characteristic(s) experimental variable(s) technology(s) measurement(s) protocols(s) 7 The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project data file(s)
- 8. One must strikea balance between • depth and breadth of information; and • sufficient information required to reuse the data The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Make annotation explicit and discoverable 8 Capture all salient features of the experimental workflow Structure the descriptions for consistency, tracking Susanna-Assunta Sansone www.ebi.ac.uk/net-project
- 9. A community mobilizationto develop standards, e.g.: Nanotechnology Working Group de jure standard organizations de facto grass-roots groups Structural and operational differences • organization types (open, close to members, society, WG etc.) • standards development (how to formulate, conduct and maintain) • adoption, uptake, outreach (link to journals, funders and commercial sector) • funds (sponsors, memberships, grants, volunteering)
- 10. Types of reportingstandards Nanotechnology Working Group Including conceptual model, conceptual schema from which an exchange format is derived to allow data to flow from one system to another Including controlled vocabularies, taxonomies, thesauri, ontologies etc. to use the same word and refer to the same „thing‟ Including minimum information reporting requirements, or checklists to report the same core, essential information
- 11. Fragmentation, duplications andgaps epidemiology plant biology microbiology Biologically-delineated views of the world Generic features (‘common core’) - description of source biomaterial - experimental design components MS Arrays Gels Columns Scanning transcriptomics Arrays & Scanning proteomics MS Technologically-delineated views of the world NMR FTIR Columns metabolomics To compare and integrate data we need interoperable standards
- 12. Growing number ofreporting standards + 303 To track provenance of the information and ensure richness of data and experimental metadata descriptions, to maximize reusability + 150 Databases, annotation, curation tools MAGE-Tab GCDML AAO SOFT GELML MITAB ISA-Tab OBI FASTA VO PATO DICOM ENVO XAO DO MIAPA MIRIAM MIQAS MIX MIGEN MOD SBRML MzML SEDML… miame CHEBI SRAxml CML Source: MIBBI, EQUATOR Estimated Source: BioPortal + 130 TEDDY PRO BTO IDO… MIAPE CIMR MIASE REMARK MIQE CONSORT MISFISHIE….
- 13. But how muchdo we know about these standards
- 14. • A coherent,curated and searchable registry of standards for describing and reporting experiments in life science, environmental, biomedical and biotechnological domains
- 15. • A coherent,curated and searchable registry of standards for describing and reporting experiments in life science, environmental, biomedical and biotechnological domains • Progressively associate standards to data policies and databases • Develop assessment criteria for usability and popularity of standards • Help stakeholders to make informed decisions on e.g. what standards or databases to use or recommend; identify efforts they have funded
- 16. 16 The International Conferenceon Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
- 18. Will the ISNI-basedORCID affiliation module cover standards organizations too?
- 19. User profiles populatedfrom ORCID... 19 The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
- 20. ... credit forcreating, contributing to, maintaining standards Ownership of open standards can be problematic in broad, grass-root collaborations 20 It requires improved models, to encourage maintenance of and contributions to these efforts, rewards and incentives need to be identified for all contributors to supporting the The International Conference on Systems Biology (ICSB), 22-28 August, 2008 continued development of standards Susanna-Assunta Sansone www.ebi.ac.uk/net-project
- 21. ... link todata records associated to publications 21 The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
- 22. ...and associated article-levelmetrics 22 The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
- 23. We need “standardsimpact metrics” to evaluate use/usability 23
- 24. working with datapublication platforms:
- 25. “Invisible” use ofstandards in data reporting tools One of the winners. Project: integration of ORCID with the ISAcreator, the editor tool, helping curators and researchers to describe experiments following community standards. The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
- 26. ODIN mission Summarizing mytalk Problem: Identification of datasets in pivotal. But meaningful sharing and (re)use also depend on how well described the datasets are. Status quo: In the life sciences there is a wealth of „reporting standards‟ set to enhance and facilitate the experimental descriptions. Challenges addressed by Identify „reporting standards‟ and their organizations, track their use, usability and impact (e.g. linking them to datasets), credit their developers, users (e.g. curators)...
- 27. Acknowledgements Philippe Rocca-Serra Alejandra Gonzalez-Beltran EamonnMaguire Collaborators: OBO Foundry COSMOS GSC Metabolomics Society Data Dryad Pistoia Alliance Elixir UK NPG‟s Scientific Data and many more….