Biosharing sansone-dryad-may13
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Biosharing sansone-dryad-may13 Biosharing sansone-dryad-may13 Presentation Transcript

  • Enriching the description of the experiments to enhance query capability: do community standards help? Working with / linking to specialized data repositories: how do identify the ‘right’ one? Associate Director, Principal Investigator Susanna-Assunta Sansone Dryad’s Annual Membership Meeting Oxford, May 2013
  • Should / could Dryad: Capture more details of the experimental workflow… Make the annotation explicit and discoverable… Allowing more query options to filter/retrieve data?
  • Growing number of reporting standards allow data to flow from one system to another use the same word and refer to the same ‘thing’ report the same core, essential information
  • + 120 Estimated + 150 Source:MIBBI, EQUATOR + 300 Source:BioPortal miame MIAPA MIRIAM MIQAS MIX MIGEN CIMR MIAPE MIASE MIQE MISFISHIE…. REMARK CONSORT MAGE-Tab GCDML SRAxml SOFT FASTA DICOM MzML SBRML SEDML… GELML CML MITAB AAO CHEBI OBI PATO ENVO MOD BTO IDO… TEDDY PRO XAO DO VO To track provenance of the information and ensure richness of data and experimental metadata descriptions, to maximize reusability Growing number of reporting standards
  • But how much do we know about these standards
  • • A coherent, curated and searchable registry of standards for describing and reporting experiments in life science, environmental, biomedical and biotechnological domains
  • • 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
  •  Existence of a formal specification, with: • good level of documentation, with scope and use cases • ease of implementation • human and machine readability  Broad adoption and implementation, outside the initial group by: • community databases (hence existence of standards-annotated datasets) • software (e.g. for reporting, editing, curating, submitting to databases)  Active user community, also providing: • support • responsiveness to community requests • examples  Interoperability with and extensibility to other standards, ranging from: • compatibility with other standards • flexibility to cover new domains • conversion and mapping, if applicable  Openness Criteria to be used in evaluating standards for adoption: Jessica D. Tenenbaum Duke Translational Medicine Institute Melissa Haendel OHSU Library Simon Lin Marshfield Clinic Research Foundation part of the NIH Clinical and Translational Science Award (CTSA) program
  •  Database name  Main resource URL  Contact information  Date resource established (year)  Conditions of use (free, or type of license)  Scope: data types captured, curation polic  Standards implemented: checklists, terminologies, formats  Taxonomic coverage  Data accessibility/output options  Data release frequency  Versioning period and access to historical files  Documentation available  User support options  Data submission policy  Relevant publications  Tools available Core attributes to describe databases and assist in evaluating scope and relevance as well as access to data: Gaudet et al. NAR Database, 2011