BUILDING THE OBO FOUNDRY – ONE POLICY AT A TIME

400 views

Published on

Policy drafting,discussion and implementation is not the most exciting or interesting thing to do when developing new resources. However, when trying to identify existing work that can be built upon in one’s project, such policies are critical to allow interoperability and reliability. We describe some tools and guidelines developed under the OBO Foundry umbrella, and show how they help realize crit- ical maintenance functions, increasing overall quality and sustainability of resources.

Published in: Health & Medicine
  • Be the first to comment

  • Be the first to like this

BUILDING THE OBO FOUNDRY – ONE POLICY AT A TIME

  1. 1. BUILDING THE OBO FOUNDRY –ONE POLICY AT A TIMEINTERNATIONAL CONFERENCE ON BIOMEDICAL ONTOLOGYWORKING WITH MULTIPLE BIOMEDICAL ONTOLOGIES WORKSHOPJULY 26TH 2011BUFFALO, NY Mélanie Courtot* , C. Mungall, R. Brinkman and A. Ruttenberg *BC Cancer Agency, Vancouver, BC, Canada
  2. 2. Working with multiple biomedicalontologies  Collaborative effort  Requires common framework to build upon  Need for shared principles Goal is to have reliable, expandable resources that can interoperate
  3. 3. Need for policies  Interoperability of resources  Reliability of resources  Common tools development   Resources handling   OBO/OWL converter, http://code.google.com/p/oboformat/   MIREOT: 1 URI  1 entity   Resources browsing and dereferencing   OntoBee: HTML for human, RDF for machine   http://ontobee.org
  4. 4. A common ID policy for reliableURIs  Specify how to perform the OBO, OBO legacy and OWL URIs interconversion  Reliable URIs, unique across OBO Foundry   Each URI denotes one entity  Common tools   ID assignment and checks   Common dereferencing platform   Stable user experience: versioning system, tracker and home project references…  http://obofoundry.org/id-policy.shtml
  5. 5. A shared metadata set to improvedocumentation  Reliance on the IAO ontology-metadata file   http://purl.obolibrary.org/obo/iao  Tools expect and can build upon iao:definition and iao:editor preferred term  Extra documentation:   Definitionsource: can be link towards website, paper…   Term editor: provides contact point   Example of usage, editor notes: further context   Curation status, obsolescence reason   OBO foundry unique label
  6. 6. Maintaining orthogonality  Avoid redundancy and duplication of work  Minimum Information to Reference and External Ontology Term (MIREOT) allows incorporation of selected terms from a source into a target ontology   MélanieCourtot, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan R. Brinkman, and Alan Ruttenberg, MIREOT: The minimum information to reference an external ontology term. Applied Ontology, Vol. 6, Nr. 1 (2011) , p. 23-33
  7. 7. Need for a common deprecationpolicy  Currently only GO and OBI policies have been formalized   http://wiki.geneontology.org/index.php/ Curator_Guide:_Obsoletion   http://obi-ontology.org/page/OBIDeprecationPolicy  Some issues with for example term merging in OBO   When terms are merged one becomes an alt_id on the other   Terms URIs disappear from the OWL translation   Issues for tools (e.g., MIREOT) which rely on URI stability   Accepted issue
  8. 8. Status and perspectives  Tools support improving   “renderby label” menu and “D” for deprecated class in P4, MIREOT protégé plugin, OntoFox  Call for contribution:   IDpolicy: feedback on OntoBee, release and versioning   Metadata set: properties for conversion OBO <-> OWL needed   MIREOT: integration with modularization algorithms   Deprecation policy: to be formalized
  9. 9. Acknowledgements  OBO consortium members  Timothy Redmond and the Protégé team  Trish Whetzel and the BioPortal team

×