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.
1. BUILDING THE OBO FOUNDRY –
ONE POLICY AT A TIME
INTERNATIONAL CONFERENCE ON BIOMEDICAL ONTOLOGY
WORKING WITH MULTIPLE BIOMEDICAL ONTOLOGIES WORKSHOP
JULY 26TH 2011
BUFFALO, NY
Mélanie Courtot* , C. Mungall, R. Brinkman and A. Ruttenberg
*BC Cancer Agency, Vancouver, BC, Canada
2. Working with multiple biomedical
ontologies
Collaborative effort
Requires common framework to build upon
Need for shared principles
Goal is to have reliable, expandable resources
that can interoperate
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. A common ID policy for reliable
URIs
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. A shared metadata set to improve
documentation
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. 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. Need for a common deprecation
policy
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. 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