Transition to OWL 2010-2012

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Revision as of 19:05, 17 August 2010 by Cjm (talk | contribs)
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Project lead: Chris Mungall

Purpose

Many tools of use to the Ontology_Development group are dependent on OWL. The GO also needs to interoperate well with OWL ontologies to leverage work done by external groups. This includes using other ontologies in computable definitions, as well as selective imports of sections of other ontologies. For example, we would like to leverage the NIF neuroscience ontologies which are managed in OWL.

Current obo2owl translations are buggy and underspecified. We need to make translation seamless. We will also explore the eventual use of OWL as the primary format used by the ontology editors, with a choice of tooling available. Of course OE could still be used to edit the ontology, and obo format will be available for downstream users.

Deliverables

obof1.4 guide

http://www.geneontology.org/GO.format.obo-1_4.shtml

Status: draft

obof1.4 syntax

Formal specification of syntax

http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html

Status: awaiting community comments

OWL2 Mapping

http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html#5

Status: awaiting community comments

Java OBO Parser

We need a ground-up rewrite of the OBO parser according to the spec. This will be a direct translation to OBO abstract syntax. This will form the basis of a future P4 parser

Status: alpha version

http://code.google.com/p/oboformat/

JUnit Test Suite

There must be a parser test suite covering all obo format tags

OWLAPI Bridge

Create a bridge layer between the OBO Parser and the OWLAPIv3 model.

Users can use the OBO Parser in its own right or seamlessly within the OWLAPI

Integration

Integrated into OWLAPIv3/Protege4

Add option to P4 to do simultaneous saves to obo/owl (this will facilitate OE/P4 synchronization)