Transition to OWL 2010-2012

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Project lead: Chris Mungall


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.


Ontology Development

Software Libraries

Additional Points of Connection

OBO-Format mail list. Subscribe on either sourceforge or googlegroups.


obof1.4 guide

Status: draft

obof1.4 syntax

Formal specification of syntax

Status: awaiting community comments

OWL2 Mapping

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

OE Bridge

  • Bridge org.obo.datamodel and org.oboformat.obodoc

short term bridge: OWL write from OE, save obo, invoke obo2owl

JUnit Test Suite

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

also -- test for roundtripping GO


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

Tools Comparison Report

A report comparing ontology development environments. The report should include a matrix of capability x tool

Tools include:

  • OE2
  • Protege4
  • WebProtege
  • CMAP
  • TopBraid
  • BioSphere
  • TermGenie

Capabilities include:

  • formats
    • obo (1.4, 1.2)
  • owl (owl1, owl2)
  • Integrated Reasoning
    • over owl
    • over obo subset of owl
  • Visualization
    • Subclass hierarchies vs all relations
    • Visualization integrated with reasoning
    • Visualization + editing
  • Search/Queries
    • Combined terminological / graph / reasoning
  • Customization/Rendering
  • QC capabilities
  • Working with multiple ontologies
  • Editing logical definitions

Other points:

  • Documentation
  • User community
  • Ease of use
  • Intended application


Integrated into OWLAPIv3/Protege4

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