Compositional Term Submission Tool

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Revision as of 17:27, 14 June 2011 by Cjm (talk | contribs) (→‎v2)
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(aka TermGenie)

Project lead: Chris

Coordinates with: ontology-editors


An increasing number of terms coming in from sourceforge are automatable compositional terms - particularly regulation terms. Ontology editors waste time performing manual tasks that could be automated, and curators experience a bottleneck during annotation.

The compositional term request system allows annotators to use a web template system to instantaneously get the term they require, provided it conforms to an existing pre-determined template. A reasoner is used to place the term automatically in the hierarchy.

Documentation for the system is available here: TermGenie


Project Dependencies


#v1 is available to curators, currently on regulation requests are live



v1 is obo-format dependent, uses a custom reasoner, and relies on various ad-hoc scripts

v1 report

A report on the v1 implementation is available:


v2 will be a port of #v1

  • implemented in Java
  • works off of OBO or OWL files
  • uses OWLAPIv3
  • runs in TomCat/Jetty
  • uses OWL reasoners

Dependencies: Transition to OWL

See: TermGenie2

Reasoner Benchmarks

Need to test various OWL reasoners, simulate evolution of GO

Feasibility Study

Determine feasibility of java version