Ontology Development Progress Report December 2012

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  • We have developed a model for modular GO annotations, which will guide the modularization of the ontology. We

refer to the model internally as Logical Extension of GO. We have vetted this model on a number of different biological cases, which has helped refine the model.

  • We completed a project with the Neuroscience Information Framework (NIF) to expand the GO cellular component ontology

such that it can replace the NIF Subcellular Anatomy Ontology (SAO) in NIF.

  • We organized a workshop in January 2012 to train GO ontology editors in the use of Protégé and the expression of GO in OWL. OWL

reasoners are now run as part of standard operating procedure to check the logical integrity of the ontology after each change is committed.

  • We have ported the OBO-Edit graph viewer component to a Protégé plugin.
  • We have switched version control system from CVS to SVN.
  • We have fully integrated internal cross-products (logical definitions) for all ‘regulation’, ‘involved in’, ‘regulation by’ ‘occurs

in’ and ‘part of cellular component’ terms.

  • We have fully integrated cross-products to CHEBI chemicals for all ‘binding’, export’, ‘import’, ‘transport’, ‘transporter’,

‘response to’ and ‘metabolism’ terms, and have a system in place to ensure all new cross-products are generated prospectively, at the time of term creation.

  • 36% of all GO terms now have cross-products associated with them.
  • We have implemented a web-based tool called

TermGenie (http://go.termgenie.org) that allows users to request template-based cross-product terms. These terms are automatically defined and placed in the ontology. This has significantly reduced annotation bottlenecks, and has freed up GO editors to work on areas of the ontology where their specialist knowledge is required.

  • We have extended TermGenie to allow submission of non-templated terms.
  • We have configured a Continuous Integration server (Jenkins) to perform OWL-based validation and deployment of the ontology, using the OBO Ontology Release Tool (OORT)
  • 784 new tracker tickets have been submitted to GO and ontology developers have closed 1,015 tickets, clearing much of the pre-existing backlog.