Ontology Development Progress Report December 2010: Difference between revisions

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====Signaling====
====Signaling====
====Taxon Triggers====
====Taxon Triggers====
The taxon trigger file is a set of taxonomic restrictions for specific GO terms that is used for automatic quality control of annotations. The file resides in [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/quality_control/annotation_checks/taxon_checks/taxon_go_triggers.obo | cvs] and is edited as new restrictions are made. A [http://www.biomedcentral.com/1471-2105/11/530|paper] on this project has recently been published in BMC Bioinformatics.
The taxon trigger file is a set of taxonomic restrictions for specific GO terms that is used for automatic quality control of annotations. The file resides in [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/quality_control/annotation_checks/taxon_checks/taxon_go_triggers.obo | cvs] and is edited as new restrictions are made. A [http://www.biomedcentral.com/1471-2105/11/530 paper] on this project has recently been published in BMC Bioinformatics.

Revision as of 09:36, 30 November 2010

Ontology Development

Metrics

GO term statistics

November 30, 2009

Current Defined Obsolete Total
Function 8657 8474 798 9455
Process 17533 17465 508 18041
Component 2613 2613 117 2731
All 28803 29976 1424 30227


November 24, 2010

Terms
Function 8898
Process 19900
Component 2773
All 31571

Note that all GO terms are now defined. The numbers above do not include the 1460 obsolete terms.

Tracker statistics (Nov. 30, 2009 - Nov 24, 2010)

  • items opened: 1158
  • items closed: 1242

Tracker report

Tracker Report for 2010

Ontology development

Internal Cross Products

We have made considerable progress this year on creating cross-products for GO terms. The first set of cross-products, between regulatory processes and regulated processes or functions, were added to the GO file at the beginning of 2010. Subsequently, two further sets have been added: biological processes involved in other biological processes, and cellular components that are part of other cellular components.

Term Genie

As a result of these changes, we have been able to develop a tool – TermGenie – that allows users to add new GO terms that conform to a cross-product template directly to the ontologies. Terms are automatically placed correctly within the ontology, and textual definitions and synonyms are automatically generated. This tool reduces the workload for ontology editors and helps reduce human error in the ontologies.

CHEBI alignment

The biggest effort this year has gone into aligning GO with the Chemical Entities of Biological Interest (CHEBI) ontology, with the aim of generating cross-products between GO and CHEBI. This work involved a 2-day meeting in September with the CHEBI ontology developers to reconcile some of the critical differences between the two ontologies. We hope the first CHEBI cross-products will be added to GO early in 2011.

OBO Foundry

We are active members of the OBO Foundry and earlier this year GO became one of the founder set of OBO Foundry ontologies, having undergone peer review and found to meet the agreed OBO Foundry standards.

Signaling

Taxon Triggers

The taxon trigger file is a set of taxonomic restrictions for specific GO terms that is used for automatic quality control of annotations. The file resides in | cvs and is edited as new restrictions are made. A paper on this project has recently been published in BMC Bioinformatics.