Ontology Development Progress Report December 2010

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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.

External cross-products: 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 July with the CHEBI ontology developers to reconcile some of the critical differences between the two ontologies. This project requires major changes to both GO and CHEBI and we hope the first CHEBI cross-products will be added to GO early in 2011. We have finished a first draft of a paper on this project to go to Nature Chemical Biology.

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.

Function-Process links

We continued to make relationships between the function and process ontologies - links between the transporters and transport terms were completed in June.

Mappings

In 2010, over 1500 enzyme reactions in GO were synchronized with MetaCyc, KEGG, RHEA and EC. The reaction text was converted to reflect ChEBI names.

GO slims

A new version of the generic (non-species specific) GO slim was developed this year, a draft is currently available.

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.

Content Projects

Transcription

A major overhaul of the transcription process and function terms was made this year. This project involved one curator attending the Gene Transcription in Yeast meeting in Sant Feliu de Guixols in Spain in late June, to obtain expert input. Several rounds of changes have been made to the ontologies so far, and we expect the project to be completed by the end of the year.

Signaling

The GO signaling working group is working to expand and improve the signaling terms in GO. At the start of 2010, signaling terms in the process ontology were restructured to include different types and mechanisms of signaling, and to connect the signaling pathways with the processes they regulate. We are currently standardising these terms to ensure more consistent annotation, and have begun to refine the signaling terms in the function ontology.

We have recently recruited three experts in signaling to help with the restructuring and to ensure that signaling is represented correctly in GO, and a two-day workshop with GO editors, GO annotators and signaling experts is scheduled for February 2011.

Kidney Development

Following a 1-day meeting with renal experts in January 2010 445 new terms relating to kidney development were added to GO. The terms represent development of the various renal systems across organisms:

  • metanephros (mammalian; 129 terms)
  • pronephros (amphibian; 24 terms)
  • mesonephros (fish; 102 terms)
  • renal system/ Malpighian tubule (insect; 18 terms).

A publication is currently in progress.

Viral terms

A project to remodel the terms related to viruses in GO was begun this year. The working group - which includes many externally collaborating groups - met several times and have come up with a broad structure for the representation of viral processes and components in GO. The new structure will be implemented in 2011.

Heart Development

A paper describing the heart development project has been submitted to Developmental Biology