Ontology Development Progress Report December 2008
Ontology Development
Metrics
GO term statistics
December 1, 2007
| Current | Defined | Obsolete | Total | |
|---|---|---|---|---|
| Function | 7986 | 7605 | 559 | 8545 |
| Process | 14307 | 14145 | 460 | 14767 |
| Component | 2046 | 2046 | 114 | 2160 |
| All | 24339 | 24929 | 1133 | 25472 |
November 30, 2008
| Current | Defined | Obsolete | Total | |
|---|---|---|---|---|
| Function | 8439 | 8137 | 765 | 9204 |
| Process | 15723 | 15594 | 479 | 16202 |
| Component | 2245 | 2245 | 117 | 2362 |
| All | 26407 | 27337 | 1361 | 27768 |
SourceForge statistics (Dec 1, 2007 - Nov. 30, 2008)
- items opened: 1037
- items closed: 1062
SourceForge reports (on SF site)
Completed work
Regulation
To improve the representation of biological regulation in the GO, three new relationship types -- regulates, negatively_regulates and positively_regulates -- have been introduced in the Biological Process ontology. Prior to this change, regulation terms were related to other terms via part_of, despite the fact that regulatory processes are not necessarily integral to the processes they regulate. Using reasoning and quality control reports, we have thoroughly reviewed the relationships involving regulatory processes and their targets to ensure internal consistency. If a term 'regulation of process X' exists in the ontology, it must be a valid subtype of 'regulation of biological process', and must have a regulates relationship with 'process X' or be a valid subtype of another regulatory process. Likewise, regulation of molecular function terms have been aligned with the corresponding terms in the molecular function ontology, and we are working to align regulation of biological quality terms with PATO. Approximately 1300 relationships have been added, and 540 deleted, as part of this work; 53 new terms were also added, and many definitions and synonyms reviewed.
We have made further progress towards creating links between the three GO ontologies, beginning with Molecular Function-Biological Process links. The regulates relationships will be used in the first links between the Molecular Function and Biological Process ontologies -- we will make the implicit regulatory relationships between 'regulation of molecular function' Biological Process terms and the corresponding Molecular Function terms explicit in early February 2009. Additional Molecular Function-Biological Process links are under development, based on single-step processes (e.g. 'protein phosphorylation'), mining external pathway resources such as Reactome and MetaCyc, and curated relationships for some metabolic pathways, are in preparation.
Other completed work
- (i.e. those that refer only to terms from one or more of the three branches of the GO) are undergoing curatorial review, and a plan for integrating them into the authoritative version of the GO has been formulated. Cross-products between GO and external ontologies such as the OBO Cell ontology are pending.
- A content meeting on lung development was held in Boston, MA, on December 5-6, 2007. Participants added 152 new terms describing the anatomical representation of lung development to a branch version of the GO flat file. Experts in the field suggestedthat the file be expanded using more description process terms. Work on this project is ongoing.
- Smaller-scale efforts include:
- Reorganization of Molecular Function terms representing peptidase activities
- 359 new terms for the Plant-Associated Microbe Gene Ontology () project
- File noting correlations between GO terms and taxon information available for use as a set of triggers for annotation quality control.
Work in progress
- Signal transduction terms
- Transcription terms
- Virus-related terms
- Biological process terms describing cellular component organization
- See Molecular Function-Biological Process links above
Ontology Quality Control
We have implemented a number of ontology quality control procedures, and more are under discussion. Several checks on text and ontology structure are built into OBO-Edit, and we also use a few custom checks. Reasoner-based checks are run periodically, external to the ontology editing cycle, and generate reports that curators use to correct errors in the ontology. At present the reasoner-based reports identify potential missing relationships, potential misplaced terms or potential term nomenclature issues.