RGD November 2011
RGD, The Rat Genome Database, November 2011
1. Staff working on GOC tasks
RGD Admin: Mindy Dwinell, Mary Shimoyama
GO Curators: Stan Laulederkind, Tim Lowry, Tom Hayman, Shur-Jen Wang, Jennifer Smith, Victoria Petri (2.5 fte, 0.8 funded by NHGRI GOC grant)
IT staff associated with GO related projects such as the development of the online curation tool and of pipelines, the updates/loads of GO ontologies in the database and the generation and submission of RGD Gene Association files: Weisong Liu, Marek Tutaj, Jeff DePons (1 fte, 0 fte funded by NHGRI GOC grant)
2. Annotation progress
| Gene Products | Annotations December 2010 | Annotations May 2011 | % Change |
|---|---|---|---|
| 23636 | 129451 non-IEA | 134760 non-IEA | +4% |
The table above is based on a review of the GOC gene_association.rgd files from May 2011 to December 2011. The number of manual annotations from RGD has increased from 39,880 to 43,590 (+ 3710 annotations, +9%) and the number of genes with manual annotations has increased from 6757 to 7617 (+860, +13.5%).
3. Methods and strategies for annotation
Because the pipelines for GO annotations are automated and updated weekly, all of the curators’ efforts are involved in manual annotation. Although RGD curators also annotate to other ontologies, approximately 75% of their curation efforts are related to GO annotations
a. Literature curation: RGD targets gene sets for manual curation and all rat papers published about those genes are curated. Since May 2011, there have been 3 major types of gene datasets curated:
- disease related: respiratory disease genes, neurological disease genes, immunological/inflammatory disease genes
- genes which are part of the Reference Genome Annotation Project
- genes involved in targeted metabolic, signaling, regulatory, and disease pathways.
b. Computational annotation strategies:
- Rat genes manually curated by other groups are brought in electronically from GOA with their associated evidence codes and the originating group acknowledged in the source.
- ISO - RGD is not currently doing manual annotation with ISO. ISO annotations are created through our automated pipelines that map GO annotations from mouse and human genes over to their rat orthologs. For each mouse or human gene that has a confirmed rat ortholog, if the GO annotation to the mouse or human gene is of evidence type IDA, IMP, IPI, IGI or IEP then the annotation is loaded onto the rat ortholog as an ISO annotation.
- IEA - rat annotations based on GO mapping to InterPro, Enzyme Commission and Swiss-Prot keywords, are brought in electronically with IEA evidence code from GOA. Annotations from GOA for all categories are updated weekly.
c. Priorities for annotation: There are several ways in which RGD assigns priorities for the annotation of genes to GO ontology terms. These include: the genes in the monthly list for the Reference Genome Annotation Project, genes associated with targeted disease, and genes involved in particular pathways.
4. Presentations and publications
a. Papers with substantial GO content
- Ontology Searching and Browsing at the Rat Genome Database. Laulederkind SJ, Tutaj M, et. al. Database (Oxford), manuscript submitted.
5. Other Highlights
A. GO terms and related contributions by RGD
RGD has contributed 74 new terms, 10 new synonyms, and 27 definition/synonym/spelling corrections to GO since May 2011.
B. Annotation outreach and user advocacy efforts
C. Other highlights