RGD November 2011

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RGD, The Rat Genome Database, December 2009

1. Staff working on GOC tasks

RGD Admin: Simon Twigger, Mary Shimoyama

GO Curators: Stan Laulederkind, Tom Hayman, Tim Lowry, Victoria Petri, Shur-Jen Wang (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: Jeff DePons (1 fte, 0 fte funded by NHGRI grant)

2. Annotation progress

Gene Products Annotations 2008 Annotations 2009 % Change
20466 169,127 191,323 (109127 non-IEA) +13%


Based on a review of the GOC gene_association.rgd files from November 2008 and December 2009, the total number of annotations from RGD has increased from 81980 to 102,728, an increase of 20,748 (25%), with annotations for 11,652 gene products (+843, 8% from 2008). The number of manual annotations from RGD has increased from 23,555 to 30,418 (+6,863 annotations, 29%) and the number of genes with manual annotations has increased from 4,785 to 5,362 (+577, 12%). Significant changes this year include the change in evidence code for our automated ortholog pipelines that map GO annotations from mouse orthologs. These were previously listed as ISS but this was changed to ISO following the evidence code guidelines.

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. In 2009, there have been 3 major types of gene datasets curated:

  1. disease related: diabetes genes
  2. genes which are part of the Reference Genome Annotation Project
  3. genes involved in targeted metabolic, signaling, regulatory, and disease pathways.

b. Computational annotation strategies:

  1. 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.
  2. ISO - RGD is not currently doing manual annotation with ISO. ISO annotations are created through our automated pipelines that map GO annotations from mouse genes over to their Rat orthologs. For each mouse gene that has a confirmed rat ortholog, if the GO annotation to the Mouse gene is of evidence type IDA, IMP, IPI, IGI or IEP then the annotation is loaded onto the rat ortholog as an ISO annotation.
  3. 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

  1. Reference Genome Group of the Gene Ontology Consortium. The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species, PLoS Comput Biol. 2009 Jul;5(7):e1000431. (PMCID: PMC2699109)
  2. The Rat Genome Database 2009: variation, ontologies and pathways. Nucleic Acids Res. 2009 Jan;37(Database issue):D744-9 (PMCID: PMC2686558)


b. Presentations including Talks and Tutorials and Teaching

  1. Simon Twigger and Jennifer Smith taught lectures on Ontologies and the Gene Ontology as part of the Bioinformatics: Tools and Tactics course, a component of the Physiology Ph.D. program at the Medical College of Wisconsin.
  2. Rat Genomics & Models, December 2 - 5, 2009, Cold Spring Harbor, NY, Workshop: "Rat Genome Database" - Presentations featuring use of gene ontology on the RGD website.
  3. Rat Genomics & Models, December 2 - 5, 2009, Cold Spring Harbor, NY, Presentation: "The Rat Genome Database Genome Viewer" - Presentation featuring gene ontology information accessed through the RGD genome viewer.


c. Poster presentations

  1. MCW Research Day, September 16, 2009, Milwaukee, WI - poster presenting information about RGD gene report pages prominantly featuring gene ontology annotations.
  2. Rat Genomics & Models, December 2 - 5, 2009, Cold Spring Harbor, NY Poster: "Multiple ontologies for prioritizing and standardizing biological information at the Rat Genome Database"

5. Other Highlights

A. GO terms contributed by RGD

RGD has contributed 23 new terms to GO this year.

B. Annotation outreach and user advocacy efforts


C. Other highlights

Ontology Education Video tutorials, available on Scivee.tv, YouTube and Vimeo.com developed in conjunction with the NCBO