RGD December 2010

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RGD, The Rat Genome Database, December 2010

1. Staff working on GOC tasks

RGD Admin: Mindy Dwinell, Mary Shimoyama

GO Curators: Stan Laulederkind, Tom Hayman, Shur-Jen Wang, Victoria Petri, Tim Lowry (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 grant)

2. Annotation progress

Gene Products Annotations 2009 Annotations 2010 % Change
28916 191,323 (109127 non-IEA) 246,172 (123,731 non-IEA) +28%


The table above is based on a review of the GOC gene_association.rgd files from December 2009 to December 2010. The number of manual annotations from RGD has increased from 30,418 to 36,791 (+ 6373 annotations, +21%) and the number of genes with manual annotations has increased from 5,362 to 5844(+482, +9%).

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 2010, there have been 3 major types of gene datasets curated:

  1. disease related: pancreato-biliary cancer genes and respiratory disease 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. RGD has also participated in the electronic reference genome curation jamborees in February and November of this year.

4. Presentations and publications

a. Papers with substantial GO content - none

b. Presentations including Talks and Tutorials and Teaching

  1. Fourth International Biocuration Conference, October 11-14, 2010, Tokyo, Japan , Presentation: “Gene Curation Software at the Rat Genome Database (RGD)” - talk focused on software used for GO curation.
  2. "Introduction to Biomedical Ontologies #4: Ontology Term Enrichment Using RatMine", video tutorial on the RGD website (http://rdg.mcw.edu) deployed in November 2010.


c. Poster presentations

  1. XVIIIth International Workshop on Genetic Systems in the Rat, November 30-December 3, 2010, Kyoto, Japan, Rat Genomics & Models, " The Rat Genome Database: Resources for Genomics Research” – included information on use of gene ontology
  2. The 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), July 11 ¬– July 13, 2010, “Increasing Curation Efficiency: RGD’s Software Suite” – included information on software for GO curation
  3. The 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), July 11 ¬– July 13, 2010, “Disease Portals at the Rat Genome Database: A Platform for Genetic and Genomic Research” – included information on curated GO data
  4. The 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), July 11 ¬– July 13, 2010, “Curating the Rat Genome: RGD’s Automated Data Integration Pipelines Maximize Coverage” – included information about GO annotation bulk downloads
  5. The 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), July 11 ¬– July 13, 2010, “The Rat Genome Database – Genome Browser” - included information about GO annotations
  6. The 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), July 11 ¬– July 13, 2010, “The Rat Genome Database Genome Viewer” - included information about GO annotations

5. Other Highlights

A. GO terms and related contributions by RGD

RGD has contributed 80 new terms, 18 new synonyms, and 19 definition/synonym/spelling corrections 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

  • Introduction to Biomedical Ontologies #4- Ontology Term Enrichment Using RatMine (Viewed 71 times during the first four days across all three video sites)
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