RGD May 2011
From GO Public
RGD, The Rat Genome Database, May 2011
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 GOC grant)
2. Annotation progress
|Gene Products||Annotations December 2010||Annotations May 2011||% Change|
|28916||246,172 (123,731 non-IEA)||251792 (129451 non-IEA)||+22%|
The table above is based on a review of the GOC gene_association.rgd files from December 2010 to May 2011. The number of manual annotations from RGD has increased from 36,791 to 39,880 (+ 3099 annotations, +8%) and the number of genes with manual annotations has increased from 5,844 to 6757 (+913, +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. In 2011, there have been 3 major types of gene datasets curated:
- disease related: respiratory 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 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.
- 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
- The Rat Genome Database curation tool suite: a set of optimized software tools enabling efficient acquisition, organization, and presentation of biological data. Laulederkind SJ, Shimoyama M, et. al. Database (Oxford). 2011 Feb 14;2011:bar002. Print 2011.
b. Presentations including Talks and Tutorials and Teaching
- International Rat Workshop 2010 in Kyoto, Japan, Nov 30 – Dec 3, RGD: A Tutorial for Data, Searches and Tools” - included information about GO annotations at RGD
c. Poster presentations
- International Rat Workshop 2010 in Kyoto, Japan, Nov 30 – Dec 3, “The Rat Genome Database: Resources for Genomics Research ” - included information about GO annotations at RGD
5. Other Highlights
A. GO terms and related contributions by RGD
RGD has contributed 15 new terms, 14 new synonyms, and 51 definition/synonym/spelling corrections to GO this year.
B. Annotation outreach and user advocacy efforts
C. Other highlights