RGD December 2014

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RGD, The Rat Genome Database, December 2014

1. Staff working on GOC tasks

RGD Admin: Mary Shimoyama

GO Curators: Stan Laulederkind, Tom Hayman, Shur-Jen Wang, Victoria Petri (~1.5 fte, 0 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 2013 Annotations 2014 % Change
39916 276,761 (180,448 non-IEA) 482,079 (235,178 non-IEA) +74%

The table above is based on a review of the GOC gene_association.rgd files from December 2013 to December 2014. The number of manual annotations from RGD has increased from 42,335 to 58,561 (+ 16,226 annotations, +38%) and the number of genes with manual annotations has increased from 6113 to 6321 (+208, +3%).

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 25% of their curation efforts have been related to GO annotations in the past year.

a. Literature curation: RGD targets gene sets for manual curation and all rat papers published about those genes are curated. In 2014, there have been 2 major types of gene datasets curated:

  1. disease related: renal disease genes and sensory organ disease genes
  2. 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: genes associated with targeted disease categories, genes involved in particular biological pathways, and genes associated with specific QTLs.

4. Presentations and publications

a. Papers with substantial GO content

  1. Shimoyama M, De Pons J, Hayman GT, Laulederkind SJ, Liu W, Nigam R, Petri V, Smith JR, Tutaj M, Wang SJ, Worthey E, Dwinell M, Jacob H. The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease. Nucleic Acids Res. 2014 Oct 29. pii: gku1026.

b. Presentations including Talks and Tutorials and Teaching

c. Poster presentations with GO content

  1. Medical College of Wisconsin Research Day 2014, September 10, 2014, Medical College of Wisconsin, Milwaukee, Wisconsin: "THE RENAL DISEASE PORTAL AT THE RAT GENOME DATABASE", G. Thomas Hayman, Jennifer R. Smith, Stanley Laulederkind, Victoria Petri, Rajni Nigam, Shur-Jen Wang, Jeff De Pons, Marek Tutaj, Weisong Liu, Elizabeth A. Worthey, Melinda R. Dwinell, Mary Shimoyama, Howard J. Jacob - included information on curated GO data

5. Other Highlights

A. GO terms and related contributions by RGD

RGD has contributed 50-60 new terms, new synonyms, or definition/synonym/spelling corrections to GO from December 2013 to December 2014.

B. Annotation outreach and user advocacy efforts

C. Other highlights

Education Video tutorials, available on Scivee.tv, YouTube and Vimeo.com.

  • Gene Annotator Tutorial- including information on using curated GO data (Viewed more than 250 times in 2014 across all three video sites)