RGD December 2015
RGD, The Rat Genome Database, December 2015
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: Marek Tutaj, Jeff DePons (1 fte, 0 fte funded by NHGRI GOC grant)
2. Annotation progress
|Gene Products||Annotations 2014||Annotations 2015||% Change|
|40204||482,079 (235,178 non-IEA)||547,064 (314,567 non-IEA)||+13%|
The table above is based on a review of the GOC gene_association.rgd files from December 2014 to December 2015. The number of manual annotations from RGD has increased from 44,967 to 49,791 (+ 4,824 annotations, +11%) and the number of genes with manual annotations has increased from 5,625 to 5,998 (+373, +7%).
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 2015, there have been 2 major types of gene datasets curated:
- disease related: sensory organ disease genes and age-related disease genes
- 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: 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
- Liu W, Laulederkind SJ, Hayman GT, Wang SJ, Nigam R, Smith JR, De Pons J, Dwinell MR, Shimoyama M. OntoMate: a text-mining tool aiding curation at the Rat Genome Database. Database (Oxford). 2015 Jan 25;2015. pii: bau129. doi: 10.1093/database/bau129. Print 2015.
- 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. 2015 Jan;43(Database issue):D743-50. doi: 10.1093/nar/gku1026.
b. Presentations including Talks and Tutorials and Teaching
- Eighth International Biocuration Conference, April 23-26, 2015, Friendship Hotel, Beijing, China: "Gene Curation Software at the Rat Genome Database: Update 2015", Stanley J. F. Laulederkind - lightning talk based on poster mentioned below, included information on curating GO data
c. Poster presentations with GO content
- Eighth International Biocuration Conference, April 23-26, 2015, Friendship Hotel, Beijing, China: "Gene Curation Software at the Rat Genome Database: Update 2015", Stanley J. F. Laulederkind, Weisong Liu, Marek Tutaj, G. Thomas Hayman, Rajni Nigam, Victoria Petri, J. R. Smith, Shur-Jen Wang, Jeff De Pons, M. R. Dwinell, Mary Shimoyama - included information on curating GO data
5. Other Highlights
A. GO terms and related contributions by RGD
RGD has contributed 400 - 450 new terms, new synonyms, or definition/synonym/spelling corrections to GO from December 2014 to December 2015.
B. Annotation outreach and user advocacy efforts
C. Other highlights
Education Video tutorials, available on YouTube, Vimeo.com, and rgd.mcw.edu.
- OLGA (Object List Generator tool) Tutorial- including information on using curated GO data
- Gene Annotator Tutorial- including information on using curated GO data