RGD, September 2009

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RGD, The Rat Genome Database, September 2009

1. Staff working on GOC tasks

GO Curators: Stan Laulederkind, Victoria Petri, Tom Hayman, Tim Lowry (2 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(0.1 fte, 0 fte funded by NHGRI grant)

2. Annotation progress

From January to September the number of manually generated GO annotations increased by 4895 from approximately 20,655 to 25,350, representing a 23% increase in the number of annotations for 2009, so far. The number of genes with manual GO annotations has increased from approximately 4,904 to 5,305 representing a 8% increase during this time period.

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 50% 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). ISS - RGD is not currently doing manual annotation with ISS. ISS annotations are brought in from MGD and GOA. The pipelines for these have been redesigned to allow weekly updates, filter out redundancies and inappropriate associations. The IT developers have closely worked with the curators to assure the robustness of the pipelines; the orthology is manually assessed.

(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 jamboree in February and July of this year. Collaborators for GO ontology development have published earlier a list of genes that have been identified in humans as drug transporters. The orthologous rat genes are going to be targeted for annotations at some point in the future.

4. Presentations and publications

a. Papers with substantial GO content - none

b. Presentations including Talks and Tutorials and Teaching

(1) "Introduction to Biomedical Ontologies #1: What is an Ontology?", video tutorial on the RGD website (http://rdg.mcw.edu) deployed in Summer of 2009

(2) “Introduction to Biomedical Ontologies #2: Anatomy of an Ontology Annotation, part 1”, video tutorial on the RGD website (http://rdg.mcw.edu) deployed in September 2009

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.

5. Other Highlights

A. GO terms contributed by RGD

RGD submitted about 55 new term/synonym requests since January 2009, which resulted in approximately 50 new terms/synonyms added to the ontology.

B. Annotation outreach and user advocacy efforts - none

C. Other highlights - none