PomBase December 2015

PomBase, December 2015

PomBase is the Model Organism Database for the fission yeast Schizosaccharomyces pombe (www.pombase.org)

1. Staff working on GOC tasks

PomBase GO curators: Valerie Wood, Midori Harris, Antonia Lock

Developers associated with GO related projects at PomBase: online curation tool, pipelines, Website, automated QC, Query tools: Mark McDowall, Kim Rutherford

NO STAFF FUNDED BY GO OR GOC GRANTS

2. Annotation progress

Annotation Type	Dec 2014	Dec 5, 2015	Change	% change
Total Number of Genes: 2014 Nos * protein coding only	5052*	5451	n/a	n/a
Total Genes with at least one (non root) GO	?????	5289	n/a	n/a
Total Genes with at least one (non root) BP	4316*	4668	n/a	n/a
Total Genes with at least one (non root) CC	4894*	5191	n/a	n/a
Total Genes with at least one (non root) MF	3682*	3958	n/a	n/a
Total Annotations:	39233	40718	+1435	+3.65
Annotation by Direct Experiment
Total genes curated by experiment	????	???	tba	tba
Total genes curated by experiment	????	???	tba	tba
Annotation by Orthology
Total Genes Annotated by Orthology	?????	3484	tba	tba
Total Orthology Annotation	????	9346	tba	tba
Annotation by PomBase	?????	9134	tba	tba
Annotation by GOA-UniProt	????	128	tba	tba
Annotation by GOC	????	4	tba	tba
IEA Annotation
Total Annotations:	5342	4290	tba	tba

3. Methods and strategies for annotation

a. Literature curation:

PomBase is primarily focussed on literature curation. PomBase does not have dedicated GO curators. PomBase curators curate all aspects of papers including GO, phenotypes (single and multi gene, alleles names and descriptions, conditiong), modifications, modifiers, upstream, downstream targets, genetic and physical interactions, complementations, orthology, disease associations, proteins features, gene co-ordinates,, other sequence features)

Community curation

b. Computational annotation strategies:

c. Priorities for annotation:

4. Presentations and publications

a. Papers with substantial GO content

b. Presentations including Talks and Tutorials and Teaching

c. Poster presentations with GO content

5. Other Highlights

A. GO terms and related contributions by PomBase

Submitted 2228 term or ontology update requests https://github.com/geneontology/go-ontology/issues?utf8=%E2%9C%93&q=+label%3APomBase+

Requested *** new terms via term Genie

Submitted 960 electronic mapping update requests https://github.com/geneontology/go-annotation/issues?utf8=%E2%9C%93&q=valwood

B. Annotation outreach and user advocacy efforts

C. Other highlights