PomBase December 2015

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Revision as of 09:08, 19 November 2015 by Valwood (talk | contribs) (Progress report)
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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:


Computational annotation strategies
Total Genes Annotated by Orthology ????? 3484 tba tba
Priorities
Total Annotations: 5342 4290 tba tba

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 http://tinyurl.com/qzz7kn9

Requested *** new terms via term Genie

Submitted 960 electronic mapping update requests http://tinyurl.com/oh45ouh


B. Annotation outreach and user advocacy efforts


C. Other highlights