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 curation focus is on literature curation. PomBase does not have dedicated GO curators but curate all aspects of papers including GO, phenotypes (single and multi gene, alleles names and descriptions, conditions), 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:
1. Literature describing the characterization of previously unknown genes, or genes previously unstudied in fission yeast
2. Legacy papers related to well studied processes, especially those providing 'direct substrate' annotation extension to build networks
Priority processes * mitotic chromosome segregation (including spindle checkpoint) (vw) * G2/M and metaphase/anaphase cell cycle transitions (vw) * cytokinesis (vw) * DNA metabolism (mah) * signalling pathways (al) * conjugation (al)
3. Approval of community curation submissions (new publications)
There are no genes with no GO annotation, or only IEA/ISO but with available literature as these are processed immediately
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