PomBase December 2015

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Revision as of 09:47, 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 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:

i. Literature describing the characterization of previously unknown genes, or genes previously unstudied in fission yeast

ii. Approval of community curation submissions (new publications)

iii. Legacy papers related to well studied processes, especially those providing 'direct substrate' annotation extension to build high quality networks/pathways based on GO data see "regulation of mitotic cell cycle" http://tinyurl.com/osp4nnq

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)

(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

See workshops and presentation above


C. Other highlights

1. Building networks based on GO annotation Dataset http://www.pombase.org/documentation/high-confidence-physical-interaction-network Access to process based high confidence interaction networks http://www.pombase.org/browse-curation/fission-yeast-go-slim-terms


2. Increasing GO slim breadth http://www.pombase.org/browse-curation/fission-yeast-go-slim-terms Proteins with a biological process annotation not covered by the slim (gene count: 115) Proteins with no GO slim or biological process annotation (gene count: 756)


3. Creating inventories of conserved and non conserved unstudied genes http://www.pombase.org/status/priority-unstudied-genes In fission yeast the "unknown" inventory is around 831 entries, many of which are apparently species-specific. However, a large number (511) are conserved, and a significant number of these (183) have orthologs in vertebrates.


4. Developing curation rules to improve curation depth and accuracy http://www.slideshare.net/ValerieWood/pombase-internal-rules-for-curation-using-ontologies Includes a) Removing IEA redundancy PomBase filters >87% of available IEA annotation (covered by manual annotation). Redundant experimental annotations are not filtered. b) Flagging high level GO terms as "not for direct annotation". PomBase excludes 1120 GO terms for direct annotation.


5. We have developed Canto, an intuitive web-based interface to support literature curation using ontologies, and a literature management environment. Canto supports GO curation and is a generic component of the GMOD project and can be easily configured for use with other organisms, and ontologies. Currently Canto is being extended to fully support annotation extensions by community curators by restricting curator options based on domain and range of terms applicable to a given relationship. We are also working to use taxon constraints to limit available term choices by species.