PomBase December 2015: Difference between revisions
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i. Literature describing the characterization of previously unknown genes, or genes previously unstudied in fission yeast | i. Literature describing the characterization of previously unknown genes, or genes previously unstudied in fission yeast | ||
ii. Approval of community curation submissions (new publications) | 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 | |||
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 | Priority processes | ||
* mitotic chromosome segregation (including spindle checkpoint) (vw) | * mitotic chromosome segregation (including spindle checkpoint) (vw) |
Revision as of 09:47, 19 November 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:
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.