MGI December 2013: Difference between revisions
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= Methods and strategies for annotation = | = Methods and strategies for annotation = | ||
'''''Literature curation:''''' | |||
Literature curation continues to be the major focus of our annotation efforts. | |||
'''''Computational annotation strategies:''''' | |||
As always, current strategies involve use of translation table to mine SwissProt keywords, InterPro domains, and EC numbers for IEA annotation. These are performed automatically on a nightly basis and require little human intervention. | |||
'''''Priorities for annotation''''' | |||
* Isoform curation (Harold, Karen, Protein Ontology project); focusing on genes that have isoforms or whose products are modified, and co-ordinate with the Protein Ontology Protein Complex project. | |||
* Genes with no GO annotation but with literature (Li and Dmitry) | |||
* Genes with only IEA annotation but with literature (Li) | |||
* Genes marked as having GO annotation completed, but now having new literature (Dmitry) | |||
* Genes that have an annotation to one of the three root nodes of GO, but have new literature (David, Karen, Dmitry) | |||
* Dmitry has been focused on annotation or miRNAs in MGI | |||
= Presentations and Publications = | = Presentations and Publications = |
Revision as of 16:02, 26 November 2013
Overview:
Staff:
[please include FTEs working on GOC tasks designating as well how many FTEs funding by GOC NIHGRI grant]
Judith Blake*
Karen R Christie*
Mary E Dolan*
Harold J Drabkin*
David Hill*
Li Ni
Dmitry Sitnikov
* Funded entirely or partially by GO
Annotation Progress
Annotation Type | Dec 5 2012 | Dec 5 2013 | Change | % change | |
---|---|---|---|---|---|
Total Genes annotated with at least one GO term of any kind | 25452 | 25406 | TBA | TBA | |
Total annotations: | 286957 | 303195 | TBA | TBA | |
Total non-IEA Annotation | |||||
Total Number of Genes: | 24550 | 24597 | TBA | TBA | |
Total Annotations: | 193088 | 208808 | |||
Annotation by Direct Experiment | |||||
MGI Curated Genes | 11104 | 11558 | |||
MGI Curated Anntations | 70615 | 75497 | |||
GOA Curated Genes: | 3475 | 4067 | |||
GOA Curated Annotations: | 18055 | 21976 | |||
Annotation by Orthology | |||||
Total Genes Annotated by Orthology | 9451 | 9826 | |||
Total Orthology Annotation | 68621 | 74777 | |||
Genes Annotated by Human Orthology Load (GOA) | 7756 | 8177 | |||
Total Annotation by Human Orthology Load | 42237 | 46001 | |||
Genes annotated by Rat Orthology Load (RGD) | 4083 | 4160 | |||
Total Annotations by Rat Orthology Load | 23323 | 24575 | |||
IEA Annotation | |||||
Total Genes with IEA | 16372 | 16786 | |||
Total IEA annotations | 93869 | 9438 | |||
Total Genes with SwissProt to GO | 15971 | 16415 | |||
Total SwissProt to GO Annotations | 64733 | 65804 | |||
Total Genes with Interpro to GO | 9792 | 10233 | |||
Total Interpro to GO Annotations | 27804 | 27418 | |||
Total Genes with EC to GO Annotations | 944 | 930 | |||
Total EC to GO annotations | 1332 | 1165 |
Methods and strategies for annotation
Literature curation:
Literature curation continues to be the major focus of our annotation efforts.
Computational annotation strategies:
As always, current strategies involve use of translation table to mine SwissProt keywords, InterPro domains, and EC numbers for IEA annotation. These are performed automatically on a nightly basis and require little human intervention.
Priorities for annotation
- Isoform curation (Harold, Karen, Protein Ontology project); focusing on genes that have isoforms or whose products are modified, and co-ordinate with the Protein Ontology Protein Complex project.
- Genes with no GO annotation but with literature (Li and Dmitry)
- Genes with only IEA annotation but with literature (Li)
- Genes marked as having GO annotation completed, but now having new literature (Dmitry)
- Genes that have an annotation to one of the three root nodes of GO, but have new literature (David, Karen, Dmitry)
- Dmitry has been focused on annotation or miRNAs in MGI
Presentations and Publications
a. Papers with substantial GO content
b. Presentations including Talks and Tutorials and Teaching
c. Poster presentations
Other Highlights:
A. Ontology Development Contributions:
B. Annotation Outreach and User Advocacy Efforts:
C. Other Highlights: