MGI December 2013: Difference between revisions

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= Methods and strategies for annotation =
= Methods and strategies for annotation =
(please note % effort on literature curation vs. computational annotation methods)
'''''Literature curation:'''''


a. Literature curation:
Literature curation continues to be the major focus of our annotation efforts.


b. Computational annotation strategies:  
'''''Computational annotation strategies:'''''


c. Priorities for annotation
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: