MGI, March 2010: Difference between revisions

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1. David Hill has worked on a team with Tanya Berardini, Chris Mungall, Midori Harris, Jen Deegan and Jane Lomax to develop cross-products within the three GO namespaces. The regulation cross-products have been released in the extended GO. David and Tanya are now quality checking the internal biological process cross products.
1. David Hill has worked on a team with Tanya Berardini, Chris Mungall, Midori Harris, Jen Deegan and Jane Lomax to develop cross-products within the three GO namespaces. The regulation cross-products have been released in the extended GO. David and Tanya are now quality checking the internal biological process cross-products.


2. David Hill has worked Tanya Berardini to continuing to add interontology links between MF and BP.
2. David Hill has worked Tanya Berardini to continuing to add interontology links between MF and BP.


3. David Hill has worked with Varsha Khodiyar, Tanya Berardini, Doug Howe, Susan Tweedie, Ruth Lovering and community experts to expand the heart development portionof the ontology.
3. David Hill has worked with Varsha Khodiyar, Tanya Berardini, Doug Howe, Susan Tweedie, Ruth Lovering and community experts to expand the heart development portion of the ontology.


4. David Hill has worked with Yasmin Alam-Faruque, Midori Harris, Becky Folger, Doug Howe, Emily Dimmer, Rachel Huntley and community experts to expand the kidney development portion of the ontology.
4. David Hill has worked with Yasmin Alam-Faruque, Midori Harris, Becky Folger, Doug Howe, Emily Dimmer, Rachel Huntley and community experts to expand the kidney development portion of the ontology.
Line 190: Line 190:
5. David Hill and Tanya Berardini are maintaining the automated quality checks of the ontology on an ongoing basis.
5. David Hill and Tanya Berardini are maintaining the automated quality checks of the ontology on an ongoing basis.


6. David Hill and Harold Drabkin are working with Jane Lomax, Midori Harris, Tanya Berardini and Jane Lomax to align the representation of chemicals in GO.  
6. David Hill and Harold Drabkin are working with Jane Lomax, Midori Harris, Tanya Berardini and Jane Lomax to align the representation of biochemicals in GO.  


7. David Hill and Tanya Berardini added or modified 231 terms as a result of attending the American Society for Cell Biology Meeting in December.
7. David Hill and Tanya Berardini added or modified 231 terms as a result of attending the American Society for Cell Biology Meeting in December.

Revision as of 15:24, 15 March 2010

Mouse Genome Informatics March, 2010

Overview

Staff:

Judith Blake

Alexander Diehl

Harold J Drabkin

David Hill

Li Ni

Dmitry Sitnikov

Mary Dolan


Annotation Progress

We continue to put emphasis on those genes selected for the Reference Genome Project. Additional emphasis has been placed on certain genes associated with lung development.


MGI GO STATS as of March 22, 2010


Annotation Type 01_Sept_09 22_Mar_10 Change % Change
Total Genes annotated (with at least one GO term of any kind):
18188
35191*
16993
93.43
Total Manual Annotation
Number of Genes
11177
33228
22051
197.29
Orthology:
708
4006
3298
465.82
IEA Annotation
SwissProt to GO
16145
15942
62
0.39
Interpro to GO
10533
10592
-3
-0.03
EC to GO
1491
1248
13
0.89
* 100% of current gene models


Methods and strategies for annotation

Literature curation:

Literature curation continues to be the major focus of our annotation efforts. Wecontinue to explore natural language processing tools to aid in identifying papers that are primarily focused on aspects of lung development, with the aid of Karen Dowel.


Computational annotation strategies:

As always current strategies involve use of translation table to mine SwissProt Keywords and InterPro domains for IEA annotation. These are performed automatically on a nightly basis and require little human intervention.


Priorities for annotation

  1. Genes assigned by Reference Genome Project (everyone)
  2. Isoform curation (Harold, Protein Ontology project); now co-ordinating with 1 by focusing on reference genes that have isoforms.
  3. Genes with no GO annotation but with literature (Li and Dmitry)
  4. Genes identified as being important in lung development (Dmitry)
  5. Genes marked as having GO annotation completed, but now having new literature (Dmitry)

Presentations and Publications

Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. (2010). Cross-Product Extensions of the Gene Ontology. J. Biomed. Inform. Feb. 9 [Epub ahead of print]

Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, Mungall C, Harris MA, Dolan ME, Blake JA, Ramoni MF. (2010). Ontology Engineering. Nature Biotechnol. Feb;28(2):128-30.

The Gene Ontology Consortium. (2010). The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 38:D331-5.

Hill DP, Berardini TZ, Howe DG, Van Auken KM. (2009). Representing Ontogeny Through Ontology: A Developmental Biologist’s Guide to The Gene Ontology. Mol Reprod. Dev. 77(4):314-29.

Dowell, KG, McAndrews-Hill MS, Hill DP, Drabkin HJ, Blake JA. (2009). Integrating Text Mining into the MGI Biocuration Workflow Database. Bap019.


b. Presentations including Talks and Tutorials and Teaching

A. Ontology Development Contributions:

1. David Hill has worked on a team with Tanya Berardini, Chris Mungall, Midori Harris, Jen Deegan and Jane Lomax to develop cross-products within the three GO namespaces. The regulation cross-products have been released in the extended GO. David and Tanya are now quality checking the internal biological process cross-products.

2. David Hill has worked Tanya Berardini to continuing to add interontology links between MF and BP.

3. David Hill has worked with Varsha Khodiyar, Tanya Berardini, Doug Howe, Susan Tweedie, Ruth Lovering and community experts to expand the heart development portion of the ontology.

4. David Hill has worked with Yasmin Alam-Faruque, Midori Harris, Becky Folger, Doug Howe, Emily Dimmer, Rachel Huntley and community experts to expand the kidney development portion of the ontology.

5. David Hill and Tanya Berardini are maintaining the automated quality checks of the ontology on an ongoing basis.

6. David Hill and Harold Drabkin are working with Jane Lomax, Midori Harris, Tanya Berardini and Jane Lomax to align the representation of biochemicals in GO.

7. David Hill and Tanya Berardini added or modified 231 terms as a result of attending the American Society for Cell Biology Meeting in December.

Annotation Outreach and User Advocacy Efforts:

The Protein Ontology project is providing a web interface (http/pir.georgetown.edu/cgi-bin/pro/race_pro ) whereby functional annotation using the GO can be applied to PRO submissions. These are reviewed by Cecilia Arighi of Georgetown. At present, only the PRO curators (Georgetown and MGI) are using the tool, but it is available to anyone.

Harold and David are mentoring Heather Wick of Tufts University, for annotation of human fetal lung development

Other Highlights:

We are now suppling a GAF 2.0 format file to GOC with column 16 and 17 data filled in. This file is also available directly from our own FTP site. Currently, the data in column 16 refers to the cell type that the experiment supporting the annotation was carried out in, by use of cell ontology terms.