MGI, March 2010

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	26_Mar_09	Change	% Change
Total Genes annotated (with at least one GO term of any kind):	18188	18159*	29	0.16
Total Manual Annotation
Number of Genes	11177	11045	132	1.2
Orthology:	708	685	23	3.4
IEA Annotation
SwissProt to GO	16145	16083	62	0.39
Interpro to GO	10533	10536	-3	-0.03
EC to GO	1491	1478	13	0.89
* 62% 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

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 between the three GO namespaces. These have not been officially released.

2. David Hill has worked with Chris Mungall and Tanya Berardini to introduce the first inter-ontology links in GO. These include regulates links between BP and MF and part_of links between MF and BP.

3. Dmitry Sitnikov and David Hill are extending the lung development branch of Biological Process to adequately annotate genes identified as being important in the development of lung cancers.

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.