MGI, September 2009

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Mouse Genome InformaticsSeptember, 2009

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 26, 2009


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

Diehl AD, Deckhut Augustine A, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, NIAID Cell Ontology Working Group, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ, 2009, “Hematopoietic Cell Types: Prototype for a Revised Cell Ontology,” Proceeding of the International Conference on Biomedical Ontology, July 24-26, 2009, University of Buffalo, NY.


Dolan ME, Blake JA. 2009. Using ontology visualization to facilitate access to knowledge about human disease genes. Applied Ontology 4(1):35-49.


Joslyn C, Baddeley B, Blake J, Bult C, Dolan M, Riensche R, Rodland K, Sanfilippo A, White A. 2009. Automated Annotation-Based Bio-Ontology Alignment with Structural Validation, submitted as conference paper to the International Conference on Biomedical Ontology, July 24-26, 2009, University of Buffalo, NY. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3518.1> (2009).

Dolan ME, Evsikov AV, Blake JA, Bult CJ. MouseCyc: a pathways approach to integration of mouse functional, phenotype and expression data. Poster presented at ISMB2009.

Reference Genome Group of the Gene Ontology Consortium. The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species, PLoS Comput Biol. 2009 Jul;5(7):e1000431. Epub 2009 Jul 3

Dowell, Karen, McAndrews-Hill, Monica, Hill, David, Drabkin, Harold, and Blake, Judith. Integrating Text Mining into the MGI Biocuration Workflow. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3262.1> (2009).


b. Presentations including Talks and Tutorials and Teaching


David gave an invited talk about using GO to study developmental biology at the MR&D meeting at Brown University.

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.


4. David Hill has expanded the development of the salivary gland, prostate gland, placenta and mammary gland in the in the BP ontology.


5. Approximately 150 terms were added to the BP ontology as a result of David Hill and Tanya Berardini attending the Society for Developmental Biology meeting.


6. Approximately 50 terms were added to the BP ontology as a result of David Hill attending the MR&D meeting.


7 Harold Drabkin and Alexander Diehl are active in the Signaling GO content development group.


8 Alexander Diehl is active in the Virus Term GO content development group.


9 Alexander Diehl continues to act as the GOC liaison to the Infectious Disease Ontology and Vaccine Ontology groups and to act on term requests for the GO from those groups.


10 Alexander Diehl is continuing his work as an acting curator of the Cell Ontology. Alex and Judy recently co-mentored Morgan V. Hightshoe, a member of the 2009 Jackson Laboratory Summer Studen.t Program, in a project to revise the representation of nervous system cell types in the Cells Ontology.

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.

Other Highlights:

We are now suppling a GAF 2.0 format file to GOC with column 17 data filled in. This file is also available directly from our own FTP site. Column 16 fill in will following, starting with specifying cell type.


Alexander Diehl co-wrote an ARRA Competitive Revision extension to the Gene Ontology Consortium grant HG000273, along with Chris Mungall and Judith Blake for the purpose of revising the Cell Ontology, and using the CL in conjunction with the GO in annotation. We hope to know the funding status prior to the September 2009 GOC meeting.


Dmitry Sitnikov continues collaboration with Larry Hunter's group (Dr. Mike Bada) to establish a large, high-quality, corpora of full-text publications, expertly annotated with expressive knowledge representations, to improve the performance of a wide variety of biochemical text mining systems and to create new approaches to text mining. This involves systematically training and evaluating a broad sample of information extraction methods for key tasks, including concept and relationship identification. This effort can also be useful in synonym improvements to the GO between GO terms and certain biological concepts and terminology used in the literature. So far, more then 70 artictles of the chosen 98 have been annotated for molecular function and process. Additionally, Dmitry is working to improve the usefulless of MGI internal GO QC reports.

As the designated coordinator of the MGI/GO project with the GO Reference Genome project, Li Ni participates in annotations of genes assigned by the Reference Genome Project, maintain the mouse Reference Genome list on MGI GO wiki and Google spreadsheet, oversees the curation of Reference Genome Genes for the mouse group.

Mary Dolan has been involved in a collaboration with Carol Bult at MGI on aligning gene ontology annotations for mouse genes assigned to MouseCyc pathways. See

See http://www.informatics.jax.org/pathways.shtml