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Mouse Genome Informatics Summary, 2010

lasted edited 9-14-10 by hjd

Overview

Staff:

Judith Blake*

Alexander Diehl*

Mary Dolan*

Harold J Drabkin*

Midori Harris*

David Hill*

Li Ni

Dmitry Sitnikov


  • Funded entirely or partially by GO

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 December, 2010


Annotation Type 09_Dec_10 09_Dec_09 Change % Change
Total Genes annotated (with at least one GO term of any kind):
34200*
18207
15993
87.84
Total Manual Annotation
Number of Genes
32410
11668
20742
177.77
Orthology:
4214
752
3462
460.37
IEA Annotation
SwissProt to GO
15667
16050
tbc
tbc
Interpro to GO
10514
10749
tbc
tbc
EC to GO
1414
1510
tbc
tbc
* 100% of current gene models


The large changes in manual (non-IEA) curated genes are the result of the addition of 5 efforts.

  1. Annotating genes with no literature annotation to one or more of the three roots. Quality control reports now alert curators for any genes annotated to one or more of the three roots when new literature is added to MGI and the literature is indexed to these genes.
  2. We have added a pipeline to create annotations inferred by sequence orthology (ISO) to mouse genes that have rat orthologs where the rat orthologs have been annotated by experiment.
  3. We have added a pipeline to load GOA annotations to mouse genes.
  4. We have added a pipeline to add annotations based on intra-ontology relationships.
  5. We have added a pipeline to add annotations by on sequence similarity (ISS)based on Panther family membership via the Reference Genome projet.

Methods and strategies for annotation

Literature curation:

Literature curation continues to be the major focus of our annotation efforts. We continue to explore natural language processing tools to aid in identifying the genes in papers selected for GO.


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

  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 with only IEA annotation but with literature (Li)
  5. Genes identified as being important in lung development (Dmitry)
  6. Genes marked as having GO annotation completed, but now having new literature (Dmitry)

Presentations and Publications

We either need a 2010 master (appears not to exist?). OR MGI should but following here. listing anything from Dec 2009 to now

Publications


Tutorials and Workshops

Posters

A. Ontology Development Contributions:

  • 1. David Hill has worked on a team with Tanya Berardini, Chris Mungall, Midori Harris and Jane Lomax to develop cross-products within and among the three GO namespaces.


  • 2. David Hill continues to work with Chris Mungall and Tanya Berardini to inter-ontology links in GO.


  • 3. David Hill has worked with Yasmin Alam-Faruque, Doug Howe, Midori Harris, Susan Tweedie, Becky Foulger and community experts to expand the kidney development portion of GO.


  • 4. Alexander Diehl is active in the GO Signaling and Virus content development groups.


  • 5. 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.


  • 6. Alexander Diehl is project leader for the Cell Ontology (with Chris Mungall) and Terry Meehan is a full-time curator working on the Cell Ontology. Terry has finished implementing cross-products for hematopoietic cell ontology terms and is working on general improvements to the CL, and has moved on to import of FMA cell types, among others. Alex is focusing improvements to the representation of neurons in the CL, part of an ongoing collaboration with the International Neuroinformatics Framework (INCF). In May 2010 we held a very successful Cell Ontology Workshop at The Jackson Laboratory where many issues regarding the longterm development of the ontology were settled. We will hold another workshop on neurons in the first quarter of 2011. (See separate progress report for the Cell Ontology)


  • 7. In summer 2010 Alexander Diehl mentored Morgan V. Hightshoe, a returned member of the Jackson Laboratory Summer Student Program, and Wade Valleau, a local high school intern in linked projects to revise the representation of nervous system cell types in the Cells Ontology. Wade received support from INCF for his work..


  • 8. David Hill and Jane Lomax oversee the biological content development of GO. In particular, all new developmental biology-related terms submitted to SourceForge are handled by David Hill and all new 'regulation' terms are handled by David Hill and Tanya Berardini.

Annotation Outreach and User Advocacy Efforts:

  • The Protein Ontology project continues to provide 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 is mentoring to curators in Donna Slonim's group at Tufts, Heather Wick and Craig Fournier. They are focusing on genes involved in human fetal development.
  • David Hill continues to serve on the GO-help rota.

Other Highlights:

We are now suppling a GAF 2.0 format file to GOC with column 16 cell type and column 17 isoform data filled in. This file is also available directly from our own FTP site.

  • 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 and in cross-product term formation. This grant was funded on September 30, 2009.
  • 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 80 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, maintain the Reference Genome status table on GO wiki, 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