2007 Progress Report

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2007 Progress Report

Aim 1: Aim 1: We will maintain comprehensive, logically rigorous and biologically accurate ontologies.

We will work closely with biological experts to ensure that the ontologies accurately reflect biological reality. We will incorporate new relationship types into the ontologies as needed and we will recast compound terms as explicit cross-products with orthogonal ontologies. We will keep the ontologies logically rigorous so that when used to query for terms associated with gene products it will neither omit relevant annotations nor return incorrect annotations.

  1. Comprehensive biological domain coverage.
    1. Request tracking, using the SourceForge system
      1. Source Forge Items submitted -
      2. Source Forge Items resolved -
    2. Special Interest Groups (SIGs)
    3. Content Meetings (2 per year)
      1. Immunology Sequence Ontology Meeting –

At the SO HLA meeting in June, it was decided that Lindsay Cowell and Alex would overhaul the representation of immunoglobulin and TCR gene segments in the SO and present a proposal. We have not done this yet, although it's on the schedule. Also, it was decided that Steve Marsh and Richard Scheuermann would prepare a separate ontology of MHC Class I and Class II structural features.

Additionally, we worked on adding a limited number of terms to the SO such as allele, that are needed to describe MHC gene variants, as well as modifying the term names or definitions of certain existing terms, such as "gene" to suit our needs better. These changes are described in the meeting notes available at http://www.sequenceontology.org/immuno_workshop.shtml and have been discussed to some extent in the SO mailing list I believe.

      1. Cardiovascular/Blood Pressure Regulation Ontology Meeting –

A 1.5 day meeting was held at the Medical College of Wisconsin to expand and refine the representation of blood pressure regulation in the Biological Process ontology. The meeting was attended by: Diane Munzenmaier, Kieth Depetrillo, Mingyu Liang, Simon Twigger, Mary Shimoyama, Jennifer Smith, Stan Laulederkind, Victoria Petri, Ruth Lovering and David Hill. The meeting was also attended virtually by Judith Blake and Jennifer Deegan.

The on-site personnel used Webex and Skype to communicate with the offsite attendees. Jennifer Deegan edited the ontologies live as discussion progressed. The meeting covered a review of previous changes to the "regulation of blood pressure" portion of the ontology that had been made over the last few months based on face-to-face and virtual meetings. Since blood pressure regulation is a complex biological process, the GOC members stepped through the graph and elicited comments from the physiology experts about term relationships and definitions. Many of the current terms in the ontology were renamed to a string that was more "useful" for a physiologist. Definitions were also refined to more accurately reflect what the terms were meant to represent. The meeting itself focused mostly on the renal control of blood pressure, which was previously only minimally represented in GO. By the end of the meeting approximately 100 new terms had been added to the ontology. The project is not complete and GOC curators are continuing to work from recommendations that were made by physiologists. Some major outstanding issues are the standardization of all term names and the addition of synonyms as well as the further expansion of some parts of the graph. The current graph can be found in the CVS scratch directory. As the graph is changed, CVS will be updated and graphical representations of the ontology will be posted on the MGI ftp site. We will continue to hold virtual meetings until the new version of blood pressure is committed to the Biological Process ontology.

      1. Muscle Development Ontology Meeting
  1. Logical Development of the GO
    1. Improving Biological Relations
    2. Providing comprehensive is_a relationships for all GO terms.
      1. “Is_a complete” Complete for all 3 domains
      2. Improving ‘regulates’ relationship in the GO.
        1. Added ‘regulates’ relationship to GO, updated ontology
      3. Generating relationships between current GO ontologies and other ontologies
      4. Completed development of cross-product representation between GO and CellType Ontologies
      5. Improving relationships within single GO ontologies.
      6. Building relationships between current GO ontologies.
        1. Support representation of biological pathways
        2. Instantiate relations between MF, BP, and CC
        3. Develop tools to maintain GO to pathway correspondence
      7. Sequence Ontology
        1. Maintain Ontology
        2. Add new relationships between terms

3. Tools and Technical Support a. Maintenance and management of the GO i. Source Forge b. Develop and support OBO_Edit for maintaining ontologies i. OBO_Edit releases ii. Addition of graphical feature c. Interoperability i. Provide GO in RDF and OWL formats