Central Nervous System Development

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Expansion of Central Nervous System Development Representation in GO

Personel

  • David Hill (GO)
  • Midori Harris (GO)
  • Jennifer Clark (GO)
  • Erika Feltrin (GO)
  • William Bug (Drexel University)
  • Maryanne Martone (University of California, San Diego)
  • Rex Chisholm (GO)
  • Kathleen Millen (University of Chicago)
  • Francis Szele (Northwestern University)
  • Judith Blake (GO)
  • Terry Hayamizu (MGI)
  • Jacqueline Finger (MGI)
  • Doug Howe (ZFIN)


Current genetic and molecular studies in many model organisms are aimed at understanding formation and development of the nervous system. Up until this point, the GO has had a very shallow representation of processes pertaining to the nervous system. In the Spring of 2006 curators decided that there should be a focus on better representation of the nervous system in GO. Cynthia Smith (MGI), Doug Howe (ZFIN) and David Hill (MGI), three curators who actively curate the literature for either GO or phenotype, chose to focus efforts on a better representation of central nervous system development. In particular, emphasis was placed on three areas that they felt were being addressed actively in current research, forebrain development, hindbrain development and neural tube development. The starting point of the ontology was a neural tube development section that contained a few dozen terms and a brain development section that contained three terms.

The effort began with the selection of approximately 10 reviews for each area of the graph that was to be expanded. All three curators read all of the reviews and then each curator took one area of expansion and worked on modifications to the GO in that area. Once the modifications were made, the new ontologies were circulated to each of the other two curators for additions, corrections and refinements. In June 2006, a two-day meeting was held in Bar Harbor where the graphs were discussed among the three original curators and experts in CNS development, neuroanatomy and ontology development. Changes to the ontologies were made directly as discussions proceeded and after the meeting further revisions to the graph were made based on the discussions. The updated ontology was then redistributed to the meeting attendees for comments and the final graph was committed to the GO in August.

Over 500 terms were added to the ontology dealing with forebrain, hindbrain and neural tube development. Most of those terms have part_of relationships to their parents due to the nature of the construction, looking at a process as a whole and deciding what processes contribute to it. We represented development from both a process-based and an anatomical-based viewpoint since both of these representations are crucial for biologists that search the ontology.

On October 12, 2006 the terms in the new CNS development portion of the ontology were made is_a complete. These terms now have is_a paths that can be traced back all the way to the root of the graph. This work was done as part of a project to make the entire biological_process ontology is_a complete.

The new CNS terms will provide a framework that will be easily extensible for the addition of new terms as they are required for literature-based curation.


Outcome

  • Project duration April 2006-October 2006
  • New term additions 537