Neurobiology Project

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Summary

To expand and improve the GO biological processes terms and annotations for neurological processes including the core cellular processes for synaptic transmission, through to some of the higher order brain processes like cognition, and to fully augment GO cc with those terms in Neurological Information Framework (NIF)

UPDATE [Jan 2016]: there is now an ongoing ontology synapse project (https://github.com/geneontology/synapse). Integration of NIF terms into GO CC was completed and published (http://www.ncbi.nlm.nih.gov/pubmed/24093723).

Personnel

GO

  • David H
  • Tanya
  • David O-S
  • Alex
  • Chris
  • Paola

External experts

  • Dr. John Chua (GWDG) - main contact
  • Dr. Mario Albrecht (Max Planck Institute)

Main interest is in biological processes concerning the synapse, particularly the presynaptic active zone (human). See their recent review below for examples of genes and processes.

The architecture of an excitatory synapse.
Chua JJ, Kindler S, Boyken J, Jahn R.
J Cell Sci. 2010 Mar 15;123(Pt 6):819-23. Review.
PMID:20200227
  • Maryann Martone (NIF, University of California)
    • Neurological cell components

Timeline

  1. Preliminary phone conference
  2. Collect SF items
  3. First draft of new terms
  4. Ontology content meeting with experts
  5. Second draft of new terms
  6. Implementation of new terms
  7. Annotations to new terms


SF items


Expansion of Central Nervous System Development Representation in GO

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. Work remains to create is_a relationships for many of the new terms. This will be our focus over the next few months and will require the addition of many ‘root’ terms to describe generic processes. In addition, the new terms will provide a framework that will be easily extensible for the addition of new terms as they are required for literature-based curation.


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