gobo - global open biology ontologies.

gobo - is an umbrella web address for structured shared controlled
vocabularies for use within the genomics and proteomics domains. 

This site both contains ontologies and points to some other efforts
within the community.

Ideally we see a range of ontologies being designed for the general
genomics and proteomics domain.  Some of these will be generic, other
more restricted in scope, for example to specific taxonomic groups.

One scheme (a meta-ontology, if you like) is shown below, with links
to some of the efforts that we know planned or being worked on.

The criteria for inclusion are:

1.  The ontologies are "open" and can be used by all without any constraint
other than that their origin must be acknowledged. 

2.  The ontologies are in, or can be instantiated in, the GO syntax, extensions
of this syntax or in DAML+OIL.  The reason for this is that they can then all be
used by the same tools and could, in principle, be combined as cross-products.

This criterion is not met in all of the ontologies that we have listed, but
we are working with those building these ontologies to have them available
in the GO syntax. Some of the links are to pages describing a project, rather
than to the ontologies themselves. For further links see:
http://www.cbil.upenn.edu/Ontology/MGED_ontology.html

3.  The ontologies are orthogonal to other ontologies already lodged with gobo. 
The major reason for this principle is to allow two different ontologies, e.g. 
anatomy and process, to be combined as cross-products.  In addition, we would 
strive for community acceptance of a single ontology for one domain, rather than rivals.

4.  The ontologies agree to share an id space.

5.  The ontologies also include definitions of their terms.


We have only done these at very high level and, in several instances, 
distinguish between what is being described (eg 'gene') and the attributes
needed to describe it.  This is not meant to be a comprehensive
specification, but the beginning of a discussion.

gobo
 gene
  gene_attribute
   gene_structure                     SO        go/gobo/sequence.ontology
   gene_variation                     ME        go/gobo/mutationevents.ontology
  gene_product 
   gene_product_attribute 
    molecular_function                GO        go/ontology/function.ontology      
    biological_process                GO        go/ontology/process.ontology
    cellular_component                GO        go/ontology/component.ontology
    protein_family                    INTERPRO  ftp://ftp.ebi.ac.uk/pub/databases/interpro/entry.list
 chemical_substance
  biochemical_substance
   biochemical_substance_attribute
    class
    physico-chemical_property
  pathway
   pathway_attribute
 development_timeline
  development_timeline.arabidopsis    TAIR      go/gobo/temporal/anatomy.tair
  development_timeline.drosophila     FBbt      go/gobo/anatomy/anatomy.fb
  development_timeline.mouse                    http://genex.hgu.mrc.ac.uk/Databases/Anatomy/new/home.shtml
 anatomy
  gross_anatomy
   gross_anatomy.arabidopsis          TAIR      go/gobo/anatomy/anatomy.tair
   gross_anatomy.drosophila           FBbt      go/gobo/anatomy/anatomy.fb
   gross_anatomy.mouse                          http://genex.hgu.mrc.ac.uk/Databases/Anatomy/new/home.shtml
  tissue
  cell_type
 phenotype
  mutant_phenotype                    PATO      go/gobo/phenotype.ontology
  traits                              TO        http://www.gramene.org/plant_ontology/trait.ontology
  pathology 
  disease
 experimental_condition                         http://www.cbil.upenn.edu/Ontology/MGED_ontology.html
 organismal_classification                      http://www.ncbi.nlm.nih.gov/Taxonomy/tax.html/
gobo_relationships
gobo_evidence                         EO        go/ontology/evidence.ontology