Ontology Structure

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Revision as of 06:13, 24 September 2007 by Jrichter (talk | contribs) (Create separate editorial version of ontology)

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Note: this page may get merged with Ontology_Development

is_a completeness

DONE

disjoint_from links

3 terms in GO are no declared mutually disjoint:

CP, MCOP, MOP

Could be done for 3 root nodes

Also for other higher level terms

Create separate editorial version of ontology

Purpose: provide buffer between ontology users and editors to allow implementation of new features in a way that is non-disruptive

Currently we have

 go/
   ontology/
     gene_ontology.obo
     gene_ontology_edit.obo

this was designed to be a separate editors and for-public version of the ontology. However, the editors version has been advertised as the file to download for the public wishing to get obof1.2 features.

One possibility is to migrate to the following:

 go/
   ontology/
     gene_ontology.obo            -- for-public, currently obof1.0, may switch to obof1.2
     gene_ontology_edit.obo       -- deprecated, obof1.2, maybe just a soft link?
     gene_ontology.1_0.obo        -- for-public, GUARANTEED obof1.0
     gene_ontology.1_2.obo        -- for-public, GUARANTEED obof1.2
     gene_ontology_editorial.obo  -- for-editors

This may be done in the context of the Versioning_Proposal

Ontology linking and cross-products

Internal (Intra-GO) links

GO currently has links within the 3 ontologies, but not between


Biological process to molecular function

Function-Process_Links

Cellular component to molecular function

Implementation

Links spanning the 3 ontologies do not differ significantly from existing DAG links. We could thus include them in the main GO file. However, users expectations will be violated - annotations cannot be propagated up these links in the same way. For this reason it may be better to capture these links in a separate file; for example:

 go/
   ontology/
     gene_ontology_editorial.obo
     function_to_process.obo
     component_to_function.obo
OBO-Edit

OBO-Edit is capable of handling these links

Hd-complex.jpg

AmiGO

AmiGO:Inter-ontology_links

Internal cross-products

Regulation cross-products

Regulation_cross-products

Other internal cross-products


External DAG links

External DAG links are different from external XPs. A DAG link is just a simple link that happens to span two ontologies.

Examples: between microvillus and hair cell

External cross-products

Cross-product meetings: [1]

We have added a Cross_Product_Guide, intended to answer all your questions about cross-products


biological_process_xp_cell

CL is currently undergoing rennovation. However, the CL cross-products can still be edited and used.

Cell cross-products

biological_process_xp_chebi

Initial set by mike Bada

Chebi cross-products

Ongoing issues:

  • plurals in ChEBI
  • roles in chebi
  • unusual DAG structure

Others

Obol