Ontology Structure

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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

This page has moved: Ontology_CVS_Directory_Layout_Overhaul

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