Ontology Structure: Difference between revisions
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=== Internal (Intra-GO) links === | === Internal (Intra-GO) links === | ||
GO currently has links within the 3 ontologies, but not between | |||
==== Biological process to molecular function ==== | ==== Biological process to molecular function ==== | ||
[[Function-Process_Links]] | |||
==== Cellular component to molecular function ==== | ==== 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 | |||
===== AmiGO ===== | |||
[[AmiGO:Inter-ontology_links]] | |||
=== Internal cross-products === | === Internal cross-products === |
Revision as of 20:20, 21 September 2007
Note: this page may get merged with Ontology_Development
is_a completeness
DONE
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 gene_ontology.obo_1_0 -- for-public, GUARANTEED obof1.0 gene_ontology.obo_1_2 -- 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
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