FP-regulates: Difference between revisions

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[[FP-regulates-GOfriends-email]]
==Summary==


[[Overview of Function-Process regulates links]]


Frequently Asked Questions:
==Frequently Asked Questions:==


== Will my parser break? ==
 
=== Which files will be affected? ===
 
The new relationships will only be present in the file:
 
go/ontology/obo_format_1_2/gene_ontology_ext.obo
 
The other OBO format ontology files (gene_ontology_edit.obo, gene_ontology.1_2.obo, gene_ontology.1_0.obo and gene_ontology.obo) will remain <b>unaffected</b> by this change, as will the database.
 
 
=== Will my parser break if I use the file with the new links? ===


Your parser or tool should NOT break unless it has been written such that it makes the assumption there are no inter-ontology links.
Your parser or tool should NOT break unless it has been written such that it makes the assumption there are no inter-ontology links.
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Even if the parser does not break, tools and databases may behave differently in that they may automatically classify gene products under an MF node where they previously did not.
Even if the parser does not break, tools and databases may behave differently in that they may automatically classify gene products under an MF node where they previously did not.


== Can I strip out the inter-ontology links? ==
We will provide a lightweight script that can do this. In addition, we may deploy a 'dumbed-down' version of the ontology with only [[is_a]] and [[part_of]] links. This will have the effect of eliminating the inter-ontology [[regulates]] links


== How do I calculate transitive closure? ==
=== How do I calculate transitive closure? ===


See [[Transitive_closure]]
See [[Transitive_closure]]


== Which files will be affected? ==


Both of the OBO format ontology files (gene_ontology_edit.obo and gene_ontology.obo) will be affected by this change, as will the database. The only files that will be unaffected are the deprecated GO format files.
[[Category:Ontology]]

Latest revision as of 09:48, 25 February 2009

Summary

Overview of Function-Process regulates links

Frequently Asked Questions:

Which files will be affected?

The new relationships will only be present in the file:

go/ontology/obo_format_1_2/gene_ontology_ext.obo

The other OBO format ontology files (gene_ontology_edit.obo, gene_ontology.1_2.obo, gene_ontology.1_0.obo and gene_ontology.obo) will remain unaffected by this change, as will the database.


Will my parser break if I use the file with the new links?

Your parser or tool should NOT break unless it has been written such that it makes the assumption there are no inter-ontology links.

Even if the parser does not break, tools and databases may behave differently in that they may automatically classify gene products under an MF node where they previously did not.


How do I calculate transitive closure?

See Transitive_closure