Overview of Function-Process regulates links

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Having successfully implemented the 'regulates' relationships in the biological process (BP) ontology, we have now added 'regulates' relationships within the molecular function (MF) ontology and between the BP and MF ontologies. These changes are only present in the file:

go/ontology/obo_format_1_2/gene_ontology_ext.obo

Specifically, we have made the implicit regulatory relationships between 'regulation of molecular function' BP terms and the corresponding MF terms explicit. For example:

   * regulation of kinase activity (BP) regulates kinase activity (MF) 

Similarly, we have made the implicit regulatory relationships between terms within the MF ontology explicit. For example:

   * calcium channel regulator activity (MF) regulates calcium channel activity (MF) 

The former are the first inter-ontology links in the GO vocabularies. Note that if software has been constructed with the assumption that there are no inter-ontology links, then this software may break when presented with these new inter-ontology links.

Adding these relationships improves the ability of the ontology to represent biology completely and accurately. The average GO user will benefit from these new links because they will be able to ask and answer more complex questions than they could previously. Users must understand what the different relationships mean and how the various GO tools utilize them.

The addition of these links also has major implications for tools that ignore relationship types when summarizing annotations. For example, it is important to understand whether a query will return all children of a term regardless of its relationship to the parent, or can discriminate between relationship types. If your tool of choice lumps annotations to 'calcium channel regulator activity' together with the regulates parent 'calcium channel activity', a query for calcium channels will also retrieve gene products that function as calcium channel regulators (and not necessarily as channels!). More sophisticated tools will allow users to customize queries to return results that better reflect their interests. For example, tools that are upgraded to take relationships into consideration will allow users to look for processes or functions, and specify whether to include or exclude their regulates children.


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