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[Gofriends] Additional inter- and intra-ontology 'regulates' links in the GO coming
alanruttenberg at gmail.com
Wed Aug 13 23:15:15 PDT 2008
Can we have a definition of "regulates" please, that allows it to be
the case that a function is regulated?
On Aug 13, 2008, at 1:37 PM, Tanya Berardini wrote:
> Dear GO Friends,
> Having successfully implemented the 'regulates' relationships in
> the biological process (BP) ontology, we now plan to add
> 'regulates' relationships within the molecular function (MF)
> ontology and between the BP and MF ontologies. The target date for
> these additions is February 9, 2009.
> These additions may have great impact on your tools and analyses
> There will be inter-ontology links between BP and MF for the first
> Loading scripts will need to be modified to take the inter-ontology
> links into account by Feb. 9, 2009.
> GO analysis tools will need to be modified to take the new
> relationships into account by Feb. 9, 2009.
> Specifically, we will make 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 will make 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 will be 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 the new ontology.
> 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.
> A test file with the BP-MF links can be found in the GO scratch
> We will provide a test file with both BP-MF and MF-MF shortly.
> As noted, we plan to implement these links in the live ontology on
> February 9, 2009.
> Please provide feedback to us regarding this plan. We have created
> a wiki page
> which will provide a more formal specification for software
> developers and database administrators. It will also provide
> answers to frequently asked questions and will be kept up to date
> with our progress.
> On behalf of the GO Consortium,
> Tanya Berardini
> David Hill
> Chris Mungall
> Gofriends mailing list
> Gofriends at geneontology.org
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