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[Gofriends] Additional inter- and intra-ontology 'regulates' links in the GO coming

Alan Ruttenberg 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?
Thanks,
Alan

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  
> because:
>
> There will be inter-ontology links between BP and MF for the first  
> time.
> 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  
> directory:
>
> http://www.geneontology.org/scratch/regulates_relations_examples/ 
> go_regtest_withPosNeg_withPF_noXP.obo
> 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
>
> http://wiki.geneontology.org/index.php/FP-regulates
> 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
> http://fafner.stanford.edu/mailman/listinfo/gofriends

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