[Ontology-editors] [Amigo-hub] inter-ontology links in AmiGO

[Seth Carbon]

On Thu, 2009-01-15 at 14:56 -0800, Chris Mungall wrote:
> See for example +regulation of lyase activity:
> http://ash.lbl.gov/cgi-bin/amigo_xp/term-details.cgi?term=GO:0051349&session_id=611amigo1229540921

As a note to the relevant groups, the above URL is functioning again. 

Cheers,

-Seth


> An important point:
> 
> *** genes should not be propagated over regulates links, unless the  
> user explicitly requests this ***
> 
> i.e. a query for lyase activity should not return +regulation of lyase  
> activity by default. The user must ask "find me genes that are  
> involved in lyase activity or regulate lyase activity"
> 
> Note that we have been doing this wrong since the inception of GO. The  
> mistake was made more explicit when we introduced the regulates  
> relation last year. With the introduction of inter-ontology links, the  
> mistake will become more egregious, because we will be inflating the  
> numbers for MF.
> 
> We will take the following steps:
> 
> - the inter-ontology links will be stripped out of the editors file  
> when creating the main public GO file. Call this go_basic.
> - an additional public GO file will be made available that will have  
> the same contents as the editors file. This is called go_full.
> 
> AmiGO will be loaded from go_basic until it has been adapter to allow  
> intelligent relation filtering, as requested in this tracker item:
> https://sourceforge.net/tracker2/?func=detail&aid=2511745&group_id=36855&atid=494390
> Then we will switch to go_full
> 
> We need to discuss the presentation of go_basic and go_full on the  
> website, and a timeline for implementing the relation filter, and  
> discuss how it will appear.
> 
> 
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