[Ontology-editors] inter-ontology links in AmiGO

[Chris Mungall]

For the hub meeting on tuesday morning I'd like to discuss the inter- 
ontology links that go live in February.

Seth has loaded a test database with two species, using a version of  
the ontology that contains inter-ontology links as they will appear in  
the editors file.

See for example +regulation of lyase activity:
http://ash.lbl.gov/cgi-bin/amigo_xp/term-details.cgi?term=GO:0051349&session_id=611amigo1229540921

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.