Add Slim documentation to Tools & GuideS section

[suzialeksander]

As mentioned in https://github.com/geneontology/amigo/issues/144, there is user interest in creating Slims. We need a walkthough in the Guides section, assuming this can be done via API.

If it can't already be done via API, what steps would be needed to make that possible??

[lpalbou]

Sorry for the delay Suzi.

There is no such API to create slims and there may never be as to my knowledge, the slims are only handled at the ontology level and all changes to the ontology have to go through github using generally protege and command lines. In addition, any change to the ontology would only reflect on production (for external users) after a monthly release.

For reference, look for "subsetdef" and "subset:" in http://current.geneontology.org/ontology/go.obo

To setup protege (more for consortium users): http://wiki.geneontology.org/index.php/Protege5_5_setup_for_GO_Eds

If you are satisfied with the answer, please close the ticket - i'll try to close a few next week -.

[suzialeksander]

@kltm I'm not super familiar with what went on in geneontology/amigo#144, does this seem like a wontfix then?

[kltm]

@suzialeksander That's not a feature currently in the roadmap.

[lpalbou]

Note that I answered about “creating slims”, which was your original question and is an ontology work like I said. The ability to map terms to higher level terms is a different question.

Mapping your gene functions to higher level terms is however something different and you can do that with the slimming function of the API which is also used for the ribbon: http://api.geneontology.org/api

[lpalbou]

As an example from the above swagger, it creates that query/url:

http://api.geneontology.org/api/bioentityset/slimmer/function?relationship_type=involved_in&subject=MGI%3A88351&slim=GO%3A0036094&slim=GO%3A0003824&exclude_automatic_assertions=false&rows=100

Which will return:

So this MGI gene has 3 annotations related to the high level term GO:0036094 (small molecule binding) and 15 annotations related to the high level term GO:0003824 (catalytic activity).