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geneontology / noctua

Graph-based modeling environment for biology, including prototype editor and services
http://noctua.geneontology.org/
BSD 3-Clause "New" or "Revised" License
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Create a slim of RO for LEGO annotation, and expose this using appropriate labels #129

Open cmungall opened 9 years ago

cmungall commented 9 years ago

cc @dosumis

We will create a subset either in RO, or as a separate bridge file. This will be used to generate the set used to construct edges in GO models. This could be achieved via some complex filtering in Noctua and/or Minerva, but it would probably be better to have some standalone functionality that generates the yaml that Noctua consumes (@hdietze to advise).

dosumis commented 9 years ago

How to choose the appropriate set of relations? Should all relations for AE be shown? What is needed in addition to this? Would it be easier just to list excluded relations?

hdietze commented 9 years ago

We already started to create a separate lego relations ontology in the GO svn repo: ontology/extensions/legorel-edit.owl which is used to create the ontology/extensions/legorel.owl The idea was not to include certain iffy c16 relations and axioms. At the moment, the file imports RO and defines a small subset of lego relevant relations. This happened quite a while ago, so this might be out-of-date.

The legorel.owl is part of the import-chain for go-lego.owl.

But the auto-complete widget is currently completely driven of Amigo, which loads the other gorel.owl!

kltm commented 9 years ago

If we just need to have our own GOlr instance, that's issue #125, and we should start adding what we wanted loaded over there.

kltm commented 9 years ago

Talking with @cmungall and @hdietze, it sounds like this needs to be maybe split out into two items.

cmungall commented 8 years ago

This may be subsumed into #165