Ontology meeting 2016-05-26: Difference between revisions
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DOS: The graph editor is invaluable for generating figures - but needs to be used with public version of the GO file in future. This is because it doesn't display intersection clauses. As we no longer duplicate intersection clauses as relationships in the editors file (e.g. with don't have both "intesersection_of: part of fu" AND "relationship: part of fu"), the graph-editor display will be incomplete in some cases. However, these clauses do appear as relationships in the various GO release files. If you need to view a graph prior to a GO nightly release, you can simply download one of the release-style GO files built by Jenkins at every build. | DOS: The graph editor is invaluable for generating figures - but needs to be used with public version of the GO file in future. This is because it doesn't display intersection clauses. As we no longer duplicate intersection clauses as relationships in the editors file (e.g. with don't have both "intesersection_of: part of fu" AND "relationship: part of fu"), the graph-editor display will be incomplete in some cases. However, these clauses do appear as relationships in the various GO release files. If you need to view a graph prior to a GO nightly release, you can simply download one of the release-style GO files built by Jenkins at every build. | ||
HJD:I use Graph viewer to look at parents and higher to make sure I’m in the right area when I browse the ontology during curation. | |||
I use the graph editor much less; mostly to make a picture when needed (like, suppose I want a picture showing just some relations and not all | |||
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Revision as of 11:36, 26 May 2016
Attendees:
Minutes: Paola
Using OBO-Edit graph viewer and graph editor
All, please report on what we use the OBO-Edit graph editor for, what we use the graph viewer for, if we use them.
[Paola] In my last 3 days of editing, I haven't used them. But I recently used the graph editor to prepare figures for papers and presentations, and I know I will need to use it again soon for the same purpose. UPDATE: I'm having trouble using the graph viewer for a 'rich' term - GO:0006915 apoptotic process. I can show this during the call. Anyone else has the same issue? Alternatives?
DOS: The graph editor is invaluable for generating figures - but needs to be used with public version of the GO file in future. This is because it doesn't display intersection clauses. As we no longer duplicate intersection clauses as relationships in the editors file (e.g. with don't have both "intesersection_of: part of fu" AND "relationship: part of fu"), the graph-editor display will be incomplete in some cases. However, these clauses do appear as relationships in the various GO release files. If you need to view a graph prior to a GO nightly release, you can simply download one of the release-style GO files built by Jenkins at every build.
HJD:I use Graph viewer to look at parents and higher to make sure I’m in the right area when I browse the ontology during curation. I use the graph editor much less; mostly to make a picture when needed (like, suppose I want a picture showing just some relations and not all