Oct 27th, 2015 Ontology Working Group Meeting

Planteome Ontology WG Zoom Meeting

• Time: Oct 27th, 2015 8:15 AM (GMT-7:00) Pacific Time (US and Canada)
• Connection info: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/672187671

• File:Ontology WG 10-27-15 video.mp4
• File:Ontology WG 10-27-15 audio.m4a

Planning for the Fall Workshop in Corvallis

Discussion of the Agenda: see link

Ontology term discussion

• see https://github.com/Planteome/plant-ontology/issues/607

Progress on Updating AmiGO 2 Browser

• Follow up call 10-27-15 with JE, LC, SC, CM

• Link to recordings:
  • File:AmiGO 2.0 10-27-2015 audio.m4a
  • File:AmiGO 2.0 10-27-2015 video p1.mp4
  • File:AmiGO 2.0 10-27-2015 video p2.mp4

Questions about Customization of the Planteome AmiGO 2.x version:

From the email:

• Customizing templates: Is there a way to just specify a new template path? I can modify the files in the current templates folder, but this seems like the wrong way to do it.
  • SC:Yes there is, although it has not been specified as a config variable (we can change that)--we kept this usecase in mind during the last major refactor. That said, it might be doable to simply have a fork that changes the template pathing variable--that way you could stay current and still make arbitrary changes.

• xrefs: How can I add new xrefs so that the links in the "Mappings"tabs work? In 1.5, I would modify Namemunger.pm, in 1.8 I would

modify go-db-perl/t/data/GO.xrf_abbs then run a modified make_dblinks.pl that didn't pull the GO.xrf_abbs file from CVS new each time, but this always seemed like a terrible hack on my part. Even so, I don't see a comparable method in AmiGO2. I'm sure there is a better way to do it.

• • SC: We're all about yaml files now https://github.com/geneontology/go-site/blob/master/metadata/db-xrefs.yaml

Depending on the exact use, the YAML files are only part of it: we also have all sorts of customizable low-level overrides for various display handlers, as well as easy overrides in the JS linker "class".

Again, it's easy enough to isolate that particular YAML pick-up as a variable and generalize it all.

>> What adds the text to "Last file loaded on"? On mine, it just has >> "???". I thought I found this once, but can't find it again, and >> thought this would be part of the golr/Makefile. This is generated by a specially structured (simple TSV) file generated by the loader; if found, as specified by a runtime variable, it will display the date, etc.

>> Lol wants to ask again about filters not being saved on clicking back >> (You already have issue >> https://github.com/geneontology/amigo/issues/50 on this, but she wants >> me to confirm this isn't something that can be fixed easily downstream) No, it's something that I'm personally not a huge fan of behavior-wise. We have a fairly good bookmarking mechanism now that could help out with that, but some nice re-draw code would have to be added so it wasn't excessively "jerky".

>> Being able to pin multiple filters, ie being able to select both >> "plant_anatomy" and "plant_trait_ontology" from the list of "Ontology >> sources" at the same time, or being able to select multiple species in >> the annotation search. I suppose this works by selecting the "-" >> rather than the "+" and choosing all the ones we don't want, but it >> seems a bit more intuitive to choose the ones we do want rather than >> those we don't. Plus we have something like 50 species, and probably >> will add more moving forward. In addition to what Chris mentioned, there are a couple of options that could be explored at the manager API level that might not be too disruptive, but would require a little work:

 https://github.com/berkeleybop/bbop-js/issues/5

While icky, this is something that can also be specified at the Solr level, but I wouldn't.

14:45:35 From cjm : http://dev.planteome.org/amigo/search/ontology

14:45:41 From cjm : Japanese

15:08:40 From sjcarbon : https://github.com/geneontology/go-site

15:12:12 From sjcarbon : https://github.com/geneontology/amigo

Other upcoming meetings and workshops

• • PAG 2016
  • ICBO 2016