Oct 27th, 2015 Ontology Working Group Meeting: Difference between revisions

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** [[File:AmiGO 2.0 10-27-2015 video p2.mp4|thumb|AmiGO 2.0 10-27-2015 video p2]]
** [[File:AmiGO 2.0 10-27-2015 video p2.mp4|thumb|AmiGO 2.0 10-27-2015 video p2]]


===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.




Revision as of 18:46, 28 October 2015

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


Planning for the Fall Workshop in Corvallis

Discussion of the Agenda: see link

Ontology term discussion

Progress on Updating AmiGO 2 Browser

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

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.

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

Revisions to the Trait Ontology

Other upcoming meetings and workshops

    • PAG 2016
    • ICBO 2016
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