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

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* '''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.
* '''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.''
** ''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.
* '''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.''
** ''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.
* '''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.
** SC: 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
** SC: 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


* '''Filters not being saved on clicking back'''- we already have issue tracker open: [https://github.com/geneontology/amigo/issues/50 #50]- Is this something that can be fixed easily downstream??
* '''Filters not being saved on clicking back'''- we already have issue tracker open: [https://github.com/geneontology/amigo/issues/50 #50]- Is this something that can be fixed easily downstream??
** ''SC: 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".''
** ''SC: 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,''' i.e. 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.
* '''Being able to pin multiple filters,''' i.e. 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.
** ''SC: 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, see:  [https://github.com/berkeleybop/bbop-js/issues/5 #5]. While icky, this is something that can also be specified at the Solr level, but I wouldn't. ''
** ''SC: 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, see:  [https://github.com/berkeleybop/bbop-js/issues/5 #5]. While icky, this is something that can also be specified at the Solr level, but I wouldn't. ''




Revision as of 18:58, 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 discussion:

  • 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.
    • SC: 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


  • Filters not being saved on clicking back- we already have issue tracker open: #50- Is this something that can be fixed easily downstream??
    • SC: 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, i.e. 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.
    • SC: 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, see: #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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