Ontology meeting 2014-09-11: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
Attendees: | Attendees: Paola, David OS, Harold, Heiko, Tanya, Jane, Judy | ||
Minutes: Paola | Minutes: Paola | ||
| Line 18: | Line 18: | ||
https://docs.google.com/document/d/1hXZs6V9Ex4zeBhqGjajsEbY50S94O5B1qxxHEghod6o/edit | https://docs.google.com/document/d/1hXZs6V9Ex4zeBhqGjajsEbY50S94O5B1qxxHEghod6o/edit | ||
We suggested to give WebProtege another 6 months before we spend significant time on it. | |||
=== Transport terms (carried over from last week) === | === Transport terms (carried over from last week) === | ||
| Line 30: | Line 32: | ||
We'll then email the GOC to alert curators that they may request new terms, use specific terms rather than generic ones, and move their existing annotations if they wish/can. | We'll then email the GOC to alert curators that they may request new terms, use specific terms rather than generic ones, and move their existing annotations if they wish/can. | ||
AI: Tanya will send Heiko slides of suggested display. | |||
DOS did some work on patterns and they're in the ontology, but not in TG yet. He put them in dead-simple owl/yaml formatting (easy to write and edit). | |||
AI: DOS will make tickets in Jira and point Heiko to these files. It may not be always easy to incorporate them. Heiko will point DOS to examples of other templates (java files). DOS will finish documenting the templates we agreed on (import across plasma membrane) and send them to Heiko for review. | |||
=== NAR paper === | |||
We briefly went over the latest draft. Judy and Harold will work on it over the weekend. Val and Jane will write the cell cycle section and will send back by end of the day on Monday (UK time). | |||
== exocytosis/endocytosis - relationship to import/export == | == exocytosis/endocytosis - relationship to import/export == | ||
| Line 36: | Line 48: | ||
Also see 'endocytic import into cell' | Also see 'endocytic import into cell' | ||
When we refer to secretion, we should specify the mechanism of secretion; exocytosis is one type of mechanism but there are others. | |||
AI: DOS will look into this further and make a proposal of how to solve this. | |||
=== Localization and establishment of localization === | |||
Note that the current ontology structure is not the final one - DOS is working on it. | |||
[[Category:Ontology]] | [[Category:Ontology]] | ||
[[Category:Meetings]] | [[Category:Meetings]] | ||
Revision as of 12:22, 11 September 2014
Attendees: Paola, David OS, Harold, Heiko, Tanya, Jane, Judy
Minutes: Paola
build-go-assert-inferences - Build # 90 - Still Failing!
Discuss in case it hasn't been solved already:
POTENTIAL REDUNDANT AXIOMS GO:0006606 'protein import into nucleus' part_of 'part_of' GO:0034504 'protein localization to nucleus' is also a simple SubClassOf.
DOS: No problem I've been fixing in branch. Struggling to finish work on branch to merge back. Have now fixed in the trunk. Assert inferences now passes. See: http://build.berkeleybop.org/job/build-go-assert-inferences-report/1120/console
WebProtege
The EBI Editors met with Matt Horridge yesterday. Report.
https://docs.google.com/document/d/1hXZs6V9Ex4zeBhqGjajsEbY50S94O5B1qxxHEghod6o/edit
We suggested to give WebProtege another 6 months before we spend significant time on it.
Transport terms (carried over from last week)
Where are we with these action items?
As discussed at SF jamboree, we will:
1) display existing transport templates in a more user-friendly way;
2) add more templates, e.g. for 'transmembrane import' and 'transmembrane export'; David OS will specify more templates if needed.
We'll then email the GOC to alert curators that they may request new terms, use specific terms rather than generic ones, and move their existing annotations if they wish/can.
AI: Tanya will send Heiko slides of suggested display.
DOS did some work on patterns and they're in the ontology, but not in TG yet. He put them in dead-simple owl/yaml formatting (easy to write and edit).
AI: DOS will make tickets in Jira and point Heiko to these files. It may not be always easy to incorporate them. Heiko will point DOS to examples of other templates (java files). DOS will finish documenting the templates we agreed on (import across plasma membrane) and send them to Heiko for review.
NAR paper
We briefly went over the latest draft. Judy and Harold will work on it over the weekend. Val and Jane will write the cell cycle section and will send back by end of the day on Monday (UK time).
exocytosis/endocytosis - relationship to import/export
see https://sourceforge.net/p/geneontology/ontology-requests/10998/#b808
Also see 'endocytic import into cell'
When we refer to secretion, we should specify the mechanism of secretion; exocytosis is one type of mechanism but there are others.
AI: DOS will look into this further and make a proposal of how to solve this.
Localization and establishment of localization
Note that the current ontology structure is not the final one - DOS is working on it.