OEWG 20090602: Difference between revisions
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[[Category:OBO-Edit working group]] | |||
OBO-Edit Working Group, Tuesday June 2nd, 2009 9.30 a.m. PST <br> | OBO-Edit Working Group, Tuesday June 2nd, 2009 9.30 a.m. PST <br> | ||
Line 7: | Line 8: | ||
Agenda/Chair: <br> | Agenda/Chair: DavidOS<br> | ||
Minutes: <br> | Minutes: Midori<br> | ||
Attendees: | Attendees: | ||
==Action items carried over== | ==Action items carried over== | ||
Amina<br> | |||
* Lock Layout option - Done | |||
* Fix logging location for OSX in 2.1 | |||
* Investigate verification check issues on a fresh install | |||
**in progress | |||
* Graph Editor Crashes | |||
** https://sourceforge.net/tracker/?func=detail&aid=2747794&group_id=36855&atid=418257 | |||
** warning before GE crashes or look into making Graph Editor quit instead of crashing the application | |||
**should be fixed in 2.1 | |||
* Ability to switch between incremental reasoning on/off states. - In Progress | |||
==Discussion items== | |||
# Jen - Filtering system in OBO-Edit. <br> | |||
* My work on cross products and taxon links is badly held back just now by the lack of a good filtered save in OBO-Edit. I'm wondering if the need is great enough that I should start adding this feature even though we are still bug fixing. I have figured out what the interface could look like:<br> | |||
1) Add a new checkbox: 'choose tags to include'<br> | |||
[[Image:save3.jpg]]<br> | [[Image:save3.jpg]]<br> | ||
2) When checked, this box calls up an auto-populated list of all the tag types in the file and the user can then choose which tags to include in each file. | |||
[[Image:save4.jpg]] | [[Image:save4.jpg]] | ||
* DOS comment: | |||
** I like this suggestion. It should allow easy filtering of any new fields that are problematic to FlyBase. I would also provide a fix for this feature request: https://sourceforge.net/tracker/?func=detail&aid=2305635&group_id=36855&atid=418260 | |||
* Chris's comment: | |||
** Hardcode an option for exporting a file with only {id,intersection_of} tags, as this would be satisfactory for the majority of use cases involving working with xps as separate files. I think this could be implemented fairly easily. <br> | |||
** Alternative approach is to always namespace links and xp defs, and have the tag filtering done automatically from this. But I think this involves more work on the editors part as they have to ensure all links are correctly namespaced | |||
*Key question is how many use cases -- enough to justify the programming time & effort? | |||
**Not sure yet, although DavidOS can envision using it. | |||
*Known use cases at present: | |||
**only id and intersection tags | |||
**everything but intersection tags | |||
more discussion ... | |||
Conclusion: remove 'typedef' from tag list; Jen will look into how hard it would be to implement the general version as mocked up | |||
* Prioritize tracker items | |||
**Action item for all wg members: comment on feature requests and bug reports that affect you | |||
* Follow OBO-Edit on Twitter! | |||
http://twitter.com/OBOEdit | |||
* new DBxref verification check requested by Susan Tweedie | |||
** Can we instigate a check for DBxrefs of the form ID:0. A number of these have slipped though in GO recently. They cause problems for chado loading. | |||
*** Ticket here: https://sourceforge.net/tracker/?func=detail&aid=2800022&group_id=36855&atid=418260 | |||
* Features that would be useful to have for Buffalo workshop: | |||
** A way to convert intersection differentia to relations when saving implied links. See ticket: save implied links misfeature - https://sourceforge.net/tracker/index.php?func=detail&aid=2305594&group_id=36855&atid=418257 | |||
** A system for saving appropriate subsets of terms from one ontology for reasoning in another: | |||
*** See ticket: https://sourceforge.net/tracker/?func=detail&aid=2116798&group_id=36855&atid=418260. Details of how this could work require some discussion. | |||
* Request for info (DOS): At the Buffalo workshop, I'd like to present both GO and FBbt approaches to working with XPs. | |||
** I would therefore like a practical guide to how GO are managing XPs and instantiating links implied using them. | |||
***Much discussion, in which DavidOS explains reasons for these requests; Tanya describes current GO workflow; DavidOS asks whether GO is asserting anything other than is_a links (answer: not at present); David wants to assert more than just is_a links. | |||
*Conclusions: | |||
**additional feature request to have 'assert implied links' assert differentiae as well as is_a, perhaps as a configurable option. This should be separate from stripping out intersection tags. | |||
**second item carried over to next week | |||
==Demos/ Tips/ Ticks== | |||
* Ontology Tree Editor - missing/new features now implemented in OBO-Edit2.1 | |||
** Distinction between local and global mode | |||
** Now implemented in OBO-Edit2 - the much awaited - Lock View feature! | |||
* Questions/Discussion points | |||
** Independent sessions for multiple OTE instances | |||
*Demo notes | |||
**Clarified a Very Important Point: the little icon for global mode is a globe. | |||
*Tree editor | |||
**Lock view is back! (much rejoicing) | |||
***Amina mentions some implementation details | |||
****do we want an icon/button in the component menu bar to lock? | |||
****some discussion; button good but not high priority | |||
*Reasoner manager - incremental reasoning off by default, and manager has option to activate it | |||
**discussion and clarifications on behavior (buttons and checkboxes) | |||
**Amina will demo next week, so wg can hash out actual workflow and desired interface | |||
Q: Do we need to be able to search for synonyms of a specified type or scope? | |||
A: Not very often, so make it a low-priority feature request | |||
=== Tip of the week === | |||
* If we don't have anything here until the meeting time - the agenda chair can pick one of the attendees and put them on the spot about their favorite tip | |||
*Suggestions: | |||
** Editing the ontology through the OTE - workflow - things to take into consideration | |||
* Query Building/ How To's | |||
** How do I search for terms with multiple synonym types that have more than one relation with their ancestors? | |||
==Action Items== | ==Action Items== | ||
* UTF8 support | |||
* OBO-Edit 2.1 release | |||
==Links== | ==Links== | ||
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]] | [[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]] |
Latest revision as of 16:48, 30 June 2014
OBO-Edit Working Group, Tuesday June 2nd, 2009 9.30 a.m. PST
Conference call details:
US: 1-888-727-6732
Outside US: 1-719-867-3417
pin: 601425
Agenda/Chair: DavidOS
Minutes: Midori
Attendees:
Action items carried over
Amina
- Lock Layout option - Done
- Fix logging location for OSX in 2.1
- Investigate verification check issues on a fresh install
- in progress
- Graph Editor Crashes
- https://sourceforge.net/tracker/?func=detail&aid=2747794&group_id=36855&atid=418257
- warning before GE crashes or look into making Graph Editor quit instead of crashing the application
- should be fixed in 2.1
- Ability to switch between incremental reasoning on/off states. - In Progress
Discussion items
- Jen - Filtering system in OBO-Edit.
- My work on cross products and taxon links is badly held back just now by the lack of a good filtered save in OBO-Edit. I'm wondering if the need is great enough that I should start adding this feature even though we are still bug fixing. I have figured out what the interface could look like:
1) Add a new checkbox: 'choose tags to include'
2) When checked, this box calls up an auto-populated list of all the tag types in the file and the user can then choose which tags to include in each file.
- DOS comment:
- I like this suggestion. It should allow easy filtering of any new fields that are problematic to FlyBase. I would also provide a fix for this feature request: https://sourceforge.net/tracker/?func=detail&aid=2305635&group_id=36855&atid=418260
- Chris's comment:
- Hardcode an option for exporting a file with only {id,intersection_of} tags, as this would be satisfactory for the majority of use cases involving working with xps as separate files. I think this could be implemented fairly easily.
- Alternative approach is to always namespace links and xp defs, and have the tag filtering done automatically from this. But I think this involves more work on the editors part as they have to ensure all links are correctly namespaced
- Hardcode an option for exporting a file with only {id,intersection_of} tags, as this would be satisfactory for the majority of use cases involving working with xps as separate files. I think this could be implemented fairly easily.
- Key question is how many use cases -- enough to justify the programming time & effort?
- Not sure yet, although DavidOS can envision using it.
- Known use cases at present:
- only id and intersection tags
- everything but intersection tags
more discussion ...
Conclusion: remove 'typedef' from tag list; Jen will look into how hard it would be to implement the general version as mocked up
- Prioritize tracker items
- Action item for all wg members: comment on feature requests and bug reports that affect you
- Follow OBO-Edit on Twitter!
- new DBxref verification check requested by Susan Tweedie
- Can we instigate a check for DBxrefs of the form ID:0. A number of these have slipped though in GO recently. They cause problems for chado loading.
- Features that would be useful to have for Buffalo workshop:
- A way to convert intersection differentia to relations when saving implied links. See ticket: save implied links misfeature - https://sourceforge.net/tracker/index.php?func=detail&aid=2305594&group_id=36855&atid=418257
- A system for saving appropriate subsets of terms from one ontology for reasoning in another:
- See ticket: https://sourceforge.net/tracker/?func=detail&aid=2116798&group_id=36855&atid=418260. Details of how this could work require some discussion.
- Request for info (DOS): At the Buffalo workshop, I'd like to present both GO and FBbt approaches to working with XPs.
- I would therefore like a practical guide to how GO are managing XPs and instantiating links implied using them.
- Much discussion, in which DavidOS explains reasons for these requests; Tanya describes current GO workflow; DavidOS asks whether GO is asserting anything other than is_a links (answer: not at present); David wants to assert more than just is_a links.
- I would therefore like a practical guide to how GO are managing XPs and instantiating links implied using them.
- Conclusions:
- additional feature request to have 'assert implied links' assert differentiae as well as is_a, perhaps as a configurable option. This should be separate from stripping out intersection tags.
- second item carried over to next week
Demos/ Tips/ Ticks
- Ontology Tree Editor - missing/new features now implemented in OBO-Edit2.1
- Distinction between local and global mode
- Now implemented in OBO-Edit2 - the much awaited - Lock View feature!
- Questions/Discussion points
- Independent sessions for multiple OTE instances
- Demo notes
- Clarified a Very Important Point: the little icon for global mode is a globe.
- Tree editor
- Lock view is back! (much rejoicing)
- Amina mentions some implementation details
- do we want an icon/button in the component menu bar to lock?
- some discussion; button good but not high priority
- Amina mentions some implementation details
- Lock view is back! (much rejoicing)
- Reasoner manager - incremental reasoning off by default, and manager has option to activate it
- discussion and clarifications on behavior (buttons and checkboxes)
- Amina will demo next week, so wg can hash out actual workflow and desired interface
Q: Do we need to be able to search for synonyms of a specified type or scope?
A: Not very often, so make it a low-priority feature request
Tip of the week
- If we don't have anything here until the meeting time - the agenda chair can pick one of the attendees and put them on the spot about their favorite tip
- Suggestions:
- Editing the ontology through the OTE - workflow - things to take into consideration
- Query Building/ How To's
- How do I search for terms with multiple synonym types that have more than one relation with their ancestors?
Action Items
- UTF8 support
- OBO-Edit 2.1 release