GO-CAM Working Group Call 2018-10-23: Difference between revisions
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== Review Action Items from Montreal Meeting == | == Review Action Items from Montreal Meeting == | ||
*Establish a GO-CAM chat room on https://gitter.im/geneontology/home | *Establish a GO-CAM chat room on https://gitter.im/geneontology/home | ||
**Seth has established a go-annotation chat room on gitter since this can be synced with the go-annotation repo wrt invitations | |||
**Will use as a way to get more timely feedback and answers to modeling questions | |||
**Monitor and collate questions for a GO-CAM FAQ | |||
**Link from Noctua? Graph editor, forms, landing page? | **Link from Noctua? Graph editor, forms, landing page? | ||
*Add an FAQ to the [http://wiki.geneontology.org/index.php/Noctua Nocuta/GO-CAM documentation] | *Add an FAQ to the [http://wiki.geneontology.org/index.php/Noctua Nocuta/GO-CAM documentation] | ||
**Landing page now linked from main Noctua documentation page | |||
**Noctua documentation page now linked from Annotation home page | |||
*Intermediate-level GO-CAM camp? | *Intermediate-level GO-CAM camp? | ||
**When? Where? Level of interest? | **When? Where? Level of interest? | ||
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**New annotations captured as GO-CAM models | **New annotations captured as GO-CAM models | ||
**Existing annotations added to GO-CAM models | **Existing annotations added to GO-CAM models | ||
== Noctua Roadmap == | |||
*[https://docs.google.com/document/d/1FSWy7mvsSN7yZ10TL5CzSeJrzverub_oYwHY25bKD9o/edit Noctua roadmap] outlining work to be done over the coming year. | |||
== Modeling Transcription == | |||
*[http://noctua.geneontology.org/editor/graph/gomodel:5a5fc23a00000137 ZDB-PUB-170709-3 clocka in mesoderm development and primitive hematopoiesis] | |||
*[http://noctua.geneontology.org/editor/graph/gomodel:5b91dbd100000370 transcription demo model] | |||
=== Key Points === | |||
*Direct vs Indirect | |||
**Direct: include target using 'has input' relation for both MF and BP | |||
**Indirect: do not include target on MF and BP | |||
**Relation between transcription process and activity of target is the same | |||
== Next Week's Meeting == | |||
*October 30th - fifth Tuesday, ad hoc meeting, if desired | |||
= Minutes = | = Minutes = | ||
*On call: | *On call: Barbara, Bob, Chris, David, Dmitry, Dustin, Edith, Giulia, Harold, Jim, Karen, Kevin M, Kimberly, Li, Marie-Claire, Penelope, Petra, Rachael, Rob, Sabrina, Seth, Stacia, Suzi A, Suzi L, Tanya | ||
== Review Action Items from Montreal Meeting == | |||
*go-annotation chat room is set up on gitter: https://gitter.im/geneontology/go-annotation | |||
**it is public and anyone can join | |||
**we will experiment with this as a forum for getting more immediate feedback on annotation issues | |||
**gitter can be accessed via a desktop app or the web, but does not work well in Safari (Chrome okay) | |||
*Landing page for GO-CAM/Noctua FAQs now linked from the [http://wiki.geneontology.org/index.php/Noctua Noctua wiki documentation] | |||
**Will begin to populate with questions about using the tool and creating models | |||
*GO-CAM camp? | |||
**Will need to gauge level of interest and funds to see if we can schedule this | |||
*Documentation for annotation flow | |||
**High priority for understanding the path of Noctua-based annotations (newly created and integrated from existing annotations) | |||
== Noctua Roadmap == | |||
*Please review and add comments | |||
*We will be fleshing this out and working from this over the coming year | |||
== Transcription Models == | |||
*Direct regulation of transcription will be captured using a TF activity MF term that is part_of regulation of transcription (could be positive or negative) | |||
*The input to the MF and BP in this case would be the same and curators would only need to create one instance of that input | |||
*Separate evidence could still be placed on the relation between the MF and BP to the input, though | |||
*This way of modeling will produce the expected output for BP in the derived GPAD (i.e. no redundancy in inputs/participants | |||
== Meeting Schedule == | |||
*May just have Alliance function calls on the first Tuesday to leave remaining Tuesday calls open for GOC | |||
*Need to confirm with Nathan if this is okay - Stacia will check with him | |||
== Alliance All-Hands Meeting == | |||
*Will schedule some time on the agenda to discuss Noctua and moving Alliance groups to using Noctua for GO curation | |||
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[[Category: | [[Category:GO-CAM]] |
Latest revision as of 05:49, 16 April 2019
Meeting URL
https://stanford.zoom.us/j/976175422
Agenda
Review Action Items from Montreal Meeting
- Establish a GO-CAM chat room on https://gitter.im/geneontology/home
- Seth has established a go-annotation chat room on gitter since this can be synced with the go-annotation repo wrt invitations
- Will use as a way to get more timely feedback and answers to modeling questions
- Monitor and collate questions for a GO-CAM FAQ
- Link from Noctua? Graph editor, forms, landing page?
- Add an FAQ to the Nocuta/GO-CAM documentation
- Landing page now linked from main Noctua documentation page
- Noctua documentation page now linked from Annotation home page
- Intermediate-level GO-CAM camp?
- When? Where? Level of interest?
- Documentation for annotation data flow
- New annotations captured as GO-CAM models
- Existing annotations added to GO-CAM models
Noctua Roadmap
- Noctua roadmap outlining work to be done over the coming year.
Modeling Transcription
- ZDB-PUB-170709-3 clocka in mesoderm development and primitive hematopoiesis
- transcription demo model
Key Points
- Direct vs Indirect
- Direct: include target using 'has input' relation for both MF and BP
- Indirect: do not include target on MF and BP
- Relation between transcription process and activity of target is the same
Next Week's Meeting
- October 30th - fifth Tuesday, ad hoc meeting, if desired
Minutes
- On call: Barbara, Bob, Chris, David, Dmitry, Dustin, Edith, Giulia, Harold, Jim, Karen, Kevin M, Kimberly, Li, Marie-Claire, Penelope, Petra, Rachael, Rob, Sabrina, Seth, Stacia, Suzi A, Suzi L, Tanya
Review Action Items from Montreal Meeting
- go-annotation chat room is set up on gitter: https://gitter.im/geneontology/go-annotation
- it is public and anyone can join
- we will experiment with this as a forum for getting more immediate feedback on annotation issues
- gitter can be accessed via a desktop app or the web, but does not work well in Safari (Chrome okay)
- Landing page for GO-CAM/Noctua FAQs now linked from the Noctua wiki documentation
- Will begin to populate with questions about using the tool and creating models
- GO-CAM camp?
- Will need to gauge level of interest and funds to see if we can schedule this
- Documentation for annotation flow
- High priority for understanding the path of Noctua-based annotations (newly created and integrated from existing annotations)
Noctua Roadmap
- Please review and add comments
- We will be fleshing this out and working from this over the coming year
Transcription Models
- Direct regulation of transcription will be captured using a TF activity MF term that is part_of regulation of transcription (could be positive or negative)
- The input to the MF and BP in this case would be the same and curators would only need to create one instance of that input
- Separate evidence could still be placed on the relation between the MF and BP to the input, though
- This way of modeling will produce the expected output for BP in the derived GPAD (i.e. no redundancy in inputs/participants
Meeting Schedule
- May just have Alliance function calls on the first Tuesday to leave remaining Tuesday calls open for GOC
- Need to confirm with Nathan if this is okay - Stacia will check with him
Alliance All-Hands Meeting
- Will schedule some time on the agenda to discuss Noctua and moving Alliance groups to using Noctua for GO curation