GO-CAM Conference Call - 2019-04-23: Difference between revisions
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**Manual models: | **Manual models: | ||
***Production, Development (in progress, test) | ***Production, Development (in progress, test) | ||
***No convention - gene names, pmids, mod paper ids, curator initials, paper titles, biological processes, model ids, etc., or combinations of these | ***No convention - gene names, species, pmids, mod paper ids, curator initials, paper titles, biological processes, model ids, etc., or combinations of these | ||
*Do models need titles? | ****The diverse titles arose partly out of a desire for curators to easily find production and development models they'd made | ||
****Do we all agree that this is not optimal and standardized model titles is desirable? | |||
*Do models need informative, human readable titles? | |||
**If yes, how should they be generated? | |||
***Proposal from Cambridge meeting: | |||
****Use controlled vocabularies and lists to generate consistent model titles | |||
*****Manual or auto-generated? | |||
*****Current tool behavior - a model can't be saved unless it has a title | |||
*****Could a temporary title (e.g. model id) be generated for saving and then curators could construct a model title from a drop-down list of terms and entities present in the completed model? | |||
******Key points: | |||
*******Aiming for organism-specific models of biological processes - BP terms would thus get preference for naming | |||
********Other key information: anatomy and/or cell type, species | |||
*******Annotations not yet part of a larger process would be added to the gene-specific model | |||
=== New Noctua "Workbenches" === | === New Noctua "Workbenches" === |
Revision as of 15:00, 22 April 2019
Call Information
- See GO's Google calendar for Zoom URL
- email Kimberly if you need access to the GO's Google calendar
Agenda
Follow-up from Cambridge GOC Meeting
Gitter for go-annotation
- Reminder that we will be trying to use gitter as an informal chat room for GO annotation questions
- https://gitter.im/geneontology/go-annotation
- login with your github account
- This doesn't replace github/go-annotation or formal documentation on the wiki, but is meant to be a place to ask questions or share ideas
- We will monitor the conversations to make sure that key issues are elevated appropriately
Annotation Imports
- Track issues on github/gocamgen
- Beginning to model has_regulation_target extensions
Naming Models
- Follow-up from breakout discussion at the Cambridge meeting
- Model titles are currently visible on the Noctua landing page as well as on the public GO-CAM site for production models only
- Current naming practice:
- MOD imports - by MOD gene ID, e.g. WB:WBGene00004732 or MGI:MGI:101757
- SynGO imports - gene/gene product name, GO aspect, number (?)
- Manual models:
- Production, Development (in progress, test)
- No convention - gene names, species, pmids, mod paper ids, curator initials, paper titles, biological processes, model ids, etc., or combinations of these
- The diverse titles arose partly out of a desire for curators to easily find production and development models they'd made
- Do we all agree that this is not optimal and standardized model titles is desirable?
- Do models need informative, human readable titles?
- If yes, how should they be generated?
- Proposal from Cambridge meeting:
- Use controlled vocabularies and lists to generate consistent model titles
- Manual or auto-generated?
- Current tool behavior - a model can't be saved unless it has a title
- Could a temporary title (e.g. model id) be generated for saving and then curators could construct a model title from a drop-down list of terms and entities present in the completed model?
- Key points:
- Aiming for organism-specific models of biological processes - BP terms would thus get preference for naming
- Other key information: anatomy and/or cell type, species
- Annotations not yet part of a larger process would be added to the gene-specific model
- Aiming for organism-specific models of biological processes - BP terms would thus get preference for naming
- Key points:
- Use controlled vocabularies and lists to generate consistent model titles
- Proposal from Cambridge meeting:
- If yes, how should they be generated?