Manager Call 2017-07-05: Difference between revisions
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*Project strategy | *Project strategy | ||
**We have an annotation call on next Tuesday, July 11th and we should have a (proposed) strategy in place for that call | **We have an annotation call on next Tuesday, July 11th and we should have a (proposed) strategy in place for that call | ||
*Recent review article: http://www.cellsignallingbiology.org/csb/002/002.pdf | |||
**Divide each ~two-week period into specific annotation and ontology issues | **Divide each ~two-week period into specific annotation and ontology issues | ||
***For example, first week would be annotation of ligands (and receptors) | ***For example, first week would be annotation of ligands (and receptors) | ||
Line 27: | Line 28: | ||
*[https://github.com/geneontology/go-ontology/issues/13791 Modification to AGR slim] | *[https://github.com/geneontology/go-ontology/issues/13791 Modification to AGR slim] | ||
*What should AGR/MOD GO curators be doing for this? | *What should AGR/MOD GO curators be doing for this? | ||
** Create a GitHub ticket in the ontology tracker | |||
=== Annotation Qualifiers === | === Annotation Qualifiers === | ||
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I have added labels to most issues: | I have added labels to most issues: | ||
https://github.com/geneontology/go-ontology/labels | https://github.com/geneontology/go-ontology/labels | ||
Topics: | |||
* 35 protein complex | |||
* 33 targeting and transport | |||
* 21 metabolism | |||
* 20 viruses and symbionts | |||
* 19 cellular processes | |||
* 19 enzymes | |||
* 19 development | |||
* 18 cell cycle and DNA processes | |||
* 16 neurobiology | |||
* 15 signaling | |||
* 13 binding | |||
* 11 transcription | |||
* 9 RNA processes | |||
* 8 regulation | |||
* 6 cell type | |||
* 5 synapse_project | |||
* 4 cellular component | |||
* 4 MF refactoring | |||
* 4 chromatin | |||
* 4 immune system | |||
* 4 multiorganism processes | |||
* 4 start_and_end | |||
* 4 translation | |||
* 3 miRNA | |||
* 3 required_for_LEGO | |||
* 2 compound terms | |||
* 2 fatty acid biosynthesis | |||
* 2 No_MF_in_GO | |||
* 2 toxin | |||
* 1 Cilia/flagella | |||
* 1 autophagy | |||
* 1 cardiac conduction | |||
* 1 Protein Complex WG | |||
* 1 recombination | |||
= Minutes = | = Minutes = |
Latest revision as of 11:51, 10 July 2017
Joining the Call on Zoom
https://stanford.zoom.us/j/754529609
Agenda
From June 21st Call
Licensing
- The DO has recently gone to a CC0 license. http://disease-ontology.org/
Attributes in Noctua Annotations
- https://github.com/geneontology/go-ontology/issues/13511
- https://github.com/geneontology/noctua/issues/458
New Issues
Signaling Project and Cambridge Meeting
- Project strategy
- We have an annotation call on next Tuesday, July 11th and we should have a (proposed) strategy in place for that call
- Recent review article: http://www.cellsignallingbiology.org/csb/002/002.pdf
- Divide each ~two-week period into specific annotation and ontology issues
- For example, first week would be annotation of ligands (and receptors)
- Make sure we strike the right balance between:
- theoretical (relations between MFs, BPs; representation in the ontology)
- practical (consistent annotations; annotation guidelines that reflect experiments reported in the literature)
- Review and flag all existing github tickets in ontology and annotation repositories
- Add signaling label to annotation repository (one exists already in ontology)
- Divide each ~two-week period into specific annotation and ontology issues
- Cambridge meeting, Sunday, October 1st
- Any funding available for non GO-funded groups?
GO AGR Slim
- Modification to AGR slim
- What should AGR/MOD GO curators be doing for this?
- Create a GitHub ticket in the ontology tracker
Annotation Qualifiers
- What are the next steps?
- Add guidelines to github documentation with examples for use of each BP qualifier (include positive and negative directionality)
- Propose a half-day online working group meeting for this
- acts_upstream_of_or_within
- acts_upstream_of
- involved_in
- regulates
- Decide on SOP for legacy annotations
- This may be different for different annotation groups.
- What would be involved in providing computational approaches to help curators?
Ontology editors
(Pascale) I have added labels to most issues: https://github.com/geneontology/go-ontology/labels
Topics:
- 35 protein complex
- 33 targeting and transport
- 21 metabolism
- 20 viruses and symbionts
- 19 cellular processes
- 19 enzymes
- 19 development
- 18 cell cycle and DNA processes
- 16 neurobiology
- 15 signaling
- 13 binding
- 11 transcription
- 9 RNA processes
- 8 regulation
- 6 cell type
- 5 synapse_project
- 4 cellular component
- 4 MF refactoring
- 4 chromatin
- 4 immune system
- 4 multiorganism processes
- 4 start_and_end
- 4 translation
- 3 miRNA
- 3 required_for_LEGO
- 2 compound terms
- 2 fatty acid biosynthesis
- 2 No_MF_in_GO
- 2 toxin
- 1 Cilia/flagella
- 1 autophagy
- 1 cardiac conduction
- 1 Protein Complex WG
- 1 recombination
Minutes
- On call: