Manager Call 2018-03-15: Difference between revisions
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'''Discussion''' | '''Discussion''' | ||
* '''GO work that is driven by priorities of alliance (Chris):''' | |||
* Get the GO API up and running (done by Nathan) | * Get the GO API up and running (done by Nathan) | ||
* Noctua being rolled out to Alliance members (Noctua is a shared Alliance tool) | * Noctua being rolled out to Alliance members (Noctua is a shared Alliance tool) | ||
* Visualization of Noctua models | * Visualization of Noctua models | ||
* GO ribbon | * GO ribbon | ||
* GO is not just 'tags on genes' anymore, but also pathways, so we need to coordinate this | |||
* See | |||
** https://docs.google.com/document/d/1WfQRoYLhoEJ-0h3JJQghEtok_DXR_vaIdV3Rti9QYro/edit | |||
** https://docs.google.com/document/d/1oTZwwNHkfA0GY02gX4z38XXGiXX1CojfJKcq5W2aOHY/edit | |||
== Working Groups/Projects == | == Working Groups/Projects == | ||
=== GO Curation Survey === | === GO Curation Survey === | ||
*[https://docs.google.com/document/d/1IEgyIHDMMZIMdFaR33jBaRg14d7-u6HKaI2couHTHXo/edit#heading=h.9nx0eh5kf2pz Draft Survey] | *[https://docs.google.com/document/d/1IEgyIHDMMZIMdFaR33jBaRg14d7-u6HKaI2couHTHXo/edit#heading=h.9nx0eh5kf2pz Draft Survey] | ||
'''Discussion''' | |||
Action to Survey monkey, make changes discussed, and send it around | |||
=== Expanded Set of Relations === | === Expanded Set of Relations === | ||
*Implementation requirements to meet our May goal of at least having acts_upstream_of_or_within | *Implementation requirements to meet our May goal of at least having acts_upstream_of_or_within | ||
Line 39: | Line 47: | ||
***Can Mary D. generate lists for all groups, put on a webpage for review? | ***Can Mary D. generate lists for all groups, put on a webpage for review? | ||
**Other software support needed for this? | **Other software support needed for this? | ||
'''Discussion''' | |||
* David: should we make it clear that this is for existing annotations? | |||
* Chris: in the NYC agenda there is a more up to date version of these relations, see http://wiki.geneontology.org/index.php/Annotation_Relations | |||
* Wiki links to RO and RO links back to the wiki pages | |||
* LOTS of discussion - we need to schedule a few calls before the GOC meeting to sort this out. We're not ready to bring this to the group yet. | |||
=== Protein Complexes === | === Protein Complexes === | ||
=== HTP Codes === | === HTP Codes === |
Latest revision as of 12:01, 21 March 2018
Call in info
https://stanford.zoom.us/j/754529609
Agenda
NYC Meeting Agenda
- Need to remind people to register & book rooms
- Start working on the agenda in more detail
- SAB agenda, plans
Alliance
- How do the priorities of the Alliance GO working group align with the priorities of the GOC overall?
- What are the most important things for GO to do in the next six months?
Discussion
- GO work that is driven by priorities of alliance (Chris):
- Get the GO API up and running (done by Nathan)
- Noctua being rolled out to Alliance members (Noctua is a shared Alliance tool)
- Visualization of Noctua models
- GO ribbon
- GO is not just 'tags on genes' anymore, but also pathways, so we need to coordinate this
- See
Working Groups/Projects
GO Curation Survey
Discussion Action to Survey monkey, make changes discussed, and send it around
Expanded Set of Relations
- Implementation requirements to meet our May goal of at least having acts_upstream_of_or_within
- Guidelines/examples for use
- acts upstream of: sperm motility, lipidation of ras, glycine transport -> heme biosynthesis
- regulation: glycolysis, signaling
- involved in: F-P links
- make use of other F-P co-annotation
- other ontology relations could be used to devise rules
- PAINT annotations
- Have a mechanism for groups to propose new rules
- Review annotations to process and regulation of process
- Can Mary D. generate lists for all groups, put on a webpage for review?
- Other software support needed for this?
- Guidelines/examples for use
Discussion
- David: should we make it clear that this is for existing annotations?
- Chris: in the NYC agenda there is a more up to date version of these relations, see http://wiki.geneontology.org/index.php/Annotation_Relations
- Wiki links to RO and RO links back to the wiki pages
- LOTS of discussion - we need to schedule a few calls before the GOC meeting to sort this out. We're not ready to bring this to the group yet.
Protein Complexes
HTP Codes
RCA Evidence Code
- Need to work with several groups to review their annotations:
- Gramene (35815 annotations)
- As an example, 2929 RCA Molecular Function annotations
- Date: 20060831
- Reference: GR_REF:8030
- Manual review of mappings; can we suggest ISM?
- GeneDB
- Some annotations from reviews, but some to papers that describe a systems analysis that is probably more in line with the original intent of RCA
- RCA -> CCA (combined computational analysis)??
- EcoCyc
- AgBase
- AspGD
- PAMGO_MGG
- If we decide to keep RCA, then we'd need to remove the one-year limit; it doesn't make sense.
Documentation
QA/QC
Working Group Meetings
- Quarterly?
- Rotate between ontology and annotation (small, focused groups)
- Test virtual meetings, but still focused on the task
Noctua
1.0 Rollout
- Merge Tremayne's fork with Noctua-dev for further testing
- Some outstanding issues on SAE
- Single source file for MODs to consume
Reactome Imports
- David, Kimberly have looked at some imports/translations
- Ben's work looks to be potentially very useful and promising for seeding templates, models
- Will probably require significant manual input, refinement, testing
End User Tools
- What plans do we have for implementing consumption and display of GO-CAM models?
- How does the AGR GO working group fit into this task?
- https://github.com/geneontology/noctua/issues/519
GO Helpdesk
Ontology
Announcing changes to the wider user community
This was brought up by Birgit in the protein complex merge ticket - she was suggesting we make an announcement. However we never made annoucements before (except for obsoletions); should we start? What would be the guidelines? For example when a merge affects more than 100, 1000 annotations ? EXP only ?
Term Genie status
This keeps on coming up at the Ontology call. What's the status ?
Minutes
- On call: