GO-CAM Working Group Call 2018-06-26: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
Line 57: | Line 57: | ||
*Landing page - please test using link above | *Landing page - please test using link above | ||
*Provide feedback to Laurent-Philippe, if needed | *Provide feedback to Laurent-Philippe, if needed | ||
== Annotation Discussion == | |||
=== Transcription === | |||
*Sabrina presented a paper and model on the clock1a transcription factor and its regulation of smad gene expression | |||
*We discussed what the correct representation of this transcriptional regulation would be | |||
*Models that Paul T. and Astrid have worked on wrt modeling transcription regulation by single vs multiple transcription factors: | |||
**[http://noctua.berkeleybop.org/editor/graph/gomodel:59bee34700000179 Template for single transcription factor activity] | |||
Revision as of 12:23, 26 June 2018
Meeting URL
https://stanford.zoom.us/j/976175422
Agenda
Logistics
- User accounts
- Follow-up from last week: Sandy L
- https://github.com/geneontology/noctua/issues/563
- Closed - all okay
- Groups
- https://github.com/geneontology/noctua-models/issues/96
- Should this be discussed on Wednesday's technical call?
- https://github.com/geneontology/noctua-models/issues/96
Noctua
- Landing Page (under development)
- Browsing GO-CAMs
- User and Group Pages
- Curators should look around the landing page, provide feedback
- Can now search using a PMID
- Green paper icons beneath model titles; mouse over shows paper data
- One question about presentation of author name(s) - first? last?
Documentation
Proposal for this group
- Focus on specific, commonly used curation modules
- For example, transcription, signaling pathways, metabolic pathways
- Groups will annotate papers of their own choosing
- We will discuss representation of the data in GO-CAMs, and any questions or issues that arise
- Choosing the appropriate relation
- Assigning evidence
- Give feedback to tool developers, ontology editors based on our discussions
- Github trackers
- Develop additional documentation
Curation Project(s) for this Group
- Will try creating models for papers that describe transcriptional regulation
- A caveat to this is that right now the MF branch for transcription factors is still under review, so we may have to make some changes to annotations in the future
- However, it would still be good to work out the relations between the MFs and the BPs wrt transcription and upstream and downstream activities and processes
- Google doc for entering papers and curation questions
- Sabrina - PMID:28687631 'Clock1a affects mesoderm development and primitive hematopoiesis by regulating Nodal-Smad3 signaling in the zebrafish embryo.'
- Kimberly - PMID: 28578929 'Morphological Diversity of C. elegans Sensory Cilia Instructed by the Differential Expression of an Immunoglobulin Domain Protein.'
Minutes
- On call: Chris G, Chris M, Dave F, David H, Dustin, Edith, Giulia, Harold, Jim, Kevin, Kimberly, Laurent-Philippe, Li, Pascale, Paul T., Penelope, Rob, Sabrina, Sandy, Seth, Stacia, Stan, Suzi A
Logistics
- Need to follow up about what the pipeline is for adding new users
- Need to discuss how to manage occasional updates to groups, both from a policy POV and a technical POV
Noctua
- Landing page - please test using link above
- Provide feedback to Laurent-Philippe, if needed
Annotation Discussion
Transcription
- Sabrina presented a paper and model on the clock1a transcription factor and its regulation of smad gene expression
- We discussed what the correct representation of this transcriptional regulation would be
- Models that Paul T. and Astrid have worked on wrt modeling transcription regulation by single vs multiple transcription factors: