GO-CAM Working Group Call 2018-06-26: Difference between revisions
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*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 | ||
*For displaying author names, curators would prefer First Name, et al., since that is what people are most used to seeing in citations in papers | |||
== Annotation Discussion == | == Annotation Discussion == | ||
=== References === | |||
*Order of preference for reference IDs: | |||
**PMID | |||
**doi | |||
**GO_REF | |||
**MOD- or group-specific IDs | |||
*Why? | |||
**Using PMIDs wherever possible allows for easier display of papers associated with a model as the software can readily retrieve paper data using the PubMed API, as opposed to retrieving paper data from many different sources | |||
=== Transcription === | === Transcription === | ||
*Sabrina presented a paper and model on the clock1a transcription factor and its regulation of smad gene expression | *Sabrina presented a paper and model on the clock1a transcription factor and its regulation of smad gene expression | ||
Line 64: | Line 74: | ||
*Models that Paul T. and Astrid have worked on wrt modeling transcription regulation by single vs multiple transcription factors: | *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] | **[http://noctua.berkeleybop.org/editor/graph/gomodel:59bee34700000179 Template for single transcription factor activity] | ||
**[http://noctua.berkeleybop.org/editor/graph/gomodel:59bee34700000193 Template for multiple required transcription factor activities] | |||
**[http://noctua.berkeleybop.org/editor/graph/gomodel:59bee34700000234 Template for two transcription factor activities that each independently activate transcription] | |||
=== New Models vs Updating Older Models === | |||
*In general, when there is new information about a process modeled as a GO-CAM, curators should try to update an existing model rather than create a new one | |||
*This allows us to build on existing knowledge to create the most comprehensive picture of a biological process rather than having multiple, distinct models that represent a snapshot of knowledge at the time a paper was published | |||
=== Annotation Relations === | |||
*'directly activates ' vs 'directly positively regulates' | |||
*Are these two relations equivalent? | |||
*Right now, in RO, 'directly activates' is a child of 'directly positively regulates' | |||
*Should these two relations be merged? What is the distinguishing feature of each? | |||
== For Next Call - July 17th == | |||
*Curators should continue to identify papers that they'd like to model for transcription factors and regulation of transcription | |||
**Particularly, look for papers that study single vs multiple TFs | |||
*We will review the three transcription template models above to make sure everyone understands the approach and the type of experimental evidence used to support the annotations | |||
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[[Category:GO-CAM]] | |||
[[Category: |
Latest revision as of 05:47, 16 April 2019
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
- For displaying author names, curators would prefer First Name, et al., since that is what people are most used to seeing in citations in papers
Annotation Discussion
References
- Order of preference for reference IDs:
- PMID
- doi
- GO_REF
- MOD- or group-specific IDs
- Why?
- Using PMIDs wherever possible allows for easier display of papers associated with a model as the software can readily retrieve paper data using the PubMed API, as opposed to retrieving paper data from many different sources
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:
New Models vs Updating Older Models
- In general, when there is new information about a process modeled as a GO-CAM, curators should try to update an existing model rather than create a new one
- This allows us to build on existing knowledge to create the most comprehensive picture of a biological process rather than having multiple, distinct models that represent a snapshot of knowledge at the time a paper was published
Annotation Relations
- 'directly activates ' vs 'directly positively regulates'
- Are these two relations equivalent?
- Right now, in RO, 'directly activates' is a child of 'directly positively regulates'
- Should these two relations be merged? What is the distinguishing feature of each?
For Next Call - July 17th
- Curators should continue to identify papers that they'd like to model for transcription factors and regulation of transcription
- Particularly, look for papers that study single vs multiple TFs
- We will review the three transcription template models above to make sure everyone understands the approach and the type of experimental evidence used to support the annotations