GO-CAM Working Group Call 2018-06-26
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- User accounts
- Follow-up from last week: Sandy L
- Closed - all okay
- Should this be discussed on Wednesday's technical call?
- 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?
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
- 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.'
- 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
- 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
- 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
- Order of preference for reference IDs:
- MOD- or group-specific IDs
- 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
- 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
- '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