Meeting URL

Agenda

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?

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

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

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

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:

In general, when there is new information 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?

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 models above to make sure everyone understands the approach and the experimental evidence used to support the annotations