LEGO September 21, 2015
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Attendance: Rama, David H., Paul T., Kimberly, Seth, Chris, Heiko
- Moving forward with LEGO-style annotation:
- Documentation
- Between now and end of November, we will work on documentation for:
- Using the tool (start from existing videos?)
- Philosophy behind LEGO-style curation (introduction to the process, how it differs from current curation paradigm)
- Specific examples of curation
- Single paper (maybe from an annotation consistency exercise)
- Conserved pathway/textbook example (glycolysis)
- Up-to-date view of a biological process (using summary figure from a recent paper or review as a starting point, annotations derived from multiple papers - sometimes this is easier for curators to model)
- Between now and end of November, we will work on documentation for:
- Roll-out
- Early December? Will need to put together some possible dates and see what works
- An in-person meeting with representatives from each group currently annotating with Column 16, and others, if funding permits
- Documentation
- Issues for discussion
- Use of TAS and NAS to create reasonable biological models when evidence is either not annotated yet or not available in the literature
- Think about how this would be visualized by users to be clear on what is known and what is proposed by authors
- Should TAS annotations point to a particular paper in With/From column? Could the PMID in the With/From column be used to fill-in annotations in a LEGO model?
- Cross-species and cross-tissue modeling
- Is used in biology, but our current annotation model doesn't quite handle the representation of these types of inferences
- New evidence code?
- Refer to other annotations (using stable IDs) to document reasoning - inter-model evidence
- How often does this occur? What is the pragmatic solution for handling this?
- Highly specific vs general models
- Curation will likely happen on the more specific models, but we can use that information to develop a more general, or common, view of a biological process
- Use of TAS and NAS to create reasonable biological models when evidence is either not annotated yet or not available in the literature