GO-CAM Conference Call - 2019-02-19
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Meeting URL
- Please see the GO's Google calendar
- Contact Kimberly if you do not have access to the GO calendar
Agenda
Recap of Berkeley Hackathon
Documentation on Google Drive
- All documents, spreadsheets related to the meeting are available on the GO's Google drive
- Other relevant information is contained in github projects and tickets:
Importing MOD annotations into Noctua: Basics
- Which MODs to start?
- MGI and WB
- Which annotations?
- Generally, all manual annotations assigned by MGI or WB
- This can be customized, e.g. specific evidence codes, for a given MOD at the time of import
- How will annotations be modeled?
- Dustin and Ben are working on the conversion code
- One gene's annotations = one GO-CAM model
- Other alternatives we considered:
- one paper = one GO-CAM (spreads potentially similar annotations and evidence out amongst many different models, harder to review and QC)
- one "organismal" process = one GO-CAM (although ultimately where we'd like to go, for this initial phase, a one gene = one GO-CAM model is probably easier to review and QC)
- Other alternatives we considered:
- Input file is GPAD
- Allows for expanded set of gp2term relations and annotation properties, e.g. contributor
- Annotations will not be 'transformed' at all upon import, i.e. what's in the file is what will be imported
- Iterative process, each round of imports is available on noctua-dev
Modeling Conventional Annotations as GO-CAMs: Rules
Molecular Function
- [GP] <- enabled_by [MF]
- [GP] contributes_to -> [MF]
Cellular Component
- [GP] part_of -> [CC]
- [GP] colocalizes_with -> [CC]
Biological Process
- Relation between MF and BP will be taken from existing gp2term relations in the GPAD. For example:
- For existing GP 'involved in' BP:
- [GP] <-enabled_by (GO:0003674 molecular_function) part_of-> BP
- For existing GP 'acts upstream of or within' BP:
- [GP] <-enabled_by (GO:0003674 molecular_function) causally_upstream_of_or_within -> BP
- For existing GP 'involved in' BP:
References
- Will import one reference ID in order of preference:
- PMID
- GO_REF
- doi
- MOD paper id
With/From Field
- github ticket on modeling multiple values in the With/From field in OWL, i.e. commas and/or pipes
- For now, import as strings?
- Future project may be to develop and use OWL Union and Intersection to represent what is meant by commas and/or pipes in the With/From field
Annotation Extensions
- Working with Dustin and Paul to devise a set of rules to convert existing annotation extensions to GO-CAM
- [https://docs.google.com/spreadsheets/d/1AEAj39mxQnBsuccIxWhpjiFKcdCJLw6uIa1eXiAG1Hs Google spreadsheet of annotation extensions for which the meaning and/or conversion needs to be clarified
- This is currently where the bulk of the curator work is being done
- For example, has_regulation_target extensions need to be modeled for GO-CAM
Minutes
- On call: David, Dmitry, Dustin, Edith, Giulia, Harold, Karen, Kevin, Kimberly, Laurent-Philippe, Li, Pascale, Patrick, Paul T., Sabrina, Seth, Shur-Jen, Stacia, Suzi A, Tanya