LEGO February 1, 2016
https://bluejeans.com/969313231
Agenda
- Software updates
- GAF updates
- Relations documentation
- Review draft?
- Plans for upcoming meetings
- ISB Meeting, Geneva, April 10-14
- GO Meeting, Geneva, April 15-16
- Models discussion
- C. elegans insulin signaling - http://noctua.berkeleybop.org/editor/graph/gomodel:5667fdd400000696
- Technical issues:
- Adding annotations for genes not yet in NEO
- Slow autocomplete for entities, GO terms, and evidence codes, especially
- Visualization options for different evidence codes, i.e. places where the evidence is strong vs underwhelming
- Add both evidence and comment with one click
- Modeling questions:
- For a signaling pathway, if/how to represent the BP without cluttering up the display
- Example of a cross-species interaction experiment as evidence for ligand-receptor binding
- Redundancy in has_input and directly_activates?
- Use of the directly_activates relation and the question of being part_of a pathway or regulating a pathway
- Using less granular MF terms, e.g. protein kinase activity vs protein serine/threonine kinase activity
- Technical issues:
- C. elegans insulin signaling - http://noctua.berkeleybop.org/editor/graph/gomodel:5667fdd400000696
Minutes
- On call: Chris, David OS, Giulia, Heiko, Helen, Kimberly, Pascale, Ruth, Seth, Stacia, Suzi
- Software updates
- Noctua front page now takes curators directly to model search/selection
- Delete model will be made a state option
- Only models marked production will be loaded into AmiGO that is visible to the public
- Large model layout issue fixed
- IDs added to term names
- GAF
- David H, Heiko, Kimberly working on this
- Need to decide how to handle regulates relations, e.g. directly_activates, when the MFs are really part_of a process
- Files for MODs to consume will be on Jenkins
- GPAD coming - need to sort out multivalue attribution
- Documentation
- Google doc is still editable
- Relations documentation needs comments from Paul T., David OS
- GO Meeting - Geneva, April 2016
- Run another Noctua workshop for GO consortium curators?
- Annotation issues
- Need to be able to annotate to non-NEO (Noctua Entity Ontology) genes/gene products
- Currently, minerva will not validate these entities
- Autocomplete is sometimes slow
- SOLR issue?
- Visual display of different evidences
- Some evidences provide stronger support than others
- Explore ideas of how to display evidence differently, e.g., bold, more colors, etc.
- Annotation comments
- May be desirable to specify type of comment, e.g. supporting evidence sentence vs curator comment
- Insulin model discussion
- Adding part_of relations to a model can make it very cluttered - display options here?
- Cross-species annotations - is there a way to provide a visual cue in the display?
- has_input - is this relation redundant when the relation to the next MF is directly_activates?
- What is the logical definition of a ligand and receptor?
- e.g., insulin-activated receptor has_part insulin binding activity?
- What is the logical definition of a ligand and receptor?
- Curators should think about what types of questions could be asked of LEGO models
- Need to be able to annotate to non-NEO (Noctua Entity Ontology) genes/gene products