WormBase-Caltech Weekly Calls
From WormBaseWiki
2013 Meetings
February 7, 2013
Person Cytoscape
- Person-person network viewing on website
- Use person lineages
- Will discuss with web team
WormBook History
- Paul editing a person history section, starting with John White
- Can use history info to link people
Binary vs. Non-binary interaction display
- Cytoscape and interaction table are only displaying interactions as binary interactions, regardless of number of interactors
- We need to assess how many interactions we have that have more than 2 interactors
- Once we have assessed that, we should discuss with web team about how to display these cases
Curation Statistics
- Wen can generate numbers for Citace AND the complete build (rather than Hinxton)?
- Will let Hinxton build the queries
- End-of-build summary for curators (with more database technical numbers) separate from the Release Notes for public (with more biologically interesting numbers)
- Will separate Wiki page into two sections to reflect this
- Public info will continue to be displayed in Release Notes
- Internal info - where should that be displayed?
Postgres info table (on Wiki page)
- Curators will continue to add info to Wiki on scripts, dependencies, ontologies, etc. for each Ontology Annotator
Intermine
- JD gave short demo yesterday
- Will give another tutorial next week (Thursday, Feb 14, 2013 - 8:30am PST)
- Curators can/should test
Nick Brown visit
- PI of FlyBase Cambridge
- Will be here tomorrow around 11am
February 21, 2013
WS237 Upload March 1, 2013
- Citace upload on February 28
WS236 will go live on April 5, 2013
- One week later than previously planned (March 29th)
New genome assemblies and gene names across species
- How do we handle independent, conflicting genome assemblies and gene models?
- Can we collect all gene models, for example, without any bias and display any info we have?
- How might we display conflicting models, etc.?
- Should we prioritize easier-to-handle, "more important" genomes?
- Can we establish automated (minimal manual effort) pipeline to handle these issues?
Expression graphs
- Wen and Daniela have been generating expression graphs
- Yanai probes need to be mapped
- Multiple probes mapped to the same gene will be averaged
- SPELL construction has changed; all data sets exist as separate flat files
Expression table
- Table of expression data to display all details of an expression pattern object
- Place in separate widgets on the gene page
- Perhaps, separate large-scale from small-scale studies
Phenotype Ontology
- How stable/complete is the current phenotype ontology?
- Good, but we may consider a reconstruction/re-ordering of existing terms
- Group phenotypes by e.g. anatomy term, life stage, etc.?
- Link anatomy terms, life stages to relevant phenotypes (at .ACE level or website level)
- Perhaps use cross-products of various ontologies to get the same effect?
- May want to consider using .OWL format as opposed to .OBO
- Need a sustainable, long-term approach to maintaining the ontologies
- AMIGO 2 only consumes .OWL format, not .OBO
- Should we consider switching to Protege, as a local ontology browser/editor (as opposed to OBO-Edit)?
