WormBase-Caltech Weekly Calls

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January

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)?

LEGO Call

• How to use annotation extensions for LEGO model?
• Consistent use?

Intermine

• Target for first release, minimal functionality for sequence-based queries
• JD working on importing sequence-based data
• How much can we get into Intermine by the first freeze/release (in April)?
• How should we prioritize?
• Can we build a "worm-version" of FlyMine (existing classes, e.g.)?
  • Probably not a good approach for first release in April, but maybe useful for long-term
• Production server (unstable) vs live/testing server (more stable)
• Major testing will start in April

Staging tests

• WS236 Staging site now available
• Everyone should test rigorously

2013 International Worm Meeting

• WormBase workshop
• What do we need to consider/prepare for, for the meeting?
• Someone should be in touch with organizers?
• Who are the organizers?
• WormBase souvenirs?

Dead genes

• Going to add "Historical_gene" tag to relevant class models (e.g. ?Interaction, ?Expr_pattern, ?Transgene, etc.)
• Will modify OA dumping scripts with Juancarlos to automate recognition of dead genes and replace them (if merged)
• Dumper will add remark about existence of dead gene in original object
• Will consider adding original gene reference through #Evidence hash under "Published_as" tag, as Other_name (gene synonym), as possibly as a separate free-text tag in the models that captures the verbatim reference to the original gene
• Will not try to re-annotate old objects WRT the gene synonyms/verbatim references, but can consider doing this going forward only

Transgenes

• CGC transgenes have been completed/unified with existing WBTransgene objects
• Updating new CGC strains will become a monthly task

GO task

• Can we link two or more genes based on ,e.g., process for enrichment analysis?
• What should we be getting out of enrichment analyses that we aren't currently?
• Link all genes as part of "FGF signaling", "DAF-2 signaling", "PAR genes", etc.
• Gene sets based on pathway, process, etc.
• Intermine should be able to filter by these means (eventually)