WormBase-Caltech Weekly Calls February 2013

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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


  • 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)?


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


  • 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?
    • Monica Colaiacovo and Ralf J. Sommer
  • 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


  • 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)

February 28, 2013

WS237 Upload

  • Upload happening today
  • May be some delay due to script issues (being fixed)
  • Transgene and Life Stage are all set

BioCurator meeting coming up

  • Karen, Kimberly, Michael, and Daniela going
  • Topics: entity recognition, curation pipelines

Kimberly attended NESCENT summit

  • Meeting: Resource Coordination for NESCENT group, Text mining for annotations
  • Kimberly spoke about Textpresso
  • Setting up Textpresso for butterfly?
  • Amer Soc Plant Bio attended, wanted to know more about Genetics/G3 markup pipeline

Galaxy workshop next Tuesday, March 5, 2013

  • Biologists workshop 11am - 2pm, in Braun 151
  • Lunch provided
  • Register here
  • Web-based platform for sequence analysis
  • Protein trees, alignments, RNA-seq data
  • Run remotely or locally as a server

Bioinformatics Club

  • Could start a LinkedIn group (Caltech BioInformatics "huddle" group?)
  • Main goal: find out who's on campus and what they do
  • What are most people interested in?
  • Create forum and wiki page?
  • Mitch Guttman coming this summer, maybe give intro talk?
  • Georgi Marinov in Wold lab

Xiaodong visited two labs in Bejing

  • Gave WormBase tutorials
  • Lab is still using legacy site
  • Said they had trouble finding things on new site
  • Xiaodong showed SPELL and modENCODE data
  • WormMart demo and some queries
  • ~30 C. elegans labs in China, and growing?
  • Xiaodong encouraged them to send questions to WormBase Help
  • Someone (WB person) should go to the Asia WormBase meeting (every 2 years)

Intermine/Wormmine workshop at 2013 IWM

  • Organizers:
    • Monica Colaiacovo (mcolaiacovo AT genetics DOT med DOT harvard DOT edu)
    • Ralf J. Sommer (ralf DOT sommer AT tuebingen DOT mpg DOT de)
  • WormMine session in WormBase workshop
  • Who (at WB) will organize workshop? Michael Paulini

WormBase website questionaire:

  • What do people find on the legacy that they can't find on the new site?
    • SNPs, validated vs. predicted
  • Have posters and/or live demos at poster sessions? Walk around with tablets?
  • We can make YouTube videos:
    • 5 minutes or less
    • Could triage topics in a topics tree on Wiki page
    • Curators could check-off certain queries as they make them


  • Building templates with genes and an "Arrow" key, with different connection types
  • They're building now (should be done soon)