WormBase-Caltech Weekly Calls

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2012 Meetings

January

February 2, 2012

EPIC data into WormBase

• Daniela spoke to John Murray
• Need to modify model and display for data
• 3D movies as ?Movie objects

Endrov

• Tom Burglin and student Johan Henriksson developed Endrov.net (http://www.endrov.net)
• May be able to incorporate Endrov visualizations of Blender model and cell lineage into WormBase website?
• Need to talk to Todd and Web team

Elsevier legal issues

• Science-direct website links to-and-from WormBase website
• Daniela still working with contacts at MGI (Mouse Genomics Institute/Jackson Labs) & Elsevier
• MGI already has established links with Elsevier

New ?Interaction model

• Update old objects and speak to web team about new model before officially incorporating new ?Interaction model

February 9, 2012

Interaction model

• Added some XREFs (in Interactor tag) and Chromatin_IP to Detection method
• Co-Immunoprecipitation would be captured under Detection method "Affinity Capture Western"
• Worked out changes needed for old *.ACE files to fit new model; will give to Juancarlos to script

Transgene

• Daniela, Juancarlos, and Karen imported Extrachromosomal array transgenes into the Transgene OA
• Extrachromosomal array transgenes for which authors have not provided a name will be named Expr####_Ex
• Maybe we will name according to paper e.g. "WBPaper########_Ex####"
• Daniela and Karen will discuss cost-benefit of objectifying Ex transgenes
• Rather than determine transgene sequence (or partial sequence), curators will (as they have been for Expr_pattern) add free-text describing the sequence
  • This includes: primer sets, restriction digest sites, etc.
  • Continue to place this info in the Reporter_gene tag
  • Maybe add an additional free-text field (Sequence_info tag?)

Displaying curator names on new website

• Should we display curators' names on their curated objects?
• Currently only on concise description; why not do all objects?
• Keep curator name info only internal?
• Prevent curator names from being dumped for build/release?
• Should include 'Date-last-updated' Evidence dump
• Curator confirmed note could be placed in Tree View for all data types

Incremental Updates

• Should we perform incremental updates?
• Update as frequently as possible?
• Web display (of updates) served from Postgres/Tazendra?
• Serve RESTful widget from Caltech?
• Caltech in agreement about pushing forward with incremental updates

February 16, 2012

Gene product annotation for variation

• Variation affects gene product: absent, disfunctional, isoform-specific effects
• How is this best captured?
• Report as a phenotype? "RNA expression variant", "protein expression variant", etc...
• Capture as a gene_regulation event? Soon will be interaction object...
• Sequence ontology?
• Captured in ?Variation?
• Ask Hinxton/Mary Ann Tuli

Interaction model

• Old objects updated OK and read into ACEDB without problems
• Need to discuss updates with Web team
• Will send all updated *.ACE files with old Gene_regulaion, Interaction, and YH objects
• Add two zeros to the Interaction IDs once all current interaction objects uploaded to the Interaction OA

Transgene naming

• New extrachromosomal arrays will get "WBPaper###_Ex###" type of ID

SPELL Issues

• Problems coming up as data size increasing
• SPELL server at Amazon running at lowest paid instance ($1000/yr)
• 4GB memory needed (more than 132-bit machine can provide) for loading data
• 64-bit machine will cost $4000 per year
• Run SPELL on canopus? Yes but, have to take care of sys-admin issues
• $500/quarter for IMSS machine maintenance
• Talk to Matt Hibbs? Maybe need to optimize the process at that step

BioCreative/BioCurator meetings

• Kimberly working with DictyBase
• Kimberly will give 2 talks (CCC and molecular function automated curation)
• WormBase workflow; Kimberly will discuss with individual curators in March
• Arun submitted abstract

GO Consotrium meeting in a week and a half

• Paul, Michael (Muller) and Kimberly going

Human diseases will be objectified