WormBase-Caltech Weekly Calls February 2012

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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 in postgres OA tables 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


February 23, 2012

BioCurator Meeting

  • Karen, Arun, Kimberly, Michael and Yuling are going
  • QCFast poster accepted for presentation


GO Consortium meeting this weekend

  • Things to bring up at meeting?
  • Responses to questionnaires


Purchase OA Domain name?

  • Move to a more formal link aside from mangolassi
  • wormbase domain name?
  • Cost? ~$11/year
  • "Ontology Annotator" may not be best name
  • "Curatool" and "Biocuratool" available; the "curinator"? Curate at your "curinal"? ;)
  • Currently only a static site
  • GO Consortium may want to use the tool


GO Upload

  • Going back and forth on deciding frequency of upload
  • Currently back to two-month uploads
  • We can certainly change frequency
  • Two-month cycle for upload (in sync with WormBase) is too long of a cycle for GO curation
  • Change GO curation upload to once per month (twice per month?)
  • Things will change when curating through a GO curation interface


SPELL server on Amazon

  • 1)Existing paid service doesn't seem to be stable
    • Looking at log file did not reveal anything
    • No reply from Matt Hibbs
  • 2)Amazon installation cannot be updated to WS229 because the dataset demands more memory
    • Raymond tried to install a 64-bit machine (free); wouldn't work
  • We're stuck without more technical support (wrt Amazon service)
  • Host ourselves (on canopus?) until OICR will take over? (When OICR is ~done with Beta site)
  • Host through IMSS?
  • WormMart is the only function of caprica; maybe setup SPELL on caprica for time being (next couple of months)
  • Will Gary Williams et al add more RNA-Seq data?
  • Athena (8GB memory?)
  • Instead of virtual machines, have one machine that does everything
  • SPELL usage? Not very much, but several (consistent users (300-900 queries per month)
  • Farm out to Matt Hibbs? Matt not serving data
  • Who is in charge of SPELL at SGD? How does SGD feel about SPELL? Ask Mike Cherry
  • Problem with hosting at OICR if SPELL needs tinkering...
  • Can Wen access and manipulate if at OICR? Not easy
  • SPELL has LOTS of data (millions of lines)
  • Will try to run locally for short term; meanwhile look for more resilient plan
  • Kimberly can ask Cara Delinsky (sp?) about SPELL


RNAi parsing script

  • Wen would like to work on
  • Updated more than a year ago
  • Should be able to parse interaction data directly into OA
  • Would like to handle new variations and transgenes
  • Script should look in Postgres tables
  • Still need to deal with DNA sequence text mapping to genome/genes
  • Elbrus a very old machine; very slow
  • Install ace-server on tazendra?
  • Ideal: OA takes/handles bulk of data; just run a script on the side to handle mapping DNA sequence to the genome
  • We will build the RNAi OA


Transgene naming strategy