WormBase-Caltech Weekly Calls June 2012

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June 7, 2012

Midbuild

  • Wen needs all .ace files ready to test the midbuild
  • Chris will send modified WS232 models.wrm to Wen
    • Chris will add all model changes proposed for WS233
    • ?Interaction model "Rearrangement" tag needs an XREF and ?Rearrangement model needs an "Interactor" tag


New Interaction OA

  • Curators should take a look at the new Interaction OA on the sandbox (mangolassi) and notify Juancarlos, Chris, and/or Xiaodong of any problems
  • All interactions, including Yeast-Two-Hybrid and Yeast-One-Hybrid experiments, are in the new OA


Paper pipeline for other species

  • Kimberly will update pipeline to include papers from other species
  • Papers can go through data tagging pipeline (SVM etc.)
  • Images could be captured from cooperating journals
  • Are PDFs available?
  • ~1600 papers for Brugia malayi, for example
  • Mapping to genomes will be an issue (e.g. RNAi)
  • We would want an automated curation mechanism in place for non-core species


June 14, 2012

Mock Upload

  • Everything was OK
  • Wen will leave files in the same directories, so curators will need to overwrite or replace if you want a new file
  • Ghost objects? Allele-phenotype didn't have correct life stages; fixed


Anatomy terms

  • Juancarlos changed obsolete anatomy terms to red text in the Term Info section of the OA
  • We will update the anatomy terms somewhat periodically
  • Some terms get deprecated; if a term gets deleted, a replacement needs to be found
  • Merges can be dealt with more automatically
  • Raymond will periodically check for "floating" anatomy terms
  • Update went smoothly
  • Not many 'obsolete' terms being used
  • Many subsumed terms
  • Paper-anatomy term associations in Citace Minus; Raymond will take care of them
  • Kimberly uses legacy data for anatomy term associations to papers
  • Cell/Cell-Group issues


Interaction OA

  • Interaction OA and dumper script essentially finished
  • Curators should check the OA on the sandbox once more before we make it live
  • Interaction summary vs. Remark
    • Interaction summary is for biological info/summary
    • Remark is more for technical details
    • We will ask Juancarlos if Remark data from old Interaction objects can be transferred to Interaction_summary field/table
  • Make Interaction type unique (single ontology field)
  • Move the "Phenotype" field to the first TAB
  • Error checks
    • 5 Fatal errors (Interaction does not get dumped) if the following are not satisfied
      • 1) There are at least two interactors
      • 2) There is a reference
      • 3) The Interactor types are compatible
      • 4) There is an Interaction ID
      • 5) There is an Interaction type
    • 1 Non-fatal error (Interaction gets dumped but error is reported in error file on dump)
      • Interaction type and directionality of interactors
  • Additional error check for Karen - duplicate interactions on multiple rows
  • "Check Data" button, what is it doing now? Can it do all the same checks as the dumper?


June 21, 2012

First Pass Forms

  • We get e-mails when first pass forms are complete, even if PDF is not ready
  • Can we set up the system to hold off on e-mailing curators until the PDF is ready?
    • Already for Author First Pass, not for Journal First Pass (GSA/DJS)
    • Right now:
      • 1) Paper gets accepted by GSA/DJS
      • 2) Journal sends Author First Pass form to authors on paper
      • 3) Journal submits XML of paper to us
      • 4) Linking script runs on XML
      • 5) Quality Control checks on linked XML performed
    • Mary Ann would rather only get alerts after PDF is available
    • We can add a note about whether or not the PDF is available to the First Pass list, so Mary Ann can sort on that parameter
  • The form currently e-mails curators whenever data is changed; do we want updated alerts?


WormMart

  • WormMart wasn't accessible from EBI
  • Raymond removed software that affects firewalls; seems to have resolved the issue


Upload deadline June 28th, 2012


High School student volunteer

  • Kristy (Yingjie) Ren from Diamond Bar High School
  • Does she want lab experience only, or would she want to do some WormBase work?
  • We should ask her
  • Work study approach? We pay 20%, govt pays 80%; better situation?


June 28, 2012

Kristy Ren (summer high school student)

  • Will come in tomorrow at 10am
  • Ranjana, Raymond, Paul, Hillel, and Karen will speak to her
  • Curation efforts may be better for college students (work study)


Itai Yanai paper

  • Daniela curating expression pattern data
  • Temporal expression patterns across 5 species during development
  • Microarray data
  • Itai wants to display his expression images in WormBase
  • He should provide sequence names instead of gene names
  • EBI will do mapping to genes
  • Should original/raw data go into SPELL? Probably
  • What do we do with images that Itai can submit?
  • How do we capture/store/process original data, and what do we display/capture in database?
  • If we get a spreadsheet of the data, place on FTP site
  • Custom Agilent arrays


Upload tomorrow at 10am

  • New models (WS233) in CitaceMinus
  • Life_stage names have not been changed yet


Yeast Two Hybrid Experiments

  • Need to update ~11,000 experiments in OA to "High throughput"
    • Can use OA batch form (or possibly script to query multiple PGIDs)
  • Requested original data from 2004 Li et al Science paper from Vidal group (Michael Calderwood)
  • Many erroneous objects need to be fixed
    • Some have only bait or only target
    • Some interactions may be wrong


Grant Application

  • Paul will submit a grant application in 3 months
  • Paul will talk to PIs about big picture goals of the project
  • What is the 5 year plan?
  • 30 pages total (short)
  • What will we need to think through?
    • Curation approach/process (incl. SVM)
    • Gene expression
      • Generating images from digital expression data
    • Gene regulation/interaction
    • Physical interactions (Protein-Protein, Protein-Nucleic Acid)
    • Function/GO
    • Pathways/Processes
      • Work study student to curate pathways via WikiPathways (potential pilot)
      • Develop process pages for the website?
    • Anatomy
    • Other species
    • Outreach
    • Documentation
    • Community Annotation
    • Life stages
    • Data retrieval/mining; querying?
    • Website/database
    • What we want to display and how?
    • Advanced Queries; Ontology Browsers; Data integration
    • Tools
    • Host/pathogen interaction (collaborate with pathogen curator groups?)
    • Behavior? Process oriented?
    • Disease/drug discovery
  • Want to determine ASAP what we may need to pilot or experiment with
  • Website
    • Ontology browsers/searches
    • Process pages
    • Molecule pages


Taking over genetics curation from EBI