WormBase-Caltech Weekly Calls

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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
• 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?