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May 3, 2012

Curator Timestamps

• Determining what data was provided directly by curator vs. what was populated automatically (e.g. mapping scripts)
• Older data provided by curators that are no longer here will be problematic
• We should archive all data-processing scripts in GitHub
• Scripts can be made to create a unique timestamp that identifies that script after the fact

Interaction model change

• Pulling Variation, Transgene, Antibody, and Expr_pattern tags out of the Interactor_info hash and into the main model
• This was originally to be able to capture intragenic interactions
• The problem is the inherent disconnect between an interactor entity (e.g. gene) and these objects
• Making this change would force a post-curation mechanism that ties these entities together for intuitive data display
  • Such a linking mechanism may be error prone, faulty, and potentially a headache for the web team
• Is there a better way to handle this type of data?
• Chris will discuss with Todd to see how much of a problem this would pose to the web team

May 17, 2012

Life_stage model

• Include species tag?
• Create an ontology of life stages for different species
• There are differences in nomenclature
• Include Matt Berriman and Mark Blaxter in conversation on this?
• Could include species abbreviation as prefix: e.g. Ppa_L1, Cbr_L3, etc.
• How should we provide descriptions for each life stage?
• Two main proposals:
  • 1. General ontology of names: L1, embryo, dauer, adult, etc.
  • 2. Go from most general to most specific
    • e.g. Larval stage -> L1 -> Ppa_L1
• Maybe make a C. elegans Slim Ontology
• Anyone requesting a new life stage should provide a description

Adding 3'UTR tag for transgene

• Capture gene name (not necessarily DNA text)
• Ignore unc-54 3'UTR
• Triage by cases that come up for interaction or gene regulation events

Transgene Names

• WBPaperIDEx vs WBPaperID_Ex (underscore)
• Would be good to have consistent naming scheme
• Juancarlos needs to know if any curator wants/needs a history of the name change
  • i.e. keep the original timestamp or create new one
  • Will likely not create new timestamp

Life_stage switch from names to IDs

• Curators need to let Juancarlos know if the OA dumper is working as expected on Mangolassi (sandbox)
• Once ready, Juancarlos can move the dumper to Tazendra

Interaction model change

• Will add two tags to the Interactor_info hash:
  • Intragenic_effector_variation
  • Intragenic_affected_variation
• Will add four tags to the main Interaction model:
  • Unaffiliated_variation
  • Unaffiliated_transgene
  • Unaffiliated_antibody
  • Unaffiliated_expression_pattern
• These changes will accommodate intragenic genetic interactions and unsuccessful object-to-gene mappings

May 24, 2012

Rearrangements vs Variations

• Deficiencies like mgDf50 should be a variation or rearrangement object?
• Many papers/authors refer to mgDf50 as an allele/variation of daf-16, but not linked in the database
• Change data model or make 'surrogate' variation/allele for this deficiency?
• To capture a deficiency as part of a Gene_regulation object, either it has to become a variation or we need to change its data model
• Easiest thing is to add rearrangements to the Interaction model (and OA)
• Rearrangements will become a type of interactor, so as to avoid the problem of mapping to many genes, and each of those mapped genes becoming an interactor in the interaction