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| [[WormBase-Caltech_Weekly_Calls_April_2012|April]] | | [[WormBase-Caltech_Weekly_Calls_April_2012|April]] |
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| + | [[WormBase-Caltech_Weekly_Calls_May_2012|May]] |
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− | == May 3, 2012 ==
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− | | + | == June 7, 2012 == |
− | Curator Timestamps
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− | *Determining what data was provided directly by curator vs. what was populated automatically (e.g. mapping scripts)
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− | *Older data provided by curators that are no longer here will be problematic
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− | *We should archive all data-processing scripts in GitHub
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− | *Scripts can be made to create a unique timestamp that identifies that script after the fact
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− | Interaction model change
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− | *Pulling Variation, Transgene, Antibody, and Expr_pattern tags out of the Interactor_info hash and into the main model
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− | *This was originally to be able to capture intragenic interactions
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− | *The problem is the inherent disconnect between an interactor entity (e.g. gene) and these objects
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− | *Making this change would force a post-curation mechanism that ties these entities together for intuitive data display
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− | **Such a linking mechanism may be error prone, faulty, and potentially a headache for the web team
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− | *Is there a better way to handle this type of data?
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− | *Chris will discuss with Todd to see how much of a problem this would pose to the web team
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− | == May 17, 2012 == | |
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− | Life_stage model
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− | *Include species tag?
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− | *Create an ontology of life stages for different species
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− | *There are differences in nomenclature
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− | *Include Matt Berriman and Mark Blaxter in conversation on this?
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− | *Could include species abbreviation as prefix: e.g. Ppa_L1, Cbr_L3, etc.
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− | *How should we provide descriptions for each life stage?
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− | *Two main proposals:
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− | ** 1. General ontology of names: L1, embryo, dauer, adult, etc.
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− | ** 2. Go from most general to most specific
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− | *** e.g. Larval stage -> L1 -> Ppa_L1
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− | *Maybe make a C. elegans Slim Ontology
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− | *Anyone requesting a new life stage should provide a description
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− | Adding 3'UTR tag for transgene
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− | *Capture gene name (not necessarily DNA text)
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− | *Ignore unc-54 3'UTR
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− | *Triage by cases that come up for interaction or gene regulation events
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− | Transgene Names
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− | *WBPaperIDEx vs WBPaperID_Ex (underscore)
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− | *Would be good to have consistent naming scheme
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− | *Juancarlos needs to know if any curator wants/needs a history of the name change
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− | **i.e. keep the original timestamp or create new one
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− | **Will likely not create new timestamp
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− | Life_stage switch from names to IDs
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− | *Curators need to let Juancarlos know if the OA dumper is working as expected on Mangolassi (sandbox)
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− | *Once ready, Juancarlos can move the dumper to Tazendra
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− | Interaction model change
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− | *Will add two tags to the Interactor_info hash:
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− | **Intragenic_effector_variation
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− | **Intragenic_affected_variation
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− | *Will add four tags to the main Interaction model:
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− | **Unaffiliated_variation
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− | **Unaffiliated_transgene
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− | **Unaffiliated_antibody
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− | **Unaffiliated_expression_pattern
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− | *These changes will accommodate intragenic genetic interactions and unsuccessful object-to-gene mappings
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− | == May 24, 2012 ==
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− | Rearrangements vs Variations
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− | *Deficiencies like mgDf50 should be a variation or rearrangement object?
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− | *Many papers/authors refer to mgDf50 as an allele/variation of daf-16, but not linked in the database
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− | *Change data model or make 'surrogate' variation/allele for this deficiency?
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− | *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
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− | *Easiest thing is to add rearrangements to the Interaction model (and OA)
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− | *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
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− | Coordinating physical interaction curation with BioGRID
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− | *Currently, BioGRID curates protein-protein interactions for C. elegans
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− | *We will now have the Interaction OA and model that can accommodate physical interactions
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− | *We can continue to curate protein-DNA and protein-RNA interactions, as BioGRID does not capture these
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− | *Need to decide how we and BioGRID share data
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− | *Can the BioGRID IMS tool communicate with Postgres/OA to coordinate assignment of WB Interaction IDs?
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− | *Conclusion: if any curator wants to curate protein-protein interactions, use the BioGRID IMS tool; if a curator wants to curate protein-DNA or protein-RNA interactions, for example, will use the Interaction OA
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− | UTR tag for Transgene
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− | *UTR_of_gene proposed tag name
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− | *Maybe not specific enough
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− | *Tag name will be 3_UTR for 3' UTRs
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− | Populating the Transgene OA with transgenes
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− | *Reg-ex for capturing transgene names from corpus
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− | *Transgenes found are attached to existing transgenes or made as new transgenes in Postgres/OA
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− | *Documentation needed on Transgene Wiki
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− | *Put all scripts and script documentation on GitHub and GitWiki?
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