Difference between revisions of "WormBase-Caltech Weekly Calls"
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**i.e. keep the original timestamp or create new one | **i.e. keep the original timestamp or create new one | ||
**Will likely not create new timestamp | **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 | ||
Revision as of 16:43, 17 May 2012
2012 Meetings
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
