WormBase-Caltech Weekly Calls

2012 Meetings

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

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

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