WormBase-Caltech Weekly Calls
Contents
Previous Years
2017 Meetings
May 11, 2017
Phenotype Strain curation (ky)
Changing Strain tag in the Phenotype class, which is used as a primary object for annotating a phenotype to, to clarify its purpose. A Strain tag also exists in phenotype assay, which is meant to capture the parent strain in which a mutant or other primary object (transgene or rearrangement) is part of. These two tags have been causing confusion for curators and it causes errors upon the dump, in addition strains entered into the Control_strain field of the phenotype form are throwing errors during the dump as they are being recognized as "Strains". The dumper does not allow more than one primary phenotype affected object, it can be Variation OR Strain.
Control_strain data from the phenotype form are being dumped as "Strain", not Control _strain.
Metabolic curation (ky)
Michael Witting has hired a student to curate elegans metabolic data. I will be talking to him to see what we can provide to help them share these curated data with WB. This might be as minimal as an spreadsheet although if they are submitting their own data, I will aim for a micropublication template. If there is another curator that wants to sit in on a call with Michael and me, that would be appreciated.
CGC login
CGC site now has a login. While we will be able to access all the info without logging in (the log in is required for placing an order or viewing an order history), do we need want a login? Aric talked with people at wormbase a while ago about the changes, was there any decision about if there will be a wormbase group login. I asked if they will be using logins to track activity on the site, he said no.
May 4, 2017
Strategies for GO-CAM (Noctua) curation
- GO-CAM (Gene Ontology - Causal Activity Model(ing))
- Proposal for curation report page (Kimberly)
- Paper-by-paper approach vs. big-picture approach
- Kimberly presented proposal for curation tool:
- Given a list of genes and keywords, tool could pull up all relevant annotations to help start with GO CAM model building
- Tool could return GO annotations, expression patterns, phenotypes, interaction-based phenotypes, etc.
- Could have a table to fill out that could then be imported into Noctua
- Can we use SObA to visualize relevant annotations for a set of genes? Help visualize common vs. distinct annotations?
- Process could highlight the need for micropublications
GO SObA
- Raymond & Juancarlos have been working on autocomplete tool for search bar; not trivial
