WormBase-Caltech Weekly Calls

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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 assa, 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 as well as people submitting data and it causes an error upon the dump.

We want two tags in the Phenotype Class called Natural_isolate and Not_in_natural_isolate to replace the Strain and Not_in_strain tags in the Phenotype class.

The data from Strain and Not_in_strain tags should be moved to the new tags, respectively.

The Strain tag in the Phenotype_assay in Phenotype_info can stay unchanged, but should be clarified on forms and the OA with the label Contained_in_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