WormBase-Caltech Weekly Calls
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Contents
Previous Years
2017 Meetings
February 2, 2017
Methods in Molecular Biology chapter
- Chris and Mary Ann will be in touch with individuals about section writing
- Karen: FlyBase chapter has small sections rather than long articles about their pages; should we keep our sections small; a few paragraphs each?
- As long as we stick to the "how to" focus, we can write as much as needed
- Raymond: We should try to write so that the content remains pertinent for a while
Pharyngeal phenotype terms
- Karen has made pharyngeal pumping phenotype terms for NemaMetrix micropublications
- It is common for many groups to involve serotonin-induced pharyngeal pumping to analyze strains; we do have a serotonin-induced pharyngeal pumping variant term- should I use this for all pumping phenotypes? In addition we have an EPG variant term and again, people tend to use EPGs to record pumping activity - should all reported pharyngeal pumping phenotypes that were measured by EPGs be annotated with this term? These questions highlight a need to revisit the pharyngeal phenotype branch and clarify how we should be focused on annotating these reported annotations.
- Karen asked Raymond/Gary and any other person interested in the group to help with pharyngeal phenotype term organization
- Raymond: Not very familiar with the existing usage of the terms and phenotype ontology structure wrt pharyngeal terms
- Authors submit phenotype data as part of the micropublication process
- Proposal for phenotype ontology going forward: create terms with logical definitions (OWL statements)
- We will start exploring more usage of logical definitions for phenotypes
- Will start meeting Thursday afternoons, starting next week (Feb 9), 1:30pm Pacific
- Karen will prepare the terms to be looked through.....
SObA graph for GO
- Juancarlos & Raymond making progress
- Added toggling for different roots of GO
- Difficult to navigate graph when lots of terms (e.g. tax-4)
- What can be done to improve the display?
- Filtering out IEA annotations; currently only for phenotype annotations; will expand to all IEA annotations
- Kimberly generating GO slim, 15-20 terms for each branch of GO, possible to use in ribbon display
- Could we distinguish between is_a, part_of, and regulates relationships?
- To simplify graph, could we further minimize the display of higher level/indirect nodes?
- Would we want parallel paths to root to be trimmed?
