WormBase-Caltech Weekly Calls

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April 6, 2017

AGR time spent

• Paul S asking about %time spent on AGR project
• Time spent on working groups, conference calls, AGR development
• Send estimates to Paul

SimpleMine

• Two tables added to SimpleMine for human orthology
• Now SimpleMine output has many columns (30+)
• We may want to give users the option to specify which output they want
• Users could specify groups of data (with checkboxes): gene IDs/names, phenotypes, orthology, etc.
• All checkboxes can be checked by default

Enrichment tools

• Raymond working on display for paper

Gene Ontology SObA graph

• Raymond, Juancarlos working on
• Working on paper

WormMine updates

• WS258 adding gene class
• WS259 adding more info (almost all meta data) on variations, laboratory and strains, RNAi phenotypes (hopefully)
• Expression data in WormMine is problematic
• Many genes being annotated to the same ~6 tissues or so
• Resulting in erroneous data for some genes
• Chris will send GitHub ticket to Todd
• Todd will discuss with Paulo today

Gene Ontology

• Some very complex terms becoming immediate children of root terms (e.g. "biological process")
• May be result of attempt to create logical definitions/equivalence axioms
• Raymond will discuss with Kimberly