WormBase-Caltech Weekly Calls
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2016 Meetings
July 21, 2016
Yuling leaving in August
- Will send out announcements to hire a replacement
- Will take time to get back up to speed
- Curators should address concerns before he leaves (documentation, SVM stuff, etc.)
AGR curator call
- Yesterday we (FlyBase, ZFIN, and WormBase) presented paper curation status tracking
- Chris Mungall will discuss phenopackets next week
Phenotypes
- Will be good to be able to compare phenotypes across DBs
- Is there a working list of Phenologs anywhere? See Ed Marcotte's paper
- Monarch/phenopackets, Chris M talks next week
- Uberon; phenotype-anatomy associations in WB could be associated with Uberon anatomy terms
GO annotation model
- Common GAF was an impetus, but were other reasons
- ACE format couldn't accommodate some aspects of GO annotations
- Ranjana considering similar model for disease annotations
WBPerson lineage graph
- Raymond requests that people take a look and send feedback
- It's not clear right now where this is intended to be displayed
Web Phenote being resurrected
- We should talk to WebPhenote people to discuss our existing OA features
July 28, 2016
WebPhenote
- Ranjana willing to test out the newest version of WebPhenote for disease annotations
- WebPhenote is currently being built for human phenotype curation
- Dan (developer) could give WB a demo at end of August
Paper curation status tracking for WB ParaSite
- Juancarlos has cloned and modified the curation status form for ParaSite
- Some paper have both Caltech species as well as ParaSite species; this creates problems in the tool
- WB Caltech standard SVMs are run on ParaSite papers as well as 3 data types (RNASeq, Proteomics, ...)
- How should we track papers separately for Caltech/ParaSite species? Add a "Curated for C. elegans" or similar standard remark?
- We may need to have separate tables for each datatype for Caltech/ParaSite
Dumping data subsets from OA
- Karen proposed having functionality in the OA to dump specific data from the OA in a human readable format
- Data can be dumped as JSON format, but isn't human readable
- Curators would need to decide on how to dump field types (single ontology, multi ontology, big text, etc.) and work with Juancarlos
AGR curator call
- We've decide to skip first Wednesdays of the month (SGD has webinar)
- Last week of the month we will set up a poll for new topics
- Curators can add topics to the Google sign-up sheet: https://docs.google.com/spreadsheets/d/16cY8qIni4XNFqHktwBZHuigvR7TdFerKxAV6lowTvQg/edit#gid=0
