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| | [[WormBase-Caltech_Weekly_Calls_June_2016|June]] | | [[WormBase-Caltech_Weekly_Calls_June_2016|June]] |
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| | + | [[WormBase-Caltech_Weekly_Calls_July_2016|July]] |
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| − | == July 21, 2016 ==
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| − | === Yuling leaving in August ===
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| − | * Will send out announcements to hire a replacement
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| − | * Will take time to get back up to speed
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| − | * Curators should address concerns before he leaves (documentation, SVM stuff, etc.)
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| − |
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| − | === AGR curator call ===
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| − | * Yesterday we (FlyBase, ZFIN, and WormBase) presented paper curation status tracking
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| − | * Chris Mungall will discuss phenopackets next week
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| − |
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| − | === Phenotypes ===
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| − | * Will be good to be able to compare phenotypes across DBs
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| − | * Is there a working list of Phenologs anywhere? See Ed Marcotte's paper
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| − | * Monarch/phenopackets, Chris M talks next week
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| − | * Uberon; phenotype-anatomy associations in WB could be associated with Uberon anatomy terms
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| − |
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| − | === GO annotation model ===
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| − | * Common GAF was an impetus, but were other reasons
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| − | * ACE format couldn't accommodate some aspects of GO annotations
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| − | * Ranjana considering similar model for disease annotations
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| − |
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| − | === WBPerson lineage graph ===
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| − | * Raymond requests that people take a look and send feedback
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| − | * It's not clear right now where this is intended to be displayed
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| − |
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| − | === Web Phenote being resurrected ===
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| − | * We should talk to WebPhenote people to discuss our existing OA features
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| − |
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| − |
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| − | == July 28, 2016 ==
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| − |
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| − | === WebPhenote ===
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| − | * Ranjana willing to test out the newest version of WebPhenote for disease annotations
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| − | * WebPhenote is currently being built for human phenotype curation
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| − | * Dan (developer) could give WB a demo at end of August
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| − |
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| − | === Paper curation status tracking for WB ParaSite ===
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| − | * Juancarlos has cloned and modified the curation status form for ParaSite
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| − | * Some paper have both Caltech species as well as ParaSite species; this creates problems in the tool
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| − | * WB Caltech standard SVMs are run on ParaSite papers as well as 3 data types (RNASeq, Proteomics, ...)
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| − | * How should we track papers separately for Caltech/ParaSite species? Add a "Curated for C. elegans" or similar standard remark?
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| − | * We may need to have separate tables for each datatype for Caltech/ParaSite
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| − | * 1094 papers have species from Caltech group and ParaSite set. SELECT joinkey FROM pap_species WHERE pap_species IN ('6239','860376','135651','6238','6239','281687','1611254','31234','497829','1561998','1195656','54126') AND joinkey IN ( SELECT joinkey FROM pap_species WHERE pap_species NOT IN ('6239','860376','135651','6238','6239','281687','1611254','31234','497829','1561998','1195656','54126') );
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| − |
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| − | === Dumping data subsets from OA ===
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| − | * Karen proposed having functionality in the OA to dump specific data from the OA in a human readable format
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| − | * Data can be dumped as JSON format, but isn't human readable (example, but change your curator_two value to your own WBPerson number : http://tazendra.caltech.edu/~postgres/cgi-bin/oa/ontology_annotator.cgi?action=jsonFieldQuery&field=id&userValue=4367,8883,12454,13163,13410,13449,13563,13567,13597,13598,13986,13987,14014,14076,14088,14090,9218&datatype=exp&curator_two=two1823&maxPerQuery=100 )
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| − | * Curators would need to decide on how to dump field types (single ontology, multi ontology, big text, etc.) and work with Juancarlos
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| − |
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| − | === AGR curator call ===
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| − | * We've decide to skip first Wednesdays of the month (SGD has webinar)
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| − | * Last week of the month we will set up a poll for new topics
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| − | * Curators can add topics to the Google sign-up sheet: https://docs.google.com/spreadsheets/d/16cY8qIni4XNFqHktwBZHuigvR7TdFerKxAV6lowTvQg/edit#gid=0
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| − | * Would be good for curators to hear from PI's about current priorities and the established working groups
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| − |
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| − | === Paper supplemental files ===
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| − | * Most papers have separate files for each supplemental document (separate PDFs, XMLs, Excel docs, Word docs, etc.)
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| − | * Some AGR groups consolidate separate docs into a single file
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| − | * File consolidation could be beneficial to WB curators as well
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| − | * Karen will look into what this would involve; if it's worthwhile
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| − |
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| − | === AGR call with NIH ===
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| − | * NIH happy with supplement proposal; would like more specifics on deliverables
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| − | * Will the MODs continue to have separate SABs? Yes, for now
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| − |
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| − | === AGR Working Groups ===
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| − | * Current proposed working groups:
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| − | ** Shared orthology
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| − | ** Disease ontology
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| − | ** Textpresso central as a common curation tool
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| − | ** Noctua as a common curation tool
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| − | ** Common web portal(s)
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| − |
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| − | === Metabolomics ===
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| − | * Discussed at TAGC
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| − | * Need to fix naming and identification of metabolites
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| − | * There is plan to work together (across organizations) and apply for funding
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| − | * Work with BioCyc? Art Edison (worm researcher) already talking to Peter Karp (BioCyc) about collaborations. Unless they've changed over the years, BioCyc does not use common ontologies - only their in-house ones - this won't work with Alliance-wide databases and collaborations with ChEBI. In addition, BioCyc might not be able to offer the flexibility in visualization and curation that is needed for grand project.
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| | == August 4, 2016 == | | == August 4, 2016 == |
