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
- 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') );
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 (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 )
- 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
- Would be good for curators to hear from PI's about current priorities and the established working groups
Paper supplemental files
- Most papers have separate files for each supplemental document (separate PDFs, XMLs, Excel docs, Word docs, etc.)
- Some AGR groups consolidate separate docs into a single file
- File consolidation could be beneficial to WB curators as well
- Karen will look into what this would involve; if it's worthwhile
AGR call with NIH
- NIH happy with supplement proposal; would like more specifics on deliverables
- Will the MODs continue to have separate SABs? Yes, for now
AGR Working Groups
- Current proposed working groups:
- Shared orthology
- Disease ontology
- Textpresso central as a common curation tool
- Noctua as a common curation tool
- Common web portal(s)
Metabolomics
- Discussed at TAGC
- Need to fix naming and identification of metabolites
- There is plan to work together (across organizations) and apply for funding
- 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.
August 4, 2016
Parasite Paper Pipeline and Curation Status Tracking
- ~4% of Journal articles (roughly, but not precisely translates, to curatable papers) mention both Caenorhabditis species and parasite species
- We discussed last week the options for accurately tracking data type flagging and curation status for these papers
- SVM does not flag data at the species level, but we need a way to distinguish curation status based on species or it will be difficult to get accurate numbers for Caltech and Hinxton
- One option would be to have separate status tables
- Lump Caltech and Hinxton species together or distinguish each species separately?
- Other options?