Difference between revisions of "WormBase-Caltech Weekly Calls"
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* How should we track papers separately for Caltech/ParaSite species? Add a "Curated for C. elegans" or similar standard remark? | * 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 | * 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 === | === Dumping data subsets from OA === |
Revision as of 20:05, 28 July 2016
Previous Years
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 establish 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? Yes, worth looking into