WormBase-Caltech Weekly Calls
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- 1 Previous Years
- 2 2017 Meetings
- 2.1 February 2, 2017
- 2.2 February 9, 2017
February 2, 2017
Methods in Molecular Biology chapter
- Chris and Mary Ann will be in touch with individuals about section writing
- Karen: FlyBase chapter has small sections rather than long articles about their pages; should we keep our sections small; a few paragraphs each?
- As long as we stick to the "how to" focus, we can write as much as needed
- Raymond: We should try to write so that the content remains pertinent for a while
Pharyngeal phenotype terms
- Karen has made pharyngeal pumping phenotype terms for NemaMetrix micropublications
- It is common for many groups to involve serotonin-induced pharyngeal pumping to analyze strains; we do have a serotonin-induced pharyngeal pumping variant term- should I use this for all pumping phenotypes? In addition we have an EPG variant term and again, people tend to use EPGs to record pumping activity - should all reported pharyngeal pumping phenotypes that were measured by EPGs be annotated with this term? These questions highlight a need to revisit the pharyngeal phenotype branch and clarify how we should be focused on annotating these reported annotations.
- Karen asked Raymond/Gary and any other person interested in the group to help with pharyngeal phenotype term organization
- Raymond: Not very familiar with the existing usage of the terms and phenotype ontology structure wrt pharyngeal terms
- Authors submit phenotype data as part of the micropublication process
- Proposal for phenotype ontology going forward: create terms with logical definitions (OWL statements)
- We will start exploring more usage of logical definitions for phenotypes
- Will start meeting Thursday afternoons, starting next week (Feb 9), 1:30pm Pacific
- Karen will prepare the terms to be looked through.....
SObA graph for GO
- Juancarlos & Raymond making progress
- Added toggling for different roots of GO
- Difficult to navigate graph when lots of terms (e.g. tax-4)
- What can be done to improve the display?
- Filtering out IEA annotations; currently only for phenotype annotations; will expand to all IEA annotations
- Kimberly generating GO slim, 15-20 terms for each branch of GO, possible to use in ribbon display
- Could we distinguish between is_a, part_of, and regulates relationships?
- To simplify graph, could we further minimize the display of higher level/indirect nodes?
- Would we want parallel paths to root to be trimmed?
February 9, 2017
AGR Disease working group
- disease association file (DAF) pretty much worked out; data quartermasters are creating DAF files for each DB
- Have a simple mockup for the display of disease data on a gene report page: https://docs.google.com/presentation/d/1YuD4_-mPS2AhIfaX41M8IIhiS63iiSy9ebcOQEZxoJQ/edit#slide=id.p4
- We should remove underscores from "is_model_of" and translate to "is a model of"
- Should spell out evidence codes
- Kevin, WB data quartermaster, working on developing the disease association file (DAF) from the WormBase build
- Ranjana working on a new ?Disease_model_annotation class and model
- Disease working group has handed off mockup to AGR UI working group to start development
C3 working group
- Proposing ontology working group to handle ontology data and display
- Juancarlos discussing with Adam, Sibyl, Matt, Kevin
- People are working on URL widgets: person widgets updated and ready for production, except for lineage widget.
- Some other URL widgets have also been completed
- Raymond was asked to collect all CIT curator uses of ACEDB, e.g. programmatic access via ACE Perl
- Send Raymond list of any CIT ACEDB-dependent processes
- Going forward, how are model changes made/proposed?
- Are we still proposing models in ACEDB and having them be converted? Not sure
- We need to establish a models migration plan
- Curators should review cronjobs that may need access to ACEDB
- Juancarlos can collect list of cronjobs using ACEDB; will send email of list
- Karen: WB Wiki page for OA forms, tables, scripts, etc. : http://wiki.wormbase.org/index.php/OA_forms,_tables,_scripts,_etc
- CIT upload February 28th? Need to check with Hinxton
- Sent two micropublications
- In review and given DOI's
Methods in Molecular Biology chapter
- Submission deadline April 1
- Mary Ann and Chris are organizing, will contact authors of older WormBook chapters
- We want to co-opt text from WormBook chapters that are specifically how-to guide with troubleshooting tips
- Everyone that has contributed this type of text, now or in this process, will be given authorship
- In future, could have small methods descriptions as micropublications; e.g. how to navigate the phenotype widget
- Content in older WormBook chapters that doesn't make it into the MIMB chapter could be micropublished
- We can review help desk inquiries to inform us as to what content should be included