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| [[WormBase-Caltech_Weekly_Calls_January_2017|January]] | | [[WormBase-Caltech_Weekly_Calls_January_2017|January]] |
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− | | + | [[WormBase-Caltech_Weekly_Calls_February_2017|February]] |
− | == February 2, 2017 ==
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− | === Methods in Molecular Biology chapter ===
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− | * Chris and Mary Ann will be in touch with individuals about section writing
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− | * Karen: FlyBase chapter has small sections rather than long articles about their pages; should we keep our sections small; a few paragraphs each?
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− | ** As long as we stick to the "how to" focus, we can write as much as needed
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− | * Raymond: We should try to write so that the content remains pertinent for a while
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− | === Pharyngeal phenotype terms ===
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− | * Karen has made pharyngeal pumping phenotype terms for NemaMetrix micropublications
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− | * 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.
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− | * Karen asked Raymond/Gary and any other person interested in the group to help with pharyngeal phenotype term organization
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− | * Raymond: Not very familiar with the existing usage of the terms and phenotype ontology structure wrt pharyngeal terms
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− | * Authors submit phenotype data as part of the micropublication process
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− | * Proposal for phenotype ontology going forward: create terms with logical definitions (OWL statements)
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− | * We will start exploring more usage of logical definitions for phenotypes
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− | * Will start meeting Thursday afternoons, starting next week (Feb 9), 1:30pm Pacific
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− | * Karen will prepare the terms to be looked through.....
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− | === SObA graph for GO ===
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− | * Juancarlos & Raymond making progress
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− | * Added toggling for different roots of GO
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− | * Difficult to navigate graph when lots of terms (e.g. tax-4)
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− | * What can be done to improve the display?
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− | * Filtering out IEA annotations; currently only for phenotype annotations; will expand to all IEA annotations
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− | * Kimberly generating GO slim, 15-20 terms for each branch of GO, possible to use in ribbon display
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− | * Could we distinguish between is_a, part_of, and regulates relationships?
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− | * To simplify graph, could we further minimize the display of higher level/indirect nodes?
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− | * Would we want parallel paths to root to be trimmed?
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− | == February 9, 2017 ==
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− | === AGR Disease working group ===
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− | * disease association file (DAF) pretty much worked out; data quartermasters are creating DAF files for each DB
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− | * 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
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− | * We should remove underscores from "is_model_of" and translate to "is a model of"
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− | * Should spell out evidence codes
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− | * Kevin, WB data quartermaster, working on developing the disease association file (DAF) from the WormBase build
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− | * Ranjana working on a new ?Disease_model_annotation class and model
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− | * Disease working group has handed off mockup to AGR UI working group to start development
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− | === C3 working group ===
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− | * Proposing ontology working group to handle ontology data and display
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− | === Datomic ===
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− | * Juancarlos discussing with Adam, Sibyl, Matt, Kevin
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− | * People are working on URL widgets: person widgets updated and ready for production, except for lineage widget.
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− | * Some other URL widgets have also been completed
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− | | |
− | === ACEDB dependencies ===
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− | * Raymond was asked to collect all CIT curator uses of ACEDB, e.g. programmatic access via ACE Perl
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− | * Send Raymond list of any CIT ACEDB-dependent processes
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− | * Going forward, how are model changes made/proposed?
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− | * Are we still proposing models in ACEDB and having them be converted? Not sure
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− | * We need to establish a models migration plan
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− | * Curators should review cronjobs that may need access to ACEDB
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− | * Juancarlos can collect list of cronjobs using ACEDB; will send email of list
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− | * Karen: WB Wiki page for OA forms, tables, scripts, etc. : http://wiki.wormbase.org/index.php/OA_forms,_tables,_scripts,_etc
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− | === Upload ===
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− | * CIT upload February 28th? Need to check with Hinxton
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− | | |
− | === Nemametrix ===
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− | * Sent two micropublications
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− | * In review and given DOI's
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− | === Methods in Molecular Biology chapter ===
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− | * Submission deadline April 1
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− | * Mary Ann and Chris are organizing, will contact authors of older WormBook chapters
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− | * We want to co-opt text from WormBook chapters that are specifically how-to guide with troubleshooting tips
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− | * Everyone that has contributed this type of text, now or in this process, will be given authorship
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− | * In future, could have small methods descriptions as micropublications; e.g. how to navigate the phenotype widget
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− | * Content in older WormBook chapters that doesn't make it into the MIMB chapter could be micropublished
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− | * We can review help desk inquiries to inform us as to what content should be included
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− | == February 16, 2017 ==
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− | === SObA graph for GO annotations ===
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− | * May be able to download a single image that can be browsed offline
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− | * Phantom.js screenshot?
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− | * Maybe download an SVG?
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− | * May need to use the unweighted view for downloadable images
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− | * Will want to create SObA graphs for expression soon
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− | === Phenotype and GO enrichment tools ===
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− | * David (Angeles) has built the tools
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− | * Raymond will send around links to the tools when ready
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− | * Something to consider for GO enrichment: consider three branches separately or together?
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− | | |
− | === Biocuration abstract deadline ===
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− | * Tomorrow (Feb 17) deadline for poster abstracts
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− | * AGR Disease working group submitted an abstract
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− | | |
− | === LEGO curation call ===
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− | * Regular Monday calls
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− | * Lots of good discussion; much about using proper relations
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− | * GO group this week discussed possibly establishing standards or recommendations
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− | * May be good to divide up biological topics among curators
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− | * Concern about over-proliferation of relations
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− | == February 23, 2017 ==
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− | === SObA graph for GO annotations ===
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− | * Added the ability to download a single image that can be browsed offline
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− | Go to a graph for say, [http://tazendra.caltech.edu/~azurebrd/cgi-bin/testing/amigo/soba_go.cgi?action=annotSummaryCytoscape&focusTermId=WBGene00002335&fakeRootFlag=1&filterLongestFlag=1 let-60]
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− | Zoom in to a level where labels are visible for all the nodes you want to show (Don' worry if some are off canvas).
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− | Click "export png", right mouse button (YMMV) to "Save Image As"
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− | Saved image is 8000 dpi wide, sufficient to show all text clearly.
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− | | |
− | === Modeling and curation future in Datomic ===
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− | * Will modeling take place directly in Datomic, or through ACEDB and the converter software?
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− | * Test trial of modeling some change in Datomic and ACEDB?
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− | * How much curator involvement in model changes?
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− | * Will there be a board to approve model changes?
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− | | |
− | === MIMB chapter ===
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− | * Thank you to those who have already submitted their contribution to the google drive.
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− | * Polite reminder to those who haven't to do so as soon as possible.
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− | | |
− | === OA cosmetic changes ===
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− | * Section heading for categories?
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− | * Tab labels changing from number to a name?
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− | * Field name font color configurable?
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