Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
= 2017 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2017|January]]
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
== 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 ===
+
= 2020 Meetings =
* 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?
 
  
 +
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
== February 9, 2017 ==
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
=== AGR Disease working group ===
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
* 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 ===
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
* Proposing ontology working group to handle ontology data and display
 
  
=== Datomic ===
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
* 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
 
  
=== ACEDB dependencies ===
+
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
* 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
 
  
=== Upload ===
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
* CIT upload February 28th? Need to check with Hinxton
 
  
=== Nemametrix ===
 
* Sent two micropublications
 
* In review and given DOI's
 
  
=== Methods in Molecular Biology chapter ===
+
==August 6th, 2020==
* Submission deadline April 1
+
===Experimental conditions data flow into Alliance===
* Mary Ann and Chris are organizing, will contact authors of older WormBook chapters
+
*Experimental conditions in disease annotations: WB has inducers (used to recapitulate the disease condition) and modifiers (a modifier can ameliorate, exacerbate, or have no effect, on the disease condition)
* We want to co-opt text from WormBook chapters that are specifically how-to guide with troubleshooting tips
+
*We use the WB Molecule CV for Inducers and Modifiers in disease annotation
* Everyone that has contributed this type of text, now or in this process, will be given authorship
+
*Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
* In future, could have small methods descriptions as micropublications; e.g. how to navigate the phenotype widget
+
*So for data flow into Alliance:
* Content in older WormBook chapters that doesn't make it into the MIMB chapter could be micropublished
+
**In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
* We can review help desk inquiries to inform us as to what content should be included
+
**Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.
 
+
* How do we handle genetic sex? Part of condition?
 
+
** Condition has been intended for external/environmental conditions, whereas genetic sex is inherent to the organism of study
 
+
** Expression pattern curation needs genetic sex; needs a model at the Alliance for capturing sex
== February 16, 2017 ==
 
 
 
=== SObA graph for GO annotations ===
 
* May be able to download a single image that can be browsed offline
 
* Phantom.js screenshot?
 
* Maybe download an SVG?
 
* May need to use the unweighted view for downloadable images
 
* Will want to create SObA graphs for expression soon
 
 
 
=== Phenotype and GO enrichment tools ===
 
* David (Angeles) has built the tools
 
* Raymond will send around links to the tools when ready
 
* Something to consider for GO enrichment: consider three branches separately or together?
 
 
 
=== Biocuration abstract deadline ===
 
* Tomorrow (Feb 17) deadline for poster abstracts
 
* AGR Disease working group submitted an abstract
 
 
 
=== LEGO curation call ===
 
* Regular Monday calls
 
* Lots of good discussion; much about using proper relations
 
* GO group this week discussed possibly establishing standards or recommendations
 
* May be good to divide up biological topics among curators
 
* Concern about over-proliferation of relations
 
 
 
== February 23, 2017 ==
 
 
 
=== SObA graph for GO annotations ===
 
* Added the ability to download a single image that can be browsed offline
 
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]
 
Zoom in to a level where labels are visible for all the nodes you want to show (Don' worry if some are off canvas).
 
Click "export png", right mouse button (YMMV) to "Save Image As"
 
Saved image is 8000 dpi wide, sufficient to show all text clearly.
 

Latest revision as of 16:36, 6 August 2020

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August 6th, 2020

Experimental conditions data flow into Alliance

  • Experimental conditions in disease annotations: WB has inducers (used to recapitulate the disease condition) and modifiers (a modifier can ameliorate, exacerbate, or have no effect, on the disease condition)
  • We use the WB Molecule CV for Inducers and Modifiers in disease annotation
  • Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
  • So for data flow into Alliance:
    • In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
    • Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.
  • How do we handle genetic sex? Part of condition?
    • Condition has been intended for external/environmental conditions, whereas genetic sex is inherent to the organism of study
    • Expression pattern curation needs genetic sex; needs a model at the Alliance for capturing sex