Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
Line 17: Line 17:
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
= 2018 Meetings =
 
  
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
 
  
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
+
= 2020 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
 +
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
== April 5, 2018 ==
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
=== GoToMeeting ===
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
* Todd would like access to run GoToMeetings
 
* Chris can send access credentials and GoToMeeting calendar details
 
  
=== Data Mining Tool comparison ===
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
* https://docs.google.com/spreadsheets/d/1vBTDBOKfXn9GcdpF1bXI62VEJ7hwyz2hOyAZcoV1_ng/edit?usp=sharing
 
* Chris and Ranjana will work on summarized blog post with link to table
 
  
=== Neuro Topic Meeting ===
+
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
* Submitting abstract for meeting, due April 13
 
* Wen will submit an abstract
 
  
=== Rutgers worm meeting ===
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
* We spoke to Andrew Singson; mentioned Rutgers meeting
 
* Kimberly will look into joining/speaking
 
  
=== Andy Golden disease and phenotype submission ===
 
* Andy had sent a sample file of alleles with disease and phenotype data
 
* Chris discussed phenotype details with Andy
 
* Andy will eventually send bulk data submission
 
  
=== Chen Institute furniture meeting ===
+
==August 6th, 2020==
* Today at new building; reviewing office furniture
+
===Experimental conditions data flow into Alliance===
* Ranjana and Valerio will go
+
*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
=== Alliance curation ===
+
*Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
* Paul needs to present on 5-year Alliance plan
+
*So for data flow into Alliance:
* Maybe could discuss curation plan
+
**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.
=== Seek/modSeek ===
+
* How do we handle genetic sex? Part of condition?
* Troyanskaya lab; have we been in touch?
+
** Condition has been intended for external/environmental conditions, whereas genetic sex is inherent to the organism of study
* They may have new version that can be used
+
** Expression pattern curation needs genetic sex; needs a model at the Alliance for capturing sex
* Paul S. will see her soon; will ask about it
 
 
 
=== Alliance Entity Summaries ===
 
* Have been working on gene summaries
 
* Do we want to start working on summaries for other entities, like variations?
 
* Ranjana can put together some proposal
 
 
 
=== Alliance Tutorial ===
 
* For reverse-site SAB meeting (April 23), need a sample query/tutorial
 
* April has worked on a script for a tutorial; maybe we can use
 
 
 
 
 
== April 12, 2018 ==
 
 
 
=== Preliminary AGR Tutorial ===
 
* https://docs.google.com/document/d/1iwKs7K87DgbDopIzg9uRlZ9eoxbza2Gd05eaEPjpxn8/edit?usp=sharing
 
* Document includes screenshots and text, which is subject to change.  Voiceover/basic video should be ready by the end of this week.  Additional video editing will be added later, including captions, an intro with footage of scientists, and visual aids (eg. arrows, boxes etc.)
 
 
 
=== Alliance data refresh ===
 
* Data refresh for 1.4 release
 
* Is this for databases that have more frequent updates, such as daily updates?  Does this apply to WB at all? Have to ask Kevin Howe if WB will have a data refresh.
 
** Kevin responded: There is a WB refresh for Alliance 1.4 release based on WS264
 
 
 
=== Phenotype graph bug ===
 
* Maybe related to https issues
 
* May need to update server to serve https requests
 
* GitHub ticket: https://github.com/WormBase/website/issues/6326
 
* Juancarlos and Raymond working on
 
 
 
=== Essential gene lists ===
 
* Several requests for the essential gene list over the years
 
* Difficult to query this out of ACEDB
 
* Chris generated a Postgres query to pull out all allele-phenotype annotations with "lethal", "sterile" or descendant phenotypes, including meta data including penetrance, background genotype, etc.
 
 
 
=== Acquiring list of ontology term descendants ===
 
* Raymond has URL constructor, for private/internal use; will share internally
 
* URL will return all ontological descendants, including all "is_a", "part_of", and "regulates"
 
* Phenotypes only have "is_a" relationships anyway, so not an issue
 
 
 
=== Gene set enrichment analysis: duplicate genes ===
 
* GitHub ticket: https://github.com/WormBase/website/issues/6300
 
* Issue where duplicate genes are not removed from input and are displayed in output
 
* We want to make clear to users that the duplicates are not counted multiple times in analysis
 
 
 
=== Gene names existing as secondary names for different genes ===
 
* Many genes (120+) have primary names that are also secondary names of other genes
 
* Causes confusion in terms of data attribution
 
* e.g. mdh-1 and mdh-2: mdh-2 has "mdh-1" as an other name even though these are distinct genes
 
* May be good for curators to make sure, for their data type, the correct genes are annotated to the correct data
 
* Jae will send around list of problematic gene names
 
 
 
== April 19, 2018 ==
 
 
 
=== Biocuration ===
 
Meeting minutes [https://docs.google.com/document/d/1U4prvuSfhWp8D9GWAjIepZL4kE0W206o5YVwkse-pcU/edit?usp=sharing]
 
 
 
=== Postgres reading access ===
 
* Coko will start generating submission forms as part of the platform build, can we have read access to postgres for them to get WB entities?
 
 
 
=== AFP ===
 

Latest revision as of 16:36, 6 August 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings



2020 Meetings

January

February

March

April

May

June

July


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