Difference between revisions of "WormBase-Caltech Weekly Calls"

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== April 19, 2018 ==
== April 19, 2018 ==
=== Genotype class ===
* Need for number of use cases
* Also good to be compliant with other MODs/Alliance members
=== Biocuration ===
=== Biocuration ===

Revision as of 16:52, 19 April 2018

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

GoToMeeting link: https://www.gotomeet.me/wormbase1

2018 Meetings




April 5, 2018


  • Todd would like access to run GoToMeetings
  • Chris can send access credentials and GoToMeeting calendar details

Data Mining Tool comparison

Neuro Topic Meeting

  • Submitting abstract for meeting, due April 13
  • Wen will submit an abstract

Rutgers worm meeting

  • 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

  • Today at new building; reviewing office furniture
  • Ranjana and Valerio will go

Alliance curation

  • Paul needs to present on 5-year Alliance plan
  • Maybe could discuss curation plan


  • Troyanskaya lab; have we been in touch?
  • They may have new version that can be used
  • 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

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

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

Genotype class

  • Need for number of use cases
  • Also good to be compliant with other MODs/Alliance members


Meeting minutes [1]

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?