WormBase-Caltech Weekly Calls

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

January

February

March

April 5, 2018

GoToMeeting

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

Data Mining Tool comparison

• 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

• 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

Seek/modSeek

• 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

• 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

Genotype class

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

Biocuration

• Meeting minutes [1]
• Wen: GEO data interface
  • May be of more use to Alliance than WormBase; fewer GEO submissions these days
  • GEO often omits relevant biological background information
  • Any GEO data sets that are unpublished? Some, not many (6-7 data sets); some have lagged publications
• Text mining tools
  • Itextmine
  • Pubtator

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

• AFP mock http://textpressocentral.org:5000/overview