WormBase-Caltech Weekly Calls

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Previous Years

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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]
  • Attn 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
      • Highly experimental (PhD project)
    • Pubtator
      • Similar to Textpresso
      • Only index (or allow annotations of) abstracts
      • Solid project; using state-of-the-art technology and techniques
  • Mike Cherry introduced Alliance
  • Not much with community curation
  • OntoChina: ontologies translated to Chinese
  • Pathway icons (Reactome)
  • Technique to identify the most relevant ontology common ancestor
    • Accounts for information content of each node
    • Valerio will send publication to Raymond
  • Automated descriptions
    • We should talk to GO about which data sources should be used to construct statements
    • Similarly, work with relevant data/curation groups for the respective data types
    • GO data coming directly from Alliance; may need to come directly from GO

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?
  • Juancarlos: Can make dumps specifically for the data objects you need, instead of giving full read access
    • Can create URL that points to all of the needed data
  • Transgenes don't come from name server; from Postgres
  • Current Postgres architecture is not setup for public access
    • Could accommodate, but need to look into what that entails
    • Probably need a server and a sys admin
    • How would it impact our other work/curation?
    • Security? Passwords?
    • How much time would we then need to devote to answering user questions, usability, user interface?


  • AFP mock http://textpressocentral.org:5000/overview
  • Update to AFP form to allow authors to confirm/validate predicted entities and data types
  • Steer authors towards data submission forms
  • Form layout tries to mirror gene page
  • Can confirm gene references, add new ones
  • Can report gene corrections and gene-sequence connections
  • Would be good to make clear to users what are the validated/accepted entities when confirming entity recognition
  • May be good to have common interface for each section; maybe one interface for data types and another for entity recognition
  • Need to make clear that the "Next" button marks the section as complete
  • Do we offer text fields for authors to indicate where the data is in the paper? May be asking too much and difficult to implement
  • Do we specify species for data types to verify it is relevant to C. elegans (e.g. physical interactions)? Again, may be asking too much; issue with what the flagging criteria are

April 26, 2018

Alliance reverse site visit

  • Went well, positive response
  • Good feedback on automated gene descriptions

Automated gene descriptions

  • Where is data coming from? GO data, from Alliance or GO?
    • Part_of relationships not loaded into Alliance GO data
    • Federated data vs. centralized data issues
  • Involves architecture discussions and decisions
  • Using same lowest-common-ancestor algorithm as GO
  • Newer WB descriptions are a big improvement

WormBase Grant

  • There may be a separation of effort/support for tools vs. database
  • Knowledgebase vs. database: which are we?

Data Commons

  • WB rep? Ask Mike Cherry (cc Kevin)


Noctua 1.0 release

  • Noctua 1.0 release coming soon
  • Worm Anatomy ontology; issue with being incorporated into the Uberon ontology
  • Worm anatomy terms not available in Noctua table annotator
  • Kimberly will send relevant GitHub ticket to Raymond
  • Raymond will follow up with Chris Mungall

Alliance phenotype face-to-face

  • June 13-14 in Eugene, Oregon
  • Working group will discuss initial and long term plans
  • Chris & Ranjana plan to go
  • Discuss travel with Sarah Torres

Datomic widgets

  • Juancarlos discussed person_lineage widget with Adam at length on Monday.
  • Adam says about 90% complete, about 20 to go.

WS266 Citace upload

  • Deposit files for Wen by May 15th, 10am Pacific time

WormBase curator candidate

  • Meet with her next Thursday