WormBase-Caltech Weekly Calls

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

2018 Meetings








August 2, 2018


  • The AFP pipeline is currently emailing authors from karen's e-mail address
  • Use same e-mail account Chris is using for phenotype community curation requests or create a new account for AFP (gmail)
  • Can use outreach@wormbase.org for consistency
  • May use the PMID in the subject line so e-mails will not be all in the same thread
  • Todd and Chris have email credentials
    • Chris will send to Valerio, Juancarlos, Daniela, and Kimberly
  • Let Valerio and Juancarlos know what pipelines use AFP before they modify
  • Do curators still want to receive emails when authors flag their data type?
    • We will leave the alert emails as is for now

August 9, 2018


  • Mei Zhen, SAB member suggested that we include disease models in the AFP form.
  • The AFP group will work with Ranjana to incorporate it. Ranjana will prepare a mock by next week.
  • We will then decide about using the existing afp_humdis tables or creating new ones.


  • Shall we move tazendra.caltech.edu to the cloud? Either WormBase cloud or Caltech cloud?

August 16, 2018


  • Moving to cloud? To avoid local hardware issues?
  • Need to discuss with Juancarlos and Paul S.
  • Need to consider logistics; put all of Tazendra functionality on cloud? Keep some things local?
    • Postgres in cloud; forms local? Paper pipeline?
    • Will consult with Textpresso

ICBO 2018 recap

  • POTATO workshop (Phenotype Ontologies Traversing All The Organisms)
    • Will work towards generating standardized logical definitions using Dead Simple OWL Design Patterns (DOSDP)
      • <Quality> and inheres_in some <Entity> (and has_modifier some <Mod>)
      • Exercise: Reconciling logical definitions for apparently equivalent phenotype terms across ontologies (e.g. MP vs. HP)
    • Can use Protege to edit the OWL ontology and ROBOT for automating generation of many terms and logical definitions in parallel
    • Will try to align WPO to UPheno as best as we can; will depend (at least in part) heavily on alignment with Uberon for anatomy
    • Some Uberon alignment challenges: e.g. Fruit fly "tibia" and human "tibia"; human "tibia" parent is "bone" but fly "tibia" is not a bone
    • Will participate in Phenotype Ontology Developer's call, every 2 weeks on Tuesdays (9am Pacific, 12pm East coast, 5pm UK)
      • Next meeting September 4, 2018
    • Crash course in Protege, ROBOT, Ontology Development Kit, using GitHub to help develop OWL ontologies
    • PATO needs work
    • Questions that arose:
      • What should the scope of an ontology term be? Context? Life stage? Conditions? Treatment?
      • Being weary of ontology term count explosion; what's the right balance?
      • When defining phenotype terms, should the cause be included or only the observation? Maybe causes as a subclass (and assuming the observation includes assessment of cause)
    • Some distinction between human phenotype terms and model organism terms: phenotype of individual vs. population
  • Xenbase is trying to develop a phenotype ontology (spoke with Troy Pell, developer)
    • Asked about WPO and how we curate
  • Lots of plant talks
  • Many talks on performing quality checks on ontology development and ontology re-use
  • Domain Informational Vocabulary Extraction (DIVE) tool
    • Entity recognition/extraction
    • Working with two plant journals
    • Tries to identify co-occurrence patterns of words
    • Web interface and curation tool
  • Semantic similarity tools and evaluation of them

WormBase Phenotype Ontology working group

  • Chris will send around Doodle poll
  • Goal is to discuss creation of logical definitions and alignment of phenotypes for Alliance

August 23, 2018

Alliance tables

  • Filtering/sorting priorities
  • Open question about which tables on the Alliance website should be prioritized for acquiring sorting and filtering functionality

Worm Phenotype Ontology working group

  • Gary S., Karen, Kimberly, and Chris have responded to Doodle poll
  • Looks like 12pm Pacific (3pm Eastern) on Thursdays is the time that works for everyone
    • May start late on days when WB CIT meeting goes past 12pm Pacific
    • May want to start a bit past 12pm to allow west coasters to get lunch, etc.?
  • Goals:
    • Work on logical definitions for WPO terms
    • Consider any restructuring of WPO that would facilitate ontology alignment with other MODs and UPheno
    • Could we eventually create a phenotype annotation tool (and term requester) that allows modular expressions of a phenotype observation to lookup existing terms or create new terms with logical definitions based on those modular elements?

Alliance anatomy

  • Data quartermasters and expression working group are looking to get updated anatomy-Uberon mappings
  • How frequent are data updates at the Alliance? Seems to be every ~2 months
  • Anatomy-Uberon mappings will affect phenotype ontology alignments

Automated Gene Descriptions

  • Working on using the anatomy ontology to perform logical trimming (as opposed to only using a file provided for neuronal term groupings provided by Oliver Hobert) for expression data summarizing
  • Playing around with thresholds to see how the sentences look
  • Working on incorporating feedback from users; e.g. referring to human ortholog, protein domains, etc.
  • Need to setup a communication between the gene description pipeline and the Postgres database
  • Need to carefully consider the benefits/drawbacks of feeding gene description info back into Postgres/OA and vice versa