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

May

June

July

August 2, 2018

AFP

• 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

AFP

• 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.

Tazendra

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

Tazendra

• Moving to cloud? To avoid local hardware issues?
• Need to discuss with Juancarlos and Paul S.

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 Onotlogy Developer's call, every 2 weeks on Tuesdays (9am Pacific, 12pm East coast, 5pm UK)
  • 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