WormBase-Caltech Weekly Calls
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Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2018 Meetings
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?
August 16, 2018
Tazendra
- 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
- Will work towards generating standardized logical definitions using Dead Simple OWL Design Patterns (DOSDP)
- 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
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