Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
= 2018 Meetings =
 
  
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
 
  
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
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= 2020 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
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[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
[[WormBase-Caltech_Weekly_Calls_May_2018|May]]
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
[[WormBase-Caltech_Weekly_Calls_June_2018|June]]
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
[[WormBase-Caltech_Weekly_Calls_July_2018|July]]
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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
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[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
== August 2, 2018 ==
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
=== AFP ===
 
  
* The AFP pipeline is currently emailing authors from karen's e-mail address
+
==August 6th, 2020==
* Use same e-mail account Chris is using for phenotype community curation requests or create a new account for AFP (gmail)
+
===Experimental conditions data flow into Alliance===
* Can use outreach@wormbase.org for consistency
+
*Experimental conditions in disease annotations: WB has inducers (used to recapitulate the disease condition) and modifiers (a modifier can ameliorate, exacerbate, or have no effect, on the disease condition)
* May use the PMID in the subject line so e-mails will not be all in the same thread
+
*We use the WB Molecule CV for Inducers and Modifiers in disease annotation
* Todd and Chris have email credentials
+
*Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
** Chris will send to Valerio, Juancarlos, Daniela, and Kimberly
+
*So for data flow into Alliance:
* Let Valerio and Juancarlos know what pipelines use AFP before they modify
+
**In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
* Do curators still want to receive emails when authors flag their data type?
+
**Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.
** We will leave the alert emails as is for now
+
* How do we handle genetic sex? Part of condition?
 
+
** Condition has been intended for external/environmental conditions, whereas genetic sex is inherent to the organism of study
 
+
** Expression pattern curation needs genetic sex; needs a model at the Alliance for capturing sex
== 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
 
* 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 [https://doodle.com/poll/xzkxet8sb57enver#table 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 ===
 
*Ranjana and Valerio working to finish the new pipeline for automated descriptions for WB, will aim to finish them for the next upload, WS268.
 
* Working on one of the last data types--tissue expression; will use the anatomy ontology to perform logical trimming for the annotation set of cell/anatomy types (for each gene) including neurons (as opposed to using a file for neuronal term groupings taken from Oliver Hobert paper in the old pipeline)
 
* Currently playing around with thresholds to see how the sentences look, will feedback any ontology related issues to Raymond
 
* Working on incorporating feedback from users for information-poor genes (defined as genes with no human orthology and no GO annotations). Will include other types of information suggested by Users such as human ortholog function and protein domains, etc.
 
* When no other data is available, will include expression cluster data.  Users have complained that they don't find this data useful as it's non-specific and from large scale studies, so will give it the lowest priority for inclusion.
 
*Suggestion to exclude the writing and storing of the thousands of automated descriptions to the Postgres database; there is really no advantage in them being in Postgres. 
 
* At the time of generation of the automated descriptions the related .ace files can also be generated; though will need to include the 6000+ manual descriptions that live in Postgres.  So will need to rethink this part a bit, though skipping Postgres will reduce the number of manual steps in the pipleline and Postgres will have less data that needs to be uploaded and downloaded from future cloud storage.
 
 
 
== August 30, 2018 ==
 
 
 
=== EPIC dataset in the Alliance import ===
 
 
 
* the EPIC dataset has fine-grained anatomy-life stage annotations (e.g. single cell per minute)
 
* This generates thousands of annotations per gene (up to 30,000) for the 127 genes analyzed in the study
 
* How to deal with this. In WB we do not display anatomy/life stage pairings but we display one list for anatomy terms and one for life stage. Also, we display the EPIC study in a separate panel on the gene page so that it does not ‘dilute’ small scale annotations (concerned raised by Oliver H at the time of the import).
 
 
 
https://www.wormbase.org/species/c_elegans/gene/WBGene00015143#1--10
 
 
 
*Possible solutions:
 
** 1. throw away the pairing information. e.g. for WBGene00020093, there are paired 10713 annotations from expression pattern Expr10421. On WormBase, we have a panel for Expr10421 (on the page for WBGene00020093) that shows 413 life-stage associations and 112 anatomy associations, with no pairing information. 
 
***This approach will still give big tables (annotation in the hundreds) for the analyzed genes and the dilution problem will still be there.
 
*** This can be implemented for 2.1 as changing the code for 2.0 is fairly involved -Kevin to do upload tomorrow
 
** 2. assign a high-level life stage term (embryo) to the EPIC expression patterns for the alliance import so they will be discoverable on the Alliance website and will be hyperlinked to the WormBase detailed records
 
 
 
* Outstanding question: what to do for the 2.0 upload. Options:
 
** Filter out the EPIC dataset and apply one of the solutions above for the long term
 
** Leave the thousands of annotations in
 
 
 
* Decision: leave the EPIC dataset out for this upload and find a global way to deal with large scale datasets
 
 
 
=== Update on AFP Form ===
 
 
 
*Daniela, Juancarlos, Kimberly, and Valerio have been working on the new iteration of the AFP form; they'll present the updates and we can discuss remaining development
 
*Currently have six test papers with varying amounts and types of information that we're using to test the functionality and performance
 
*For entity recognition, we're not able to restrict by paper section, so this presents a challenge
 
**We are implementing a threshold value, but the actual value will likely need to be entity-specific and we will probably err on the side of precision rather than recall
 

Latest revision as of 16:36, 6 August 2020

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August 6th, 2020

Experimental conditions data flow into Alliance

  • Experimental conditions in disease annotations: WB has inducers (used to recapitulate the disease condition) and modifiers (a modifier can ameliorate, exacerbate, or have no effect, on the disease condition)
  • We use the WB Molecule CV for Inducers and Modifiers in disease annotation
  • Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
  • So for data flow into Alliance:
    • In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
    • Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.
  • How do we handle genetic sex? Part of condition?
    • Condition has been intended for external/environmental conditions, whereas genetic sex is inherent to the organism of study
    • Expression pattern curation needs genetic sex; needs a model at the Alliance for capturing sex