Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
Line 17: Line 17:
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
= 2018 Meetings =
+
= 2021 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
+
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
+
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
+
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
[[WormBase-Caltech_Weekly_Calls_May_2018|May]]
+
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
[[WormBase-Caltech_Weekly_Calls_June_2018|June]]
+
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
  
[[WormBase-Caltech_Weekly_Calls_July_2018|July]]
 
  
 +
== July 1, 2021 ==
  
== August 2, 2018 ==
+
=== Importing genes for tm alleles from GeneACE ===
 +
* https://github.com/WormBase/website/issues/8262
 +
* Nightly dump currently excludes tm allele genes
 +
* Most tm (Mitani) alleles are not being manually connected to specific genes in GeneACE
 +
* Should pull the data from WS release (into Postgres) after the build has mapped the alleles to genes
 +
* ~100,000 alleles in Postgres; ~70,000 don't have a gene connection
 +
* Would Hinxton be willing to take WS-mapped allele-to-gene associations and populate GeneACE with associations not already in there?
  
=== AFP ===
+
=== Citace upload ===
 +
* Curators upload files to Spica for citace upload on Tuesday (July 6)
  
* The AFP pipeline is currently emailing authors from karen's e-mail address
+
=== Chen B1 kitchen Usage Considerations ===
* Use same e-mail account Chris is using for phenotype community curation requests or create a new account for AFP (gmail)
+
* Clean up after oneself.
* Can use outreach@wormbase.org for consistency
+
* Mark food storage with name and date.
* May use the PMID in the subject line so e-mails will not be all in the same thread
+
* Mark storage drawers
* Todd and Chris have email credentials
+
* Consumables
** 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 ==
+
== July 8, 2021 ==
  
=== AFP ===
+
=== Alliance work ===
* Mei Zhen, SAB member suggested that we include disease models in the AFP form.
+
* Orange team presenting initial plans at Alliance PI meeting tomorrow
* The AFP group will work with Ranjana to incorporate it. Ranjana will prepare a mock by next week.
+
* What working groups are still meeting? What are their responsibilities?
* We will then decide about using the existing afp_humdis tables or creating new ones.
+
** Expression
 +
** Variants
 +
** Disease & Phenotype
 +
** Technical working groups
 +
*** Technical call
 +
*** Data quartermasters
 +
*** DevOps
 +
* Expression working group working on LinkML model with Gil (FB)
 +
** Includes work on antibody class, image class, movie class
 +
** Are species-specific anatomy ontologies being utilized for expression annotations or still just Uberon?
 +
* Creating a curation interface/tool:
 +
** Will require loading auxiliary data types in addition to primary data types (e.g. if we are focused on disease annotation curation, we will need to load genes, alleles, strains, etc. in addition to the disease annotations themselves) to be available to make connections to
 +
** One requirement already expressed by curators is the need to generate new entities, like alleles, and have them quickly (immediately?) available for use in curation
 +
** Maybe this could be handled by an Alliance central name server that mints new IDs (Alliance IDs and maybe also MOD IDs?) for the objects to make them available (also with a mechanism for these new objects/IDs to make their way back to the MODs as well)
 +
** Micropublication curation forms have tackled a lot of issues of collecting lexica and entity names and IDs; should consider work already done with Micropubs
  
=== Tazendra ===
+
== July 15, 2021 ==
  
* Shall we move tazendra.caltech.edu to the cloud? Either WormBase cloud or Caltech cloud?
+
=== hlh-34 expression ===
 +
* Rebecca Mcwhirter (Miller lab) contacted WB saying that the annotations to AVJ for hlh-34 are incorrect. 4 evidences list AVJ -> the authors of the first paper that describes hlh-34 expression (Cunningham et al, 2012 : http://dx.doi.org/10.1016/j.cmet.2012.05.014) had to pick one neuron per reviewer's request. The neuron should instead be AVH.
 +
* Oliver is putting together a micropub to clarify the issue
 +
* How to deal with existing  annotations? Add a comment in the remarks that points to the microPub? remove AVJ from the anatomy association list?
 +
* Should we also add public comments to the relevant papers?
  
 +
== July 22, 2021 ==
  
 
+
=== Copying data from textpresso-dev to tazendra ===
== August 16, 2018 ==
+
* Michael has been asking curators to retrieve any data they might still want on textpresso-dev before the machine dies
 
+
* Can we copy files to tazendra?
=== Tazendra ===
+
* If so, do we need to have a more general approach/strategy other than creating new folders in the individual curator directories?
* Moving to cloud? To avoid local hardware issues?
+
* Are there any size considerations for what we copy over? There are 1.1T free in /home2 which is not backed up
* 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 18:00, 22 July 2021

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

January

February

March

April

May

June


July 1, 2021

Importing genes for tm alleles from GeneACE

  • https://github.com/WormBase/website/issues/8262
  • Nightly dump currently excludes tm allele genes
  • Most tm (Mitani) alleles are not being manually connected to specific genes in GeneACE
  • Should pull the data from WS release (into Postgres) after the build has mapped the alleles to genes
  • ~100,000 alleles in Postgres; ~70,000 don't have a gene connection
  • Would Hinxton be willing to take WS-mapped allele-to-gene associations and populate GeneACE with associations not already in there?

Citace upload

  • Curators upload files to Spica for citace upload on Tuesday (July 6)

Chen B1 kitchen Usage Considerations

  • Clean up after oneself.
  • Mark food storage with name and date.
  • Mark storage drawers
  • Consumables


July 8, 2021

Alliance work

  • Orange team presenting initial plans at Alliance PI meeting tomorrow
  • What working groups are still meeting? What are their responsibilities?
    • Expression
    • Variants
    • Disease & Phenotype
    • Technical working groups
      • Technical call
      • Data quartermasters
      • DevOps
  • Expression working group working on LinkML model with Gil (FB)
    • Includes work on antibody class, image class, movie class
    • Are species-specific anatomy ontologies being utilized for expression annotations or still just Uberon?
  • Creating a curation interface/tool:
    • Will require loading auxiliary data types in addition to primary data types (e.g. if we are focused on disease annotation curation, we will need to load genes, alleles, strains, etc. in addition to the disease annotations themselves) to be available to make connections to
    • One requirement already expressed by curators is the need to generate new entities, like alleles, and have them quickly (immediately?) available for use in curation
    • Maybe this could be handled by an Alliance central name server that mints new IDs (Alliance IDs and maybe also MOD IDs?) for the objects to make them available (also with a mechanism for these new objects/IDs to make their way back to the MODs as well)
    • Micropublication curation forms have tackled a lot of issues of collecting lexica and entity names and IDs; should consider work already done with Micropubs

July 15, 2021

hlh-34 expression

  • Rebecca Mcwhirter (Miller lab) contacted WB saying that the annotations to AVJ for hlh-34 are incorrect. 4 evidences list AVJ -> the authors of the first paper that describes hlh-34 expression (Cunningham et al, 2012 : http://dx.doi.org/10.1016/j.cmet.2012.05.014) had to pick one neuron per reviewer's request. The neuron should instead be AVH.
  • Oliver is putting together a micropub to clarify the issue
  • How to deal with existing annotations? Add a comment in the remarks that points to the microPub? remove AVJ from the anatomy association list?
  • Should we also add public comments to the relevant papers?

July 22, 2021

Copying data from textpresso-dev to tazendra

  • Michael has been asking curators to retrieve any data they might still want on textpresso-dev before the machine dies
  • Can we copy files to tazendra?
  • If so, do we need to have a more general approach/strategy other than creating new folders in the individual curator directories?
  • Are there any size considerations for what we copy over? There are 1.1T free in /home2 which is not backed up