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]]
  
  
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= 2018 Meetings =
+
= 2019 Meetings =
 
 
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_May_2018|May]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_June_2018|June]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_July_2018|July]]
 
  
 +
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
  
== August 2, 2018 ==
+
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
  
=== AFP ===
+
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
  
* The AFP pipeline is currently emailing authors from karen's e-mail address
+
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
* 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
 
  
 +
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
  
== August 9, 2018 ==
+
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
  
=== AFP ===
+
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
* 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 ===
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
  
* Shall we move tazendra.caltech.edu to the cloud? Either WormBase cloud or Caltech cloud?
+
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
  
  
 +
== October 3, 2019 ==
  
== August 16, 2018 ==
+
=== SObA comparison graphs ===
 +
* Raymond and Juancarlos have worked on a SObA-graph based comparison tool to compare two genes for ontology-based annotations
 +
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 1]
 +
** [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=annotSummaryCytoscape&filterForLcaFlag=1&filterLongestFlag=1&showControlsFlag=0&datatype=phenotype&geneOneValue=lin-3%20(Caenorhabditis%20elegans,%20WB:WBGene00002992,%20-,%20F36H1.4)&autocompleteValue=let-23%20(Caenorhabditis%20elegans,%20WB:WBGene00002299,%20-,%20ZK1067.1 Example comparison between lin-3 and let-23]
 +
* [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 2]
 +
** [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=annotSummaryCytoscape&filterForLcaFlag=1&filterLongestFlag=1&showControlsFlag=0&datatype=phenotype&geneOneValue=lin-3%20(Caenorhabditis%20elegans,%20WB:WBGene00002992,%20-,%20F36H1.4)&autocompleteValue=let-23%20(Caenorhabditis%20elegans,%20WB:WBGene00002299,%20-,%20ZK1067.1) Example comparison between lin-3 and let-23]
 +
* What information does a user most care about?
 +
# What terms (nodes) are annotated to gene 1 and what terms to gene 2
 +
# For a given term, what is the relative number of annotations between gene 1 and gene 2.
 +
# For a given node, what is the relative number of annotations each gene has to the total annotations of that gene.
 +
* # 3 is actually what we applied to size the nodes in the single-gene version of SObA. Thus, not surprisingly, I think it is important.
 +
* Generally people like Prototype 2 as a default view; we could possibly have a toggle to see the other view
 +
* In either case users need a good legend and/or documentation
 +
* Jae, it would be good if a user could specifically highlight nodes specific to each gene and gray-out or de-emphasize the common nodes
  
=== Tazendra ===
+
=== Germ line discussion ===
* Moving to cloud? To avoid local hardware issues?
+
* Currently, the anatomy ontology has "germ line" as a type of "Cell" and a type of "Tissue", and "germ cell" as a type of "germ line"
* Need to discuss with Juancarlos and Paul S.
+
* Chris would like to (1) remove "germ line" from under "Cell" and leave it under "Tissue" and (2) move "germ cell" out from under "germ line" and place directly under "Cell"
* Need to consider logistics; put all of Tazendra functionality on cloud? Keep some things local?
+
** [https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/pull/23 Made pull request]
** Postgres in cloud; forms local? Paper pipeline?
+
* Chris will update pull request to include a change to move "germline precursor cell" out from under "germ line" and place it under "Cell" (done)
** Will consult with Textpresso
 
  
=== ICBO 2018 recap ===
+
=== Script to remove blank entries from Postgres ===
* POTATO workshop (Phenotype Ontologies Traversing All The Organisms)
+
* Chris stumbled across several entries in the OA that were blank (empty strings) or consisted of only whitespace, some of which were causing errors upon upload to ACEDB
** Will work towards generating standardized logical definitions using Dead Simple OWL Design Patterns (DOSDP)
+
* Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
*** <Quality> and inheres_in some <Entity> (and has_modifier some <Mod>)
+
* Does anyone object to removing these entries throughout Postgres?
*** Exercise: Reconciling logical definitions for apparently equivalent phenotype terms across ontologies (e.g. MP vs. HP)
+
* Juancarlos will remove all the empty fields identified by his script
** 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 ==
+
== October 10, 2019 ==
  
=== Alliance tables ===
+
=== Biocuration 2020 ===
*Filtering/sorting priorities
+
* Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
 +
* Dates: Sunday May 17th to Wednesday May 20th, 2020
 +
* Will have 3rd POTATO workshop
 +
* [https://www.jax.org/education-and-learning/education-calendar/2020/05-may/biocuration-2020-conference Meeting website]
 +
* Key Dates
 +
** October 31, 2019 - Paper Submission Deadline
 +
** January 24, 2020 - Abstract  and Workshop Submission Deadline
 +
** March 6, 2020 - Notification of Acceptance
 +
** April 6, 2020 - Early Bird Registration Ends
 +
** May 8, 2020 - Registration Deadline
 +
* Academic ISB Member, early bird registration fee is $250
 +
* Author First Pass form paper, submitting to Database, biocuration issue (managed by biocuration group); authors have an opportunity to present at Biocuration conference
  
=== Worm Phenotype Ontology working group ===
+
=== ICBO 2020 ===
* Gary S., Karen, Kimberly, and Chris have responded to [https://doodle.com/poll/xzkxet8sb57enver#table Doodle poll]
+
* International Conference on Biomedical Ontologies
* Looks like 12pm Pacific (3pm Eastern) on Thursdays is the time that works for everyone
+
* [https://icbo2020.inf.unibz.it/ Meeting website]
** May start late on days when WB CIT meeting goes past 12pm Pacific
+
* Held in Bozen-Bolzano, Italy
** May want to start a bit past 12pm to allow west coasters to get lunch, etc.?
+
* 16 - 19 September 2020
* 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 ===
+
=== SObA comparison tool ===
* Data quartermasters and expression working group are looking to get updated anatomy-Uberon mappings
+
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
* 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 ===
+
=== Textpresso derived paper connections ===
* 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
+
* For example for strains and constructs, maybe anatomy terms?
* Playing around with thresholds to see how the sentences look
+
* May want to flag Textpresso predictions (as opposed to manually connected)
* Working on incorporating feedback from users; e.g. referring to human ortholog, protein domains, etc.
+
* Couple of options:
 +
** 1) At time of build, populate the papers (in ACEDB/Datomic) into a 'Putative_reference' tag and display in a distinct 'Putative references' widget
 +
** 2) Not part of database build, but make associations live (using RESTful API to link out to Textpresso and submit search with URL) using Textpresso with links to Textpresso and Textpresso results, giving users chance to see context of matches in sentences at the Textpresso site
 +
*** A link to Textpresso could be done regardless of other approaches; low-hanging fruit?
 +
*** Do a diff so that Textpresso pulls up only additional papers (not already associated)?
 +
** 3) Could populate WB page with connections made through a Textpresso API call (could cache results? maybe, but might as well choose 1st option?)
 +
* Transgene pipeline:
 +
** Arun wrote script, matching transgene names (using regex; Is and Si transgenes) to papers, automatically populate OA
 +
** Another script, captures Ex transgenes as well, automatically connects to construct objects
 +
** WB only displays verified papers; unverified (predicted) associations are not dumped
 +
* Could integrate author verification as part of AFP pipeline, even for older papers? Would we want to re-request AFP results for authors that have already replied in the past? Probably not
 +
* Could embed AFP predictions in WB display with link to AFP form for authors (and others?) to verify, via logged-in users? Or via a validation token sent via email?
 +
* Chris will make GitHub ticket to ask WB web team to add a link to Textpresso search from References widget on respective page; will require a Textpresso URL constructor
 +
* Can apply to: genes, transgenes, constructs, strains, alleles, AFP-vetted entities

Revision as of 15:06, 11 October 2019

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings


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


2019 Meetings

January

February

March

April

May

June

July

August

September


October 3, 2019

SObA comparison graphs

  1. What terms (nodes) are annotated to gene 1 and what terms to gene 2
  2. For a given term, what is the relative number of annotations between gene 1 and gene 2.
  3. For a given node, what is the relative number of annotations each gene has to the total annotations of that gene.
  • # 3 is actually what we applied to size the nodes in the single-gene version of SObA. Thus, not surprisingly, I think it is important.
  • Generally people like Prototype 2 as a default view; we could possibly have a toggle to see the other view
  • In either case users need a good legend and/or documentation
  • Jae, it would be good if a user could specifically highlight nodes specific to each gene and gray-out or de-emphasize the common nodes

Germ line discussion

  • Currently, the anatomy ontology has "germ line" as a type of "Cell" and a type of "Tissue", and "germ cell" as a type of "germ line"
  • Chris would like to (1) remove "germ line" from under "Cell" and leave it under "Tissue" and (2) move "germ cell" out from under "germ line" and place directly under "Cell"
  • Chris will update pull request to include a change to move "germline precursor cell" out from under "germ line" and place it under "Cell" (done)

Script to remove blank entries from Postgres

  • Chris stumbled across several entries in the OA that were blank (empty strings) or consisted of only whitespace, some of which were causing errors upon upload to ACEDB
  • Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
  • Does anyone object to removing these entries throughout Postgres?
  • Juancarlos will remove all the empty fields identified by his script


October 10, 2019

Biocuration 2020

  • Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
  • Dates: Sunday May 17th to Wednesday May 20th, 2020
  • Will have 3rd POTATO workshop
  • Meeting website
  • Key Dates
    • October 31, 2019 - Paper Submission Deadline
    • January 24, 2020 - Abstract and Workshop Submission Deadline
    • March 6, 2020 - Notification of Acceptance
    • April 6, 2020 - Early Bird Registration Ends
    • May 8, 2020 - Registration Deadline
  • Academic ISB Member, early bird registration fee is $250
  • Author First Pass form paper, submitting to Database, biocuration issue (managed by biocuration group); authors have an opportunity to present at Biocuration conference

ICBO 2020

  • International Conference on Biomedical Ontologies
  • Meeting website
  • Held in Bozen-Bolzano, Italy
  • 16 - 19 September 2020

SObA comparison tool

Textpresso derived paper connections

  • For example for strains and constructs, maybe anatomy terms?
  • May want to flag Textpresso predictions (as opposed to manually connected)
  • Couple of options:
    • 1) At time of build, populate the papers (in ACEDB/Datomic) into a 'Putative_reference' tag and display in a distinct 'Putative references' widget
    • 2) Not part of database build, but make associations live (using RESTful API to link out to Textpresso and submit search with URL) using Textpresso with links to Textpresso and Textpresso results, giving users chance to see context of matches in sentences at the Textpresso site
      • A link to Textpresso could be done regardless of other approaches; low-hanging fruit?
      • Do a diff so that Textpresso pulls up only additional papers (not already associated)?
    • 3) Could populate WB page with connections made through a Textpresso API call (could cache results? maybe, but might as well choose 1st option?)
  • Transgene pipeline:
    • Arun wrote script, matching transgene names (using regex; Is and Si transgenes) to papers, automatically populate OA
    • Another script, captures Ex transgenes as well, automatically connects to construct objects
    • WB only displays verified papers; unverified (predicted) associations are not dumped
  • Could integrate author verification as part of AFP pipeline, even for older papers? Would we want to re-request AFP results for authors that have already replied in the past? Probably not
  • Could embed AFP predictions in WB display with link to AFP form for authors (and others?) to verify, via logged-in users? Or via a validation token sent via email?
  • Chris will make GitHub ticket to ask WB web team to add a link to Textpresso search from References widget on respective page; will require a Textpresso URL constructor
  • Can apply to: genes, transgenes, constructs, strains, alleles, AFP-vetted entities