Difference between revisions of "WormBase-Caltech Weekly Calls"

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GoToMeeting link: https://www.gotomeet.me/wormbase1
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
  
  
 
= 2019 Meetings =
 
= 2019 Meetings =
  
== January 3, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
 
 
=== WS270 Citace upload ===
 
* Next Tuesday, Jan 8th, 10am Pacific
 
 
 
=== Gene descriptions ===
 
* Valerio generated new files to ignore/filter-out problematic genes
 
* Still need to validate new pipeline
 
* Barring any major issues, will submit new files for WS270 (can load old files if needed)
 
* Maybe should define a test set (random sample) to test each release? Already have a test set
 
  
=== Protege Tutorial ===
+
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
* Doodle poll open: https://doodle.com/poll/kn49rd3rggymn68g
 
* Please fill out poll if you are interested in attending; have responses from Kimberly and Gary S.
 
  
 +
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
  
==January 11th, 2019==
+
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
  
===WB workshop at IWM 2019===
+
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
Here's a draft, need to finalize as Jan 15th is the deadline
 
<pre style="white-space: pre-wrap;
 
white-space: -moz-pre-wrap;
 
white-space: -pre-wrap;
 
white-space: -o-pre-wrap;
 
word-wrap: break-word">
 
Possible Title 1: Data in WormBase and how to query it
 
Possible Title 2: WormBase 2019 - Data, Tools and Community Curation
 
This workshop will be an interactive session with users in order to discuss the types of data in WormBase and how to query them using specific tools.  We will discuss recent changes to WormBase community annotation forms and how to use them to contribute data to WormBase.  We will also present updates to ParaSite, a portal to parasitic worm genomic data, and how to find cross-species data at the Alliance of Genome Research.
 
  
1:00 pm 
+
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
Keep your widgets open: a wealth of data on the gene page - Ranjana Kishore
 
(This will be a quick introduction of the gene page for orienting Users before we jump into the tools section)
 
     
 
1:05 pm 
 
Use the right tool for the right data:
 
Get simple lists using SimpleMine - Wen Chen
 
Tools for RNA seq data - Wen Chen
 
Tools for enrichment analysis - Kimberly Van Auken
 
Get gene data using the WormBase Ontology Browser - Raymond Lee
 
Get the big picture: visualize annotations using the SOBA tool - Raymond Lee
 
     
 
1.45-2.00 pm 
 
WormBase ParaSite: Exploring lots of genomes - Kevin Howe
 
  
Find cross-species data at the Alliance of Genome Research - Chris Grove
+
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
  
Be a Community Curator: submit your data to WormBase - Daniela Raciti
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
  
2.00-2.30pm. Open forum for questions
+
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
</pre>
 
  
=== Finalize Protege tutorial time ===
 
* Best final options:
 
** Wed, Jan 16th, 1pm Pacific/4pm Eastern
 
** Thurs, Jan 17th, 11am Pacific/2pm Eastern
 
** Thurs, Jan 17th, 1pm Pacific/4pm Eastern
 
* Propose we go with Wed, Jan 16th, 1pm Pacific/4pm Eastern
 
  
=== Automated descriptions ===
+
== October 3, 2019 ==
* Distinguishing information rich vs. poor genes
 
* Information poor genes can take advantage of information across MODs/species
 
* Need more robust QC pipeline; can work on for WormBase, and later apply to Alliance once worked out
 
* Working on expression statements for Alliance genes
 
* Considering rearrangement of description so disease features more prominently
 
  
=== Disease curation ===
+
=== SObA comparison graphs ===
* Disease model curation progressing; Lots of discussions about data standards and entities in Alliance Disease Working Group
+
* Raymond and Juancarlos have worked on a SObA-graph based comparison tool to compare two genes for ontology-based annotations
* Considering SVM for disease; current paper flagging pipeline is rather broad
+
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 1]
*200+ papers as positive training set available
+
** [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]
* Results section are not being extracted in latest Textpresso (paper sectioning in general not happening)
+
* [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
  
=== Noctua / GO-CAM ===
+
=== Germ line discussion ===
* Making progress on best practices
+
* 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"
* Can use Noctua to generate GO annotations
+
* 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"
* Starting to incorporate proteins
+
** [https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/pull/23 Made pull request]
* Working with an ever changing Noctua platform; bugs emerge as it is developed; may benefit from frozen release of the software
+
* 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)
* Next month or two, will import entire set of C. elegans GO annotations into Noctua
 
** Many decisions to make: how to model?
 
** Each gene will become a single Noctua model; not linked to each other initially
 
** Working on batch updates/uploads to Noctua
 
  
=== Expression cluster curation ===
+
=== Script to remove blank entries from Postgres ===
* Wen working on 40 paper backlog; hoping to finish by WS271
+
* 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
* Wen wants to work on RNA-Seq tools next
+
* Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
** FPKM tools
+
* Does anyone object to removing these entries throughout Postgres?
** Filtering by datasets
+
* Juancarlos will remove all the empty fields identified by his script
** Would like tools ready before International C. elegans Meeting (June 2019)
 
  
=== Neural function curation ===
 
* Raymond: want to use design pattern strategy to curate
 
  
=== WOBr ===
+
== October 10, 2019 ==
* Now incororating non-IEA disease annotations into WOBr
 
* Using disease-association file
 
  
=== Phenotype curation ===
+
=== Biocuration 2020 ===
* Will run a new round of phenotype requests on ~3,000 papers in next few weeks (last one ran in October)
+
* Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
* Processing community curation submissions
+
* Dates: Sunday May 17th to Wednesday May 20th, 2020
* Will recurate some community curation papers to check:
+
* Will have 3rd POTATO workshop
** 1. completeness of community curation
+
* [https://www.jax.org/education-and-learning/education-calendar/2020/05-may/biocuration-2020-conference Meeting website]
** 2. the time-savings of the phenotype form pipeline
+
* Key Dates
* Have made recent improvements to phenotype request emails, allowing authors more feedback options which are now being readily used
+
** October 31, 2019 - Paper Submission Deadline
* Working with new phenotype ontology GitHub repository
+
** January 24, 2020 - Abstract  and Workshop Submission Deadline
** OBO Foundry now pointing phenotype ontology at the GitHub repository (both OBO and OWL files)
+
** March 6, 2020 - Notification of Acceptance
** Need to update the citace upload procedure to generate phenotype .ACE file; currently the script is still running on the old OBO Tazendra location; need to update to work off new OBO file at GitHub
+
** 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
  
=== Metabolomics ===
+
=== ICBO 2020 ===
* Karen working with Michael Witting to pull in metabolomics data
+
* International Conference on Biomedical Ontologies
* Integrating information about endogenous concentrations of metabolites
+
* [https://icbo2020.inf.unibz.it/ Meeting website]
 +
* Held in Bozen-Bolzano, Italy
 +
* 16 - 19 September 2020
  
=== Automated descriptions React tool ===
+
=== SObA comparison tool ===
* Juancarlos developed tool to request versions of the automated descriptions
+
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
* Will update pipeline to pull data from Alliance; currently coming from Tazendra
 
* Tracking how the descriptions are changing, by data module for example
 
* React tool currently on mangolassi but will move to Alliance at a location of Olin's choosing (AWS resource)
 
  
=== Transgenes in the Alliance ===
+
=== Textpresso derived paper connections ===
* Are transgenes being discussed at the Alliance?
+
* For example for strains and constructs, maybe anatomy terms?
* Yes, the phenotype and disease working group has been discussing
+
* May want to flag Textpresso predictions (as opposed to manually connected)
* Hasn't come up in recent weeks, but was discussed at face-to-face meeting
+
* Couple of options:
* One significant issue is that WormBase uniquely has extra-chromosomal arrays, whereas other MODS (always?) have integrated transgenes and consider them types of alleles
+
** 1) At time of build, populate the papers (in ACEDB/Datomic) into a 'Putative_reference' tag and display in a distinct 'Putative references' widget
* Chris will give Karen a heads up next time the issue is intended to be discussed within the Alliance
+
** 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