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 ===
 
* 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.
 
 
 
 
 
==January 10th, 2019==
 
 
 
===WB workshop at IWM 2019===
 
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">
 
 
 
Title: 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 for parasitic worm genomic data, and guide participants on how to find data across model organisms at the Alliance of Genome Research.
 
 
 
Format: 90 minutes: 1 section of 40 minutes, followed by a second section of 20 mins and a third section which will be a 30 minute open discussion/Q&A session.  Talks in each section will also be tailored to allow time for questions from the audience.
 
 
 
Section 1: Introduction to the WormBase gene page and tools such as SimpleMine, Tools for RNA seq data and enrichment analysis, gene-related data using WormBase Ontology Browser and Annotation Visualization tools.
 
  
Section 2: WormBase Parasite database, Model Organism data at the Alliance of Genome Research and Community Curation forms
+
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
  
Section 3: Open forum for discussion and Q&A.
+
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
</pre>
 
  
=== Finalize Protege tutorial time ===
+
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
* 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 ===
+
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
* 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 ===
+
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
* Disease model curation progressing; Lots of discussions about data standards and entities in Alliance Disease Working Group
 
* Considering SVM for disease; current paper flagging pipeline is rather broad
 
*200+ papers as positive training set available
 
* Results section are not being extracted in latest Textpresso (paper sectioning in general not happening)
 
  
=== Noctua / GO-CAM ===
+
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
* Making progress on best practices
 
* Can use Noctua to generate GO annotations
 
* Starting to incorporate proteins
 
* Working with an ever changing Noctua platform; bugs emerge as it is developed; may benefit from frozen release of the software
 
* 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 ===
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
* Wen working on 40 paper backlog; hoping to finish by WS271
 
* Wen wants to work on RNA-Seq tools next
 
** FPKM tools
 
** Filtering by datasets
 
** Would like tools ready before International C. elegans Meeting (June 2019)
 
  
=== Neural function curation ===
+
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
* Raymond: want to use design pattern strategy to curate
 
  
=== WOBr ===
 
* Now incororating non-IEA disease annotations into WOBr
 
* Using disease-association file
 
  
=== Phenotype curation ===
+
== October 3, 2019 ==
* Will run a new round of phenotype requests on ~3,000 papers in next few weeks (last one ran in October)
 
* Processing community curation submissions
 
* Will recurate some community curation papers to check:
 
** 1. completeness of community curation
 
** 2. the time-savings of the phenotype form pipeline
 
* Have made recent improvements to phenotype request emails, allowing authors more feedback options which are now being readily used
 
* Working with new phenotype ontology GitHub repository
 
** OBO Foundry now pointing phenotype ontology at the GitHub repository (both OBO and OWL files)
 
** 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
 
  
=== Metabolomics ===
+
=== SObA comparison graphs ===
* Karen working with Michael Witting to pull in metabolomics data
+
* Raymond and Juancarlos have worked on a SObA-graph based comparison tool to compare two genes for ontology-based annotations
* Integrating information about endogenous concentrations of metabolites
+
* [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
  
=== Automated descriptions React tool ===
+
=== Germ line discussion ===
* Juancarlos developed tool to request versions of the automated descriptions
+
* 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"
* Will update pipeline to pull data from Alliance; currently coming from Tazendra
+
* 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"
* Tracking how the descriptions are changing, by data module for example
+
** [https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/pull/23 Made pull request]
* React tool currently on mangolassi but will move to Alliance at a location of Olin's choosing (AWS resource)
+
* 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)
  
=== Transgenes in the Alliance ===
+
=== Script to remove blank entries from Postgres ===
* Are transgenes being discussed at the Alliance?
+
* 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
* Yes, the phenotype and disease working group has been discussing
+
* Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
* Hasn't come up in recent weeks, but was discussed at face-to-face meeting
+
* Does anyone object to removing these entries throughout Postgres?
* One significant issue is that WormBase uniquely has extra-chromosomal arrays, whereas other MODS (always?) have integrated transgenes and consider them types of alleles
+
* Juancarlos will remove all the empty fields identified by his script
* Chris will give Karen a heads up next time the issue is intended to be discussed within the Alliance
 
  
  
==January 17th, 2019==
+
== October 10, 2019 ==
  
=== Alliance Grant ===
+
=== Biocuration 2020 ===
* Review grant and see if anything important is missing or if there are any needed edits
+
* Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
* Tight on space but feel free to add a sentence here or there
+
* Dates: Sunday May 17th to Wednesday May 20th, 2020
* Doc: https://docs.google.com/document/d/1HtTBnQYISfrMjnfFKEDaSjSazlyVBkvacOA8VWo8INY/edit?usp=sharing
+
* 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
  
 +
=== ICBO 2020 ===
 +
* International Conference on Biomedical Ontologies
 +
* [https://icbo2020.inf.unibz.it/ Meeting website]
 +
* Held in Bozen-Bolzano, Italy
 +
* 16 - 19 September 2020
  
==January 24th, 2019==
+
=== SObA comparison tool ===
 +
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
  
=== Author First Pass ===
+
=== Textpresso derived paper connections ===
*For strain identification, we are using the obo_name_strain table.
+
* For example for strains and constructs, maybe anatomy terms?
*There is an entry for 'Strain' in that table that leads to false positives.
+
* May want to flag Textpresso predictions (as opposed to manually connected)
*Is this entry needed for curation?
+
* Couple of options:
*If so, we will just filter it out for the purposes of AFP.
+
** 1) At time of build, populate the papers (in ACEDB/Datomic) into a 'Putative_reference' tag and display in a distinct 'Putative references' widget
* In Tazendra with timestamp Jan 23, 2019; on Mangolassi with timestamp Nov 15, 2018
+
** 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
* In WS269 with timestamp '2018-09-25_17:00:39_pad'
+
*** A link to Textpresso could be done regardless of other approaches; low-hanging fruit?
* Linked to paper WBPaper00055300; Location 'PS'; species C. elegans
+
*** 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