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]]
  
[[WormBase-Caltech_Weekly_Calls_August_2018|August]]
+
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
  
 +
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
  
== September 6, 2018 ==
+
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
  
=== Genotype class ===
+
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
* Chris started initial document to draw up ?Genotype class and make appropriate changes to ?Strain class
 
**  https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing
 
* Would be good for people to look at so we can discuss next time
 
* Would also be good to have Kevin H take a look and provide feedback
 
  
=== Citace Upload ===
+
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
* Send citace files to Wen by Sept 18, 10am Pacific
 
  
=== Automated gene descriptions ===
+
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
* Group making improvements
 
* Added disease, protein domains
 
** When direct experimental evidence for disease relevance, will say "gene has been used to study"
 
* When minimal data (information-poor genes), we can refer to human ortholog and data stored for that human gene in Alliance
 
* Continue to receive feedback from users; include enrichment information, etc.
 
* Now have good trimming algorithms to retain important info without flooding a description with too many granular terms
 
* Will not store automated descriptions in Postgres
 
* Wen will modify SimpleMine scripts to accommodate change
 
* Would be good to write a paper on automated concise descriptions
 
* Came up at GO meeting/hackathon: Translating GO-CAM models into concise descriptions?
 
** Should be doable; just need to develop code when we're ready to do that
 
  
=== Textpresso presentation at next Alliance all-hands call ===
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
* Who should present? Maybe have several people? Kimberly, Valerio, Michael for sections?
 
* We can discuss at next Textpresso meeting
 
* Should cover techniques and software, but keep it generally simple and comprehensible for a larger audience
 
  
 +
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
  
== September 13, 2018 ==
 
  
=== Citace upload ===
+
== October 3, 2019 ==
* Send files to Wen by 10am Tuesday (18th)
 
  
=== Genotype class ===
+
=== SObA comparison graphs ===
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing ?Genotype class proposal]
+
* Raymond and Juancarlos have worked on a SObA-graph based comparison tool to compare two genes for ontology-based annotations
* Genotype_name tag: free text summary of the genotype
+
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 1]
** Can this be automatically generated from components? Ideally, yes, but may be difficult
+
** [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]
** Otherwise, can be manually written, as we have been doing, but is a bit denormalized and may require maintenance
+
* [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 2]
* Genotype_description tag: free-text description of the genotype
+
** [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]
** No precedent and probably not going to start now, so will remove from model
+
* What information does a user most care about?
* Genotype_components supertag: to collect genotype component objects and, where necessary, free text
+
# What terms (nodes) are annotated to gene 1 and what terms to gene 2
** We want to be able to express zygosity for each referenced object, likely requires a #Zygosity hash (and hence a ?Zygosity model)
+
# For a given term, what is the relative number of annotations between gene 1 and gene 2.
** ?Zygosity model can have three main tags: "Homozygous", "Heterozygous_with_wild_type", or "Heteroallelic_combination_with"
+
# For a given node, what is the relative number of annotations each gene has to the total annotations of that gene.
*** Heteroallelic_combination_with tag could further specify the type and identity of the object that is in heteroallelic combination with the original object
+
* # 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.
*** Since it is not ideal to store an arbitrary component in the #Zygosity hash, we should probably just state the zygosity as "Heteroallelic_combination" and for display purposes have an automated way to calculate which components affect the same locus/loci (if necessary)
+
* 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"
 +
** [https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/pull/23 Made pull request]
 +
* 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
  
== September 20, 2018 ==
 
  
=== Kimberly's talk at Rutgers ===
+
== October 10, 2019 ==
* Kimberly went to worm meeting at Rutgers (10 labs using C. elegans? 6-7 totally worm-centric)
 
* 30-40 attendees (PIs, postdocs, grad students)
 
* Discussed tools and features at WB
 
* Presented Alliance pages and Textpresso
 
* PIs are enthusiastic about WB
 
* Monica Driscoll made a good plug for Textpresso
 
* People requesting FAQs and user guides (text and videos)
 
* Monica suggested a WB tutorial for PIs ;p
 
* Some people surprised about what they can accomplish using the tools available, like SimpleMine
 
* Covered gene set enrichment, WormMine, SPELL, SimpleMine, ParaSite BioMart, Textpresso
 
* Would be good to show people how to use Textpresso Central
 
* Discussed micropublications, asked about negative results (precedent?)
 
* Some asked about WB funding and Alliance plans
 
* Can we make a within-page search available to find, for example, field names etc.
 
* Some challenges in find genes/proteins of certain class
 
** Had question about histone genes recently
 
** Repeatedly have had questions about finding "ion channels"
 
** Searching gene class with text pulls out lots of false positives
 
** Could perform an analysis on particular classes of genes (e.g. histones or ion channels) and generate a micropublication providing the curated list
 
** Can generate a WormMine template query to pull these out for each release
 
** What classes of genes would we want to identify: histones, transcription factors, ion channels, protein kinases
 
** Chris will look into WormMine templates using gene class info and look into pulling in protein motif information
 
** We will ask other MODs and UniProt about how they deal with this issue
 
  
 +
=== 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
 +
* [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
  
== September 27, 2018 ==
+
=== ICBO 2020 ===
=== Update on the new AFP form and pipeline ===
+
* International Conference on Biomedical Ontologies
*Daniela, KImberly, Juancarlos, and Valerio will update on the current status of the new AFP form and pipeline
+
* [https://icbo2020.inf.unibz.it/ Meeting website]
**Overall, the goal has been to incorporate as much Textpresso-based entity and data-type flagging as possible into the form
+
* Held in Bozen-Bolzano, Italy
**Move from author data flagging to author data validation wherever we can
+
* 16 - 19 September 2020
**Provide opportunities for authors to submit more detailed curation if they want
 
* General: Positive thru SVM gets checked checkbox
 
* General: Question mark icons with help text
 
* Gene recognition
 
** Need to set a threshold of mentions; don't necessarily want all genes mentioned once
 
*** Can we show all genes, ranked by occurrence?
 
** Don't want to overwhelm users
 
** How are the genes identified? Via the Textpresso pipeline, string matching, consolidate multiple instances (protein, gene, etc.) into single gene result
 
** Searches include supplemental materials
 
** Cannot search by section of paper
 
** Can we identify genes other than C. elegans/worm? Are not doing now, and will stick to C. elegans for now
 
** Will expand to non-elegans nematodes in future; will expand to other species when extending to other MODs/Alliance members
 
** Chris: should we show the name of the gene as mentioned, verbatim, from the paper?
 
*** Karen: No, we should insist authors use the proper names
 
*** Chris: Meant referencing sequence names in paper, but public name comes out by the time AFP goes to authors, causing confusion
 
** Can we pull genes from tables? We are pulling from PDF tables, but not supplemental Excel tables, for example
 
* Gene model updates: checkbox yes/no
 
* Species in paper
 
** Including worm, mouse, human, yeast
 
** Still more work to do on this front
 
* Alleles recognized
 
** Show list of allele names and WBVar IDs for confirmation
 
** Can submit new alleles within the AFP form (just allele names, no genes or other info; keeping it simple)
 
* Allele sequence change checkbox yes/no (link to Allele sequence info form)
 
* Can there be a feedback option readily available? There is a comments section toward the end of the form under "Anything else?"
 
* Transgenes handled like alleles
 
* Antibodies
 
** Newly generated antibodies checkbox and text field (ask for details? consistency with alleles?) maybe shouldn't ask for antibody details; can make details optional
 
** Form for existing antibodies
 
* Expression data
 
** Anatomic expression in WT
 
** Site of action (may be difficult to interpret user input; ask for example; make text details required)
 
** Time of action
 
** RNAseq data
 
* Microarrays - just link out to GEO
 
* Interactions (all SVM based, three checkboxes)
 
* Phenotypes (SVMs, link to phenotype form)
 
* Disease
 
** Checkbox for worm orthologs of human disease gene, etc.
 
* Comments section (to point out missing data types, provide general comments on form)
 
** Ask for unpublished data and suggest micropublication
 
* Final thank you and update contact info and lineage
 
* CIT feedback
 
** Maybe make font size larger
 
** Mobile device compatible? Yes
 
** Change "Anything else?" to "Anything else? Comments?"
 
** Can people save and return later? Yes
 
*** How do we know they're finished? There is a "Finish and submit" button at end (but authors can still go back and make changes later)
 
*** Maybe move "Finish and submit" button to left panel so it is always visible? Maybe make the button stand alone?
 
** If authors indicate there are physical interactions, can we distinguish elegans-elegans interactions vs. non-elegans or interspecies interactions? No, we cannot yet distinguish
 
  
=== Genetics and G3 papers in Textpresso ===
+
=== SObA comparison tool ===
* These papers don't get a PMID yet (when they first enter WB), only DOI (most of time DOI doesn't work (yet))
+
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
* DOI should work right away; Karen will look into if there's a problem/typo
 
* Daniel needs to keep track, go back and merge WBPapers once PMID goes live
 
* Kimberly or Karen may have to send papers directly to Daniel for uploading
 
* Should Daniel only download papers with a PubMed ID? Yes, except for micropublications?
 
* Need a separate pipeline for micropublications? Daniel is currently downloading the papers
 
  
=== ParaSite (non-elegans) papers ===
+
=== Textpresso derived paper connections ===
* Should Daniel be trying to download all of these papers? Many are hard to track down
+
* For example for strains and constructs, maybe anatomy terms?
* Daniel should ask Michael Paulini
+
* 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

Revision as of 15:06, 11 October 2019

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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