Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
 
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
  
== April 4, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
  
=== Paul's Biocuration Keynote ===
+
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
* At Biocuration keynote, Paul S. will talk about web forms, including Author First Pass form
 
* Can someone send Paul the latest AFP form location and documentation
 
* Will also discuss the future of micropublications
 
  
=== IWM Swag ===
+
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
* Stickers vs. screen cloths
 
* Daniela had contacted Jessie to make new graphic; she's interested, but do we still need a new graphic?
 
* Plan was to make ~2,000 screen cloths (4x4 inch or 6x6 inch?)
 
** As for design would be nice to have new design
 
** Gary had made cartoon for community curation (proposal might be offensive to some)
 
* Include water bottles for special contributors? In addition to shot glasses?
 
* Turn around time? ~ 1 month; designs done in April; submit request by mid-May at latest
 
* Worm in apple graphic? Dragon worm cartooon? Maybe some variation on it?
 
** We can ask Jessie if she can draw up a couple quick sketch ideas
 
  
=== Collaborators tool ===
+
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
* Juancarlos worked on a tool to extract WBPerson collaborators
 
* WB staff generally had ~100 collaborators, Paul S has 670
 
* Distinguish between collaborators and coauthors? Manual (self reported) vs. automatic associations?
 
* Make modification to ACEDB model?
 
* Maybe 'collaborators' should be restricted to the laboratory level?
 
  
 +
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
  
== April 11, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
  
=== Canadian C. elegans meeting ===
 
the "Canadian C. elegans meeting” that will follow the 2019 annual conference of the Canadian Society for Molecular Biosciences. The CSMB conference is held at Université de Montréal on June 2-5, 2019 and will focus on Model systems in cancer research (https://www.fourwav.es/view/1174/info/). The C. elegans conference will be held at the CHUM Research Center in downtown Montréal on Thursday June 6, 2019, and will offer opportunities for both oral and poster presentations. The schedule is not finalized yet but it should start around 8:30am and end around 6pm, followed by an apero in a nearby pub. The costs of registrations will depend on the number of participants but will be between 35 and 50 $ per person (it will cover the costs of lunch, coffee break and logistics).
 
* Karen may be able to go; she will contact Kimberly for any pertinent information
 
  
=== Feedback from small RNA meeting April 3-5, 2019 ===
+
== October 3, 2019 ==
* Future meeting invitations and summer workshop?
 
* Dustin Updike - in Maine - interested in running a summer workshop for students
 
** Maybe one or two week-long (5-10 days); unconfirmed
 
** Wen followed up with him: WormBase curator could attend and present on JBrowse, scientific writing, micropublications
 
** Hopefully they can cover travel costs of WB curators
 
** Dustin will get back to us about details as they emerge
 
* Julie Claycomb interested in having WB curator at Toronto's worm meeting
 
  
=== New SVM approach ===
+
=== SObA comparison graphs ===
* Michael will send around paper list with new and old results in the same file
+
* Raymond and Juancarlos have worked on a SObA-graph based comparison tool to compare two genes for ontology-based annotations
* Raymond looked at his data types; at first glance thinks there may be quite a few false positives and false negatives
+
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 1]
* Can represent new SVM scores as histograms, presumably produce Gaussian curves, can we accept the overlap in distribution tails?
+
** [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]
* Old thresholds were not necessarily gold standards, probably somewhat arbitrarily chosen initially; we can use the old metrics to roughly choose a new set of corresponding thresholds for the new SVM scores
+
* [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
  
=== IWM workshop ===
+
=== Germ line discussion ===
* On Saturday of meeting
+
* 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)
  
=== NIH workshop on Trustworthiness ===
+
=== Script to remove blank entries from Postgres ===
* Chris attended on Monday and Tuesday
+
* 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
* Not quite clear that there is or will be any mandate from funders; just encouragement
+
* Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
* FAIR data and TRUST-worthy repositories
+
* Does anyone object to removing these entries throughout Postgres?
** FAIR = Findable, Accessible, Interoperable, Reusable
+
* Juancarlos will remove all the empty fields identified by his script
** TRUST = Transparency, Responsibility, User community, Sustainability, Technology
 
* Chris will review briefly at next site-wide call
 
* Karen: This is something the data commons really wants
 
** Maybe just need to make sure that the Alliance meets these requirements going forward, not so much for WormBase (?)
 
  
  
== April 18, 2019 ==
+
== October 10, 2019 ==
  
=== IWM swag ===
+
=== Biocuration 2020 ===
* Stickers, screen cloths?
+
* Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
* Jessie's design(s)?
+
* Dates: Sunday May 17th to Wednesday May 20th, 2020
* Daniel reaching out to Caltech security who has nice screen cloths
+
* Will have 3rd POTATO workshop
* Print list of WormBase tools or user guide on cloth (one side; logo on the other?)?
+
* [https://www.jax.org/education-and-learning/education-calendar/2020/05-may/biocuration-2020-conference Meeting website]
* Will get quote (maybe ≤$1 per cloth?)
+
* 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
  
=== Life stage and anatomy ontologies ===
+
=== ICBO 2020 ===
* Each ontology now has an ODK GitHub repository (thanks Nico!):
+
* International Conference on Biomedical Ontologies
** Anatomy ontology: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology
+
* [https://icbo2020.inf.unibz.it/ Meeting website]
** Life stage ontology: https://github.com/obophenotype/c-elegans-development-ontology
+
* Held in Bozen-Bolzano, Italy
* We will perform a round of comparisons between the original OBO files and the ODK-generated OBO files
+
* 16 - 19 September 2020
* Will follow up with quality control fixes (e.g. duplicate or missing definitions)
 
  
=== Biocurator meeting ===
+
=== SObA comparison tool ===
* EuroPMC - have access to 80-90% full text of open access papers
+
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
** Would be good for WormBase & Textpresso to work with them
 
* Lots of groups working together on pathways
 
** SwissProt, GO, Reactome
 
* SwissLipids
 
** Metabolomics database pilot
 
** https://www.swisslipids.org/#/
 
* RHEA to replace KEGG (which is well curated but not (no longer) open)
 
** https://www.rhea-db.org/home
 
* Author First Pass poster presented (won 3rd place out of ~200 posters!)
 
** Analogous to FlyBase's 'Fast Track Your Paper' (FTYP)
 
** FTYP does not extract entities
 
** Should evolve into an Alliance pipeline
 
* Data visualization talk (Sean O'Donoghue)
 
** Don't use rainbow heatmaps
 
** Oval representation of time course
 
** Valerio spoke to him; D3 is now a standard library for data visualization
 
  
=== GO CAM ===
+
=== Textpresso derived paper connections ===
* Could try to generate automated descriptions using GO CAM models
+
* For example for strains and constructs, maybe anatomy terms?
* Group is trying to come up with model naming scheme
+
* May want to flag Textpresso predictions (as opposed to manually connected)
 
+
* Couple of options:
=== Gene Expression Omnibus (GEO) ===
+
** 1) At time of build, populate the papers (in ACEDB/Datomic) into a 'Putative_reference' tag and display in a distinct 'Putative references' widget
* GEO data has user submission forms that refer to life stages, anatomy but don't map to WB unique IDs
+
** 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
* Maybe we can ask GEO to update their data submission forms to use standard IDs
+
*** A link to Textpresso could be done regardless of other approaches; low-hanging fruit?
* Would help reduce amount of effort required by WB to curate the entries after submission to GEO
+
*** Do a diff so that Textpresso pulls up only additional papers (not already associated)?
* GEO forms apply to all species; controlled vocabularies/ontologies could be submitted to GEO for incorporation into their forms
+
** 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:
=== RNA-Seq data processing pipeline (Alaska) ===
+
** Arun wrote script, matching transgene names (using regex; Is and Si transgenes) to papers, automatically populate OA
* Raymond, Juancarlos, David Angeles and Joseph developed automated data processing pipeline
+
** Another script, captures Ex transgenes as well, automatically connects to construct objects
* http://alaska.caltech.edu/
+
** WB only displays verified papers; unverified (predicted) associations are not dumped
* Maps reads to the genome; will it return FPKM values for each gene?
+
* 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
== April 25, 2019 ==
+
* Can apply to: genes, transgenes, constructs, strains, alleles, AFP-vetted entities
 
 
=== WormBase plans for coming year ===
 
* Jae
 
** help develop better usability of data and tools for expression and regulation
 
** Venn diagrams
 
** Get more up to date on protein-DNA and protein-RNA interactions, may distinguish small scale from large scale
 
** GO CAM curation, once there are defined best practices for editing with Noctua
 
* Kimberly
 
** Migration of all manual GO annotations to Noctua as GO CAM models; Jae may want to wait until the migration is done (aiming for mid-summer)
 
*** Will write rules for converting individual simple annotations and complex annotations (with LEGO extensions) into GO-CAM models
 
** Will continue to develop GO CAM models and tools to help/expedite GO CAM model development
 
*** Will work with developers to create next generation of annotation forms; some more table-based input forms
 
*** Annotation review tool: Once annotations are in, this will allow for efficient annotation search and editing
 
*** Will continue to work on defining best practices for Noctua usage
 
** Will keep working on developing the gene ontology
 
* Ranjana
 
** Gene descriptions: need to bring in pathway data; processes alone are insufficient; will try to use GO CAM models (proof of concept)
 
*** Paul S: would be good to identify low information genes for curation priorities
 
*** Can include information about relevant chemicals
 
** Human disease curation: WB disease data into the Alliance
 
*** Improved text-mining approach to identify disease model papers
 
*** Paul S: May want to work on pathways/GO-CAM models for disease genes
 
* Wen
 
** Proteomics curation, tool development
 
*** Work with Hinxton to curate proteomics data at Caltech
 
*** 50 existing datasets
 
*** Common follow up to RNA Seq experiments
 
*** Jae: will we handle single-cell proteomics? Wen: Can consider part of sample condition, and include with all other proteomics data
 
** Expression clusters - will focus on 'high quality' papers, i.e. useful to community; some have poor metadata and authors don't respond to emails
 
** Outreach - will explore possibility of having local institutes invite WormBase staff to give talks (pay travel costs?); coincide with meetings?
 
*** Northwest worm meeting in Seattle? Chicago worm meeting?
 
*** Bar Harbor tutorial this summer; good precedent/model for future visits to other institutes?
 
** RNA Seq, don't want to step on Hinxton's toes WRT RNA-seq curation
 
* Raymond
 
** Focused cell function curation; want to use Noctua, but not sure we can use all relevant (WB-specific) ontologies in Noctua
 
** Are supported relations in Noctua good enough for this purpose? May need development
 
** Re-working the anatomy ontology; work on logical definitions; e.g. how do we define a single cell type?
 
* Marie Claire
 
** Finishing a micropublication on a GO CAM model; continuing to work with Noctua and improve usage
 
* Daniela
 
** Gene expression - want to attempt to automate expression curation; using AFP-like pipelines and other automation
 
*** ~150 expression pattern papers coming in every two months; many are reassessing expression using CRISPR constructs
 
*** Wen: focus on genes whose expression have never been studied?
 
*** Will still do manual steps of curation pipeline, but would begin to automate certain steps of curation pipeline
 
*** Complex patterns are difficult to automate
 
** Micropublication, Wen: is there anything else we can do to help?
 
*** Daniela: Trial attempts to submit a paper to test and provide feedback on submission pipeline
 
*** Will continue to develop methods to calculate metrics and citation indices, etc.
 
* Chris
 
** Will continue with mass email and community curation pipeline
 
*** Want to evaluate existing issues and how to improve efficiency and minimize technical and submission errors
 
** Will continue working on relevant sentence detection for phenotype, maybe expand to genetic interactions
 
** Will continue to develop phenotype ontology and alignment with other phenotype ontologies; patternization and logical definitions
 
** Will also work on life stage and anatomy ontologies with Raymond
 
** Paul S: maybe we can present authors with predicted genetic interactions and ask for confirmation of binary interactions which can then feed into GO-CAM models and pathway curation; can stick to simple binary associations for now, forgoing details like interaction type and alleles etc.
 
* Gary
 
** Continue working on phenotype ontology
 
** Prioritizing genes that don't have phenotype info; working with Juancarlos to identify papers that may have high value, novel annotations
 
* Juancarlos
 
** General tool maintenance and development
 
** Working with Ranjana and Valerio to work on automated gene description tools: React forms for curators to do QC check, using filters and search options
 
 
 
=== Screen cloths for IWM swag ===
 
* Daniel got quotes
 
* Give feedback on style
 
* Maybe use the cartoon (Dick & Jane) for community curators and tool menu for general meeting participants
 
* Will try to order next week
 

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