Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
  
  
= 2019 Meetings =
 
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
+
= 2020 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
+
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
+
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
  
 +
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
  
== October 3, 2019 ==
 
  
=== SObA comparison graphs ===
+
== October 1, 2020 ==
* 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
 
  
=== Germ line discussion ===
+
=== Gene association file formats on FTP ===
* 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"
+
* For example, current production release ONTOLOGY directory: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/ONTOLOGY/
* 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"
+
* Our association files have format "*.wb"; is this useful or necessary?
** [https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/pull/23 Made pull request]
+
* Other than referring to GAF in the header, it isn't clear to users what the columns refer to or what the column headers should be
* 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)
+
* We could add a README file and/or convert to the new [https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md GAF 2.2 format] which would have a more expressive file header and possibly column headers(?)
 +
** File headers could possibly link to the format specification page
  
=== Script to remove blank entries from Postgres ===
+
=== Phenotype association file idiosyncrasy ===
* 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
+
* As we've discussed previously, there is an oddity to how the phenotype association file we provide lists, or doesn't, references
* Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
+
* According to the GAF spec, column 6 is for reference and is required, whereas column 8 is "With (or) From" and is optional
* Does anyone object to removing these entries throughout Postgres?
+
* When we have a reference, the WBPaper ID is provided in column 6 and the WBVar ID or RNAi ID is provided in column 8
* Juancarlos will remove all the empty fields identified by his script
+
* However, when we have no reference (personal communication, e.g. from NBP allele submissions), the WBVar ID is instead put in column 6 (because we need something there), and column 8 is blank.
 +
** This results in (1) column 6 having a mix of paper/reference IDs (good) and WBVar IDs (not good) and (2) WBVar IDs split between column 6 and 8; thus making it tedious to parse this file
 +
* Proposed solution: Can we come up with some type of reference object ID to associate to the personal communications (or any annotations currently lacking a formal reference)?
 +
* With the proposed solution, we can always have a reference ID in column 6 (the intended purpose of the column) and WBVar IDs for alleles can always remain consistently in column 8
 +
* Proposal is to put WBPerson IDs in column 6 for personal communications. Chris & Karen will check if this will work.
  
 +
=== Server space in Chen Building ===
 +
* It looks like that we will not have a specific space for server computers.
  
== October 10, 2019 ==
 
  
=== Biocuration 2020 ===
+
== October 8, 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
 
  
=== ICBO 2020 ===
+
=== Webinar Announcement ===
* International Conference on Biomedical Ontologies
+
* Here is the live registration site: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/webinar.cgi
* [https://icbo2020.inf.unibz.it/ Meeting website]
+
* Caltech zoom allows 300 attendees.
* Held in Bozen-Bolzano, Italy
 
* 16 - 19 September 2020
 
  
=== SObA comparison tool ===
+
=== Descriptions from GO-CAM models ===
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
+
* One suggestion for the Alliance is to create a description based on a GO-CAM model
 +
* Could also micropublish some descriptions (semi-automated?)
 +
* Can make curators authors of micropublications for GO-CAM models/pathways
  
=== Textpresso derived paper connections ===
+
=== Transcription Factors in WormBase ===
* For example for strains and constructs, maybe anatomy terms?
+
* WormBase has a ?Transcription_factor class that is currently underutilized
* May want to flag Textpresso predictions (as opposed to manually connected)
+
* Chris spoke with Gary Williams about the status as he has done much of the work on the class
* Couple of options:
+
* Because transcription factors can often be complexes, it was decided to create the ?Transcription_factor class rather than simply an extension of tags to the existing ?Gene class
** 1) At time of build, populate the papers (in ACEDB/Datomic) into a 'Putative_reference' tag and display in a distinct 'Putative references' widget
+
* The class seems reasonably complete; it's important to note that some TFs are general transcription factors, not necessarily gene-specific or sequence-specific DNA-binding TFs; it will be good to make that distinction clear to users
** 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
+
* Chris has compiled a [https://docs.google.com/spreadsheets/d/1KdmvybWDWHXdlJwZgfleL4xHDoyPoYR13WAUcERF82g/edit?usp=sharing Google sheet] to assess the class before Gary W. leaves WB in the next couple of weeks
*** A link to Textpresso could be done regardless of other approaches; low-hanging fruit?
+
* The Google sheet has several tabs/worksheets, including one for the ACEDB data model (and notes about usage of tags), a summary table of associated genes, bound sequence features, existence of other protein-DNA binding data, etc.
*** Do a diff so that Textpresso pulls up only additional papers (not already associated)?
+
* It would be good to make TF binding info (per gene and globally) more accessibly to our users, maybe via a new widget on gene pages (e.g. list incoming, regulating TFs and, for TF genes themselves, list potential target genes)
** 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
 
  
 +
== October 15, 2020 ==
  
== October 17, 2019 ==
+
=== BioGRID data sharing ===
 +
* Rose from BioGRID proposed that BioGRID curate high-throughput C. elegans interaction datasets, capturing confidence scores when available, and making those annotations available to WormBase for regular ingest
 +
* Will need to consider a few points:
 +
** BioGRID doesn't curate protein-DNA interactions
 +
** We don't yet know the turn-around timeline for BioGRID curation of worm datasets; WB may be able to curate them much sooner
 +
* Chris and Jae will work with Rose et al. to coordinate HTP curation
  
=== Alliance All Hands Face-to-Face ===
+
=== Enriched genes ===
* Flights: has everyone already booked? No, not yet
+
* Some genes are considered "enriched" for an expression cluster data set even if the enrichment was in comparison to another cell or tissue (not whole animal)
* Any coordination of flights from Pasadena/LA?  
+
* We should reconsider the ?Expression_cluster model to make sure we can appropriately model and communicate enrichment or subtypes thereof
** Ranjana and Valerio got a direct flight from Burbank to Boston on Sunday for premeetings
 
  
=== SObA Comparison Tool ===
 
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
 
* Prototype discussed last week, updated with feedback from prior discussions
 
* Would this be a stand-alone tool discoverable under the Tools menu?
 
** Possibly; could be a gene page widget, but may be out of place
 
** Stand-alone tool probably makes more sense
 
* Life stage graph doesn't specify expression pattern vs. expression cluster; pretty much only expression patterns (no clusters)
 
  
=== SObA ===
+
== October 22, 2020 ==
* Raymond intending to share progress on SObA at December Alliance All-Hands Face-to-Face
 
* For example, share GO SObA graph for other species
 
* Will need to be dependent on a SOLR server with all species data
 
** Raymond has run into problems trying to setup his own SOLR server
 
** Raymond asked Seth Carbon if we could us GO server, but he prefers not
 
** Appear to be software versioning issues, possible memory issues
 
  
=== GO meeting ===
+
=== CHEBI ===
* Kimberly can give update on recent updates to GO from the recent GO meeting
+
* Karen spoke to CHEBI personnel on Tuesday
* Slides are shared online
+
* CHEBI only has ~2 curators to create new entities
 +
* CHEBI had submitted a proposal to establish pipelines to process requests from MODs
 +
* Chemical Translation Service (CTS)
 +
* OxO = https://www.ebi.ac.uk/spot/oxo/search
  
=== "all stages Ce" life stage ===
+
=== Training Webinar ===
* Currently used to annotate that RNA was collected from, or a gene was observed to be expressed during, all C. elegans life stages
+
* Scheduled for tomorrow at 1pm Pacific/4pm Eastern
* "all stages Ce" is currently the root node of the C. elegans branch, but needs to change to generic "C. elegans life stage"
+
 
* Should we:
+
 
** 1) Create a "C. elegans life span" or "C. elegans life cycle" term to represent the entire life span and annotate to that?
+
== October 29, 2020 ==
*** Does this mean that, for example, a gene is expressed at some point during the life cycle or consistently throughout the entire life span?
+
 
** 2) Annotate instead to, for example, "embryo Ce", "larva Ce", and "adult Ce" individually
+
=== Overview Webinar debriefing ===
* Note: authors are often vague in their descriptions simply saying "during all stages" possibly stating a beginning and end of the range
+
* What's Good
* Wen: not comfortable making a decision right now; want to discuss with Gary Williams and with other MOD members about how to handle large scale expression data
+
* What needs improvement
* Daniela: will look through existing (old and new) expression pattern annotations made to "all stages Ce" to see if it would be reasonable to annotate each case individually to "embryo Ce", "larva Ce", and "adult Ce" individually
+
* Participant requests:
 +
  A place to look for Worm methods (a public {moderated} wiki page?)
 +
 
 +
 
 +
=== New alleles extraction pipeline ===
 +
* current pipeline (on textpresso-dev) is sending data to Sanger RT system, which is being retired
 +
* the plan is to build a new pipeline to send AFP-like alerts with new entities
 +
* current pipeline reads alleles data from GSA and gene lists from Sanger, but I (Valerio) would need help from curators to understand how to get these data

Latest revision as of 18:06, 29 October 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings



2020 Meetings

January

February

March

April

May

June

July

August

September


October 1, 2020

Gene association file formats on FTP

  • For example, current production release ONTOLOGY directory: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/ONTOLOGY/
  • Our association files have format "*.wb"; is this useful or necessary?
  • Other than referring to GAF in the header, it isn't clear to users what the columns refer to or what the column headers should be
  • We could add a README file and/or convert to the new GAF 2.2 format which would have a more expressive file header and possibly column headers(?)
    • File headers could possibly link to the format specification page

Phenotype association file idiosyncrasy

  • As we've discussed previously, there is an oddity to how the phenotype association file we provide lists, or doesn't, references
  • According to the GAF spec, column 6 is for reference and is required, whereas column 8 is "With (or) From" and is optional
  • When we have a reference, the WBPaper ID is provided in column 6 and the WBVar ID or RNAi ID is provided in column 8
  • However, when we have no reference (personal communication, e.g. from NBP allele submissions), the WBVar ID is instead put in column 6 (because we need something there), and column 8 is blank.
    • This results in (1) column 6 having a mix of paper/reference IDs (good) and WBVar IDs (not good) and (2) WBVar IDs split between column 6 and 8; thus making it tedious to parse this file
  • Proposed solution: Can we come up with some type of reference object ID to associate to the personal communications (or any annotations currently lacking a formal reference)?
  • With the proposed solution, we can always have a reference ID in column 6 (the intended purpose of the column) and WBVar IDs for alleles can always remain consistently in column 8
  • Proposal is to put WBPerson IDs in column 6 for personal communications. Chris & Karen will check if this will work.

Server space in Chen Building

  • It looks like that we will not have a specific space for server computers.


October 8, 2020

Webinar Announcement

Descriptions from GO-CAM models

  • One suggestion for the Alliance is to create a description based on a GO-CAM model
  • Could also micropublish some descriptions (semi-automated?)
  • Can make curators authors of micropublications for GO-CAM models/pathways

Transcription Factors in WormBase

  • WormBase has a ?Transcription_factor class that is currently underutilized
  • Chris spoke with Gary Williams about the status as he has done much of the work on the class
  • Because transcription factors can often be complexes, it was decided to create the ?Transcription_factor class rather than simply an extension of tags to the existing ?Gene class
  • The class seems reasonably complete; it's important to note that some TFs are general transcription factors, not necessarily gene-specific or sequence-specific DNA-binding TFs; it will be good to make that distinction clear to users
  • Chris has compiled a Google sheet to assess the class before Gary W. leaves WB in the next couple of weeks
  • The Google sheet has several tabs/worksheets, including one for the ACEDB data model (and notes about usage of tags), a summary table of associated genes, bound sequence features, existence of other protein-DNA binding data, etc.
  • It would be good to make TF binding info (per gene and globally) more accessibly to our users, maybe via a new widget on gene pages (e.g. list incoming, regulating TFs and, for TF genes themselves, list potential target genes)

October 15, 2020

BioGRID data sharing

  • Rose from BioGRID proposed that BioGRID curate high-throughput C. elegans interaction datasets, capturing confidence scores when available, and making those annotations available to WormBase for regular ingest
  • Will need to consider a few points:
    • BioGRID doesn't curate protein-DNA interactions
    • We don't yet know the turn-around timeline for BioGRID curation of worm datasets; WB may be able to curate them much sooner
  • Chris and Jae will work with Rose et al. to coordinate HTP curation

Enriched genes

  • Some genes are considered "enriched" for an expression cluster data set even if the enrichment was in comparison to another cell or tissue (not whole animal)
  • We should reconsider the ?Expression_cluster model to make sure we can appropriately model and communicate enrichment or subtypes thereof


October 22, 2020

CHEBI

  • Karen spoke to CHEBI personnel on Tuesday
  • CHEBI only has ~2 curators to create new entities
  • CHEBI had submitted a proposal to establish pipelines to process requests from MODs
  • Chemical Translation Service (CTS)
  • OxO = https://www.ebi.ac.uk/spot/oxo/search

Training Webinar

  • Scheduled for tomorrow at 1pm Pacific/4pm Eastern


October 29, 2020

Overview Webinar debriefing

  • What's Good
  • What needs improvement
  • Participant requests:
 A place to look for Worm methods (a public {moderated} wiki page?)


New alleles extraction pipeline

  • current pipeline (on textpresso-dev) is sending data to Sanger RT system, which is being retired
  • the plan is to build a new pipeline to send AFP-like alerts with new entities
  • current pipeline reads alleles data from GSA and gene lists from Sanger, but I (Valerio) would need help from curators to understand how to get these data