Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
m
(108 intermediate revisions by 5 users not shown)
Line 35: Line 35:
 
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
 
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
  
 +
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
  
== June 6, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
  
=== New SObA graphs ===
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
* May put graphs within existing widgets, but don't need to rush to get that ready for IWM
 
  
=== Phenotype association file format ===
+
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
* May be best to leave the format as is
 
* There are problems; paper IDs keep switching columns
 
* Would need to revisit the reasoning for why we do it that way
 
* When will the Alliance produce a similar/replacement file? Not sure
 
  
=== Phenotype requests ===
 
* Sent out 1140 emails on May 30
 
* Since have received 374 annotations from 54 papers (42 requested, 12 additional)
 
* 21 papers flagged as not having phenotypes
 
* Of 1140 papers emailed about, 35 emails bounced, and have received some flagging or curation on 63 (63/1105 = ~6% response rate), in first week
 
  
 +
== October 3, 2019 ==
  
== June 13, 2019 ==
+
=== SObA comparison graphs ===
 +
* 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
  
=== IWM ===
+
=== Germ line discussion ===
* Coordinating transportation of swag boxes to Pauley Pavilion
+
* 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"
* Workshop on Saturday June 22, from 1pm to 2:30pm
+
* 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"
* Saturday morning micropublication breakfast 7:30 - 8:30am
+
** [https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/pull/23 Made pull request]
* Workshop
+
* 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)
** Presenters: it may be best to present as use cases rather than a research project
 
** Chris will cover SimpleMine for Wen
 
** Chris: won't do live demo; only screenshots, maybe some video
 
* Paul's lab will do marathon bibs to show lab affiliation and graphical abstract
 
* Paul's talk
 
** Cover Alliance
 
** New features
 
*** SObA (for new data)
 
*** Complete for protein-protein interactions
 
*** RNASeq tools
 
*** Updated automated gene concise descriptions?
 
** Phenotype community curation
 
*** Chris will send Paul numbers on: top community curators, overall stats (number of annotations, papers, curators)
 
** Author First Pass
 
** Micropublication
 
  
=== SGD SAB ===
+
=== Script to remove blank entries from Postgres ===
* Paul attended
+
* 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
* Alliance publicity was discussed
+
* Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
* SAB likes the Alliance orthology features
+
* Does anyone object to removing these entries throughout Postgres?
* Working on topics: displaying papers and data
+
* Juancarlos will remove all the empty fields identified by his script
* Pathways: discussion about best approach
 
* Metabolic engineering
 
* Meta data about RNASeq data
 
** SPELL tool, basically only tool of its kind available; need new tools
 
* Species-specific proteins: how best to find them? HMMs (Jackhammer)?
 
  
=== Concise descriptions ===
 
* Progress being made within the Alliance to update the automated concise gene descriptions
 
* We will still accept manually written descriptions and display them in parallel with automated descriptions
 
  
=== Micropublications ===
+
== October 10, 2019 ==
* If people are requesting manually written gene descriptions, they could submit a microreview
 
* Concern was expressed about how to handle a really high throughput of submissions:
 
** Daniela: Working towards automating as much of the processing pipeline as possible
 
** Raymond: The throughput will be handled appropriately depending on demand; priority scheme will help
 
** Not getting lots of submissions yet, probably won't be inundated in the near future
 
** Karen: tools are still being developed; the platform is not being advertised as much as it could be; will ramp up outreach and communication once tools are in place to handle more submissions
 
* Karen: Micropublications team will reach out to curators to help build submission forms for respective data types
 
  
=== Undiagnosed Disease Network data ===
+
=== Biocuration 2020 ===
* Andy Golden will meet with Ranjana and Chris at IWM to discuss
+
* Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
* Andy asked about protocol pages at WormBase?
+
* Dates: Sunday May 17th to Wednesday May 20th, 2020
* Paul: Bioprotocols and Protocols IO
+
* Will have 3rd POTATO workshop
* Maybe we could interface with those existing resources to link to relevant protocols from WormBase (and WormBook)
+
* [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
  
==June 27th, 2019==
+
=== SObA comparison tool ===
 +
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
  
===IWM 2019: Feedback from Users===
+
=== Textpresso derived paper connections ===
* Anatomy term synonym search
+
* For example for strains and constructs, maybe anatomy terms?
** User pointed out that "RnB" search returns 0 results; GitHub ticket made to index anatomy synonyms
+
* May want to flag Textpresso predictions (as opposed to manually connected)
* Ciliated neurons
+
* Couple of options:
** User pointed out that male ciliated neurons are missing as a subclass of term "ciliated neuron"; GitHub ticket made, easy fix
+
** 1) At time of build, populate the papers (in ACEDB/Datomic) into a 'Putative_reference' tag and display in a distinct 'Putative references' widget
* Import of 22G and 26G RNAs
+
** 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
** Spoke to Julie Claycomb
+
*** A link to Textpresso could be done regardless of other approaches; low-hanging fruit?
** These are short RNAs transcribed by RNA-dependent RNA Polymerase (RdRP) off of mRNA molecules
+
*** Do a diff so that Textpresso pulls up only additional papers (not already associated)?
** Should these be instantiated as gene objects in WormBase? Julie argues that these are not 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?)
*** Should these just be transcript objects? Would they be linked to a gene? Or maybe also to any transcripts from which they could be derived?
+
* Transgene pipeline:
** Many map uniquely to the genome, but some map in multiple locations
+
** Arun wrote script, matching transgene names (using regex; Is and Si transgenes) to papers, automatically populate OA
** Associated data for now would likely just be protein-RNA interactions (Argonaute-RNA interactions)
+
** Another script, captures Ex transgenes as well, automatically connects to construct objects
*** May eventually include phenotype and/or gene ontology (biological process) annotations
+
** WB only displays verified papers; unverified (predicted) associations are not dumped
* Ranjana & Chris spoke with Andy Golden
+
* 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
** Andy and his lab will submit phenotype and disease data as they become available (likely pre-publication); we will likely point to a consortium as source until paper is published
+
* 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?
** There is still a strong need for cross-species variant mapping/visualization
+
* 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
* miRNA binding sites
+
* Can apply to: genes, transgenes, constructs, strains, alleles, AFP-vetted entities
** User asked at workshop and at booth; can we show miRNA binding sites in JBrowse? We would need to collect the data
 
** There are many sources of miRNA-target interactions, some experimental, most predicted
 
*** Chris compiled [https://docs.google.com/spreadsheets/d/19-txXrGi-ROFuByyLnQYvWbKl3o12KZON56qto3MN6g/edit?usp=sharing list of interaction databases] for Alliance interactions working group
 
* Ontology aware diffs of annotations (gene1 expression vs. gene2 expression)
 
* Promoter sequence in experimental constructs
 
* Workshop went well
 
** Next time, maybe have people bring laptops and follow along; be more interactive
 
** We could do webinars, for WormMine for example, allow people to work along with the presentation
 
*** Do other MODs/groups do webinars? How have they been? Useful?
 
** Competing with other workshops during the IWM
 
** Can focus on new, less-used features for webinars, tutorial videos
 
* Hawaiian genome in JBrowse
 
* Had internet stability issues at UCLA; can we get a local, dedicated WiFi?
 
* Next meeting (2021) will likely be in Europe (Cambridge UK?)
 
* User at cGal workshop asked about tissue-specific promoters/transgenes
 
** Have ~30 drivers and ~30 effectors; will WB take them in unpublished? Could make BioRXiv preprint (quick, before peer-review) and/or micropublication (after peer-review)
 
* Protocols
 
** Would be good to establish (for Alliance/WB) framework for serving protocols maintained by community
 
  
=== TAGC meeting ===
 
* Next April (2020)
 
* Alliance representation needed
 
  
===Giving disease model annotations a stable identifier===
+
== October 17, 2019 ==
*Currently disease model annotations get a temporary ID at the time of dump,
 
<pre style="white-space: pre-wrap;
 
white-space: -moz-pre-wrap;
 
white-space: -pre-wrap;
 
white-space: -o-pre-wrap;
 
word-wrap: break-word">
 
Disease_model_annotation : "00000004"
 
Disease_term "DOID:0050833"
 
Disease_of_species "Homo sapiens"
 
Variation "WBVar00275555"
 
Disease_relevant_gene "WBGene00011559"
 
Inferred_gene "WBGene00011559"
 
Association_type "is_implicated_in"
 
Evidence_code "IMP"
 
Genetic_sex "hermaphrodite"
 
Paper_evidence "WBPaper00035924"
 
Database "OMIM" "gene" "613891 "
 
Database "OMIM" "disease" "258900"
 
Curator_confirmed "WBPerson324"
 
Date_last_updated "2017-04-24"
 
</pre>
 
*Would like to institute stable identifiers across releases, so the plan is to call these objects, 'WBDisease_annotation:<number>', so then the above identifier would become 'WBDisease_annotation:00000004', or 'WBDiseaseannot:00000004' or 'WBDiseaseAnnot:00000004'
 
*ID convention--is underscore allowed?
 
*Is 'WBDisease_annotation:00000004' too long for acedb?
 
* Need to ask Kevin, Hinxton; what are the other implications for maintaining and generating persistent, unique IDs
 
  
=== Anatomy ontology issues ===
+
=== Alliance All Hands Face-to-Face ===
* Currently, "intestinal muscle" is considered "part of" intestine
+
* Flights: has everyone already booked? No, not yet
** User asked for intestinally expressed genes; using WOBr would also retrieve genes in intestinal muscle
+
* Any coordination of flights from Pasadena/LA?
** David Hall confirmed that instestinal muscle cells are not part of intestine
+
** Ranjana and Valerio got a direct flight from Burbank to Boston on Sunday for premeetings
** Maybe we can change to: "intestinal muscle" part_of "alimentary system"
 
* Currently, "amphid process" is considered "part of" each type of amphid neuron like AWC, AFD, etc.
 
** Problem is that users looking in WOBr for AWC-expressed genes will be given genes expressed in ANY amphid process regardless of which cell
 
** Propose to change to: "amphid process" part_of "amphid neuron" only
 
  
 +
=== 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)
  
== July 11th, 2019 ==
+
=== SObA ===
 +
* 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
  
=== Alliance all hands meeting ===
+
=== GO meeting ===
* Raymond: would be interested in discussing ontologies and their usage in the Alliance
+
* Kimberly can give update on recent updates to GO from the recent GO meeting
** Phenotype, anatomy ontologies, GO, etc.
+
* Slides are shared online
** Ontology browsers, SObA
+
 
 +
=== "all stages Ce" life stage ===
 +
* Currently used to annotate that RNA was collected from, or a gene was observed to be expressed during, all C. elegans life stages
 +
* "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?
 +
*** 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
 +
* Note: authors are often vague in their descriptions simply saying "during all stages" possibly stating a beginning and end of the range
 +
* 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
 +
* 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
 +
 
 +
=== Gene class missing description ===
 +
* The gene class "aatf" has no description, so in the aatf-1 gene page Overview widget, the gene has empty parentheses next to the gene name where there should be a description of what "aatf" stands for (coming from the ?Gene_class description)
 +
* Jae or Ranjana will create a ticket and assign it to someone at Hinxton

Revision as of 17:12, 17 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


October 17, 2019

Alliance All Hands Face-to-Face

  • Flights: has everyone already booked? No, not yet
  • Any coordination of flights from Pasadena/LA?
    • 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

  • 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

  • Kimberly can give update on recent updates to GO from the recent GO meeting
  • Slides are shared online

"all stages Ce" life stage

  • Currently used to annotate that RNA was collected from, or a gene was observed to be expressed during, all C. elegans life stages
  • "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?
      • 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
  • Note: authors are often vague in their descriptions simply saying "during all stages" possibly stating a beginning and end of the range
  • 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
  • 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

Gene class missing description

  • The gene class "aatf" has no description, so in the aatf-1 gene page Overview widget, the gene has empty parentheses next to the gene name where there should be a description of what "aatf" stands for (coming from the ?Gene_class description)
  • Jae or Ranjana will create a ticket and assign it to someone at Hinxton