Difference between revisions of "WormBase-Caltech Weekly Calls"

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= Previous Years =
 +
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
  
==February 10, 2011==
+
[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 +
 
 +
 
 +
GoToMeeting link: https://www.gotomeet.me/wormbase1
 +
 
 +
 
 +
= 2019 Meetings =
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
  
*Should we have a Caltech project/site manager? We'll look at the issues to be solved first
+
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
  
*Todd would like to know more about what's going on at Caltech
+
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
**What would Todd like to know about? New ideas, data types?
 
**What can we communicate more effectively to Todd?
 
  
*Should we take minutes of Caltech WormBase group meetings and send around?
+
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
  
*Kimberly: helpful (for off site individuals) if we go around the room to talk about what each of us is working on
+
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
  
*Bitbucket use
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
**How do we see only what pertains to us, individually?
 
**Paul: good way to document bugs and fixes, problems/solutions
 
**Bitbucket Wiki - does that capture what people want/need to see?
 
**Who should Todd follow? What would Todd like to know about?
 
**Raymond: used for code development/versioning by OICR; may be the best use for Bitbucket
 
**Should we develop best practices guideline for Bitbucket use?
 
***Avoid posting topics that are too specific or too vague?
 
***What do we want most to get out of Bitbucket?
 
**Curation efforts? No
 
  
*SAB Meeting
+
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
**Not much feedback for literature curators
 
**User interface stuff took precedence
 
**Paul: Testing, spot-checking website for errors
 
**Web issues, e-mails from Gary and Oliver
 
  
*WormBase-wide conference call twice per month
 
**First & third Thursday of the month
 
**Starting next Thursday (2-17) @ 8:30am PST
 
**Web redesign meetings on Thursdays will have to be every other week? Do both same day?
 
  
*Raymond: WormBase mirrors
+
== October 3, 2019 ==
**Do we want to implement the Genome Browser for the mirror(s)? If practical
 
**It seems as though Caltech mirror has been crashing often
 
**Has the Caltech mirror been working for people lately? Yes, more or less
 
  
 +
=== 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
  
== February 17, 2011 ==
+
=== 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)
  
Interaction dumping script
+
=== Script to remove blank entries from Postgres ===
*Spot check table
+
* 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
*Push changes to Git? Yes, to main branch
+
* 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
  
  
Interactions automatically downloaded to FTP every release? Yes
+
== October 10, 2019 ==
*People should check their own curation data
 
*Users query frequently?
 
*Can WormMart work instead?
 
*Ruihua - feature can be added
 
*Todd - good to have pre-defined queries generated automatically
 
*Parse/remove predicted interactions (400,000) from others during dump? Yes
 
*Paul - Wei Wei wants to help with updates - who should she contact at WB?
 
  
 +
=== 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
  
Ranjana - Solar flares causing static on phone? ;)
+
=== ICBO 2020 ===
 +
* International Conference on Biomedical Ontologies
 +
* [https://icbo2020.inf.unibz.it/ Meeting website]
 +
* Held in Bozen-Bolzano, Italy
 +
* 16 - 19 September 2020
  
 +
=== SObA comparison tool ===
 +
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
  
Newsletter for new website release? Yes
+
=== Textpresso derived paper connections ===
*Todd - 5 development milestones
+
* For example for strains and constructs, maybe anatomy terms?
**teleconference with Gary Ruvkun's lab next week
+
* May want to flag Textpresso predictions (as opposed to manually connected)
**Go live with Beta version in June (@IWM)
+
* Couple of options:
**Go live live with new site in September
+
** 1) At time of build, populate the papers (in ACEDB/Datomic) into a 'Putative_reference' tag and display in a distinct 'Putative references' widget
**Retire old site at end of year
+
** 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
**Need outreach, documentation, screencasts
+
*** 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
  
  
BioGRID
+
== October 17, 2019 ==
*WormBase to BioGRID curation
 
*Issues of mapping interaction types: WB -> BioGRID vs. BioGRID -> WB
 
*Moving towards using WB interaction types
 
*Definitions of our interaction types
 
*Rose will propose to BioGRID community
 
*Physical interactions - BioGRID has a better format
 
**break physical interactions away from other interaction types?
 
**Kimberly can propose changes to model: YH separate from other interactions?
 
**Physical vs Genetic interactions? keep separate
 
*We need an interaction ontology, of some sort
 
*Who should Wei Wei contact, how to coordinate with Hinxton; getting data from FlyBase and SGD?
 
**Automation?
 
*Interaction pages - explain what the interaction is based on; provenance/reference
 
*Gene Orienteer shows data, but user has to link out
 
  
 +
=== 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
  
WormBase IWM souvenir?
+
=== SObA Comparison Tool ===
*Computer stress ball? with new site address?
+
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
*bouncy ball?
+
* Prototype discussed last week, updated with feedback from prior discussions
*worm rubber band thing?
+
* Would this be a stand-alone tool discoverable under the Tools menu?
*Screen shield?
+
** Possibly; could be a gene page widget, but may be out of place
*Complementary iPads? ;)
+
** Stand-alone tool probably makes more sense
*Antifungal socks? wristbands?
+
* 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
  
SPELL
+
=== GO meeting ===
*new data doesn't load; problem runnning search engine; can load it on athena, not generalizable problem?
+
* Kimberly can give update on recent updates to GO from the recent GO meeting
*OS was not complete with an update; try again
+
* Slides are shared online
*two virtual machines working back and forth for support
 
*how often is SPELL being used? log?; had 6-7 users within two weeks complaining of SPELL problems
 
*Todd - can send Google analytic tool to put at bottom of page
 
*Wen - SPELL testing server; official and mirror; want a separate testing server for new releases; mirror on athena (Wen's working machine); Raymond says don't want to attract users to that machine; WB's running SPELL on altair; heavily loaded and has had problems; relying on athena may be problematic
 
*maybe we need analysis of all of our machines to see big picture; can we consolidate machines; make use of ones we have? If not we can get another machine.
 
*what type of machine do we need?
 
*Log of all machines with purchase date and functionality?
 
*Linux vs Mac curators? athena development machine;
 
*how much power do the scripts need? can check
 
*may not be appropriate as official server if main machine goes down
 
*WB and athena can run SPELL server, but not others. security problems?
 
*prefer work machine is readily re-bootable; reconfigure software easily without affecting other things that people rely on
 
*need 10GB space; 4GB memory? SPELL production server; want it stable for outside world; hardware designed for that purpose; farm it out to IMSS?
 
*complexity of the application; Linux can run multiple applications; caprica has SVM production and WormMart; understand demand of the application; requirements; development vs running scripts, how often? Efficient use of machines. Have 2 computers, getting a third; for WormMart need power; traffic suddenly increased yesterday; monitor traffic; not much personal experience with server maintenance; cluster needs lots of expertise
 
*building official sever of SPELL at OICR? Yes
 
  
 +
=== "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
  
WormMart
+
=== Gene class missing description ===
*with WormMart and WormBase, people just want to know if it's down, just to know to lessen frustration; Official statement from dev team
+
* 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)
*WormMart - we give users testing url; can we just change WormBase link to that testing server?
+
* Jae or Ranjana will create a ticket and assign it to someone at Hinxton
*going to change HTML to update users with most recent information; discuss with Lincoln, 5 datasets on testing server; remaining 3 datasets. if WormMart not working, put a message on main site
 
*it doesn't look good to have a link to a tool linked from a production server; if we don't trust the data we shouldn't put it up.
 
*would like to keep the html page as a testing server; could modify page
 
*if WormMart is working OK but not perfect, that's OK; Comment in the banner
 
*the html page is a useful tool to get feedback from users
 

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