Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to: navigation, search
m (June 13, 2019)
m (August 22, 2019)
 
(68 intermediate revisions by 4 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 ===
 
* May put graphs within existing widgets, but don't need to rush to get that ready for IWM
 
  
=== Phenotype association file format ===
+
== August 1, 2019 ==
* 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 ===
+
=== Life stage public names missing in WS271 ===
* Sent out 1140 emails on May 30
+
* Did we ever get a patch in for this?
* Since have received 374 annotations from 54 papers (42 requested, 12 additional)
+
* WormMine only has WBls IDs (no public name) for almost all life stages
* 21 papers flagged as not having phenotypes
+
* Wen will resend the patch file
* 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
+
  
 +
=== 2020 WB NAR paper ===
 +
* Who's contributing?
 +
** Raymond, Chris, Ranjana, Valerio, Daniela, Kimberly
 +
* Topics
 +
** Automated descriptions
 +
** Ontology tools (SObA)
 +
** Community curation
 +
** Author first pass
  
== June 13, 2019 ==
+
=== 2019 IWM Workshop videos ===
 +
* On YouTube, but not public yet
 +
* Chris will make them public and send links to Ranjana for the blog post
  
=== IWM ===
 
* Coordinating transportation of swag boxes to Pauley Pavilion
 
* Workshop on Saturday June 22, from 1pm to 2:30pm
 
* Saturday morning micropublication breakfast 7:30 - 8:30am
 
* Workshop
 
** 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 ===
+
== August 15, 2019 ==
* Paul attended
+
 
* Alliance publicity was discussed
+
=== GO Alliance slim terms ===
* SAB likes the Alliance orthology features
+
* We need to update our GO slim terms for WB GO ribbons to be in sync with Alliance
* Working on topics: displaying papers and data
+
* May need to watch out for terms that don't apply to worms
* Pathways: discussion about best approach
+
* Raymond gets slim terms into Solr from OBO release file; Sibyl collecting from different source; should make the same (pull from WB FTP site?)
* Metabolic engineering
+
 
* Meta data about RNASeq data
+
=== Phenotype ontology patternization ===
** SPELL tool, basically only tool of its kind available; need new tools
+
* Now have 676 terms patternized (27% of 2,506 terms total)
* Species-specific proteins: how best to find them? HMMs (Jackhammer)?
+
* Have reviewed the class hierarchy, collecting list of unexpected class subsumptions
 +
* Issues to address collected here: https://docs.google.com/document/d/1IWtQbEQ-elM-U5SQyU4VfIH3vdJp6taVMGViIjGyVks/edit?usp=sharing
 +
 
 +
 
 +
== August 22, 2019 ==
 +
 
 +
=== Obsolete ontology terms in Postgres ===
 +
* There are currently 172 GO annotations in the GO OA, 94 in Expr OA, and 54 in Pic OA referring to obsolete GO terms
 +
** https://docs.google.com/spreadsheets/d/14iG3-s0GrZ3_W87iOjD6tZiQiUJklRRjgs6ARFWi9E4/edit?usp=sharing
 +
* We would like a mechanism for detecting and alerting curators to obsolete ontology terms in the OA/Postgres
 +
 
 +
=== Community phenotype requests ===
 +
* Sent out new round of phenotype requests on August 20, 21, and 22 (today) 2019
 +
* 2,627 emails/papers requested
 +
* 112 emails bounced; 4 resent to new addresses
 +
* 205 Phenotype OA community annotations; 55 RNAi OA annotations, from 47 papers, by 42 distinct community curators (so far)
 +
* Also, 3 worksheets submitted, for 4 papers
 +
* 35 papers flagged as not having phenotypes
 +
* 86 papers with responses (3% response; still early)
 +
* Need to coordinate with the AFP request pipeline
 +
 
 +
=== GO slim terms ===
 +
* SObA highlights Alliance slim terms, but doesn't correspond to ribbon
 +
* Want to use same slim terms used for ribbons
 +
* Add slim terms into ACEDB? One option
 +
* Ribbon order of slim terms is an issue
 +
* Decided not to store ribbon info (slim terms and term order) in ACEDB, but rather in web code
 +
* Will have to manually synchronize with Alliance if Alliance changes its ribbon

Latest revision as of 18:30, 22 August 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 1, 2019

Life stage public names missing in WS271

  • Did we ever get a patch in for this?
  • WormMine only has WBls IDs (no public name) for almost all life stages
  • Wen will resend the patch file

2020 WB NAR paper

  • Who's contributing?
    • Raymond, Chris, Ranjana, Valerio, Daniela, Kimberly
  • Topics
    • Automated descriptions
    • Ontology tools (SObA)
    • Community curation
    • Author first pass

2019 IWM Workshop videos

  • On YouTube, but not public yet
  • Chris will make them public and send links to Ranjana for the blog post


August 15, 2019

GO Alliance slim terms

  • We need to update our GO slim terms for WB GO ribbons to be in sync with Alliance
  • May need to watch out for terms that don't apply to worms
  • Raymond gets slim terms into Solr from OBO release file; Sibyl collecting from different source; should make the same (pull from WB FTP site?)

Phenotype ontology patternization


August 22, 2019

Obsolete ontology terms in Postgres

Community phenotype requests

  • Sent out new round of phenotype requests on August 20, 21, and 22 (today) 2019
  • 2,627 emails/papers requested
  • 112 emails bounced; 4 resent to new addresses
  • 205 Phenotype OA community annotations; 55 RNAi OA annotations, from 47 papers, by 42 distinct community curators (so far)
  • Also, 3 worksheets submitted, for 4 papers
  • 35 papers flagged as not having phenotypes
  • 86 papers with responses (3% response; still early)
  • Need to coordinate with the AFP request pipeline

GO slim terms

  • SObA highlights Alliance slim terms, but doesn't correspond to ribbon
  • Want to use same slim terms used for ribbons
  • Add slim terms into ACEDB? One option
  • Ribbon order of slim terms is an issue
  • Decided not to store ribbon info (slim terms and term order) in ACEDB, but rather in web code
  • Will have to manually synchronize with Alliance if Alliance changes its ribbon