Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
 
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
  
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[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
  
== July 11th, 2019 ==
 
  
=== Alliance all hands meeting ===
+
== August 1, 2019 ==
* Raymond: would be interested in discussing ontologies and their usage in the Alliance
 
** Phenotype, anatomy ontologies, GO, etc.
 
** Ontology browsers, SObA
 
  
=== IWM workshop ===
+
=== Life stage public names missing in WS271 ===
* Videos ready for upload
+
* Did we ever get a patch in for this?
* Wen and Raymond now have access to outreach@wormbase.org account; will upload videos
+
* WormMine only has WBls IDs (no public name) for almost all life stages
 +
* Wen will resend the patch file
  
=== Protocol videos ===
+
=== 2020 WB NAR paper ===
* Wen met Craig Mello at the IWM; he is interested in putting up microinjection videos online; linkable from WormBase?
+
* Who's contributing?
* Can make each video a Video Weblog so people can make comments, etc.
+
** 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
  
== July 25, 2019 ==
 
  
=== Anatomy ontology ===
+
== August 15, 2019 ==
* Raymond added back some deprecated cell group terms as obsolete terms
 
  
=== Life stage ontology ===
+
=== GO Alliance slim terms ===
* Who will take charge of it? Raymond or Chris?
+
* We need to update our GO slim terms for WB GO ribbons to be in sync with Alliance
* OBO-to-ACE script is working
+
* May need to watch out for terms that don't apply to worms
* OBO is working (?) in SObA and WOBr
+
* Raymond gets slim terms into Solr from OBO release file; Sibyl collecting from different source; should make the same (pull from WB FTP site?)
* Chris will take over life stage ontology; Daniela & Raymond will send Chris location of OBO-to-ACE script
 
* Chris will send release OBO to Raymond to test WOBr and SObA
 
  
=== Anatomy term acronyms ===
+
=== Phenotype ontology patternization ===
* Some anatomy terms: can the name be changed?
+
* Now have 676 terms patternized (27% of 2,506 terms total)
** e.g. "DTC" is main label for "distal tip cell"
+
* Have reviewed the class hierarchy, collecting list of unexpected class subsumptions
** e.g. "HMC" is main label for "head mesodermal cell"
+
* Issues to address collected here: https://docs.google.com/document/d/1IWtQbEQ-elM-U5SQyU4VfIH3vdJp6taVMGViIjGyVks/edit?usp=sharing
** e.g. "gon herm dtca" is main label for "anterior distal tip cell"
 
* Karen: would be good to still point out a "public name" or "common name"
 
** Chris: we may need to select a specific OWL annotation property to dump into OBO so our scripts can recognize them and populate ACEDB/Datomic; will look into; may require model change
 
  
=== Author first pass ===
+
 
* Paul: spent about 30-40 minutes doing author first pass for a micropublication
+
== August 22, 2019 ==
* Entities need to be listed 10+ times (fixed threshold) to be recognized, but micropubs won't usually have this many occurrences of terms
+
 
* Need a better way to report allele details; curation of alleles can happen at Caltech or Hinxton; need to discuss
+
=== Obsolete ontology terms in Postgres ===
* Google summer of code: add to schedule so we can post requests/openings
+
* There are currently 172 GO annotations in the GO OA referring to obsolete GO terms
* Karen: Could implement something like Apollo? Talk to Nathan?
+
** https://docs.google.com/spreadsheets/d/14iG3-s0GrZ3_W87iOjD6tZiQiUJklRRjgs6ARFWi9E4/edit?usp=sharing
* How can we optimize micropub author first pass?
+
* We would like a mechanism for detecting and alerting curators to obsolete ontology terms in the OA/Postgres
* Need to minimize/eliminate redundant curation effort
 
* Curation forms could hide fields that have already been curated; OR, show existing curated data to form users
 
* Paul: Can we have submission form build a report to send to user, but possibly not store locally?
 
** Karen: May be counter to the intent of micropublication where we want authors to submit data in parallel to submission/publication process
 
* Eventually there shouldn't be any author first pass for micropublications
 
* For now we will exclude micropublications from AFP
 
* Can NIH funded groups be pressured to submit data? We need the pipeline to operate smoothly (and properly) before making a requirement
 

Revision as of 19:27, 16 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