Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
= 2018 Meetings =
+
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
 
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_May_2018|May]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_June_2018|June]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_July_2018|July]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_August_2018|August]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_September_2018|September]]
 
 
 
 
 
== October 4, 2018 ==
 
 
 
=== SimpleMine ===
 
* Automated descriptions will be removed from Postgres/OA
 
* SimpleMine needed to update where it pulls the automated descriptions from
 
* Will add expression cluster and automated description columns output (in addition to concise description)
 
* Added RNAseq FPKM download function for 9 species: http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/fpkmmine.cgi
 
* Added SimpleMine-like topic search: http://tazendra.caltech.edu/%7Eazurebrd/cgi-bin/forms/spellmine.cgi
 
* Should put the new tools under the WormBase Tools menu
 
 
 
 
 
== October 11, 2018 ==
 
 
 
=== Ready for new round of phenotype requests ===
 
* Some users are getting confused about the name & email prepopulation based on IP address
 
** May want to stop autopopulating name and email or autopopulate based on email recipient only (encode in URL sent in email)
 
** Could we use cookies? Possibly, but may only help if a computer is shared but the browser isn't
 
* Current autocomplete expects exact match to person primary name; e.g. "Scott Emmons" will not match the official name "Scott Wilson Emmons"
 
** Maybe we could improve search matching; algorithm from Cecilia/Juancarlos? Elastic search by Valerio?
 
** Can we capture incomplete sessions? We may be able to learn from them. May be flooded by robot visits? Is it worth going through all the logs/sessions? Info is there if we want to look at it.
 
* Will go ahead and send emails for only new set of papers (won't resend requests for papers that had emails sent in June/July)
 
* Maybe go back to papers that already had a request sent at the 6 month time point
 
* Include other papers in need of curation at bottom of email; possibly, would it turn off users?
 
 
 
=== Worm Phenotype Ontology ===
 
* WPO has a new home on GitHub
 
** https://github.com/obophenotype/c-elegans-phenotype-ontology
 
* Edits should only be made to the edit file
 
** https://github.com/obophenotype/c-elegans-phenotype-ontology/blob/master/src/ontology/wbphenotype-edit.owl
 
* Anyone interested in contributing to the WPO should contact Chris for update pipeline info
 
* Need to make sure that all users of the WPO have the updated link information
 
 
 
=== Provide provenance in query tools ===
 
* Prompted by user question/request
 
* Specifically in WOBr, Anatomy pages
 
* WOBr provides genes annotated to term; should provide provenance of each gene and its annotations
 
* Expression pattern and expression cluster gene lists (in context of Anatomy WOBr); want to provide provenance for this data
 
* Provenance = an object ID, like "Expr1234" or "WBPaper00032062:age_regulated_genes" with link to relevant page
 
 
 
=== WOBr disease associations ===
 
* Ranjana wondering if WOBr is using updated disease-gene associations
 
* Gene association file (for disease) being generated by script; likely need to update where the data is coming from
 
* Ranjana will discuss with Raymond and Kevin
 
  
=== New WormMine superuser ===
+
= 2020 Meetings =
* Now all template queries are owned by a new superuser
 
* If people are interested in adding or editing templates talk to Chris or Paulo for superuser access
 
* We were running into login, template ownership, and consistency issues
 
  
=== Next upload Nov 16 ===
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
* WS269 citace upload Tuesday, November 13
 
* Can we add upload dates to Google calendar for WormBase?
 
  
  
== October 18, 2018 ==
+
== February 6, 2020 ==
  
=== Upload for WS269===
+
=== Worcester Area Worm Meeting talk ===
* To Hinxton Nov 16
+
* Confirmed for December 2020 or February 2021
* Citace upload to Wen Nov 13
 
  
=== Data provenance in WOBr tools ===
+
=== Alaska software ===
* Juancarlos and Raymond have been working on
+
* Code developed and maintained by Joseph, but not long term solution
* Awaiting pull request
+
* Raymond and Eduardo talked about taking it over
* Can test: juancarlos.wormbase.org
+
* Why have a web application vs. a command-line application?
** Go to WOBr and test anatomy ontology
+
** Wanted to make it easy, but also to capture meta data for WB
** Now WOBr gene count results show data objects from which the associations come (Expr_pattern and Expression_cluster objects)
+
* Should/will find out from Joseph about how hard it is to maintain the software
 +
* Maybe it could be taken over by Alliance, as RNA-Seq/Microarray meta data are getting harmonized
 +
* Expression working group working with Brian Oliver to have GEO take in more structured meta data
 +
* Array Express tried requiring more structured meta data, but authors stopped submitting
 +
* May be possible to build a form that collects meta data while simultaneously submitting to GEO in parallel
  
=== New SPELL server ===
 
* New server on Amazon (modifying server SGD uses)
 
* Raymond, Wen, and Todd working on
 
* Currently only have an SGD mirror running
 
* Wen will swap the data later today
 
* WormBase header link (to WormBase) or only link to Alliance site? We want a unified site for Alliance
 
* Each MOD would still support their own server for their data (MOD-specific grants support each server, for now)
 
  
=== Alliance expression data ===
+
== February 13, 2020 ==
* Anatomy-LifeStage pair required for Alliance expression annotations
 
* Since many expression pattern annotations don't have both, the missing entity would default to ontology root term
 
* Need to link anatomy root term to Uberon for ribbon display; root term annotations fall under the "Other" category in the ribbon slim
 
* Create "Anatomical_part" term to serve as the default "Other"/root term?
 
* All life-stage-only annotations will fall into anatomy "Other" and flood the list; should these be filtered out?
 
  
 +
=== Alliance Literature Group ===
 +
* Held first meeting on Monday, February 10th
 +
* Regular meetings will be on Tuesdays at 10am/1pm/6pm
 +
* Representatives from each group will give a brief overview of their literature pipelines before the group gets into details about deliverables
 +
* Question about centralized paper repository; group needs guidance from Alliance PIs on how to proceed
  
== October 25, 2018 ==
+
=== ?Genotype class model ===
 +
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?pli=1#bookmark=id.7r3e8pg19rd8 Proposal]
 +
* Can aim to implement for WS277 but may have to wait until WS278
  
=== WormBase SPELL on Amazon Web Service ===
+
=== Genotype OA ===
* http://34.224.93.60/ is running WormBase SPELL on WS267, based on the SPELL code supported by SGD. It is more stable and faster than the current Caltech server
+
* Will put documentation [[Genotype|here]]
* Waiting for Todd to respond if we can use this site as the official server for WormBase SPELL.
 
* Also need to get an instance (preferably also from WormBase AWS as a development site of WormBase SPELL.
 
* Caltech will focus on generating new data instead of SPELL code development.
 
  
=== Linking annotation evidence to Anatomy Ontology Browser ===
+
=== WB All-Hands Meeting ===
Each gene expression annotation shown on WOBr is linked to the object so that users can more easily examine the evidence.
+
* [https://doodle.com/poll/7f65p4ba6d88ztzt Doodle poll]
[https://juancarlos.wormbase.org/tools/ontology_browser/show_genes?focusTermName=neuron&focusTermId=WBbt:0003681 Example]
+
* Any thoughts at this point? Still need to discuss with Hinxton, Toronto.

Latest revision as of 19:30, 13 February 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings


GoToMeeting link: https://www.gotomeet.me/wormbase1

2020 Meetings

January


February 6, 2020

Worcester Area Worm Meeting talk

  • Confirmed for December 2020 or February 2021

Alaska software

  • Code developed and maintained by Joseph, but not long term solution
  • Raymond and Eduardo talked about taking it over
  • Why have a web application vs. a command-line application?
    • Wanted to make it easy, but also to capture meta data for WB
  • Should/will find out from Joseph about how hard it is to maintain the software
  • Maybe it could be taken over by Alliance, as RNA-Seq/Microarray meta data are getting harmonized
  • Expression working group working with Brian Oliver to have GEO take in more structured meta data
  • Array Express tried requiring more structured meta data, but authors stopped submitting
  • May be possible to build a form that collects meta data while simultaneously submitting to GEO in parallel


February 13, 2020

Alliance Literature Group

  • Held first meeting on Monday, February 10th
  • Regular meetings will be on Tuesdays at 10am/1pm/6pm
  • Representatives from each group will give a brief overview of their literature pipelines before the group gets into details about deliverables
  • Question about centralized paper repository; group needs guidance from Alliance PIs on how to proceed

?Genotype class model

  • Proposal
  • Can aim to implement for WS277 but may have to wait until WS278

Genotype OA

  • Will put documentation here

WB All-Hands Meeting

  • Doodle poll
  • Any thoughts at this point? Still need to discuss with Hinxton, Toronto.