Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
(187 intermediate revisions by 9 users not shown)
Line 22: Line 22:
  
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
 
  
 
= 2020 Meetings =
 
= 2020 Meetings =
Line 30: Line 30:
 
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
 
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
 +
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
== March 5, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
 
 
=== WormBase curation ===
 
* Tim Schedl: WB needs to do more curation for phenotype and variation
 
* Doing community curation, but not fast enough
 
* Would like to work on more automation; e.g. having Textpresso return all sentences mentioning an allele in papers that are predicted to have phenotype data
 
 
 
=== Alaksa ===
 
* Joesph may be able to meet with Raymond
 
* How can the tool be maintained? If it can't it needs to be pulled
 
 
 
=== Single cell expression tool ===
 
* Tool is here: http://de.wormcells.com/
 
* What do we need to consider for pulling into WormBase?
 
* Where does the data sit and how does the tool access it? Can we integrate the data more into WormBase (e.g. local curation databases)?
 
** Would want it to be in sync with WormBase releases
 
** May not need to reprocess with every release with current (small-ish) data set
 
* Fully integrated tool versus an embedded tool?
 
 
 
=== Name service updates ===
 
* For now we will stick to the CGIs that Juancarlos has built for variations and strains
 
* Juancarlos can discuss with Matt R. and Sibyl the possibility of integrating API requests to the Name service into a CGI form for the OA
 
 
 
 
 
== March 12, 2020 ==
 
 
 
=== Cancelled meetings ===
 
* Meetings are being cancelled, including Biocuration 2020. Ranjana will update our Wormbase meeting page with a note to users (done)
 
* We should start doing online advertisement for micropublications with webinars
 
 
 
=== Storing invalid/avoided WBPersons and email addresses in Postgres ===
 
* Currently Chris has been maintaining ([https://docs.google.com/spreadsheets/d/1FHhQk_IZIBLYkOUdVf9Kfh5zx66rkHOEVFQQ6wzT2ks/edit?usp=sharing on Google sheets]) a list of papers, people, and email addresses to omit from future WormBase outreach requests
 
* Valerio would like to add these to Postgres to keep a more central repository of them
 
* Chris would still like to be able to readily update/edit the content of those lists
 
 
 
* Proposed solutions: Keep the list in a flat file and have a cron job to sync the data to postgres daily or create a simple form to create/modify entries directly in postgres
 
 
 
=== Updates on Alaska ===
 
 
 
Raymond and Eduardo met with Joseph and decided to have the tool running as is for now even though maintaining it can be hard
 
The future plan is to move the platform to Google colab to reduce maintainance work.
 
 
 
==Nameservice discussion==
 
*Getting a token has worked for Chris and Ranjana
 
*Karen and Daniela need to get tokens
 
 
 
==Noctua GO-CAM updates==
 
*Noctua is a production tool available for annotations right now
 
*Create as many interconnected models and make available for curators is the ongoing goal
 
*Reactome models are in the process of being imported
 
*Real time validation messages as curation is being done, is being worked on
 
*Kimberly will send out the details for logging into Noctua and make sure all curators are on the login list
 
 
 
 
 
== March 19, 2020 ==
 
 
 
=== Citace Upload ===
 
* Tuesday, March 31st
 
 
 
=== Latest ACEDB ===
 
* Getting latest ACEDB build from staging FTP (for descriptions, etc.)
 
 
 
=== Storing email addresses/persons to omit from requests ===
 
* Chris and Juancarlos will work on a form to submit email addresses and WBPerson IDs to Postgres
 
 
 
=== Mailing lists ===
 
* Let Todd know if you want to keep your caltech.edu account on the mailing lists
 
  
 +
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
==March 26th==
+
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
===Community curation===
 
*Do we need to publicize any data form and urge Users to contribute? The AFP and phenotype forms already send targeted e-mail
 
* Paul S. is getting people from the lab to do phenotype curation; Chris G will run a tutorial for interested people
 
* Blog about phenotype form to make people generally aware
 
* Could the phenotype form be adapted for other species? Possibly but depends on:
 
** Whether genotypes could be loaded and recognized
 
  
=== AFP for older papers ===
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
* Discussed recently
 
* Many (all?) Old papers have already gone through the old AFP pipeline
 
* Need to check what has already been curated
 
  
=== Omit form ===
 
* http://tazendra.caltech.edu/~postgres/cgi-bin/omit_form.cgi
 
* Can view, add, or edit persons, email addresses, and IP addresses to omit from email requests (and IP addresses to block)
 
  
=== Problems accessing Textpresso Central ===
+
==August 6th, 2020==
* Ranjana had noticed that the server was acting slow
+
===Experimental conditions data flow into Alliance===
* Unknown problem; hard to pin down
+
*Experimental conditions in disease annotations: WB has inducers (used to recapitulate the disease condition) and modifiers (a modifier can ameliorate, exacerbate, or have no effect, on the disease condition)
* Definitely a Caltech network system
+
*We use the WB Molecule CV for Inducers and Modifiers in disease annotation
 +
*Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
 +
*So for data flow into Alliance:
 +
**In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
 +
**Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.

Latest revision as of 23:18, 5 August 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings



2020 Meetings

January

February

March

April

May

June

July


August 6th, 2020

Experimental conditions data flow into Alliance

  • Experimental conditions in disease annotations: WB has inducers (used to recapitulate the disease condition) and modifiers (a modifier can ameliorate, exacerbate, or have no effect, on the disease condition)
  • We use the WB Molecule CV for Inducers and Modifiers in disease annotation
  • Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
  • So for data flow into Alliance:
    • In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
    • Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.