Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
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[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
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= 2021 Meetings =
  
= 2020 Meetings =
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[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
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[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
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[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
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[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
== March 5, 2020 ==
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[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
=== WormBase curation ===
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[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
* 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 ===
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[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
* 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 ===
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[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
* 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
 
  
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== September 2, 2021 ==
  
== March 12, 2020 ==
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1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking<br>
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Needed for
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*AFP community curation
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*microPublication author tracking for all species
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*stub of person Alliance model already exists made by Adam http://dev.alliancegenome.org:11223/redoc#tag/Person
  
=== Cancelled meetings ===
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Problems:
* Meetings are being cancelled, including Biocuration 2020. Ranjana will update our Wormbase meeting page with a note to users (done)
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*this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
* We should start doing online advertisement for micropublications with webinars
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*need to do this outside of Alliance
  
=== Storing invalid/avoided WBPersons and email addresses in Postgres ===
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Action
* 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
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*Paul talks to zfin about interest in person pages
* Valerio would like to add these to Postgres to keep a more central repository of them
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*Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
* Chris would still like to be able to readily update/edit the content of those lists
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*Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite
  
* 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
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Will do
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*create biolink model based on current WB postgres/Caltech model
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*Adam will add tables when we have them
  
=== Updates on Alaska ===
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2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.
  
Raymond and Eduardo met with Joseph and decided to have the tool running as is for now even though maintaining it can be hard
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== September 16, 2021 ==
The future plan is to move the platform to Google colab to reduce maintainance work.
 
  
==Nameservice discussion==
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1. CeNGEN enriched genes per cell type data targeted for WS283.
*Getting a token has worked for Chris and Ranjana
 
*Karen and Daniela need to get tokens
 
  
==Noctua GO-CAM updates==
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2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump.  Juancarlos changed the OA population script script to exclude those.
*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
 
  
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== September 23, 2021 ==
  
== March 19, 2020 ==
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1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?
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* Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
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* Update the WB page on citing WormBase
  
=== Citace Upload ===
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2. CeNGEN data on Gene page for WS282. A short blog to highlight.
* Tuesday, March 31st
 
  
=== Latest ACEDB ===
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3. Server room in Braun power down for no apparent reason. Reset.
* 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
 

Latest revision as of 18:17, 23 September 2021

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

January

February

March

April

May

June

July

August


September 2, 2021

1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking
Needed for

Problems:

  • this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
  • need to do this outside of Alliance

Action

  • Paul talks to zfin about interest in person pages
  • Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
  • Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite

Will do

  • create biolink model based on current WB postgres/Caltech model
  • Adam will add tables when we have them

2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.

September 16, 2021

1. CeNGEN enriched genes per cell type data targeted for WS283.

2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump. Juancarlos changed the OA population script script to exclude those.

September 23, 2021

1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?

  • Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
  • Update the WB page on citing WormBase

2. CeNGEN data on Gene page for WS282. A short blog to highlight.

3. Server room in Braun power down for no apparent reason. Reset.