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]]
  
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= 2021 Meetings =
  
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[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
= 2020 Meetings =
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[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
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[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
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[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
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[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
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[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
  
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
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[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
  
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
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[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
  
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
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[[WormBase-Caltech_Weekly_Calls_September_2021|September]]
  
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[[WormBase-Caltech_Weekly_Calls_October_2021|October]]
  
==July 9th, 2020==
 
===Gene names issue in SimpleMine and other mining tools===
 
*Wen: Last week, Jonathan Ewbank raised the issue of gene names that may refer to multiple objects.
 
*this can be an issue for multiple data mining tools including WormMine, BioMart, and Gene Set Enrichment.
 
*Perhaps have a standalone approach to check if any gene name among a list may refer to multiple objects (users check their name lists before submitting them to any data mining tool).
 
*Jae: The public name issue has heterogeneous natures. That means there may be no single solution to solve all those problems.
 
*Gene list curation from high-throughput studies, confusing usage of public names probably less than 2% (still cannot be ignored). See examples below--
 
**single public name is assigned to multiple WBgene ID, Wen has a list of these genes
 
**overlapped or dicistronic genes, ex. mrpl-44 and F02A9.10
 
**overlapped or dicistronic, but has a single sequence name, examples:
 
    exos-4.1 and tin-9.2 (B0564.1)
 
    eat-18 and lev-10 (Y105E8A.7)
 
    cha-1 and unc-17 (ZC416.8)
 
  
**simple confusion from authors, ex. mdh-1 and mdh-2
 
*One of the most significant problems is a propagation to other DB and papers of  these gene name issues.
 
*We can make a special note for each gene page, but the people using batch analysis could not catch that easily.
 
*Conclusion: Jae and Wen will work on a tool that lets Users "sanitize" their gene lists before submission to data mining tools.  They will also write a microPub explaining this issue to the community.
 
  
===Wormicloud===
+
== November 4 2021 ==
*Please test and leave any feedback on the word cloud tool (Wormicloud), https://wormicloud.textpressolab.com/
 
*Valerio and Jae have worked on a tool that uses data in Textpresso; given a keyword, eg. "transposon", the tool generates a word cloud and word trend.
 
*Any keyword can generate a graph that plots trends of occurence across the years in publication abstracts.
 
  
===Noctua 2.0 form ready to use===
+
=== Migrating Paper Pipeline to Alliance ===
*Caltech summer student will try using Noctua initially for dauer (neuronal signaling) pathways
+
*Meeting abstracts
 +
**Continuing to review what we have and standardize bibliographic info before we migrate
 +
**QC checks highlight some older abstracts with little-to-no data - propose to invalidate these so we don't migrate poor quality paper data to the Alliance
 +
**We can always respond to individual requests to add old meeting abstracts if they arise
  
===Nightly names service updates to postgres===
 
*Nightly using Matt's wb-names-export.jar to get full output of genes from datomic/names service, and updating postgres based on that.
 
  
 +
== November 11 2021 ==
  
==July 16th, 2020==
+
=== WS284 upload dates for Caltech ===
===Citing ontologies and their versions===
+
* When are files due for the Caltech group?
*Came up in the context of the Alliance: It would be best practice to provide users with the list of ontologies used and their versions/date.
+
 
*If WB ontology developers could make sure their ontology file headers (WB anatomy ontology, WB life stage, etc.) conformed to obo file header specifications, then it would be easy to pull in version and date information into the Alliance.
+
===Minutes===
*Some useful links (from DQM meeting minutes)
+
*WS284 upload-Better to upload before the holidays or in Jan 2022
**http://www.obofoundry.org/principles/fp-004-versioning.html
+
*Wen will contact Paul D/Hinxton to find out when the WS284 models will be released
**http://obo-dashboard-test.ontodev.com/ (you can see that wbbt, wbls version metadata attribute is generating a warning
+
 
**Note: OBO-foundry may not have been updated, but good practice to check your headers, anyway.
+
 
 +
== November 18 2021 ==
 +
Proposal for upgrading tanzendra/mangolassi computing resources
 +
1. Move them to Chen. (done)
 +
  monitor stability of network
 +
 
 +
Old hardware and out of support OS (Ubuntu 14.04)
 +
 
 +
2. Establish a development environment for Dockerizing services (curation OA, other web forms, postgres DB)
 +
  (use Valerio's local server/desktop)
 +
 
 +
3. Establish a local file server for storage and download access (PDFs, dump files)
 +
 
 +
4. Run dockerized services from AWS
 +
 
 +
5. Continuous development and integration locally -> AWS
 +
 
 +
===Commercial antibodies===
 +
* Daniela contacted ZFIN and FlyBase. ZFIN does curate commercial antibodies only if found in publications. Waiting for FlyBase feedback (Sian out).
 +
* TODO: Contact TAIR and see if they including commercial antibodies and if  they charge companies  (Daniela sent a message on slack). Tanya: We have not charged for placing the links but have strongly encouraged a corporate subscription for the two companies.
 +
* This can be an  Alliance project. Need to contact companies and see who is interested (need to have a price in mind for that).
 +
* Can pilot text mining for commercial antibodies
 +
* GeneCards charges for inclusion of commercial reagents on their website: "Companies that wish to provide deep links to their products (e.g. reagents, assays, antibodies, clones, etc) in the Services and other relevant sections of GeneCards, should contact sales@lifemapsc.com." From https://www.genecards.org/Guide/FAQ

Latest revision as of 17:51, 18 November 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

October


November 4 2021

Migrating Paper Pipeline to Alliance

  • Meeting abstracts
    • Continuing to review what we have and standardize bibliographic info before we migrate
    • QC checks highlight some older abstracts with little-to-no data - propose to invalidate these so we don't migrate poor quality paper data to the Alliance
    • We can always respond to individual requests to add old meeting abstracts if they arise


November 11 2021

WS284 upload dates for Caltech

  • When are files due for the Caltech group?

Minutes

  • WS284 upload-Better to upload before the holidays or in Jan 2022
  • Wen will contact Paul D/Hinxton to find out when the WS284 models will be released


November 18 2021

Proposal for upgrading tanzendra/mangolassi computing resources

1. Move them to Chen. (done)
  monitor stability of network
Old hardware and out of support OS (Ubuntu 14.04)
2. Establish a development environment for Dockerizing services (curation OA, other web forms, postgres DB)
  (use Valerio's local server/desktop)
3. Establish a local file server for storage and download access (PDFs, dump files)
4. Run dockerized services from AWS
5. Continuous development and integration locally -> AWS

Commercial antibodies

  • Daniela contacted ZFIN and FlyBase. ZFIN does curate commercial antibodies only if found in publications. Waiting for FlyBase feedback (Sian out).
  • TODO: Contact TAIR and see if they including commercial antibodies and if they charge companies (Daniela sent a message on slack). Tanya: We have not charged for placing the links but have strongly encouraged a corporate subscription for the two companies.
  • This can be an Alliance project. Need to contact companies and see who is interested (need to have a price in mind for that).
  • Can pilot text mining for commercial antibodies
  • GeneCards charges for inclusion of commercial reagents on their website: "Companies that wish to provide deep links to their products (e.g. reagents, assays, antibodies, clones, etc) in the Services and other relevant sections of GeneCards, should contact sales@lifemapsc.com." From https://www.genecards.org/Guide/FAQ