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]]
  
==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.
 
* How do we handle genetic sex? Part of condition?
 
** Condition has been intended for external/environmental conditions, whereas genetic sex is inherent to the organism of study
 
** Expression pattern curation needs genetic sex; needs a model at the Alliance for capturing sex
 
  
 +
== November 4 2021 ==
  
== August 13, 2020 ==
+
=== 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
  
=== Species in Postgres and ACEDB/Datomic ===
 
* Want to dump "Affected By Pathogen" fields in Phenotype OA and RNAi OA
 
* Want to be sure that what gets dumped aligns with species loaded into ACEDB
 
* Currently one species annotated not in WS277: Streptococcus gallolyticus subsp. gallolyticus
 
* We currently have multiple Postgres tables for storing species lists:
 
** pap_species_index (used by "Affected By Pathogen" fields, AFP); Kimberly uses to assign species to papers and occasionally adds new ones
 
** obo_name_ncbitaxonid
 
** obo_name_taxon (original, smaller list)
 
** h_pap_species_index (history for pap_species_index)
 
* How do species get loaded into ACEDB? Dumps from Postgres? Which table(s)?
 
* WS277 has 7,906 species (1,936 have no NCBI Taxon ID)
 
* Kimberly has occasionally uploaded a species.ace file in the context of GO curation; but Hinxton otherwise handles it; should ask them
 
* New species are associated with paper objects, but otherwise no additional data for those species come from Caltech
 
* It might be useful to have species pages in WB that at least list papers for which we have species associations, maybe include other information?
 
  
=== WS279 Citace upload ===
+
== November 11 2021 ==
* When is it happening? Not sure; not on release schedule right now
 
  
=== SOLR server security (IMSS) ===
+
=== WS284 upload dates for Caltech ===
* IMSS network security blocked network on our server due to its open SOLR web access.
+
* When are files due for the Caltech group?
* Part of AMIGO stack, very old version, drives our ontology browser directly, SObA, Enrichment tools indirectly.
 
* Added some firewall/URL filter and IMSS opens up the network (for now). IMSS still gripes about its service is open to the world.
 
  
=== Alzheimer's disease portal ===
+
===Minutes===
* Supplement grant awarded to Alliance for an Alzheimer's disease portal
+
*WS284 upload-Better to upload before the holidays or in Jan 2022
* Could involve automated/concise descriptions, interactions, etc.
+
*Wen will contact Paul D/Hinxton to find out when the WS284 models will be released
* Could establish useful pipelines that could be reused in other contexts
 
  
  
==August 20th, 2020==
+
== November 18 2021 ==
 +
Proposal for upgrading tanzendra/mangolassi computing resources
 +
1. Move them to Chen. (done)
 +
  monitor stability of network
  
=== Expression in sex ===
+
Old hardware and out of support OS (Ubuntu 14.04)
* In Alliance Expression group, talking about how to handle sex in expression
+
 
* In WB, will start collecting sex in a separate field
+
2. Establish a development environment for Dockerizing services (curation OA, other web forms, postgres DB)
* Daniela will capture sexually dimorphic expression in remarks/comments
+
  (use Valerio's local server/desktop)
* Will eventually figure out how to handle/display at the Alliance
+
 
 +
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