Difference between revisions of "WormBase-Caltech Weekly Calls"

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= Previous Years =
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[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
  
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[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
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[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
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 +
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
 +
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[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 +
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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
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 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
==2011 Meetings==
 
  
[[WormBase-Caltech_Weekly_Calls_February_2011|February]]
 
  
[[WormBase-Caltech_Weekly_Calls_March_2011|March]]
 
  
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= 2020 Meetings =
  
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[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
==April 7, 2011==
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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
Transgene Model
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
*On Wiki
 
*Sent out to people
 
*Have a look; report any concerns
 
*Can follow on BitBucket; search for transgene; link to Wiki
 
*No objections at Caltech; Karen will send to Paul Davis
 
*Changes to ACE dumping script; Karen will talk to Juancarlos
 
*Changes needed in OA (softer deadline than dump)
 
  
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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
Interactions
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[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
*Murky genetic interaction curation?
 
*Err on the side of generality/trusting author statements
 
*When in doubt, curate as "genetic interaction"
 
*Chris is working on decision tree/pipeline for curation
 
*Kimberly working on Physical Interaction model
 
  
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[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
BioGRID meeting at Princeton in May
 
*Call in
 
*What will Rose propose?
 
  
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==August 6th, 2020==
  
Expression Pattern Curation (Daniela/Wen)
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===Experimental conditions data flow into Alliance===
*Daniela sent out picture page for review
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*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)
*Expr Pattern OA wiki is in place:
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*We use the WB Molecule CV for Inducers and Modifiers in disease annotation
**http://wiki.wormbase.org/index.php/Expression_Pattern
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*Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
*As soon as Juancarlos is done with the modularization will start working on the code.
+
*So for data flow into Alliance:
*In the meanwhile Daniela will curate expression pattern writing .ace files
+
**In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
*Expr_pattern OA should be ready by the next upload (May26th).
+
**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
  
  
Patch file/Interbuild (Raymond)
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== August 13, 2020 ==
*Developed good patch file
 
*Tested patch file to update WS224 to WS225 - seems OK
 
*Less than 5 minutes for upload
 
*Testing now should be done by Todd/OICR team
 
  
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=== 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
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** 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?
  
Uma started
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=== WS279 Citace upload ===
*Working on concise descriptions of gene classes
+
* When is it happening? Not sure; not on release schedule right now
*Karen has reviewed with Uma; Uma is reading papers
 
*Discussing details of descriptions
 
*Inconsistencies/discrepancies of gene class names
 
*>2400 gene classes
 
*Can work on generating formula for this curation
 
*Arun can help with automation
 
*May need to get Uma an interface to enter data into postgres
 
*Adapt concise description CGI for her?
 
*Gene class name and a text field
 
*Using Textpresso/WormMart output; sentence saver?
 
  
 +
=== SOLR server security (IMSS) ===
 +
* IMSS network security blocked network on our server due to its open SOLR web access.
 +
* 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.
  
eggNOG data into citace?
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=== Alzheimer's disease portal ===
*Who's going to handle the data? curate?
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* Supplement grant awarded to Alliance for an Alzheimer's disease portal
*Michael? OK
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* Could involve automated/concise descriptions, interactions, etc.
 +
* Could establish useful pipelines that could be reused in other contexts

Revision as of 21:01, 13 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.
  • 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


August 13, 2020

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

  • When is it happening? Not sure; not on release schedule right now

SOLR server security (IMSS)

  • IMSS network security blocked network on our server due to its open SOLR web access.
  • 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

  • Supplement grant awarded to Alliance for an Alzheimer's disease portal
  • Could involve automated/concise descriptions, interactions, etc.
  • Could establish useful pipelines that could be reused in other contexts