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]]
  
  
==August 6th, 2020==
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== October 14, 2021 ==
  
===Experimental conditions data flow into Alliance===
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=== WormBase HD YouTube channel has ads ===
*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)
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* Is there a way to turn them off? Seems like we cannot remove them entirely
*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
 
  
 
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=== Form headers and footers no longer updating ===
== August 13, 2020 ==
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* WS version number falls out of date; Juancarlos will manually update
 
 
=== 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
 

Latest revision as of 18:27, 14 October 2021

Previous Years

2009 Meetings

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2019 Meetings

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2021 Meetings

January

February

March

April

May

June

July

August

September


October 14, 2021

WormBase HD YouTube channel has ads

  • Is there a way to turn them off? Seems like we cannot remove them entirely

Form headers and footers no longer updating

  • WS version number falls out of date; Juancarlos will manually update