Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
  
  
= 2019 Meetings =
 
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
+
= 2020 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
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[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
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[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
  
== September 12, 2019 ==
+
==August 6th, 2020==
  
=== Update on SVM pipeline ===
+
===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
  
=== Clarifying definitions of "defective" and "deficient" for phenotypes ===
+
 
* WB phenotype ontology has many "variant/abnormal" terms and distinct subclass terms for "defective/deficient"
+
== August 13, 2020 ==
* Have tried to create a logical definition pattern for these terms, but the vagueness of the meaning of "defective" and how it is distinct from "abnormal" has stalled the process
+
 
* What do we mean exactly by "defective" and how, specifically, is this distinct from "abnormal"?
+
=== Species in Postgres and ACEDB/Datomic ===
* Definitions include meanings or words:
+
* Want to dump "Affected By Pathogen" fields in Phenotype OA and RNAi OA
** "aberrant"
+
* Want to be sure that what gets dumped aligns with species loaded into ACEDB
** "defective"
+
* Currently one species annotated not in WS277: Streptococcus gallolyticus subsp. gallolyticus
** "defect"
+
* We currently have multiple Postgres tables for storing species lists:
** "defects"
+
** pap_species_index (used by "Affected By Pathogen" fields, AFP); Kimberly uses to assign species to papers and occasionally adds new ones
** "deficiency"
+
** obo_name_ncbitaxonid
** "disrupted"
+
** obo_name_taxon (original, smaller list)
** "ineffective"
+
** h_pap_species_index (history for pap_species_index)
** "perturbation that disrupts"
+
* How do species get loaded into ACEDB? Dumps from Postgres? Which table(s)?
** "variations in the ability"
+
* WS277 has 7,906 species (1,936 have no NCBI Taxon ID)
** failure to execute the characteristic response = abnormal?
+
* Kimberly used to upload a species.ace file; now Hinxton handles it; should ask them
** abnormal
+
 
** abnormality leading to specific outcomes
+
=== WS279 Citace upload ===
** fail to exhibit the same taxis behavior = abnormal?
+
* When is it happening? Not sure; not on release schedule right now
** failure
+
 
** failure OR delayed
+
=== SOLR server security (IMSS) ===
** failure/abnormal
+
* 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 19:09, 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 used to upload a species.ace file; now Hinxton handles it; should ask them

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