Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
= 2018 Meetings =
 
  
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
 
  
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
+
= 2020 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
 +
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
== May 3, 2018 ==
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
=== SimpleMine output ===
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
* Wen was working on simplification of SimpleMine output
 
* Considering removing general terms in an ontology when more specific terms exist
 
* Concern that we would be removing information; will keep terms
 
  
=== SPELL topics ===
+
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
* Topics in SPELL need some organization, possibly trimming
 
* We could create a graph (SObA) display of topics (based on GO process)
 
  
=== SPELL problem with WS265 ===
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
* Wen had to debug; SPELL has limit of how many genes can be processed per data set (46,340)
 
* Wen trying to accommodate, deleting some genes from data set that had no expression (kludge)
 
* Wen will write to Matt Hibbs to ask how to deal with
 
* Will Alliance work together on a system to analyze large scale expression data?
 
  
=== Curator candidate ===
 
* Will arrive at 10am
 
* Skype calls with remote curators
 
* Curators will send group Skype handle and requested time to talk
 
  
== May 10, 2018 ==
+
==August 6th, 2020==
  
=== ECO terms for genome editing ===
+
===Experimental conditions data flow into Alliance===
* Asking group's feedback on ECO terms for genome editing
+
*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

Latest 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