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_May_2020|May]]
  
== June 6, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
=== New SObA graphs ===
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
* May put graphs within existing widgets, but don't need to rush to get that ready for IWM
 
  
=== Phenotype association file format ===
 
* May be best to leave the format as is
 
* There are problems; paper IDs keep switching columns
 
* Would need to revisit the reasoning for why we do it that way
 
* When will the Alliance produce a similar/replacement file? Not sure
 
  
=== Phenotype requests ===
+
==August 6th, 2020==
* Sent out 1140 emails on May 30
 
* Since have received 374 annotations from 54 papers (42 requested, 12 additional)
 
* 21 papers flagged as not having phenotypes
 
* Of 1140 papers emailed about, 35 emails bounced, and have received some flagging or curation on 63 (63/1105 = ~6% response rate), in first week
 
  
 +
===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
  
== June 13, 2019 ==
 
  
=== IWM ===
+
== August 13, 2020 ==
* Coordinating transportation of swag boxes to Pauley Pavilion
 
* Workshop on Saturday June 22, from 1pm to 2:30pm
 
* Saturday morning micropublication breakfast 7:30 - 8:30am
 
* Workshop
 
** Presenters: it may be best to present as use cases rather than a research project
 
** Chris will cover SimpleMine for Wen
 
** Chris: won't do live demo; only screenshots, maybe some video
 
* Paul's lab will do marathon bibs to show lab affiliation and graphical abstract
 
* Paul's talk
 
** Cover Alliance
 
** New features
 
*** SObA (for new data)
 
*** Complete for protein-protein interactions
 
*** RNASeq tools
 
*** Updated automated gene concise descriptions?
 
** Phenotype community curation
 
*** Chris will send Paul numbers on: top community curators, overall stats (number of annotations, papers, curators)
 
** Author First Pass
 
** Micropublication
 
  
=== SGD SAB ===
+
=== Species in Postgres and ACEDB/Datomic ===
* Paul attended
+
* Want to dump "Affected By Pathogen" fields in Phenotype OA and RNAi OA
* Alliance publicity was discussed
+
* Want to be sure that what gets dumped aligns with species loaded into ACEDB
* SAB likes the Alliance orthology features
+
* Currently one species annotated not in WS277: Streptococcus gallolyticus subsp. gallolyticus
* Working on topics: displaying papers and data
+
* We currently have multiple Postgres tables for storing species lists:
* Pathways: discussion about best approach
+
** pap_species_index (used by "Affected By Pathogen" fields, AFP); Kimberly uses to assign species to papers and occasionally adds new ones
* Metabolic engineering
+
** obo_name_ncbitaxonid
* Meta data about RNASeq data
+
** obo_name_taxon (original, smaller list)
** SPELL tool, basically only tool of its kind available; need new tools
+
** h_pap_species_index (history for pap_species_index)
* Species-specific proteins: how best to find them? HMMs (Jackhammer)?
+
* 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
  
=== Concise descriptions ===
+
=== WS279 Citace upload ===
* Progress being made within the Alliance to update the automated concise gene descriptions
+
* When is it happening? Not sure; not on release schedule right now
* We will still accept manually written descriptions and display them in parallel with automated descriptions
 
  
=== Micropublications ===
+
=== SOLR server security (IMSS) ===
* If people are requesting manually written gene descriptions, they could submit a microreview
+
* IMSS network security blocked network on our server due to its open SOLR web access.
* Concern was expressed about how to handle a really high throughput of submissions:
+
* Part of AMIGO stack, very old version, drives our ontology browser directly, SObA, Enrichment tools indirectly.
** Daniela: Working towards automating as much of the processing pipeline as possible
+
* Added some firewall/URL filter and IMSS opens up the network (for now). IMSS still gripes about its service is open to the world.
** Raymond: The throughput will be handled appropriately depending on demand; priority scheme will help
+
 
** Not getting lots of submissions yet, probably won't be inundated in the near future
+
=== Alzheimer's disease portal ===
** Karen: tools are still being developed; the platform is not being advertised as much as it could be; will ramp up outreach and communication once tools are in place to handle more submissions
+
* Supplement grant awarded to Alliance for an Alzheimer's disease portal
* Karen: Micropublications team will reach out to curators to help build submission forms for respective data types
+
* 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