Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
m
Line 1: Line 1:
 +
= Previous Years =
 +
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
  
==2011 Meetings==
+
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
 
 
[[WormBase-Caltech_Weekly_Calls_February_2011|February]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_March_2011|March]]
 
 
 
 
 
 
 
==April 7, 2011==
 
 
 
 
 
Transgene Model
 
*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)
 
 
 
 
 
Interactions
 
*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
 
 
 
 
 
BioGRID meeting at Princeton in May
 
*Call in
 
*What will Rose propose?
 
 
 
 
 
Expression Pattern Curation (Daniela/Wen)
 
*Daniela sent out picture page for review
 
*Expr Pattern OA wiki is in place:
 
**http://wiki.wormbase.org/index.php/Expression_Pattern
 
*As soon as Juancarlos is done with the modularization will start working on the code.
 
*In the meanwhile Daniela will curate expression pattern writing .ace files
 
*Expr_pattern OA should be ready by the next upload (May26th). (I really doubt this, parsing in data, writing dumpers, and checking it take a long time.  Picture and Interaction each probably took longer than 2 months, and we're not starting Expr until May at the earliest -- Juancarlos)
 
 
 
 
 
Patch file/Interbuild (Raymond)
 
*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
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
  
Uma started
+
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
*Working on concise descriptions of gene classes
 
*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? (probably write a whole new interface depending on goal -- Juancarlos)
 
*Gene class name and a text field
 
*Using Textpresso/WormMart output; sentence saver?
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
eggNOG data into citace?
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
*Who's going to handle the data? curate?
 
*Michael? OK
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
==April 14, 2011==
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
Gene Class Descriptions
 
*Concerns about maintenance and redundancy
 
*Uma here for ~ 3 months
 
*How many gene classes have alleles?
 
*How many are named by phenotype rather than just molecular data?
 
*How is this different from gene concise descriptions?
 
*Should it be a summary of all gene concise descriptions of the class?
 
*Things currently focused on:
 
**using WormMart to look at genes in a class
 
**pulls out all concise descriptions
 
**look at similarities
 
**interesting things to highlight
 
*Gene concise descriptions vs class descriptions
 
**Gene-centric vs Class-centric
 
**Consolidating/pooling all concise descriptions from individual genes?
 
*Going for maintenance-free statements
 
*Potentially building an interface
 
*Richard Durbin: development vs behavior?
 
*Prioritization?
 
*Focus on phenotype-based classes like UNC?
 
*Factors for prioritization:
 
**Numbers of genes curated
 
**molecular vs phenotype-based
 
**Amount of info currently available?
 
**Historical points
 
**Most actively worked currently? (most mentioned in last year's publications?)
 
*Uma and Karen could communicate with Kimberly and Ranjana about
 
*What is most efficient for Uma to focus on?
 
*Uma can look at gene class description makes sense
 
*Skip gene classes for which only one gene exists
 
*GO term stats on each class?
 
  
  
Papers missing from Textpresso
 
*Issue: Genetics papers for GSA markup are missing from SVM analysis
 
*Juancarlos' file on caprica
 
*Discrepancy between papers on Textpresso and those gone through SVM
 
*SVM doesn't pick up GSA papers
 
*Generate a filtering to detect which ones have been missed by SVM
 
*Michael looking into reasons why the pipeline isn't working
 
*Tazendra vs Textpresso discrepancies?
 
*Ruihua will process 56 missing papers retroactively
 
*Still working on how to avoid this in the future
 
  
 +
= 2020 Meetings =
  
 +
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
==April 21, 2011==
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
 +
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
WormMart
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
*Stable for IWM?
 
*WormMart presentation for WormBase workshop
 
**Query examples
 
**Data content
 
**Features
 
**Plans for the next year; what data to be made available
 
**Discuss stability?
 
  
 +
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
Igor's machine: elbrus
+
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
*Can have problems
 
*Input info has changed for WS225
 
*RNAi script stopped working
 
*Migration issues
 
**Decide on priorities
 
**Who will maintain what?
 
**Migrate things over to newer machines, locally
 
*On elbrus now:
 
**RNAi scripts (sequence mapping); Migrating to EBI
 
**Anatomy ontology browser (optional)
 
**Microarray tool (Wen will take over)
 
**Get-Sequence CGI (how many people use it?)
 
*Meet with Norie at IWM?
 
*We should write everything down first
 
  
 +
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
BioGRID-WormBase data exchange:
 
*Questions about how to best do this
 
*How to handle/organize genetic interactions
 
*BioGRID meeting in May; will not be sufficient to solve the genetic interaction issues
 
*Chris still working on genetic interaction organization scheme
 
  
 +
==August 6th, 2020==
  
SPELL/Microarray
+
===Experimental conditions data flow into Alliance===
*Discuss at IWM?
+
*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)
*Patching changes into WS225
+
*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
  
  
ModENCODE Meeting
+
== August 13, 2020 ==
*Gary Williams should go
 
  
 +
=== 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?
  
Picture Page
+
=== WS279 Citace upload ===
*New developments
+
* When is it happening? Not sure; not on release schedule right now
*Elsevier publishing; how to handle them? ($17.5 per figure!!!)
 
  
 +
=== 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.
  
Informatics Resources Assessment
+
=== Alzheimer's disease portal ===
*Can we develop plan to determine informatics resources available
+
* Supplement grant awarded to Alliance for an Alzheimer's disease portal
*Long-term plans for sustainable informatics resources
+
* 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