Difference between revisions of "WormBase-Caltech Weekly Calls"

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==June 11, 2009==
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= Previous Years =
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*Discussion of allele-paper connections
 
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**Jolene has a Textpresso-based pipeline for identifying alleles in papers
 
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**Alleles get associated with a paper if there is phenotypic or molecular data
 
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**List of all alleles associated with a paper could possibly be passed on to Sanger for subsequent connection
 
  
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*Discussion of gene-paper connections
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[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
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**What criteria should be used for associating genes with papers?
 
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**Currently being associated manually by a curator during first-pass
 
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**Could Textpresso be harnessed for this task?
 
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**There are different evidences attached to gene-paper connections
 
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**Genes associated with a paper via Textpresso searches could be presented to the first-pass curator for approval in the first-pass form
 
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**Need to fix current abstract-gene associating script to include proteins (e.g. PIE-1)
 
  
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*Incorporate a customized Textpresso query on WormBase object pages so users could look for additional info if they want
+
[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
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**Data type curator could help design a useful query
 
  
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*Other gene-object connections
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[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
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**Develop a canned query for all objects that should be associated with the gene page
 
  
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*Worm Meeting
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[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
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**Pre-meeting - meeting rooms?
 
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**Pre-meeting - practice talks for WormBase workshop
 
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**Storage for swag - pavillion should be okay
 
  
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==June 18, 2009==
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[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
  
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*Worm Meeting and Pre-Meeting
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[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
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**WormBase Help Desk Schedule - set for worm meeting
 
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**Wen may need help carrying boxes of swag
 
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**Do any Sanger or WashU people need rides to UCLA?
 
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**Mary Alvarez is working on finding rooms for the pre-meeting
 
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**Be prepared to report on curation status of your data type and what we might need
 
  
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*Author contact information on first-pass form
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[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
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**email goes to the first email address found by Textpresso
 
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**Raymond - we do care where this data comes from
 
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**Erich - can we send it to the designated corresponding author
 
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**first-pass curation could capture the corresponding author
 
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**if the email didn't go to the corresponding author, it may affect our response rate
 
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**two-stage approach proposal
 
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***respond to Bernard - we'll try to find corresponding author in the future and add his name to the comments field for now
 
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***going forward, how best to determine corresponding author?
 
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***keep track of IP address from which the data was sent?
 
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***add text to email saying that authors may include their contact information in the comments box, if they wish
 
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***Raymond will proof-read papers to check on corresponding author designation and email addresses
 
  
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*Zfin visit - PATO progress, worth looking at
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[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
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**Erich noted no genome browser - what is the issue?
 
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**Their experience with getting figures from journals might be helpful.
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
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==February 10, 2011==
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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
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*Should we have a Caltech project/site manager? We'll look at the issues to be solved first
 
  
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*Todd would like to know more about what's going on at Caltech
 
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**What would Todd like to know about? New ideas, data types?
 
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**What can we communicate more effectively to Todd?
 
  
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*Should we take minutes of Caltech WormBase group meetings and send around?
 
  
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*Kimberly: helpful (for off site individuals) if we go around the room to talk about what each of us is working on
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= 2020 Meetings =
  
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*Bitbucket use
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[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
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**How do we see only what pertains to us, individually?
 
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**Paul: good way to document bugs and fixes, problems/solutions
 
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**Bitbucket Wiki - does that capture what people want/need to see?
 
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**Who should Todd follow? What would Todd like to know about?
 
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**Raymond: used for code development/versioning by OICR; may be the best use for Bitbucket
 
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**Should we develop best practices guideline for Bitbucket use?
 
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***Avoid posting topics that are too specific or too vague?
 
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***What do we want most to get out of Bitbucket?
 
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**Curation efforts? No
 
  
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*SAB Meeting
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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
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**Not much feedback for literature curators
 
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**User interface stuff took precedence
 
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**Paul: Testing, spot-checking website for errors
 
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**Web issues, e-mails from Gary and Oliver
 
  
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*WormBase-wide conference call twice per month
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
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**First & third Thursday of the month
 
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**Starting next Thursday (2-17) @ 8:30am PST
 
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**Web redesign meetings on Thursdays will have to be every other week? Do both same day?
 
  
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*Raymond: WormBase mirrors
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
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**Do we want to implement the Genome Browser for the mirror(s)? If practical
+
 
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**It seems as though Caltech mirror has been crashing often
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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
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**Has the Caltech mirror been working for people lately? Yes, more or less
+
 
 +
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_July_2020|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

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
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