Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
 
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
 +
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
== June 4, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
=== Citace (tentative) upload ===
 
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
 
* Citace upload to Hinxton on Friday, July 10th
 
  
=== Caltech reopening ===
+
==August 6th, 2020==
* Paul looking to get plan approved
 
* People that want to come to campus need to watch training video
 
* Masks available in Paul's lab
 
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
 
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
 
* Need to coordinate, maybe make a Google calendar to do so (also Slack)
 
* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
 
* Also, need to submit who you were in contact with for contact tracing
 
* Form is used all week, and hold on to it until asked to be submitted
 
* If someone goes in to the office, they could print several forms for people to pick up in WB offices
 
  
=== Nameserver ===
+
===Experimental conditions data flow into Alliance===
* Nameserver was down
+
*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)
* CIT curators would still like to have a single form to interact with
+
*We use the WB Molecule CV for Inducers and Modifiers in disease annotation
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
+
*Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
* Still putting genotype and all info for a strain in the reason/why field in the nameserver
+
*So for data flow into Alliance:
* We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
+
**In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
* Hinxton is pulling in CGC strains, how often?
+
**Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.
* Caltech could possibly get a block of IDs
+
* 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
  
=== Alliance SimpleMine ===
 
* Any updates? 3.1 feature freeze is tomorrow
 
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
 
  
 +
== August 13, 2020 ==
  
== June 11, 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?
  
=== Name Service ===
+
=== WS279 Citace upload ===
* Testing site now up; linked to Mangolassi
+
* When is it happening? Not sure; not on release schedule right now
* CGI from Juancarlos not accepting all characters, including double quotes like "
 
* Example submission that fails via CGI
 
WBPaper000XXXX; genotype: blah::' " ` / < > [ ] { } ? , . ( ) * ^ & % $ # @ ! \ | &alpha; &beta; Ω ≈ µ ≤ ≥ ÷ æ … ˚ ∆ ∂ ß œ ∑ † ¥ ¨ ü i î ø π “  ‘ « • – ≠ Å ´ ∏ » ± — ‚ °
 
* Juancarlos will look into and try to fix
 
  
=== Alliance Literature group ===
+
=== SOLR server security (IMSS) ===
* Textpresso vs. OntoMate vs. PubMed
+
* IMSS network security blocked network on our server due to its open SOLR web access.
* Still some confusion about what the different tasks can be performed in each tool
+
* Part of AMIGO stack, very old version, drives our ontology browser directly, SObA, Enrichment tools indirectly.
* Working on collecting different use cases on spreadsheet
+
* Added some firewall/URL filter and IMSS opens up the network (for now). IMSS still gripes about its service is open to the world.
* Sentence-based search is big strength of Textpresso
 
* At latest meeting performed some large searches for OntoMate and Textpresso
 
* Literature acquisition: still needs work
 
** Using SVM vs. Textpresso search to find relevant papers
 
** Species based SVM? Currently use string matching to derive different corpora
 
** Finding genes and determining which species those genes belong to?
 
  
=== Alliance priorities? ===
+
=== Alzheimer's disease portal ===
* Transcription regulatory networks
+
* Supplement grant awarded to Alliance for an Alzheimer's disease portal
* Interactions can focus on network viewer eventually
+
* Could involve automated/concise descriptions, interactions, etc.
** May want different versions/flavors of interaction viewers
+
* Could establish useful pipelines that could be reused in other contexts
** May also want to work closely with GO and GO-CAMs
 
* Gene descriptions can focus on information poor genes, protein domains, etc.
 
 
 
=== Sandbox visual cues ===
 
* Juancarlos and Daniela will discuss ways to provide visual cues that a curator is on a sandbox form (on Mangolassi) vs live form (on Tazendra)
 
* AFP and Micropub dev sites have indicators
 
* Could play with changing the background color? Maybe too hard to look at?
 
* Change the color of the title of the form, e.g. the OA?
 
* Will add red text "Development Site" at top of the OA form
 
 
 
=== Evidence Code Ontology ===
 
* Kimberly and Juancarlos have worked on a parser
 
* Will load into ACEDB soon
 
 
 
 
 
== June 18, 2020 ==
 
 
 
=== Undergrad phenotype submissions ===
 
* Chris gave presentation to Lina Dahlberg's class about community phenotype curation
 
* Class took survey about experience with presentation and experience trying to curate worm phenotypes
 
** Survey results: https://www.dropbox.com/s/00cit5aitv8yu27/Dahlberg_class_survey_results.xlsx?dl=0
 
** Some students didn't benefit, but most did; nice feedback!
 
** Lina intends to publish/micropublish the survey results so please don't share
 
 
 
=== Special characters in OA/Postgres ===
 
* There are many special characters in free text entries in the OA; probably all from copy-pasting directly from PDF
 
* In some cases it seems the special characters cause problems for downstream scripts (e.g. FTP interactions file generator)
 
* It would probably be good to script the replacement of special characters with their appropriate simple characters or encoded characters
 

Latest revision as of 21:01, 13 August 2020

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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