WormBase-Caltech Weekly Calls

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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