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HIPC Dashboard pipeline v1.3.0
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@kcs3 kcs3 released this 09 Feb 17:11
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v1.3.0
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HIPC Dashboard Pipeline

Changes in version 1.3.0

  • Support new exposure type: infection (COVID-19 studies)
  • For subject type "cell_subset", use cell ontology ids instead of display names.
    This concerns tissue types (column tissue_type_term_id) and cell-type response components (column response_component_id)
  • For subject type "pathogen", use NCBI taxonomy ids instead of display names
    (columns target_pathogen_taxonid for vaccine, exposure_material_id for infection).
  • For tissue types, support parsing out cell ontology IDs from curator-oriented data validation pulldown values added to templates:
    -- The pulldown value is shown first. Just the term is also permitted:
    CL:0000624 (CD4-positive, alpha-beta T cell)
    CL:0000624
  • For target pathogens in the vaccine templates, support parsing out NCBI taxonomy IDs
    from curator-oriented data validation pulldown values added to templates:
    -- The pulldown value is shown first. The other values are also accepted:
    “ncbi_taxid:11090 (Yellow fever virus 17D)”
    “ncbi_taxid:11090”
    “11090” (defaults to NCBI taxonomy id)
  • In the target_pathogen_taxonid column of vaccine templates, for influenza vaccine entries,
    allow use of lookup tags for taxonomy ids. The tags will be replaced by the actual viral
    components of the vaccine, looked up in the file "vaccine_years.txt. Multiple entries are allowed.
    -- For example
    “influ:2008” will be substituted with the several actual viral components of the vaccine for year 2008.
    “influ:2007; influ:2008; influ:2009” will be substituted with the union of the three year's viral components.
  • Add ability to return vaccine pathogen component NCBI taxonomy ids to lookup function.
  • Gene lookup using the NCBI data file now also checks the nomenclature_authority column (HGNC).
    If a query symbol is not found in the official NCBI symbols or aliases,
    but IS found in the nomenclature_authority column, the NCBI official symbol is substituted.

HIPC data/curation sheet-related changes

Changes in version 1.3.0

  • Add two infection (COVID-19) studies:
    -- Odak et al., 2020
    -- Arunachalam et al., 2020
  • Create pathogen and cell_subset lookup-values for curation sheets. Format is e.g.
    -- “ncbi_taxid:11090 (Yellow fever virus 17D)”
    -- "CL:2000001 (peripheral blood mononuclear cell)"
  • The following formats are also accepted
    -- “ncbi_taxid:11090”
    -- "CL:2000001"
    -- “11090” (tissues only, defaults to NCBI taxonomy id)
  • Add cell ontology and NCBI taxonomy IDs to existing data as needed.
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