HOBOrganismTaxonomy
type: Library
node role: treeRoot
id:
  v: HOBOrganismTaxonomy
text:
  status:
    v: extensions
  div:
    v: Metadata Title HOB Organism Taxonomy Logic Version 2026.1.0 Status Draft Experimental true Topic FHIR Topic CQL Description DRAFT Data elements used to determine organism taxonomy as part of the calculation of Hospital-onset Bacteremia and Fungemia measures. Type logic-library from http://terminology.hl7.org/CodeSystem/library-type Parameter Name: OrganismTaxonomy Use: Out Min Cardinality: 0 Max Cardinality: * Type: Resource Library Content CQL Content library HOBOrganismTaxonomy // TODO: Need to construct more concise tables here define "OrganismTaxonomy": { { "snomed_preferred_term": '(Cholera) or (Vibrio cholerae)', "snomed_concept_id": '186087007', "roll_up_genus_level": '1', "roll_up_genus_name": 'Vibrio', "roll_up_genus_conceptid": '34872001', "roll_up_species_level": '1', "roll_up_species_name": 'Vibrio cholerae', "roll_up_species_conceptid": '75953000', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '0' } } define fluent function species(organism Concept): OrganismTaxonomy T where exists (organism.codes C where C.system = 'http://snomed.info/sct' and C.code = T.snomed_concept_id) return T.roll_up_species_conceptid define fluent function genus(organism Concept): OrganismTaxonomy T where exists (organism.codes C where C.system = 'http://snomed.info/sct' and C.code = T.snomed_concept_id) return T.roll_up_genus_conceptid define fluent function organismMatches(organismA Concept, organismB Concept): organismA ~ organismB or organismA.species() = organismB.species() or ( organismA.species() is null and organismB.species() is null and organismA.genus() = organismB.genus() ) ELM XML Content Encoded data (42380 characters) ELM JSON Content Encoded data (78744 characters) Generated using version 0.5.0 of the sample-content-ig Liquid templates
extension:
  url:
    v: http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm
  value: integer
    v: 1
extension:
  url:
    v: http://hl7.org/fhir/StructureDefinition/structuredefinition-wg
  value: code
    v: cds
extension:
  url:
    v: http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status
  value: code
    v: informative
url:
  v: https://madie.cms.gov/Library/HOBOrganismTaxonomy
version:
  v: 2026.1.0
name:
  v: HOBOrganismTaxonomy
title:
  v: HOB Organism Taxonomy Logic
status:
  v: draft
experimental:
  v: true
type:
  coding:
    system:
      v: http://terminology.hl7.org/CodeSystem/library-type
    code:
      v: logic-library
date:
  v: 2026-06-16T17:19:32+00:00
description:
  v: DRAFT Data elements used to determine organism taxonomy as part of the calculation of Hospital-onset Bacteremia and Fungemia measures.
topic:
  text:
    v: FHIR
topic:
  text:
    v: CQL
parameter:
  name:
    v: OrganismTaxonomy
  use:
    v: out
  min:
    v: 0
  max:
    v: *
  type:
    v: Resource
content:
  content type:
    v: text/cql
content:
  content type:
    v: application/elm+xml
content:
  content type:
    v: application/elm+json