{
  "resourceType" : "CodeSystem",
  "id" : "hob-organism-taxonomy",
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: CodeSystem hob-organism-taxonomy</b></p><a name=\"hob-organism-taxonomy\"> </a><a name=\"hchob-organism-taxonomy\"> </a><p><b>Properties</b></p><p><b>This code system defines the following properties for its concepts</b></p><table class=\"grid\"><tr><td><b>Name</b></td><td><b>Code</b></td><td><b>Type</b></td><td><b>Description</b></td></tr><tr><td>roll-up-genus</td><td>roll-up-genus</td><td>Coding</td><td>Genus-level SNOMED CT concept this organism rolls up to (roll_up_genus_conceptid / roll_up_genus_name).</td></tr><tr><td>roll-up-species</td><td>roll-up-species</td><td>Coding</td><td>Species-level SNOMED CT concept this organism rolls up to (roll_up_species_conceptid / roll_up_species_name). Absent for genus-level or higher concepts.</td></tr><tr><td>nhsn-community-associated</td><td>nhsn-community-associated</td><td>boolean</td><td>NHSN classification: organism is community-associated (source nhsn_community_associated, 1=true).</td></tr><tr><td>nhsn-skin-commensal</td><td>nhsn-skin-commensal</td><td>boolean</td><td>NHSN classification: organism is a common skin commensal (source nhsn_skin_commensal, 1=true).</td></tr><tr><td>snomed-status</td><td>snomed-status</td><td>code</td><td>SNOMED status flag as recorded in the source taxonomy ('0'/'1'). Exact semantics to be confirmed (likely active=1).</td></tr></table><p><b>Concepts</b></p><p>This code system supplement <code>https://example.org/fhir/CodeSystem/hob-organism-taxonomy</code> defines properties on the following codes:</p><table class=\"codes\"><tr><td style=\"white-space:nowrap\"><b>Code</b></td><td><b>Display</b></td><td><b>roll-up-genus</b></td><td><b>roll-up-species</b></td><td><b>nhsn-community-associated</b></td><td><b>nhsn-skin-commensal</b></td><td><b>snomed-status</b></td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/186087007\">186087007</a><a name=\"hob-organism-taxonomy-186087007\"> </a></td><td>(Cholera) or (Vibrio cholerae)</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 34872001}\">Vibrio</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 75953000}\">Vibrio cholerae</a></td><td>false</td><td>false</td><td>0</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/266186009\">266186009</a><a name=\"hob-organism-taxonomy-266186009\"> </a></td><td>(Legionella) or (Legionnaire's disease)</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 7527002}\">Legionella</a></td><td/><td>false</td><td>false</td><td>0</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/154315008\">154315008</a><a name=\"hob-organism-taxonomy-154315008\"> </a></td><td>(Legionella) or (Legionnaire's disease)</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 7527002}\">Legionella</a></td><td/><td>false</td><td>false</td><td>0</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/186103005\">186103005</a><a name=\"hob-organism-taxonomy-186103005\"> </a></td><td>(Shigella dysenteriae - group A) or (bacillary dysentery)</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 77352002}\">Shigella</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 43612004}\">Shigella dysenteriae</a></td><td>false</td><td>false</td><td>0</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/186350009\">186350009</a><a name=\"hob-organism-taxonomy-186350009\"> </a></td><td>(Whooping cough) or (Bordetella)</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 46466005}\">Bordetella</a></td><td/><td>false</td><td>false</td><td>0</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/115161005\">115161005</a><a name=\"hob-organism-taxonomy-115161005\"> </a></td><td>Abiotrophia</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 115161005}\">Abiotrophia</a></td><td/><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/113714003\">113714003</a><a name=\"hob-organism-taxonomy-113714003\"> </a></td><td>Abiotrophia defectiva</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 115161005}\">Abiotrophia</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 113714003}\">Abiotrophia defectiva</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/409815006\">409815006</a><a name=\"hob-organism-taxonomy-409815006\"> </a></td><td>Abiotrophia para-adiacens</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 115161005}\">Abiotrophia</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 409815006}\">Abiotrophia para-adiacens</a></td><td>false</td><td>false</td><td>0</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/372391001\">372391001</a><a name=\"hob-organism-taxonomy-372391001\"> </a></td><td>Abiotrophia species</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 115161005}\">Abiotrophia</a></td><td/><td>false</td><td>false</td><td>0</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/736080001\">736080001</a><a name=\"hob-organism-taxonomy-736080001\"> </a></td><td>Abortiporus</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 736080001}\">Abortiporus</a></td><td/><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/736079004\">736079004</a><a name=\"hob-organism-taxonomy-736079004\"> </a></td><td>Abortiporus biennis</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 736080001}\">Abortiporus</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 736079004}\">Abortiporus biennis</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/57145009\">57145009</a><a name=\"hob-organism-taxonomy-57145009\"> </a></td><td>Absidia</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 57145009}\">Absidia</a></td><td/><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/2591000146102\">2591000146102</a><a name=\"hob-organism-taxonomy-2591000146102\"> </a></td><td>Absidia caerulea</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 57145009}\">Absidia</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 2591000146102}\">Absidia caerulea</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/243420008\">243420008</a><a name=\"hob-organism-taxonomy-243420008\"> </a></td><td>Absidia corymbifera</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 57145009}\">Absidia</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 243420008}\">Absidia corymbifera</a></td><td>false</td><td>false</td><td>0</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/49931000087108\">49931000087108</a><a name=\"hob-organism-taxonomy-49931000087108\"> </a></td><td>Absidia cylindrospora</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 57145009}\">Absidia</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 49931000087108}\">Absidia cylindrospora</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/785768009\">785768009</a><a name=\"hob-organism-taxonomy-785768009\"> </a></td><td>Absidia glauca</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 57145009}\">Absidia</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 785768009}\">Absidia glauca</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/8296004\">8296004</a><a name=\"hob-organism-taxonomy-8296004\"> </a></td><td>Absidia halospora</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 57145009}\">Absidia</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 8296004}\">Absidia halospora</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/359802007\">359802007</a><a name=\"hob-organism-taxonomy-359802007\"> </a></td><td>Absidia lichtheimii</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 57145009}\">Absidia</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 359802007}\">Absidia lichtheimii</a></td><td>false</td><td>false</td><td>0</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/36013002\">36013002</a><a name=\"hob-organism-taxonomy-36013002\"> </a></td><td>Absidia ramosa</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 57145009}\">Absidia</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 36013002}\">Absidia ramosa</a></td><td>false</td><td>false</td><td>0</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/404226006\">404226006</a><a name=\"hob-organism-taxonomy-404226006\"> </a></td><td>Absidia species</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 57145009}\">Absidia</a></td><td/><td>false</td><td>false</td><td>0</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/541341000124105\">541341000124105</a><a name=\"hob-organism-taxonomy-541341000124105\"> </a></td><td>Abyssicoccus</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 541341000124105}\">Abyssicoccus</a></td><td/><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/541351000124107\">541351000124107</a><a name=\"hob-organism-taxonomy-541351000124107\"> </a></td><td>Abyssicoccus albus</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 541341000124105}\">Abyssicoccus</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 541351000124107}\">Abyssicoccus albus</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/28861000087102\">28861000087102</a><a name=\"hob-organism-taxonomy-28861000087102\"> </a></td><td>Acaromyces</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 28861000087102}\">Acaromyces</a></td><td/><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/28871000087106\">28871000087106</a><a name=\"hob-organism-taxonomy-28871000087106\"> </a></td><td>Acaromyces ingoldii</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 28861000087102}\">Acaromyces</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 28871000087106}\">Acaromyces ingoldii</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/785735002\">785735002</a><a name=\"hob-organism-taxonomy-785735002\"> </a></td><td>Acaulium</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 785735002}\">Acaulium</a></td><td/><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/59520005\">59520005</a><a name=\"hob-organism-taxonomy-59520005\"> </a></td><td>Acaulium acremonium</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 785735002}\">Acaulium</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 59520005}\">Acaulium acremonium</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/423947001\">423947001</a><a name=\"hob-organism-taxonomy-423947001\"> </a></td><td>Acetanaerobacterium</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 423947001}\">Acetanaerobacterium</a></td><td/><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/423867006\">423867006</a><a name=\"hob-organism-taxonomy-423867006\"> </a></td><td>Acetanaerobacterium elongatum</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 423947001}\">Acetanaerobacterium</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 423867006}\">Acetanaerobacterium elongatum</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/424162006\">424162006</a><a name=\"hob-organism-taxonomy-424162006\"> </a></td><td>Acetitomaculum</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 424162006}\">Acetitomaculum</a></td><td/><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/425276005\">425276005</a><a name=\"hob-organism-taxonomy-425276005\"> </a></td><td>Acetitomaculum ruminis</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 424162006}\">Acetitomaculum</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 425276005}\">Acetitomaculum ruminis</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/72806006\">72806006</a><a name=\"hob-organism-taxonomy-72806006\"> </a></td><td>Acetivibrio</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 72806006}\">Acetivibrio</a></td><td/><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/432614007\">432614007</a><a name=\"hob-organism-taxonomy-432614007\"> </a></td><td>Acetivibrio aldrichii</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 72806006}\">Acetivibrio</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 432614007}\">Acetivibrio aldrichii</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/86860008\">86860008</a><a name=\"hob-organism-taxonomy-86860008\"> </a></td><td>Acetivibrio cellulolyticus</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 72806006}\">Acetivibrio</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 86860008}\">Acetivibrio cellulolyticus</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/64755006\">64755006</a><a name=\"hob-organism-taxonomy-64755006\"> </a></td><td>Acetivibrio ethanolgignens</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 72806006}\">Acetivibrio</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 64755006}\">Acetivibrio ethanolgignens</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/131199002\">131199002</a><a name=\"hob-organism-taxonomy-131199002\"> </a></td><td>Acetivibrio species</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 72806006}\">Acetivibrio</a></td><td/><td>false</td><td>false</td><td>0</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/432622000\">432622000</a><a name=\"hob-organism-taxonomy-432622000\"> </a></td><td>Acetivibrio straminisolvens</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 72806006}\">Acetivibrio</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 432622000}\">Acetivibrio straminisolvens</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/68100006\">68100006</a><a name=\"hob-organism-taxonomy-68100006\"> </a></td><td>Acetivibrio thermocellus</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 72806006}\">Acetivibrio</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 68100006}\">Acetivibrio thermocellus</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/423611000\">423611000</a><a name=\"hob-organism-taxonomy-423611000\"> </a></td><td>Acetoanaerobium</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 423611000}\">Acetoanaerobium</a></td><td/><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/422656003\">422656003</a><a name=\"hob-organism-taxonomy-422656003\"> </a></td><td>Acetoanaerobium noterae</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 423611000}\">Acetoanaerobium</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 422656003}\">Acetoanaerobium noterae</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/78437006\">78437006</a><a name=\"hob-organism-taxonomy-78437006\"> </a></td><td>Acetoanaerobium sticklandii</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 423611000}\">Acetoanaerobium</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 78437006}\">Acetoanaerobium sticklandii</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/396949003\">396949003</a><a name=\"hob-organism-taxonomy-396949003\"> </a></td><td>Acetobacter</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td/><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/396950003\">396950003</a><a name=\"hob-organism-taxonomy-396950003\"> </a></td><td>Acetobacter aceti</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396950003}\">Acetobacter aceti</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/413398000\">413398000</a><a name=\"hob-organism-taxonomy-413398000\"> </a></td><td>Acetobacter calcoaceticus</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 413398000}\">Acetobacter calcoaceticus</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/413399008\">413399008</a><a name=\"hob-organism-taxonomy-413399008\"> </a></td><td>Acetobacter cerevisiae</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 413399008}\">Acetobacter cerevisiae</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/413400001\">413400001</a><a name=\"hob-organism-taxonomy-413400001\"> </a></td><td>Acetobacter cibinongensis</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 413400001}\">Acetobacter cibinongensis</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/413401002\">413401002</a><a name=\"hob-organism-taxonomy-413401002\"> </a></td><td>Acetobacter estunensis</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 413401002}\">Acetobacter estunensis</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/116881000181108\">116881000181108</a><a name=\"hob-organism-taxonomy-116881000181108\"> </a></td><td>Acetobacter fabarum</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 116881000181108}\">Acetobacter fabarum</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/23731000181109\">23731000181109</a><a name=\"hob-organism-taxonomy-23731000181109\"> </a></td><td>Acetobacter ghanensis</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 23731000181109}\">Acetobacter ghanensis</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/396953001\">396953001</a><a name=\"hob-organism-taxonomy-396953001\"> </a></td><td>Acetobacter hansenii</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396953001}\">Acetobacter hansenii</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/413402009\">413402009</a><a name=\"hob-organism-taxonomy-413402009\"> </a></td><td>Acetobacter indonesiensis</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 413402009}\">Acetobacter indonesiensis</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/23741000181102\">23741000181102</a><a name=\"hob-organism-taxonomy-23741000181102\"> </a></td><td>Acetobacter lambici</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 23741000181102}\">Acetobacter lambici</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/396951004\">396951004</a><a name=\"hob-organism-taxonomy-396951004\"> </a></td><td>Acetobacter liquefaciens</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396951004}\">Acetobacter liquefaciens</a></td><td>false</td><td>false</td><td>0</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/413403004\">413403004</a><a name=\"hob-organism-taxonomy-413403004\"> </a></td><td>Acetobacter lovaniensis</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 413403004}\">Acetobacter lovaniensis</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/413404005\">413404005</a><a name=\"hob-organism-taxonomy-413404005\"> </a></td><td>Acetobacter malorum</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 413404005}\">Acetobacter malorum</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/23751000181104\">23751000181104</a><a name=\"hob-organism-taxonomy-23751000181104\"> </a></td><td>Acetobacter musti</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 23751000181104}\">Acetobacter musti</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/23761000181101\">23761000181101</a><a name=\"hob-organism-taxonomy-23761000181101\"> </a></td><td>Acetobacter nitrogenifigens</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 23761000181101}\">Acetobacter nitrogenifigens</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/23771000181106\">23771000181106</a><a name=\"hob-organism-taxonomy-23771000181106\"> </a></td><td>Acetobacter oeni</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 23771000181106}\">Acetobacter oeni</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/413405006\">413405006</a><a name=\"hob-organism-taxonomy-413405006\"> </a></td><td>Acetobacter orientalis</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 413405006}\">Acetobacter orientalis</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/413406007\">413406007</a><a name=\"hob-organism-taxonomy-413406007\"> </a></td><td>Acetobacter orleanensis</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 413406007}\">Acetobacter orleanensis</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/396952006\">396952006</a><a name=\"hob-organism-taxonomy-396952006\"> </a></td><td>Acetobacter pasteurianus</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396952006}\">Acetobacter pasteurianus</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/413407003\">413407003</a><a name=\"hob-organism-taxonomy-413407003\"> </a></td><td>Acetobacter peroxydans</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 413407003}\">Acetobacter peroxydans</a></td><td>false</td><td>false</td><td>0</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/708522006\">708522006</a><a name=\"hob-organism-taxonomy-708522006\"> </a></td><td>Acetobacter persici</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 708522006}\">Acetobacter persici</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/413408008\">413408008</a><a name=\"hob-organism-taxonomy-413408008\"> </a></td><td>Acetobacter polyoxogenes</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 413408008}\">Acetobacter polyoxogenes</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/413409000\">413409000</a><a name=\"hob-organism-taxonomy-413409000\"> </a></td><td>Acetobacter pomorum</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 413409000}\">Acetobacter pomorum</a></td><td>false</td><td>false</td><td>1</td></tr><tr><td><a style=\"white-space:nowrap\" href=\"http://snomed.info/id/413410005\">413410005</a><a name=\"hob-organism-taxonomy-413410005\"> </a></td><td>Acetobacter species</td><td><a href=\"http://hl7.org/fhir/R4/codesystem-snomedct.html\" title=\"{http://snomed.info/sct 396949003}\">Acetobacter</a></td><td/><td>false</td><td>false</td><td>0</td></tr></table></div>"
  },
  "url" : "https://example.org/fhir/CodeSystem/hob-organism-taxonomy",
  "version" : "0.1.0",
  "name" : "HOBOrganismTaxonomy",
  "title" : "HOB Organism Taxonomy - SNOMED CT Supplement",
  "status" : "draft",
  "experimental" : true,
  "date" : "2026-07-30T20:17:17+00:00",
  "publisher" : "CQF (local starter)",
  "description" : "SNOMED CT code system supplement carrying the NHSN HOB organism-taxonomy rollup and classification properties. Generated from the OrganismTaxonomy expression in the HOBOrganismTaxonomy CQL library (the source is a work-in-progress alphabetical fragment, so this supplement is incomplete). The source columns roll_up_genus_level / roll_up_species_level are omitted because they are fully implied by the presence of the roll-up-genus / roll-up-species properties, and the always-null 'L' column is omitted. Genus/species preferred terms are carried as the display of each Coding-valued property.",
  "content" : "supplement",
  "supplements" : "http://snomed.info/sct",
  "count" : 65,
  "property" : [{
    "code" : "roll-up-genus",
    "description" : "Genus-level SNOMED CT concept this organism rolls up to (roll_up_genus_conceptid / roll_up_genus_name).",
    "type" : "Coding"
  },
  {
    "code" : "roll-up-species",
    "description" : "Species-level SNOMED CT concept this organism rolls up to (roll_up_species_conceptid / roll_up_species_name). Absent for genus-level or higher concepts.",
    "type" : "Coding"
  },
  {
    "code" : "nhsn-community-associated",
    "description" : "NHSN classification: organism is community-associated (source nhsn_community_associated, 1=true).",
    "type" : "boolean"
  },
  {
    "code" : "nhsn-skin-commensal",
    "description" : "NHSN classification: organism is a common skin commensal (source nhsn_skin_commensal, 1=true).",
    "type" : "boolean"
  },
  {
    "code" : "snomed-status",
    "description" : "SNOMED status flag as recorded in the source taxonomy ('0'/'1'). Exact semantics to be confirmed (likely active=1).",
    "type" : "code"
  }],
  "concept" : [{
    "code" : "186087007",
    "display" : "(Cholera) or (Vibrio cholerae)",
    "property" : [{
      "code" : "roll-up-genus",
      "valueCoding" : {
        "system" : "http://snomed.info/sct",
        "code" : "34872001",
        "display" : "Vibrio"
      }
    },
    {
      "code" : "roll-up-species",
      "valueCoding" : {
        "system" : "http://snomed.info/sct",
        "code" : "75953000",
        "display" : "Vibrio cholerae"
      }
    },
    {
      "code" : "nhsn-community-associated",
      "valueBoolean" : false
    },
    {
      "code" : "nhsn-skin-commensal",
      "valueBoolean" : false
    },
    {
      "code" : "snomed-status",
      "valueCode" : "0"
    }]
  },
  {
    "code" : "266186009",
    "display" : "(Legionella) or (Legionnaire's disease)",
    "property" : [{
      "code" : "roll-up-genus",
      "valueCoding" : {
        "system" : "http://snomed.info/sct",
        "code" : "7527002",
        "display" : "Legionella"
      }
    },
    {
      "code" : "nhsn-community-associated",
      "valueBoolean" : false
    },
    {
      "code" : "nhsn-skin-commensal",
      "valueBoolean" : false
    },
    {
      "code" : "snomed-status",
      "valueCode" : "0"
    }]
  },
  {
    "code" : "154315008",
    "display" : "(Legionella) or (Legionnaire's disease)",
    "property" : [{
      "code" : "roll-up-genus",
      "valueCoding" : {
        "system" : "http://snomed.info/sct",
        "code" : "7527002",
        "display" : "Legionella"
      }
    },
    {
      "code" : "nhsn-community-associated",
      "valueBoolean" : false
    },
    {
      "code" : "nhsn-skin-commensal",
      "valueBoolean" : false
    },
    {
      "code" : "snomed-status",
      "valueCode" : "0"
    }]
  },
  {
    "code" : "186103005",
    "display" : "(Shigella dysenteriae - group A) or (bacillary dysentery)",
    "property" : [{
      "code" : "roll-up-genus",
      "valueCoding" : {
        "system" : "http://snomed.info/sct",
        "code" : "77352002",
        "display" : "Shigella"
      }
    },
    {
      "code" : "roll-up-species",
      "valueCoding" : {
        "system" : "http://snomed.info/sct",
        "code" : "43612004",
        "display" : "Shigella dysenteriae"
      }
    },
    {
      "code" : "nhsn-community-associated",
      "valueBoolean" : false
    },
    {
      "code" : "nhsn-skin-commensal",
      "valueBoolean" : false
    },
    {
      "code" : "snomed-status",
      "valueCode" : "0"
    }]
  },
  {
    "code" : "186350009",
    "display" : "(Whooping cough) or (Bordetella)",
    "property" : [{
      "code" : "roll-up-genus",
      "valueCoding" : {
        "system" : "http://snomed.info/sct",
        "code" : "46466005",
        "display" : "Bordetella"
      }
    },
    {
      "code" : "nhsn-community-associated",
      "valueBoolean" : false
    },
    {
      "code" : "nhsn-skin-commensal",
      "valueBoolean" : false
    },
    {
      "code" : "snomed-status",
      "valueCode" : "0"
    }]
  },
  {
    "code" : "115161005",
    "display" : "Abiotrophia",
    "property" : [{
      "code" : "roll-up-genus",
      "valueCoding" : {
        "system" : "http://snomed.info/sct",
        "code" : "115161005",
        "display" : "Abiotrophia"
      }
    },
    {
      "code" : "nhsn-community-associated",
      "valueBoolean" : false
    },
    {
      "code" : "nhsn-skin-commensal",
      "valueBoolean" : false
    },
    {
      "code" : "snomed-status",
      "valueCode" : "1"
    }]
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  {
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        "system" : "http://snomed.info/sct",
        "code" : "413409000",
        "display" : "Acetobacter pomorum"
      }
    },
    {
      "code" : "nhsn-community-associated",
      "valueBoolean" : false
    },
    {
      "code" : "nhsn-skin-commensal",
      "valueBoolean" : false
    },
    {
      "code" : "snomed-status",
      "valueCode" : "1"
    }]
  },
  {
    "code" : "413410005",
    "display" : "Acetobacter species",
    "property" : [{
      "code" : "roll-up-genus",
      "valueCoding" : {
        "system" : "http://snomed.info/sct",
        "code" : "396949003",
        "display" : "Acetobacter"
      }
    },
    {
      "code" : "nhsn-community-associated",
      "valueBoolean" : false
    },
    {
      "code" : "nhsn-skin-commensal",
      "valueBoolean" : false
    },
    {
      "code" : "snomed-status",
      "valueCode" : "0"
    }]
  }]
}