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', "L": null as String },
{ "snomed_preferred_term": '(Legionella) or (Legionnaire\'s disease)', "snomed_concept_id": '266186009', "roll_up_genus_level": '1', "roll_up_genus_name": 'Legionella', "roll_up_genus_conceptid": '7527002', "roll_up_species_level": '0', "roll_up_species_name": null as String, "roll_up_species_conceptid": null as String, "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '0', "L": null as String },
{ "snomed_preferred_term": '(Legionella) or (Legionnaire\'s disease)', "snomed_concept_id": '154315008', "roll_up_genus_level": '1', "roll_up_genus_name": 'Legionella', "roll_up_genus_conceptid": '7527002', "roll_up_species_level": '0', "roll_up_species_name": null as String, "roll_up_species_conceptid": null as String, "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '0', "L": null as String },
{ "snomed_preferred_term": '(Shigella dysenteriae - group A) or (bacillary dysentery)', "snomed_concept_id": '186103005', "roll_up_genus_level": '1', "roll_up_genus_name": 'Shigella', "roll_up_genus_conceptid": '77352002', "roll_up_species_level": '1', "roll_up_species_name": 'Shigella dysenteriae', "roll_up_species_conceptid": '43612004', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '0', "L": null as String },
{ "snomed_preferred_term": '(Whooping cough) or (Bordetella)', "snomed_concept_id": '186350009', "roll_up_genus_level": '1', "roll_up_genus_name": 'Bordetella', "roll_up_genus_conceptid": '46466005', "roll_up_species_level": '0', "roll_up_species_name": null as String, "roll_up_species_conceptid": null as String, "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '0', "L": null as String },
{ "snomed_preferred_term": 'Abiotrophia', "snomed_concept_id": '115161005', "roll_up_genus_level": '1', "roll_up_genus_name": 'Abiotrophia', "roll_up_genus_conceptid": '115161005', "roll_up_species_level": '0', "roll_up_species_name": null as String, "roll_up_species_conceptid": null as String, "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Abiotrophia defectiva', "snomed_concept_id": '113714003', "roll_up_genus_level": '1', "roll_up_genus_name": 'Abiotrophia', "roll_up_genus_conceptid": '115161005', "roll_up_species_level": '1', "roll_up_species_name": 'Abiotrophia defectiva', "roll_up_species_conceptid": '113714003', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Abiotrophia para-adiacens', "snomed_concept_id": '409815006', "roll_up_genus_level": '1', "roll_up_genus_name": 'Abiotrophia', "roll_up_genus_conceptid": '115161005', "roll_up_species_level": '1', "roll_up_species_name": 'Abiotrophia para-adiacens', "roll_up_species_conceptid": '409815006', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '0', "L": null as String },
{ "snomed_preferred_term": 'Abiotrophia species', "snomed_concept_id": '372391001', "roll_up_genus_level": '1', "roll_up_genus_name": 'Abiotrophia', "roll_up_genus_conceptid": '115161005', "roll_up_species_level": '0', "roll_up_species_name": null as String, "roll_up_species_conceptid": null as String, "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '0', "L": null as String },
{ "snomed_preferred_term": 'Abortiporus', "snomed_concept_id": '736080001', "roll_up_genus_level": '1', "roll_up_genus_name": 'Abortiporus', "roll_up_genus_conceptid": '736080001', "roll_up_species_level": '0', "roll_up_species_name": null as String, "roll_up_species_conceptid": null as String, "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Abortiporus biennis', "snomed_concept_id": '736079004', "roll_up_genus_level": '1', "roll_up_genus_name": 'Abortiporus', "roll_up_genus_conceptid": '736080001', "roll_up_species_level": '1', "roll_up_species_name": 'Abortiporus biennis', "roll_up_species_conceptid": '736079004', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Absidia', "snomed_concept_id": '57145009', "roll_up_genus_level": '1', "roll_up_genus_name": 'Absidia', "roll_up_genus_conceptid": '57145009', "roll_up_species_level": '0', "roll_up_species_name": null as String, "roll_up_species_conceptid": null as String, "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Absidia caerulea', "snomed_concept_id": '2591000146102', "roll_up_genus_level": '1', "roll_up_genus_name": 'Absidia', "roll_up_genus_conceptid": '57145009', "roll_up_species_level": '1', "roll_up_species_name": 'Absidia caerulea', "roll_up_species_conceptid": '2591000146102', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Absidia corymbifera', "snomed_concept_id": '243420008', "roll_up_genus_level": '1', "roll_up_genus_name": 'Absidia', "roll_up_genus_conceptid": '57145009', "roll_up_species_level": '1', "roll_up_species_name": 'Absidia corymbifera', "roll_up_species_conceptid": '243420008', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '0', "L": null as String },
{ "snomed_preferred_term": 'Absidia cylindrospora', "snomed_concept_id": '49931000087108', "roll_up_genus_level": '1', "roll_up_genus_name": 'Absidia', "roll_up_genus_conceptid": '57145009', "roll_up_species_level": '1', "roll_up_species_name": 'Absidia cylindrospora', "roll_up_species_conceptid": '49931000087108', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Absidia glauca', "snomed_concept_id": '785768009', "roll_up_genus_level": '1', "roll_up_genus_name": 'Absidia', "roll_up_genus_conceptid": '57145009', "roll_up_species_level": '1', "roll_up_species_name": 'Absidia glauca', "roll_up_species_conceptid": '785768009', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Absidia halospora', "snomed_concept_id": '8296004', "roll_up_genus_level": '1', "roll_up_genus_name": 'Absidia', "roll_up_genus_conceptid": '57145009', "roll_up_species_level": '1', "roll_up_species_name": 'Absidia halospora', "roll_up_species_conceptid": '8296004', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Absidia lichtheimii', "snomed_concept_id": '359802007', "roll_up_genus_level": '1', "roll_up_genus_name": 'Absidia', "roll_up_genus_conceptid": '57145009', "roll_up_species_level": '1', "roll_up_species_name": 'Absidia lichtheimii', "roll_up_species_conceptid": '359802007', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '0', "L": null as String },
{ "snomed_preferred_term": 'Absidia ramosa', "snomed_concept_id": '36013002', "roll_up_genus_level": '1', "roll_up_genus_name": 'Absidia', "roll_up_genus_conceptid": '57145009', "roll_up_species_level": '1', "roll_up_species_name": 'Absidia ramosa', "roll_up_species_conceptid": '36013002', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '0', "L": null as String },
{ "snomed_preferred_term": 'Absidia species', "snomed_concept_id": '404226006', "roll_up_genus_level": '1', "roll_up_genus_name": 'Absidia', "roll_up_genus_conceptid": '57145009', "roll_up_species_level": '0', "roll_up_species_name": null as String, "roll_up_species_conceptid": null as String, "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '0', "L": null as String },
{ "snomed_preferred_term": 'Abyssicoccus', "snomed_concept_id": '541341000124105', "roll_up_genus_level": '1', "roll_up_genus_name": 'Abyssicoccus', "roll_up_genus_conceptid": '541341000124105', "roll_up_species_level": '0', "roll_up_species_name": null as String, "roll_up_species_conceptid": null as String, "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Abyssicoccus albus', "snomed_concept_id": '541351000124107', "roll_up_genus_level": '1', "roll_up_genus_name": 'Abyssicoccus', "roll_up_genus_conceptid": '541341000124105', "roll_up_species_level": '1', "roll_up_species_name": 'Abyssicoccus albus', "roll_up_species_conceptid": '541351000124107', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acaromyces', "snomed_concept_id": '28861000087102', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acaromyces', "roll_up_genus_conceptid": '28861000087102', "roll_up_species_level": '0', "roll_up_species_name": null as String, "roll_up_species_conceptid": null as String, "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acaromyces ingoldii', "snomed_concept_id": '28871000087106', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acaromyces', "roll_up_genus_conceptid": '28861000087102', "roll_up_species_level": '1', "roll_up_species_name": 'Acaromyces ingoldii', "roll_up_species_conceptid": '28871000087106', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acaulium', "snomed_concept_id": '785735002', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acaulium', "roll_up_genus_conceptid": '785735002', "roll_up_species_level": '0', "roll_up_species_name": null as String, "roll_up_species_conceptid": null as String, "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acaulium acremonium', "snomed_concept_id": '59520005', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acaulium', "roll_up_genus_conceptid": '785735002', "roll_up_species_level": '1', "roll_up_species_name": 'Acaulium acremonium', "roll_up_species_conceptid": '59520005', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetanaerobacterium', "snomed_concept_id": '423947001', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetanaerobacterium', "roll_up_genus_conceptid": '423947001', "roll_up_species_level": '0', "roll_up_species_name": null as String, "roll_up_species_conceptid": null as String, "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetanaerobacterium elongatum', "snomed_concept_id": '423867006', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetanaerobacterium', "roll_up_genus_conceptid": '423947001', "roll_up_species_level": '1', "roll_up_species_name": 'Acetanaerobacterium elongatum', "roll_up_species_conceptid": '423867006', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetitomaculum', "snomed_concept_id": '424162006', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetitomaculum', "roll_up_genus_conceptid": '424162006', "roll_up_species_level": '0', "roll_up_species_name": null as String, "roll_up_species_conceptid": null as String, "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetitomaculum ruminis', "snomed_concept_id": '425276005', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetitomaculum', "roll_up_genus_conceptid": '424162006', "roll_up_species_level": '1', "roll_up_species_name": 'Acetitomaculum ruminis', "roll_up_species_conceptid": '425276005', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetivibrio', "snomed_concept_id": '72806006', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetivibrio', "roll_up_genus_conceptid": '72806006', "roll_up_species_level": '0', "roll_up_species_name": null as String, "roll_up_species_conceptid": null as String, "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetivibrio aldrichii', "snomed_concept_id": '432614007', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetivibrio', "roll_up_genus_conceptid": '72806006', "roll_up_species_level": '1', "roll_up_species_name": 'Acetivibrio aldrichii', "roll_up_species_conceptid": '432614007', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetivibrio cellulolyticus', "snomed_concept_id": '86860008', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetivibrio', "roll_up_genus_conceptid": '72806006', "roll_up_species_level": '1', "roll_up_species_name": 'Acetivibrio cellulolyticus', "roll_up_species_conceptid": '86860008', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetivibrio ethanolgignens', "snomed_concept_id": '64755006', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetivibrio', "roll_up_genus_conceptid": '72806006', "roll_up_species_level": '1', "roll_up_species_name": 'Acetivibrio ethanolgignens', "roll_up_species_conceptid": '64755006', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetivibrio species', "snomed_concept_id": '131199002', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetivibrio', "roll_up_genus_conceptid": '72806006', "roll_up_species_level": '0', "roll_up_species_name": null as String, "roll_up_species_conceptid": null as String, "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '0', "L": null as String },
{ "snomed_preferred_term": 'Acetivibrio straminisolvens', "snomed_concept_id": '432622000', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetivibrio', "roll_up_genus_conceptid": '72806006', "roll_up_species_level": '1', "roll_up_species_name": 'Acetivibrio straminisolvens', "roll_up_species_conceptid": '432622000', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetivibrio thermocellus', "snomed_concept_id": '68100006', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetivibrio', "roll_up_genus_conceptid": '72806006', "roll_up_species_level": '1', "roll_up_species_name": 'Acetivibrio thermocellus', "roll_up_species_conceptid": '68100006', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetoanaerobium', "snomed_concept_id": '423611000', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetoanaerobium', "roll_up_genus_conceptid": '423611000', "roll_up_species_level": '0', "roll_up_species_name": null as String, "roll_up_species_conceptid": null as String, "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetoanaerobium noterae', "snomed_concept_id": '422656003', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetoanaerobium', "roll_up_genus_conceptid": '423611000', "roll_up_species_level": '1', "roll_up_species_name": 'Acetoanaerobium noterae', "roll_up_species_conceptid": '422656003', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetoanaerobium sticklandii', "snomed_concept_id": '78437006', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetoanaerobium', "roll_up_genus_conceptid": '423611000', "roll_up_species_level": '1', "roll_up_species_name": 'Acetoanaerobium sticklandii', "roll_up_species_conceptid": '78437006', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter', "snomed_concept_id": '396949003', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '0', "roll_up_species_name": null as String, "roll_up_species_conceptid": null as String, "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter aceti', "snomed_concept_id": '396950003', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter aceti', "roll_up_species_conceptid": '396950003', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter calcoaceticus', "snomed_concept_id": '413398000', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter calcoaceticus', "roll_up_species_conceptid": '413398000', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter cerevisiae', "snomed_concept_id": '413399008', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter cerevisiae', "roll_up_species_conceptid": '413399008', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter cibinongensis', "snomed_concept_id": '413400001', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter cibinongensis', "roll_up_species_conceptid": '413400001', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter estunensis', "snomed_concept_id": '413401002', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter estunensis', "roll_up_species_conceptid": '413401002', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter fabarum', "snomed_concept_id": '116881000181108', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter fabarum', "roll_up_species_conceptid": '116881000181108', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter ghanensis', "snomed_concept_id": '23731000181109', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter ghanensis', "roll_up_species_conceptid": '23731000181109', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter hansenii', "snomed_concept_id": '396953001', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter hansenii', "roll_up_species_conceptid": '396953001', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter indonesiensis', "snomed_concept_id": '413402009', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter indonesiensis', "roll_up_species_conceptid": '413402009', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter lambici', "snomed_concept_id": '23741000181102', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter lambici', "roll_up_species_conceptid": '23741000181102', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter liquefaciens', "snomed_concept_id": '396951004', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter liquefaciens', "roll_up_species_conceptid": '396951004', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '0', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter lovaniensis', "snomed_concept_id": '413403004', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter lovaniensis', "roll_up_species_conceptid": '413403004', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter malorum', "snomed_concept_id": '413404005', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter malorum', "roll_up_species_conceptid": '413404005', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter musti', "snomed_concept_id": '23751000181104', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter musti', "roll_up_species_conceptid": '23751000181104', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter nitrogenifigens', "snomed_concept_id": '23761000181101', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter nitrogenifigens', "roll_up_species_conceptid": '23761000181101', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter oeni', "snomed_concept_id": '23771000181106', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter oeni', "roll_up_species_conceptid": '23771000181106', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter orientalis', "snomed_concept_id": '413405006', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter orientalis', "roll_up_species_conceptid": '413405006', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter orleanensis', "snomed_concept_id": '413406007', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter orleanensis', "roll_up_species_conceptid": '413406007', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter pasteurianus', "snomed_concept_id": '396952006', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter pasteurianus', "roll_up_species_conceptid": '396952006', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter peroxydans', "snomed_concept_id": '413407003', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter peroxydans', "roll_up_species_conceptid": '413407003', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '0', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter persici', "snomed_concept_id": '708522006', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter persici', "roll_up_species_conceptid": '708522006', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter polyoxogenes', "snomed_concept_id": '413408008', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter polyoxogenes', "roll_up_species_conceptid": '413408008', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter pomorum', "snomed_concept_id": '413409000', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '1', "roll_up_species_name": 'Acetobacter pomorum', "roll_up_species_conceptid": '413409000', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Acetobacter species', "snomed_concept_id": '413410005', "roll_up_genus_level": '1', "roll_up_genus_name": 'Acetobacter', "roll_up_genus_conceptid": '396949003', "roll_up_species_level": '0', "roll_up_species_name": null as String, "roll_up_species_conceptid": null as String, "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '0', "L": null as String },
{ "snomed_preferred_term": 'Staphylococcus aureus', "snomed_concept_id": '3092008', "roll_up_genus_level": '1', "roll_up_genus_name": 'Staphylococcus', "roll_up_genus_conceptid": '65119002', "roll_up_species_level": '1', "roll_up_species_name": 'Staphylococcus aureus', "roll_up_species_conceptid": '3092008', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Staphylococcus aureus complex', "snomed_concept_id": '44651000087108', "roll_up_genus_level": '1', "roll_up_genus_name": 'Staphylococcus', "roll_up_genus_conceptid": '65119002', "roll_up_species_level": '0', "roll_up_species_name": null as String, "roll_up_species_conceptid": null as String, "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Staphylococcus aureus ss aureus', "snomed_concept_id": '113961008', "roll_up_genus_level": '1', "roll_up_genus_name": 'Staphylococcus', "roll_up_genus_conceptid": '65119002', "roll_up_species_level": '1', "roll_up_species_name": 'Staphylococcus aureus', "roll_up_species_conceptid": '3092008', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String },
{ "snomed_preferred_term": 'Staphylococcus aureus ss. anaerobius', "snomed_concept_id": '50269000', "roll_up_genus_level": '1', "roll_up_genus_name": 'Staphylococcus', "roll_up_genus_conceptid": '65119002', "roll_up_species_level": '1', "roll_up_species_name": 'Staphylococcus aureus', "roll_up_species_conceptid": '3092008', "nhsn_community_associated": '0', "nhsn_skin_commensal": '0', "snomed_status": '1', "L": null as String }
}
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()
)
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