From 821465d9f1a8d55de75d542fce1a911f0b59bfd7 Mon Sep 17 00:00:00 2001 From: cbarcl01 Date: Thu, 18 Jul 2024 15:29:13 -0700 Subject: [PATCH 1/4] Add NCBI_schema --- convast/schema/NCBI_schema.yaml | 149 ++++++++++++++++++++++++++++++++ 1 file changed, 149 insertions(+) create mode 100644 convast/schema/NCBI_schema.yaml diff --git a/convast/schema/NCBI_schema.yaml b/convast/schema/NCBI_schema.yaml new file mode 100644 index 0000000..d051e46 --- /dev/null +++ b/convast/schema/NCBI_schema.yaml @@ -0,0 +1,149 @@ +id: https://example.com/NCBI_antibiogram +name: PHA4GE +description: 'Schema for validation of AST antibiogram data' +version: 1.0.0 +imports: + - linkml:types +prefixes: + linkml: https://w3id.org/linkml/ +classes: + NCBI_antibiogram: + description: Class representing an antibiogram + slots: + - biosample_accession + - organism + - antibiotic + - resistance_phenotype + - measurement + - measurement_units + - measurement_sign + - laboratory_typing_method + - laboratory_typing_platform + - vendor +slots: + biosample_accession: + title: biosample_accession + range: string + description: The identifier assigned to a BioSample in INSDC archives + examples: SAMN14180202 + exact_mappings: GENEPIO:0001139 + organism: + title: organism + range: string + description: Taxonomic name of the organism + examples: + antibiotic: + title: antibiotic + range: string + description: Name of the antibiotic + examples: + resistance_phenotype: + title: resistance_phenotype + range: resistance_phenotype_menu + description: The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic + examples: susceptible + measurement: + title: measurement + range: float + description: The measured value of antimicrobial resistance + examples: + measurement_units: + title: measurement_units + range: measurement_units_menu + description: The units of measurement for antimicrobial resistance measurement + examples: + measurement_sign: + title: measurement_sign + range: measurement_sign_menu + description: The qualifier associated with the antibiotic susceptibility measurement + examples: + laboratory_typing_method: + title: laboratory_typing_method + range: laboratory_typing_method_menu + description: The general method used for antibiotic susceptibility testing + examples: + laboratory_typing_platform: + title: laboratory_typing_platform + range: laboratory_typing_platform_menu + description: The brand/platform used for antibiotic susceptibility testing + examples: + vendor: + title: vendor + range: vendor_menu + description: The name of the vendor of the testing platform used + examples: +enums: + resistance_phenotype_menu: + permissible_values: + resistant: + text: resistant + meaning: ARO:3004301 + susceptible: + text: susceptible + meaning: ARO:3004302 + intermediate: + text: intermediate + meaning: ARO:3004300 + nonsusceptible: + text: nonsusceptible + meaning: ARO:3004303 + not_defined: + text: not_defined + susceptible-dose dependent: + text: susceptible-dose dependent + meaning: ARO:3004304 + measurement_units_menu: + permissible_values: + mg_per_L: + text: mg/L + meaning: UO:0000273 + mm: + text: mm + meaning: UO:0000016 + measurement_sign_menu: + permissible_values: + less_than: + text: '<' + less_than_or_equal: + text: '<=' + equal_to: + text: '==' + greater_than: + text: '>' + greater_than_or_equal: + text: '>=' + laboratory_typing_method_menu: + permissable_values: + MIC: + text: MIC + agar dilution: + text: agar dilution + disk diffusion: + text: disk diffusion + missing: + text: missing + laboratory_typing_platform_menu: + permissible_values: + Microscan: + text: Microscan + meaning: ARO:3004400 + Phoenix: + text: Phoenix + meaning: ARO:3004401 + Sensititre: + text: Sensititre + meaning: ARO:3004402 + Vitek: + text: Vitek + meaning: ARO:3004403 + vendor_menu: + permissible_values: + Becton Dickinson: + Biomérieux: + Siemens: + Trek: + + + + + From bbd8790a8a9b1499ee90be49ac021ed810a9f0d8 Mon Sep 17 00:00:00 2001 From: Charlie Barclay <77304067+cbarcl01@users.noreply.github.com> Date: Thu, 18 Jul 2024 15:32:18 -0700 Subject: [PATCH 2/4] Update NCBI_schema.yaml --- convast/schema/NCBI_schema.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/convast/schema/NCBI_schema.yaml b/convast/schema/NCBI_schema.yaml index d051e46..15d0be1 100644 --- a/convast/schema/NCBI_schema.yaml +++ b/convast/schema/NCBI_schema.yaml @@ -1,5 +1,5 @@ id: https://example.com/NCBI_antibiogram -name: PHA4GE +name: NCBI_antibiogram description: 'Schema for validation of AST antibiogram data' version: 1.0.0 imports: From 4091088e5a40ec5f7875a203ad96a7d94f1279f7 Mon Sep 17 00:00:00 2001 From: cbarcl01 Date: Thu, 18 Jul 2024 18:12:37 -0700 Subject: [PATCH 3/4] Update NCBI_schema.yaml --- convast/schema/NCBI_schema.yaml | 411 +++++++++++++++++++++++++++++++- 1 file changed, 410 insertions(+), 1 deletion(-) diff --git a/convast/schema/NCBI_schema.yaml b/convast/schema/NCBI_schema.yaml index d051e46..e9ac1b5 100644 --- a/convast/schema/NCBI_schema.yaml +++ b/convast/schema/NCBI_schema.yaml @@ -20,6 +20,8 @@ classes: - laboratory_typing_method - laboratory_typing_platform - vendor + - laboratory_typing_method_version_or_reagent + - testing_standard slots: biosample_accession: title: biosample_accession @@ -34,7 +36,7 @@ slots: examples: antibiotic: title: antibiotic - range: string + range: antibiotic_menu description: Name of the antibiotic examples: resistance_phenotype: @@ -72,7 +74,361 @@ slots: range: vendor_menu description: The name of the vendor of the testing platform used examples: + laboratory_typing_method_version_or_reagent: + title: laboratory_typing_method_version_or_reagent + range: laboratory_typing_method_version_or_reagent_menu + description: + examples: + testing_standard: + title: testing_standard + range: testing_standard_menu + description: + examples: enums: + antibiotic_menu: + permissible_values: + acridine dye: + acriflavin: + actinomycin: + actinomycin D: + amikacin: + amoxicillin: + amoxicillin-clavulanic acid: + amphotericin B: + ampicillin: + ampicillin-sulbactam: + amythiamicin A: + anidulafungin: + antibiotic A40926: + antibiotic A47934: + apramycin: + arbekacin: + arsphenamine: + arylomycin: + astromicin: + aurodox: + avoparcin: + azamulin: + azdimycin: + azidamfenicol: + azithromycin: + azlocillin: + aztreonam: + bacitracin: + bacitracin A: + bacitracin B: + bacitracin F: + balhimycin: + benzylpenicillin: + bicyclomycin: + bleomycin: + bleomycin A2: + bleomycin B2: + bleomycinic acid: + brodimoprim: + butirosin: + capreomycin: + carbenicillin: + carbomycin: + caspofungin: + cefaclor: + cefadroxil: + cefalexin: + cefalotin: + cefamandole: + cefazolin: + cefdinir: + cefditoren: + cefepime: + cefetamet: + cefideroco: + cefixime: + cefmetazole: + cefonicid: + cefoperazone: + cefotaxime: + cefotaxime-clavulanic acid: + cefotetan: + cefotiam: + cefoxitin: + cefpodoxime: + cefpodoxime-proxetil: + cefprozil: + ceftaroline: + ceftazidime: + ceftazidime-avibactam: + ceftazidime-clavulanic acid: + ceftibuten: + ceftiofur: + ceftizoxime: + ceftobiprole: + ceftolozane-tazobactam: + ceftriaxone: + cefuroxime: + celesticetin: + cephalexin: + cephalothin: + cephamycin: + cephapirin: + cephem: + cephradine: + chalcomycin: + chloramphenicol: + chloroeremomycin: + chlortetracycline: + cinoxacin: + ciprofloxacin: + clarithromycin: + clavulanic acid: + clinafloxacin: + clindamycin: + clofazimine: + clorobiocin: + cloxacillin: + colistin: + colistin A: + colistin B: + coumermycin A1: + cyclic thiazolyl peptide elfamycin: + cycloserine: + dalbavancin: + dalfopristin: + danofloxacin: + daptomycin: + defensin: + delafloxacin: + demeclocycline: + diaminopyrimidine: + dibekacin: + dicloxacillin: + dihydromocimycin: + dirithromycin: + doripenem: + doxycycline: + edeine: + edeine A: + edeine B: + edeine D: + edeine F: + efrotomycin: + elfamycin: + enacyloxin IIa: + enoxacin: + enrofloxacin: + eravacycline: + ertapenem: + erythromycin: + ethambutol: + ethionamide: + factumycin: + fidaxomicin: + fleroxacin: + flomoxef: + florfenicol: + flucloxacillin: + fluconazole: + flucytosine: + fluoroquinolone: + fosfomycin: + fosfomycin-glucose-6-phosphate: + fosmidomycin: + furazolidone: + fusidic acid: + G418: + ganefromycin: + gatifloxacin: + GE2270A: + GE37468: + gentamicin: + gentamicin B: + gentamicin C: + glycylcycline: + gramicidin: + gramicidin A: + gramicidin B: + gramicidin C: + gramicidin D: + gramicidin S: + grepafloxacin: + griseoviridin: + heneicomycin: + hygromycin B: + iclaprim: + imipenem: + Imipenem-EDTA-PA: + imipenem-relebactam: + isavuconazole: + isepamicin: + isoniazid: + isopenicillin N: + itraconazole: + josamycin: + kanamycin: + kanamycin A: + kasugamicin: + kirromycin: + kirrothricin: + kitasamycin: + L-681,217: + levofloxacin: + lincomycin: + lincosamide: + linezolid: + lipopeptide antibiotic: + lividomycin: + lividomycin A: + lividomycin B: + lomefloxacin: + loracarbef: + madumycin II: + mafenide: + magainin: + mecillinam: + megalomycin: + meropenem: + meropenem-vaborbactam: + methicillin: + methymycin: + metronidazole: + mezlocillin: + micafungin: + midecamycin: + minocycline: + moenomycin: + moenomycin A1: + moxalactam: + moxifloxacin: + mupirocin: + mycinamicin: + nafcillin: + nalidixic acid: + narbomycin: + neomycin: + netilmicin: + nicotinamide: + niddamycin: + nitrofurantoin: + norfloxacin: + novobiocin: + ofloxacin: + oleandomycin: + omadacycline: + oritavancin: + ostreogrycin B3: + oxacillin: + oxytetracycline: + para-aminosalicylic acid: + paromomycin: + patricin A: + patricin B: + pefloxacin: + penam: + penicillin: + penicillin N: + phenelfamycin A: + phenelfamycin B: + phenelfamycin C: + phenelfamycin D: + phenelfamycin E: + phenelfamycin F: + phenelfamycin G: + phenelfamycin H: + phenicol: + phenoxymethylpenicillin: + pikromycin: + piperacillin: + piperacillin-sulbactam: + piperacillin-tazobactam: + plazomicin: + pleuromutilin: + polymyxin: + polymyxin B: + polymyxin B1: + polymyxin B2: + polymyxin B3: + polymyxin B4: + posaconazole: + pristinamycin IA: + pristinamycin IB: + pristinamycin IIA: + propicillin: + prothionamide: + pulvomycin: + puromycin: + pyrazinamide: + quinupristin: + quinupristin-dalfopristin: + retapamulin: + ribostamycin: + rifabutin: + rifampin: + rifamycin: + rifapentine: + rifaximin: + ristocetin: + rosaramicin: + roxithromycin: + SB22484: + sisomicin: + sparfloxacin: + spectinomycin: + spiramycin: + streptogramin: + streptogramin A antibiotic: + streptogramin B antibiotic: + streptomycin: + streptothricin: + sulbactam: + sulfacetamide: + sulfadiazine: + sulfadimethoxine: + sulfadimidine: + sulfadoxine: + sulfamethizole: + sulfamethoxazole: + sulfasalazine: + sulfisoxazole: + sulfonamide: + surotomycin: + synercid: + tazobactam: + tedizolid: + teicoplanin: + telavancin: + telithromycin: + temocillin: + tetracycline: + tetroxoprim: + thiamphenicol: + thiostrepton: + tiamulin: + ticarcillin: + ticarcillin-clavulanic acid: + tigecycline: + tilmicosin: + timentin: + tinidazole: + tobramycin: + triclosan: + trimethoprim: + trimethoprim-sulfamethoxazole: + trovafloxacin: + tuberactinomycin: + tulathromycin: + tunicamycin: + tylosin: + tyrothricin: + UK-69,753: + unphenelfamycin: + valnemulin: + vancomycin: + verdamicin: + vernamycin B-gamma: + vernamycin C: + vertilimicin: + viomycin: + virginiamycin S2: + voriconazole: resistance_phenotype_menu: permissible_values: resistant: @@ -139,9 +495,62 @@ enums: vendor_menu: permissible_values: Becton Dickinson: + text: Becton Dickinson + meaning: ARO:3004405 Biomérieux: + text: Biomérieux + meaning: ARO:3004406 Siemens: + text: Siemens + meaning: ARO:3004407 Trek: + text: Trek + meaning: ARO:3004409 + laboratory_typing_method_version_or_reagent_menu: + permissible_values: + 96-Well Plate: + text: 96-Well Plate + meaning: BAO:0000513 + E-Test: + text: E-Test + meaning: NCIT:85596 + GM-NEG: + text: GM-NEG + meaning: + testing_standard_menu: + permissible_values: + BSAC: + text: British Society for Antimicrobial Chemotherapy (BSAC) + meaning: ARO:3004365 + CLSI: + text: Clinical Laboratory and Standards Institute (CLSI) + meaning: ARO:3004366 + DIN: + text: Deutsches Institut für Normung (DIN) + meaning: ARO:3004367 + EUCAST: + text: European Committee on Antimicrobial Susceptibility Testing (EUCAST) + meaning: ARO:3004368 + NARMS: + text: National Antimicrobial Resistance Monitoring System (NARMS) + meaning: ARO:3007195 + NCCLS: + text: National Committee for Clinical Laboratory Standards (NCCLS) + meaning: ARO:3007193 + SFM: + text: Société Française de Microbiologie (SFM) + meaning: ARO:3004369 + SIR: + text: Swedish Reference Group for Antibiotics (SIR) + meaning: ARO:3007397 + WRG: + text: Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) + meaning: ARO:3007398 + missing: + text: missing + meaning: data is missing + + From 60f269b2ffc428897434fc6eabd98395ed36f32b Mon Sep 17 00:00:00 2001 From: cbarcl01 Date: Thu, 18 Jul 2024 18:23:29 -0700 Subject: [PATCH 4/4] Update NCBI_schema.yaml --- convast/schema/NCBI_schema.yaml | 29 +++++++++++++++-------------- 1 file changed, 15 insertions(+), 14 deletions(-) diff --git a/convast/schema/NCBI_schema.yaml b/convast/schema/NCBI_schema.yaml index c53bd67..5576f81 100644 --- a/convast/schema/NCBI_schema.yaml +++ b/convast/schema/NCBI_schema.yaml @@ -1,11 +1,13 @@ id: https://example.com/NCBI_antibiogram name: NCBI_antibiogram -description: 'Schema for validation of AST antibiogram data' +description: 'Schema for validation of NCBI antibiogram data' version: 1.0.0 imports: - linkml:types prefixes: linkml: https://w3id.org/linkml/ + GENEPIO: http://purl.obolibrary.org/obo/GENEPIO_ + ARO: http://purl.obolibrary.org/obo/ARO_ classes: NCBI_antibiogram: description: Class representing an antibiogram @@ -28,7 +30,6 @@ slots: range: string description: The identifier assigned to a BioSample in INSDC archives examples: SAMN14180202 - exact_mappings: GENEPIO:0001139 organism: title: organism range: string @@ -37,8 +38,8 @@ slots: antibiotic: title: antibiotic range: antibiotic_menu - description: Name of the antibiotic - examples: + description: The name of the antibiotic that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans + examples: actinomycin resistance_phenotype: title: resistance_phenotype range: resistance_phenotype_menu @@ -48,42 +49,42 @@ slots: title: measurement range: float description: The measured value of antimicrobial resistance - examples: + examples: 4 measurement_units: title: measurement_units range: measurement_units_menu description: The units of measurement for antimicrobial resistance measurement - examples: + examples: mg/L measurement_sign: title: measurement_sign range: measurement_sign_menu description: The qualifier associated with the antibiotic susceptibility measurement - examples: + examples: laboratory_typing_method: title: laboratory_typing_method range: laboratory_typing_method_menu description: The general method used for antibiotic susceptibility testing - examples: + examples: disk diffusion laboratory_typing_platform: title: laboratory_typing_platform range: laboratory_typing_platform_menu description: The brand/platform used for antibiotic susceptibility testing - examples: + examples: Microscan vendor: title: vendor range: vendor_menu description: The name of the vendor of the testing platform used - examples: + examples: Trek laboratory_typing_method_version_or_reagent: title: laboratory_typing_method_version_or_reagent range: laboratory_typing_method_version_or_reagent_menu - description: - examples: + description: The specific type or version of reagents and methods used in laboratory typing + examples: 96-Well Plate testing_standard: title: testing_standard range: testing_standard_menu - description: - examples: + description: The testing standard used for determination of resistance phenotype + examples: BSAC enums: antibiotic_menu: permissible_values: