From 774390aa7cc5701c92dfa6fb78be15a565e2e987 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Thu, 8 Feb 2024 09:57:39 -0700 Subject: [PATCH 01/14] Update Demographics enums --- modules/enums/Demographics.yaml | 574 +++++++++++++++++--------------- 1 file changed, 305 insertions(+), 269 deletions(-) diff --git a/modules/enums/Demographics.yaml b/modules/enums/Demographics.yaml index 28aa45a..fc31f0a 100644 --- a/modules/enums/Demographics.yaml +++ b/modules/enums/Demographics.yaml @@ -1,284 +1,320 @@ enums: SexEnum: permissible_values: - unknown: null - Not Reported: null - female: null - male: null - unspecified: null + Female: + Male: + Unspecified: + Unknown: + CauseofDeathEnum: permissible_values: - Not Reported: null - Renal Disorder NOS: null - Toxicity: null - Cardiovascular Disorder NOS: null - unknown: null - Not Applicable: null - Infection: null - Spinal Muscular Atrophy: null - Cancer Related: null - End-stage Renal Disease: null - Surgical Complications: null - Not Cancer Related: null + Not Reported: + Renal Disorder NOS: + Toxicity: + Cardiovascular Disorder NOS: + Unknown: + Not Applicable: + Infection: + Spinal Muscular Atrophy: + Cancer Related: + End-stage Renal Disease: + Surgical Complications: + Not Cancer Related: + EthnicityEnum: permissible_values: - unknown: null - Not Reported: null - hispanic or latino: null - not hispanic or latino: null - not allowed to collect: null + Hispanic or Latino: + 'Non-Hispanic/Non-Latino': + Jewish: + NA: + Not Reported: + Unknown: + RaceEnum: permissible_values: - american indian or alaska native: null - Not Reported: null - white: null - unknown: null - black or african american: null - not allowed to collect: null - asian: null - Other: null - native hawaiian or other pacific islander: null + American Indian or Alaska Native: + White: + Black: + Asian: + Native Hawaiian or Other Pacific Islander: + NA: + Not Reported: + Unknown: + Other: + AgeIsObfuscatedEnum: permissible_values: - 'True': null - 'False': null + 'True': + 'False': + CountryofResidenceEnum: permissible_values: - Trinidad and Tobago: null - Botswana: null - Malaysia: null - Suriname: null - Uruguay: null - Gibraltar: null - Andorra: null - Cayman Islands: null - Mozambique: null - Dominica: null - Tajikistan: null - Barbados: null - Seychelles: null - Curacao: null - Cote d'Ivoire: null - Albania: null - China: null - Oman: null - Congo: null - Burundi: null - Falkland Islands (Malvinas): null - Kazakhstan: null - Australia: null - France: null - Bahrain: null - Solomon Islands: null - Tanzania: null - French Guiana: null - Federated States of Micronesia: null - Antigua and Barbuda: null - Colombia: null - Fiji: null - Sao Tome and Principe: null - Brazil: null - Guam: null - South Africa: null - Denmark: null - Kyrgyzstan: null - Tunisia: null - Mexico: null - Martinique: null - Burkina Faso: null - India: null - Myanmar: null - Malawi: null - Sweden: null - Macau: null - Cambodia: null - Equatorial Guinea: null - Senegal: null - Guernsey: null - Azerbaijan: null - Angola: null - Kuwait: null - Papua New Guinea: null - Central African Republic: null - Bhutan: null - Uzbekistan: null - Portugal: null - Isle of Man: null - Guatemala: null - Saint Helena Ascension and Tristan da Cunha: null - Kiribati: null - Peru: null - South Sudan: null - North Macedonia: null - Democratic Republic of the Congo: null - Belarus: null - Madagascar: null - Singapore: null - Togo: null - Gambia: null - Georgia: null - Italy: null - Tuvalu: null - Eswatini: null - Nepal: null - Kenya: null - Niger: null - Israel: null - Iran: null - Liberia: null - Mali: null - Belize: null - Hungary: null - Holy See: null - Serbia: null - Belgium: null - Bermuda: null - Anguilla: null - Jamaica: null - Lebanon: null - Svalbard & Jan Mayen Islands: null - Cyprus: null - Norway: null - Somalia: null - Japan: null - Guyana: null - Paraguay: null - New Zealand: null - Palau: null - Laos: null - Latvia: null - Ethiopia: null - Cuba: null - French Polynesia: null - Slovenia: null - Philippines: null - Mongolia: null - Switzerland: null - Bahamas: null - Samoa: null - El Salvador: null - Chad: null - Honduras: null - Bangladesh: null - Tonga: null - Croatia: null - Bosnia and Herzegovina: null - Eritrea: null - Saint Kitts and Nevis: null - Vietnam: null - Northern Mariana Islands: null - Cape Verde: null - Cook Islands: null - Turkmenistan: null - Western Sahara: null - Jordan: null - Romania: null - Uganda: null - Aruba: null - Hong Kong: null - Syria: null - Germany: null - Chile: null - Austria: null - Gabon: null - Kosovo: null - Qatar: null - Comoros: null - Mayotte: null - Spain: null - Libya: null - Costa Rica: null - Bolivia: null - Taiwan: null - Iraq: null - Finland: null - Netherlands: null - Venezuela: null - Malta: null - Niue: null - Algeria: null - Guinea: null - Ireland: null - Montenegro: null - United Arab Emirates: null - Maldives: null - Zambia: null - Slovakia: null - Lesotho: null - Dominican Republic: null - Saint Pierre and Miquelon: null - Moldova: null - San Marino: null - Nauru: null - Luxembourg: null - Monaco: null - Zimbabwe: null - Saudi Arabia: null - Mauritania: null - Panama: null - United States: null - Montserrat: null - Nicaragua: null - Faroe Islands: null - United Kingdom: null - Canada: null - Ghana: null - Armenia: null - Bulgaria: null - Egypt: null - Reunion: null - Cameroon: null - Rwanda: null - Timor-Leste: null - Yemen: null - Saint Lucia: null - Poland: null - Namibia: null - Guinea-Bissau: null - Thailand: null - Argentina: null - Turkey: null - Djibouti: null - Greece: null - Jersey: null - Mauritius: null - Wallis and Futuna: null - Pakistan: null - Ukraine: null - State of Palestine: null - Ecuador: null - South Korea: null - Russia: null - Greenland: null - Liechtenstein: null - Nigeria: null - Benin: null - Vanuatu: null - Sri Lanka: null - Tokelau: null - Czech Republic (Czechia): null - Marshall Islands: null - Estonia: null - Saint Vincent and the Grenadines: null - Puerto Rico: null - Grenada: null - Guadeloupe: null - Sierra Leone: null - Afghanistan: null - Haiti: null - Lithuania: null - Indonesia: null - Virgin Islands British: null - Virgin Islands U.S.: null - Sudan: null - Morocco: null - Iceland: null - North Korea: null - New Caledonia: null - Brunei: null + Trinidad and Tobago: + Botswana: + Malaysia: + Suriname: + Uruguay: + Gibraltar: + Andorra: + Cayman Islands: + Mozambique: + Dominica: + Tajikistan: + Barbados: + Seychelles: + Curacao: + Cote d'Ivoire: + Albania: + China: + Oman: + Congo: + Burundi: + Falkland Islands (Malvinas): + Kazakhstan: + Australia: + France: + Bahrain: + Solomon Islands: + Tanzania: + French Guiana: + Federated States of Micronesia: + Antigua and Barbuda: + Colombia: + Fiji: + Sao Tome and Principe: + Brazil: + Guam: + South Africa: + Denmark: + Kyrgyzstan: + Tunisia: + Mexico: + Martinique: + Burkina Faso: + India: + Myanmar: + Malawi: + Sweden: + Macau: + Cambodia: + Equatorial Guinea: + Senegal: + Guernsey: + Azerbaijan: + Angola: + Kuwait: + Papua New Guinea: + Central African Republic: + Bhutan: + Uzbekistan: + Portugal: + Isle of Man: + Guatemala: + Saint Helena Ascension and Tristan da Cunha: + Kiribati: + Peru: + South Sudan: + North Macedonia: + Democratic Republic of the Congo: + Belarus: + Madagascar: + Singapore: + Togo: + Gambia: + Georgia: + Italy: + Tuvalu: + Eswatini: + Nepal: + Kenya: + Niger: + Israel: + Iran: + Liberia: + Mali: + Belize: + Hungary: + Holy See: + Serbia: + Belgium: + Bermuda: + Anguilla: + Jamaica: + Lebanon: + Svalbard & Jan Mayen Islands: + Cyprus: + Norway: + Somalia: + Japan: + Guyana: + Paraguay: + New Zealand: + Palau: + Laos: + Latvia: + Ethiopia: + Cuba: + French Polynesia: + Slovenia: + Philippines: + Mongolia: + Switzerland: + Bahamas: + Samoa: + El Salvador: + Chad: + Honduras: + Bangladesh: + Tonga: + Croatia: + Bosnia and Herzegovina: + Eritrea: + Saint Kitts and Nevis: + Vietnam: + Northern Mariana Islands: + Cape Verde: + Cook Islands: + Turkmenistan: + Western Sahara: + Jordan: + Romania: + Uganda: + Aruba: + Hong Kong: + Syria: + Germany: + Chile: + Austria: + Gabon: + Kosovo: + Qatar: + Comoros: + Mayotte: + Spain: + Libya: + Costa Rica: + Bolivia: + Taiwan: + Iraq: + Finland: + Netherlands: + Venezuela: + Malta: + Niue: + Algeria: + Guinea: + Ireland: + Montenegro: + United Arab Emirates: + Maldives: + Zambia: + Slovakia: + Lesotho: + Dominican Republic: + Saint Pierre and Miquelon: + Moldova: + San Marino: + Nauru: + Luxembourg: + Monaco: + Zimbabwe: + Saudi Arabia: + Mauritania: + Panama: + United States: + Montserrat: + Nicaragua: + Faroe Islands: + United Kingdom: + Canada: + Ghana: + Armenia: + Bulgaria: + Egypt: + Reunion: + Cameroon: + Rwanda: + Timor-Leste: + Yemen: + Saint Lucia: + Poland: + Namibia: + Guinea-Bissau: + Thailand: + Argentina: + Turkey: + Djibouti: + Greece: + Jersey: + Mauritius: + Wallis and Futuna: + Pakistan: + Ukraine: + State of Palestine: + Ecuador: + South Korea: + Russia: + Greenland: + Liechtenstein: + Nigeria: + Benin: + Vanuatu: + Sri Lanka: + Tokelau: + Czech Republic (Czechia): + Marshall Islands: + Estonia: + Saint Vincent and the Grenadines: + Puerto Rico: + Grenada: + Guadeloupe: + Sierra Leone: + Afghanistan: + Haiti: + Lithuania: + Indonesia: + Virgin Islands British: + Virgin Islands U.S.: + Sudan: + Morocco: + Iceland: + North Korea: + New Caledonia: + Brunei: + VitalStatusEnum: permissible_values: - Dead: null - unknown: null - Not Reported: null - Alive: null + Dead: + unknown: + Not Reported: + Alive: + + SurgeryReasonEnum: + permissible_values: + # For both breast/ovarian: + Risk Reduction: + Gender Affirmation: + # For breast surgery + # For ovarian surgery + Ovarian Cyst: + Tubal Sterilization: + Ovarian Serous Cystadenoma: + Endometriosis: + Uterine Fibroids: + 'Uterine Fibroids + Endometriosis': + 'Uterine Fibroids + Adenomyosis': + Cesarean Section: + Menorrhagia: + Adnexal Mass: + Pelvic Mass: + Unknown: + + MenstrualCyclePhaseEnum: + permissible_values: + Inactive: + Secretory: + Proliferative: + Weakly Proliferative: + Late Proliferative/Early Secretory: + Unknown: + From bf14b05499d84a28071cb14c6d53202b6c38894c Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Thu, 8 Feb 2024 09:58:34 -0700 Subject: [PATCH 02/14] Add prop per issue #85 --- modules/slots.yaml | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/modules/slots.yaml b/modules/slots.yaml index fd82cd4..5e8baa6 100644 --- a/modules/slots.yaml +++ b/modules/slots.yaml @@ -30,13 +30,13 @@ slots: Age: title: Age required: true - description: Age of individual as a positive number such as 40 or 56.5. If not available, cannot leave blank and must use "unknown". + description: Age (in years) of individual when samples are contributed/biobanked, as a positive number such as 40 or 56.5. If not available, cannot leave blank and must use "unknown". annotations: - validationRules: regex match ^\d*\.?\d*$|^unknown$ + validationRules: regex match ^\d*\.?\d*$|^Unknown$ AgeAtMenarche: title: Age At Menarche required: false - description: TBD + description: Age at menarche. annotations: AgeIsObfuscated: title: Age Is Obfuscated @@ -47,7 +47,7 @@ slots: AgeatDiagnosis: title: Age at Diagnosis required: false - description: Age at the time of diagnosis expressed in number of days since birth. + description: Age at the time of diagnosis in years. annotations: AlcoholDaysPerWeek: title: Alcohol Days Per Week @@ -1468,6 +1468,11 @@ slots: required: false description: TBD annotations: + SurgeryReason: + title: Surgery Reason + required: false + description: Reason for individual obtaining surgery + range: SurgeryReasonEnum SatelliteMetastasisPresentIndicator: title: Satellite Metastasis Present Indicator required: false From 73e81a6c194711e00d3bede26326f6ee91629ef3 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Thu, 8 Feb 2024 09:58:53 -0700 Subject: [PATCH 03/14] Update CohortCore template --- modules/classes/patient_and_specimen.yaml | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/modules/classes/patient_and_specimen.yaml b/modules/classes/patient_and_specimen.yaml index 64fc3c1..36ecfd6 100644 --- a/modules/classes/patient_and_specimen.yaml +++ b/modules/classes/patient_and_specimen.yaml @@ -1,5 +1,12 @@ classes: + Patient: + annotations: + requiresComponent: '' + required: false + slots: + - Component + CohortCoreTemplate: is_a: Patient annotations: @@ -7,14 +14,15 @@ classes: required: false slots: - ParticipantID + - TimepointLabel - Age - Sex - - BMI - Race - Ethnicity - VitalStatus - Height - Weight + - BMI - Gravidity - Parity - AgeAtMenarche @@ -29,21 +37,15 @@ classes: - PackYearsSmoked - AlcoholUse - NumberofDrinksPerWeek + - ContraceptiveUse - AntibioticUse - SampleCollectionCenter - SampleCollectionYear - ERStatus - PRStatus - HER2Status + - SurgeryReason - Patient: - annotations: - requiresComponent: '' - required: false - slots: - - Component - - ParticipantID - - TimepointLabel PatientExtended: is_a: Patient From c23828cc6e4b93b7c992ea8884ff102cd2c57c38 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Thu, 8 Feb 2024 10:55:53 -0700 Subject: [PATCH 04/14] Update for #86 --- modules/classes/patient_and_specimen.yaml | 1 - modules/enums/Device.yaml | 18 ++++++++++++++++++ modules/slots.yaml | 5 +++++ 3 files changed, 23 insertions(+), 1 deletion(-) diff --git a/modules/classes/patient_and_specimen.yaml b/modules/classes/patient_and_specimen.yaml index 36ecfd6..9197d97 100644 --- a/modules/classes/patient_and_specimen.yaml +++ b/modules/classes/patient_and_specimen.yaml @@ -37,7 +37,6 @@ classes: - PackYearsSmoked - AlcoholUse - NumberofDrinksPerWeek - - ContraceptiveUse - AntibioticUse - SampleCollectionCenter - SampleCollectionYear diff --git a/modules/enums/Device.yaml b/modules/enums/Device.yaml index ad89045..d65b6ba 100644 --- a/modules/enums/Device.yaml +++ b/modules/enums/Device.yaml @@ -34,3 +34,21 @@ enums: Revio: Ultima Genomics UG100: Unknown: + + Contraceptive: + permissible_values: + Oral: + Oral (estrogen): + Oral (progesterone): + Male sterilization: + Condoms: + Patch: + Vaginal ring: + IUD: + IUD (progesterone): + Implant: + Implant (progesterone): + Injection (progesterone): + Bilateral tubal ligation: + Natural family planning: + Unknown: \ No newline at end of file diff --git a/modules/slots.yaml b/modules/slots.yaml index 5e8baa6..2a505ee 100644 --- a/modules/slots.yaml +++ b/modules/slots.yaml @@ -1808,6 +1808,11 @@ slots: description: Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints) annotations: range: TumorTissueTypeEnum + TypeContraceptiveUse: + title: Type of Contraceptive Use + required: false + description: Type of contraceptive(s) used within the individual's history. + range: Contraceptive TypeofSmokeExposure: title: Type of Smoke Exposure required: false From 871fdbf4d03a9e69cf8a8718322a55cb48df37c8 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Thu, 8 Feb 2024 10:57:11 -0700 Subject: [PATCH 05/14] Lint --- modules/enums/Device.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/enums/Device.yaml b/modules/enums/Device.yaml index d65b6ba..73bf6ba 100644 --- a/modules/enums/Device.yaml +++ b/modules/enums/Device.yaml @@ -51,4 +51,5 @@ enums: Injection (progesterone): Bilateral tubal ligation: Natural family planning: - Unknown: \ No newline at end of file + Unknown: + From 92ee99c9eed6fd89f7cf19686dbc242236c8a9e9 Mon Sep 17 00:00:00 2001 From: gf-dcc-service Date: Thu, 8 Feb 2024 18:00:11 +0000 Subject: [PATCH 06/14] Build jsonld --- GF.jsonld | 5967 ++++++++++++++++++++++++++++------------------------- 1 file changed, 3210 insertions(+), 2757 deletions(-) diff --git a/GF.jsonld b/GF.jsonld index f17016d..a519bf2 100644 --- a/GF.jsonld +++ b/GF.jsonld @@ -27,15 +27,13 @@ }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:unknown" - }, { - "@id" : "bts:NotReported" + "@id" : "bts:Female" }, { - "@id" : "bts:female" + "@id" : "bts:Male" }, { - "@id" : "bts:male" + "@id" : "bts:Unspecified" }, { - "@id" : "bts:unspecified" + "@id" : "bts:Unknown" } ], "rdfs:label" : "RelationshipGender", "rdfs:comment" : "The text term used to describe the gender of the patient's relative with a history of cancer.", @@ -587,7 +585,7 @@ }, { "@id" : "bts:CardiovascularDisorderNOS" }, { - "@id" : "bts:unknown" + "@id" : "bts:Unknown" }, { "@id" : "bts:NotApplicable" }, { @@ -3560,15 +3558,13 @@ }, "sms:required" : "sms:true", "schema:rangeIncludes" : [ { - "@id" : "bts:unknown" + "@id" : "bts:Female" }, { - "@id" : "bts:NotReported" - }, { - "@id" : "bts:female" + "@id" : "bts:Male" }, { - "@id" : "bts:male" + "@id" : "bts:Unspecified" }, { - "@id" : "bts:unspecified" + "@id" : "bts:Unknown" } ], "rdfs:label" : "Sex", "rdfs:comment" : "Sex of individual", @@ -6470,10 +6466,50 @@ "rdfs:comment" : "Did all channels pass QC (if not add free text Comment)", "@type" : "rdfs:Class", "sms:displayName" : "PassedQC" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:SurgeryReason", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:RiskReduction" + }, { + "@id" : "bts:GenderAffirmation" + }, { + "@id" : "bts:OvarianCyst" + }, { + "@id" : "bts:TubalSterilization" + }, { + "@id" : "bts:OvarianSerousCystadenoma" + }, { + "@id" : "bts:Endometriosis" + }, { + "@id" : "bts:UterineFibroids" + }, { + "@id" : "bts:UterineFibroids+Endometriosis" + }, { + "@id" : "bts:UterineFibroids+Adenomyosis" + }, { + "@id" : "bts:CesareanSection" + }, { + "@id" : "bts:Menorrhagia" + }, { + "@id" : "bts:AdnexalMass" + }, { + "@id" : "bts:PelvicMass" + }, { + "@id" : "bts:Unknown" + } ], + "rdfs:label" : "SurgeryReason", + "rdfs:comment" : "Reason for individual obtaining surgery", + "@type" : "rdfs:Class", + "sms:displayName" : "SurgeryReason" }, { "@id" : "bts:AgeAtMenarche", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", + "rdfs:comment" : "Age at menarche.", "rdfs:label" : "AgeAtMenarche", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { @@ -6573,15 +6609,17 @@ }, "sms:required" : "sms:true", "schema:rangeIncludes" : [ { - "@id" : "bts:unknown" + "@id" : "bts:HispanicorLatino" }, { - "@id" : "bts:NotReported" + "@id" : "bts:Non-Hispanic/Non-Latino" }, { - "@id" : "bts:hispanicorlatino" + "@id" : "bts:Jewish" }, { - "@id" : "bts:nothispanicorlatino" + "@id" : "bts:NA" + }, { + "@id" : "bts:NotReported" }, { - "@id" : "bts:notallowedtocollect" + "@id" : "bts:Unknown" } ], "rdfs:label" : "Ethnicity", "rdfs:comment" : "An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.", @@ -7400,7 +7438,7 @@ }, { "@id" : "bts:AgeatDiagnosis", "@type" : "rdfs:Class", - "rdfs:comment" : "Age at the time of diagnosis expressed in number of days since birth.", + "rdfs:comment" : "Age at the time of diagnosis in years.", "rdfs:label" : "AgeatDiagnosis", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { @@ -7720,15 +7758,13 @@ }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:unknown" - }, { - "@id" : "bts:NotReported" + "@id" : "bts:Female" }, { - "@id" : "bts:female" + "@id" : "bts:Male" }, { - "@id" : "bts:male" + "@id" : "bts:Unspecified" }, { - "@id" : "bts:unspecified" + "@id" : "bts:Unknown" } ], "rdfs:label" : "Gender", "rdfs:comment" : "Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]", @@ -8287,6 +8323,48 @@ }, "sms:displayName" : "SectionThicknessValue", "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:TypeContraceptiveUse", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Oral" + }, { + "@id" : "bts:Oral(estrogen)" + }, { + "@id" : "bts:Oral(progesterone)" + }, { + "@id" : "bts:Malesterilization" + }, { + "@id" : "bts:Condoms" + }, { + "@id" : "bts:Patch" + }, { + "@id" : "bts:Vaginalring" + }, { + "@id" : "bts:IUD" + }, { + "@id" : "bts:IUD(progesterone)" + }, { + "@id" : "bts:Implant" + }, { + "@id" : "bts:Implant(progesterone)" + }, { + "@id" : "bts:Injection(progesterone)" + }, { + "@id" : "bts:Bilateraltuballigation" + }, { + "@id" : "bts:Naturalfamilyplanning" + }, { + "@id" : "bts:Unknown" + } ], + "rdfs:label" : "TypeContraceptiveUse", + "rdfs:comment" : "Type of contraceptive(s) used within the individual's history.", + "@type" : "rdfs:Class", + "sms:displayName" : "TypeContraceptiveUse" }, { "@id" : "bts:SoftwareandVersion", "@type" : "rdfs:Class", @@ -8401,23 +8479,23 @@ }, "sms:required" : "sms:true", "schema:rangeIncludes" : [ { - "@id" : "bts:americanindianoralaskanative" + "@id" : "bts:AmericanIndianorAlaskaNative" }, { - "@id" : "bts:NotReported" + "@id" : "bts:White" }, { - "@id" : "bts:white" + "@id" : "bts:Black" }, { - "@id" : "bts:unknown" + "@id" : "bts:Asian" }, { - "@id" : "bts:blackorafricanamerican" + "@id" : "bts:NativeHawaiianorOtherPacificIslander" }, { - "@id" : "bts:notallowedtocollect" + "@id" : "bts:NA" }, { - "@id" : "bts:asian" + "@id" : "bts:NotReported" }, { - "@id" : "bts:Other" + "@id" : "bts:Unknown" }, { - "@id" : "bts:nativehawaiianorotherpacificislander" + "@id" : "bts:Other" } ], "rdfs:label" : "Race", "rdfs:comment" : "An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.", @@ -8535,9 +8613,9 @@ "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:true", - "sms:validationRules" : [ "regex match ^\\d*\\.?\\d*$|^unknown$" ], + "sms:validationRules" : [ "regex match ^\\d*\\.?\\d*$|^Unknown$" ], "rdfs:label" : "Age", - "rdfs:comment" : "Age of individual as a positive number such as 40 or 56.5. If not available, cannot leave blank and must use \"unknown\".", + "rdfs:comment" : "Age (in years) of individual when samples are contributed/biobanked, as a positive number such as 40 or 56.5. If not available, cannot leave blank and must use \"unknown\".", "@type" : "rdfs:Class", "sms:displayName" : "Age" }, { @@ -8735,1252 +8813,1182 @@ "sms:displayName" : "CancerIncidenceLocation", "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Assay" - } ], - "@id" : "bts:ImagingLevel2", + "@id" : "bts:IndicatorEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "IndicatorEnum", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "ImagingLevel2", - "rdfs:comment" : "TBD", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:Filename" - }, { - "@id" : "bts:FileFormat" - }, { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:ChannelMetadataFilename" - }, { - "@id" : "bts:ImagingAssayType" - }, { - "@id" : "bts:ProtocolLink" - }, { - "@id" : "bts:SoftwareandVersion" - }, { - "@id" : "bts:Microscope" - }, { - "@id" : "bts:Objective" - }, { - "@id" : "bts:NominalMagnification" - }, { - "@id" : "bts:LensNA" - }, { - "@id" : "bts:WorkingDistance" - }, { - "@id" : "bts:WorkingDistanceUnit" - }, { - "@id" : "bts:Immersion" - }, { - "@id" : "bts:Pyramid" - }, { - "@id" : "bts:Zstack" - }, { - "@id" : "bts:Tseries" - }, { - "@id" : "bts:PassedQC" - }, { - "@id" : "bts:Comment" - }, { - "@id" : "bts:FOVnumber" - }, { - "@id" : "bts:FOVX" - }, { - "@id" : "bts:FOVXUnit" - }, { - "@id" : "bts:FOVY" - }, { - "@id" : "bts:FOVYUnit" - }, { - "@id" : "bts:FrameAveraging" - }, { - "@id" : "bts:ImageID" - }, { - "@id" : "bts:DimensionOrder" - }, { - "@id" : "bts:PhysicalSizeX" - }, { - "@id" : "bts:PhysicalSizeXUnit" - }, { - "@id" : "bts:PhysicalSizeY" - }, { - "@id" : "bts:PhysicalSizeYUnit" - }, { - "@id" : "bts:PhysicalSizeZ" - }, { - "@id" : "bts:PhysicalSizeZUnit" - }, { - "@id" : "bts:PixelsBigEndian" - }, { - "@id" : "bts:PlaneCount" - }, { - "@id" : "bts:SizeC" - }, { - "@id" : "bts:SizeT" - }, { - "@id" : "bts:SizeX" - }, { - "@id" : "bts:SizeY" - }, { - "@id" : "bts:SizeZ" - }, { - "@id" : "bts:PixelType" - } ], - "sms:displayName" : "ImagingLevel2" + "sms:displayName" : "IndicatorEnum", + "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Publication" - } ], - "@id" : "bts:PublicationTemplate", + "@id" : "bts:BreastCancerAssessmentTestsEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "BreastCancerAssessmentTestsEnum", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "PublicationTemplate", - "rdfs:comment" : "TBD", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:PublicationDOI" - }, { - "@id" : "bts:Title" - }, { - "@id" : "bts:Authors" - }, { - "@id" : "bts:LinkedProject" - }, { - "@id" : "bts:LinkedDatasets" - } ], - "sms:displayName" : "PublicationTemplate" + "sms:displayName" : "BreastCancerAssessmentTestsEnum", + "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Patient" - } ], - "@id" : "bts:Exposure", + "@id" : "bts:HereditaryCancerPredispositionSyndromeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "HereditaryCancerPredispositionSyndromeEnum", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "Exposure", - "rdfs:comment" : "TBD", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:TimepointLabel" - }, { - "@id" : "bts:StartDaysfromIndex" - }, { - "@id" : "bts:SmokingExposure" - }, { - "@id" : "bts:AlcoholExposure" - }, { - "@id" : "bts:EnvironmentalTobaccoSmokeExposure" - } ], - "sms:displayName" : "Exposure" + "sms:displayName" : "HereditaryCancerPredispositionSyndromeEnum", + "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Exposure" - } ], - "@id" : "bts:Yes-SmokingExposure", + "@id" : "bts:BreastCarcinomaDetectionMethodTypeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "BreastCarcinomaDetectionMethodTypeEnum", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "Yes-SmokingExposure", + "sms:displayName" : "BreastCarcinomaDetectionMethodTypeEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:CancerAssociatedGeneMutationsEnum", + "@type" : "rdfs:Class", "rdfs:comment" : "TBD", + "rdfs:label" : "CancerAssociatedGeneMutationsEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "CancerAssociatedGeneMutationsEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:RelativewithCancerHistoryEnum", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:TimepointLabel" - }, { - "@id" : "bts:StartDaysfromIndex" - }, { - "@id" : "bts:SmokingExposure" - }, { - "@id" : "bts:AlcoholExposure" - }, { - "@id" : "bts:EnvironmentalTobaccoSmokeExposure" - }, { - "@id" : "bts:YearsSmoked" - }, { - "@id" : "bts:PackYearsSmoked" - }, { - "@id" : "bts:CigarettesperDay" - }, { - "@id" : "bts:SmokingFrequency" - }, { - "@id" : "bts:TypeofSmokeExposure" - }, { - "@id" : "bts:TimebetweenWakingandFirstSmoke" - }, { - "@id" : "bts:TobaccoSmokingOnsetYear" - }, { - "@id" : "bts:TobaccoSmokingQuitYear" - }, { - "@id" : "bts:TobaccoSmokingStatus" - }, { - "@id" : "bts:TypeofTobaccoUsed" - }, { - "@id" : "bts:SecondhandSmokeasChild" - }, { - "@id" : "bts:SmokeExposureDuration" - }, { - "@id" : "bts:TobaccoUseperDay" - }, { - "@id" : "bts:SmokelessTobaccoQuitAge" - } ], - "sms:displayName" : "Yes-SmokingExposure" + "rdfs:comment" : "TBD", + "rdfs:label" : "RelativewithCancerHistoryEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "RelativewithCancerHistoryEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:EthnicityEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "EthnicityEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:MolecularTest", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "MolecularTest", + "sms:displayName" : "EthnicityEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:ImmersionEnum", + "@type" : "rdfs:Class", "rdfs:comment" : "TBD", + "rdfs:label" : "ImmersionEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ImmersionEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:BreastCancerGenomicTestPerformedEnum", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:TimepointLabel" - }, { - "@id" : "bts:StartDaysfromIndex" - }, { - "@id" : "bts:StopDaysfromIndex" - }, { - "@id" : "bts:GeneSymbol" - }, { - "@id" : "bts:MolecularAnalysisMethod" - }, { - "@id" : "bts:TestResult" - }, { - "@id" : "bts:AAChange" - }, { - "@id" : "bts:Antigen" - }, { - "@id" : "bts:ClinicalBiospecimenType" - }, { - "@id" : "bts:BloodTestNormalRangeUpper" - }, { - "@id" : "bts:BloodTestNormalRangeLower" - }, { - "@id" : "bts:CellCount" - }, { - "@id" : "bts:Chromosome" - }, { - "@id" : "bts:Clonality" - }, { - "@id" : "bts:CopyNumber" - }, { - "@id" : "bts:Cytoband" - }, { - "@id" : "bts:Exon" - }, { - "@id" : "bts:HistoneFamily" - }, { - "@id" : "bts:HistoneVariant" - }, { - "@id" : "bts:Intron" - }, { - "@id" : "bts:LaboratoryTest" - }, { - "@id" : "bts:LociAbnormalCount" - }, { - "@id" : "bts:LociCount" - }, { - "@id" : "bts:Locus" - }, { - "@id" : "bts:MismatchRepairMutation" - }, { - "@id" : "bts:MolecularConsequence" - }, { - "@id" : "bts:Pathogenicity" - }, { - "@id" : "bts:Ploidy" - }, { - "@id" : "bts:SecondExon" - }, { - "@id" : "bts:SecondGeneSymbol" - }, { - "@id" : "bts:SpecializedMolecularTest" - }, { - "@id" : "bts:TestAnalyteType" - }, { - "@id" : "bts:TestUnits" - }, { - "@id" : "bts:TestValue" - }, { - "@id" : "bts:Transcript" - }, { - "@id" : "bts:VariantOrigin" - }, { - "@id" : "bts:VariantType" - }, { - "@id" : "bts:Zygosity" - } ], - "sms:displayName" : "MolecularTest" + "rdfs:comment" : "TBD", + "rdfs:label" : "BreastCancerGenomicTestPerformedEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BreastCancerGenomicTestPerformedEnum", + "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:FamilyHistory" - } ], - "@id" : "bts:Yes-CancerHistoryRelative", + "@id" : "bts:FileFormatEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "FileFormatEnum", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "Yes-CancerHistoryRelative", + "sms:displayName" : "FileFormatEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:DimensionOrderEnum", + "@type" : "rdfs:Class", "rdfs:comment" : "TBD", + "rdfs:label" : "DimensionOrderEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "DimensionOrderEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:SexEnum", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:TimepointLabel" - }, { - "@id" : "bts:RelativewithCancerHistory" - }, { - "@id" : "bts:RelativeswithCancerHistoryCount" - }, { - "@id" : "bts:RelationshipType" - }, { - "@id" : "bts:RelationshipPrimaryDiagnosis" - }, { - "@id" : "bts:RelationshipGender" - }, { - "@id" : "bts:RelationshipAgeatDiagnosis" - } ], - "sms:displayName" : "Yes-CancerHistoryRelative" + "rdfs:comment" : "TBD", + "rdfs:label" : "SexEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SexEnum", + "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Patient" - } ], - "@id" : "bts:PatientExtended", + "@id" : "bts:AlcoholIntensityEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "AlcoholIntensityEnum", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "PatientExtended", + "sms:displayName" : "AlcoholIntensityEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:ImagingAssayTypeEnum", + "@type" : "rdfs:Class", "rdfs:comment" : "TBD", + "rdfs:label" : "ImagingAssayTypeEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ImagingAssayTypeEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:PassedQCEnum", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:TimepointLabel" - }, { - "@id" : "bts:StartDaysfromIndex" - }, { - "@id" : "bts:StopDaysfromIndex" - }, { - "@id" : "bts:SentinelLymphNodeCount" - }, { - "@id" : "bts:SentinelNodePositiveAssessmentCount" - }, { - "@id" : "bts:TumorExtranodalExtensionIndicator" - }, { - "@id" : "bts:SatelliteMetastasisPresentIndicator" - }, { - "@id" : "bts:OtherBiopsyResectionSite" - }, { - "@id" : "bts:ExtentofTumorResection" - }, { - "@id" : "bts:PrecancerousConditionType" - }, { - "@id" : "bts:PriorSitesofRadiation" - }, { - "@id" : "bts:Immunosuppression" - }, { - "@id" : "bts:ConcomitantMedicationReceivedType" - }, { - "@id" : "bts:FamilyMemberVitalStatusIndicator" - }, { - "@id" : "bts:COVID19OccurrenceIndicator" - }, { - "@id" : "bts:COVID19CurrentStatus" - }, { - "@id" : "bts:COVID19PositiveLabTestIndicator" - }, { - "@id" : "bts:COVID19AntibodyTesting" - }, { - "@id" : "bts:COVID19ComplicationsSeverity" - }, { - "@id" : "bts:COVID19CancerTreatmentFollowup" - }, { - "@id" : "bts:Ecigvapeuse" - }, { - "@id" : "bts:Ecigvape30dayusenum" - }, { - "@id" : "bts:Ecigvapetimesperday" - }, { - "@id" : "bts:Typeofsmokeexposurecumulativeyears" - }, { - "@id" : "bts:Chewingtobaccodailyusecount" - }, { - "@id" : "bts:Secondhandsmokeexposureyears" - }, { - "@id" : "bts:KnownGeneticPredispositionMutation" - }, { - "@id" : "bts:HereditaryCancerPredispositionSyndrome" - }, { - "@id" : "bts:CancerAssociatedGeneMutations" - }, { - "@id" : "bts:MutationalSignatures" - }, { - "@id" : "bts:MismatchRepairSystemStatus" - }, { - "@id" : "bts:LabTestsforMMRStatus" - }, { - "@id" : "bts:ModeofCancerDetection" - }, { - "@id" : "bts:EducationLevel" - }, { - "@id" : "bts:CountryofBirth" - }, { - "@id" : "bts:MedicallyUnderservedArea" - }, { - "@id" : "bts:RuralvsUrban" - }, { - "@id" : "bts:CancerIncidence" - }, { - "@id" : "bts:CancerIncidenceLocation" - } ], - "sms:displayName" : "PatientExtended" + "rdfs:comment" : "TBD", + "rdfs:label" : "PassedQCEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "PassedQCEnum", + "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:SingleCellSequencing" - } ], - "@id" : "bts:ScRNA-seqLevel3", + "@id" : "bts:ExtentofTumorResectionEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ExtentofTumorResectionEnum", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "ScRNA-seqLevel3", + "sms:displayName" : "ExtentofTumorResectionEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:ReverseTranscriptionPrimerEnum", + "@type" : "rdfs:Class", "rdfs:comment" : "TBD", + "rdfs:label" : "ReverseTranscriptionPrimerEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ReverseTranscriptionPrimerEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:CountryofResidenceEnum", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:Filename" - }, { - "@id" : "bts:FileFormat" - }, { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:SampleID" - }, { - "@id" : "bts:AltSampleID" - }, { - "@id" : "bts:SequencingPlatform" - }, { - "@id" : "bts:NucleicAcidSource" - }, { - "@id" : "bts:LibraryConstructionMethod" - }, { - "@id" : "bts:LibrarySelectionMethod" - }, { - "@id" : "bts:LibraryLayout" - }, { - "@id" : "bts:LibraryPrepKitName" - }, { - "@id" : "bts:LibraryPrepKitVersion" - }, { - "@id" : "bts:LibraryPrepKitVendor" - }, { - "@id" : "bts:ReadIndicator" - }, { - "@id" : "bts:ReadContent" - }, { - "@id" : "bts:TargetDepth" - }, { - "@id" : "bts:AdapterName" - }, { - "@id" : "bts:AdapterSequence" - }, { - "@id" : "bts:BatchID" - }, { - "@id" : "bts:LaneNumber" - }, { - "@id" : "bts:TechnicalReplicateGroup" - }, { - "@id" : "bts:DissociationMethod" - }, { - "@id" : "bts:CryopreservedCellsinSample" - }, { - "@id" : "bts:SingleCellIsolationMethod" - }, { - "@id" : "bts:TotalNumberofInputCells" - }, { - "@id" : "bts:InputCellsandNuclei" - }, { - "@id" : "bts:ReverseTranscriptionPrimer" - }, { - "@id" : "bts:SpikeIn" - }, { - "@id" : "bts:EndBias" - }, { - "@id" : "bts:DataCategory" - }, { - "@id" : "bts:MatrixType" - }, { - "@id" : "bts:LinkedMatrices" - }, { - "@id" : "bts:CellMedianNumberReads" - }, { - "@id" : "bts:CellMedianNumberGenes" - }, { - "@id" : "bts:CellTotal" - }, { - "@id" : "bts:ScRNAseqWorkflowType" - }, { - "@id" : "bts:ScRNAseqWorkflowParametersDescription" - }, { - "@id" : "bts:WorkflowLink" - }, { - "@id" : "bts:WorkflowVersion" - } ], - "sms:displayName" : "ScRNA-seqLevel3" + "rdfs:comment" : "TBD", + "rdfs:label" : "CountryofResidenceEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "CountryofResidenceEnum", + "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Biospecimen" - } ], - "@id" : "bts:AnalyteBiospecimenType", + "@id" : "bts:TobaccoSmokingStatusEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "TobaccoSmokingStatusEnum", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "AnalyteBiospecimenType", + "sms:displayName" : "TobaccoSmokingStatusEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:OncotypeRiskGroupEnum", + "@type" : "rdfs:Class", "rdfs:comment" : "TBD", + "rdfs:label" : "OncotypeRiskGroupEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "OncotypeRiskGroupEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:PathogenicityEnum", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:BiospecimenID" - }, { - "@id" : "bts:ParentID" - }, { - "@id" : "bts:ParentBiospecimenID" - }, { - "@id" : "bts:AdjacentBiospecimenIDs" - }, { - "@id" : "bts:BiospecimenType" - }, { - "@id" : "bts:TimepointLabel" - }, { - "@id" : "bts:SpecimenLaterality" - }, { - "@id" : "bts:AnalyteType" - }, { - "@id" : "bts:FixationDuration" - }, { - "@id" : "bts:SlideChargeType" - }, { - "@id" : "bts:SectionThicknessValue" - }, { - "@id" : "bts:SectioningDaysfromIndex" - }, { - "@id" : "bts:ShippingConditionType" - }, { - "@id" : "bts:IschemicTime" - }, { - "@id" : "bts:IschemicTemperature" - } ], - "sms:displayName" : "AnalyteBiospecimenType" + "rdfs:comment" : "TBD", + "rdfs:label" : "PathogenicityEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "PathogenicityEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:LabTestsforMMRStatusEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "LabTestsforMMRStatusEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "LabTestsforMMRStatusEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:LibraryConstructionMethodEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "LibraryConstructionMethodEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "LibraryConstructionMethodEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:BisulfiteConversionKitEnum", + 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"sms:displayName" : "LibraryLayoutEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:BreastCancerAllredEstrogenReceptorScoreEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "BreastCancerAllredEstrogenReceptorScoreEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BreastCancerAllredEstrogenReceptorScoreEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:PrecancerousConditionTypeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "PrecancerousConditionTypeEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "PrecancerousConditionTypeEnum", + "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Exposure" - } ], - "@id" : "bts:Yes-AlcoholExposure", + "@id" : "bts:VariantTypeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : 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"bts:AlcoholDaysPerWeek" - }, { - "@id" : "bts:AlcoholDrinksPerDay" - }, { - "@id" : "bts:AlcoholHistory" - }, { - "@id" : "bts:AlcoholIntensity" - }, { - "@id" : "bts:AlcoholType" - } ], - "sms:displayName" : "Yes-AlcoholExposure" + "rdfs:comment" : "TBD", + "rdfs:label" : "SmokingExposureEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SmokingExposureEnum", + "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:File" - } ], - "@id" : "bts:BulkMethylation-seqLevel3", + "@id" : "bts:OvarianCancerPlatinumStatusEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "OvarianCancerPlatinumStatusEnum", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "BulkMethylation-seqLevel3", - "rdfs:comment" : "Sample level summary data for bulk methylation sequencing, such as t-SNE plot coordinates, etc.", + "sms:displayName" : "OvarianCancerPlatinumStatusEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:HistoneFamilyEnum", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:Filename" - }, { - "@id" : "bts:FileFormat" - }, { - "@id" : "bts:DMCallingTool" - }, { - "@id" : "bts:WorkflowLink" - }, { - "@id" : "bts:PUC19methylationratio" - }, { - "@id" : "bts:Lambdamethylationratio" - } ], - "sms:displayName" : "BulkMethylation-seqLevel3" + "rdfs:comment" : "TBD", + "rdfs:label" : "HistoneFamilyEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "HistoneFamilyEnum", + "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:SingleCellSequencing" - } ], - "@id" : "bts:ScRNA-seqLevel1", + "@id" : "bts:ChromosomeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ChromosomeEnum", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "ScRNA-seqLevel1", + "sms:displayName" : "ChromosomeEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:OvarianCancerHistologicSubtypeEnum", + "@type" : "rdfs:Class", "rdfs:comment" : "TBD", + "rdfs:label" : "OvarianCancerHistologicSubtypeEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "OvarianCancerHistologicSubtypeEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:MicroscopyUnitEnum", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:Filename" - }, { - "@id" : "bts:FileFormat" - }, { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:SampleID" - }, { - "@id" : "bts:AltSampleID" - }, { - "@id" : "bts:SequencingPlatform" - }, { - "@id" : "bts:NucleicAcidSource" - }, { - "@id" : "bts:LibraryConstructionMethod" - }, { - "@id" : "bts:LibrarySelectionMethod" - }, { - "@id" : "bts:LibraryLayout" - }, { - "@id" : "bts:LibraryPrepKitName" - }, { - "@id" : "bts:LibraryPrepKitVersion" - }, { - "@id" : "bts:LibraryPrepKitVendor" - }, { - "@id" : "bts:ReadIndicator" - }, { - "@id" : "bts:ReadContent" - }, { - "@id" : "bts:TargetDepth" - }, { - "@id" : "bts:AdapterName" - }, { - "@id" : "bts:AdapterSequence" - }, { - "@id" : "bts:BatchID" - }, { - "@id" : "bts:LaneNumber" - }, { - "@id" : "bts:TechnicalReplicateGroup" - }, { - "@id" : "bts:DissociationMethod" - }, { - "@id" : "bts:CryopreservedCellsinSample" - }, { - "@id" : "bts:SingleCellIsolationMethod" - }, { - "@id" : "bts:TotalNumberofInputCells" - }, { - "@id" : "bts:InputCellsandNuclei" - }, { - "@id" : "bts:ReverseTranscriptionPrimer" - }, { - "@id" : "bts:SpikeIn" - }, { - "@id" : "bts:EndBias" - }, { - "@id" : "bts:UMIBarcodeOffset" - }, { - "@id" : "bts:UMIBarcodeLength" - }, { - "@id" : "bts:MedianUMIsperCellNumber" - }, { - "@id" : "bts:CellBarcodeOffset" - }, { - "@id" : "bts:CellBarcodeLength" - }, { - "@id" : "bts:ValidBarcodesCellNumber" - } ], - "sms:displayName" : "ScRNA-seqLevel1" + "rdfs:comment" : "TBD", + "rdfs:label" : "MicroscopyUnitEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "MicroscopyUnitEnum", + "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Patient" - } ], - "@id" : "bts:BreastCancerPatient", + "@id" : "bts:HistoryEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "HistoryEnum", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "BreastCancerPatient", + "sms:displayName" : "HistoryEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:CauseofDeathEnum", + "@type" : "rdfs:Class", "rdfs:comment" : "TBD", + "rdfs:label" : "CauseofDeathEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "CauseofDeathEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:TestResultEnum", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:TimepointLabel" - }, { - "@id" : "bts:BreastCarcinomaDetectionMethodType" - }, { - "@id" : "bts:BreastCarcinomaHistologyCategory" - }, { - "@id" : "bts:InvasiveLobularBreastCarcinomaHistologicCategory" - }, { - "@id" : "bts:InvasiveDuctalBreastCarcinomaHistologicCategory" - }, { - "@id" : "bts:BreastBiopsyProcedureFindingType" - }, { - "@id" : "bts:BreastQuadrantSite" - }, { - "@id" : "bts:BreastCancerAssessmentTests" - }, { - "@id" : "bts:BreastCancerGenomicTestPerformed" - }, { - "@id" : "bts:MammaprintRiskGroup" - }, { - "@id" : "bts:OncotypeRiskGroup" - }, { - "@id" : "bts:ERReceptorStatus" - }, { - "@id" : "bts:PRReceptorStatus" - }, { - "@id" : "bts:BreastCancerAllredEstrogenReceptorScore" - }, { - "@id" : "bts:PriorInvasiveBreastDisease" - }, { - "@id" : "bts:BreastCarcinomaERStatusPercentageValue" - }, { - "@id" : "bts:BreastCarcinomaPRStatusPercentageValue" - }, { - "@id" : "bts:HER2BreastCarcinomaCopyNumberTotal" - }, { - "@id" : "bts:BreastCarcinomaCentromere17CopyNumber" - }, { - "@id" : "bts:BreastCarcinomaHER2Centromere17CopynumberTotal" - }, { - "@id" : "bts:BreastCarcinomaHER2Chromosome17Ratio" - }, { - "@id" : "bts:BreastCarcinomaSurgicalProcedureName" - }, { - "@id" : "bts:BreastCarcinomaHER2RatioDiagnosis" - }, { - "@id" : "bts:BreastCarcinomaHER2Status" - }, { - "@id" : "bts:HormoneTherapyBreastCancerPreventionIndicator" - }, { - "@id" : "bts:ERStainingIntensity" - }, { - "@id" : "bts:PRStainingIntensity" - }, { - "@id" : "bts:OncotypeScore" - }, { - "@id" : "bts:BreastImagingPerformedType" - }, { - "@id" : "bts:MultifocalBreastCarcinomaPresentIndicator" - }, { - "@id" : "bts:MulticentricBreastCarcinomaPresentIndicator" - }, { - "@id" : "bts:BIRADSMammographyBreastDensityCategory" - } ], - "sms:displayName" : "BreastCancerPatient" + "rdfs:comment" : "TBD", + "rdfs:label" : "TestResultEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "TestResultEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:AntigenEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "AntigenEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:Patient", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "Patient", + "sms:displayName" : "AntigenEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:MolecularConsequenceEnum", + "@type" : "rdfs:Class", "rdfs:comment" : "TBD", + "rdfs:label" : "MolecularConsequenceEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "MolecularConsequenceEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:ReceptorStatusEnum", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:TimepointLabel" - } ], - "sms:displayName" : "Patient" + "rdfs:comment" : "TBD", + "rdfs:label" : "ReceptorStatusEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ReceptorStatusEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:TumorTissueTypeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "TumorTissueTypeEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:File", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "File", - "rdfs:comment" : "Basic metadata for a file entity that contains data (whether sequencing, imaging, etc.) will inherit.", + "sms:displayName" : "TumorTissueTypeEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:BreastQuadrantSiteEnum", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:Filename" - }, { - "@id" : "bts:FileFormat" - } ], - "sms:displayName" : "File" + "rdfs:comment" : "TBD", + "rdfs:label" : "BreastQuadrantSiteEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BreastQuadrantSiteEnum", + "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:SingleCellSequencing" - } ], - "@id" : "bts:ScRNA-seqLevel2", + "@id" : "bts:PloidyEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "PloidyEnum", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "ScRNA-seqLevel2", + "sms:displayName" : "PloidyEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:SpecimenLateralityEnum", + "@type" : "rdfs:Class", "rdfs:comment" : "TBD", + "rdfs:label" : "SpecimenLateralityEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SpecimenLateralityEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:FamilyMemberVitalStatusIndicatorEnum", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:Filename" - }, { - "@id" : "bts:FileFormat" - }, { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:SampleID" - }, { - "@id" : "bts:AltSampleID" - }, { - "@id" : "bts:SequencingPlatform" - }, { - "@id" : "bts:NucleicAcidSource" - }, { - "@id" : "bts:LibraryConstructionMethod" - }, { - "@id" : "bts:LibrarySelectionMethod" - }, { - "@id" : "bts:LibraryLayout" - }, { - "@id" : "bts:LibraryPrepKitName" - }, { - "@id" : "bts:LibraryPrepKitVersion" - }, { - "@id" : "bts:LibraryPrepKitVendor" - }, { - "@id" : "bts:ReadIndicator" - }, { - "@id" : "bts:ReadContent" - }, { - "@id" : "bts:TargetDepth" - }, { - "@id" : "bts:AdapterName" - }, { - "@id" : "bts:AdapterSequence" - }, { - "@id" : "bts:BatchID" - }, { - "@id" : "bts:LaneNumber" - }, { - "@id" : "bts:TechnicalReplicateGroup" - }, { - "@id" : "bts:DissociationMethod" - }, { - "@id" : "bts:CryopreservedCellsinSample" - }, { - "@id" : "bts:SingleCellIsolationMethod" - }, { - "@id" : "bts:TotalNumberofInputCells" - }, { - "@id" : "bts:InputCellsandNuclei" - }, { - "@id" : "bts:ReverseTranscriptionPrimer" - }, { - "@id" : "bts:SpikeIn" - }, { - "@id" : "bts:EndBias" - }, { - "@id" : "bts:ScRNAseqWorkflowType" - }, { - "@id" : "bts:ScRNAseqWorkflowParametersDescription" - }, { - "@id" : "bts:WorkflowVersion" - }, { - "@id" : "bts:WorkflowLink" - }, { - "@id" : "bts:GenomicReference" - }, { - "@id" : 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"rdfs:comment" : "TBD", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:VascularInvasionType" - } ], - "sms:displayName" : "Yes-VascularInvasionPresent" + "sms:displayName" : "SequencingPlatformEnum", + "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:SequencingData" - } ], - "@id" : "bts:SingleCellSequencing", + "@id" : "bts:VariantOriginEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "VariantOriginEnum", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "SingleCellSequencing", - "rdfs:comment" : "TBD", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:Filename" - }, { - "@id" : "bts:FileFormat" - }, { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:SampleID" - }, { - "@id" : "bts:AltSampleID" - }, { - "@id" : 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"SingleCellSequencing" + "sms:displayName" : "VariantOriginEnum", + "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:SingleCellSequencing" - } ], - "@id" : "bts:ScATAC-seqLevel1", + "@id" : "bts:AnaplasiaPresentTypeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "AnaplasiaPresentTypeEnum", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "ScATAC-seqLevel1", - "rdfs:comment" : "TBD", + "sms:displayName" : "AnaplasiaPresentTypeEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:TranspositionReactionEnum", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:Filename" - }, { - "@id" : "bts:FileFormat" - }, { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:SampleID" - }, { - "@id" : "bts:AltSampleID" - }, { - "@id" : "bts:SequencingPlatform" - }, { - "@id" : "bts:NucleicAcidSource" - }, { - "@id" : "bts:LibraryConstructionMethod" - }, { - "@id" : "bts:LibrarySelectionMethod" - }, { - "@id" : "bts:LibraryLayout" - }, { - "@id" : "bts:LibraryPrepKitName" - }, { - "@id" : "bts:LibraryPrepKitVersion" - }, { - "@id" : "bts:LibraryPrepKitVendor" - }, { - "@id" : "bts:ReadIndicator" - }, { - "@id" : "bts:ReadContent" - }, { - "@id" : "bts:TargetDepth" - }, { - "@id" : "bts:AdapterName" - }, { - "@id" : "bts:AdapterSequence" - }, { - "@id" : "bts:BatchID" - }, { - "@id" : "bts:LaneNumber" - }, { - "@id" : "bts:TechnicalReplicateGroup" - }, { - "@id" : "bts:DissociationMethod" - }, { - "@id" : "bts:CryopreservedCellsinSample" - }, { - "@id" : "bts:SingleCellIsolationMethod" - }, { - "@id" : "bts:TotalNumberofInputCells" - }, { - "@id" : "bts:InputCellsandNuclei" - }, { - "@id" : "bts:ReverseTranscriptionPrimer" - }, { - "@id" : "bts:SpikeIn" - }, { - "@id" : "bts:EndBias" - }, { - "@id" : "bts:SingleNucleusBuffer" - }, { - "@id" : "bts:TranspositionReaction" - }, { - "@id" : "bts:NucleusIdentifier" - }, { - "@id" : "bts:NucleiBarcodeLength" - }, { - "@id" : "bts:NucleiBarcodeRead" - } ], - "sms:displayName" : "ScATAC-seqLevel1" + "rdfs:comment" : "TBD", + "rdfs:label" : "TranspositionReactionEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "TranspositionReactionEnum", + "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Biospecimen" - } ], - "@id" : "bts:TotalVolume", + "@id" : "bts:EndBiasEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "EndBiasEnum", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "TotalVolume", + "sms:displayName" : "EndBiasEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:HistoneVariantEnum", + "@type" : "rdfs:Class", "rdfs:comment" : "TBD", + "rdfs:label" : "HistoneVariantEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "HistoneVariantEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:BreastCarcinomaHistologyCategoryEnum", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:BiospecimenID" - }, { - "@id" : "bts:ParentID" - }, { - "@id" : "bts:ParentBiospecimenID" - }, { - "@id" : "bts:AdjacentBiospecimenIDs" - }, { - "@id" : "bts:BiospecimenType" - }, { - "@id" : "bts:TimepointLabel" - }, { - "@id" : "bts:SpecimenLaterality" - }, { - "@id" : "bts:TotalVolumeUnit" - } ], - "sms:displayName" : "TotalVolume" + "rdfs:comment" : "TBD", + "rdfs:label" : "BreastCarcinomaHistologyCategoryEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BreastCarcinomaHistologyCategoryEnum", + "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:File" - } ], - "@id" : "bts:BulkMethylation-seqLevel1", + "@id" : "bts:BreastImagingPerformedTypeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "BreastImagingPerformedTypeEnum", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "BulkMethylation-seqLevel1", - "rdfs:comment" : "Raw data for bulk methylation sequencing, such as FASTQs and unaligned BAMs", + "sms:displayName" : "BreastImagingPerformedTypeEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:AlcoholExposureEnum", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:Filename" - }, { - "@id" : "bts:FileFormat" - }, { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:SampleID" - }, { - "@id" : "bts:AltSampleID" - }, { - "@id" : "bts:NucleicAcidSource" - }, { - "@id" : "bts:BisulfiteConversionKit" - }, { - "@id" : "bts:BulkMethylationAssayType" - }, { - "@id" : "bts:SequencingPlatform" - }, { - "@id" : "bts:TechnicalReplicateGroup" - } ], - "sms:displayName" : "BulkMethylation-seqLevel1" + "rdfs:comment" : "TBD", + "rdfs:label" : "AlcoholExposureEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "AlcoholExposureEnum", + "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Biospecimen" - } ], - "@id" : "bts:UrineBiospecimenType", + "@id" : "bts:SlideChargeTypeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "SlideChargeTypeEnum", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "UrineBiospecimenType", + "sms:displayName" : "SlideChargeTypeEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:ShippingConditionTypeEnum", + "@type" : "rdfs:Class", "rdfs:comment" : "TBD", + "rdfs:label" : "ShippingConditionTypeEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ShippingConditionTypeEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:SingleCellIsolationMethodEnum", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:BiospecimenID" - }, { - "@id" : "bts:ParentID" - }, { - "@id" : "bts:ParentBiospecimenID" - }, { - "@id" : "bts:AdjacentBiospecimenIDs" - }, { - "@id" : "bts:BiospecimenType" - }, { - "@id" : "bts:TimepointLabel" - }, { - "@id" : "bts:SpecimenLaterality" - }, { - "@id" : "bts:IschemicTime" - }, { - "@id" : "bts:IschemicTemperature" - }, { - "@id" : "bts:SiteofResectionorBiopsy" - }, { - "@id" : "bts:PortionWeight" - }, { - "@id" : "bts:TotalVolume" - }, { - "@id" : "bts:TumorTissueType" - }, { - "@id" : "bts:HistologicMorphologyCode" - }, { - "@id" : "bts:PreservationMethod" - } ], - "sms:displayName" : "UrineBiospecimenType" + "rdfs:comment" : "TBD", + "rdfs:label" : "SingleCellIsolationMethodEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SingleCellIsolationMethodEnum", + "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ { - "@id" : "bts:ImagingLevel2" + "@id" : "bts:Assay" } ], - "@id" : "bts:ImagingLevel2Channels", + "@id" : "bts:ImagingLevel2", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "sms:requiresComponent" : "", - "rdfs:label" : "ImagingLevel2Channels", + "rdfs:label" : "ImagingLevel2", "rdfs:comment" : "TBD", "@type" : "rdfs:Class", "sms:requiresDependency" : [ { @@ -10014,264 +10022,97 @@ }, { "@id" : "bts:Immersion" }, { - "@id" : "bts:Pyramid" - }, { - "@id" : "bts:Zstack" - }, { - "@id" : "bts:Tseries" - }, { - "@id" : "bts:PassedQC" - }, { - "@id" : "bts:Comment" - }, { - "@id" : "bts:FOVnumber" - }, { - "@id" : "bts:FOVX" - }, { - "@id" : "bts:FOVXUnit" - }, { - "@id" : "bts:FOVY" - }, { - "@id" : "bts:FOVYUnit" - }, { - "@id" : "bts:FrameAveraging" - }, { - "@id" : "bts:ImageID" - }, { - "@id" : "bts:DimensionOrder" - }, { - "@id" : "bts:PhysicalSizeX" - }, { - "@id" : "bts:PhysicalSizeXUnit" - }, { - "@id" : "bts:PhysicalSizeY" - }, { - "@id" : "bts:PhysicalSizeYUnit" - }, { - "@id" : "bts:PhysicalSizeZ" - }, { - "@id" : "bts:PhysicalSizeZUnit" - }, { - "@id" : "bts:PixelsBigEndian" - }, { - "@id" : "bts:PlaneCount" - }, { - "@id" : "bts:SizeC" - }, { - "@id" : "bts:SizeT" - }, { - "@id" : "bts:SizeX" - }, { - "@id" : "bts:SizeY" - }, { - "@id" : "bts:SizeZ" - }, { - "@id" : "bts:PixelType" - }, { - "@id" : "bts:ChannelID" - }, { - "@id" : "bts:ChannelName" - }, { - "@id" : "bts:ChannelPassedQC" - }, { - "@id" : "bts:CycleNumber" - }, { - "@id" : "bts:SubCycleNumber" - }, { - "@id" : "bts:TargetName" - }, { - "@id" : "bts:AntibodyName" - }, { - "@id" : "bts:RRIDidentifier" - }, { - "@id" : "bts:Fluorophore" - }, { - "@id" : "bts:Clone" - }, { - "@id" : "bts:Lot" - }, { - "@id" : "bts:Vendor" - }, { - "@id" : "bts:CatalogNumber" - }, { - "@id" : "bts:ExcitationWavelength" - }, { - "@id" : "bts:EmissionWavelength" - }, { - "@id" : "bts:ExcitationBandwidth" - }, { - "@id" : "bts:EmissionBandwidth" - }, { - "@id" : "bts:MetalIsotopeElement" - }, { - "@id" : "bts:MetalIsotopeMass" - }, { - "@id" : "bts:OligoBarcodeUpperStrand" - }, { - "@id" : "bts:OligoBarcodeLowerStrand" - }, { - "@id" : "bts:Dilution" - }, { - "@id" : "bts:Concentration" - } ], - "sms:displayName" : "ImagingLevel2Channels" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:SampleCoreTemplate", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "SampleCoreTemplate", - "rdfs:comment" : "TBD", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:SampleID" - }, { - "@id" : "bts:DetailedSampleID" - }, { - "@id" : "bts:AdjacentSampleIDs" - }, { - "@id" : "bts:SampleSite" - }, { - "@id" : "bts:ERStatus" - }, { - "@id" : "bts:PRStatus" - }, { - "@id" : "bts:HER2Status" - }, { - "@id" : "bts:Laterality" - } ], - "sms:displayName" : "SampleCoreTemplate" - }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:File" - } ], - "@id" : "bts:SequencingData", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "SequencingData", - "rdfs:comment" : "Base template for some type of sequencing data file, for which below properties are relevant/in common.", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:Filename" - }, { - "@id" : "bts:FileFormat" + "@id" : "bts:Pyramid" }, { - "@id" : "bts:ParticipantID" + "@id" : "bts:Zstack" }, { - "@id" : "bts:SampleID" + "@id" : "bts:Tseries" }, { - "@id" : "bts:AltSampleID" + "@id" : "bts:PassedQC" }, { - "@id" : "bts:SequencingPlatform" + "@id" : "bts:Comment" }, { - "@id" : "bts:NucleicAcidSource" + "@id" : "bts:FOVnumber" }, { - "@id" : "bts:LibraryConstructionMethod" + "@id" : "bts:FOVX" }, { - "@id" : "bts:LibrarySelectionMethod" + "@id" : "bts:FOVXUnit" }, { - "@id" : "bts:LibraryLayout" + "@id" : "bts:FOVY" }, { - "@id" : "bts:LibraryPrepKitName" + "@id" : "bts:FOVYUnit" }, { - "@id" : "bts:LibraryPrepKitVersion" + "@id" : "bts:FrameAveraging" }, { - "@id" : "bts:LibraryPrepKitVendor" + "@id" : "bts:ImageID" }, { - "@id" : "bts:ReadIndicator" + "@id" : "bts:DimensionOrder" }, { - "@id" : "bts:ReadContent" + "@id" : "bts:PhysicalSizeX" }, { - "@id" : "bts:TargetDepth" + "@id" : "bts:PhysicalSizeXUnit" }, { - "@id" : "bts:AdapterName" + "@id" : "bts:PhysicalSizeY" }, { - "@id" : "bts:AdapterSequence" + "@id" : "bts:PhysicalSizeYUnit" }, { - "@id" : "bts:BatchID" + "@id" : "bts:PhysicalSizeZ" }, { - "@id" : "bts:LaneNumber" + "@id" : "bts:PhysicalSizeZUnit" }, { - "@id" : "bts:TechnicalReplicateGroup" - } ], - "sms:displayName" : "SequencingData" - }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:File" - } ], - "@id" : "bts:BulkMethylation-seqLevel2", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "BulkMethylation-seqLevel2", - "rdfs:comment" : "Aligned primary data for bulk methylation sequencing, such as gene expression matrix files, VCFs, etc.", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" + "@id" : "bts:PixelsBigEndian" }, { - "@id" : "bts:Filename" + "@id" : "bts:PlaneCount" }, { - "@id" : "bts:FileFormat" + "@id" : "bts:SizeC" }, { - "@id" : "bts:WorkflowVersion" + "@id" : "bts:SizeT" }, { - "@id" : "bts:WorkflowLink" + "@id" : "bts:SizeX" }, { - "@id" : "bts:GenomicReference" + "@id" : "bts:SizeY" }, { - "@id" : "bts:GenomicReferenceURL" + "@id" : "bts:SizeZ" }, { - "@id" : "bts:ProportionofMinimumCpGCoverage10X" + "@id" : "bts:PixelType" } ], - "sms:displayName" : "BulkMethylation-seqLevel2" + "sms:displayName" : "ImagingLevel2" }, { "rdfs:subClassOf" : [ { - "@id" : "bts:Diagnosis" + "@id" : "bts:Publication" } ], - "@id" : "bts:Yes-ProgressionorRecurrence", + "@id" : "bts:PublicationTemplate", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "sms:requiresComponent" : "", - "rdfs:label" : "Yes-ProgressionorRecurrence", + "rdfs:label" : "PublicationTemplate", "rdfs:comment" : "TBD", "@type" : "rdfs:Class", "sms:requiresDependency" : [ { - "@id" : "bts:ProgressionorRecurrenceType" + "@id" : "bts:PublicationDOI" }, { - "@id" : "bts:DaystoProgression" + "@id" : "bts:Title" }, { - "@id" : "bts:DaystoProgressionFree" + "@id" : "bts:Authors" }, { - "@id" : "bts:DaystoRecurrence" + "@id" : "bts:LinkedProject" }, { - "@id" : "bts:ProgressionorRecurrenceAnatomicSite" + "@id" : "bts:LinkedDatasets" } ], - "sms:displayName" : "Yes-ProgressionorRecurrence" + "sms:displayName" : "PublicationTemplate" }, { "rdfs:subClassOf" : [ { "@id" : "bts:Patient" } ], - "@id" : "bts:OvarianCancerPatient", + "@id" : "bts:Exposure", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "sms:requiresComponent" : "", - "rdfs:label" : "OvarianCancerPatient", + "rdfs:label" : "Exposure", "rdfs:comment" : "TBD", "@type" : "rdfs:Class", "sms:requiresDependency" : [ { @@ -10279,140 +10120,79 @@ }, { "@id" : "bts:ParticipantID" }, { - "@id" : "bts:TimepointLabel" - }, { - "@id" : "bts:OvarianCancerHistologicSubtype" - }, { - "@id" : "bts:OvarianCancerSurgicalOutcome" - }, { - "@id" : "bts:OvarianCancerPlatinumStatus" - } ], - "sms:displayName" : "OvarianCancerPatient" - }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Biospecimen" - } ], - "@id" : "bts:BoneMarrowBiospecimenType", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "BoneMarrowBiospecimenType", - "rdfs:comment" : "TBD", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:BiospecimenID" - }, { - "@id" : "bts:ParentID" - }, { - "@id" : "bts:ParentBiospecimenID" - }, { - "@id" : "bts:AdjacentBiospecimenIDs" - }, { - "@id" : "bts:BiospecimenType" - }, { - "@id" : "bts:TimepointLabel" - }, { - "@id" : "bts:SpecimenLaterality" - }, { - "@id" : "bts:IschemicTime" - }, { - "@id" : "bts:IschemicTemperature" - }, { - "@id" : "bts:SiteofResectionorBiopsy" - }, { - "@id" : "bts:PortionWeight" - }, { - "@id" : "bts:TotalVolume" - }, { - "@id" : "bts:TumorTissueType" - }, { - "@id" : "bts:HistologicMorphologyCode" - }, { - "@id" : "bts:PreservationMethod" - }, { - "@id" : "bts:BiospecimenDimension1" + "@id" : "bts:StartDaysfromIndex" }, { - "@id" : "bts:BiospecimenDimension2" + "@id" : "bts:SmokingExposure" }, { - "@id" : "bts:BiospecimenDimension3" + "@id" : "bts:AlcoholExposure" }, { - "@id" : "bts:SectionNumberinSequence" + "@id" : "bts:EnvironmentalTobaccoSmokeExposure" } ], - "sms:displayName" : "BoneMarrowBiospecimenType" + "sms:displayName" : "Exposure" }, { "rdfs:subClassOf" : [ { - "@id" : "bts:SequencingData" + "@id" : "bts:Exposure" } ], - "@id" : "bts:BulkDNA-seqLevel1", + "@id" : "bts:Yes-SmokingExposure", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "sms:requiresComponent" : "", - "rdfs:label" : "BulkDNA-seqLevel1", + "rdfs:label" : "Yes-SmokingExposure", "rdfs:comment" : "TBD", "@type" : "rdfs:Class", "sms:requiresDependency" : [ { "@id" : "bts:Component" - }, { - "@id" : "bts:Filename" - }, { - "@id" : "bts:FileFormat" }, { "@id" : "bts:ParticipantID" }, { - "@id" : "bts:SampleID" - }, { - "@id" : "bts:AltSampleID" + "@id" : "bts:StartDaysfromIndex" }, { - "@id" : "bts:SequencingPlatform" + "@id" : "bts:SmokingExposure" }, { - "@id" : "bts:NucleicAcidSource" + "@id" : "bts:AlcoholExposure" }, { - "@id" : "bts:LibraryConstructionMethod" + "@id" : "bts:EnvironmentalTobaccoSmokeExposure" }, { - "@id" : "bts:LibrarySelectionMethod" + "@id" : "bts:YearsSmoked" }, { - "@id" : "bts:LibraryLayout" + "@id" : "bts:PackYearsSmoked" }, { - "@id" : "bts:LibraryPrepKitName" + "@id" : "bts:CigarettesperDay" }, { - "@id" : "bts:LibraryPrepKitVersion" + "@id" : "bts:SmokingFrequency" }, { - "@id" : "bts:LibraryPrepKitVendor" + "@id" : "bts:TypeofSmokeExposure" }, { - "@id" : "bts:ReadIndicator" + "@id" : "bts:TimebetweenWakingandFirstSmoke" }, { - "@id" : "bts:ReadContent" + "@id" : "bts:TobaccoSmokingOnsetYear" }, { - "@id" : "bts:TargetDepth" + "@id" : "bts:TobaccoSmokingQuitYear" }, { - "@id" : "bts:AdapterName" + "@id" : "bts:TobaccoSmokingStatus" }, { - "@id" : "bts:AdapterSequence" + "@id" : "bts:TypeofTobaccoUsed" }, { - "@id" : "bts:BatchID" + "@id" : "bts:SecondhandSmokeasChild" }, { - "@id" : "bts:LaneNumber" + "@id" : "bts:SmokeExposureDuration" }, { - "@id" : "bts:TechnicalReplicateGroup" + "@id" : "bts:TobaccoUseperDay" }, { - "@id" : "bts:TargetCaptureKit" + "@id" : "bts:SmokelessTobaccoQuitAge" } ], - "sms:displayName" : "BulkDNA-seqLevel1" + "sms:displayName" : "Yes-SmokingExposure" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Patient" - } ], - "@id" : "bts:CohortCoreTemplate", + "rdfs:subClassOf" : [ ], + "@id" : "bts:MolecularTest", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "sms:requiresComponent" : "", - "rdfs:label" : "CohortCoreTemplate", + "rdfs:label" : "MolecularTest", "rdfs:comment" : "TBD", "@type" : "rdfs:Class", "sms:requiresDependency" : [ { @@ -10422,284 +10202,216 @@ }, { "@id" : "bts:TimepointLabel" }, { - "@id" : "bts:Age" - }, { - "@id" : "bts:Sex" - }, { - "@id" : "bts:BMI" - }, { - "@id" : "bts:Race" - }, { - "@id" : "bts:Ethnicity" - }, { - "@id" : "bts:VitalStatus" - }, { - "@id" : "bts:Height" - }, { - "@id" : "bts:Weight" - }, { - "@id" : "bts:Gravidity" - }, { - "@id" : "bts:Parity" + "@id" : "bts:StartDaysfromIndex" }, { - "@id" : "bts:AgeAtMenarche" + "@id" : "bts:StopDaysfromIndex" }, { - "@id" : "bts:MenstrualCyclePhase" + "@id" : "bts:GeneSymbol" }, { - "@id" : "bts:MenopauseStatus" + "@id" : "bts:MolecularAnalysisMethod" }, { - "@id" : "bts:PrimaryDiagnosis" + "@id" : "bts:TestResult" }, { - "@id" : "bts:AgeatDiagnosis" + "@id" : "bts:AAChange" }, { - "@id" : "bts:DiagnosisStatusType" + "@id" : "bts:Antigen" }, { - "@id" : "bts:ClassBRCA1" + "@id" : "bts:ClinicalBiospecimenType" }, { - "@id" : "bts:ClassBRCA2" + "@id" : "bts:BloodTestNormalRangeUpper" }, { - "@id" : "bts:TobaccoUse" + "@id" : "bts:BloodTestNormalRangeLower" }, { - "@id" : "bts:PackYearsSmoked" + "@id" : "bts:CellCount" }, { - "@id" : "bts:AlcoholUse" + "@id" : "bts:Chromosome" }, { - "@id" : "bts:NumberofDrinksPerWeek" + "@id" : "bts:Clonality" }, { - "@id" : "bts:AntibioticUse" + "@id" : "bts:CopyNumber" }, { - "@id" : "bts:SampleCollectionCenter" + "@id" : "bts:Cytoband" }, { - "@id" : "bts:SampleCollectionYear" + "@id" : "bts:Exon" }, { - "@id" : "bts:ERStatus" + "@id" : "bts:HistoneFamily" }, { - "@id" : "bts:PRStatus" + "@id" : "bts:HistoneVariant" }, { - "@id" : "bts:HER2Status" - } ], - "sms:displayName" : "CohortCoreTemplate" - }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Biospecimen" - } ], - "@id" : "bts:TissueBiospecimenType", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "TissueBiospecimenType", - "rdfs:comment" : "TBD", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:BiospecimenID" + "@id" : "bts:Intron" }, { - "@id" : "bts:ParentID" + "@id" : "bts:LaboratoryTest" }, { - "@id" : "bts:ParentBiospecimenID" + "@id" : "bts:LociAbnormalCount" }, { - "@id" : "bts:AdjacentBiospecimenIDs" + "@id" : "bts:LociCount" }, { - "@id" : "bts:BiospecimenType" + "@id" : "bts:Locus" }, { - "@id" : "bts:TimepointLabel" + "@id" : "bts:MismatchRepairMutation" }, { - "@id" : "bts:SpecimenLaterality" + "@id" : "bts:MolecularConsequence" }, { - "@id" : "bts:IschemicTime" + "@id" : "bts:Pathogenicity" }, { - "@id" : "bts:IschemicTemperature" + "@id" : "bts:Ploidy" }, { - "@id" : "bts:SiteofResectionorBiopsy" + "@id" : "bts:SecondExon" }, { - "@id" : "bts:PortionWeight" + "@id" : "bts:SecondGeneSymbol" }, { - "@id" : "bts:TotalVolume" + "@id" : "bts:SpecializedMolecularTest" }, { - "@id" : "bts:TumorTissueType" + "@id" : "bts:TestAnalyteType" }, { - "@id" : "bts:HistologicMorphologyCode" + "@id" : "bts:TestUnits" }, { - "@id" : "bts:PreservationMethod" + "@id" : "bts:TestValue" }, { - "@id" : "bts:BiospecimenDimension1" + "@id" : "bts:Transcript" }, { - "@id" : "bts:BiospecimenDimension2" + "@id" : "bts:VariantOrigin" }, { - "@id" : "bts:BiospecimenDimension3" + "@id" : "bts:VariantType" }, { - "@id" : "bts:SectionNumberinSequence" + "@id" : "bts:Zygosity" } ], - "sms:displayName" : "TissueBiospecimenType" + "sms:displayName" : "MolecularTest" }, { "rdfs:subClassOf" : [ { - "@id" : "bts:Patient" + "@id" : "bts:FamilyHistory" } ], - "@id" : "bts:FamilyHistory", + "@id" : "bts:Yes-CancerHistoryRelative", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "sms:requiresComponent" : "", - "rdfs:label" : "FamilyHistory", + "rdfs:label" : "Yes-CancerHistoryRelative", "rdfs:comment" : "TBD", "@type" : "rdfs:Class", "sms:requiresDependency" : [ { "@id" : "bts:Component" }, { - "@id" : "bts:ParticipantID" + "@id" : "bts:RelativewithCancerHistory" }, { - "@id" : "bts:TimepointLabel" + "@id" : "bts:RelativeswithCancerHistoryCount" }, { - "@id" : "bts:RelativewithCancerHistory" + "@id" : "bts:RelationshipType" + }, { + "@id" : "bts:RelationshipPrimaryDiagnosis" + }, { + "@id" : "bts:RelationshipGender" + }, { + "@id" : "bts:RelationshipAgeatDiagnosis" } ], - "sms:displayName" : "FamilyHistory" + "sms:displayName" : "Yes-CancerHistoryRelative" }, { "rdfs:subClassOf" : [ { - "@id" : "bts:SingleCellSequencing" + "@id" : "bts:Patient" } ], - "@id" : "bts:ScRNA-seqLevel4", + "@id" : "bts:PatientExtended", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "sms:requiresComponent" : "", - "rdfs:label" : "ScRNA-seqLevel4", + "rdfs:label" : "PatientExtended", "rdfs:comment" : "TBD", "@type" : "rdfs:Class", "sms:requiresDependency" : [ { "@id" : "bts:Component" }, { - "@id" : "bts:Filename" - }, { - "@id" : "bts:FileFormat" + "@id" : "bts:StartDaysfromIndex" }, { - "@id" : "bts:ParticipantID" + "@id" : "bts:StopDaysfromIndex" }, { - "@id" : "bts:SampleID" + "@id" : "bts:SentinelLymphNodeCount" }, { - "@id" : "bts:AltSampleID" + "@id" : "bts:SentinelNodePositiveAssessmentCount" }, { - "@id" : "bts:SequencingPlatform" + "@id" : "bts:TumorExtranodalExtensionIndicator" }, { - "@id" : "bts:NucleicAcidSource" + "@id" : "bts:SatelliteMetastasisPresentIndicator" }, { - "@id" : "bts:LibraryConstructionMethod" + "@id" : "bts:OtherBiopsyResectionSite" }, { - "@id" : "bts:LibrarySelectionMethod" + "@id" : "bts:ExtentofTumorResection" }, { - "@id" : "bts:LibraryLayout" + "@id" : "bts:PrecancerousConditionType" }, { - "@id" : "bts:LibraryPrepKitName" + "@id" : "bts:PriorSitesofRadiation" }, { - "@id" : "bts:LibraryPrepKitVersion" + "@id" : "bts:Immunosuppression" }, { - "@id" : "bts:LibraryPrepKitVendor" + "@id" : "bts:ConcomitantMedicationReceivedType" }, { - "@id" : "bts:ReadIndicator" + "@id" : "bts:FamilyMemberVitalStatusIndicator" }, { - "@id" : "bts:ReadContent" + "@id" : "bts:COVID19OccurrenceIndicator" }, { - "@id" : "bts:TargetDepth" + "@id" : "bts:COVID19CurrentStatus" }, { - "@id" : "bts:AdapterName" + "@id" : "bts:COVID19PositiveLabTestIndicator" }, { - "@id" : "bts:AdapterSequence" + "@id" : "bts:COVID19AntibodyTesting" }, { - "@id" : "bts:BatchID" + "@id" : "bts:COVID19ComplicationsSeverity" }, { - "@id" : "bts:LaneNumber" + "@id" : "bts:COVID19CancerTreatmentFollowup" }, { - "@id" : "bts:TechnicalReplicateGroup" + "@id" : "bts:Ecigvapeuse" }, { - "@id" : "bts:DissociationMethod" + "@id" : "bts:Ecigvape30dayusenum" }, { - "@id" : "bts:CryopreservedCellsinSample" + "@id" : "bts:Ecigvapetimesperday" }, { - "@id" : "bts:SingleCellIsolationMethod" + "@id" : "bts:Typeofsmokeexposurecumulativeyears" }, { - "@id" : "bts:TotalNumberofInputCells" + "@id" : "bts:Chewingtobaccodailyusecount" }, { - "@id" : "bts:InputCellsandNuclei" + "@id" : "bts:Secondhandsmokeexposureyears" }, { - "@id" : "bts:ReverseTranscriptionPrimer" + "@id" : "bts:KnownGeneticPredispositionMutation" }, { - "@id" : "bts:SpikeIn" + "@id" : "bts:HereditaryCancerPredispositionSyndrome" }, { - "@id" : "bts:EndBias" + "@id" : "bts:CancerAssociatedGeneMutations" }, { - "@id" : "bts:DataCategory" + "@id" : "bts:MutationalSignatures" }, { - "@id" : "bts:MatrixType" + "@id" : "bts:MismatchRepairSystemStatus" }, { - "@id" : "bts:LinkedMatrices" + "@id" : "bts:LabTestsforMMRStatus" }, { - "@id" : "bts:CellMedianNumberReads" + "@id" : "bts:ModeofCancerDetection" }, { - "@id" : "bts:CellMedianNumberGenes" + "@id" : "bts:EducationLevel" }, { - "@id" : "bts:CellTotal" + "@id" : "bts:CountryofBirth" }, { - "@id" : "bts:ScRNAseqWorkflowType" + "@id" : "bts:MedicallyUnderservedArea" }, { - "@id" : "bts:ScRNAseqWorkflowParametersDescription" + "@id" : "bts:RuralvsUrban" }, { - "@id" : "bts:WorkflowLink" + "@id" : "bts:CancerIncidence" }, { - "@id" : "bts:WorkflowVersion" + "@id" : "bts:CancerIncidenceLocation" } ], - "sms:displayName" : "ScRNA-seqLevel4" + "sms:displayName" : "PatientExtended" }, { "rdfs:subClassOf" : [ { - "@id" : "bts:Patient" + "@id" : "bts:SingleCellSequencing" } ], - "@id" : "bts:Demographics", + "@id" : "bts:ScRNA-seqLevel3", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "sms:requiresComponent" : "", - "rdfs:label" : "Demographics", + "rdfs:label" : "ScRNA-seqLevel3", "rdfs:comment" : "TBD", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:TimepointLabel" - }, { - "@id" : "bts:Ethnicity" - }, { - "@id" : "bts:Gender" - }, { - "@id" : "bts:Race" - }, { - "@id" : "bts:VitalStatus" - }, { - "@id" : "bts:DaystoBirth" - }, { - "@id" : "bts:CountryofResidence" - }, { - "@id" : "bts:AgeIsObfuscated" - }, { - "@id" : "bts:YearOfBirth" - } ], - "sms:displayName" : "Demographics" - }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:ScRNA-seqLevel1" - } ], - "@id" : "bts:CEL-seq2", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "CEL-seq2", - "rdfs:comment" : "Highly-multiplexed plate-based single-cell RNA-Seq assay (so a subtype of scRNA-seq, and some additional metadata parameters are collected)", - "@type" : "rdfs:Class", "sms:requiresDependency" : [ { "@id" : "bts:Component" }, { @@ -10761,61 +10473,38 @@ }, { "@id" : "bts:EndBias" }, { - "@id" : "bts:UMIBarcodeOffset" - }, { - "@id" : "bts:UMIBarcodeLength" - }, { - "@id" : "bts:MedianUMIsperCellNumber" - }, { - "@id" : "bts:CellBarcodeOffset" - }, { - "@id" : "bts:CellBarcodeLength" + "@id" : "bts:DataCategory" }, { - "@id" : "bts:ValidBarcodesCellNumber" + "@id" : "bts:MatrixType" }, { - "@id" : "bts:EmptyWellBarcode" + "@id" : "bts:LinkedMatrices" }, { - "@id" : "bts:WellIndex" - } ], - "sms:displayName" : "CEL-seq2" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:Biospecimen", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "Biospecimen", - "rdfs:comment" : "TBD", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:BiospecimenID" + "@id" : "bts:CellMedianNumberReads" }, { - "@id" : "bts:ParentID" + "@id" : "bts:CellMedianNumberGenes" }, { - "@id" : "bts:ParentBiospecimenID" + "@id" : "bts:CellTotal" }, { - "@id" : "bts:AdjacentBiospecimenIDs" + "@id" : "bts:ScRNAseqWorkflowType" }, { - "@id" : "bts:BiospecimenType" + "@id" : "bts:ScRNAseqWorkflowParametersDescription" }, { - "@id" : "bts:TimepointLabel" + "@id" : "bts:WorkflowLink" }, { - "@id" : "bts:SpecimenLaterality" + "@id" : "bts:WorkflowVersion" } ], - "sms:displayName" : "Biospecimen" + "sms:displayName" : "ScRNA-seqLevel3" }, { "rdfs:subClassOf" : [ { "@id" : "bts:Biospecimen" } ], - "@id" : "bts:BiospecimenDimension1", + "@id" : "bts:AnalyteBiospecimenType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "sms:requiresComponent" : "", - "rdfs:label" : "BiospecimenDimension1", + "rdfs:label" : "AnalyteBiospecimenType", "rdfs:comment" : "TBD", "@type" : "rdfs:Class", "sms:requiresDependency" : [ { @@ -10833,1173 +10522,1563 @@ }, { "@id" : "bts:SpecimenLaterality" }, { - "@id" : "bts:DimensionsUnit" + "@id" : "bts:AnalyteType" + }, { + "@id" : "bts:FixationDuration" + }, { + "@id" : "bts:SlideChargeType" + }, { + "@id" : "bts:SectionThicknessValue" + }, { + "@id" : "bts:SectioningDaysfromIndex" + }, { + "@id" : "bts:ShippingConditionType" + }, { + "@id" : "bts:IschemicTime" + }, { + "@id" : "bts:IschemicTemperature" } ], - "sms:displayName" : "BiospecimenDimension1" + "sms:displayName" : "AnalyteBiospecimenType" }, { "rdfs:subClassOf" : [ { - "@id" : "bts:Biospecimen" + "@id" : "bts:Exposure" } ], - "@id" : "bts:BloodBiospecimenType", + "@id" : "bts:Yes-AlcoholExposure", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "sms:requiresComponent" : "", - "rdfs:label" : "BloodBiospecimenType", + "rdfs:label" : "Yes-AlcoholExposure", "rdfs:comment" : "TBD", "@type" : "rdfs:Class", "sms:requiresDependency" : [ { - "@id" : "bts:BiospecimenID" + "@id" : "bts:Component" }, { - "@id" : "bts:ParentID" + "@id" : "bts:ParticipantID" }, { - "@id" : "bts:ParentBiospecimenID" + "@id" : "bts:StartDaysfromIndex" }, { - "@id" : "bts:AdjacentBiospecimenIDs" + "@id" : "bts:SmokingExposure" }, { - "@id" : "bts:BiospecimenType" + "@id" : "bts:AlcoholExposure" }, { - "@id" : "bts:TimepointLabel" + "@id" : "bts:EnvironmentalTobaccoSmokeExposure" }, { - "@id" : "bts:SpecimenLaterality" + "@id" : "bts:AlcoholDaysPerWeek" }, { - "@id" : "bts:ShippingConditionType" - } ], - "sms:displayName" : "BloodBiospecimenType" - }, { - "@id" : "bts:IndicatorEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "IndicatorEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "IndicatorEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:BreastCancerAssessmentTestsEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BreastCancerAssessmentTestsEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "BreastCancerAssessmentTestsEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:HereditaryCancerPredispositionSyndromeEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "HereditaryCancerPredispositionSyndromeEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "HereditaryCancerPredispositionSyndromeEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:BreastCarcinomaDetectionMethodTypeEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BreastCarcinomaDetectionMethodTypeEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "BreastCarcinomaDetectionMethodTypeEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:CancerAssociatedGeneMutationsEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "CancerAssociatedGeneMutationsEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "CancerAssociatedGeneMutationsEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:RelativewithCancerHistoryEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "RelativewithCancerHistoryEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "RelativewithCancerHistoryEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:EthnicityEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "EthnicityEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "EthnicityEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:ImmersionEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ImmersionEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "ImmersionEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:BreastCancerGenomicTestPerformedEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BreastCancerGenomicTestPerformedEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "BreastCancerGenomicTestPerformedEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:FileFormatEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "FileFormatEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "FileFormatEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:DimensionOrderEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "DimensionOrderEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "DimensionOrderEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:SexEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "SexEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "SexEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:AlcoholIntensityEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "AlcoholIntensityEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "AlcoholIntensityEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:ImagingAssayTypeEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ImagingAssayTypeEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "ImagingAssayTypeEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:PassedQCEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "PassedQCEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "PassedQCEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:ExtentofTumorResectionEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ExtentofTumorResectionEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "ExtentofTumorResectionEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:ReverseTranscriptionPrimerEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ReverseTranscriptionPrimerEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "ReverseTranscriptionPrimerEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:CountryofResidenceEnum", - "@type" : 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"@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "AlcoholTypeEnum", - "rdfs:subClassOf" : [ ], + "rdfs:subClassOf" : [ { + "@id" : "bts:File" + } ], + "@id" : "bts:BulkMethylation-seqLevel3", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "AlcoholTypeEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:VitalStatusEnum", + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "BulkMethylation-seqLevel3", + "rdfs:comment" : "Sample level summary data for bulk methylation sequencing, such as t-SNE plot coordinates, etc.", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "VitalStatusEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "VitalStatusEnum", - "sms:required" : "sms:false" + "sms:requiresDependency" : [ { + "@id" : "bts:Component" + }, { + "@id" : "bts:Filename" + }, { + "@id" : "bts:FileFormat" + }, { + "@id" : "bts:DMCallingTool" + }, { + "@id" : "bts:WorkflowLink" + }, { + "@id" : "bts:PUC19methylationratio" + }, { + "@id" : "bts:Lambdamethylationratio" + } ], + "sms:displayName" : "BulkMethylation-seqLevel3" }, { - "@id" : "bts:InvasiveLobularBreastCarcinomaHistologicCategoryEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "InvasiveLobularBreastCarcinomaHistologicCategoryEnum", - "rdfs:subClassOf" : [ ], + "rdfs:subClassOf" : [ { + "@id" : "bts:SingleCellSequencing" + } ], + "@id" : "bts:ScRNA-seqLevel1", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "InvasiveLobularBreastCarcinomaHistologicCategoryEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:DimensionsUnitEnum", - "@type" : "rdfs:Class", + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "ScRNA-seqLevel1", "rdfs:comment" : "TBD", - "rdfs:label" : "DimensionsUnitEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - 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: "sms:false" + "sms:requiresDependency" : [ { + "@id" : "bts:Component" + } ], + "sms:displayName" : "Patient" }, { - "@id" : "bts:BreastCarcinomaSurgicalProcedureNameEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BreastCarcinomaSurgicalProcedureNameEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:File", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BreastCarcinomaSurgicalProcedureNameEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:SmokingFrequencyEnum", + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "File", + "rdfs:comment" : "Basic metadata for a file entity that contains data (whether sequencing, imaging, etc.) will inherit.", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "SmokingFrequencyEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "SmokingFrequencyEnum", - "sms:required" : "sms:false" + "sms:requiresDependency" : [ { + "@id" : "bts:Component" + }, { + "@id" : "bts:Filename" + }, { + "@id" : "bts:FileFormat" + } ], + "sms:displayName" : "File" }, { - "@id" : "bts:PixelTypeEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "PixelTypeEnum", - "rdfs:subClassOf" : [ ], + "rdfs:subClassOf" : [ { + "@id" : "bts:SingleCellSequencing" + } ], + "@id" : "bts:ScRNA-seqLevel2", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "PixelTypeEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:SpikeInEnum", - "@type" : "rdfs:Class", + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "ScRNA-seqLevel2", "rdfs:comment" : "TBD", - "rdfs:label" : "SpikeInEnum", - "rdfs:subClassOf" : [ ], + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:Component" + }, { + "@id" : "bts:Filename" + }, { + "@id" : "bts:FileFormat" + }, { + "@id" : 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"bts:ReverseTranscriptionPrimer" + }, { + "@id" : "bts:SpikeIn" + }, { + "@id" : "bts:EndBias" + }, { + "@id" : "bts:ScRNAseqWorkflowType" + }, { + "@id" : "bts:ScRNAseqWorkflowParametersDescription" + }, { + "@id" : "bts:WorkflowVersion" + }, { + "@id" : "bts:WorkflowLink" + }, { + "@id" : "bts:GenomicReference" + }, { + "@id" : "bts:GenomicReferenceURL" + }, { + "@id" : "bts:GenomeAnnotationURL" + }, { + "@id" : "bts:WhitelistCellBarcodeFileLink" + }, { + "@id" : "bts:CellBarcodeTag" + }, { + "@id" : "bts:UMITag" + }, { + "@id" : "bts:AppliedHardTrimming" + } ], + "sms:displayName" : "ScRNA-seqLevel2" + }, { + "rdfs:subClassOf" : [ { + "@id" : "bts:Diagnosis" + } ], + "@id" : "bts:Yes-VascularInvasionPresent", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SpikeInEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:ReadEnum", - "@type" : "rdfs:Class", + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "Yes-VascularInvasionPresent", "rdfs:comment" : "TBD", - "rdfs:label" : "ReadEnum", - "rdfs:subClassOf" : [ ], + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:VascularInvasionType" + } ], + "sms:displayName" : "Yes-VascularInvasionPresent" + }, { + "rdfs:subClassOf" : [ { + "@id" : "bts:SequencingData" + } ], + "@id" : "bts:SingleCellSequencing", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ReadEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "SingleCellSequencing", + "rdfs:comment" : "TBD", + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:Component" + }, { + "@id" : "bts:Filename" + }, { + "@id" : "bts:FileFormat" + }, { + "@id" : "bts:ParticipantID" + }, { + "@id" : "bts:SampleID" + }, { + "@id" : "bts:AltSampleID" + }, { + "@id" : "bts:SequencingPlatform" + }, { + "@id" : "bts:NucleicAcidSource" + }, { + "@id" : "bts:LibraryConstructionMethod" + }, { + "@id" : "bts:LibrarySelectionMethod" + }, { + "@id" : "bts:LibraryLayout" + }, { + "@id" : "bts:LibraryPrepKitName" + }, { + "@id" : "bts:LibraryPrepKitVersion" + }, { + "@id" : "bts:LibraryPrepKitVendor" + }, { + "@id" : "bts:ReadIndicator" + }, { + "@id" : "bts:ReadContent" + }, { + "@id" : "bts:TargetDepth" + }, { + "@id" : "bts:AdapterName" + }, { + "@id" : "bts:AdapterSequence" + }, { + "@id" : "bts:BatchID" + }, { + "@id" : "bts:LaneNumber" + }, { + "@id" : "bts:TechnicalReplicateGroup" + }, { + "@id" : "bts:DissociationMethod" + }, { + "@id" : "bts:CryopreservedCellsinSample" + }, { + "@id" : "bts:SingleCellIsolationMethod" + }, { + "@id" : "bts:TotalNumberofInputCells" + }, { + "@id" : "bts:InputCellsandNuclei" + }, { + "@id" : "bts:ReverseTranscriptionPrimer" + }, { + "@id" : "bts:SpikeIn" + }, { + "@id" : "bts:EndBias" + } ], + "sms:displayName" : "SingleCellSequencing" }, { - "@id" : "bts:BreastCarcinomaHER2StatusEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BreastCarcinomaHER2StatusEnum", - "rdfs:subClassOf" : [ ], + "rdfs:subClassOf" : [ { + "@id" : "bts:SingleCellSequencing" + } ], + "@id" : "bts:ScATAC-seqLevel1", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BreastCarcinomaHER2StatusEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:ClinicalBiospecimenTypeEnum", - "@type" : "rdfs:Class", + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "ScATAC-seqLevel1", "rdfs:comment" : "TBD", - "rdfs:label" : "ClinicalBiospecimenTypeEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "ClinicalBiospecimenTypeEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:RelationshipPrimaryDiagnosisEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "RelationshipPrimaryDiagnosisEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "RelationshipPrimaryDiagnosisEnum", - "sms:required" : "sms:false" + "sms:requiresDependency" : [ { + "@id" : "bts:Component" + }, { + "@id" : "bts:Filename" + }, { + "@id" : "bts:FileFormat" + }, { + "@id" : "bts:ParticipantID" + }, { + "@id" : "bts:SampleID" + }, { + "@id" : "bts:AltSampleID" + }, { + "@id" : "bts:SequencingPlatform" + }, { + "@id" : "bts:NucleicAcidSource" + }, { + "@id" : "bts:LibraryConstructionMethod" + }, { + "@id" : "bts:LibrarySelectionMethod" + }, { + "@id" : "bts:LibraryLayout" + }, { + "@id" : "bts:LibraryPrepKitName" + }, { + "@id" : "bts:LibraryPrepKitVersion" + }, { + "@id" : "bts:LibraryPrepKitVendor" + }, { + "@id" : "bts:ReadIndicator" + }, { + "@id" : "bts:ReadContent" + }, { + "@id" : "bts:TargetDepth" + }, { + "@id" : "bts:AdapterName" + }, { + "@id" : "bts:AdapterSequence" + }, { + "@id" : "bts:BatchID" + }, { + "@id" : "bts:LaneNumber" + }, { + "@id" : "bts:TechnicalReplicateGroup" + }, { + "@id" : "bts:DissociationMethod" + }, { + "@id" : "bts:CryopreservedCellsinSample" + }, { + "@id" : "bts:SingleCellIsolationMethod" + }, { + "@id" : "bts:TotalNumberofInputCells" + }, { + "@id" : "bts:InputCellsandNuclei" + }, { + "@id" : "bts:ReverseTranscriptionPrimer" + }, { + "@id" : "bts:SpikeIn" + }, { + "@id" : "bts:EndBias" + }, { + "@id" : "bts:SingleNucleusBuffer" + }, { + "@id" : "bts:TranspositionReaction" + }, { + "@id" : "bts:NucleusIdentifier" + }, { + "@id" : "bts:NucleiBarcodeLength" + }, { + "@id" : "bts:NucleiBarcodeRead" + } ], + "sms:displayName" : "ScATAC-seqLevel1" }, { - "@id" : "bts:BIRADSMammographyBreastDensityCategoryEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BIRADSMammographyBreastDensityCategoryEnum", - "rdfs:subClassOf" : [ ], + "rdfs:subClassOf" : [ { + "@id" : "bts:Biospecimen" + } ], + "@id" : "bts:TotalVolume", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BIRADSMammographyBreastDensityCategoryEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:SingleNucleusBufferEnum", - "@type" : "rdfs:Class", + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "TotalVolume", "rdfs:comment" : "TBD", - "rdfs:label" : "SingleNucleusBufferEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "SingleNucleusBufferEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:BiospecimenTypeEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BiospecimenTypeEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "BiospecimenTypeEnum", - "sms:required" : "sms:false" + "sms:requiresDependency" : [ { + "@id" : "bts:BiospecimenID" + }, { + "@id" : "bts:ParentID" + }, { + "@id" : "bts:ParentBiospecimenID" + }, { + "@id" : "bts:AdjacentBiospecimenIDs" + }, { + "@id" : "bts:BiospecimenType" + }, { + "@id" : "bts:TimepointLabel" + }, { + "@id" : "bts:SpecimenLaterality" + }, { + "@id" : "bts:TotalVolumeUnit" + } ], + "sms:displayName" : "TotalVolume" }, { - "@id" : "bts:AntibioticUseEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "AntibioticUseEnum", - "rdfs:subClassOf" : [ ], + "rdfs:subClassOf" : [ { + "@id" : "bts:File" + } ], + "@id" : "bts:BulkMethylation-seqLevel1", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "AntibioticUseEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:HormoneTherapyBreastCancerPreventionIndicatorEnum", + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "BulkMethylation-seqLevel1", + "rdfs:comment" : "Raw data for bulk methylation sequencing, such as FASTQs and unaligned BAMs", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "HormoneTherapyBreastCancerPreventionIndicatorEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "HormoneTherapyBreastCancerPreventionIndicatorEnum", - "sms:required" : "sms:false" + "sms:requiresDependency" : [ { + "@id" : "bts:Component" + }, { + "@id" : "bts:Filename" + }, { + "@id" : "bts:FileFormat" + }, { + "@id" : "bts:ParticipantID" + }, { + "@id" : "bts:SampleID" + }, { + "@id" : "bts:AltSampleID" + }, { + "@id" : "bts:NucleicAcidSource" + }, { + "@id" : "bts:BisulfiteConversionKit" + }, { + "@id" : "bts:BulkMethylationAssayType" + }, { + "@id" : "bts:SequencingPlatform" + }, { + "@id" : "bts:TechnicalReplicateGroup" + } ], + "sms:displayName" : "BulkMethylation-seqLevel1" }, { - "@id" : "bts:PreservationMethodEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "PreservationMethodEnum", - "rdfs:subClassOf" : [ ], + "rdfs:subClassOf" : [ { + "@id" : "bts:Biospecimen" + } ], + "@id" : "bts:UrineBiospecimenType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "PreservationMethodEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:TumorExtranodalExtensionIndicatorEnum", - "@type" : "rdfs:Class", + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "UrineBiospecimenType", "rdfs:comment" : "TBD", - "rdfs:label" : "TumorExtranodalExtensionIndicatorEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "TumorExtranodalExtensionIndicatorEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:TseriesEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "TseriesEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "TseriesEnum", - "sms:required" : "sms:false" + "sms:requiresDependency" : [ { + "@id" : "bts:BiospecimenID" + }, { + "@id" : "bts:ParentID" + }, { + "@id" : "bts:ParentBiospecimenID" + }, { + "@id" : "bts:AdjacentBiospecimenIDs" + }, { + "@id" : "bts:BiospecimenType" + }, { + "@id" : "bts:TimepointLabel" + }, { + "@id" : "bts:SpecimenLaterality" + }, { + "@id" : "bts:IschemicTime" + }, { + "@id" : "bts:IschemicTemperature" + }, { + "@id" : "bts:SiteofResectionorBiopsy" + }, { + "@id" : "bts:PortionWeight" + }, { + "@id" : "bts:TotalVolume" + }, { + "@id" : "bts:TumorTissueType" + }, { + "@id" : "bts:HistologicMorphologyCode" + }, { + "@id" : "bts:PreservationMethod" + } ], + "sms:displayName" : "UrineBiospecimenType" }, { - "@id" : "bts:DissociationMethodEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "DissociationMethodEnum", - "rdfs:subClassOf" : [ ], + "rdfs:subClassOf" : [ { + "@id" : "bts:ImagingLevel2" + } ], + "@id" : "bts:ImagingLevel2Channels", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "DissociationMethodEnum", - "sms:required" : "sms:false" - }, { - "@id" : 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"sms:requiresComponent" : "", + "rdfs:label" : "SampleCoreTemplate", "rdfs:comment" : "TBD", - "rdfs:label" : "BreastCancerAllredEstrogenReceptorScoreEnum", - "rdfs:subClassOf" : [ ], + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:ParticipantID" + }, { + "@id" : "bts:SampleID" + }, { + "@id" : "bts:DetailedSampleID" + }, { + "@id" : "bts:AdjacentSampleIDs" + }, { + "@id" : "bts:SampleSite" + }, { + "@id" : "bts:ERStatus" + }, { + "@id" : "bts:PRStatus" + }, { + "@id" : "bts:HER2Status" + }, { + "@id" : "bts:Laterality" + } ], + "sms:displayName" : "SampleCoreTemplate" + }, { + "rdfs:subClassOf" : [ { + "@id" : "bts:File" + } ], + "@id" : "bts:SequencingData", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BreastCancerAllredEstrogenReceptorScoreEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "SequencingData", + "rdfs:comment" : "Base template for some type of sequencing data file, for which below properties are relevant/in common.", + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:Component" + }, { + "@id" : "bts:Filename" + }, { + "@id" : "bts:FileFormat" + }, { + "@id" : "bts:ParticipantID" + }, { + "@id" : "bts:SampleID" + }, { + "@id" : "bts:AltSampleID" + }, { + "@id" : "bts:SequencingPlatform" + }, { + "@id" : "bts:NucleicAcidSource" + }, { + "@id" : "bts:LibraryConstructionMethod" + }, { + "@id" : "bts:LibrarySelectionMethod" + }, { + "@id" : "bts:LibraryLayout" + }, { + "@id" : "bts:LibraryPrepKitName" + }, { + "@id" : "bts:LibraryPrepKitVersion" + }, { + "@id" : "bts:LibraryPrepKitVendor" + }, { + "@id" : "bts:ReadIndicator" + }, { + "@id" : "bts:ReadContent" + }, { + "@id" : "bts:TargetDepth" + }, { + "@id" : "bts:AdapterName" + }, { + "@id" : "bts:AdapterSequence" + }, { + "@id" : "bts:BatchID" + }, { + "@id" : "bts:LaneNumber" + }, { + "@id" : "bts:TechnicalReplicateGroup" + } ], + 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"HistoneFamilyEnum", - "rdfs:subClassOf" : [ ], + "rdfs:subClassOf" : [ { + "@id" : "bts:Patient" + } ], + "@id" : "bts:OvarianCancerPatient", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "HistoneFamilyEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:ChromosomeEnum", - "@type" : "rdfs:Class", + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "OvarianCancerPatient", "rdfs:comment" : "TBD", - "rdfs:label" : "ChromosomeEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "ChromosomeEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:OvarianCancerHistologicSubtypeEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "OvarianCancerHistologicSubtypeEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "OvarianCancerHistologicSubtypeEnum", - 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"rdfs:comment" : "TBD", - "rdfs:label" : "VariantOriginEnum", - "rdfs:subClassOf" : [ ], + "rdfs:subClassOf" : [ { + "@id" : "bts:ScRNA-seqLevel1" + } ], + "@id" : "bts:CEL-seq2", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "VariantOriginEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:AnaplasiaPresentTypeEnum", + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "CEL-seq2", + "rdfs:comment" : "Highly-multiplexed plate-based single-cell RNA-Seq assay (so a subtype of scRNA-seq, and some additional metadata parameters are collected)", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "AnaplasiaPresentTypeEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "AnaplasiaPresentTypeEnum", - "sms:required" : "sms:false" + "sms:requiresDependency" : [ { + "@id" : "bts:Component" + }, { + "@id" : "bts:Filename" + }, { + "@id" : "bts:FileFormat" + }, { + "@id" : "bts:ParticipantID" + }, { + "@id" : "bts:SampleID" + }, { + "@id" : "bts:AltSampleID" + }, { + "@id" : "bts:SequencingPlatform" + }, { + "@id" : "bts:NucleicAcidSource" + }, { + "@id" : "bts:LibraryConstructionMethod" + }, { + "@id" : "bts:LibrarySelectionMethod" + }, { + "@id" : "bts:LibraryLayout" + }, { + "@id" : "bts:LibraryPrepKitName" + }, { + "@id" : "bts:LibraryPrepKitVersion" + }, { + "@id" : "bts:LibraryPrepKitVendor" + }, { + "@id" : "bts:ReadIndicator" + }, { + "@id" : "bts:ReadContent" + }, { + "@id" : "bts:TargetDepth" + }, { + "@id" : "bts:AdapterName" + }, { + "@id" : "bts:AdapterSequence" + }, { + "@id" : "bts:BatchID" + }, { + "@id" : "bts:LaneNumber" + }, { + "@id" : "bts:TechnicalReplicateGroup" + }, { + "@id" : "bts:DissociationMethod" + }, { + "@id" : "bts:CryopreservedCellsinSample" + }, { + "@id" : "bts:SingleCellIsolationMethod" + }, { + "@id" : "bts:TotalNumberofInputCells" + }, { + "@id" : "bts:InputCellsandNuclei" + }, { + "@id" : "bts:ReverseTranscriptionPrimer" + }, { + "@id" : "bts:SpikeIn" + }, { + "@id" : "bts:EndBias" + }, { + "@id" : "bts:UMIBarcodeOffset" + }, { + "@id" : "bts:UMIBarcodeLength" + }, { + "@id" : "bts:MedianUMIsperCellNumber" + }, { + "@id" : "bts:CellBarcodeOffset" + }, { + "@id" : "bts:CellBarcodeLength" + }, { + "@id" : "bts:ValidBarcodesCellNumber" + }, { + "@id" : "bts:EmptyWellBarcode" + }, { + "@id" : "bts:WellIndex" + } ], + "sms:displayName" : "CEL-seq2" }, { - "@id" : "bts:TranspositionReactionEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "TranspositionReactionEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:Biospecimen", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TranspositionReactionEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:EndBiasEnum", - "@type" : "rdfs:Class", + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "Biospecimen", "rdfs:comment" : "TBD", - "rdfs:label" : "EndBiasEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "EndBiasEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:HistoneVariantEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "HistoneVariantEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "HistoneVariantEnum", - "sms:required" : "sms:false" + "sms:requiresDependency" : [ { + "@id" : "bts:BiospecimenID" + }, { + "@id" : "bts:ParentID" + }, { + "@id" : "bts:ParentBiospecimenID" + }, { + "@id" : "bts:AdjacentBiospecimenIDs" + }, { + "@id" : "bts:BiospecimenType" + }, { + "@id" : "bts:TimepointLabel" + }, { + "@id" : "bts:SpecimenLaterality" + } ], + "sms:displayName" : "Biospecimen" }, { - "@id" : "bts:BreastCarcinomaHistologyCategoryEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BreastCarcinomaHistologyCategoryEnum", - "rdfs:subClassOf" : [ ], + "rdfs:subClassOf" : [ { + "@id" : "bts:Biospecimen" + } ], + "@id" : "bts:BiospecimenDimension1", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BreastCarcinomaHistologyCategoryEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:BreastImagingPerformedTypeEnum", - "@type" : "rdfs:Class", + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "BiospecimenDimension1", "rdfs:comment" : "TBD", - "rdfs:label" : "BreastImagingPerformedTypeEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "BreastImagingPerformedTypeEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:AlcoholExposureEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "AlcoholExposureEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "AlcoholExposureEnum", - "sms:required" : "sms:false" + "sms:requiresDependency" : [ { + "@id" : "bts:BiospecimenID" + }, { + "@id" : "bts:ParentID" + }, { + "@id" : "bts:ParentBiospecimenID" + }, { + "@id" : "bts:AdjacentBiospecimenIDs" + }, { + "@id" : "bts:BiospecimenType" + }, { + "@id" : "bts:TimepointLabel" + }, { + "@id" : "bts:SpecimenLaterality" + }, { + "@id" : "bts:DimensionsUnit" + } ], + "sms:displayName" : "BiospecimenDimension1" }, { - "@id" : "bts:SlideChargeTypeEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "SlideChargeTypeEnum", - "rdfs:subClassOf" : [ ], + "rdfs:subClassOf" : [ { + "@id" : "bts:Biospecimen" + } ], + "@id" : "bts:BloodBiospecimenType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SlideChargeTypeEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:ShippingConditionTypeEnum", - "@type" : "rdfs:Class", + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "BloodBiospecimenType", "rdfs:comment" : "TBD", - "rdfs:label" : "ShippingConditionTypeEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "ShippingConditionTypeEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:SingleCellIsolationMethodEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "SingleCellIsolationMethodEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "SingleCellIsolationMethodEnum", - "sms:required" : "sms:false" + "sms:requiresDependency" : [ { + "@id" : "bts:BiospecimenID" + }, { + "@id" : "bts:ParentID" + }, { + "@id" : "bts:ParentBiospecimenID" + }, { + "@id" : "bts:AdjacentBiospecimenIDs" + }, { + "@id" : "bts:BiospecimenType" + }, { + "@id" : "bts:TimepointLabel" + }, { + "@id" : "bts:SpecimenLaterality" + }, { + "@id" : "bts:ShippingConditionType" + } ], + "sms:displayName" : "BloodBiospecimenType" }, { "@id" : "bts:Skinofupperlimbandshoulder", "@type" : "rdfs:Class", @@ -12099,6 +12178,17 @@ }, "sms:displayName" : "Pakistan", "sms:required" : "sms:false" + }, { + "@id" : "bts:Menorrhagia", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Menorrhagia", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Menorrhagia", + "sms:required" : "sms:false" }, { "@id" : "bts:Togo", "@type" : "rdfs:Class", @@ -12968,6 +13058,17 @@ }, "sms:displayName" : "Mixed medullary-follicular carcinoma", "sms:required" : "sms:false" + }, { + "@id" : "bts:Malesterilization", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Malesterilization", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Male sterilization", + "sms:required" : "sms:false" }, { "@id" : "bts:Fresh", "@type" : "rdfs:Class", @@ -13573,17 +13674,6 @@ }, "sms:displayName" : "Abdomen NOS", "sms:required" : "sms:false" - }, { - "@id" : "bts:blackorafricanamerican", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "blackorafricanamerican", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "black or african american", - "sms:required" : "sms:false" }, { "@id" : "bts:IKZF1mutation", "@type" : "rdfs:Class", @@ -13870,6 +13960,17 @@ }, "sms:displayName" : "Portugal", "sms:required" : "sms:false" + }, { + "@id" : "bts:Black", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Black", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Black", + "sms:required" : "sms:false" }, { "@id" : "bts:Epididymis", "@type" : "rdfs:Class", @@ -13892,6 +13993,17 @@ }, "sms:displayName" : "Dysplastic nevus", "sms:required" : "sms:false" + }, { + "@id" : "bts:Endometriosis", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Endometriosis", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Endometriosis", + "sms:required" : "sms:false" }, { "@id" : "bts:CurrentReformedSmokerfor>15yrs", "@type" : "rdfs:Class", @@ -14046,17 +14158,6 @@ }, "sms:displayName" : "Microsatellite instability high MSIH", "sms:required" : "sms:false" - }, { - "@id" : "bts:white", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "white", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "white", - "sms:required" : "sms:false" }, { "@id" : "bts:Nepal", "@type" : "rdfs:Class", @@ -14959,6 +15060,17 @@ }, "sms:displayName" : "bgzip", "sms:required" : "sms:false" + }, { + "@id" : "bts:TubalSterilization", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "TubalSterilization", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Tubal Sterilization", + "sms:required" : "sms:false" }, { "@id" : "bts:Mixedpancreaticendocrineandexocrinetumormalignant", "@type" : "rdfs:Class", @@ -15025,6 +15137,17 @@ }, "sms:displayName" : "Cancer Related", "sms:required" : "sms:false" + }, { + "@id" : "bts:Inactive", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Inactive", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Inactive", + "sms:required" : "sms:false" }, { "@id" : "bts:IntraductalpapillaryadenocarcinomaNOS", "@type" : "rdfs:Class", @@ -15498,6 +15621,17 @@ }, "sms:displayName" : "Transcript Ablation", "sms:required" : "sms:false" + }, { + "@id" : "bts:GenderAffirmation", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "GenderAffirmation", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Gender Affirmation", + "sms:required" : "sms:false" }, { "@id" : "bts:NewZealand", "@type" : "rdfs:Class", @@ -15740,6 +15874,17 @@ }, "sms:displayName" : "United Kingdom", "sms:required" : "sms:false" + }, { + "@id" : "bts:Condoms", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Condoms", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Condoms", + "sms:required" : "sms:false" }, { "@id" : "bts:Signature13", "@type" : "rdfs:Class", @@ -15883,6 +16028,17 @@ }, "sms:displayName" : "Medulla of adrenal gland", "sms:required" : "sms:false" + }, { + "@id" : "bts:HispanicorLatino", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "HispanicorLatino", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Hispanic or Latino", + "sms:required" : "sms:false" }, { "@id" : "bts:gentleMACS", "@type" : "rdfs:Class", @@ -16466,6 +16622,17 @@ }, "sms:displayName" : "Scattered fibroglandular densities", "sms:required" : "sms:false" + }, { + "@id" : "bts:Non-Hispanic/Non-Latino", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Non-Hispanic/Non-Latino", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Non-Hispanic/Non-Latino", + "sms:required" : "sms:false" }, { "@id" : "bts:Pyriformsinus", "@type" : "rdfs:Class", @@ -17148,6 +17315,17 @@ }, "sms:displayName" : "Liquid Nitrogen", "sms:required" : "sms:false" + }, { + "@id" : "bts:Naturalfamilyplanning", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Naturalfamilyplanning", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Natural family planning", + "sms:required" : "sms:false" }, { "@id" : "bts:TumorcellsNOS", "@type" : "rdfs:Class", @@ -17852,6 +18030,17 @@ }, "sms:displayName" : "Translocation", "sms:required" : "sms:false" + }, { + "@id" : "bts:CesareanSection", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "CesareanSection", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Cesarean Section", + "sms:required" : "sms:false" }, { "@id" : "bts:Heterogeneouslydense", "@type" : "rdfs:Class", @@ -18446,6 +18635,17 @@ }, "sms:displayName" : "Coding Sequence Variant", "sms:required" : "sms:false" + }, { + "@id" : "bts:Proliferative", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Proliferative", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Proliferative", + "sms:required" : "sms:false" }, { "@id" : "bts:fasta", "@type" : "rdfs:Class", @@ -18578,6 +18778,17 @@ }, "sms:displayName" : "Nervous system NOS", "sms:required" : "sms:false" + }, { + "@id" : "bts:Asian", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Asian", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Asian", + "sms:required" : "sms:false" }, { "@id" : "bts:Lowerouterquadrant", "@type" : "rdfs:Class", @@ -19128,6 +19339,17 @@ }, "sms:displayName" : "PolE mutation", "sms:required" : "sms:false" + }, { + "@id" : "bts:Oral(estrogen)", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Oral(estrogen)", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Oral (estrogen)", + "sms:required" : "sms:false" }, { "@id" : "bts:Signature14", "@type" : "rdfs:Class", @@ -19469,6 +19691,17 @@ }, "sms:displayName" : "Penis NOS", "sms:required" : "sms:false" + }, { + "@id" : "bts:Oral", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Oral", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Oral", + "sms:required" : "sms:false" }, { "@id" : "bts:ClassicalHodgkinlymphomanodularsclerosiscellularphase", "@type" : "rdfs:Class", @@ -20393,6 +20626,17 @@ }, "sms:displayName" : "Barbados", "sms:required" : "sms:false" + }, { + "@id" : "bts:Bilateraltuballigation", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Bilateraltuballigation", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Bilateral tubal ligation", + "sms:required" : "sms:false" }, { "@id" : "bts:Estonia", "@type" : "rdfs:Class", @@ -20404,6 +20648,17 @@ }, "sms:displayName" : "Estonia", "sms:required" : "sms:false" + }, { + "@id" : "bts:UterineFibroids+Endometriosis", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "UterineFibroids+Endometriosis", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Uterine Fibroids + Endometriosis", + "sms:required" : "sms:false" }, { "@id" : "bts:CellBarcode", "@type" : "rdfs:Class", @@ -20448,6 +20703,17 @@ }, "sms:displayName" : "Papillary squamous cell carcinoma", "sms:required" : "sms:false" + }, { + "@id" : "bts:White", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "White", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "White", + "sms:required" : "sms:false" }, { "@id" : "bts:Methylation", "@type" : "rdfs:Class", @@ -21075,17 +21341,6 @@ }, "sms:displayName" : "CENP-A", "sms:required" : "sms:false" - }, { - "@id" : "bts:asian", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "asian", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "asian", - "sms:required" : "sms:false" }, { "@id" : "bts:FalklandIslands(Malvinas)", "@type" : "rdfs:Class", @@ -21504,17 +21759,6 @@ }, "sms:displayName" : "Fresh dissociated", "sms:required" : "sms:false" - }, { - "@id" : "bts:nativehawaiianorotherpacificislander", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "nativehawaiianorotherpacificislander", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "native hawaiian or other pacific islander", - "sms:required" : "sms:false" }, { "@id" : "bts:None", "@type" : "rdfs:Class", @@ -21636,6 +21880,17 @@ }, "sms:displayName" : "Medulloblastoma NOS", "sms:required" : "sms:false" + }, { + "@id" : "bts:Jewish", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Jewish", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Jewish", + "sms:required" : "sms:false" }, { "@id" : "bts:Alpha-1antitrypsin", "@type" : "rdfs:Class", @@ -21999,17 +22254,6 @@ }, "sms:displayName" : "GeoMX-DSP", "sms:required" : "sms:false" - }, { - "@id" : "bts:male", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "male", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "male", - "sms:required" : "sms:false" }, { "@id" : "bts:Splice", "@type" : "rdfs:Class", @@ -22043,6 +22287,17 @@ }, "sms:displayName" : "Maternal Great Aunt", "sms:required" : "sms:false" + }, { + "@id" : "bts:Vaginalring", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Vaginalring", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Vaginal ring", + "sms:required" : "sms:false" }, { "@id" : "bts:FosterFather", "@type" : "rdfs:Class", @@ -22098,17 +22353,6 @@ }, "sms:displayName" : "Tonsillar pillar", "sms:required" : "sms:false" - }, { - "@id" : "bts:hispanicorlatino", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "hispanicorlatino", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "hispanic or latino", - "sms:required" : "sms:false" }, { "@id" : "bts:Intermediate", "@type" : "rdfs:Class", @@ -22725,17 +22969,6 @@ }, "sms:displayName" : "Mucosa of lip NOS", "sms:required" : "sms:false" - }, { - "@id" : "bts:americanindianoralaskanative", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "americanindianoralaskanative", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "american indian or alaska native", - "sms:required" : "sms:false" }, { "@id" : "bts:Rscript", "@type" : "rdfs:Class", @@ -23187,6 +23420,28 @@ }, "sms:displayName" : "Rectum NOS", "sms:required" : "sms:false" + }, { + "@id" : "bts:Male", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Male", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Male", + "sms:required" : "sms:false" + }, { + "@id" : "bts:IUD(progesterone)", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "IUD(progesterone)", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "IUD (progesterone)", + "sms:required" : "sms:false" }, { "@id" : "bts:Mauritania", "@type" : "rdfs:Class", @@ -23385,6 +23640,17 @@ }, "sms:displayName" : "Platinum-sensitive", "sms:required" : "sms:false" + }, { + "@id" : "bts:Secretory", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Secretory", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Secretory", + "sms:required" : "sms:false" }, { "@id" : "bts:Russia", "@type" : "rdfs:Class", @@ -23858,6 +24124,17 @@ }, "sms:displayName" : "Parametrium", "sms:required" : "sms:false" + }, { + "@id" : "bts:Injection(progesterone)", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Injection(progesterone)", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Injection (progesterone)", + "sms:required" : "sms:false" }, { "@id" : "bts:DomesticPartner", "@type" : "rdfs:Class", @@ -24969,6 +25246,17 @@ }, "sms:displayName" : "XYTZC", "sms:required" : "sms:false" + }, { + "@id" : "bts:IUD", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "IUD", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "IUD", + "sms:required" : "sms:false" }, { "@id" : "bts:Non-clonal", "@type" : "rdfs:Class", @@ -25574,17 +25862,6 @@ }, "sms:displayName" : "WXS", "sms:required" : "sms:false" - }, { - "@id" : "bts:female", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "female", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "female", - "sms:required" : "sms:false" }, { "@id" : "bts:NeutrophilBands", "@type" : "rdfs:Class", @@ -25629,6 +25906,17 @@ }, "sms:displayName" : "ARF mutation", "sms:required" : "sms:false" + }, { + "@id" : "bts:Female", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Female", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Female", + "sms:required" : "sms:false" }, { "@id" : "bts:Drinker", "@type" : "rdfs:Class", @@ -26058,6 +26346,17 @@ }, "sms:displayName" : "Signature 21", "sms:required" : "sms:false" + }, { + "@id" : "bts:Unspecified", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Unspecified", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Unspecified", + "sms:required" : "sms:false" }, { "@id" : "bts:mzML", "@type" : "rdfs:Class", @@ -26201,6 +26500,17 @@ }, "sms:displayName" : "Grandfather", "sms:required" : "sms:false" + }, { + "@id" : "bts:RiskReduction", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "RiskReduction", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Risk Reduction", + "sms:required" : "sms:false" }, { "@id" : "bts:Lentigomalignatype", "@type" : "rdfs:Class", @@ -26333,17 +26643,6 @@ }, "sms:displayName" : "CD23", "sms:required" : "sms:false" - }, { - "@id" : "bts:nothispanicorlatino", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "nothispanicorlatino", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "not hispanic or latino", - "sms:required" : "sms:false" }, { "@id" : "bts:Upper-innerquadrantofbreast", "@type" : "rdfs:Class", @@ -26509,17 +26808,6 @@ }, "sms:displayName" : "Paternal Aunt", "sms:required" : "sms:false" - }, { - "@id" : "bts:notallowedtocollect", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "notallowedtocollect", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "not allowed to collect", - "sms:required" : "sms:false" }, { "@id" : "bts:PaternalUncle", "@type" : "rdfs:Class", @@ -27565,6 +27853,17 @@ }, "sms:displayName" : "Tonsil NOS", "sms:required" : "sms:false" + }, { + "@id" : "bts:OvarianCyst", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "OvarianCyst", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Ovarian Cyst", + "sms:required" : "sms:false" }, { "@id" : "bts:int8", "@type" : "rdfs:Class", @@ -27906,6 +28205,17 @@ }, "sms:displayName" : "Urine Biospecimen Type", "sms:required" : "sms:false" + }, { + "@id" : "bts:OvarianSerousCystadenoma", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "OvarianSerousCystadenoma", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Ovarian Serous Cystadenoma", + "sms:required" : "sms:false" }, { "@id" : "bts:CarcinosarcomaNOS", "@type" : "rdfs:Class", @@ -29116,6 +29426,17 @@ }, "sms:displayName" : "APC mutation", "sms:required" : "sms:false" + }, { + "@id" : "bts:UterineFibroids+Adenomyosis", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "UterineFibroids+Adenomyosis", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Uterine Fibroids + Adenomyosis", + "sms:required" : "sms:false" }, { "@id" : "bts:Cryopreservationinliquidnitrogen-deadtissue", "@type" : "rdfs:Class", @@ -29248,6 +29569,17 @@ }, "sms:displayName" : "other", "sms:required" : "sms:false" + }, { + "@id" : "bts:AmericanIndianorAlaskaNative", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "AmericanIndianorAlaskaNative", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "American Indian or Alaska Native", + "sms:required" : "sms:false" }, { "@id" : "bts:OrbitNOS", "@type" : "rdfs:Class", @@ -29347,6 +29679,17 @@ }, "sms:displayName" : "Pelvis NOS", "sms:required" : "sms:false" + }, { + "@id" : "bts:LateProliferative/EarlySecretory", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "LateProliferative/EarlySecretory", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Late Proliferative/Early Secretory", + "sms:required" : "sms:false" }, { "@id" : "bts:Thailand", "@type" : "rdfs:Class", @@ -30491,6 +30834,17 @@ }, "sms:displayName" : "10xV3.1", "sms:required" : "sms:false" + }, { + "@id" : "bts:Implant(progesterone)", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Implant(progesterone)", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Implant (progesterone)", + "sms:required" : "sms:false" }, { "@id" : "bts:EpendymomaNOS", "@type" : "rdfs:Class", @@ -31305,6 +31659,17 @@ }, "sms:displayName" : "Mauritius", "sms:required" : "sms:false" + }, { + "@id" : "bts:WeaklyProliferative", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "WeaklyProliferative", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Weakly Proliferative", + "sms:required" : "sms:false" }, { "@id" : "bts:DiffuselargeB-celllymphomaNOS", "@type" : "rdfs:Class", @@ -33131,6 +33496,17 @@ }, "sms:displayName" : "Dermatofibroma NOS", "sms:required" : "sms:false" + }, { + "@id" : "bts:PelvicMass", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "PelvicMass", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Pelvic Mass", + "sms:required" : "sms:false" }, { "@id" : "bts:Benign", "@type" : "rdfs:Class", @@ -33164,6 +33540,17 @@ }, "sms:displayName" : "Bronchiolo-alveolar adenocarcinoma NOS", "sms:required" : "sms:false" + }, { + "@id" : "bts:Implant", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Implant", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Implant", + "sms:required" : "sms:false" }, { "@id" : "bts:PaternalGrandfather", "@type" : "rdfs:Class", @@ -34275,6 +34662,17 @@ }, "sms:displayName" : "SMARCB1 mutation", "sms:required" : "sms:false" + }, { + "@id" : "bts:Oral(progesterone)", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Oral(progesterone)", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Oral (progesterone)", + "sms:required" : "sms:false" }, { "@id" : "bts:TubularandroblastomaNOS", "@type" : "rdfs:Class", @@ -34572,6 +34970,17 @@ }, "sms:displayName" : "Saudi Arabia", "sms:required" : "sms:false" + }, { + "@id" : "bts:NativeHawaiianorOtherPacificIslander", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "NativeHawaiianorOtherPacificIslander", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Native Hawaiian or Other Pacific Islander", + "sms:required" : "sms:false" }, { "@id" : "bts:Chondrosarcomagrade2/3", "@type" : "rdfs:Class", @@ -34660,6 +35069,17 @@ }, "sms:displayName" : "Renal cell carcinoma NOS", "sms:required" : "sms:false" + }, { + "@id" : "bts:Patch", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Patch", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Patch", + "sms:required" : "sms:false" }, { "@id" : "bts:cm", "@type" : "rdfs:Class", @@ -35166,6 +35586,17 @@ }, "sms:displayName" : "Strong", "sms:required" : "sms:false" + }, { + "@id" : "bts:UterineFibroids", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "UterineFibroids", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Uterine Fibroids", + "sms:required" : "sms:false" }, { "@id" : "bts:Overlappinglesionofperipheralnervesandautonomicnervoussystem", "@type" : "rdfs:Class", @@ -35595,6 +36026,17 @@ }, "sms:displayName" : "Bladder Cancer", "sms:required" : "sms:false" + }, { + "@id" : "bts:AdnexalMass", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "AdnexalMass", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Adnexal Mass", + "sms:required" : "sms:false" }, { "@id" : "bts:MalegenitalorgansNOS", "@type" : "rdfs:Class", @@ -35606,6 +36048,17 @@ }, "sms:displayName" : "Male genital organs NOS", "sms:required" : "sms:false" + }, { + "@id" : "bts:NA", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "NA", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "NA", + "sms:required" : "sms:false" }, { "@id" : "bts:MalignantlymphomalargecellNOS", "@type" : "rdfs:Class", From 8d53f502421327479397fb122c0aecd27e69be40 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Thu, 8 Feb 2024 11:41:04 -0700 Subject: [PATCH 07/14] Update description --- modules/slots.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/slots.yaml b/modules/slots.yaml index 2a505ee..b985cdc 100644 --- a/modules/slots.yaml +++ b/modules/slots.yaml @@ -30,7 +30,7 @@ slots: Age: title: Age required: true - description: Age (in years) of individual when samples are contributed/biobanked, as a positive number such as 40 or 56.5. If not available, cannot leave blank and must use "unknown". + description: Age (in years) of individual when samples are contributed/biobanked, as a positive number such as 40 or 56.5. If not available/missing, fill in with value "Unknown". annotations: validationRules: regex match ^\d*\.?\d*$|^Unknown$ AgeAtMenarche: From 486c23c82abf119a599598b6d8742844e3423545 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Thu, 8 Feb 2024 11:42:36 -0700 Subject: [PATCH 08/14] Update description and range --- modules/slots.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/slots.yaml b/modules/slots.yaml index b985cdc..a3de455 100644 --- a/modules/slots.yaml +++ b/modules/slots.yaml @@ -1015,7 +1015,8 @@ slots: MenstrualCyclePhase: title: Menstrual Cycle Phase required: false - description: TBD + description: Phase of the menstrual cycle at patient sample collection. + range: MenstrualCyclePhaseEnum annotations: MetalIsotopeElement: title: Metal Isotope Element From e2b0dea89959115ed351c440874c9a21ae38f2da Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Thu, 8 Feb 2024 12:03:36 -0700 Subject: [PATCH 09/14] Clean up unnecessary nulls --- modules/enums/Biospecimen.yaml | 180 ++-- modules/enums/Diagnosis.yaml | 1852 ++++++++++++++++---------------- 2 files changed, 1016 insertions(+), 1016 deletions(-) diff --git a/modules/enums/Biospecimen.yaml b/modules/enums/Biospecimen.yaml index a3182c6..4b1dcc8 100644 --- a/modules/enums/Biospecimen.yaml +++ b/modules/enums/Biospecimen.yaml @@ -1,111 +1,111 @@ enums: TotalVolumeUnitEnum: permissible_values: - mL: null - mm^3: null - cm^2: null + mL: + mm^3: + cm^2: IschemicTemperatureEnum: permissible_values: - unknown: null - Liquid Nitrogen: null - Warm Ischemia: null - Cold Ischemia: null - Ambient air: null - 4C wet ice: null - Negative -20C: null - Dry Ice: null + unknown: + Liquid Nitrogen: + Warm Ischemia: + Cold Ischemia: + Ambient air: + 4C wet ice: + Negative -20C: + Dry Ice: AnalyteTypeEnum: permissible_values: - Tissue Section Analyte: null - Serum Analyte: null - PBMCs or Plasma or Serum Analyte: null - Plasma: null - Tissue Block Analyte: null - cfDNA Analyte: null - DNA Analyte: null - RNA Analyte: null - cDNA Libraries Analyte: null - PBMCs: null - Total RNA Analyte: null + Tissue Section Analyte: + Serum Analyte: + PBMCs or Plasma or Serum Analyte: + Plasma: + Tissue Block Analyte: + cfDNA Analyte: + DNA Analyte: + RNA Analyte: + cDNA Libraries Analyte: + PBMCs: + Total RNA Analyte: DimensionsUnitEnum: permissible_values: - cm: null - mm: null + cm: + mm: BiospecimenTypeEnum: permissible_values: - Fluids Biospecimen Type: null - Sputum Biospecimen Type: null - Tissue Biospecimen Type: null - Mouth Rinse Biospecimen Type: null - Ascites Biospecimen Type: null - Cells Biospecimen Type: null - Blood Biospecimen Type: null - Analyte Biospecimen Type: null - Bone Marrow Biospecimen Type: null - Urine Biospecimen Type: null - Stool Biospecimen Type: null + Fluids Biospecimen Type: + Sputum Biospecimen Type: + Tissue Biospecimen Type: + Mouth Rinse Biospecimen Type: + Ascites Biospecimen Type: + Cells Biospecimen Type: + Blood Biospecimen Type: + Analyte Biospecimen Type: + Bone Marrow Biospecimen Type: + Urine Biospecimen Type: + Stool Biospecimen Type: PreservationMethodEnum: permissible_values: - Negative 80 Deg C: null - Not Reported: null - Cryopreservation in dry ice - dead tissue: null - unknown: null - Fresh: null - Cryopreservation in liquid nitrogen - dead tissue: null - Formalin fixed paraffin embedded - FFPE: null - Archival: null - Formalin fixed-buffered: null - Formalin fixed-unbuffered: null - Cryopreserved: null - Frozen: null - Fresh dissociated and single cell sorted: null - Fresh dissociated and single cell sorted into plates in NP40 buffer: null - Methacarn fixed paraffin embedded - MFPE: null - Fresh dissociated: null - Fresh dissociated and single cell sorted into plates: null - Cryopreservation in liquid nitrogen - live cells: null - OCT: null - Snap Frozen: null - Liquid Nitrogen: null + Negative 80 Deg C: + Not Reported: + Cryopreservation in dry ice - dead tissue: + unknown: + Fresh: + Cryopreservation in liquid nitrogen - dead tissue: + Formalin fixed paraffin embedded - FFPE: + Archival: + Formalin fixed-buffered: + Formalin fixed-unbuffered: + Cryopreserved: + Frozen: + Fresh dissociated and single cell sorted: + Fresh dissociated and single cell sorted into plates in NP40 buffer: + Methacarn fixed paraffin embedded - MFPE: + Fresh dissociated: + Fresh dissociated and single cell sorted into plates: + Cryopreservation in liquid nitrogen - live cells: + OCT: + Snap Frozen: + Liquid Nitrogen: TumorTissueTypeEnum: permissible_values: - Normal: null - Normal adjacent: null - Recurrent: null - Post therapy neoadjuvant: null - Normal distant: null - Post therapy adjuvant: null - Post therapy: null - Atypia - hyperplasia: null - Not Otherwise Specified: null - Metastatic: null - Local recurrence: null - Premalignant - in situ: null - Additional Primary: null - Premalignant: null - Primary: null + Normal: + Normal adjacent: + Recurrent: + Post therapy neoadjuvant: + Normal distant: + Post therapy adjuvant: + Post therapy: + Atypia - hyperplasia: + Not Otherwise Specified: + Metastatic: + Local recurrence: + Premalignant - in situ: + Additional Primary: + Premalignant: + Primary: SpecimenLateralityEnum: permissible_values: - Not Applicable: null - unknown: null - Not Reported: null - Bilateral: null - Left: null - Right: null + Not Applicable: + unknown: + Not Reported: + Bilateral: + Left: + Right: SlideChargeTypeEnum: permissible_values: - Other: null - Uncharged: null - Charged: null - Coverslip: null - Not applicable: null + Other: + Uncharged: + Charged: + Coverslip: + Not applicable: ShippingConditionTypeEnum: permissible_values: - Liquid Nitrogen: null - Dry Ice: null - Ambient Pack: null - Cold Pack: null - Ice Pack: null - Specimen at Room Temperature: null - Other Shipping Environment: null - Not Shipped: null + Liquid Nitrogen: + Dry Ice: + Ambient Pack: + Cold Pack: + Ice Pack: + Specimen at Room Temperature: + Other Shipping Environment: + Not Shipped: diff --git a/modules/enums/Diagnosis.yaml b/modules/enums/Diagnosis.yaml index 23d6d1c..437bae3 100644 --- a/modules/enums/Diagnosis.yaml +++ b/modules/enums/Diagnosis.yaml @@ -1,944 +1,944 @@ enums: ExtentofTumorResectionEnum: permissible_values: - Minor: null - Open Biopsy: null - Not Reported: null - Gross Total Resection: null - unknown: null - Not Applicable: null - Segmental: null - NTR: null - Suboptimal debulking: null - Subtotal Resection: null - Other: null - Partial debulking: null - Suboptimal: null - Optimal debulking: null - Extensive Subtotal: null + Minor: + Open Biopsy: + Not Reported: + Gross Total Resection: + unknown: + Not Applicable: + Segmental: + NTR: + Suboptimal debulking: + Subtotal Resection: + Other: + Partial debulking: + Suboptimal: + Optimal debulking: + Extensive Subtotal: SiteofResectionorBiopsyEnum: permissible_values: - Tonsillar fossa: null - Overlapping lesion of lung: null - Overlapping lesion of other and unspecified parts of mouth: null - Endometrium: null - Bone of limb NOS: null - Posterior wall of nasopharynx: null - Small intestine NOS: null - Anterior wall of nasopharynx: null - Thoracic esophagus: null - Parietal lobe: null - Head face or neck NOS: null - Endocervix: null - Supraglottis: null - Ethmoid sinus: null - Ileum: null - Overlapping lesion of heart mediastinum and pleura: null - Exocervix: null - Pancreas NOS: null - Epididymis: null - Kidney NOS: null - Anus NOS: null - Cerebrum: null - Overlapping lesion of breast: null - Overlapping lesion of peripheral nerves and autonomic nervous system: null - Fundus of stomach: null - Oropharynx NOS: null - Urachus: null - Labium majus: null - Parametrium: null - Vestibule of mouth: null - Lower third of esophagus: null - Overlapping lesion of digestive system: null - Bones of skull and face and associated joints: null - Lymph nodes of axilla or arm: null - Soft palate NOS: null - Hepatic flexure of colon: null - Subglottis: null - Overlapping lesion of lip: null - Extrahepatic bile duct: null - Vallecula: null - Tongue NOS: null - Liver: null - Overlapping lesion of bones joints and articular cartilage: null - Not Reported: null - Peripheral nerves and autonomic nervous system of upper limb and shoulder: null - Lymph nodes of multiple regions: null - Duodenum: null - Maxillary sinus: null - Intrahepatic bile duct: null - Lateral wall of bladder: null - Overlapping lesion of hypopharynx: null - Overlapping lesion of rectum anus and anal canal: null - Middle third of esophagus: null - Lateral floor of mouth: null - Anterior mediastinum: null - Anterior floor of mouth: null - Nervous system NOS: null - Waldeyer ring: null - Rib sternum clavicle and associated joints: null - Long bones of lower limb and associated joints: null - Frontal sinus: null - Uterine adnexa: null - Trachea: null - Rectum NOS: null - Adrenal gland NOS: null - Pleura NOS: null - Lower limb NOS: null - Transverse colon: null - Lymph nodes of head face and neck: null - Greater curvature of stomach NOS: null - Upper respiratory tract NOS: null - Overlapping lesion of pancreas: null - Cerebellum NOS: null - Overlapping lesions of oropharynx: null - Axillary tail of breast: null - unknown: null - Vulva NOS: null - Floor of mouth NOS: null - Overlapping lesion of male genital organs: null - Uterus NOS: null - Body of stomach: null - Urethra: null - Middle lobe lung: null - Tail of pancreas: null - Pineal gland: null - Spermatic cord: null - Carotid body: null - Reticuloendothelial system NOS: null - Other specified parts of pancreas: null - External ear: null - Meckel diverticulum: null - Penis NOS: null - Lower-inner quadrant of breast: null - Superior wall of nasopharynx: null - Retina: null - Border of tongue: null - Intra-abdominal lymph nodes: null - Peripheral nerves and autonomic nervous system of thorax: null - Cauda equina: null - Overlapping lesion of palate: null - Nasopharynx NOS: null - Placenta: null - External lip NOS: null - Bone NOS: null - Ciliary body: null - Hematopoietic system NOS: null - Prepuce: null - Pelvic lymph nodes: null - Postcricoid region: null - External upper lip: null - Peripheral nerves and autonomic nervous system of pelvis: null - Pelvis NOS: null - Connective subcutaneous and other soft tissues of abdomen: null - Vertebral column: null - Body of pancreas: null - Trigone of bladder: null - Commissure of lip: null - Peripheral nerves and autonomic nervous system of abdomen: null - Upper-inner quadrant of breast: null - Palate NOS: null - Hypopharyngeal aspect of aryepiglottic fold: null - Upper gum: null - Thorax NOS: null - Spinal cord: null - Brain NOS: null - Mouth NOS: null - Connective subcutaneous and other soft tissues of upper limb and shoulder: null - Retroperitoneum: null - Long bones of upper limb scapula and associated joints: null - Hard palate: null - Gallbladder: null - Endocrine gland NOS: null - Brain stem: null - Cornea NOS: null - Overlapping lesion of nasopharynx: null - Dorsal surface of tongue NOS: null - Major salivary gland NOS: null - Abdominal esophagus: null - Olfactory nerve: null - Short bones of upper limb and associated joints: null - Overlapping lesion of tonsil: null - Autonomic nervous system NOS: null - Ill-defined sites within respiratory system: null - Lymph nodes of inguinal region or leg: null - Overlapping lesion of major salivary glands: null - Peripheral nerves and autonomic nervous system of trunk NOS: null - Fundus uteri: null - Testis NOS: null - Parotid gland: null - Ampulla of Vater: null - Cardia NOS: null - Skin of lip NOS: null - Overlapping lesion of stomach: null - Rectosigmoid junction: null - Gastric antrum: null - Cortex of adrenal gland: null - Renal pelvis: null - Middle ear: null - Overlapping lesion of female genital organs: null - Gastrointestinal tract NOS: null - Connective subcutaneous and other soft tissues of thorax: null - Skin NOS: null - Parathyroid gland: null - Pituitary gland: null - Overlapping lesion of tongue: null - Lung NOS: null - Cervix uteri: null - Skin of other and unspecified parts of face: null - Submandibular gland: null - Clitoris: null - Central portion of breast: null - Ovary: null - Lateral wall of oropharynx: null - Stomach NOS: null - Ventral surface of tongue NOS: null - Overlapping lesion of urinary organs: null - Sigmoid colon: null - Overlapping lesion of brain: null - Overlapping lesion of colon: null - Glans penis: null - Mediastinum NOS: null - Vagina NOS: null - Lower-outer quadrant of breast: null - Pharynx NOS: null - Intestinal tract NOS: null - Peripheral nerves and autonomic nervous system of head face and neck: null - Overlapping lesion of bladder: null - Pyriform sinus: null - Conjunctiva: null - Connective subcutaneous and other soft tissues NOS: null - Acoustic nerve: null - Lesser curvature of stomach NOS: null - Mucosa of lower lip: null - Bladder NOS: null - Intrathoracic lymph nodes: null - Pylorus: null - Blood: null - Biliary tract NOS: null - Accessory sinus NOS: null - Mandible: null - Overlapping lesion of retroperitoneum and peritoneum: null - Urinary system NOS: null - Sublingual gland: null - Tonsil NOS: null - Anterior surface of epiglottis: null - Branchial cleft: null - Peritoneum NOS: null - Lacrimal gland: null - Spleen: null - Optic nerve: null - Cervical esophagus: null - Fallopian tube: null - Base of tongue NOS: null - Skin of upper limb and shoulder: null - Craniopharyngeal duct: null - Specified parts of peritoneum: null - Pancreatic duct: null - External lower lip: null - Overlapping lesion of cervix uteri: null - Anterior wall of bladder: null - Uvula: null - Upper-outer quadrant of breast: null - Overlapping lesion of esophagus: null - Short bones of lower limb and associated joints: null - Ascending colon: null - Mucosa of upper lip: null - Connective subcutaneous and other soft tissues of head face and neck: null - Anal canal: null - Hypopharynx NOS: null - Aortic body and other paraganglia: null - Overlapping lesion of endocrine glands and related structures: null - Larynx NOS: null - Ureter: null - Eye NOS: null - Medulla of adrenal gland: null - Colon NOS: null - Lower lobe lung: null - Eyelid: null - Overlapping lesion of respiratory system and intrathoracic organs: null - Overlapping lesion of connective subcutaneous and other soft tissues: null - Esophagus NOS: null - Overlapping lesion of brain and central nervous system: null - Choroid: null - Bladder neck: null - Overlapping lesion of skin: null - Thyroid gland: null - Sphenoid sinus: null - Round ligament: null - Breast NOS: null - Upper lobe lung: null - Splenic flexure of colon: null - Cranial nerve NOS: null - Paraurethral gland: null - Posterior wall of oropharynx: null - Other specified parts of male genital organs: null - Undescended testis: null - Nasal cavity: null - Cerebral meninges: null - Overlapping lesion of floor of mouth: null - Overlapping lesion of corpus uteri: null - Lip NOS: null - Cheek mucosa: null - Upper limb NOS: null - Dome of bladder: null - Connective subcutaneous and other soft tissues of pelvis: null - unknown primary site: null - Posterior mediastinum: null - Ureteric orifice: null - Other ill-defined sites: null - Bone marrow: null - Peripheral nerves and autonomic nervous system of lower limb and hip: null - Lymph node NOS: null - Skin of scalp and neck: null - Retromolar area: null - Overlapping lesion of lip oral cavity and pharynx: null - Overlapping lesion of accessory sinuses: null - Overlapping lesion of penis: null - Overlapping lesion of vulva: null - Overlapping lesion of ill-defined sites: null - Occipital lobe: null - Overlapping lesion of eye and adnexa: null - Lingual tonsil: null - Gum NOS: null - Thymus: null - Male genital organs NOS: null - Islets of Langerhans: null - Isthmus uteri: null - Spinal meninges: null - Myometrium: null - Pelvic bones sacrum coccyx and associated joints: null - Connective subcutaneous and other soft tissues of lower limb and hip: null - Anterior 2/3 of tongue NOS: null - Upper third of esophagus: null - Meninges NOS: null - Prostate gland: null - Overlapping lesion of small intestine: null - Lower gum: null - Paraspinal: null - Appendix: null - Scrotum NOS: null - Overlapping lesion of larynx: null - Main bronchus: null - Descended testis: null - Cloacogenic zone: null - Connective subcutaneous and other soft tissues of trunk NOS: null - Heart: null - Mucosa of lip NOS: null - Broad ligament: null - Head of pancreas: null - Overlapping lesion of bones joints and articular cartilage of limbs: null - Temporal lobe: null - Body of penis: null - Overlapping lesion of biliary tract: null - Labium minus: null - Descending colon: null - Lateral wall of nasopharynx: null - Posterior wall of hypopharynx: null - Nipple: null - Jejunum: null - Posterior wall of bladder: null - Laryngeal cartilage: null - Cecum: null - Skin of lower limb and hip: null - Corpus uteri: null - Female genital tract NOS: null - Abdomen NOS: null - Tonsillar pillar: null - Other specified parts of female genital organs: null - Glottis: null - Orbit NOS: null - Skin of trunk: null - Ventricle NOS: null - Frontal lobe: null + Tonsillar fossa: + Overlapping lesion of lung: + Overlapping lesion of other and unspecified parts of mouth: + Endometrium: + Bone of limb NOS: + Posterior wall of nasopharynx: + Small intestine NOS: + Anterior wall of nasopharynx: + Thoracic esophagus: + Parietal lobe: + Head face or neck NOS: + Endocervix: + Supraglottis: + Ethmoid sinus: + Ileum: + Overlapping lesion of heart mediastinum and pleura: + Exocervix: + Pancreas NOS: + Epididymis: + Kidney NOS: + Anus NOS: + Cerebrum: + Overlapping lesion of breast: + Overlapping lesion of peripheral nerves and autonomic nervous system: + Fundus of stomach: + Oropharynx NOS: + Urachus: + Labium majus: + Parametrium: + Vestibule of mouth: + Lower third of esophagus: + Overlapping lesion of digestive system: + Bones of skull and face and associated joints: + Lymph nodes of axilla or arm: + Soft palate NOS: + Hepatic flexure of colon: + Subglottis: + Overlapping lesion of lip: + Extrahepatic bile duct: + Vallecula: + Tongue NOS: + Liver: + Overlapping lesion of bones joints and articular cartilage: + Not Reported: + Peripheral nerves and autonomic nervous system of upper limb and shoulder: + Lymph nodes of multiple regions: + Duodenum: + Maxillary sinus: + Intrahepatic bile duct: + Lateral wall of bladder: + Overlapping lesion of hypopharynx: + Overlapping lesion of rectum anus and anal canal: + Middle third of esophagus: + Lateral floor of mouth: + Anterior mediastinum: + Anterior floor of mouth: + Nervous system NOS: + Waldeyer ring: + Rib sternum clavicle and associated joints: + Long bones of lower limb and associated joints: + Frontal sinus: + Uterine adnexa: + Trachea: + Rectum NOS: + Adrenal gland NOS: + Pleura NOS: + Lower limb NOS: + Transverse colon: + Lymph nodes of head face and neck: + Greater curvature of stomach NOS: + Upper respiratory tract NOS: + Overlapping lesion of pancreas: + Cerebellum NOS: + Overlapping lesions of oropharynx: + Axillary tail of breast: + unknown: + Vulva NOS: + Floor of mouth NOS: + Overlapping lesion of male genital organs: + Uterus NOS: + Body of stomach: + Urethra: + Middle lobe lung: + Tail of pancreas: + Pineal gland: + Spermatic cord: + Carotid body: + Reticuloendothelial system NOS: + Other specified parts of pancreas: + External ear: + Meckel diverticulum: + Penis NOS: + Lower-inner quadrant of breast: + Superior wall of nasopharynx: + Retina: + Border of tongue: + Intra-abdominal lymph nodes: + Peripheral nerves and autonomic nervous system of thorax: + Cauda equina: + Overlapping lesion of palate: + Nasopharynx NOS: + Placenta: + External lip NOS: + Bone NOS: + Ciliary body: + Hematopoietic system NOS: + Prepuce: + Pelvic lymph nodes: + Postcricoid region: + External upper lip: + Peripheral nerves and autonomic nervous system of pelvis: + Pelvis NOS: + Connective subcutaneous and other soft tissues of abdomen: + Vertebral column: + Body of pancreas: + Trigone of bladder: + Commissure of lip: + Peripheral nerves and autonomic nervous system of abdomen: + Upper-inner quadrant of breast: + Palate NOS: + Hypopharyngeal aspect of aryepiglottic fold: + Upper gum: + Thorax NOS: + Spinal cord: + Brain NOS: + Mouth NOS: + Connective subcutaneous and other soft tissues of upper limb and shoulder: + Retroperitoneum: + Long bones of upper limb scapula and associated joints: + Hard palate: + Gallbladder: + Endocrine gland NOS: + Brain stem: + Cornea NOS: + Overlapping lesion of nasopharynx: + Dorsal surface of tongue NOS: + Major salivary gland NOS: + Abdominal esophagus: + Olfactory nerve: + Short bones of upper limb and associated joints: + Overlapping lesion of tonsil: + Autonomic nervous system NOS: + Ill-defined sites within respiratory system: + Lymph nodes of inguinal region or leg: + Overlapping lesion of major salivary glands: + Peripheral nerves and autonomic nervous system of trunk NOS: + Fundus uteri: + Testis NOS: + Parotid gland: + Ampulla of Vater: + Cardia NOS: + Skin of lip NOS: + Overlapping lesion of stomach: + Rectosigmoid junction: + Gastric antrum: + Cortex of adrenal gland: + Renal pelvis: + Middle ear: + Overlapping lesion of female genital organs: + Gastrointestinal tract NOS: + Connective subcutaneous and other soft tissues of thorax: + Skin NOS: + Parathyroid gland: + Pituitary gland: + Overlapping lesion of tongue: + Lung NOS: + Cervix uteri: + Skin of other and unspecified parts of face: + Submandibular gland: + Clitoris: + Central portion of breast: + Ovary: + Lateral wall of oropharynx: + Stomach NOS: + Ventral surface of tongue NOS: + Overlapping lesion of urinary organs: + Sigmoid colon: + Overlapping lesion of brain: + Overlapping lesion of colon: + Glans penis: + Mediastinum NOS: + Vagina NOS: + Lower-outer quadrant of breast: + Pharynx NOS: + Intestinal tract NOS: + Peripheral nerves and autonomic nervous system of head face and neck: + Overlapping lesion of bladder: + Pyriform sinus: + Conjunctiva: + Connective subcutaneous and other soft tissues NOS: + Acoustic nerve: + Lesser curvature of stomach NOS: + Mucosa of lower lip: + Bladder NOS: + Intrathoracic lymph nodes: + Pylorus: + Blood: + Biliary tract NOS: + Accessory sinus NOS: + Mandible: + Overlapping lesion of retroperitoneum and peritoneum: + Urinary system NOS: + Sublingual gland: + Tonsil NOS: + Anterior surface of epiglottis: + Branchial cleft: + Peritoneum NOS: + Lacrimal gland: + Spleen: + Optic nerve: + Cervical esophagus: + Fallopian tube: + Base of tongue NOS: + Skin of upper limb and shoulder: + Craniopharyngeal duct: + Specified parts of peritoneum: + Pancreatic duct: + External lower lip: + Overlapping lesion of cervix uteri: + Anterior wall of bladder: + Uvula: + Upper-outer quadrant of breast: + Overlapping lesion of esophagus: + Short bones of lower limb and associated joints: + Ascending colon: + Mucosa of upper lip: + Connective subcutaneous and other soft tissues of head face and neck: + Anal canal: + Hypopharynx NOS: + Aortic body and other paraganglia: + Overlapping lesion of endocrine glands and related structures: + Larynx NOS: + Ureter: + Eye NOS: + Medulla of adrenal gland: + Colon NOS: + Lower lobe lung: + Eyelid: + Overlapping lesion of respiratory system and intrathoracic organs: + Overlapping lesion of connective subcutaneous and other soft tissues: + Esophagus NOS: + Overlapping lesion of brain and central nervous system: + Choroid: + Bladder neck: + Overlapping lesion of skin: + Thyroid gland: + Sphenoid sinus: + Round ligament: + Breast NOS: + Upper lobe lung: + Splenic flexure of colon: + Cranial nerve NOS: + Paraurethral gland: + Posterior wall of oropharynx: + Other specified parts of male genital organs: + Undescended testis: + Nasal cavity: + Cerebral meninges: + Overlapping lesion of floor of mouth: + Overlapping lesion of corpus uteri: + Lip NOS: + Cheek mucosa: + Upper limb NOS: + Dome of bladder: + Connective subcutaneous and other soft tissues of pelvis: + unknown primary site: + Posterior mediastinum: + Ureteric orifice: + Other ill-defined sites: + Bone marrow: + Peripheral nerves and autonomic nervous system of lower limb and hip: + Lymph node NOS: + Skin of scalp and neck: + Retromolar area: + Overlapping lesion of lip oral cavity and pharynx: + Overlapping lesion of accessory sinuses: + Overlapping lesion of penis: + Overlapping lesion of vulva: + Overlapping lesion of ill-defined sites: + Occipital lobe: + Overlapping lesion of eye and adnexa: + Lingual tonsil: + Gum NOS: + Thymus: + Male genital organs NOS: + Islets of Langerhans: + Isthmus uteri: + Spinal meninges: + Myometrium: + Pelvic bones sacrum coccyx and associated joints: + Connective subcutaneous and other soft tissues of lower limb and hip: + Anterior 2/3 of tongue NOS: + Upper third of esophagus: + Meninges NOS: + Prostate gland: + Overlapping lesion of small intestine: + Lower gum: + Paraspinal: + Appendix: + Scrotum NOS: + Overlapping lesion of larynx: + Main bronchus: + Descended testis: + Cloacogenic zone: + Connective subcutaneous and other soft tissues of trunk NOS: + Heart: + Mucosa of lip NOS: + Broad ligament: + Head of pancreas: + Overlapping lesion of bones joints and articular cartilage of limbs: + Temporal lobe: + Body of penis: + Overlapping lesion of biliary tract: + Labium minus: + Descending colon: + Lateral wall of nasopharynx: + Posterior wall of hypopharynx: + Nipple: + Jejunum: + Posterior wall of bladder: + Laryngeal cartilage: + Cecum: + Skin of lower limb and hip: + Corpus uteri: + Female genital tract NOS: + Abdomen NOS: + Tonsillar pillar: + Other specified parts of female genital organs: + Glottis: + Orbit NOS: + Skin of trunk: + Ventricle NOS: + Frontal lobe: VascularInvasionTypeEnum: permissible_values: - unknown: null - Not Reported: null - Extramural: null - Intramural: null - Macro: null - Micro: null - No Vascular Invasion: null + unknown: + Not Reported: + Extramural: + Intramural: + Macro: + Micro: + No Vascular Invasion: ModeofCancerDetectionEnum: permissible_values: - Data not available: null - Standard of Care Screening: null - Clinical Examination of unrelated cancer symptoms: null - Incidentaloma: null - Interval Cancer: null - PrimaryDiagnosisEnum: + Data not available: + Standard of Care Screening: + Clinical Examination of unrelated cancer symptoms: + Incidentaloma: + Interval Cancer: + DiagnosisEnum: permissible_values: - Paget disease and intraductal carcinoma of breast: null - Papillary microcarcinoma: null - Kaposi sarcoma: null - Carcinoma NOS: null - Acute myeloid leukemia NOS: null - Tumor NOS: null - Renal cell adenocarcinoma: null - Malignant lymphoma lymphoblastic NOS: null - Mammary carcinoma in situ: null - Adenocarcinoma in situ in tubular adenoma: null - Malignant lymphoma small B lymphocytic NOS: null - Eosinophilic leukemia: null - Acute lymphoblastic leukemia NOS: null - Malignant lymphoma lymphocytic nodular NOS: null - Basal cell epithelioma: null - Intracystic papilloma: null - Lobular and ductal carcinoma: null - Cancer: null - T lymphoblastic leukemia/lymphoma: null - Classical Hodgkin lymphoma lymphocyte-rich: null - Esophageal intraepithelial neoplasia high grade: null - Burkitt cell leukemia: null - Monocytic leukemia NOS: null - Acute leukemia NOS: null - Renal medullary carcinoma: null - Diffuse melanocytosis: null - Intraductal and lobular carcinoma: null - Melanotic psammomatous MPNST: null - Malignant melanoma in Hutchinson melanotic freckle: null - Pigmented adenoma: null - Chronic granulocytic leukemia BCR/ABL: null - Cervical intraepithelial neoplasia grade III: null - High-grade serous carcinoma: null - Classical Hodgkin lymphoma nodular sclerosis grade 1: null - Meningioma malignant: null - Interstitial cell tumor NOS: null - Bronchial adenoma NOS: null - Precursor T-cell lymphoblastic lymphoma: null - Tubular androblastoma with lipid storage: null - Combined large cell neuroendocrine carcinoma: null - Nephroblastoma NOS: null - Tumor cells benign: null - Tumorlet benign: null - Pleomorphic lipoma: null - Adenocarcinoma of anal ducts: null - Gastrointestinal stromal tumor malignant: null - Malignant melanoma in junctional nevus: null - Rhabdosarcoma: null - Endometrioid adenoma NOS: null - Hodgkin sarcoma: null - Malignant lymphoma immunoblastic NOS: null - Small congenital nevus: null - Tumor malignant NOS: null - Undifferentiated epithelioid sarcoma: null - Neuroendocrine carcinoma NOS: null - Acute lymphoblastic leukemia precursor cell type: null - Inflammatory adenocarcinoma: null - Tubular adenocarcinoma: null - Combined small cell-adenocarcinoma: null - Classical Hodgkin lymphoma nodular sclerosis cellular phase: null - Mixed adenocarcinoma and epidermoid carcinoma: null - Epidermoid carcinoma in situ NOS: null - Undifferentiated high-grade pleomorphic sarcoma: null - Sclerosing hepatic carcinoma: null - Pagetoid reticulosis: null - Central neurocytoma: null - Bronchiolo-alveolar carcinoma NOS: null - Chronic lymphoid leukemia: null - Paraganglioma malignant: null - Classical Hodgkin lymphoma nodular sclerosis grade 2: null - B-ALL: null - Skin appendage carcinoma: null - Epithelial tumor benign: null - B lymphoblastic leukemia/lymphoma NOS: null - Hodgkin lymphoma nodular sclerosis NOS: null - Malignant lymphoma lymphocytic diffuse NOS: null - Pro-B ALL: null - Gastrinoma NOS: null - Intraductal carcinoma clinging: null - Non-invasive low grade serous carcinoma: null - Acute promyelocytic leukemia NOS: null - Malignant lymphoma non-Hodgkin NOS: null - Not Reported: null - Melanotic schwannoma: null - Splenic marginal zone lymphoma NOS: null - Transitional cell carcinoma in situ: null - Chronic monocytic leukemia: null - Gastrin cell tumor: null - Papillary serous cystadenocarcinoma: null - Teratoma malignant NOS: null - Classical Hodgkin lymphoma lymphocyte depletion reticular: null - Tumor cells uncertain whether benign or malignant: null - Epithelial tumor malignant: null - Tubular androblastoma NOS: null - Papillary carcinoma in situ: null - Pituitary carcinoma NOS: null - Typical carcinoid: null - Non-small cell carcinoma: null - Meningioma NOS: null - Endometrial sarcoma NOS: null - Neuroblastoma NOS: null - B cell lymphoma NOS: null - Peripheral T-cell lymphoma large cell: null - Renal cell carcinoma NOS: null - Renal cell carcinoma spindle cell: null - Hepatocholangiocarcinoma: null - Malignant lymphoma nodular NOS: null - Bronchiolo-alveolar carcinoma non-mucinous: null - unknown: null - Bronchiolo-alveolar carcinoma indeterminate type: null - Pleomorphic carcinoma: null - Papillary cystadenoma NOS: null - Burkitt tumor: null - Basal cell carcinoma NOS: null - Hepatocellular carcinoma NOS: null - Undifferentiated leukaemia: null - Gastrin cell tumor malignant: null - Melanoameloblastoma: null - Prostatic intraepithelial neoplasia grade III: null - Mixed pineal tumor: null - Small cell sarcoma: null - Carcinoma in adenomatous polyp: null - Paget disease extramammary: null - Intraductal carcinoma solid type: null - Liver cell carcinoma: null - Undifferentiated sarcoma: null - Squamous cell carcinoma clear cell type: null - Pituitary adenoma NOS: null - Endometrioid carcinoma NOS: null - Papillary adenocarcinoma NOS: null - Duct carcinoma desmoplastic type: null - Chronic lymphatic leukemia: null - Squamous cell carcinoma in situ NOS: null - Intraductal papillary adenocarcinoma with invasion: null - Adenocarcinoma combined with other types of carcinoma: null - Combined hepatocellular carcinoma and cholangiocarcinoma: null - Primary amyloidosis: null - Preleukemia: null - Adenocarcinoma of anal glands: null - Secondary carcinoma: null - Dermal nevus: null - Infiltrating duct and cribriform carcinoma: null - Eosinophil adenocarcinoma: null - Chronic myeloproliferative disorder: null - Malignant melanoma regressing: null - Osteoblastoma malignant: null - Papillotubular adenocarcinoma: null - Carcinoma metastatic NOS: null - Sclerosing hemangioma: null - Lymphocytic leukemia NOS: null - Precursor cell lymphoblastic leukemia NOS: null - Papillary carcinoma NOS: null - Bronchio-alveolar carcinoma mucinous: null - Carcinoma in a polyp NOS: null - Acute myeloid leukemia MLL: null - Tubulocystic renal cell carcinoma: null - Melanocytoma NOS: null - Chronic myelogenous leukemia Philadelphia chromosome (Ph 1) positive: null - Ewing sarcoma: null - Glioma NOS: null - Bronchial-associated lymphoid tissue lymphoma: null - Papillotubular adenoma: null - Papilloma of bladder: null - Bronchio-alveolar carcinoma mixed mucinous and non-mucinous: null - Carcinoma in pleomorphic adenoma: null - Chondrosarcoma grade 2/3: null - Neoplasm secondary: null - Rhabdomyosarcoma with ganglionic differentiation: null - Chronic lymphocytic leukemia: null - Liposarcoma well differentiated: null - Undifferentiated pleomorphic sarcoma: null - Secretory carcinoma of breast: null - Lobular carcinoma noninfiltrating: null - Mixed adenocarcinoma and squamous cell carcinoma: null - Melanotic neurofibroma: null - Chronic granulocytic leukemia Philadelphia chromosome (Ph1) positive: null - Hepatocellular adenoma: null - Burkitt lymphoma NOS (Includes all variants): null - Paraganglioma NOS: null - Diffuse large B-cell lymphoma NOS: null - Nevus NOS: null - Hepatoid carcinoma: null - Mixed tumor malignant NOS: null - Rhabdoid sarcoma: null - Tubulolobular carcinoma: null - Papillomatosis glandular: null - Bronchial adenoma carcinoid: null - Tumor embolus: null - Duct carcinoma NOS: null - Rhabdomyosarcoma NOS: null - Lobular carcinoma NOS: null - Bronchial adenoma cylindroid: null - Epidermoid carcinoma NOS: null - Papillary glioneuronal tumor: null - Ductal carcinoma in situ NOS: null - Unclassified tumor malignant uncertain whether primary or metastatic: null - Glioblastoma: null - Papillary and follicular carcinoma: null - Ductal carcinoma NOS: null - Tumor benign: null - Paget disease mammary: null - Diffuse astrocytoma low grade: null - Duct cell carcinoma: null - Preleukemic syndrome: null - Carcinoma diffuse type: null - Neurosarcoma: null - Papillomatosis NOS: null - Therapy related myeloid neoplasm: null - Renal carcinoma collecting duct type: null - Neurofibroma NOS: null - Meningioma anaplastic: null - Cementoma NOS: null - Dermatofibroma NOS: null - Astrocytoma NOS: null - Liver cell adenoma: null - Tubulovillous adenoma NOS: null - Melanoma NOS: null - Papilloma NOS: null - Esophageal glandular dysplasia (intraepithelial neoplasia) high grade: null - Tumor cells malignant: null - Malignant lymphoma diffuse NOS: null - Renal cell carcinoma chromophobe type: null - Tubular carcinoid: null - Nonpigmented nevus: null - Rodent ulcer: null - Hodgkin disease NOS: null - Acinar cell carcinoma: null - Papillary adenofibroma: null - Oat cell carcinoma: null - Adenocarcinoma in adenomatous polyp: null - Spindle cell carcinoma NOS: null - Adenocarcinoma in polypoid adenoma: null - Papillary serous adenocarcinoma: null - Splenic diffuse red pulp small B-cell lymphoma: null - Chondroma NOS: null - Bile duct adenoma: null - Adenocarcinoma in villous adenoma: null - Spindle cell melanoma NOS: null - Classical Hodgkin lymphoma mixed cellularity NOS: null - Combined small cell-large carcinoma: null - Eosinophil carcinoma: null - Pancreatic endocrine tumor NOS: null - Adenocarcinoma NOS: null - Sarcoma NOS: null - Chronic myelocytic leukemia NOS: null - Adenocarcinoma in situ non-mucinous: null - Chronic leukemia NOS: null - Pro-T ALL: null - Esophageal glandular dysplasia (intraepithelial neoplasia) low grade: null - Lymphoblastoma: null - Mixed medullary-papillary carcinoma: null - Classical Hodgkin lymphoma nodular sclerosis NOS: null - Osteoblastoma NOS: null - Cerebellar sarcoma NOS: null - Paraganglioma benign: null - Intraductal tubular-papillary neoplasm low grade: null - Familial adenomatous polyposis: null - Mixed squamous cell and glandular papilloma: null - Intraductal carcinoma NOS: null - Transitional carcinoma: null - Gastrinoma malignant: null - Melanocytoma eyeball: null - Mixed medullary-follicular carcinoma: null - Chronic myelogenous leukemia BCR-ABL positive: null - Basophil carcinoma: null - Neuroepithelioma NOS: null - Adenocarcinoma pancreatobiliary type: null - Precancerous melanosis NOS: null - Undifferentiated round cell sarcoma: null - Malignant lymphoma large cell NOS: null - Tubulo-papillary adenoma: null - Classical Hodgkin lymphoma lymphocyte depletion diffuse fibrosis: null - Cerebellar liponeurocytoma: null - Pulmonary blastoma: null - Burkitt-like lymphoma: null - Ganglioglioma NOS: null - T-cell lymphoma NOS: null - Papillary tumor of the pineal region: null - Intraductal papillary adenocarcinoma NOS: null - Malignant lymphoma NOS: null - Hepatoid adenocarcinoma: null - Papillary adenoma NOS: null - Carcinoma in situ in adenomatous polyp: null - Eosinophilic granuloma: null - Medullary adenocarcinoma: null - Malignant lymphoma mixed cell type nodular: null - Intraductal carcinoma noninfiltrating NOS: null - Interstitial cell tumor malignant: null - Lymphoma NOS: null - Unclassified tumor borderline malignancy: null - Adenocarcinoma in tubular adenoma: null - Intraductal papillary carcinoma: null - Myelocytic leukemia NOS: null - Tumor cells NOS: null - Liposarcoma NOS: null - Interstitial cell tumor benign: null - Neoplasm metastatic: null - Chronic neutrophilic leukemia: null - Bronchiolo-alveolar carcinoma goblet cell type: null - Papillary adenocarcinoma follicular variant: null - Hepatocarcinoma: null - Undifferentiated uterine sarcoma: null - Renal cell carcinoma unclassified: null - Papillary epidermoid carcinoma: null - Pigmented nevus NOS: null - Myeloid leukemia NOS: null - Esophageal squamous intraepithelial neoplasia (dysplasia) high grade: null - Malignant lymphoma large B-cell NOS: null - Non-lymphocytic leukemia NOS: null - Basal cell adenocarcinoma: null - Adult T-cell lymphoma/leukemia: null - Mixed pancreatic endocrine and exocrine tumor malignant: null - Ependymoma NOS: null - Peripheral T-cell lymphoma NOS: null - Pulmonary adenomatosis: null - Pleomorphic lobular carcinoma: null - Paget disease of breast: null - Hodgkin paragranuloma NOS: null - Malignant melanoma NOS: null - Papillary transitional cell carcinoma: null - Acute lymphocytic leukemia: null - Serous surface papillary carcinoma: null - Basal cell tumor: null - Chronic myelomonocytic leukemia NOS: null - Lymphatic leukemic NOS: null - Teratoma NOS: null - Malignant lymphoma mixed cell type follicular: null - Bronchiolar adenocarcinoma: null - Basophil adenocarcinoma: null - Non-Hodgkin lymphoma NOS: null - Haemangioblastoma: null - Intraductal tubular-papillary neoplasm high grade: null - Chronic myeloproliferative disease NOS: null - Rhabdoid meningioma: null - Rhabdoid tumor NOS: null - Carcinoma intestinal type: null - Classical Hodgkin lymphoma lymphocyte depletion NOS: null - Chronic myeloid leukemia NOS: null - Melanotic medulloblastoma: null - Melanotic neuroectodermal tumor: null - Lobular carcinoma in situ NOS: null - Mixed small cell carcinoma: null - Intradermal nevus: null - Bronchiolo-alveolar carcinoma Clara cell: null - Papillary squamous cell carcinoma in situ: null - Small cell neuroendocrine carcinoma: null - Malignant melanoma in precancerous melanosis: null - Carcinoma anaplastic NOS: null - Dysplastic nevus: null - Liposarcoma differentiated: null - Combined small cell-squamous cell carcinoma: null - Acute lymphatic leukemia: null - Glioma malignant: null - Adenocarcinoma in situ NOS: null - Mucosal-associated lymphoid tissue lymphoma: null - Splenic lymphoma with villous lymphocytes: null - Large cell carcinoma NOS: null - Micropapillary carcinoma NOS: null - Undifferentiated spindle cell sarcoma: null - Intraepidermal squamous cell carcinoma Bowen type: null - Endometrioid adenofibroma NOS: null - Medullary carcinoma NOS: null - T-cell large granular lymphocytosis: null - Intraductal adenocarcinoma noninfiltrating NOS: null - Osteosarcoma NOS: null - Pancreatobiliary-type carcinoma: null - Adenocarcinoid tumor: null - Diffuse astrocytoma IDH-mutant: null - Medullary osteosarcoma: null - Adenocarcinoma intestinal type: null - Carcinoma in situ in a polyp NOS: null - Carcinosarcoma NOS: null - Basal cell adenoma: null - Adult T-cell lymphoma: null - Lobular adenocarcinoma: null - Melanocytic nevus: null - Adenocarcinoma metastatic NOS: null - Pigmented basal cell carcinoma: null - Astrocytoma anaplastic: null - Melanoma malignant of soft parts: null - Small cell osteosarcoma: null - Unclassified tumor uncertain whether benign or malignant: null - Transitional cell carcinoma: null - Intraductal carcinoma and lobular carcinoma in situ: null - Rhabdomyoma NOS: null - B-cell lymphocytic leukemia/small lymphocytic lymphoma: null - Capillary hemangioma: null - Precursor B-cell lymphoblastic leukemia: null - Bronchiolo-alveolar carcinoma Clara cell and goblet cell type: null - Eosinophil adenoma: null - Splenic B-cell lymphoma/leukemia unclassifiable: null - Composite Hodgkin and non-Hodgkin lymphoma: null - Paget disease and infiltrating duct carcinoma of breast: null - Neurofibromatosis NOS: null - Hodgkin lymphoma NOS: null - Melanoma in situ: null - Serous cystadenocarcinoma NOS: null - Malignant lymphoma Hodgkin: null - Acute lymphoblastic leukemia-lymphoma NOS: null - Unclassified tumor malignant: null - Adult rhabdomyoma: null - Neoplasm uncertain whether benign or malignant: null - Chronic myelomonocytic leukemia Type 1: null - Duct adenoma NOS: null - Neoplasm benign: null - Carcinoma undifferentiated NOS: null - Malignancy: null - Adenocarcinoma in situ mucinous: null - Papillary squamous cell carcinoma: null - B lymphoblastic leukemia/lymphoma with hyperdiploidy: null - Precursor T-cell lymphoblastic leukemia: null - Tumor secondary: null - Pancreatobiliary neoplasm non-invasive: null - Malignant melanoma in giant pigmented nevus: null - Squamous cell carcinoma adenoid: null - Acute myelomonocytic leukemia: null - Bile duct cystadenocarcinoma: null - Pancreatic endocrine tumor nonfunctioning: null - Pleomorphic adenoma: null - B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL): null - Renal cell carcinoma sarcomatoid: null - Splenic marginal zone B-cell lymphoma: null - Malignant lymphoma large B-cell diffuse NOS: null - Infiltrating duct and colloid carcinoma: null - Chronic myelomonocytic leukemia Type II: null - Duct adenocarcinoma NOS: null - Combined/mixed carcinoid and adenocarcinoma: null - Haemangiosarcoma: null - Acute lymphoid leukemia: null - Diffuse astrocytoma IDH-wildtype: null - Intraductal tubulopapillary neoplasm: null - Acute basophilic leukaemia: null - Unclassified tumor benign: null - Intraductal micropapillary carcinoma: null - Hodgkin granuloma: null - Chronic lymphocytic leukemia B-cell type (includes all variants of BCLL): null - Pancreatoblastoma: null - Bile duct adenocarcinoma: null - Meningeal melanocytoma: null - Hodgkin lymphoma mixed cellularity NOS: null - Infiltrating duct carcinoma NOS: null - Esophageal squamous intraepithelial neoplasia (dysplasia) low grade: null - Small cell carcinoma NOS: null - Inflammatory carcinoma: null - Papillary urothelial carcinoma: null - Melanotic progonoma: null - Central neuroblastoma: null - Malignant lymphoma lymphocytic NOS: null - Myeloma NOS: null - Adenocarcinoma endocervical type: null - Adenocarcinoma in situ in a polyp NOS: null - Neoplasm malignant uncertain whether primary or metastatic: null - Pulmonary artery intimal sarcoma: null - Intraepidermal carcinoma NOS: null - Papillary serous cystadenoma NOS: null - Carcinoma in situ NOS: null - Tubular adenoma NOS: null - Tubulopapillary adenocarcinoma: null - Pancreatic microadenoma: null - Acute lymphoblastic leukemia mature B-cell type: null - c-ALL: null - Acute leukemia Burkitt type: null - Cervical intraepithelial neoplasia low grade: null - Mixed tumor NOS: null - Bronchiolo-alveolar adenocarcinoma NOS: null - Myoepithelioma: null - Pancreatic endocrine tumor malignant: null - Endometrioid adenocarcinoma NOS: null - Infiltrating basal cell carcinoma NOS: null - Precursor B-cell lymphoblastic lymphoma: null - Pleomorphic lobular carcinoma in situ: null - Mucous adenocarcinoma: null - Meningeal melanoma: null - Acute myeloid leukemia minimal differentiation: null - Lymphoblastic leukemia NOS: null - Melanotic MPNST: null - Astrocytoma low grade: null - Multiple myeloma: null - Papillary renal cell carcinoma: null - Medulloblastoma NOS: null - Adenocarcinoma in a polyp NOS: null - Combined small cell carcinoma: null - Bile duct carcinoma: null - Chronic granulocytic leukemia NOS: null - Juvenile myelomonocytic leukemia: null - Neoplasm NOS: null - Capillary lymphangioma: null - Malignant lymphoma mixed cell type diffuse: null - Neoplasm malignant: null - Papillary meningioma: null - Bile duct cystadenoma: null - Malignant melanoma in congenital melanocytic nevus: null - Adenocarcinoma diffuse type: null - Pancreatic endocrine tumor benign: null - Squamous cell carcinoma NOS: null - Chronic myelomonocytic leukemia in transformation: null - T-cell large granular lymphocytic leukemia: null - Basophil adenoma: null - Bronchiolar carcinoma: null - Tubular carcinoma: null - Neurofibrosarcoma: null - Adenocarcinoma in situ in adenomatous polyp: null - Intravascular B-cell lymphoma: null - Pleomorphic liposarcoma: null - Tumor metastatic: null + Paget disease and intraductal carcinoma of breast: + Papillary microcarcinoma: + Kaposi sarcoma: + Carcinoma NOS: + Acute myeloid leukemia NOS: + Tumor NOS: + Renal cell adenocarcinoma: + Malignant lymphoma lymphoblastic NOS: + Mammary carcinoma in situ: + Adenocarcinoma in situ in tubular adenoma: + Malignant lymphoma small B lymphocytic NOS: + Eosinophilic leukemia: + Acute lymphoblastic leukemia NOS: + Malignant lymphoma lymphocytic nodular NOS: + Basal cell epithelioma: + Intracystic papilloma: + Lobular and ductal carcinoma: + Cancer: + T lymphoblastic leukemia/lymphoma: + Classical Hodgkin lymphoma lymphocyte-rich: + Esophageal intraepithelial neoplasia high grade: + Burkitt cell leukemia: + Monocytic leukemia NOS: + Acute leukemia NOS: + Renal medullary carcinoma: + Diffuse melanocytosis: + Intraductal and lobular carcinoma: + Melanotic psammomatous MPNST: + Malignant melanoma in Hutchinson melanotic freckle: + Pigmented adenoma: + Chronic granulocytic leukemia BCR/ABL: + Cervical intraepithelial neoplasia grade III: + High-grade serous carcinoma: + Classical Hodgkin lymphoma nodular sclerosis grade 1: + Meningioma malignant: + Interstitial cell tumor NOS: + Bronchial adenoma NOS: + Precursor T-cell lymphoblastic lymphoma: + Tubular androblastoma with lipid storage: + Combined large cell neuroendocrine carcinoma: + Nephroblastoma NOS: + Tumor cells benign: + Tumorlet benign: + Pleomorphic lipoma: + Adenocarcinoma of anal ducts: + Gastrointestinal stromal tumor malignant: + Malignant melanoma in junctional nevus: + Rhabdosarcoma: + Endometrioid adenoma NOS: + Hodgkin sarcoma: + Malignant lymphoma immunoblastic NOS: + Small congenital nevus: + Tumor malignant NOS: + Undifferentiated epithelioid sarcoma: + Neuroendocrine carcinoma NOS: + Acute lymphoblastic leukemia precursor cell type: + Inflammatory adenocarcinoma: + Tubular adenocarcinoma: + Combined small cell-adenocarcinoma: + Classical Hodgkin lymphoma nodular sclerosis cellular phase: + Mixed adenocarcinoma and epidermoid carcinoma: + Epidermoid carcinoma in situ NOS: + Undifferentiated high-grade pleomorphic sarcoma: + Sclerosing hepatic carcinoma: + Pagetoid reticulosis: + Central neurocytoma: + Bronchiolo-alveolar carcinoma NOS: + Chronic lymphoid leukemia: + Paraganglioma malignant: + Classical Hodgkin lymphoma nodular sclerosis grade 2: + B-ALL: + Skin appendage carcinoma: + Epithelial tumor benign: + B lymphoblastic leukemia/lymphoma NOS: + Hodgkin lymphoma nodular sclerosis NOS: + Malignant lymphoma lymphocytic diffuse NOS: + Pro-B ALL: + Gastrinoma NOS: + Intraductal carcinoma clinging: + Non-invasive low grade serous carcinoma: + Acute promyelocytic leukemia NOS: + Malignant lymphoma non-Hodgkin NOS: + Not Reported: + Melanotic schwannoma: + Splenic marginal zone lymphoma NOS: + Transitional cell carcinoma in situ: + Chronic monocytic leukemia: + Gastrin cell tumor: + Papillary serous cystadenocarcinoma: + Teratoma malignant NOS: + Classical Hodgkin lymphoma lymphocyte depletion reticular: + Tumor cells uncertain whether benign or malignant: + Epithelial tumor malignant: + Tubular androblastoma NOS: + Papillary carcinoma in situ: + Pituitary carcinoma NOS: + Typical carcinoid: + Non-small cell carcinoma: + Meningioma NOS: + Endometrial sarcoma NOS: + Neuroblastoma NOS: + B cell lymphoma NOS: + Peripheral T-cell lymphoma large cell: + Renal cell carcinoma NOS: + Renal cell carcinoma spindle cell: + Hepatocholangiocarcinoma: + Malignant lymphoma nodular NOS: + Bronchiolo-alveolar carcinoma non-mucinous: + unknown: + Bronchiolo-alveolar carcinoma indeterminate type: + Pleomorphic carcinoma: + Papillary cystadenoma NOS: + Burkitt tumor: + Basal cell carcinoma NOS: + Hepatocellular carcinoma NOS: + Undifferentiated leukaemia: + Gastrin cell tumor malignant: + Melanoameloblastoma: + Prostatic intraepithelial neoplasia grade III: + Mixed pineal tumor: + Small cell sarcoma: + Carcinoma in adenomatous polyp: + Paget disease extramammary: + Intraductal carcinoma solid type: + Liver cell carcinoma: + Undifferentiated sarcoma: + Squamous cell carcinoma clear cell type: + Pituitary adenoma NOS: + Endometrioid carcinoma NOS: + Papillary adenocarcinoma NOS: + Duct carcinoma desmoplastic type: + Chronic lymphatic leukemia: + Squamous cell carcinoma in situ NOS: + Intraductal papillary adenocarcinoma with invasion: + Adenocarcinoma combined with other types of carcinoma: + Combined hepatocellular carcinoma and cholangiocarcinoma: + Primary amyloidosis: + Preleukemia: + Adenocarcinoma of anal glands: + Secondary carcinoma: + Dermal nevus: + Infiltrating duct and cribriform carcinoma: + Eosinophil adenocarcinoma: + Chronic myeloproliferative disorder: + Malignant melanoma regressing: + Osteoblastoma malignant: + Papillotubular adenocarcinoma: + Carcinoma metastatic NOS: + Sclerosing hemangioma: + Lymphocytic leukemia NOS: + Precursor cell lymphoblastic leukemia NOS: + Papillary carcinoma NOS: + Bronchio-alveolar carcinoma mucinous: + Carcinoma in a polyp NOS: + Acute myeloid leukemia MLL: + Tubulocystic renal cell carcinoma: + Melanocytoma NOS: + Chronic myelogenous leukemia Philadelphia chromosome (Ph 1) positive: + Ewing sarcoma: + Glioma NOS: + Bronchial-associated lymphoid tissue lymphoma: + Papillotubular adenoma: + Papilloma of bladder: + Bronchio-alveolar carcinoma mixed mucinous and non-mucinous: + Carcinoma in pleomorphic adenoma: + Chondrosarcoma grade 2/3: + Neoplasm secondary: + Rhabdomyosarcoma with ganglionic differentiation: + Chronic lymphocytic leukemia: + Liposarcoma well differentiated: + Undifferentiated pleomorphic sarcoma: + Secretory carcinoma of breast: + Lobular carcinoma noninfiltrating: + Mixed adenocarcinoma and squamous cell carcinoma: + Melanotic neurofibroma: + Chronic granulocytic leukemia Philadelphia chromosome (Ph1) positive: + Hepatocellular adenoma: + Burkitt lymphoma NOS (Includes all variants): + Paraganglioma NOS: + Diffuse large B-cell lymphoma NOS: + Nevus NOS: + Hepatoid carcinoma: + Mixed tumor malignant NOS: + Rhabdoid sarcoma: + Tubulolobular carcinoma: + Papillomatosis glandular: + Bronchial adenoma carcinoid: + Tumor embolus: + Duct carcinoma NOS: + Rhabdomyosarcoma NOS: + Lobular carcinoma NOS: + Bronchial adenoma cylindroid: + Epidermoid carcinoma NOS: + Papillary glioneuronal tumor: + Ductal carcinoma in situ NOS: + Unclassified tumor malignant uncertain whether primary or metastatic: + Glioblastoma: + Papillary and follicular carcinoma: + Ductal carcinoma NOS: + Tumor benign: + Paget disease mammary: + Diffuse astrocytoma low grade: + Duct cell carcinoma: + Preleukemic syndrome: + Carcinoma diffuse type: + Neurosarcoma: + Papillomatosis NOS: + Therapy related myeloid neoplasm: + Renal carcinoma collecting duct type: + Neurofibroma NOS: + Meningioma anaplastic: + Cementoma NOS: + Dermatofibroma NOS: + Astrocytoma NOS: + Liver cell adenoma: + Tubulovillous adenoma NOS: + Melanoma NOS: + Papilloma NOS: + Esophageal glandular dysplasia (intraepithelial neoplasia) high grade: + Tumor cells malignant: + Malignant lymphoma diffuse NOS: + Renal cell carcinoma chromophobe type: + Tubular carcinoid: + Nonpigmented nevus: + Rodent ulcer: + Hodgkin disease NOS: + Acinar cell carcinoma: + Papillary adenofibroma: + Oat cell carcinoma: + Adenocarcinoma in adenomatous polyp: + Spindle cell carcinoma NOS: + Adenocarcinoma in polypoid adenoma: + Papillary serous adenocarcinoma: + Splenic diffuse red pulp small B-cell lymphoma: + Chondroma NOS: + Bile duct adenoma: + Adenocarcinoma in villous adenoma: + Spindle cell melanoma NOS: + Classical Hodgkin lymphoma mixed cellularity NOS: + Combined small cell-large carcinoma: + Eosinophil carcinoma: + Pancreatic endocrine tumor NOS: + Adenocarcinoma NOS: + Sarcoma NOS: + Chronic myelocytic leukemia NOS: + Adenocarcinoma in situ non-mucinous: + Chronic leukemia NOS: + Pro-T ALL: + Esophageal glandular dysplasia (intraepithelial neoplasia) low grade: + Lymphoblastoma: + Mixed medullary-papillary carcinoma: + Classical Hodgkin lymphoma nodular sclerosis NOS: + Osteoblastoma NOS: + Cerebellar sarcoma NOS: + Paraganglioma benign: + Intraductal tubular-papillary neoplasm low grade: + Familial adenomatous polyposis: + Mixed squamous cell and glandular papilloma: + Intraductal carcinoma NOS: + Transitional carcinoma: + Gastrinoma malignant: + Melanocytoma eyeball: + Mixed medullary-follicular carcinoma: + Chronic myelogenous leukemia BCR-ABL positive: + Basophil carcinoma: + Neuroepithelioma NOS: + Adenocarcinoma pancreatobiliary type: + Precancerous melanosis NOS: + Undifferentiated round cell sarcoma: + Malignant lymphoma large cell NOS: + Tubulo-papillary adenoma: + Classical Hodgkin lymphoma lymphocyte depletion diffuse fibrosis: + Cerebellar liponeurocytoma: + Pulmonary blastoma: + Burkitt-like lymphoma: + Ganglioglioma NOS: + T-cell lymphoma NOS: + Papillary tumor of the pineal region: + Intraductal papillary adenocarcinoma NOS: + Malignant lymphoma NOS: + Hepatoid adenocarcinoma: + Papillary adenoma NOS: + Carcinoma in situ in adenomatous polyp: + Eosinophilic granuloma: + Medullary adenocarcinoma: + Malignant lymphoma mixed cell type nodular: + Intraductal carcinoma noninfiltrating NOS: + Interstitial cell tumor malignant: + Lymphoma NOS: + Unclassified tumor borderline malignancy: + Adenocarcinoma in tubular adenoma: + Intraductal papillary carcinoma: + Myelocytic leukemia NOS: + Tumor cells NOS: + Liposarcoma NOS: + Interstitial cell tumor benign: + Neoplasm metastatic: + Chronic neutrophilic leukemia: + Bronchiolo-alveolar carcinoma goblet cell type: + Papillary adenocarcinoma follicular variant: + Hepatocarcinoma: + Undifferentiated uterine sarcoma: + Renal cell carcinoma unclassified: + Papillary epidermoid carcinoma: + Pigmented nevus NOS: + Myeloid leukemia NOS: + Esophageal squamous intraepithelial neoplasia (dysplasia) high grade: + Malignant lymphoma large B-cell NOS: + Non-lymphocytic leukemia NOS: + Basal cell adenocarcinoma: + Adult T-cell lymphoma/leukemia: + Mixed pancreatic endocrine and exocrine tumor malignant: + Ependymoma NOS: + Peripheral T-cell lymphoma NOS: + Pulmonary adenomatosis: + Pleomorphic lobular carcinoma: + Paget disease of breast: + Hodgkin paragranuloma NOS: + Malignant melanoma NOS: + Papillary transitional cell carcinoma: + Acute lymphocytic leukemia: + Serous surface papillary carcinoma: + Basal cell tumor: + Chronic myelomonocytic leukemia NOS: + Lymphatic leukemic NOS: + Teratoma NOS: + Malignant lymphoma mixed cell type follicular: + Bronchiolar adenocarcinoma: + Basophil adenocarcinoma: + Non-Hodgkin lymphoma NOS: + Haemangioblastoma: + Intraductal tubular-papillary neoplasm high grade: + Chronic myeloproliferative disease NOS: + Rhabdoid meningioma: + Rhabdoid tumor NOS: + Carcinoma intestinal type: + Classical Hodgkin lymphoma lymphocyte depletion NOS: + Chronic myeloid leukemia NOS: + Melanotic medulloblastoma: + Melanotic neuroectodermal tumor: + Lobular carcinoma in situ NOS: + Mixed small cell carcinoma: + Intradermal nevus: + Bronchiolo-alveolar carcinoma Clara cell: + Papillary squamous cell carcinoma in situ: + Small cell neuroendocrine carcinoma: + Malignant melanoma in precancerous melanosis: + Carcinoma anaplastic NOS: + Dysplastic nevus: + Liposarcoma differentiated: + Combined small cell-squamous cell carcinoma: + Acute lymphatic leukemia: + Glioma malignant: + Adenocarcinoma in situ NOS: + Mucosal-associated lymphoid tissue lymphoma: + Splenic lymphoma with villous lymphocytes: + Large cell carcinoma NOS: + Micropapillary carcinoma NOS: + Undifferentiated spindle cell sarcoma: + Intraepidermal squamous cell carcinoma Bowen type: + Endometrioid adenofibroma NOS: + Medullary carcinoma NOS: + T-cell large granular lymphocytosis: + Intraductal adenocarcinoma noninfiltrating NOS: + Osteosarcoma NOS: + Pancreatobiliary-type carcinoma: + Adenocarcinoid tumor: + Diffuse astrocytoma IDH-mutant: + Medullary osteosarcoma: + Adenocarcinoma intestinal type: + Carcinoma in situ in a polyp NOS: + Carcinosarcoma NOS: + Basal cell adenoma: + Adult T-cell lymphoma: + Lobular adenocarcinoma: + Melanocytic nevus: + Adenocarcinoma metastatic NOS: + Pigmented basal cell carcinoma: + Astrocytoma anaplastic: + Melanoma malignant of soft parts: + Small cell osteosarcoma: + Unclassified tumor uncertain whether benign or malignant: + Transitional cell carcinoma: + Intraductal carcinoma and lobular carcinoma in situ: + Rhabdomyoma NOS: + B-cell lymphocytic leukemia/small lymphocytic lymphoma: + Capillary hemangioma: + Precursor B-cell lymphoblastic leukemia: + Bronchiolo-alveolar carcinoma Clara cell and goblet cell type: + Eosinophil adenoma: + Splenic B-cell lymphoma/leukemia unclassifiable: + Composite Hodgkin and non-Hodgkin lymphoma: + Paget disease and infiltrating duct carcinoma of breast: + Neurofibromatosis NOS: + Hodgkin lymphoma NOS: + Melanoma in situ: + Serous cystadenocarcinoma NOS: + Malignant lymphoma Hodgkin: + Acute lymphoblastic leukemia-lymphoma NOS: + Unclassified tumor malignant: + Adult rhabdomyoma: + Neoplasm uncertain whether benign or malignant: + Chronic myelomonocytic leukemia Type 1: + Duct adenoma NOS: + Neoplasm benign: + Carcinoma undifferentiated NOS: + Malignancy: + Adenocarcinoma in situ mucinous: + Papillary squamous cell carcinoma: + B lymphoblastic leukemia/lymphoma with hyperdiploidy: + Precursor T-cell lymphoblastic leukemia: + Tumor secondary: + Pancreatobiliary neoplasm non-invasive: + Malignant melanoma in giant pigmented nevus: + Squamous cell carcinoma adenoid: + Acute myelomonocytic leukemia: + Bile duct cystadenocarcinoma: + Pancreatic endocrine tumor nonfunctioning: + Pleomorphic adenoma: + B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL): + Renal cell carcinoma sarcomatoid: + Splenic marginal zone B-cell lymphoma: + Malignant lymphoma large B-cell diffuse NOS: + Infiltrating duct and colloid carcinoma: + Chronic myelomonocytic leukemia Type II: + Duct adenocarcinoma NOS: + Combined/mixed carcinoid and adenocarcinoma: + Haemangiosarcoma: + Acute lymphoid leukemia: + Diffuse astrocytoma IDH-wildtype: + Intraductal tubulopapillary neoplasm: + Acute basophilic leukaemia: + Unclassified tumor benign: + Intraductal micropapillary carcinoma: + Hodgkin granuloma: + Chronic lymphocytic leukemia B-cell type (includes all variants of BCLL): + Pancreatoblastoma: + Bile duct adenocarcinoma: + Meningeal melanocytoma: + Hodgkin lymphoma mixed cellularity NOS: + Infiltrating duct carcinoma NOS: + Esophageal squamous intraepithelial neoplasia (dysplasia) low grade: + Small cell carcinoma NOS: + Inflammatory carcinoma: + Papillary urothelial carcinoma: + Melanotic progonoma: + Central neuroblastoma: + Malignant lymphoma lymphocytic NOS: + Myeloma NOS: + Adenocarcinoma endocervical type: + Adenocarcinoma in situ in a polyp NOS: + Neoplasm malignant uncertain whether primary or metastatic: + Pulmonary artery intimal sarcoma: + Intraepidermal carcinoma NOS: + Papillary serous cystadenoma NOS: + Carcinoma in situ NOS: + Tubular adenoma NOS: + Tubulopapillary adenocarcinoma: + Pancreatic microadenoma: + Acute lymphoblastic leukemia mature B-cell type: + c-ALL: + Acute leukemia Burkitt type: + Cervical intraepithelial neoplasia low grade: + Mixed tumor NOS: + Bronchiolo-alveolar adenocarcinoma NOS: + Myoepithelioma: + Pancreatic endocrine tumor malignant: + Endometrioid adenocarcinoma NOS: + Infiltrating basal cell carcinoma NOS: + Precursor B-cell lymphoblastic lymphoma: + Pleomorphic lobular carcinoma in situ: + Mucous adenocarcinoma: + Meningeal melanoma: + Acute myeloid leukemia minimal differentiation: + Lymphoblastic leukemia NOS: + Melanotic MPNST: + Astrocytoma low grade: + Multiple myeloma: + Papillary renal cell carcinoma: + Medulloblastoma NOS: + Adenocarcinoma in a polyp NOS: + Combined small cell carcinoma: + Bile duct carcinoma: + Chronic granulocytic leukemia NOS: + Juvenile myelomonocytic leukemia: + Neoplasm NOS: + Capillary lymphangioma: + Malignant lymphoma mixed cell type diffuse: + Neoplasm malignant: + Papillary meningioma: + Bile duct cystadenoma: + Malignant melanoma in congenital melanocytic nevus: + Adenocarcinoma diffuse type: + Pancreatic endocrine tumor benign: + Squamous cell carcinoma NOS: + Chronic myelomonocytic leukemia in transformation: + T-cell large granular lymphocytic leukemia: + Basophil adenoma: + Bronchiolar carcinoma: + Tubular carcinoma: + Neurofibrosarcoma: + Adenocarcinoma in situ in adenomatous polyp: + Intravascular B-cell lymphoma: + Pleomorphic liposarcoma: + Tumor metastatic: TumorExtranodalExtensionIndicatorEnum: permissible_values: - Absent: null - Not applicable: null - 'YES': null - unspecified: null - No source documentation: null - UNKNOWN: null - Present: null - Present - extensive: null - Not sampled or dissected: null - Present - minimal: null - 'NO': null - Indeterminate: null + Absent: + Not applicable: + 'YES': + unspecified: + No source documentation: + UNKNOWN: + Present: + Present - extensive: + Not sampled or dissected: + Present - minimal: + 'NO': + Indeterminate: PrecancerousConditionTypeEnum: permissible_values: - Carcinoma NOS: null - Atypical melanocytic proliferation: null - Superficial spreading: null - Melanoma in situ arising in a giant congenital nevus: null - Invasive melanoma: null - Invasive melanoma - acral lentiginous: null - Melanoma in situ not otherwise classified: null - Mild dysplasia: null - Adenocarcinoma in situ - non mucinous: null - Reserve cell hyperplasia: null - Invasive melanoma - nevoid: null - No diagnosis possible: null - Hamartoma: null - Adenocarcinoma in situ - mucinous: null - Squamous metaplasia - immature: null - Severe dysplasia: null - Invasive melanoma - lentigo maligna: null - Squamous metaplasia - mature: null - Acral-lentiginous: null - Invasive melanoma - superficial spreading: null - Atypical adenomatous hyperplasia: null - Moderate dysplasia: null - Atypical Adenomatous Lung Hyperplasia: null - Normal WDA: null - Other: null - Persistent melanoma in situ: null - Pancreatic Intraepithelial Neoplasia: null - Ductal Carcinoma In Situ: null - Pancreatic Intraductal Papillary-Mucinous Neoplasm: null - Melanocytic hyperplasia: null - Melanoma in situ: null - Invasive melanoma - desmoplastic: null - Benign tumor NOS: null - Lentigo maligna type: null - Scar - no residual melanoma: null - Invasive melanoma - nodular type: null - Prostatic Intraepithelial Neoplasia: null + Carcinoma NOS: + Atypical melanocytic proliferation: + Superficial spreading: + Melanoma in situ arising in a giant congenital nevus: + Invasive melanoma: + Invasive melanoma - acral lentiginous: + Melanoma in situ not otherwise classified: + Mild dysplasia: + Adenocarcinoma in situ - non mucinous: + Reserve cell hyperplasia: + Invasive melanoma - nevoid: + No diagnosis possible: + Hamartoma: + Adenocarcinoma in situ - mucinous: + Squamous metaplasia - immature: + Severe dysplasia: + Invasive melanoma - lentigo maligna: + Squamous metaplasia - mature: + Acral-lentiginous: + Invasive melanoma - superficial spreading: + Atypical adenomatous hyperplasia: + Moderate dysplasia: + Atypical Adenomatous Lung Hyperplasia: + Normal WDA: + Other: + Persistent melanoma in situ: + Pancreatic Intraepithelial Neoplasia: + Ductal Carcinoma In Situ: + Pancreatic Intraductal Papillary-Mucinous Neoplasm: + Melanocytic hyperplasia: + Melanoma in situ: + Invasive melanoma - desmoplastic: + Benign tumor NOS: + Lentigo maligna type: + Scar - no residual melanoma: + Invasive melanoma - nodular type: + Prostatic Intraepithelial Neoplasia: IndicatorEnum: permissible_values: - 'Yes': null - 'No': null - unknown: null + 'Yes': + 'No': + unknown: AnaplasiaPresentTypeEnum: permissible_values: - unknown: null - Not Reported: null - Equivocal: null - Absent: null - Present: null - Diffuse: null - Focal: null - Sclerosis: null + unknown: + Not Reported: + Equivocal: + Absent: + Present: + Diffuse: + Focal: + Sclerosis: From ffc5a5b2fb4b0a4c6c53c5dd21f1fdfca5677c08 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Thu, 8 Feb 2024 12:06:24 -0700 Subject: [PATCH 10/14] Revise diagnosis-related attributes per RFC --- modules/classes/patient_and_specimen.yaml | 4 ++-- modules/enums/Demographics.yaml | 7 +++++++ modules/slots.yaml | 19 +++++++++++++------ 3 files changed, 22 insertions(+), 8 deletions(-) diff --git a/modules/classes/patient_and_specimen.yaml b/modules/classes/patient_and_specimen.yaml index 9197d97..61f1154 100644 --- a/modules/classes/patient_and_specimen.yaml +++ b/modules/classes/patient_and_specimen.yaml @@ -28,9 +28,9 @@ classes: - AgeAtMenarche - MenstrualCyclePhase - MenopauseStatus - - PrimaryDiagnosis - - AgeatDiagnosis - DiagnosisStatusType + - PreviousDiagnosis + - AgeAtDiagnosis - ClassBRCA1 - ClassBRCA2 - TobaccoUse diff --git a/modules/enums/Demographics.yaml b/modules/enums/Demographics.yaml index fc31f0a..9928d60 100644 --- a/modules/enums/Demographics.yaml +++ b/modules/enums/Demographics.yaml @@ -318,3 +318,10 @@ enums: Late Proliferative/Early Secretory: Unknown: + DiagnosisStatusTypeEnum: + permissible_values: + Never received diagnosis of cancer: + Previous diagnosis of cancer: + Current diagnosis of cancer: + Unknown: + diff --git a/modules/slots.yaml b/modules/slots.yaml index a3de455..4913e37 100644 --- a/modules/slots.yaml +++ b/modules/slots.yaml @@ -44,10 +44,10 @@ slots: description: The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified. annotations: range: AgeIsObfuscatedEnum - AgeatDiagnosis: + AgeAtDiagnosis: title: Age at Diagnosis required: false - description: Age at the time of diagnosis in years. + description: If applicable and known, age at the time of diagnosis in years. annotations: AlcoholDaysPerWeek: title: Alcohol Days Per Week @@ -141,7 +141,7 @@ slots: BMI: title: BMI required: false - description: TBD + description: Body mass index. Note that more direct height/weight information are preferred, if available. annotations: BiospecimenDimension1: title: Biospecimen Dimension 1 @@ -531,7 +531,8 @@ slots: DiagnosisStatusType: title: Diagnosis Status Type required: false - description: TBD + description: Diagnosis status to provide information on any history with cancer (if applicable). + range: DiagnosisStatusTypeEnum annotations: Dilution: title: Dilution @@ -1299,12 +1300,18 @@ slots: description: Text term that represents the method used to preserve the sample. annotations: range: PreservationMethodEnum + PreviousDiagnosis: + title: Previous Diagnosis + required: false + description: Name of cancer corresponding to a previous diagnosis. + annotations: + range: DiagnosisEnum PrimaryDiagnosis: title: Primary Diagnosis required: false - description: Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O). + description: If applicable, patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O). annotations: - range: PrimaryDiagnosisEnum + range: DiagnosisEnum PriorInvasiveBreastDisease: title: Prior Invasive Breast Disease required: false From 211af0ec56558c96fcf8a4f310a5aeec5c7f2aa8 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Thu, 8 Feb 2024 12:33:01 -0700 Subject: [PATCH 11/14] Reorganize and add descriptions --- modules/classes/patient_and_specimen.yaml | 4 ++-- modules/slots.yaml | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/modules/classes/patient_and_specimen.yaml b/modules/classes/patient_and_specimen.yaml index 61f1154..82b3600 100644 --- a/modules/classes/patient_and_specimen.yaml +++ b/modules/classes/patient_and_specimen.yaml @@ -38,12 +38,12 @@ classes: - AlcoholUse - NumberofDrinksPerWeek - AntibioticUse - - SampleCollectionCenter - - SampleCollectionYear - ERStatus - PRStatus - HER2Status - SurgeryReason + - SampleCollectionCenter + - SampleCollectionYear PatientExtended: diff --git a/modules/slots.yaml b/modules/slots.yaml index 4913e37..9d07f00 100644 --- a/modules/slots.yaml +++ b/modules/slots.yaml @@ -417,12 +417,12 @@ slots: ClassBRCA1: title: Class BRCA1 required: false - description: TBD + description: BRCA1 grouping. annotations: ClassBRCA2: title: Class BRCA2 required: false - description: TBD + description: BRCA2 grouping. annotations: ClinicalBiospecimenType: title: Clinical Biospecimen Type @@ -1459,12 +1459,12 @@ slots: SampleCollectionCenter: title: Sample Collection Center required: false - description: TBD + description: Name of center/institution/site where the individual contributed samples. annotations: SampleCollectionYear: title: Sample Collection Year required: false - description: TBD + description: Year the sample was collected from the individual. annotations: SampleID: title: Sample ID From a036f0fc87bf22d608a0039dc7d69aea7d04bc1d Mon Sep 17 00:00:00 2001 From: gf-dcc-service Date: Thu, 8 Feb 2024 19:33:42 +0000 Subject: [PATCH 12/14] Build jsonld --- GF.jsonld | 1370 +++++++++++++++++++++++++++++++++++++++++++++++------ 1 file changed, 1229 insertions(+), 141 deletions(-) diff --git a/GF.jsonld b/GF.jsonld index a519bf2..16033be 100644 --- a/GF.jsonld +++ b/GF.jsonld @@ -2079,6 +2079,17 @@ }, "sms:displayName" : "CellBarcodeTag", "sms:required" : "sms:false" + }, { + "@id" : "bts:AgeAtDiagnosis", + "@type" : "rdfs:Class", + "rdfs:comment" : "If applicable and known, age at the time of diagnosis in years.", + "rdfs:label" : "AgeAtDiagnosis", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "AgeAtDiagnosis", + "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:ReadContent", @@ -2206,7 +2217,7 @@ }, { "@id" : "bts:ClassBRCA1", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", + "rdfs:comment" : "BRCA1 grouping.", "rdfs:label" : "ClassBRCA1", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { @@ -2228,7 +2239,7 @@ }, { "@id" : "bts:SampleCollectionCenter", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", + "rdfs:comment" : "Name of center/institution/site where the individual contributed samples.", "rdfs:label" : "SampleCollectionCenter", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { @@ -3701,7 +3712,7 @@ }, { "@id" : "bts:BMI", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", + "rdfs:comment" : "Body mass index. Note that more direct height/weight information are preferred, if available.", "rdfs:label" : "BMI", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { @@ -5200,25 +5211,1128 @@ }, { "@id" : "bts:MultipleendocrineneoplasiatypeI" }, { - "@id" : "bts:Birt-Hogg-Dubesyndrome" + "@id" : "bts:Birt-Hogg-Dubesyndrome" + }, { + "@id" : "bts:Familialpancreaticcancer" + }, { + "@id" : "bts:Hereditarybreast–ovariancancersyndrome" + }, { + "@id" : "bts:Familialprostatecancer" + }, { + "@id" : "bts:Melanoma–astrocytomasyndrome" + }, { + "@id" : "bts:Alpha-1antitrypsin" + } ], + "rdfs:label" : "HereditaryCancerPredispositionSyndrome", + "rdfs:comment" : "History of presence of inherited genetic predisposition syndrome that confers heightened susceptibility to cancer in the patient.", + "@type" : "rdfs:Class", + "sms:displayName" : "HereditaryCancerPredispositionSyndrome" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:PrimaryDiagnosis", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Pagetdiseaseandintraductalcarcinomaofbreast" + }, { + "@id" : "bts:Papillarymicrocarcinoma" + }, { + "@id" : "bts:Kaposisarcoma" + }, { + "@id" : "bts:CarcinomaNOS" + }, { + "@id" : "bts:AcutemyeloidleukemiaNOS" + }, { + "@id" : "bts:TumorNOS" + }, { + "@id" : "bts:Renalcelladenocarcinoma" + }, { + "@id" : "bts:MalignantlymphomalymphoblasticNOS" + }, { + "@id" : "bts:Mammarycarcinomainsitu" + }, { + "@id" : "bts:Adenocarcinomainsituintubularadenoma" + }, { + "@id" : "bts:MalignantlymphomasmallBlymphocyticNOS" + }, { + "@id" : "bts:Eosinophilicleukemia" + }, { + "@id" : "bts:AcutelymphoblasticleukemiaNOS" + }, { + "@id" : "bts:MalignantlymphomalymphocyticnodularNOS" + }, { + "@id" : "bts:Basalcellepithelioma" + }, { + "@id" : "bts:Intracysticpapilloma" + }, { + "@id" : "bts:Lobularandductalcarcinoma" + }, { + "@id" : "bts:Cancer" + }, { + "@id" : "bts:Tlymphoblasticleukemia/lymphoma" + }, { + "@id" : "bts:ClassicalHodgkinlymphomalymphocyte-rich" + }, { + "@id" : "bts:Esophagealintraepithelialneoplasiahighgrade" + }, { + "@id" : "bts:Burkittcellleukemia" + }, { + "@id" : "bts:MonocyticleukemiaNOS" + }, { + "@id" : "bts:AcuteleukemiaNOS" + }, { + "@id" : "bts:Renalmedullarycarcinoma" + }, { + "@id" : "bts:Diffusemelanocytosis" + }, { + "@id" : "bts:Intraductalandlobularcarcinoma" + }, { + "@id" : "bts:MelanoticpsammomatousMPNST" + }, { + "@id" : "bts:MalignantmelanomainHutchinsonmelanoticfreckle" + }, { + "@id" : "bts:Pigmentedadenoma" + }, { + "@id" : "bts:ChronicgranulocyticleukemiaBCR/ABL" + }, { + "@id" : "bts:CervicalintraepithelialneoplasiagradeIII" + }, { + "@id" : "bts:High-gradeserouscarcinoma" + }, { + "@id" : "bts:ClassicalHodgkinlymphomanodularsclerosisgrade1" + }, { + "@id" : "bts:Meningiomamalignant" + }, { + "@id" : "bts:InterstitialcelltumorNOS" + }, { + "@id" : "bts:BronchialadenomaNOS" + }, { + "@id" : "bts:PrecursorT-celllymphoblasticlymphoma" + }, { + "@id" : "bts:Tubularandroblastomawithlipidstorage" + }, { + "@id" : "bts:Combinedlargecellneuroendocrinecarcinoma" + }, { + "@id" : "bts:NephroblastomaNOS" + }, { + "@id" : "bts:Tumorcellsbenign" + }, { + "@id" : "bts:Tumorletbenign" + }, { + "@id" : "bts:Pleomorphiclipoma" + }, { + "@id" : "bts:Adenocarcinomaofanalducts" + }, { + "@id" : "bts:Gastrointestinalstromaltumormalignant" + }, { + "@id" : "bts:Malignantmelanomainjunctionalnevus" + }, { + "@id" : "bts:Rhabdosarcoma" + }, { + "@id" : "bts:EndometrioidadenomaNOS" + }, { + "@id" : "bts:Hodgkinsarcoma" + }, { + "@id" : "bts:MalignantlymphomaimmunoblasticNOS" + }, { + "@id" : "bts:Smallcongenitalnevus" + }, { + "@id" : "bts:TumormalignantNOS" + }, { + "@id" : "bts:Undifferentiatedepithelioidsarcoma" + }, { + "@id" : "bts:NeuroendocrinecarcinomaNOS" + }, { + "@id" : "bts:Acutelymphoblasticleukemiaprecursorcelltype" + }, { + "@id" : "bts:Inflammatoryadenocarcinoma" + }, { + "@id" : "bts:Tubularadenocarcinoma" + }, { + "@id" : "bts:Combinedsmallcell-adenocarcinoma" + }, { + "@id" : "bts:ClassicalHodgkinlymphomanodularsclerosiscellularphase" + }, { + "@id" : "bts:Mixedadenocarcinomaandepidermoidcarcinoma" + }, { + "@id" : "bts:EpidermoidcarcinomainsituNOS" + }, { + "@id" : "bts:Undifferentiatedhigh-gradepleomorphicsarcoma" + }, { + "@id" : "bts:Sclerosinghepaticcarcinoma" + }, { + "@id" : "bts:Pagetoidreticulosis" + }, { + "@id" : "bts:Centralneurocytoma" + }, { + "@id" : "bts:Bronchiolo-alveolarcarcinomaNOS" + }, { + "@id" : "bts:Chroniclymphoidleukemia" + }, { + "@id" : "bts:Paragangliomamalignant" + }, { + "@id" : "bts:ClassicalHodgkinlymphomanodularsclerosisgrade2" + }, { + "@id" : "bts:B-ALL" + }, { + "@id" : "bts:Skinappendagecarcinoma" + }, { + "@id" : "bts:Epithelialtumorbenign" + }, { + "@id" : "bts:Blymphoblasticleukemia/lymphomaNOS" + }, { + "@id" : "bts:HodgkinlymphomanodularsclerosisNOS" + }, { + "@id" : "bts:MalignantlymphomalymphocyticdiffuseNOS" + }, { + "@id" : "bts:Pro-BALL" + }, { + "@id" : "bts:GastrinomaNOS" + }, { + "@id" : "bts:Intraductalcarcinomaclinging" + }, { + "@id" : "bts:Non-invasivelowgradeserouscarcinoma" + }, { + "@id" : "bts:AcutepromyelocyticleukemiaNOS" + }, { + "@id" : "bts:Malignantlymphomanon-HodgkinNOS" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:Melanoticschwannoma" + }, { + "@id" : "bts:SplenicmarginalzonelymphomaNOS" + }, { + "@id" : "bts:Transitionalcellcarcinomainsitu" + }, { + "@id" : "bts:Chronicmonocyticleukemia" + }, { + "@id" : "bts:Gastrincelltumor" + }, { + "@id" : "bts:Papillaryserouscystadenocarcinoma" + }, { + "@id" : "bts:TeratomamalignantNOS" + }, { + "@id" : "bts:ClassicalHodgkinlymphomalymphocytedepletionreticular" + }, { + "@id" : "bts:Tumorcellsuncertainwhetherbenignormalignant" + }, { + "@id" : "bts:Epithelialtumormalignant" + }, { + "@id" : "bts:TubularandroblastomaNOS" + }, { + "@id" : "bts:Papillarycarcinomainsitu" + }, { + "@id" : "bts:PituitarycarcinomaNOS" + }, { + "@id" : "bts:Typicalcarcinoid" + }, { + "@id" : "bts:Non-smallcellcarcinoma" + }, { + "@id" : "bts:MeningiomaNOS" + }, { + "@id" : "bts:EndometrialsarcomaNOS" + }, { + "@id" : "bts:NeuroblastomaNOS" + }, { + "@id" : "bts:BcelllymphomaNOS" + }, { + "@id" : "bts:PeripheralT-celllymphomalargecell" + }, { + "@id" : "bts:RenalcellcarcinomaNOS" + }, { + "@id" : "bts:Renalcellcarcinomaspindlecell" + }, { + "@id" : "bts:Hepatocholangiocarcinoma" + }, { + "@id" : "bts:MalignantlymphomanodularNOS" + }, { + "@id" : "bts:Bronchiolo-alveolarcarcinomanon-mucinous" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Bronchiolo-alveolarcarcinomaindeterminatetype" + }, { + "@id" : "bts:Pleomorphiccarcinoma" + }, { + "@id" : "bts:PapillarycystadenomaNOS" + }, { + "@id" : "bts:Burkitttumor" + }, { + "@id" : "bts:BasalcellcarcinomaNOS" + }, { + "@id" : "bts:HepatocellularcarcinomaNOS" + }, { + "@id" : "bts:Undifferentiatedleukaemia" + }, { + "@id" : "bts:Gastrincelltumormalignant" + }, { + "@id" : "bts:Melanoameloblastoma" + }, { + "@id" : "bts:ProstaticintraepithelialneoplasiagradeIII" + }, { + "@id" : "bts:Mixedpinealtumor" + }, { + "@id" : "bts:Smallcellsarcoma" + }, { + "@id" : "bts:Carcinomainadenomatouspolyp" + }, { + "@id" : "bts:Pagetdiseaseextramammary" + }, { + "@id" : "bts:Intraductalcarcinomasolidtype" + }, { + "@id" : "bts:Livercellcarcinoma" + }, { + "@id" : "bts:Undifferentiatedsarcoma" + }, { + "@id" : "bts:Squamouscellcarcinomaclearcelltype" + }, { + "@id" : "bts:PituitaryadenomaNOS" + }, { + "@id" : "bts:EndometrioidcarcinomaNOS" + }, { + "@id" : "bts:PapillaryadenocarcinomaNOS" + }, { + "@id" : "bts:Ductcarcinomadesmoplastictype" + }, { + "@id" : "bts:Chroniclymphaticleukemia" + }, { + "@id" : "bts:SquamouscellcarcinomainsituNOS" + }, { + "@id" : "bts:Intraductalpapillaryadenocarcinomawithinvasion" + }, { + "@id" : "bts:Adenocarcinomacombinedwithothertypesofcarcinoma" + }, { + "@id" : "bts:Combinedhepatocellularcarcinomaandcholangiocarcinoma" + }, { + "@id" : "bts:Primaryamyloidosis" + }, { + "@id" : "bts:Preleukemia" + }, { + "@id" : "bts:Adenocarcinomaofanalglands" + }, { + "@id" : "bts:Secondarycarcinoma" + }, { + "@id" : "bts:Dermalnevus" + }, { + "@id" : "bts:Infiltratingductandcribriformcarcinoma" + }, { + "@id" : "bts:Eosinophiladenocarcinoma" + }, { + "@id" : "bts:Chronicmyeloproliferativedisorder" + }, { + "@id" : "bts:Malignantmelanomaregressing" + }, { + "@id" : "bts:Osteoblastomamalignant" + }, { + "@id" : "bts:Papillotubularadenocarcinoma" + }, { + "@id" : "bts:CarcinomametastaticNOS" + }, { + "@id" : "bts:Sclerosinghemangioma" + }, { + "@id" : "bts:LymphocyticleukemiaNOS" + }, { + "@id" : "bts:PrecursorcelllymphoblasticleukemiaNOS" + }, { + "@id" : "bts:PapillarycarcinomaNOS" + }, { + "@id" : "bts:Bronchio-alveolarcarcinomamucinous" + }, { + "@id" : "bts:CarcinomainapolypNOS" + }, { + "@id" : "bts:AcutemyeloidleukemiaMLL" + }, { + "@id" : "bts:Tubulocysticrenalcellcarcinoma" + }, { + "@id" : "bts:MelanocytomaNOS" + }, { + "@id" : "bts:ChronicmyelogenousleukemiaPhiladelphiachromosome(Ph1)positive" + }, { + "@id" : "bts:Ewingsarcoma" + }, { + "@id" : "bts:GliomaNOS" + }, { + "@id" : "bts:Bronchial-associatedlymphoidtissuelymphoma" + }, { + "@id" : "bts:Papillotubularadenoma" + }, { + "@id" : "bts:Papillomaofbladder" + }, { + "@id" : "bts:Bronchio-alveolarcarcinomamixedmucinousandnon-mucinous" + }, { + "@id" : "bts:Carcinomainpleomorphicadenoma" + }, { + "@id" : "bts:Chondrosarcomagrade2/3" + }, { + "@id" : "bts:Neoplasmsecondary" + }, { + "@id" : "bts:Rhabdomyosarcomawithganglionicdifferentiation" + }, { + "@id" : "bts:Chroniclymphocyticleukemia" + }, { + "@id" : "bts:Liposarcomawelldifferentiated" + }, { + "@id" : "bts:Undifferentiatedpleomorphicsarcoma" + }, { + "@id" : "bts:Secretorycarcinomaofbreast" + }, { + "@id" : "bts:Lobularcarcinomanoninfiltrating" + }, { + "@id" : "bts:Mixedadenocarcinomaandsquamouscellcarcinoma" + }, { + "@id" : "bts:Melanoticneurofibroma" + }, { + "@id" : "bts:ChronicgranulocyticleukemiaPhiladelphiachromosome(Ph1)positive" + }, { + "@id" : "bts:Hepatocellularadenoma" + }, { + "@id" : "bts:BurkittlymphomaNOS(Includesallvariants)" + }, { + "@id" : "bts:ParagangliomaNOS" + }, { + "@id" : "bts:DiffuselargeB-celllymphomaNOS" + }, { + "@id" : "bts:NevusNOS" + }, { + "@id" : "bts:Hepatoidcarcinoma" + }, { + "@id" : "bts:MixedtumormalignantNOS" + }, { + "@id" : "bts:Rhabdoidsarcoma" + }, { + "@id" : "bts:Tubulolobularcarcinoma" + }, { + "@id" : "bts:Papillomatosisglandular" + }, { + "@id" : "bts:Bronchialadenomacarcinoid" + }, { + "@id" : "bts:Tumorembolus" + }, { + "@id" : "bts:DuctcarcinomaNOS" + }, { + "@id" : "bts:RhabdomyosarcomaNOS" + }, { + "@id" : "bts:LobularcarcinomaNOS" + }, { + "@id" : "bts:Bronchialadenomacylindroid" + }, { + "@id" : "bts:EpidermoidcarcinomaNOS" + }, { + "@id" : "bts:Papillaryglioneuronaltumor" + }, { + "@id" : "bts:DuctalcarcinomainsituNOS" + }, { + "@id" : 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Diseases for Oncology (ICD-O).", + "@type" : "rdfs:Class", + "sms:displayName" : "PrimaryDiagnosis" + }, { + "@id" : "bts:Gravidity", + "@type" : "rdfs:Class", + "rdfs:comment" : "Total number of pregnancies regardless of outcome", + "rdfs:label" : "Gravidity", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Gravidity", + "sms:required" : "sms:false" + }, { + "@id" : "bts:TotalNumberofPassingNuclei", + "@type" : "rdfs:Class", + "rdfs:comment" : "Number of nuclei sequenced", + "rdfs:label" : "TotalNumberofPassingNuclei", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "TotalNumberofPassingNuclei", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Objective", + "@type" : "rdfs:Class", + "rdfs:comment" : "Objective", + "rdfs:label" : "Objective", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Objective", + "sms:required" : "sms:false" + }, { + "@id" : "bts:BatchID", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "BatchID", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BatchID", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:VascularInvasionType", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" + }, { + "@id" : "bts:NotReported" }, { - "@id" : "bts:Familialpancreaticcancer" + "@id" : "bts:Extramural" }, { - "@id" : "bts:Hereditarybreast–ovariancancersyndrome" + "@id" : "bts:Intramural" }, { - "@id" : "bts:Familialprostatecancer" + "@id" : "bts:Macro" }, { - "@id" : "bts:Melanoma–astrocytomasyndrome" + "@id" : "bts:Micro" }, { - "@id" : "bts:Alpha-1antitrypsin" + "@id" : "bts:NoVascularInvasion" } ], - "rdfs:label" : "HereditaryCancerPredispositionSyndrome", - "rdfs:comment" : "History of presence of inherited genetic predisposition syndrome that confers heightened susceptibility to cancer in the patient.", + "rdfs:label" : "VascularInvasionType", + "rdfs:comment" : "Text term that represents the type of vascular tumor invasion.", "@type" : "rdfs:Class", - "sms:displayName" : "HereditaryCancerPredispositionSyndrome" + "sms:displayName" : "VascularInvasionType" + }, { + "@id" : "bts:AntibodyName", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "AntibodyName", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "AntibodyName", + "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:PrimaryDiagnosis", + "@id" : "bts:PreviousDiagnosis", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, @@ -6234,91 +7348,10 @@ }, { "@id" : "bts:Tumormetastatic" } ], - "rdfs:label" : "PrimaryDiagnosis", - "rdfs:comment" : "Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", - "@type" : "rdfs:Class", - "sms:displayName" : "PrimaryDiagnosis" - }, { - "@id" : "bts:Gravidity", - "@type" : "rdfs:Class", - "rdfs:comment" : "Total number of pregnancies regardless of outcome", - "rdfs:label" : "Gravidity", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "Gravidity", - "sms:required" : "sms:false" - }, { - "@id" : "bts:TotalNumberofPassingNuclei", - "@type" : "rdfs:Class", - "rdfs:comment" : "Number of nuclei sequenced", - "rdfs:label" : "TotalNumberofPassingNuclei", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "TotalNumberofPassingNuclei", - "sms:required" : "sms:false" - }, { - "@id" : "bts:Objective", - "@type" : "rdfs:Class", - "rdfs:comment" : "Objective", - "rdfs:label" : "Objective", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "Objective", - "sms:required" : "sms:false" - }, { - "@id" : "bts:BatchID", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BatchID", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "BatchID", - "sms:required" : "sms:false" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:VascularInvasionType", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:unknown" - }, { - "@id" : "bts:NotReported" - }, { - "@id" : "bts:Extramural" - }, { - "@id" : "bts:Intramural" - }, { - "@id" : "bts:Macro" - }, { - "@id" : "bts:Micro" - }, { - "@id" : "bts:NoVascularInvasion" - } ], - "rdfs:label" : "VascularInvasionType", - "rdfs:comment" : "Text term that represents the type of vascular tumor invasion.", - "@type" : "rdfs:Class", - "sms:displayName" : "VascularInvasionType" - }, { - "@id" : "bts:AntibodyName", + "rdfs:label" : "PreviousDiagnosis", + "rdfs:comment" : "Name of cancer corresponding to a previous diagnosis.", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "AntibodyName", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "AntibodyName", - "sms:required" : "sms:false" + "sms:displayName" : "PreviousDiagnosis" }, { "@id" : "bts:TestValue", "@type" : "rdfs:Class", @@ -6894,16 +7927,29 @@ "sms:displayName" : "SmokeExposureDuration", "sms:required" : "sms:false" }, { - "@id" : "bts:MenstrualCyclePhase", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "MenstrualCyclePhase", "rdfs:subClassOf" : [ ], + "@id" : "bts:MenstrualCyclePhase", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "MenstrualCyclePhase", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Inactive" + }, { + "@id" : "bts:Secretory" + }, { + "@id" : "bts:Proliferative" + }, { + "@id" : "bts:WeaklyProliferative" + }, { + "@id" : "bts:LateProliferative/EarlySecretory" + }, { + "@id" : "bts:Unknown" + } ], + "rdfs:label" : "MenstrualCyclePhase", + "rdfs:comment" : "Phase of the menstrual cycle at patient sample collection.", + "@type" : "rdfs:Class", + "sms:displayName" : "MenstrualCyclePhase" }, { "@id" : "bts:ThresholdforMinimumPassingReads", "@type" : "rdfs:Class", @@ -7061,7 +8107,7 @@ }, { "@id" : "bts:SampleCollectionYear", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", + "rdfs:comment" : "Year the sample was collected from the individual.", "rdfs:label" : "SampleCollectionYear", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { @@ -7435,17 +8481,6 @@ "rdfs:comment" : "Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", "@type" : "rdfs:Class", "sms:displayName" : "FOVYUnit" - }, { - "@id" : "bts:AgeatDiagnosis", - "@type" : "rdfs:Class", - "rdfs:comment" : "Age at the time of diagnosis in years.", - "rdfs:label" : "AgeatDiagnosis", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "AgeatDiagnosis", - "sms:required" : "sms:false" }, { "@id" : "bts:Cytoband", "@type" : "rdfs:Class", @@ -8253,7 +9288,7 @@ }, { "@id" : "bts:ClassBRCA2", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", + "rdfs:comment" : "BRCA2 grouping.", "rdfs:label" : "ClassBRCA2", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { @@ -8596,16 +9631,25 @@ "sms:displayName" : "Clone", "sms:required" : "sms:false" }, { - "@id" : "bts:DiagnosisStatusType", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "DiagnosisStatusType", "rdfs:subClassOf" : [ ], + "@id" : "bts:DiagnosisStatusType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "DiagnosisStatusType", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Neverreceiveddiagnosisofcancer" + }, { + "@id" : "bts:Previousdiagnosisofcancer" + }, { + "@id" : "bts:Currentdiagnosisofcancer" + }, { + "@id" : "bts:Unknown" + } ], + "rdfs:label" : "DiagnosisStatusType", + "rdfs:comment" : "Diagnosis status to provide information on any history with cancer (if applicable).", + "@type" : "rdfs:Class", + "sms:displayName" : "DiagnosisStatusType" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:Age", @@ -8615,7 +9659,7 @@ "sms:required" : "sms:true", "sms:validationRules" : [ "regex match ^\\d*\\.?\\d*$|^Unknown$" ], "rdfs:label" : "Age", - "rdfs:comment" : "Age (in years) of individual when samples are contributed/biobanked, as a positive number such as 40 or 56.5. If not available, cannot leave blank and must use \"unknown\".", + "rdfs:comment" : "Age (in years) of individual when samples are contributed/biobanked, as a positive number such as 40 or 56.5. If not available/missing, fill in with value \"Unknown\".", "@type" : "rdfs:Class", "sms:displayName" : "Age" }, { @@ -9252,6 +10296,17 @@ }, "sms:displayName" : "ModeofCancerDetectionEnum", "sms:required" : "sms:false" + }, { + "@id" : "bts:DiagnosisEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "DiagnosisEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "DiagnosisEnum", + "sms:required" : "sms:false" }, { "@id" : "bts:BreastBiopsyProcedureFindingTypeEnum", "@type" : "rdfs:Class", @@ -9307,17 +10362,6 @@ }, "sms:displayName" : "DimensionsUnitEnum", "sms:required" : "sms:false" - }, { - "@id" : "bts:PrimaryDiagnosisEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "PrimaryDiagnosisEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "PrimaryDiagnosisEnum", - "sms:required" : "sms:false" }, { "@id" : "bts:TestAnalyteTypeEnum", "@type" : "rdfs:Class", @@ -9461,6 +10505,17 @@ }, "sms:displayName" : "BreastCarcinomaHER2StatusEnum", "sms:required" : "sms:false" + }, { + "@id" : "bts:DiagnosisStatusTypeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "DiagnosisStatusTypeEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "DiagnosisStatusTypeEnum", + "sms:required" : "sms:false" }, { "@id" : "bts:ClinicalBiospecimenTypeEnum", "@type" : "rdfs:Class", @@ -11666,11 +12721,11 @@ }, { "@id" : "bts:MenopauseStatus" }, { - "@id" : "bts:PrimaryDiagnosis" + "@id" : "bts:DiagnosisStatusType" }, { - "@id" : "bts:AgeatDiagnosis" + "@id" : "bts:PreviousDiagnosis" }, { - "@id" : "bts:DiagnosisStatusType" + "@id" : "bts:AgeAtDiagnosis" }, { "@id" : "bts:ClassBRCA1" }, { @@ -11685,10 +12740,6 @@ "@id" : "bts:NumberofDrinksPerWeek" }, { "@id" : "bts:AntibioticUse" - }, { - "@id" : "bts:SampleCollectionCenter" - }, { - "@id" : "bts:SampleCollectionYear" }, { "@id" : "bts:ERStatus" }, { @@ -11697,6 +12748,10 @@ "@id" : "bts:HER2Status" }, { "@id" : "bts:SurgeryReason" + }, { + "@id" : "bts:SampleCollectionCenter" + }, { + "@id" : "bts:SampleCollectionYear" } ], "sms:displayName" : "CohortCoreTemplate" }, { @@ -17403,6 +18458,17 @@ }, "sms:displayName" : "Constitutional mismatch repair deficiency", "sms:required" : "sms:false" + }, { + "@id" : "bts:Neverreceiveddiagnosisofcancer", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Neverreceiveddiagnosisofcancer", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Never received diagnosis of cancer", + "sms:required" : "sms:false" }, { "@id" : "bts:chr18", "@type" : "rdfs:Class", @@ -18877,6 +19943,17 @@ }, "sms:displayName" : "Intraductal carcinoma clinging", "sms:required" : "sms:false" + }, { + "@id" : "bts:Previousdiagnosisofcancer", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Previousdiagnosisofcancer", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Previous diagnosis of cancer", + "sms:required" : "sms:false" }, { "@id" : "bts:Lowerlobelung", "@type" : "rdfs:Class", @@ -30757,6 +31834,17 @@ }, "sms:displayName" : "Choroid", "sms:required" : "sms:false" + }, { + "@id" : "bts:Currentdiagnosisofcancer", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Currentdiagnosisofcancer", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Current diagnosis of cancer", + "sms:required" : "sms:false" }, { "@id" : "bts:MEN1mutation", "@type" : "rdfs:Class", From d05cf5c6deaabfbd73143bc17f2b9bdaad298c88 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu Date: Thu, 8 Feb 2024 12:50:26 -0700 Subject: [PATCH 13/14] Update exposure enums --- modules/enums/Biospecimen.yaml | 7 +++ modules/enums/Exposure.yaml | 102 +++++++++++++++++---------------- modules/slots.yaml | 6 +- 3 files changed, 65 insertions(+), 50 deletions(-) diff --git a/modules/enums/Biospecimen.yaml b/modules/enums/Biospecimen.yaml index 4b1dcc8..d393b4d 100644 --- a/modules/enums/Biospecimen.yaml +++ b/modules/enums/Biospecimen.yaml @@ -109,3 +109,10 @@ enums: Specimen at Room Temperature: Other Shipping Environment: Not Shipped: + MarkerStatus: + permissible_values: + Strongly Positive: + Positive: + Weakly Positive: + Negative: + Equivocal: diff --git a/modules/enums/Exposure.yaml b/modules/enums/Exposure.yaml index 38b9aa1..7773e97 100644 --- a/modules/enums/Exposure.yaml +++ b/modules/enums/Exposure.yaml @@ -1,57 +1,63 @@ enums: - AlcoholTypeEnum: - permissible_values: - Other: - unknown: - Not Reported: - Beer: - Liquor: - Wine: - TobaccoSmokingStatusEnum: - permissible_values: - Not Reported: - unknown: - Current Reformed Smoker: - Current Smoker: - Current Reformed Smoker for > 15 yrs: - Duration Not Specified: - Smoking history not documented: - Lifelong Non-Smoker: - Current Reformed Smoker for < or = 15 yrs: - SmokingFrequencyEnum: - permissible_values: - unknown: - Every day: - Some days: AlcoholExposureEnum: permissible_values: - Yes - Alcohol Exposure: - Not Reported: - No - Alcohol Exposure: - HistoryEnum: - permissible_values: - 'Yes': - 'No': - unknown: - Not Reported: + No - Alcohol Exposure: + Not Reported: + Yes - Alcohol Exposure: AlcoholIntensityEnum: permissible_values: - unknown: - Not Reported: - Drinker: - Heavy Drinker: - Lifelong Non-Drinker: - Non-Drinker: - Occasional Drinker: + Drinker: + Heavy Drinker: + Lifelong Non-Drinker: + Non-Drinker: + Not Reported: + Occasional Drinker: + unknown: + AlcoholTypeEnum: + permissible_values: + Beer: + Liquor: + Not Reported: + Other: + Wine: + unknown: + AlcoholUseEnum: + permissible_values: + Former Drinker: + Never Drinker: + Not Reported: + Unknown: AntibioticUseEnum: permissible_values: - 'No': - unknown: - Yes - within last monthh: - Yes - within last 1-6 months: - Yes - over 6 months ago: + 'No': + Yes - over 6 months ago: + Yes - within last 1-6 months: + Yes - within last monthh: + Unknown: + HistoryEnum: + permissible_values: + 'No': + Not Reported: + 'Yes': + unknown: SmokingExposureEnum: permissible_values: - Yes - Smoking Exposure: - Not Reported: - No - Smoking Exposure: + No - Smoking Exposure: + Not Reported: + Yes - Smoking Exposure: + SmokingFrequencyEnum: + permissible_values: + Every day: + Some days: + unknown: + TobaccoUseEnum: + permissible_values: + Current Smoker: + Current Reformed Smoker: + Current Reformed Smoker for < or = 15 yrs: + Current Reformed Smoker for > 15 yrs: + Duration Not Specified: + Never Smoker: + Not Reported: + Unknown: + diff --git a/modules/slots.yaml b/modules/slots.yaml index 9d07f00..59dff8f 100644 --- a/modules/slots.yaml +++ b/modules/slots.yaml @@ -86,8 +86,9 @@ slots: AlcoholUse: title: Alcohol Use required: false - description: TBD + description: Alcohol use characterization. More quantitative data may be available in NumberofDrinksPerWeek. annotations: + range: AlcoholUseEnum AnalyteType: title: Analyte Type required: false @@ -1749,7 +1750,8 @@ slots: TobaccoUse: title: Tobacco Use required: false - description: TBD + description: Tobacco use characterization. More quantitative data may be available in PackYearsSmoked. + range: TobaccoUseEnum annotations: TobaccoUseperDay: title: Tobacco Use per Day From 636669f07075585bbbfc8e6ec47b35adc425f293 Mon Sep 17 00:00:00 2001 From: gf-dcc-service Date: Thu, 8 Feb 2024 19:55:07 +0000 Subject: [PATCH 14/14] Build jsonld --- GF.jsonld | 235 ++++++++++++++++++++++++++++++++++-------------------- 1 file changed, 149 insertions(+), 86 deletions(-) diff --git a/GF.jsonld b/GF.jsonld index 16033be..0c65bf2 100644 --- a/GF.jsonld +++ b/GF.jsonld @@ -528,25 +528,7 @@ "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:NotReported" - }, { - "@id" : "bts:unknown" - }, { - "@id" : "bts:CurrentReformedSmoker" - }, { - "@id" : "bts:CurrentSmoker" - }, { - "@id" : "bts:CurrentReformedSmokerfor>15yrs" - }, { - "@id" : "bts:DurationNotSpecified" - }, { - "@id" : "bts:Smokinghistorynotdocumented" - }, { - "@id" : "bts:LifelongNon-Smoker" - }, { - "@id" : "bts:CurrentReformedSmokerfor15yrs" + }, { + "@id" : "bts:DurationNotSpecified" + }, { + "@id" : "bts:NeverSmoker" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:Unknown" + } ], + "rdfs:label" : "TobaccoUse", + "rdfs:comment" : "Tobacco use characterization. More quantitative data may be available in PackYearsSmoked.", + "@type" : "rdfs:Class", + "sms:displayName" : "TobaccoUse" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:Zstack", @@ -10044,26 +10052,26 @@ "sms:displayName" : "ReverseTranscriptionPrimerEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:CountryofResidenceEnum", + "@id" : "bts:TobaccoUseEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "CountryofResidenceEnum", + "rdfs:label" : "TobaccoUseEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "CountryofResidenceEnum", + "sms:displayName" : "TobaccoUseEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:TobaccoSmokingStatusEnum", + "@id" : "bts:CountryofResidenceEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "TobaccoSmokingStatusEnum", + "rdfs:label" : "CountryofResidenceEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TobaccoSmokingStatusEnum", + "sms:displayName" : "CountryofResidenceEnum", "sms:required" : "sms:false" }, { "@id" : "bts:OncotypeRiskGroupEnum", @@ -10219,6 +10227,17 @@ }, "sms:displayName" : "SiteofResectionorBiopsyEnum", "sms:required" : "sms:false" + }, { + "@id" : "bts:AlcoholUseEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "AlcoholUseEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "AlcoholUseEnum", + "sms:required" : "sms:false" }, { "@id" : "bts:VascularInvasionTypeEnum", "@type" : "rdfs:Class", @@ -10362,6 +10381,17 @@ }, "sms:displayName" : "DimensionsUnitEnum", "sms:required" : "sms:false" + }, { + "@id" : "bts:MarkerStatus", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "MarkerStatus", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "MarkerStatus", + "sms:required" : "sms:false" }, { "@id" : "bts:TestAnalyteTypeEnum", "@type" : "rdfs:Class", @@ -14256,17 +14286,6 @@ }, "sms:displayName" : "Not applicable", "sms:required" : "sms:false" - }, { - "@id" : "bts:Smokinghistorynotdocumented", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Smokinghistorynotdocumented", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "Smoking history not documented", - "sms:required" : "sms:false" }, { "@id" : "bts:Conjunctiva", "@type" : "rdfs:Class", @@ -14476,6 +14495,17 @@ }, "sms:displayName" : "Cambodia", "sms:required" : "sms:false" + }, { + "@id" : "bts:FormerDrinker", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "FormerDrinker", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Former Drinker", + "sms:required" : "sms:false" }, { "@id" : "bts:HodgkinlymphomaNOS", "@type" : "rdfs:Class", @@ -15818,6 +15848,17 @@ }, "sms:displayName" : "Malignant lymphoma Hodgkin", "sms:required" : "sms:false" + }, { + "@id" : "bts:NeverDrinker", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "NeverDrinker", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Never Drinker", + "sms:required" : "sms:false" }, { "@id" : "bts:NaturalSon", "@type" : "rdfs:Class", @@ -19261,17 +19302,6 @@ }, "sms:displayName" : "Malignant melanoma in giant pigmented nevus", "sms:required" : "sms:false" - }, { - "@id" : "bts:LifelongNon-Smoker", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "LifelongNon-Smoker", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "Lifelong Non-Smoker", - "sms:required" : "sms:false" }, { "@id" : "bts:MaternalGrandparent", "@type" : "rdfs:Class", @@ -24211,6 +24241,17 @@ }, "sms:displayName" : "Greece", "sms:required" : "sms:false" + }, { + "@id" : "bts:WeaklyPositive", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "WeaklyPositive", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Weakly Positive", + "sms:required" : "sms:false" }, { "@id" : "bts:AdrenalglandNOS", "@type" : "rdfs:Class", @@ -32659,6 +32700,17 @@ }, "sms:displayName" : "Signature 7", "sms:required" : "sms:false" + }, { + "@id" : "bts:NeverSmoker", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "NeverSmoker", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Never Smoker", + "sms:required" : "sms:false" }, { "@id" : "bts:Upperinnerquadrant", "@type" : "rdfs:Class", @@ -33979,6 +34031,17 @@ }, "sms:displayName" : "Peripheral nerves and autonomic nervous system of pelvis", "sms:required" : "sms:false" + }, { + "@id" : "bts:StronglyPositive", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "StronglyPositive", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Strongly Positive", + "sms:required" : "sms:false" }, { "@id" : "bts:Invasivemelanoma-lentigomaligna", "@type" : "rdfs:Class",