diff --git a/src/valuesets/enums/medical/oncology/__init__.py b/src/valuesets/enums/medical/oncology/__init__.py new file mode 100644 index 00000000..633c553c --- /dev/null +++ b/src/valuesets/enums/medical/oncology/__init__.py @@ -0,0 +1 @@ +"""Auto-generated package.""" diff --git a/src/valuesets/enums/medical/oncology/icdo.py b/src/valuesets/enums/medical/oncology/icdo.py new file mode 100644 index 00000000..44b0eae3 --- /dev/null +++ b/src/valuesets/enums/medical/oncology/icdo.py @@ -0,0 +1,196 @@ +""" +ICD-O Cancer Classification Value Sets + +Value sets based on the International Classification of Diseases for Oncology (ICD-O) bi-axial classification system. ICD-O uses two independent axes: topography (anatomic site) and morphology (histological type and behavior). + +Generated from: medical/oncology/icdo.yaml +""" + +from __future__ import annotations + +from valuesets.generators.rich_enum import RichEnum + +class TumorTopography(RichEnum): + """ + Major anatomic sites for tumor classification based on ICD-O topography codes (C00-C80). These represent primary sites where neoplasms occur. + """ + # Enum members + LIP_ORAL_CAVITY_PHARYNX = "LIP_ORAL_CAVITY_PHARYNX" + DIGESTIVE_ORGANS = "DIGESTIVE_ORGANS" + ESOPHAGUS = "ESOPHAGUS" + STOMACH = "STOMACH" + COLON = "COLON" + RECTUM = "RECTUM" + LIVER = "LIVER" + PANCREAS = "PANCREAS" + RESPIRATORY_INTRATHORACIC = "RESPIRATORY_INTRATHORACIC" + LUNG = "LUNG" + BONE_ARTICULAR_CARTILAGE = "BONE_ARTICULAR_CARTILAGE" + SKIN = "SKIN" + SOFT_TISSUE = "SOFT_TISSUE" + BREAST = "BREAST" + FEMALE_GENITAL = "FEMALE_GENITAL" + CERVIX_UTERI = "CERVIX_UTERI" + OVARY = "OVARY" + MALE_GENITAL = "MALE_GENITAL" + PROSTATE = "PROSTATE" + TESTIS = "TESTIS" + URINARY_TRACT = "URINARY_TRACT" + KIDNEY = "KIDNEY" + BLADDER = "BLADDER" + EYE_BRAIN_CNS = "EYE_BRAIN_CNS" + BRAIN = "BRAIN" + THYROID_ENDOCRINE = "THYROID_ENDOCRINE" + THYROID = "THYROID" + LYMPH_NODES = "LYMPH_NODES" + UNKNOWN_PRIMARY = "UNKNOWN_PRIMARY" + +# Set metadata after class creation +TumorTopography._metadata = { + "LIP_ORAL_CAVITY_PHARYNX": {'description': 'Malignant neoplasms of lip, oral cavity and pharynx (C00-C14)', 'annotations': {'icdo_range': 'C00-C14'}}, + "DIGESTIVE_ORGANS": {'description': 'Malignant neoplasms of digestive organs (C15-C26)', 'annotations': {'icdo_range': 'C15-C26'}}, + "ESOPHAGUS": {'description': 'Malignant neoplasm of esophagus (C15)', 'annotations': {'icdo_code': 'C15', 'uberon': 'UBERON:0001043'}}, + "STOMACH": {'description': 'Malignant neoplasm of stomach (C16)', 'annotations': {'icdo_code': 'C16', 'uberon': 'UBERON:0000945'}}, + "COLON": {'description': 'Malignant neoplasm of colon (C18)', 'annotations': {'icdo_code': 'C18', 'uberon': 'UBERON:0001155'}}, + "RECTUM": {'description': 'Malignant neoplasm of rectum (C20)', 'annotations': {'icdo_code': 'C20', 'uberon': 'UBERON:0001052'}}, + "LIVER": {'description': 'Malignant neoplasm of liver and intrahepatic bile ducts (C22)', 'annotations': {'icdo_code': 'C22', 'uberon': 'UBERON:0002107'}}, + "PANCREAS": {'description': 'Malignant neoplasm of pancreas (C25)', 'annotations': {'icdo_code': 'C25', 'uberon': 'UBERON:0001264'}}, + "RESPIRATORY_INTRATHORACIC": {'description': 'Malignant neoplasms of respiratory and intrathoracic organs (C30-C39)', 'annotations': {'icdo_range': 'C30-C39'}}, + "LUNG": {'description': 'Malignant neoplasm of bronchus and lung (C34)', 'annotations': {'icdo_code': 'C34', 'uberon': 'UBERON:0002048'}}, + "BONE_ARTICULAR_CARTILAGE": {'description': 'Malignant neoplasms of bone and articular cartilage (C40-C41)', 'annotations': {'icdo_range': 'C40-C41'}}, + "SKIN": {'description': 'Melanoma and other malignant neoplasms of skin (C43-C44)', 'annotations': {'icdo_range': 'C43-C44', 'uberon': 'UBERON:0002097'}}, + "SOFT_TISSUE": {'description': 'Malignant neoplasms of mesothelial and soft tissues (C45-C49)', 'annotations': {'icdo_range': 'C45-C49'}}, + "BREAST": {'description': 'Malignant neoplasm of breast (C50)', 'annotations': {'icdo_code': 'C50', 'uberon': 'UBERON:0000310'}}, + "FEMALE_GENITAL": {'description': 'Malignant neoplasms of female genital organs (C51-C58)', 'annotations': {'icdo_range': 'C51-C58'}}, + "CERVIX_UTERI": {'description': 'Malignant neoplasm of cervix uteri (C53)', 'annotations': {'icdo_code': 'C53'}}, + "OVARY": {'description': 'Malignant neoplasm of ovary (C56)', 'annotations': {'icdo_code': 'C56', 'uberon': 'UBERON:0000992'}}, + "MALE_GENITAL": {'description': 'Malignant neoplasms of male genital organs (C60-C63)', 'annotations': {'icdo_range': 'C60-C63'}}, + "PROSTATE": {'description': 'Malignant neoplasm of prostate (C61)', 'annotations': {'icdo_code': 'C61', 'uberon': 'UBERON:0002367'}}, + "TESTIS": {'description': 'Malignant neoplasm of testis (C62)', 'annotations': {'icdo_code': 'C62', 'uberon': 'UBERON:0000473'}}, + "URINARY_TRACT": {'description': 'Malignant neoplasms of urinary tract (C64-C68)', 'annotations': {'icdo_range': 'C64-C68'}}, + "KIDNEY": {'description': 'Malignant neoplasm of kidney (C64)', 'annotations': {'icdo_code': 'C64', 'uberon': 'UBERON:0002113'}}, + "BLADDER": {'description': 'Malignant neoplasm of bladder (C67)', 'annotations': {'icdo_code': 'C67', 'uberon': 'UBERON:0001255'}}, + "EYE_BRAIN_CNS": {'description': 'Malignant neoplasms of eye, brain and other parts of CNS (C69-C72)', 'annotations': {'icdo_range': 'C69-C72'}}, + "BRAIN": {'description': 'Malignant neoplasm of brain (C71)', 'annotations': {'icdo_code': 'C71', 'uberon': 'UBERON:0000955'}}, + "THYROID_ENDOCRINE": {'description': 'Malignant neoplasms of thyroid and other endocrine glands (C73-C75)', 'annotations': {'icdo_range': 'C73-C75'}}, + "THYROID": {'description': 'Malignant neoplasm of thyroid gland (C73)', 'annotations': {'icdo_code': 'C73', 'uberon': 'UBERON:0002046'}}, + "LYMPH_NODES": {'description': 'Malignant neoplasms of lymph nodes (C77)', 'annotations': {'icdo_code': 'C77'}}, + "UNKNOWN_PRIMARY": {'description': 'Malignant neoplasm of unknown primary site (C80)', 'annotations': {'icdo_code': 'C80'}}, +} + +class TumorMorphology(RichEnum): + """ + Major histological types for tumor classification based on ICD-O morphology codes. These represent the cell type and histological pattern of neoplasms. + """ + # Enum members + CARCINOMA_NOS = "CARCINOMA_NOS" + ADENOCARCINOMA_NOS = "ADENOCARCINOMA_NOS" + SQUAMOUS_CELL_CARCINOMA = "SQUAMOUS_CELL_CARCINOMA" + TRANSITIONAL_CELL_CARCINOMA = "TRANSITIONAL_CELL_CARCINOMA" + SMALL_CELL_CARCINOMA = "SMALL_CELL_CARCINOMA" + LARGE_CELL_CARCINOMA = "LARGE_CELL_CARCINOMA" + SARCOMA_NOS = "SARCOMA_NOS" + OSTEOSARCOMA = "OSTEOSARCOMA" + CHONDROSARCOMA = "CHONDROSARCOMA" + LIPOSARCOMA = "LIPOSARCOMA" + LEIOMYOSARCOMA = "LEIOMYOSARCOMA" + RHABDOMYOSARCOMA = "RHABDOMYOSARCOMA" + LYMPHOMA_NOS = "LYMPHOMA_NOS" + HODGKIN_LYMPHOMA = "HODGKIN_LYMPHOMA" + NON_HODGKIN_LYMPHOMA = "NON_HODGKIN_LYMPHOMA" + DIFFUSE_LARGE_B_CELL_LYMPHOMA = "DIFFUSE_LARGE_B_CELL_LYMPHOMA" + LEUKEMIA_NOS = "LEUKEMIA_NOS" + ACUTE_LYMPHOBLASTIC_LEUKEMIA = "ACUTE_LYMPHOBLASTIC_LEUKEMIA" + ACUTE_MYELOID_LEUKEMIA = "ACUTE_MYELOID_LEUKEMIA" + CHRONIC_LYMPHOCYTIC_LEUKEMIA = "CHRONIC_LYMPHOCYTIC_LEUKEMIA" + CHRONIC_MYELOID_LEUKEMIA = "CHRONIC_MYELOID_LEUKEMIA" + MELANOMA = "MELANOMA" + MESOTHELIOMA = "MESOTHELIOMA" + GERM_CELL_TUMOR = "GERM_CELL_TUMOR" + NEUROENDOCRINE_TUMOR = "NEUROENDOCRINE_TUMOR" + +# Set metadata after class creation +TumorMorphology._metadata = { + "CARCINOMA_NOS": {'description': 'Malignant epithelial neoplasm, not otherwise specified. General term for cancers arising from epithelial cells.', 'meaning': 'NCIT:C2916', 'annotations': {'icdo_code': 8010}}, + "ADENOCARCINOMA_NOS": {'description': 'Malignant glandular epithelial neoplasm. Cancer arising from glandular epithelium.', 'meaning': 'NCIT:C2852', 'annotations': {'icdo_code': 8140}}, + "SQUAMOUS_CELL_CARCINOMA": {'description': 'Malignant neoplasm arising from squamous epithelium. Common in skin, lung, esophagus, and cervix.', 'meaning': 'NCIT:C2929', 'annotations': {'icdo_code': 8070}}, + "TRANSITIONAL_CELL_CARCINOMA": {'description': 'Malignant neoplasm arising from transitional epithelium (urothelium). Most common in bladder and urinary tract.', 'meaning': 'NCIT:C2930', 'annotations': {'icdo_code': 8120}}, + "SMALL_CELL_CARCINOMA": {'description': 'Highly malignant neuroendocrine carcinoma with small cells. Most common in lung.', 'meaning': 'NCIT:C3915', 'annotations': {'icdo_code': 8041}}, + "LARGE_CELL_CARCINOMA": {'description': 'Undifferentiated carcinoma with large cells.', 'annotations': {'icdo_code': 8012}}, + "SARCOMA_NOS": {'description': 'Malignant mesenchymal neoplasm, not otherwise specified. Cancers arising from connective tissue, bone, cartilage, fat, muscle, or blood vessels.', 'meaning': 'NCIT:C9118', 'annotations': {'icdo_code': 8800}}, + "OSTEOSARCOMA": {'description': 'Malignant bone-forming tumor. Most common primary malignant bone tumor.', 'meaning': 'NCIT:C9145', 'annotations': {'icdo_code': 9180}}, + "CHONDROSARCOMA": {'description': 'Malignant cartilage-forming tumor.', 'meaning': 'NCIT:C2946', 'annotations': {'icdo_code': 9220}}, + "LIPOSARCOMA": {'description': 'Malignant tumor arising from adipose tissue.', 'meaning': 'NCIT:C3194', 'annotations': {'icdo_code': 8850}}, + "LEIOMYOSARCOMA": {'description': 'Malignant tumor arising from smooth muscle.', 'meaning': 'NCIT:C3158', 'annotations': {'icdo_code': 8890}}, + "RHABDOMYOSARCOMA": {'description': 'Malignant tumor arising from skeletal muscle.', 'meaning': 'NCIT:C3359', 'annotations': {'icdo_code': 8900}}, + "LYMPHOMA_NOS": {'description': 'Malignant neoplasm of lymphoid tissue, not otherwise specified. Includes Hodgkin and non-Hodgkin lymphomas.', 'meaning': 'NCIT:C3208', 'annotations': {'icdo_code': 9590}}, + "HODGKIN_LYMPHOMA": {'description': 'Lymphoma characterized by presence of Reed-Sternberg cells and specific histological patterns.', 'meaning': 'NCIT:C9357', 'annotations': {'icdo_code': 9650}}, + "NON_HODGKIN_LYMPHOMA": {'description': 'All lymphomas other than Hodgkin lymphoma. Includes B-cell and T-cell lymphomas.', 'meaning': 'NCIT:C3211', 'annotations': {'icdo_codes': '9591, 9670-9729'}}, + "DIFFUSE_LARGE_B_CELL_LYMPHOMA": {'description': 'Most common type of non-Hodgkin lymphoma.', 'meaning': 'NCIT:C8851', 'annotations': {'icdo_code': 9680}}, + "LEUKEMIA_NOS": {'description': 'Malignant neoplasm of blood-forming tissues, not otherwise specified.', 'meaning': 'NCIT:C3161', 'annotations': {'icdo_code': 9800}}, + "ACUTE_LYMPHOBLASTIC_LEUKEMIA": {'description': 'Acute leukemia of lymphoid precursor cells.', 'meaning': 'NCIT:C3167', 'annotations': {'icdo_code': 9811}}, + "ACUTE_MYELOID_LEUKEMIA": {'description': 'Acute leukemia of myeloid precursor cells.', 'meaning': 'NCIT:C3171', 'annotations': {'icdo_code': 9861}}, + "CHRONIC_LYMPHOCYTIC_LEUKEMIA": {'description': 'Chronic leukemia of mature B lymphocytes.', 'meaning': 'NCIT:C3163', 'annotations': {'icdo_code': 9823}}, + "CHRONIC_MYELOID_LEUKEMIA": {'description': 'Chronic leukemia characterized by BCR-ABL1 fusion gene.', 'meaning': 'NCIT:C3174', 'annotations': {'icdo_code': 9875}}, + "MELANOMA": {'description': 'Malignant neoplasm arising from melanocytes.', 'meaning': 'NCIT:C3224', 'annotations': {'icdo_code': 8720}}, + "MESOTHELIOMA": {'description': 'Malignant tumor arising from mesothelial cells lining pleura, peritoneum, or pericardium. Strongly associated with asbestos exposure.', 'meaning': 'NCIT:C3234', 'annotations': {'icdo_code': 9050}}, + "GERM_CELL_TUMOR": {'description': 'Tumor arising from germ cells. Includes seminoma, teratoma, etc.', 'meaning': 'NCIT:C3708', 'annotations': {'icdo_codes': '9060-9110'}}, + "NEUROENDOCRINE_TUMOR": {'description': 'Tumor arising from neuroendocrine cells.', 'annotations': {'icdo_codes': '8240-8249'}}, +} + +class TumorBehavior(RichEnum): + """ + Biological behavior codes used in ICD-O morphology (5th digit). Indicates whether a neoplasm is benign, uncertain, in situ, or malignant. + """ + # Enum members + BENIGN = "BENIGN" + UNCERTAIN_BORDERLINE = "UNCERTAIN_BORDERLINE" + IN_SITU = "IN_SITU" + MALIGNANT_PRIMARY = "MALIGNANT_PRIMARY" + MALIGNANT_METASTATIC = "MALIGNANT_METASTATIC" + MALIGNANT_UNCERTAIN_PRIMARY_METASTATIC = "MALIGNANT_UNCERTAIN_PRIMARY_METASTATIC" + +# Set metadata after class creation +TumorBehavior._metadata = { + "BENIGN": {'description': 'Non-cancerous neoplasm that does not invade surrounding tissue or metastasize.', 'meaning': 'NCIT:C3677', 'annotations': {'icdo_behavior': '/0'}}, + "UNCERTAIN_BORDERLINE": {'description': 'Neoplasm with borderline malignancy or uncertain behavior. May recur but typically does not metastasize.', 'annotations': {'icdo_behavior': '/1'}}, + "IN_SITU": {'description': 'Malignant cells confined to epithelium without invasion through basement membrane. Pre-invasive cancer.', 'meaning': 'NCIT:C2917', 'annotations': {'icdo_behavior': '/2'}}, + "MALIGNANT_PRIMARY": {'description': 'Invasive malignant neoplasm at primary site. Cancer that has invaded through basement membrane.', 'annotations': {'icdo_behavior': '/3'}}, + "MALIGNANT_METASTATIC": {'description': 'Malignant neoplasm that has spread from primary site to secondary (metastatic) site.', 'annotations': {'icdo_behavior': '/6'}}, + "MALIGNANT_UNCERTAIN_PRIMARY_METASTATIC": {'description': 'Malignant neoplasm where it is uncertain if this is the primary site or a metastatic site.', 'annotations': {'icdo_behavior': '/9'}}, +} + +class TumorGrade(RichEnum): + """ + Histological grade/differentiation codes used in ICD-O (6th digit). Indicates how abnormal the tumor cells appear compared to normal cells. + """ + # Enum members + GRADE_1 = "GRADE_1" + GRADE_2 = "GRADE_2" + GRADE_3 = "GRADE_3" + GRADE_4 = "GRADE_4" + GRADE_NOT_DETERMINED = "GRADE_NOT_DETERMINED" + T_CELL = "T_CELL" + B_CELL = "B_CELL" + NULL_CELL = "NULL_CELL" + NK_CELL = "NK_CELL" + +# Set metadata after class creation +TumorGrade._metadata = { + "GRADE_1": {'description': 'Tumor cells closely resemble normal cells. Typically slow-growing with better prognosis.', 'annotations': {'icdo_grade': 1, 'differentiation': 'well differentiated'}}, + "GRADE_2": {'description': 'Tumor cells show moderate resemblance to normal cells. Intermediate behavior.', 'annotations': {'icdo_grade': 2, 'differentiation': 'moderately differentiated'}}, + "GRADE_3": {'description': 'Tumor cells show little resemblance to normal cells. More aggressive with poorer prognosis.', 'annotations': {'icdo_grade': 3, 'differentiation': 'poorly differentiated'}}, + "GRADE_4": {'description': 'Tumor cells bear no resemblance to normal cells. Most aggressive with poorest prognosis.', 'annotations': {'icdo_grade': 4, 'differentiation': 'undifferentiated, anaplastic'}}, + "GRADE_NOT_DETERMINED": {'description': 'Histological grade has not been assessed or is not applicable.', 'annotations': {'icdo_grade': 9}}, + "T_CELL": {'description': 'Lymphoma/leukemia of T-cell origin.', 'annotations': {'icdo_grade': 5, 'use': 'lymphomas/leukemias'}}, + "B_CELL": {'description': 'Lymphoma/leukemia of B-cell origin.', 'annotations': {'icdo_grade': 6, 'use': 'lymphomas/leukemias'}}, + "NULL_CELL": {'description': 'Lymphoma/leukemia of neither T-cell nor B-cell origin.', 'annotations': {'icdo_grade': 7, 'use': 'lymphomas/leukemias'}}, + "NK_CELL": {'description': 'Lymphoma/leukemia of natural killer cell origin.', 'annotations': {'icdo_grade': 8, 'use': 'lymphomas/leukemias'}}, +} + +__all__ = [ + "TumorTopography", + "TumorMorphology", + "TumorBehavior", + "TumorGrade", +] \ No newline at end of file diff --git a/src/valuesets/enums/medical/pediatric_oncology/__init__.py b/src/valuesets/enums/medical/pediatric_oncology/__init__.py new file mode 100644 index 00000000..633c553c --- /dev/null +++ b/src/valuesets/enums/medical/pediatric_oncology/__init__.py @@ -0,0 +1 @@ +"""Auto-generated package.""" diff --git a/src/valuesets/enums/medical/pediatric_oncology/diagnosis_categories.py b/src/valuesets/enums/medical/pediatric_oncology/diagnosis_categories.py new file mode 100644 index 00000000..c9cbf342 --- /dev/null +++ b/src/valuesets/enums/medical/pediatric_oncology/diagnosis_categories.py @@ -0,0 +1,85 @@ +""" +Pediatric Oncology Diagnosis Categories + +High-level pediatric cancer diagnosis groupings based on CCDI CDE 16607972 (Diagnosis Pediatric Oncology Grouping Category). These categories were developed through consensus by St. Jude, CBTN, Treehouse, and NCI to enable cohort aggregation across federated pediatric cancer data resources. Categories are aligned with WHO CNS5, WHO-HAEM5, and WHO Pediatric Blue Book. + +Generated from: medical/pediatric_oncology/diagnosis_categories.yaml +""" + +from __future__ import annotations + +from valuesets.generators.rich_enum import RichEnum + +class PediatricOncologyDiagnosisCategory(RichEnum): + """ + High-level groupings for pediatric cancer diagnoses per CCDI CDE 16607972. Designed for cohort aggregation across federated data resources. Each diagnosis maps to a single dominant category. + """ + # Enum members + ATYPICAL_TERATOID_RHABDOID_TUMOR = "ATYPICAL_TERATOID_RHABDOID_TUMOR" + CHOROID_PLEXUS_TUMOR = "CHOROID_PLEXUS_TUMOR" + CNS_GERM_CELL_TUMOR = "CNS_GERM_CELL_TUMOR" + CNS_SARCOMA = "CNS_SARCOMA" + CRANIOPHARYNGIOMA = "CRANIOPHARYNGIOMA" + EPENDYMOMA = "EPENDYMOMA" + GLIONEURONAL_AND_NEURONAL_TUMOR = "GLIONEURONAL_AND_NEURONAL_TUMOR" + HIGH_GRADE_GLIOMA = "HIGH_GRADE_GLIOMA" + LOW_GRADE_GLIOMA = "LOW_GRADE_GLIOMA" + MEDULLOBLASTOMA = "MEDULLOBLASTOMA" + OTHER_CNS_EMBRYONAL_TUMOR = "OTHER_CNS_EMBRYONAL_TUMOR" + OTHER_GLIOMA = "OTHER_GLIOMA" + OTHER_BRAIN_TUMOR = "OTHER_BRAIN_TUMOR" + LYMPHOBLASTIC_LEUKEMIA = "LYMPHOBLASTIC_LEUKEMIA" + MYELOID_LEUKEMIA = "MYELOID_LEUKEMIA" + HODGKIN_LYMPHOMA = "HODGKIN_LYMPHOMA" + NON_HODGKIN_LYMPHOMA = "NON_HODGKIN_LYMPHOMA" + LYMPHOPROLIFERATIVE_DISEASE = "LYMPHOPROLIFERATIVE_DISEASE" + OTHER_HEME_TUMOR = "OTHER_HEME_TUMOR" + NEUROBLASTOMA = "NEUROBLASTOMA" + OSTEOSARCOMA = "OSTEOSARCOMA" + EWING_SARCOMA = "EWING_SARCOMA" + RHABDOMYOSARCOMA = "RHABDOMYOSARCOMA" + SOFT_TISSUE_TUMOR = "SOFT_TISSUE_TUMOR" + RHABDOID_TUMOR = "RHABDOID_TUMOR" + RENAL_TUMOR = "RENAL_TUMOR" + RETINOBLASTOMA = "RETINOBLASTOMA" + GERM_CELL_TUMOR = "GERM_CELL_TUMOR" + ENDOCRINE_AND_NEUROENDOCRINE_TUMOR = "ENDOCRINE_AND_NEUROENDOCRINE_TUMOR" + OTHER_SOLID_TUMOR = "OTHER_SOLID_TUMOR" + +# Set metadata after class creation +PediatricOncologyDiagnosisCategory._metadata = { + "ATYPICAL_TERATOID_RHABDOID_TUMOR": {'description': 'Highly malignant embryonal CNS tumor characterized by loss of SMARCB1 (INI1) or SMARCA4 expression. Predominantly occurs in young children.', 'meaning': 'NCIT:C6807', 'annotations': {'category': 'brain_tumor', 'who_classification': 'WHO CNS5'}}, + "CHOROID_PLEXUS_TUMOR": {'description': 'Neoplasms arising from the choroid plexus epithelium, including papilloma, atypical papilloma, and carcinoma.', 'meaning': 'NCIT:C3698', 'annotations': {'category': 'brain_tumor', 'who_classification': 'WHO CNS5'}}, + "CNS_GERM_CELL_TUMOR": {'description': 'Germ cell tumors arising within the central nervous system, including germinoma and non-germinomatous germ cell tumors.', 'meaning': 'NCIT:C6286', 'annotations': {'category': 'brain_tumor', 'who_classification': 'WHO CNS5'}}, + "CNS_SARCOMA": {'description': 'Sarcomas arising primarily in the central nervous system, including Ewing sarcoma and rhabdomyosarcoma of CNS.', 'meaning': 'NCIT:C121624', 'annotations': {'category': 'brain_tumor'}}, + "CRANIOPHARYNGIOMA": {'description': 'Benign epithelial tumors arising from remnants of Rathke pouch, including adamantinomatous and papillary subtypes.', 'meaning': 'NCIT:C2998', 'annotations': {'category': 'brain_tumor', 'who_classification': 'WHO CNS5'}}, + "EPENDYMOMA": {'description': 'Glial tumors arising from ependymal cells lining the ventricular system and central canal. Includes molecular subtypes defined by WHO CNS5.', 'meaning': 'NCIT:C3017', 'annotations': {'category': 'brain_tumor', 'who_classification': 'WHO CNS5'}}, + "GLIONEURONAL_AND_NEURONAL_TUMOR": {'description': 'Tumors with neuronal differentiation including ganglioglioma, dysembryoplastic neuroepithelial tumor (DNET), and central neurocytoma.', 'meaning': 'NCIT:C6927', 'annotations': {'category': 'brain_tumor', 'who_classification': 'WHO CNS5'}}, + "HIGH_GRADE_GLIOMA": {'description': 'Aggressive glial tumors including pediatric-type diffuse high-grade gliomas (H3 K27-altered, H3 G34-mutant, and H3/IDH-wildtype), as well as glioblastoma.', 'meaning': 'NCIT:C129355', 'annotations': {'category': 'brain_tumor', 'who_classification': 'WHO CNS5', 'grade': 'high'}}, + "LOW_GRADE_GLIOMA": {'description': 'Indolent glial tumors including pilocytic astrocytoma and pediatric-type diffuse low-grade gliomas (MYB/MYBL1-altered, MAPK pathway-altered).', 'meaning': 'NCIT:C129354', 'annotations': {'category': 'brain_tumor', 'who_classification': 'WHO CNS5', 'grade': 'low'}}, + "MEDULLOBLASTOMA": {'description': 'Embryonal tumor of the cerebellum, classified by molecular subgroups (WNT-activated, SHH-activated, Group 3, Group 4) per WHO CNS5.', 'meaning': 'NCIT:C3222', 'annotations': {'category': 'brain_tumor', 'who_classification': 'WHO CNS5'}}, + "OTHER_CNS_EMBRYONAL_TUMOR": {'description': 'Embryonal tumors of the CNS other than medulloblastoma and ATRT, including embryonal tumor with multilayered rosettes (ETMR), CNS neuroblastoma, and pineoblastoma.', 'meaning': 'NCIT:C6774', 'annotations': {'category': 'brain_tumor', 'who_classification': 'WHO CNS5'}, 'aliases': ['CNS Embryonal Tumor, NOS']}, + "OTHER_GLIOMA": {'description': 'Glial tumors not classified as high-grade or low-grade glioma, including angiocentric glioma and astroblastoma.', 'meaning': 'NCIT:C3059', 'annotations': {'category': 'brain_tumor'}}, + "OTHER_BRAIN_TUMOR": {'description': 'CNS tumors not fitting other brain tumor categories, including meningioma, schwannoma, and hemangioblastoma.', 'meaning': 'NCIT:C2907', 'annotations': {'category': 'brain_tumor'}}, + "LYMPHOBLASTIC_LEUKEMIA": {'description': 'Acute lymphoblastic leukemia (ALL) including B-ALL and T-ALL with all molecular subtypes (BCR::ABL1, ETV6::RUNX1, KMT2A-r, DUX4, MEF2D, etc.).', 'meaning': 'NCIT:C3167', 'annotations': {'category': 'hematologic', 'who_classification': 'WHO-HAEM5'}, 'aliases': ['ALL', 'Acute Lymphoblastic Leukemia']}, + "MYELOID_LEUKEMIA": {'description': 'Acute myeloid leukemia (AML) and related myeloid neoplasms including AML with defining genetic abnormalities, therapy-related AML, and juvenile myelomonocytic leukemia (JMML).', 'meaning': 'NCIT:C3171', 'annotations': {'category': 'hematologic', 'who_classification': 'WHO-HAEM5'}, 'aliases': ['AML', 'Acute Myeloid Leukemia']}, + "HODGKIN_LYMPHOMA": {'description': 'Lymphoid neoplasm characterized by Reed-Sternberg cells, including classical Hodgkin lymphoma and nodular lymphocyte predominant Hodgkin lymphoma.', 'meaning': 'NCIT:C9357', 'annotations': {'category': 'hematologic', 'who_classification': 'WHO-HAEM5'}}, + "NON_HODGKIN_LYMPHOMA": {'description': 'Lymphoid neoplasms other than Hodgkin lymphoma, including Burkitt lymphoma, diffuse large B-cell lymphoma, anaplastic large cell lymphoma, and lymphoblastic lymphoma.', 'meaning': 'NCIT:C3211', 'annotations': {'category': 'hematologic', 'who_classification': 'WHO-HAEM5'}, 'aliases': ['NHL']}, + "LYMPHOPROLIFERATIVE_DISEASE": {'description': 'Disorders characterized by abnormal lymphocyte proliferation, including post-transplant lymphoproliferative disorder (PTLD) and hemophagocytic lymphohistiocytosis (HLH).', 'meaning': 'NCIT:C3138', 'annotations': {'category': 'hematologic'}}, + "OTHER_HEME_TUMOR": {'description': 'Hematologic malignancies not classified elsewhere, including histiocytic disorders, myelodysplastic syndromes, and myeloproliferative neoplasms.', 'meaning': 'NCIT:C27134', 'annotations': {'category': 'hematologic'}}, + "NEUROBLASTOMA": {'description': 'Embryonal tumor of the peripheral sympathetic nervous system, arising from neural crest cells. Includes ganglioneuroblastoma and ganglioneuroma.', 'meaning': 'NCIT:C3270', 'annotations': {'category': 'solid_tumor', 'who_classification': 'WHO Pediatric Blue Book'}}, + "OSTEOSARCOMA": {'description': 'Primary malignant bone tumor characterized by osteoid production, including conventional, telangiectatic, and small cell variants.', 'meaning': 'NCIT:C9145', 'annotations': {'category': 'solid_tumor', 'who_classification': 'WHO Bone/Soft Tissue'}}, + "EWING_SARCOMA": {'description': 'Small round cell sarcoma typically harboring EWSR1 rearrangements, arising in bone or soft tissue. Includes Ewing sarcoma family of tumors.', 'meaning': 'NCIT:C4817', 'annotations': {'category': 'solid_tumor', 'who_classification': 'WHO Bone/Soft Tissue'}}, + "RHABDOMYOSARCOMA": {'description': 'Malignant soft tissue tumor with skeletal muscle differentiation, including embryonal, alveolar, and spindle cell/sclerosing subtypes.', 'meaning': 'NCIT:C3359', 'annotations': {'category': 'solid_tumor', 'who_classification': 'WHO Bone/Soft Tissue'}}, + "SOFT_TISSUE_TUMOR": {'description': 'Soft tissue neoplasms other than rhabdomyosarcoma and Ewing sarcoma, including synovial sarcoma, fibrosarcoma, and other sarcomas. Also includes non-sarcomatous soft tissue tumors.', 'meaning': 'NCIT:C3399', 'annotations': {'category': 'solid_tumor'}, 'aliases': ['Soft Tissue Sarcoma']}, + "RHABDOID_TUMOR": {'description': 'Highly aggressive tumors characterized by SMARCB1 loss, occurring outside the CNS (extracranial rhabdoid tumor). Includes malignant rhabdoid tumor of kidney.', 'meaning': 'NCIT:C3769', 'annotations': {'category': 'solid_tumor'}}, + "RENAL_TUMOR": {'description': 'Kidney tumors including Wilms tumor (nephroblastoma), clear cell sarcoma of kidney, renal cell carcinoma, and congenital mesoblastic nephroma.', 'meaning': 'NCIT:C7548', 'annotations': {'category': 'solid_tumor', 'who_classification': 'WHO Pediatric Blue Book'}, 'aliases': ['Kidney Tumor', 'Wilms Tumor']}, + "RETINOBLASTOMA": {'description': 'Malignant neoplasm of the retina arising from developing retinal cells, associated with RB1 mutations.', 'meaning': 'NCIT:C7541', 'annotations': {'category': 'solid_tumor', 'who_classification': 'WHO Pediatric Blue Book'}}, + "GERM_CELL_TUMOR": {'description': 'Tumors arising from primordial germ cells, occurring in gonadal or extragonadal sites. Includes teratoma, yolk sac tumor, germinoma, choriocarcinoma, and mixed germ cell tumors. Excludes CNS germ cell tumors.', 'meaning': 'NCIT:C3708', 'annotations': {'category': 'solid_tumor'}}, + "ENDOCRINE_AND_NEUROENDOCRINE_TUMOR": {'description': 'Tumors of endocrine glands and neuroendocrine cells, including thyroid carcinoma, adrenocortical carcinoma, pheochromocytoma, and paraganglioma.', 'meaning': 'NCIT:C3010', 'annotations': {'category': 'solid_tumor'}}, + "OTHER_SOLID_TUMOR": {'description': 'Solid tumors not classified elsewhere, including hepatoblastoma, pleuropulmonary blastoma, nasopharyngeal carcinoma, melanoma, and carcinomas.', 'meaning': 'NCIT:C9107', 'annotations': {'category': 'solid_tumor'}}, +} + +__all__ = [ + "PediatricOncologyDiagnosisCategory", +] \ No newline at end of file diff --git a/src/valuesets/enums/medical/pediatric_oncology/iccc3.py b/src/valuesets/enums/medical/pediatric_oncology/iccc3.py new file mode 100644 index 00000000..00e50f41 --- /dev/null +++ b/src/valuesets/enums/medical/pediatric_oncology/iccc3.py @@ -0,0 +1,154 @@ +""" +International Classification of Childhood Cancer, Third Edition (ICCC-3) + +Value sets based on the International Classification of Childhood Cancer, Third Edition (ICCC-3). The ICCC is the standard classification for childhood cancers, emphasizing tumor morphology rather than primary site (as used for adult cancers). ICCC-3 classifies tumors coded according to ICD-O-3 into 12 main groups and 47 subgroups. + +Generated from: medical/pediatric_oncology/iccc3.yaml +""" + +from __future__ import annotations + +from valuesets.generators.rich_enum import RichEnum + +class ICCC3MainGroup(RichEnum): + """ + The 12 main diagnostic groups of the International Classification of Childhood Cancer, Third Edition. Based on tumor morphology and primary site with emphasis on morphology. + """ + # Enum members + I_LEUKEMIAS_MYELOPROLIFERATIVE_MYELODYSPLASTIC = "I_LEUKEMIAS_MYELOPROLIFERATIVE_MYELODYSPLASTIC" + II_LYMPHOMAS_RETICULOENDOTHELIAL = "II_LYMPHOMAS_RETICULOENDOTHELIAL" + III_CNS_INTRACRANIAL_INTRASPINAL = "III_CNS_INTRACRANIAL_INTRASPINAL" + IV_NEUROBLASTOMA_PERIPHERAL_NERVOUS = "IV_NEUROBLASTOMA_PERIPHERAL_NERVOUS" + V_RETINOBLASTOMA = "V_RETINOBLASTOMA" + VI_RENAL_TUMORS = "VI_RENAL_TUMORS" + VII_HEPATIC_TUMORS = "VII_HEPATIC_TUMORS" + VIII_MALIGNANT_BONE_TUMORS = "VIII_MALIGNANT_BONE_TUMORS" + IX_SOFT_TISSUE_SARCOMAS = "IX_SOFT_TISSUE_SARCOMAS" + X_GERM_CELL_GONADAL = "X_GERM_CELL_GONADAL" + XI_EPITHELIAL_MELANOMA = "XI_EPITHELIAL_MELANOMA" + XII_OTHER_UNSPECIFIED = "XII_OTHER_UNSPECIFIED" + +# Set metadata after class creation +ICCC3MainGroup._metadata = { + "I_LEUKEMIAS_MYELOPROLIFERATIVE_MYELODYSPLASTIC": {'description': 'Includes lymphoid leukemias, acute myeloid leukemias, chronic myeloproliferative diseases, myelodysplastic syndrome and other myeloproliferative diseases, and unspecified and other specified leukemias.', 'meaning': 'NCIT:C3161', 'annotations': {'iccc_code': 'I', 'subgroup_count': 5}}, + "II_LYMPHOMAS_RETICULOENDOTHELIAL": {'description': 'Includes Hodgkin lymphomas, non-Hodgkin lymphomas (except Burkitt lymphoma), Burkitt lymphoma, and miscellaneous lymphoreticular neoplasms.', 'meaning': 'NCIT:C7058', 'annotations': {'iccc_code': 'II', 'subgroup_count': 4}}, + "III_CNS_INTRACRANIAL_INTRASPINAL": {'description': 'Includes ependymomas and choroid plexus tumor, astrocytomas, intracranial and intraspinal embryonal tumors, other gliomas, other specified intracranial and intraspinal neoplasms, and unspecified intracranial and intraspinal neoplasms. Also includes nonmalignant CNS tumors.', 'meaning': 'NCIT:C2907', 'annotations': {'iccc_code': 'III', 'subgroup_count': 6, 'includes_nonmalignant': True}}, + "IV_NEUROBLASTOMA_PERIPHERAL_NERVOUS": {'description': 'Includes neuroblastoma and ganglioneuroblastoma, and other peripheral nervous cell tumors.', 'meaning': 'NCIT:C3270', 'annotations': {'iccc_code': 'IV', 'subgroup_count': 2}}, + "V_RETINOBLASTOMA": {'description': 'Malignant neoplasm of the retina. Single group with no subgroups.', 'meaning': 'NCIT:C7541', 'annotations': {'iccc_code': 'V', 'subgroup_count': 1}}, + "VI_RENAL_TUMORS": {'description': 'Includes nephroblastoma and other nonepithelial renal tumors, renal carcinomas, and unspecified malignant renal tumors.', 'meaning': 'NCIT:C7548', 'annotations': {'iccc_code': 'VI', 'subgroup_count': 3}}, + "VII_HEPATIC_TUMORS": {'description': 'Includes hepatoblastoma, hepatic carcinomas, and unspecified malignant hepatic tumors.', 'meaning': 'NCIT:C7927', 'annotations': {'iccc_code': 'VII', 'subgroup_count': 3}}, + "VIII_MALIGNANT_BONE_TUMORS": {'description': 'Includes osteosarcomas, chondrosarcomas, Ewing tumor and related sarcomas of bone, other specified malignant bone tumors, and unspecified malignant bone tumors.', 'meaning': 'NCIT:C4882', 'annotations': {'iccc_code': 'VIII', 'subgroup_count': 5}}, + "IX_SOFT_TISSUE_SARCOMAS": {'description': 'Includes rhabdomyosarcomas, fibrosarcomas/peripheral nerve sheath tumors/other fibrous neoplasms, Kaposi sarcoma, other specified soft tissue sarcomas, and unspecified soft tissue sarcomas.', 'meaning': 'NCIT:C9306', 'annotations': {'iccc_code': 'IX', 'subgroup_count': 5}}, + "X_GERM_CELL_GONADAL": {'description': 'Includes intracranial and intraspinal germ cell tumors, malignant extracranial and extragonadal germ cell tumors, malignant gonadal germ cell tumors, gonadal carcinomas, and other and unspecified malignant gonadal tumors.', 'meaning': 'NCIT:C3708', 'annotations': {'iccc_code': 'X', 'subgroup_count': 5}}, + "XI_EPITHELIAL_MELANOMA": {'description': 'Includes adrenocortical carcinomas, thyroid carcinomas, nasopharyngeal carcinomas, malignant melanomas, skin carcinomas, and other and unspecified carcinomas.', 'meaning': 'NCIT:C3709', 'annotations': {'iccc_code': 'XI', 'subgroup_count': 6}}, + "XII_OTHER_UNSPECIFIED": {'description': 'Includes other specified malignant tumors and other unspecified malignant tumors not classifiable in groups I-XI.', 'meaning': 'NCIT:C3262', 'annotations': {'iccc_code': 'XII', 'subgroup_count': 2}}, +} + +class ICCC3Subgroup(RichEnum): + """ + The 47 diagnostic subgroups of the International Classification of Childhood Cancer, Third Edition. These provide more detailed classification within each of the 12 main groups. + """ + # Enum members + IA_LYMPHOID_LEUKEMIAS = "Ia_LYMPHOID_LEUKEMIAS" + IB_ACUTE_MYELOID_LEUKEMIAS = "Ib_ACUTE_MYELOID_LEUKEMIAS" + IC_CHRONIC_MYELOPROLIFERATIVE = "Ic_CHRONIC_MYELOPROLIFERATIVE" + ID_MYELODYSPLASTIC_OTHER_MYELOPROLIFERATIVE = "Id_MYELODYSPLASTIC_OTHER_MYELOPROLIFERATIVE" + IE_UNSPECIFIED_OTHER_LEUKEMIAS = "Ie_UNSPECIFIED_OTHER_LEUKEMIAS" + IIA_HODGKIN_LYMPHOMAS = "IIa_HODGKIN_LYMPHOMAS" + IIB_NON_HODGKIN_LYMPHOMAS = "IIb_NON_HODGKIN_LYMPHOMAS" + IIC_BURKITT_LYMPHOMA = "IIc_BURKITT_LYMPHOMA" + IID_MISC_LYMPHORETICULAR = "IId_MISC_LYMPHORETICULAR" + IIIA_EPENDYMOMAS = "IIIa_EPENDYMOMAS" + IIIB_ASTROCYTOMAS = "IIIb_ASTROCYTOMAS" + IIIC_INTRACRANIAL_EMBRYONAL = "IIIc_INTRACRANIAL_EMBRYONAL" + IIID_OTHER_GLIOMAS = "IIId_OTHER_GLIOMAS" + IIIE_OTHER_INTRACRANIAL_INTRASPINAL = "IIIe_OTHER_INTRACRANIAL_INTRASPINAL" + IIIF_UNSPECIFIED_INTRACRANIAL = "IIIf_UNSPECIFIED_INTRACRANIAL" + IVA_NEUROBLASTOMA_GANGLIONEUROBLASTOMA = "IVa_NEUROBLASTOMA_GANGLIONEUROBLASTOMA" + IVB_OTHER_PERIPHERAL_NERVOUS = "IVb_OTHER_PERIPHERAL_NERVOUS" + V_RETINOBLASTOMA = "V_RETINOBLASTOMA" + VIA_NEPHROBLASTOMA = "VIa_NEPHROBLASTOMA" + VIB_RENAL_CARCINOMAS = "VIb_RENAL_CARCINOMAS" + VIC_UNSPECIFIED_RENAL = "VIc_UNSPECIFIED_RENAL" + VIIA_HEPATOBLASTOMA = "VIIa_HEPATOBLASTOMA" + VIIB_HEPATIC_CARCINOMAS = "VIIb_HEPATIC_CARCINOMAS" + VIIC_UNSPECIFIED_HEPATIC = "VIIc_UNSPECIFIED_HEPATIC" + VIIIA_OSTEOSARCOMAS = "VIIIa_OSTEOSARCOMAS" + VIIIB_CHONDROSARCOMAS = "VIIIb_CHONDROSARCOMAS" + VIIIC_EWING_TUMOR_BONE = "VIIIc_EWING_TUMOR_BONE" + VIIID_OTHER_BONE = "VIIId_OTHER_BONE" + VIIIE_UNSPECIFIED_BONE = "VIIIe_UNSPECIFIED_BONE" + IXA_RHABDOMYOSARCOMAS = "IXa_RHABDOMYOSARCOMAS" + IXB_FIBROSARCOMAS = "IXb_FIBROSARCOMAS" + IXC_KAPOSI_SARCOMA = "IXc_KAPOSI_SARCOMA" + IXD_OTHER_SOFT_TISSUE = "IXd_OTHER_SOFT_TISSUE" + IXE_UNSPECIFIED_SOFT_TISSUE = "IXe_UNSPECIFIED_SOFT_TISSUE" + XA_INTRACRANIAL_GERM_CELL = "Xa_INTRACRANIAL_GERM_CELL" + XB_EXTRACRANIAL_EXTRAGONADAL_GERM_CELL = "Xb_EXTRACRANIAL_EXTRAGONADAL_GERM_CELL" + XC_GONADAL_GERM_CELL = "Xc_GONADAL_GERM_CELL" + XD_GONADAL_CARCINOMAS = "Xd_GONADAL_CARCINOMAS" + XE_OTHER_GONADAL = "Xe_OTHER_GONADAL" + XIA_ADRENOCORTICAL_CARCINOMAS = "XIa_ADRENOCORTICAL_CARCINOMAS" + XIB_THYROID_CARCINOMAS = "XIb_THYROID_CARCINOMAS" + XIC_NASOPHARYNGEAL_CARCINOMAS = "XIc_NASOPHARYNGEAL_CARCINOMAS" + XID_MALIGNANT_MELANOMAS = "XId_MALIGNANT_MELANOMAS" + XIE_SKIN_CARCINOMAS = "XIe_SKIN_CARCINOMAS" + XIF_OTHER_CARCINOMAS = "XIf_OTHER_CARCINOMAS" + XIIA_OTHER_SPECIFIED = "XIIa_OTHER_SPECIFIED" + XIIB_OTHER_UNSPECIFIED = "XIIb_OTHER_UNSPECIFIED" + +# Set metadata after class creation +ICCC3Subgroup._metadata = { + "IA_LYMPHOID_LEUKEMIAS": {'description': 'Precursor cell lymphoblastic leukemia, NOS; precursor cell lymphoblastic leukemia, B-cell; precursor cell lymphoblastic leukemia, T-cell; Burkitt cell leukemia; and other lymphoid leukemias.', 'meaning': 'NCIT:C3167', 'annotations': {'main_group': 'I', 'icdo3_codes': '9820-9827, 9835-9837'}}, + "IB_ACUTE_MYELOID_LEUKEMIAS": {'description': 'Acute myeloid leukemia and variants including AML with maturation, acute promyelocytic leukemia, acute myelomonocytic leukemia, acute monoblastic leukemia, acute megakaryoblastic leukemia, etc.', 'meaning': 'NCIT:C3171', 'annotations': {'main_group': 'I', 'icdo3_codes': '9840, 9861, 9866-9867, 9870-9874, 9891, 9895-9897, 9910, 9920, 9931'}}, + "IC_CHRONIC_MYELOPROLIFERATIVE": {'description': 'Chronic myeloid leukemia, NOS; juvenile myelomonocytic leukemia; and other chronic myeloproliferative diseases.', 'meaning': 'NCIT:C4345', 'annotations': {'main_group': 'I', 'icdo3_codes': '9863, 9875-9876, 9945-9946, 9950, 9960-9964'}}, + "ID_MYELODYSPLASTIC_OTHER_MYELOPROLIFERATIVE": {'description': 'Myelodysplastic syndrome, NOS; refractory anemia; refractory anemia with ringed sideroblasts; refractory anemia with excess blasts.', 'meaning': 'NCIT:C3247', 'annotations': {'main_group': 'I', 'icdo3_codes': '9945, 9980, 9982-9983, 9985-9989'}}, + "IE_UNSPECIFIED_OTHER_LEUKEMIAS": {'description': 'Leukemia, NOS and other specified leukemias not elsewhere classified.', 'meaning': 'NCIT:C3161', 'annotations': {'main_group': 'I', 'icdo3_codes': '9800-9801, 9805-9809, 9860, 9930'}}, + "IIA_HODGKIN_LYMPHOMAS": {'description': 'Classical Hodgkin lymphoma and nodular lymphocyte predominant Hodgkin lymphoma.', 'meaning': 'NCIT:C9357', 'annotations': {'main_group': 'II', 'icdo3_codes': '9650-9655, 9659, 9661-9665, 9667'}}, + "IIB_NON_HODGKIN_LYMPHOMAS": {'description': 'Diffuse large B-cell lymphoma, follicular lymphoma, peripheral T-cell lymphoma, anaplastic large cell lymphoma, and other non-Hodgkin lymphomas.', 'meaning': 'NCIT:C3211', 'annotations': {'main_group': 'II', 'icdo3_codes': '9591, 9670-9686, 9689-9691, 9695, 9698-9702, 9705, 9708-9709, 9714-9719, 9727-9729'}}, + "IIC_BURKITT_LYMPHOMA": {'description': 'Burkitt lymphoma and Burkitt-like lymphoma.', 'meaning': 'NCIT:C8150', 'annotations': {'main_group': 'II', 'icdo3_codes': '9687'}}, + "IID_MISC_LYMPHORETICULAR": {'description': 'Lymphoreticular neoplasms not elsewhere classified including lymphomatoid granulomatosis and post-transplant lymphoproliferative disorder.', 'meaning': 'NCIT:C27134', 'annotations': {'main_group': 'II', 'icdo3_codes': '9740-9742, 9750, 9754-9758, 9930, 9970'}}, + "IIIA_EPENDYMOMAS": {'description': 'Ependymoma, anaplastic ependymoma, myxopapillary ependymoma, and choroid plexus papilloma and carcinoma.', 'meaning': 'NCIT:C3017', 'annotations': {'main_group': 'III', 'icdo3_codes': '9383, 9390-9394'}}, + "IIIB_ASTROCYTOMAS": {'description': 'Pilocytic astrocytoma, diffuse astrocytoma, anaplastic astrocytoma, glioblastoma, and other astrocytic tumors.', 'meaning': 'NCIT:C60781', 'annotations': {'main_group': 'III', 'icdo3_codes': '9380, 9384, 9400-9411, 9420, 9424'}}, + "IIIC_INTRACRANIAL_EMBRYONAL": {'description': 'Medulloblastoma, primitive neuroectodermal tumor, medulloepithelioma, atypical teratoid/rhabdoid tumor, and other embryonal tumors.', 'meaning': 'NCIT:C6774', 'annotations': {'main_group': 'III', 'icdo3_codes': '9470-9474, 9480, 9490, 9500-9508'}}, + "IIID_OTHER_GLIOMAS": {'description': 'Oligodendroglioma, anaplastic oligodendroglioma, mixed glioma, and other gliomas not elsewhere classified.', 'meaning': 'NCIT:C3059', 'annotations': {'main_group': 'III', 'icdo3_codes': '9380-9382, 9430, 9440-9460'}}, + "IIIE_OTHER_INTRACRANIAL_INTRASPINAL": {'description': 'Pituitary adenoma, craniopharyngioma, pineal tumors, and other specified intracranial neoplasms.', 'meaning': 'NCIT:C2907', 'annotations': {'main_group': 'III'}}, + "IIIF_UNSPECIFIED_INTRACRANIAL": {'description': 'Intracranial and intraspinal neoplasms, NOS.', 'meaning': 'NCIT:C2907', 'annotations': {'main_group': 'III', 'icdo3_codes': '8000-8005'}}, + "IVA_NEUROBLASTOMA_GANGLIONEUROBLASTOMA": {'description': 'Neuroblastoma, NOS and ganglioneuroblastoma.', 'meaning': 'NCIT:C3270', 'annotations': {'main_group': 'IV', 'icdo3_codes': '9490, 9500'}}, + "IVB_OTHER_PERIPHERAL_NERVOUS": {'description': 'Other peripheral nerve tumors including ganglioneuroma and peripheral nerve sheath tumors.', 'meaning': 'NCIT:C4969', 'annotations': {'main_group': 'IV', 'icdo3_codes': '9501-9504, 9520-9523'}}, + "V_RETINOBLASTOMA": {'description': 'Retinoblastoma.', 'meaning': 'NCIT:C7541', 'annotations': {'main_group': 'V', 'icdo3_codes': '9510-9514'}}, + "VIA_NEPHROBLASTOMA": {'description': 'Wilms tumor (nephroblastoma), clear cell sarcoma of kidney, rhabdoid tumor of kidney, and other nonepithelial renal tumors.', 'meaning': 'NCIT:C3267', 'annotations': {'main_group': 'VI', 'icdo3_codes': '8960, 8963-8964'}}, + "VIB_RENAL_CARCINOMAS": {'description': 'Renal cell carcinoma and other renal carcinomas.', 'meaning': 'NCIT:C9385', 'annotations': {'main_group': 'VI'}}, + "VIC_UNSPECIFIED_RENAL": {'description': 'Malignant renal tumors, NOS.', 'meaning': 'NCIT:C7548', 'annotations': {'main_group': 'VI'}}, + "VIIA_HEPATOBLASTOMA": {'description': 'Hepatoblastoma.', 'meaning': 'NCIT:C3728', 'annotations': {'main_group': 'VII', 'icdo3_codes': '8970'}}, + "VIIB_HEPATIC_CARCINOMAS": {'description': 'Hepatocellular carcinoma, cholangiocarcinoma, and other hepatic carcinomas.', 'meaning': 'NCIT:C3099', 'annotations': {'main_group': 'VII'}}, + "VIIC_UNSPECIFIED_HEPATIC": {'description': 'Malignant hepatic tumors, NOS.', 'meaning': 'NCIT:C7927', 'annotations': {'main_group': 'VII'}}, + "VIIIA_OSTEOSARCOMAS": {'description': 'Osteosarcoma, NOS and variants including chondroblastic, fibroblastic, telangiectatic, and small cell osteosarcoma.', 'meaning': 'NCIT:C9145', 'annotations': {'main_group': 'VIII', 'icdo3_codes': '9180-9187, 9191-9195'}}, + "VIIIB_CHONDROSARCOMAS": {'description': 'Chondrosarcoma, NOS and variants.', 'meaning': 'NCIT:C2946', 'annotations': {'main_group': 'VIII', 'icdo3_codes': '9220-9231, 9240-9243'}}, + "VIIIC_EWING_TUMOR_BONE": {'description': 'Ewing sarcoma of bone and peripheral primitive neuroectodermal tumor of bone.', 'meaning': 'NCIT:C4817', 'annotations': {'main_group': 'VIII', 'icdo3_codes': '9260, 9364'}}, + "VIIID_OTHER_BONE": {'description': 'Other specified malignant bone tumors including giant cell tumor of bone, malignant and adamantinoma.', 'meaning': 'NCIT:C4882', 'annotations': {'main_group': 'VIII'}}, + "VIIIE_UNSPECIFIED_BONE": {'description': 'Malignant bone tumors, NOS.', 'meaning': 'NCIT:C4882', 'annotations': {'main_group': 'VIII'}}, + "IXA_RHABDOMYOSARCOMAS": {'description': 'Rhabdomyosarcoma, NOS; embryonal rhabdomyosarcoma; alveolar rhabdomyosarcoma; and other rhabdomyosarcomas.', 'meaning': 'NCIT:C3359', 'annotations': {'main_group': 'IX', 'icdo3_codes': '8900-8905, 8910, 8912, 8920'}}, + "IXB_FIBROSARCOMAS": {'description': 'Fibrosarcoma, NOS; infantile fibrosarcoma; dermatofibrosarcoma; and malignant peripheral nerve sheath tumor.', 'meaning': 'NCIT:C3043', 'annotations': {'main_group': 'IX', 'icdo3_codes': '8810-8815, 8820-8823, 8830, 8832-8833, 9540, 9560-9561'}}, + "IXC_KAPOSI_SARCOMA": {'description': 'Kaposi sarcoma.', 'meaning': 'NCIT:C9087', 'annotations': {'main_group': 'IX', 'icdo3_codes': '9140'}}, + "IXD_OTHER_SOFT_TISSUE": {'description': 'Includes liposarcoma, leiomyosarcoma, synovial sarcoma, hemangiosarcoma, and other specified soft tissue sarcomas.', 'meaning': 'NCIT:C9306', 'annotations': {'main_group': 'IX'}}, + "IXE_UNSPECIFIED_SOFT_TISSUE": {'description': 'Soft tissue sarcomas, NOS.', 'meaning': 'NCIT:C9306', 'annotations': {'main_group': 'IX'}}, + "XA_INTRACRANIAL_GERM_CELL": {'description': 'CNS germ cell tumors including germinoma, teratoma, and nongerminomatous germ cell tumors.', 'meaning': 'NCIT:C6286', 'annotations': {'main_group': 'X', 'icdo3_codes': '9060-9102'}}, + "XB_EXTRACRANIAL_EXTRAGONADAL_GERM_CELL": {'description': 'Extracranial germ cell tumors not involving the gonads including sacrococcygeal, retroperitoneal, and mediastinal germ cell tumors.', 'meaning': 'NCIT:C6545', 'annotations': {'main_group': 'X'}}, + "XC_GONADAL_GERM_CELL": {'description': 'Germ cell tumors of the ovary and testis including dysgerminoma, yolk sac tumor, embryonal carcinoma, and mixed germ cell tumors.', 'meaning': 'NCIT:C3708', 'annotations': {'main_group': 'X'}}, + "XD_GONADAL_CARCINOMAS": {'description': 'Carcinomas arising in the ovary and testis.', 'meaning': 'NCIT:C3709', 'annotations': {'main_group': 'X'}}, + "XE_OTHER_GONADAL": {'description': 'Other specified and unspecified gonadal tumors.', 'meaning': 'NCIT:C3708', 'annotations': {'main_group': 'X'}}, + "XIA_ADRENOCORTICAL_CARCINOMAS": {'description': 'Adrenocortical carcinoma.', 'meaning': 'NCIT:C9325', 'annotations': {'main_group': 'XI', 'icdo3_codes': '8370'}}, + "XIB_THYROID_CARCINOMAS": {'description': 'Papillary thyroid carcinoma, follicular thyroid carcinoma, and medullary thyroid carcinoma.', 'meaning': 'NCIT:C7510', 'annotations': {'main_group': 'XI'}}, + "XIC_NASOPHARYNGEAL_CARCINOMAS": {'description': 'Nasopharyngeal carcinoma and related carcinomas.', 'meaning': 'NCIT:C3871', 'annotations': {'main_group': 'XI'}}, + "XID_MALIGNANT_MELANOMAS": {'description': 'Cutaneous and non-cutaneous malignant melanomas.', 'meaning': 'NCIT:C3224', 'annotations': {'main_group': 'XI'}}, + "XIE_SKIN_CARCINOMAS": {'description': 'Basal cell carcinoma, squamous cell carcinoma of skin, and other skin carcinomas.', 'meaning': 'NCIT:C3372', 'annotations': {'main_group': 'XI'}}, + "XIF_OTHER_CARCINOMAS": {'description': 'Carcinomas at other sites and carcinomas, NOS.', 'meaning': 'NCIT:C3709', 'annotations': {'main_group': 'XI'}}, + "XIIA_OTHER_SPECIFIED": {'description': 'Malignant tumors not classifiable in groups I-XI but with specified histology.', 'meaning': 'NCIT:C3262', 'annotations': {'main_group': 'XII'}}, + "XIIB_OTHER_UNSPECIFIED": {'description': 'Malignant tumors, NOS not classifiable in groups I-XI.', 'meaning': 'NCIT:C3262', 'annotations': {'main_group': 'XII'}}, +} + +__all__ = [ + "ICCC3MainGroup", + "ICCC3Subgroup", +] \ No newline at end of file diff --git a/src/valuesets/enums/medical/pediatric_oncology/staging/__init__.py b/src/valuesets/enums/medical/pediatric_oncology/staging/__init__.py new file mode 100644 index 00000000..633c553c --- /dev/null +++ b/src/valuesets/enums/medical/pediatric_oncology/staging/__init__.py @@ -0,0 +1 @@ +"""Auto-generated package.""" diff --git a/src/valuesets/enums/medical/pediatric_oncology/staging/neuroblastoma.py b/src/valuesets/enums/medical/pediatric_oncology/staging/neuroblastoma.py new file mode 100644 index 00000000..f5e92b5d --- /dev/null +++ b/src/valuesets/enums/medical/pediatric_oncology/staging/neuroblastoma.py @@ -0,0 +1,124 @@ +""" +Neuroblastoma Staging Value Sets + +Staging systems for neuroblastoma including the International Neuroblastoma Risk Group Staging System (INRGSS) and International Neuroblastoma Staging System (INSS). INRGSS is the current standard (effective 2024+) based on imaging and image-defined risk factors. INSS is the legacy surgical staging system still used for historical data. + +Generated from: medical/pediatric_oncology/staging/neuroblastoma.yaml +""" + +from __future__ import annotations + +from valuesets.generators.rich_enum import RichEnum + +class INRGSSStage(RichEnum): + """ + International Neuroblastoma Risk Group Staging System (INRGSS) stages. A clinical staging system based on imaging and image-defined risk factors (IDRFs), effective for diagnosis years 2024+. Allows staging before any treatment, unlike the surgical INSS system. + """ + # Enum members + L1 = "L1" + L2 = "L2" + M = "M" + MS = "MS" + +# Set metadata after class creation +INRGSSStage._metadata = { + "L1": {'description': 'Localized tumor not involving vital structures as defined by the list of image-defined risk factors and confined to one body compartment (neck, chest, abdomen, or pelvis).', 'meaning': 'NCIT:C133427', 'annotations': {'localized': True, 'idrfs_present': False}}, + "L2": {'description': 'Locoregional tumor with presence of one or more image-defined risk factors. The tumor has not spread far from where it started but has at least one IDRF.', 'meaning': 'NCIT:C133428', 'annotations': {'localized': True, 'idrfs_present': True}}, + "M": {'description': 'Distant metastatic disease (except as defined for MS). The tumor has spread (metastasized) to distant parts of the body.', 'meaning': 'NCIT:C133429', 'annotations': {'metastatic': True}}, + "MS": {'description': 'Metastatic disease in children younger than 18 months with metastases confined to skin, liver, and/or bone marrow (bone marrow involvement limited to <10% tumor cells). This stage has a favorable prognosis despite metastatic disease.', 'meaning': 'NCIT:C133430', 'annotations': {'metastatic': True, 'special_category': True, 'age_restriction': '<18 months', 'favorable_prognosis': True}, 'aliases': ['Stage 4S equivalent']}, +} + +class INSSStage(RichEnum): + """ + International Neuroblastoma Staging System (INSS) stages. A post-surgical staging system based on extent of tumor resection, lymph node involvement, and metastatic spread. This is the legacy system; INRGSS is now preferred for diagnosis years 2024+. + """ + # Enum members + STAGE_1 = "STAGE_1" + STAGE_2A = "STAGE_2A" + STAGE_2B = "STAGE_2B" + STAGE_3 = "STAGE_3" + STAGE_4 = "STAGE_4" + STAGE_4S = "STAGE_4S" + +# Set metadata after class creation +INSSStage._metadata = { + "STAGE_1": {'description': 'Localized tumor with complete gross excision, with or without microscopic residual disease; representative ipsilateral lymph nodes negative for tumor microscopically.', 'meaning': 'NCIT:C6639', 'annotations': {'localized': True, 'resection': 'complete'}}, + "STAGE_2A": {'description': 'Localized tumor with incomplete gross excision; representative ipsilateral nonadherent lymph nodes negative for tumor microscopically.', 'meaning': 'NCIT:C6640', 'annotations': {'localized': True, 'resection': 'incomplete', 'lymph_nodes': 'negative'}}, + "STAGE_2B": {'description': 'Localized tumor with or without complete gross excision, with ipsilateral nonadherent lymph nodes positive for tumor. Enlarged contralateral lymph nodes must be negative microscopically.', 'meaning': 'NCIT:C6641', 'annotations': {'localized': True, 'lymph_nodes': 'ipsilateral_positive'}}, + "STAGE_3": {'description': 'Unresectable unilateral tumor infiltrating across the midline, with or without regional lymph node involvement; or localized unilateral tumor with contralateral regional lymph node involvement; or midline tumor with bilateral extension by infiltration (unresectable) or by lymph node involvement.', 'meaning': 'NCIT:C6642', 'annotations': {'localized': False, 'crosses_midline': True}}, + "STAGE_4": {'description': 'Any primary tumor with dissemination to distant lymph nodes, bone, bone marrow, liver, skin, and/or other organs (except as defined for stage 4S).', 'meaning': 'NCIT:C6643', 'annotations': {'metastatic': True}}, + "STAGE_4S": {'description': 'Localized primary tumor (as defined for stage 1, 2A, or 2B) with dissemination limited to skin, liver, and/or bone marrow (limited to infants <1 year of age). Marrow involvement should be minimal (<10% of total nucleated cells).', 'meaning': 'NCIT:C6644', 'annotations': {'metastatic': True, 'special_category': True, 'age_restriction': '<12 months', 'favorable_prognosis': True}, 'aliases': ['Special stage 4']}, +} + +class NeuroblastomaRiskGroup(RichEnum): + """ + International Neuroblastoma Risk Group (INRG) pretreatment risk classification groups. Combines INRGSS stage with tumor histology, MYCN status, ploidy, and other prognostic factors. + """ + # Enum members + VERY_LOW = "VERY_LOW" + LOW = "LOW" + INTERMEDIATE = "INTERMEDIATE" + HIGH = "HIGH" + +# Set metadata after class creation +NeuroblastomaRiskGroup._metadata = { + "VERY_LOW": {'description': 'Very low risk neuroblastoma with excellent prognosis. Typically includes L1 tumors and MS without MYCN amplification.', 'meaning': 'NCIT:C103236', 'annotations': {'expected_efs': '>85%'}}, + "LOW": {'description': 'Low risk neuroblastoma with favorable prognosis. Treatment may include surgery alone or observation.', 'meaning': 'NCIT:C103237', 'annotations': {'expected_efs': '>75%'}}, + "INTERMEDIATE": {'description': 'Intermediate risk neuroblastoma requiring multimodal treatment including chemotherapy.', 'meaning': 'NCIT:C103238', 'annotations': {'expected_efs': '50-75%'}}, + "HIGH": {'description': 'High risk neuroblastoma with poor prognosis. Requires intensive multimodal therapy including high-dose chemotherapy with autologous stem cell rescue, surgery, radiation, and immunotherapy.', 'meaning': 'NCIT:C103239', 'annotations': {'expected_efs': '<50%', 'mycn_amplified': 'often'}}, +} + +class ImageDefinedRiskFactor(RichEnum): + """ + Image-defined risk factors (IDRFs) used in INRGSS staging to determine surgical risk. Presence of any IDRF upgrades a tumor from L1 to L2. + """ + # Enum members + IPSILATERAL_TUMOR_EXTENSION_TO_BODY_CAVITIES = "IPSILATERAL_TUMOR_EXTENSION_TO_BODY_CAVITIES" + NECK_ENCASING_CAROTID_OR_VERTEBRAL = "NECK_ENCASING_CAROTID_OR_VERTEBRAL" + NECK_ENCASING_JUGULAR = "NECK_ENCASING_JUGULAR" + NECK_EXTENDING_TO_SKULL_BASE = "NECK_EXTENDING_TO_SKULL_BASE" + NECK_COMPRESSING_TRACHEA = "NECK_COMPRESSING_TRACHEA" + CERVICOTHORACIC_ENCASING_BRACHIAL_PLEXUS = "CERVICOTHORACIC_ENCASING_BRACHIAL_PLEXUS" + CERVICOTHORACIC_ENCASING_SUBCLAVIAN = "CERVICOTHORACIC_ENCASING_SUBCLAVIAN" + CERVICOTHORACIC_COMPRESSING_TRACHEA = "CERVICOTHORACIC_COMPRESSING_TRACHEA" + THORAX_ENCASING_AORTA = "THORAX_ENCASING_AORTA" + THORAX_COMPRESSING_TRACHEA_BRONCHI = "THORAX_COMPRESSING_TRACHEA_BRONCHI" + THORAX_LOWER_MEDIASTINUM_INFILTRATING = "THORAX_LOWER_MEDIASTINUM_INFILTRATING" + THORACOABDOMINAL_ENCASING_AORTA_CELIAC = "THORACOABDOMINAL_ENCASING_AORTA_CELIAC" + ABDOMEN_PELVIS_ENCASING_CELIAC_SMA = "ABDOMEN_PELVIS_ENCASING_CELIAC_SMA" + ABDOMEN_PELVIS_ENCASING_RENAL_VESSELS = "ABDOMEN_PELVIS_ENCASING_RENAL_VESSELS" + ABDOMEN_PELVIS_ENCASING_AORTA_IVC = "ABDOMEN_PELVIS_ENCASING_AORTA_IVC" + ABDOMEN_PELVIS_ENCASING_ILIAC_VESSELS = "ABDOMEN_PELVIS_ENCASING_ILIAC_VESSELS" + ABDOMEN_PELVIS_PELVIC_CROSSING_SCIATIC_NOTCH = "ABDOMEN_PELVIS_PELVIC_CROSSING_SCIATIC_NOTCH" + INTRASPINAL_EXTENSION = "INTRASPINAL_EXTENSION" + ADJACENT_ORGAN_INFILTRATION = "ADJACENT_ORGAN_INFILTRATION" + +# Set metadata after class creation +ImageDefinedRiskFactor._metadata = { + "IPSILATERAL_TUMOR_EXTENSION_TO_BODY_CAVITIES": {'description': 'Tumor extension from neck to chest, chest to abdomen, or abdomen to pelvis.'}, + "NECK_ENCASING_CAROTID_OR_VERTEBRAL": {'description': 'Tumor encasing carotid artery and/or vertebral artery.'}, + "NECK_ENCASING_JUGULAR": {'description': 'Tumor encasing internal jugular vein.'}, + "NECK_EXTENDING_TO_SKULL_BASE": {'description': 'Tumor extending to base of skull.'}, + "NECK_COMPRESSING_TRACHEA": {'description': 'Tumor compressing the trachea.'}, + "CERVICOTHORACIC_ENCASING_BRACHIAL_PLEXUS": {'description': 'Tumor encasing brachial plexus roots (C5-T1).'}, + "CERVICOTHORACIC_ENCASING_SUBCLAVIAN": {'description': 'Tumor encasing subclavian vessels and/or vertebral artery and/or carotid artery.'}, + "CERVICOTHORACIC_COMPRESSING_TRACHEA": {'description': 'Tumor compressing the trachea.'}, + "THORAX_ENCASING_AORTA": {'description': 'Tumor encasing aorta and/or major branches.'}, + "THORAX_COMPRESSING_TRACHEA_BRONCHI": {'description': 'Tumor compressing trachea and/or principal bronchi.'}, + "THORAX_LOWER_MEDIASTINUM_INFILTRATING": {'description': 'Lower mediastinal tumor infiltrating the costo-vertebral junction between T9 and T12.'}, + "THORACOABDOMINAL_ENCASING_AORTA_CELIAC": {'description': 'Tumor encasing the aorta and/or vena cava.'}, + "ABDOMEN_PELVIS_ENCASING_CELIAC_SMA": {'description': 'Tumor encasing celiac axis and/or superior mesenteric artery.'}, + "ABDOMEN_PELVIS_ENCASING_RENAL_VESSELS": {'description': 'Tumor encasing origin of renal vessels.'}, + "ABDOMEN_PELVIS_ENCASING_AORTA_IVC": {'description': 'Tumor encasing aorta and/or inferior vena cava.'}, + "ABDOMEN_PELVIS_ENCASING_ILIAC_VESSELS": {'description': 'Tumor encasing iliac vessels.'}, + "ABDOMEN_PELVIS_PELVIC_CROSSING_SCIATIC_NOTCH": {'description': 'Pelvic tumor crossing the sciatic notch.'}, + "INTRASPINAL_EXTENSION": {'description': 'Intraspinal tumor extension provided that more than one third of the spinal canal in the axial plane is invaded and/or the perimedullary leptomeningeal spaces are not visible and/or spinal cord signal is abnormal.'}, + "ADJACENT_ORGAN_INFILTRATION": {'description': 'Infiltration of adjacent organs/structures such as pericardium, diaphragm, kidney, liver, duodeno-pancreatic block, and mesentery.'}, +} + +__all__ = [ + "INRGSSStage", + "INSSStage", + "NeuroblastomaRiskGroup", + "ImageDefinedRiskFactor", +] \ No newline at end of file diff --git a/src/valuesets/enums/units/quantity_kinds.py b/src/valuesets/enums/units/quantity_kinds.py new file mode 100644 index 00000000..a11c64cf --- /dev/null +++ b/src/valuesets/enums/units/quantity_kinds.py @@ -0,0 +1,121 @@ +""" +QUDT Quantity Kinds Value Set + +Value set for physical quantity kinds based on QUDT (Quantities, Units, Dimensions and Types). Quantity kinds represent the abstract type of a physical quantity, independent of its units. For example, "length" is a quantity kind that can be measured in meters, feet, etc. + +Generated from: units/quantity_kinds.yaml +""" + +from __future__ import annotations + +from valuesets.generators.rich_enum import RichEnum + +class QuantityKindEnum(RichEnum): + """ + Physical quantity kinds based on QUDT. These represent abstract types of physical quantities independent of the units used to measure them. + """ + # Enum members + LENGTH = "LENGTH" + MASS = "MASS" + TIME = "TIME" + THERMODYNAMIC_TEMPERATURE = "THERMODYNAMIC_TEMPERATURE" + AMOUNT_OF_SUBSTANCE = "AMOUNT_OF_SUBSTANCE" + ELECTRIC_CURRENT = "ELECTRIC_CURRENT" + LUMINOUS_INTENSITY = "LUMINOUS_INTENSITY" + AREA = "AREA" + VOLUME = "VOLUME" + ANGLE = "ANGLE" + SOLID_ANGLE = "SOLID_ANGLE" + VELOCITY = "VELOCITY" + SPEED = "SPEED" + ACCELERATION = "ACCELERATION" + FORCE = "FORCE" + PRESSURE = "PRESSURE" + ENERGY = "ENERGY" + WORK = "WORK" + POWER = "POWER" + MOMENTUM = "MOMENTUM" + TORQUE = "TORQUE" + ANGULAR_VELOCITY = "ANGULAR_VELOCITY" + ANGULAR_ACCELERATION = "ANGULAR_ACCELERATION" + DENSITY = "DENSITY" + VISCOSITY = "VISCOSITY" + KINEMATIC_VISCOSITY = "KINEMATIC_VISCOSITY" + FREQUENCY = "FREQUENCY" + MASS_CONCENTRATION = "MASS_CONCENTRATION" + AMOUNT_CONCENTRATION = "AMOUNT_CONCENTRATION" + ELECTRIC_CHARGE = "ELECTRIC_CHARGE" + ELECTRIC_POTENTIAL = "ELECTRIC_POTENTIAL" + ELECTRIC_RESISTANCE = "ELECTRIC_RESISTANCE" + ELECTRICAL_CONDUCTIVITY = "ELECTRICAL_CONDUCTIVITY" + CAPACITANCE = "CAPACITANCE" + INDUCTANCE = "INDUCTANCE" + MAGNETIC_FLUX = "MAGNETIC_FLUX" + MAGNETIC_FLUX_DENSITY = "MAGNETIC_FLUX_DENSITY" + HEAT_CAPACITY = "HEAT_CAPACITY" + SPECIFIC_HEAT_CAPACITY = "SPECIFIC_HEAT_CAPACITY" + THERMAL_CONDUCTIVITY = "THERMAL_CONDUCTIVITY" + LUMINOUS_FLUX = "LUMINOUS_FLUX" + ILLUMINANCE = "ILLUMINANCE" + RADIANT_INTENSITY = "RADIANT_INTENSITY" + ACTIVITY = "ACTIVITY" + ABSORBED_DOSE = "ABSORBED_DOSE" + DOSE_EQUIVALENT = "DOSE_EQUIVALENT" + INFORMATION_ENTROPY = "INFORMATION_ENTROPY" + DATA_RATE = "DATA_RATE" + +# Set metadata after class creation +QuantityKindEnum._metadata = { + "LENGTH": {'description': 'A 1-D extent quality representing distance between two points', 'meaning': 'quantitykind:Length', 'annotations': {'si_base': 'true', 'dimension': 'L'}}, + "MASS": {'description': 'The amount of matter in an object', 'meaning': 'quantitykind:Mass', 'annotations': {'si_base': 'true', 'dimension': 'M'}}, + "TIME": {'description': 'Duration or temporal extent', 'meaning': 'quantitykind:Time', 'annotations': {'si_base': 'true', 'dimension': 'T', 'pato_label': 'duration'}}, + "THERMODYNAMIC_TEMPERATURE": {'description': 'The thermal energy of a system', 'meaning': 'quantitykind:ThermodynamicTemperature', 'annotations': {'si_base': 'true', 'dimension': 'Θ', 'pato_label': 'temperature'}}, + "AMOUNT_OF_SUBSTANCE": {'description': 'The number of elementary entities (atoms, molecules, etc.)', 'meaning': 'quantitykind:AmountOfSubstance', 'annotations': {'si_base': 'true', 'dimension': 'N', 'pato_label': 'amount'}}, + "ELECTRIC_CURRENT": {'description': 'Flow of electric charge per unit time', 'meaning': 'quantitykind:ElectricCurrent', 'annotations': {'si_base': 'true', 'dimension': 'I'}}, + "LUMINOUS_INTENSITY": {'description': 'Luminous power per unit solid angle emitted by a point light source', 'meaning': 'quantitykind:LuminousIntensity', 'annotations': {'si_base': 'true', 'dimension': 'J', 'pato_label': 'luminance'}}, + "AREA": {'description': 'A 2-D extent representing the size of a surface', 'meaning': 'quantitykind:Area', 'annotations': {'dimension': 'L²'}}, + "VOLUME": {'description': 'A 3-D extent representing the amount of space occupied', 'meaning': 'quantitykind:Volume', 'annotations': {'dimension': 'L³'}}, + "ANGLE": {'description': 'The figure formed by two rays sharing a common endpoint', 'meaning': 'quantitykind:Angle', 'annotations': {'dimension': 'dimensionless'}}, + "SOLID_ANGLE": {'description': 'A 3-D angular measure', 'meaning': 'quantitykind:SolidAngle', 'annotations': {'dimension': 'dimensionless'}}, + "VELOCITY": {'description': 'Rate of change of position with direction', 'meaning': 'quantitykind:Velocity', 'annotations': {'dimension': 'L·T⁻¹'}}, + "SPEED": {'description': 'Scalar rate of change of position', 'meaning': 'quantitykind:Speed', 'annotations': {'dimension': 'L·T⁻¹'}}, + "ACCELERATION": {'description': 'Rate of change of velocity', 'meaning': 'quantitykind:Acceleration', 'annotations': {'dimension': 'L·T⁻²'}}, + "FORCE": {'description': 'Rate of change of momentum', 'meaning': 'quantitykind:Force', 'annotations': {'dimension': 'M·L·T⁻²'}}, + "PRESSURE": {'description': 'Force per unit area', 'meaning': 'quantitykind:Pressure', 'annotations': {'dimension': 'M·L⁻¹·T⁻²'}}, + "ENERGY": {'description': 'Capacity to do work', 'meaning': 'quantitykind:Energy', 'annotations': {'dimension': 'M·L²·T⁻²'}}, + "WORK": {'description': 'Energy transferred by a force', 'meaning': 'quantitykind:Work', 'annotations': {'dimension': 'M·L²·T⁻²'}}, + "POWER": {'description': 'Rate of doing work or transferring energy', 'meaning': 'quantitykind:Power', 'annotations': {'dimension': 'M·L²·T⁻³'}}, + "MOMENTUM": {'description': 'Product of mass and velocity', 'meaning': 'quantitykind:Momentum', 'annotations': {'dimension': 'M·L·T⁻¹'}}, + "TORQUE": {'description': 'Rotational force or moment of force', 'meaning': 'quantitykind:Torque', 'annotations': {'dimension': 'M·L²·T⁻²'}}, + "ANGULAR_VELOCITY": {'description': 'Rate of change of angular position', 'meaning': 'quantitykind:AngularVelocity', 'annotations': {'dimension': 'T⁻¹'}}, + "ANGULAR_ACCELERATION": {'description': 'Rate of change of angular velocity', 'meaning': 'quantitykind:AngularAcceleration', 'annotations': {'dimension': 'T⁻²'}}, + "DENSITY": {'description': 'Mass per unit volume', 'meaning': 'quantitykind:Density', 'annotations': {'dimension': 'M·L⁻³', 'pato_label': 'mass density'}}, + "VISCOSITY": {'description': 'Internal resistance to flow', 'meaning': 'quantitykind:DynamicViscosity', 'annotations': {'dimension': 'M·L⁻¹·T⁻¹'}}, + "KINEMATIC_VISCOSITY": {'description': 'Dynamic viscosity divided by density', 'meaning': 'quantitykind:KinematicViscosity', 'annotations': {'dimension': 'L²·T⁻¹'}}, + "FREQUENCY": {'description': 'Number of repetitive events per unit time', 'meaning': 'quantitykind:Frequency', 'annotations': {'dimension': 'T⁻¹'}}, + "MASS_CONCENTRATION": {'description': 'Mass of a substance per unit volume', 'meaning': 'quantitykind:MassConcentration', 'annotations': {'dimension': 'M·L⁻³', 'pato_label': 'concentration of'}}, + "AMOUNT_CONCENTRATION": {'description': 'Amount of substance per unit volume (molarity)', 'meaning': 'quantitykind:AmountConcentration', 'annotations': {'dimension': 'N·L⁻³'}}, + "ELECTRIC_CHARGE": {'description': 'Fundamental property of matter causing electromagnetic interaction', 'meaning': 'quantitykind:ElectricCharge', 'annotations': {'dimension': 'I·T'}}, + "ELECTRIC_POTENTIAL": {'description': 'Potential energy per unit charge (voltage)', 'meaning': 'quantitykind:ElectricPotential', 'annotations': {'dimension': 'M·L²·T⁻³·I⁻¹'}, 'aliases': ['voltage']}, + "ELECTRIC_RESISTANCE": {'description': 'Opposition to electric current flow', 'meaning': 'quantitykind:Resistance', 'annotations': {'dimension': 'M·L²·T⁻³·I⁻²'}}, + "ELECTRICAL_CONDUCTIVITY": {'description': 'Ability to conduct electric current', 'meaning': 'quantitykind:Conductivity', 'annotations': {'dimension': 'I²·T³·M⁻¹·L⁻³'}}, + "CAPACITANCE": {'description': 'Ability to store electric charge', 'meaning': 'quantitykind:Capacitance', 'annotations': {'dimension': 'I²·T⁴·M⁻¹·L⁻²'}}, + "INDUCTANCE": {'description': 'Property relating magnetic flux to electric current', 'meaning': 'quantitykind:Inductance', 'annotations': {'dimension': 'M·L²·T⁻²·I⁻²'}}, + "MAGNETIC_FLUX": {'description': 'Measure of total magnetic field passing through a surface', 'meaning': 'quantitykind:MagneticFlux', 'annotations': {'dimension': 'M·L²·T⁻²·I⁻¹'}}, + "MAGNETIC_FLUX_DENSITY": {'description': 'Magnetic flux per unit area', 'meaning': 'quantitykind:MagneticFluxDensity', 'annotations': {'dimension': 'M·T⁻²·I⁻¹'}}, + "HEAT_CAPACITY": {'description': 'Heat required to raise temperature by one unit', 'meaning': 'quantitykind:HeatCapacity', 'annotations': {'dimension': 'M·L²·T⁻²·Θ⁻¹'}}, + "SPECIFIC_HEAT_CAPACITY": {'description': 'Heat capacity per unit mass', 'meaning': 'quantitykind:SpecificHeatCapacity', 'annotations': {'dimension': 'L²·T⁻²·Θ⁻¹'}}, + "THERMAL_CONDUCTIVITY": {'description': 'Ability to conduct heat', 'meaning': 'quantitykind:ThermalConductivity', 'annotations': {'dimension': 'M·L·T⁻³·Θ⁻¹', 'pato_label': 'heat conductivity'}}, + "LUMINOUS_FLUX": {'description': 'Total perceived light power emitted', 'meaning': 'quantitykind:LuminousFlux', 'annotations': {'dimension': 'J'}}, + "ILLUMINANCE": {'description': 'Luminous flux per unit area', 'meaning': 'quantitykind:Illuminance', 'annotations': {'dimension': 'J·L⁻²'}}, + "RADIANT_INTENSITY": {'description': 'Radiant power per unit solid angle', 'meaning': 'quantitykind:RadiantIntensity', 'annotations': {'dimension': 'M·L²·T⁻³'}}, + "ACTIVITY": {'description': 'Number of nuclear disintegrations per unit time', 'meaning': 'quantitykind:Activity', 'annotations': {'dimension': 'T⁻¹'}}, + "ABSORBED_DOSE": {'description': 'Energy deposited per unit mass by ionizing radiation', 'meaning': 'quantitykind:AbsorbedDose', 'annotations': {'dimension': 'L²·T⁻²'}}, + "DOSE_EQUIVALENT": {'description': 'Absorbed dose weighted by radiation type', 'meaning': 'quantitykind:DoseEquivalent', 'annotations': {'dimension': 'L²·T⁻²'}}, + "INFORMATION_ENTROPY": {'description': 'Measure of information content or uncertainty', 'meaning': 'quantitykind:InformationEntropy', 'annotations': {'dimension': 'dimensionless'}}, + "DATA_RATE": {'description': 'Amount of data transferred per unit time', 'meaning': 'quantitykind:DataRate', 'annotations': {'dimension': 'T⁻¹'}}, +} + +__all__ = [ + "QuantityKindEnum", +] \ No newline at end of file diff --git a/src/valuesets/schema/medical/pediatric_oncology/diagnosis_categories.yaml b/src/valuesets/schema/medical/pediatric_oncology/diagnosis_categories.yaml new file mode 100644 index 00000000..847ea1bf --- /dev/null +++ b/src/valuesets/schema/medical/pediatric_oncology/diagnosis_categories.yaml @@ -0,0 +1,346 @@ +name: pediatric_oncology_diagnosis_categories +title: Pediatric Oncology Diagnosis Categories +description: >- + High-level pediatric cancer diagnosis groupings based on CCDI CDE 16607972 + (Diagnosis Pediatric Oncology Grouping Category). These categories were + developed through consensus by St. Jude, CBTN, Treehouse, and NCI to enable + cohort aggregation across federated pediatric cancer data resources. + Categories are aligned with WHO CNS5, WHO-HAEM5, and WHO Pediatric Blue Book. +id: https://w3id.org/linkml/valuesets/medical/pediatric_oncology/diagnosis_categories +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + valuesets: https://w3id.org/valuesets/ + NCIT: http://purl.obolibrary.org/obo/NCIT_ + MONDO: http://purl.obolibrary.org/obo/MONDO_ + EFO: http://www.ebi.ac.uk/efo/EFO_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ + caDSR: https://cadsr.cancer.gov/onedata/cde/ +default_prefix: valuesets +enums: + PediatricOncologyDiagnosisCategory: + title: Pediatric Oncology Diagnosis Category + description: >- + High-level groupings for pediatric cancer diagnoses per CCDI CDE 16607972. + Designed for cohort aggregation across federated data resources. Each + diagnosis maps to a single dominant category. + status: RELEASED + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://github.com/CBIIT/ccdi-federation-api/discussions/160 + - https://docs.stjude.cloud/cc4k + annotations: + caDSR_CDE: "16607972" + source: CCDI Federation API + alignment: WHO CNS5, WHO-HAEM5, WHO Pediatric Blue Book + permissible_values: + # ===== BRAIN TUMORS (13 categories) ===== + ATYPICAL_TERATOID_RHABDOID_TUMOR: + title: Atypical Teratoid/Rhabdoid Tumors + description: >- + Highly malignant embryonal CNS tumor characterized by loss of + SMARCB1 (INI1) or SMARCA4 expression. Predominantly occurs in + young children. + meaning: NCIT:C6807 + annotations: + category: brain_tumor + who_classification: WHO CNS5 + CHOROID_PLEXUS_TUMOR: + title: Choroid Plexus Tumors + description: >- + Neoplasms arising from the choroid plexus epithelium, including + papilloma, atypical papilloma, and carcinoma. + meaning: NCIT:C3698 + annotations: + category: brain_tumor + who_classification: WHO CNS5 + CNS_GERM_CELL_TUMOR: + title: CNS Germ Cell Tumors + description: >- + Germ cell tumors arising within the central nervous system, + including germinoma and non-germinomatous germ cell tumors. + meaning: NCIT:C6286 + annotations: + category: brain_tumor + who_classification: WHO CNS5 + CNS_SARCOMA: + title: CNS Sarcomas + description: >- + Sarcomas arising primarily in the central nervous system, + including Ewing sarcoma and rhabdomyosarcoma of CNS. + meaning: NCIT:C121624 + annotations: + category: brain_tumor + CRANIOPHARYNGIOMA: + title: Craniopharyngiomas + description: >- + Benign epithelial tumors arising from remnants of Rathke pouch, + including adamantinomatous and papillary subtypes. + meaning: NCIT:C2998 + annotations: + category: brain_tumor + who_classification: WHO CNS5 + EPENDYMOMA: + title: Ependymoma + description: >- + Glial tumors arising from ependymal cells lining the ventricular + system and central canal. Includes molecular subtypes defined + by WHO CNS5. + meaning: NCIT:C3017 + annotations: + category: brain_tumor + who_classification: WHO CNS5 + GLIONEURONAL_AND_NEURONAL_TUMOR: + title: Glioneuronal and Neuronal Tumors + description: >- + Tumors with neuronal differentiation including ganglioglioma, + dysembryoplastic neuroepithelial tumor (DNET), and central + neurocytoma. + meaning: NCIT:C6927 + annotations: + category: brain_tumor + who_classification: WHO CNS5 + HIGH_GRADE_GLIOMA: + title: High-Grade Gliomas + description: >- + Aggressive glial tumors including pediatric-type diffuse high-grade + gliomas (H3 K27-altered, H3 G34-mutant, and H3/IDH-wildtype), + as well as glioblastoma. + meaning: NCIT:C129355 + annotations: + category: brain_tumor + who_classification: WHO CNS5 + grade: high + LOW_GRADE_GLIOMA: + title: Low-Grade Gliomas + description: >- + Indolent glial tumors including pilocytic astrocytoma and + pediatric-type diffuse low-grade gliomas (MYB/MYBL1-altered, + MAPK pathway-altered). + meaning: NCIT:C129354 + annotations: + category: brain_tumor + who_classification: WHO CNS5 + grade: low + MEDULLOBLASTOMA: + title: Medulloblastoma + description: >- + Embryonal tumor of the cerebellum, classified by molecular + subgroups (WNT-activated, SHH-activated, Group 3, Group 4) + per WHO CNS5. + meaning: NCIT:C3222 + annotations: + category: brain_tumor + who_classification: WHO CNS5 + OTHER_CNS_EMBRYONAL_TUMOR: + title: Other CNS Embryonal Tumors + description: >- + Embryonal tumors of the CNS other than medulloblastoma and ATRT, + including embryonal tumor with multilayered rosettes (ETMR), + CNS neuroblastoma, and pineoblastoma. + meaning: NCIT:C6774 + aliases: + - CNS Embryonal Tumor, NOS + annotations: + category: brain_tumor + who_classification: WHO CNS5 + OTHER_GLIOMA: + title: Other Gliomas + description: >- + Glial tumors not classified as high-grade or low-grade glioma, + including angiocentric glioma and astroblastoma. + meaning: NCIT:C3059 + annotations: + category: brain_tumor + OTHER_BRAIN_TUMOR: + title: Other Brain Tumors + description: >- + CNS tumors not fitting other brain tumor categories, including + meningioma, schwannoma, and hemangioblastoma. + meaning: NCIT:C2907 + annotations: + category: brain_tumor + + # ===== HEMATOLOGIC MALIGNANCIES (6 categories) ===== + LYMPHOBLASTIC_LEUKEMIA: + title: Lymphoblastic Leukemia + description: >- + Acute lymphoblastic leukemia (ALL) including B-ALL and T-ALL + with all molecular subtypes (BCR::ABL1, ETV6::RUNX1, KMT2A-r, + DUX4, MEF2D, etc.). + meaning: NCIT:C3167 + aliases: + - ALL + - Acute Lymphoblastic Leukemia + annotations: + category: hematologic + who_classification: WHO-HAEM5 + MYELOID_LEUKEMIA: + title: Myeloid Leukemia + description: >- + Acute myeloid leukemia (AML) and related myeloid neoplasms + including AML with defining genetic abnormalities, therapy-related + AML, and juvenile myelomonocytic leukemia (JMML). + meaning: NCIT:C3171 + aliases: + - AML + - Acute Myeloid Leukemia + annotations: + category: hematologic + who_classification: WHO-HAEM5 + HODGKIN_LYMPHOMA: + title: Hodgkin Lymphoma + description: >- + Lymphoid neoplasm characterized by Reed-Sternberg cells, + including classical Hodgkin lymphoma and nodular lymphocyte + predominant Hodgkin lymphoma. + meaning: NCIT:C9357 + annotations: + category: hematologic + who_classification: WHO-HAEM5 + NON_HODGKIN_LYMPHOMA: + title: Non-Hodgkin Lymphoma + description: >- + Lymphoid neoplasms other than Hodgkin lymphoma, including + Burkitt lymphoma, diffuse large B-cell lymphoma, anaplastic + large cell lymphoma, and lymphoblastic lymphoma. + meaning: NCIT:C3211 + aliases: + - NHL + annotations: + category: hematologic + who_classification: WHO-HAEM5 + LYMPHOPROLIFERATIVE_DISEASE: + title: Lymphoproliferative Diseases + description: >- + Disorders characterized by abnormal lymphocyte proliferation, + including post-transplant lymphoproliferative disorder (PTLD) + and hemophagocytic lymphohistiocytosis (HLH). + meaning: NCIT:C3138 + annotations: + category: hematologic + OTHER_HEME_TUMOR: + title: Other Heme Tumors + description: >- + Hematologic malignancies not classified elsewhere, including + histiocytic disorders, myelodysplastic syndromes, and + myeloproliferative neoplasms. + meaning: NCIT:C27134 + annotations: + category: hematologic + + # ===== SOLID TUMORS (11 categories) ===== + NEUROBLASTOMA: + title: Neuroblastoma + description: >- + Embryonal tumor of the peripheral sympathetic nervous system, + arising from neural crest cells. Includes ganglioneuroblastoma + and ganglioneuroma. + meaning: NCIT:C3270 + annotations: + category: solid_tumor + who_classification: WHO Pediatric Blue Book + OSTEOSARCOMA: + title: Osteosarcoma + description: >- + Primary malignant bone tumor characterized by osteoid production, + including conventional, telangiectatic, and small cell variants. + meaning: NCIT:C9145 + annotations: + category: solid_tumor + who_classification: WHO Bone/Soft Tissue + EWING_SARCOMA: + title: Ewing Sarcoma + description: >- + Small round cell sarcoma typically harboring EWSR1 rearrangements, + arising in bone or soft tissue. Includes Ewing sarcoma family + of tumors. + meaning: NCIT:C4817 + annotations: + category: solid_tumor + who_classification: WHO Bone/Soft Tissue + RHABDOMYOSARCOMA: + title: Rhabdomyosarcoma + description: >- + Malignant soft tissue tumor with skeletal muscle differentiation, + including embryonal, alveolar, and spindle cell/sclerosing subtypes. + meaning: NCIT:C3359 + annotations: + category: solid_tumor + who_classification: WHO Bone/Soft Tissue + SOFT_TISSUE_TUMOR: + title: Soft Tissue Tumors + description: >- + Soft tissue neoplasms other than rhabdomyosarcoma and Ewing sarcoma, + including synovial sarcoma, fibrosarcoma, and other sarcomas. + Also includes non-sarcomatous soft tissue tumors. + meaning: NCIT:C3399 + aliases: + - Soft Tissue Sarcoma + annotations: + category: solid_tumor + RHABDOID_TUMOR: + title: Rhabdoid Tumors + description: >- + Highly aggressive tumors characterized by SMARCB1 loss, + occurring outside the CNS (extracranial rhabdoid tumor). + Includes malignant rhabdoid tumor of kidney. + meaning: NCIT:C3769 + annotations: + category: solid_tumor + RENAL_TUMOR: + title: Renal Tumors + description: >- + Kidney tumors including Wilms tumor (nephroblastoma), clear cell + sarcoma of kidney, renal cell carcinoma, and congenital + mesoblastic nephroma. + meaning: NCIT:C7548 + aliases: + - Kidney Tumor + - Wilms Tumor + annotations: + category: solid_tumor + who_classification: WHO Pediatric Blue Book + RETINOBLASTOMA: + title: Retinoblastoma + description: >- + Malignant neoplasm of the retina arising from developing + retinal cells, associated with RB1 mutations. + meaning: NCIT:C7541 + annotations: + category: solid_tumor + who_classification: WHO Pediatric Blue Book + GERM_CELL_TUMOR: + title: Germ Cell Tumors + description: >- + Tumors arising from primordial germ cells, occurring in gonadal + or extragonadal sites. Includes teratoma, yolk sac tumor, + germinoma, choriocarcinoma, and mixed germ cell tumors. + Excludes CNS germ cell tumors. + meaning: NCIT:C3708 + annotations: + category: solid_tumor + ENDOCRINE_AND_NEUROENDOCRINE_TUMOR: + title: Endocrine and Neuroendocrine Tumors + description: >- + Tumors of endocrine glands and neuroendocrine cells, including + thyroid carcinoma, adrenocortical carcinoma, pheochromocytoma, + and paraganglioma. + meaning: NCIT:C3010 + annotations: + category: solid_tumor + OTHER_SOLID_TUMOR: + title: Other Solid Tumors + description: >- + Solid tumors not classified elsewhere, including hepatoblastoma, + pleuropulmonary blastoma, nasopharyngeal carcinoma, melanoma, + and carcinomas. + meaning: NCIT:C9107 + annotations: + category: solid_tumor diff --git a/src/valuesets/schema/medical/pediatric_oncology/iccc3.yaml b/src/valuesets/schema/medical/pediatric_oncology/iccc3.yaml new file mode 100644 index 00000000..e67e0b15 --- /dev/null +++ b/src/valuesets/schema/medical/pediatric_oncology/iccc3.yaml @@ -0,0 +1,573 @@ +name: iccc3 +title: International Classification of Childhood Cancer, Third Edition (ICCC-3) +description: >- + Value sets based on the International Classification of Childhood Cancer, + Third Edition (ICCC-3). The ICCC is the standard classification for childhood + cancers, emphasizing tumor morphology rather than primary site (as used for + adult cancers). ICCC-3 classifies tumors coded according to ICD-O-3 into + 12 main groups and 47 subgroups. +id: https://w3id.org/linkml/valuesets/medical/pediatric_oncology/iccc3 +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + valuesets: https://w3id.org/valuesets/ + NCIT: http://purl.obolibrary.org/obo/NCIT_ + ICDO: http://purl.obolibrary.org/obo/ICDO_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ + seer: https://seer.cancer.gov/ +default_prefix: valuesets +enums: + ICCC3MainGroup: + title: ICCC-3 Main Diagnostic Group + description: >- + The 12 main diagnostic groups of the International Classification of + Childhood Cancer, Third Edition. Based on tumor morphology and primary + site with emphasis on morphology. + status: RELEASED + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://seer.cancer.gov/iccc/ + - https://seer.cancer.gov/iccc/iccc3.html + - https://pubmed.ncbi.nlm.nih.gov/15712273/ + annotations: + source: SEER/IARC + version: ICCC-3 + coding_system: ICD-O-3 + permissible_values: + I_LEUKEMIAS_MYELOPROLIFERATIVE_MYELODYSPLASTIC: + title: "I. Leukemias, myeloproliferative diseases, and myelodysplastic diseases" + description: >- + Includes lymphoid leukemias, acute myeloid leukemias, chronic + myeloproliferative diseases, myelodysplastic syndrome and other + myeloproliferative diseases, and unspecified and other specified + leukemias. + meaning: NCIT:C3161 + annotations: + iccc_code: I + subgroup_count: 5 + II_LYMPHOMAS_RETICULOENDOTHELIAL: + title: "II. Lymphomas and reticuloendothelial neoplasms" + description: >- + Includes Hodgkin lymphomas, non-Hodgkin lymphomas (except Burkitt + lymphoma), Burkitt lymphoma, and miscellaneous lymphoreticular + neoplasms. + meaning: NCIT:C7058 + annotations: + iccc_code: II + subgroup_count: 4 + III_CNS_INTRACRANIAL_INTRASPINAL: + title: "III. CNS and miscellaneous intracranial and intraspinal neoplasms" + description: >- + Includes ependymomas and choroid plexus tumor, astrocytomas, + intracranial and intraspinal embryonal tumors, other gliomas, + other specified intracranial and intraspinal neoplasms, and + unspecified intracranial and intraspinal neoplasms. Also includes + nonmalignant CNS tumors. + meaning: NCIT:C2907 + annotations: + iccc_code: III + subgroup_count: 6 + includes_nonmalignant: true + IV_NEUROBLASTOMA_PERIPHERAL_NERVOUS: + title: "IV. Neuroblastoma and other peripheral nervous cell tumors" + description: >- + Includes neuroblastoma and ganglioneuroblastoma, and other + peripheral nervous cell tumors. + meaning: NCIT:C3270 + annotations: + iccc_code: IV + subgroup_count: 2 + V_RETINOBLASTOMA: + title: "V. Retinoblastoma" + description: >- + Malignant neoplasm of the retina. Single group with no subgroups. + meaning: NCIT:C7541 + annotations: + iccc_code: V + subgroup_count: 1 + VI_RENAL_TUMORS: + title: "VI. Renal tumors" + description: >- + Includes nephroblastoma and other nonepithelial renal tumors, + renal carcinomas, and unspecified malignant renal tumors. + meaning: NCIT:C7548 + annotations: + iccc_code: VI + subgroup_count: 3 + VII_HEPATIC_TUMORS: + title: "VII. Hepatic tumors" + description: >- + Includes hepatoblastoma, hepatic carcinomas, and unspecified + malignant hepatic tumors. + meaning: NCIT:C7927 + annotations: + iccc_code: VII + subgroup_count: 3 + VIII_MALIGNANT_BONE_TUMORS: + title: "VIII. Malignant bone tumors" + description: >- + Includes osteosarcomas, chondrosarcomas, Ewing tumor and related + sarcomas of bone, other specified malignant bone tumors, and + unspecified malignant bone tumors. + meaning: NCIT:C4882 + annotations: + iccc_code: VIII + subgroup_count: 5 + IX_SOFT_TISSUE_SARCOMAS: + title: "IX. Soft tissue and other extraosseous sarcomas" + description: >- + Includes rhabdomyosarcomas, fibrosarcomas/peripheral nerve sheath + tumors/other fibrous neoplasms, Kaposi sarcoma, other specified + soft tissue sarcomas, and unspecified soft tissue sarcomas. + meaning: NCIT:C9306 + annotations: + iccc_code: IX + subgroup_count: 5 + X_GERM_CELL_GONADAL: + title: "X. Germ cell tumors, trophoblastic tumors, and neoplasms of gonads" + description: >- + Includes intracranial and intraspinal germ cell tumors, malignant + extracranial and extragonadal germ cell tumors, malignant gonadal + germ cell tumors, gonadal carcinomas, and other and unspecified + malignant gonadal tumors. + meaning: NCIT:C3708 + annotations: + iccc_code: X + subgroup_count: 5 + XI_EPITHELIAL_MELANOMA: + title: "XI. Other malignant epithelial neoplasms and malignant melanomas" + description: >- + Includes adrenocortical carcinomas, thyroid carcinomas, + nasopharyngeal carcinomas, malignant melanomas, skin carcinomas, + and other and unspecified carcinomas. + meaning: NCIT:C3709 + annotations: + iccc_code: XI + subgroup_count: 6 + XII_OTHER_UNSPECIFIED: + title: "XII. Other and unspecified malignant neoplasms" + description: >- + Includes other specified malignant tumors and other unspecified + malignant tumors not classifiable in groups I-XI. + meaning: NCIT:C3262 + annotations: + iccc_code: XII + subgroup_count: 2 + + ICCC3Subgroup: + title: ICCC-3 Diagnostic Subgroup + description: >- + The 47 diagnostic subgroups of the International Classification of + Childhood Cancer, Third Edition. These provide more detailed classification + within each of the 12 main groups. + status: RELEASED + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://seer.cancer.gov/iccc/iccc3.html + - https://seer.cancer.gov/iccc/iccc3_ext.html + annotations: + source: SEER/IARC + version: ICCC-3 + permissible_values: + # ===== Group I: Leukemias ===== + Ia_LYMPHOID_LEUKEMIAS: + title: "Ia. Lymphoid leukemias" + description: >- + Precursor cell lymphoblastic leukemia, NOS; precursor cell + lymphoblastic leukemia, B-cell; precursor cell lymphoblastic + leukemia, T-cell; Burkitt cell leukemia; and other lymphoid leukemias. + meaning: NCIT:C3167 + annotations: + main_group: I + icdo3_codes: "9820-9827, 9835-9837" + Ib_ACUTE_MYELOID_LEUKEMIAS: + title: "Ib. Acute myeloid leukemias" + description: >- + Acute myeloid leukemia and variants including AML with maturation, + acute promyelocytic leukemia, acute myelomonocytic leukemia, + acute monoblastic leukemia, acute megakaryoblastic leukemia, etc. + meaning: NCIT:C3171 + annotations: + main_group: I + icdo3_codes: "9840, 9861, 9866-9867, 9870-9874, 9891, 9895-9897, 9910, 9920, 9931" + Ic_CHRONIC_MYELOPROLIFERATIVE: + title: "Ic. Chronic myeloproliferative diseases" + description: >- + Chronic myeloid leukemia, NOS; juvenile myelomonocytic leukemia; + and other chronic myeloproliferative diseases. + meaning: NCIT:C4345 + annotations: + main_group: I + icdo3_codes: "9863, 9875-9876, 9945-9946, 9950, 9960-9964" + Id_MYELODYSPLASTIC_OTHER_MYELOPROLIFERATIVE: + title: "Id. Myelodysplastic syndrome and other myeloproliferative diseases" + description: >- + Myelodysplastic syndrome, NOS; refractory anemia; refractory + anemia with ringed sideroblasts; refractory anemia with excess blasts. + meaning: NCIT:C3247 + annotations: + main_group: I + icdo3_codes: "9945, 9980, 9982-9983, 9985-9989" + Ie_UNSPECIFIED_OTHER_LEUKEMIAS: + title: "Ie. Unspecified and other specified leukemias" + description: Leukemia, NOS and other specified leukemias not elsewhere classified. + meaning: NCIT:C3161 + annotations: + main_group: I + icdo3_codes: "9800-9801, 9805-9809, 9860, 9930" + + # ===== Group II: Lymphomas ===== + IIa_HODGKIN_LYMPHOMAS: + title: "IIa. Hodgkin lymphomas" + description: >- + Classical Hodgkin lymphoma and nodular lymphocyte predominant + Hodgkin lymphoma. + meaning: NCIT:C9357 + annotations: + main_group: II + icdo3_codes: "9650-9655, 9659, 9661-9665, 9667" + IIb_NON_HODGKIN_LYMPHOMAS: + title: "IIb. Non-Hodgkin lymphomas (except Burkitt lymphoma)" + description: >- + Diffuse large B-cell lymphoma, follicular lymphoma, peripheral + T-cell lymphoma, anaplastic large cell lymphoma, and other + non-Hodgkin lymphomas. + meaning: NCIT:C3211 + annotations: + main_group: II + icdo3_codes: "9591, 9670-9686, 9689-9691, 9695, 9698-9702, 9705, 9708-9709, 9714-9719, 9727-9729" + IIc_BURKITT_LYMPHOMA: + title: "IIc. Burkitt lymphoma" + description: Burkitt lymphoma and Burkitt-like lymphoma. + meaning: NCIT:C8150 + annotations: + main_group: II + icdo3_codes: "9687" + IId_MISC_LYMPHORETICULAR: + title: "IId. Miscellaneous lymphoreticular neoplasms" + description: >- + Lymphoreticular neoplasms not elsewhere classified including + lymphomatoid granulomatosis and post-transplant lymphoproliferative + disorder. + meaning: NCIT:C27134 + annotations: + main_group: II + icdo3_codes: "9740-9742, 9750, 9754-9758, 9930, 9970" + + # ===== Group III: CNS and Intracranial ===== + IIIa_EPENDYMOMAS: + title: "IIIa. Ependymomas and choroid plexus tumor" + description: >- + Ependymoma, anaplastic ependymoma, myxopapillary ependymoma, + and choroid plexus papilloma and carcinoma. + meaning: NCIT:C3017 + annotations: + main_group: III + icdo3_codes: "9383, 9390-9394" + IIIb_ASTROCYTOMAS: + title: "IIIb. Astrocytomas" + description: >- + Pilocytic astrocytoma, diffuse astrocytoma, anaplastic astrocytoma, + glioblastoma, and other astrocytic tumors. + meaning: NCIT:C60781 + annotations: + main_group: III + icdo3_codes: "9380, 9384, 9400-9411, 9420, 9424" + IIIc_INTRACRANIAL_EMBRYONAL: + title: "IIIc. Intracranial and intraspinal embryonal tumors" + description: >- + Medulloblastoma, primitive neuroectodermal tumor, medulloepithelioma, + atypical teratoid/rhabdoid tumor, and other embryonal tumors. + meaning: NCIT:C6774 + annotations: + main_group: III + icdo3_codes: "9470-9474, 9480, 9490, 9500-9508" + IIId_OTHER_GLIOMAS: + title: "IIId. Other gliomas" + description: >- + Oligodendroglioma, anaplastic oligodendroglioma, mixed glioma, + and other gliomas not elsewhere classified. + meaning: NCIT:C3059 + annotations: + main_group: III + icdo3_codes: "9380-9382, 9430, 9440-9460" + IIIe_OTHER_INTRACRANIAL_INTRASPINAL: + title: "IIIe. Other specified intracranial and intraspinal neoplasms" + description: >- + Pituitary adenoma, craniopharyngioma, pineal tumors, and other + specified intracranial neoplasms. + meaning: NCIT:C2907 + annotations: + main_group: III + IIIf_UNSPECIFIED_INTRACRANIAL: + title: "IIIf. Unspecified intracranial and intraspinal neoplasms" + description: Intracranial and intraspinal neoplasms, NOS. + meaning: NCIT:C2907 + annotations: + main_group: III + icdo3_codes: "8000-8005" + + # ===== Group IV: Neuroblastoma ===== + IVa_NEUROBLASTOMA_GANGLIONEUROBLASTOMA: + title: "IVa. Neuroblastoma and ganglioneuroblastoma" + description: >- + Neuroblastoma, NOS and ganglioneuroblastoma. + meaning: NCIT:C3270 + annotations: + main_group: IV + icdo3_codes: "9490, 9500" + IVb_OTHER_PERIPHERAL_NERVOUS: + title: "IVb. Other peripheral nervous cell tumors" + description: >- + Other peripheral nerve tumors including ganglioneuroma and + peripheral nerve sheath tumors. + meaning: NCIT:C4969 + annotations: + main_group: IV + icdo3_codes: "9501-9504, 9520-9523" + + # ===== Group V: Retinoblastoma ===== + V_RETINOBLASTOMA: + title: "V. Retinoblastoma" + description: Retinoblastoma. + meaning: NCIT:C7541 + annotations: + main_group: V + icdo3_codes: "9510-9514" + + # ===== Group VI: Renal tumors ===== + VIa_NEPHROBLASTOMA: + title: "VIa. Nephroblastoma and other nonepithelial renal tumors" + description: >- + Wilms tumor (nephroblastoma), clear cell sarcoma of kidney, + rhabdoid tumor of kidney, and other nonepithelial renal tumors. + meaning: NCIT:C3267 + annotations: + main_group: VI + icdo3_codes: "8960, 8963-8964" + VIb_RENAL_CARCINOMAS: + title: "VIb. Renal carcinomas" + description: Renal cell carcinoma and other renal carcinomas. + meaning: NCIT:C9385 + annotations: + main_group: VI + VIc_UNSPECIFIED_RENAL: + title: "VIc. Unspecified malignant renal tumors" + description: Malignant renal tumors, NOS. + meaning: NCIT:C7548 + annotations: + main_group: VI + + # ===== Group VII: Hepatic tumors ===== + VIIa_HEPATOBLASTOMA: + title: "VIIa. Hepatoblastoma" + description: Hepatoblastoma. + meaning: NCIT:C3728 + annotations: + main_group: VII + icdo3_codes: "8970" + VIIb_HEPATIC_CARCINOMAS: + title: "VIIb. Hepatic carcinomas" + description: >- + Hepatocellular carcinoma, cholangiocarcinoma, and other hepatic + carcinomas. + meaning: NCIT:C3099 + annotations: + main_group: VII + VIIc_UNSPECIFIED_HEPATIC: + title: "VIIc. Unspecified malignant hepatic tumors" + description: Malignant hepatic tumors, NOS. + meaning: NCIT:C7927 + annotations: + main_group: VII + + # ===== Group VIII: Bone tumors ===== + VIIIa_OSTEOSARCOMAS: + title: "VIIIa. Osteosarcomas" + description: >- + Osteosarcoma, NOS and variants including chondroblastic, + fibroblastic, telangiectatic, and small cell osteosarcoma. + meaning: NCIT:C9145 + annotations: + main_group: VIII + icdo3_codes: "9180-9187, 9191-9195" + VIIIb_CHONDROSARCOMAS: + title: "VIIIb. Chondrosarcomas" + description: Chondrosarcoma, NOS and variants. + meaning: NCIT:C2946 + annotations: + main_group: VIII + icdo3_codes: "9220-9231, 9240-9243" + VIIIc_EWING_TUMOR_BONE: + title: "VIIIc. Ewing tumor and related sarcomas of bone" + description: >- + Ewing sarcoma of bone and peripheral primitive neuroectodermal + tumor of bone. + meaning: NCIT:C4817 + annotations: + main_group: VIII + icdo3_codes: "9260, 9364" + VIIId_OTHER_BONE: + title: "VIIId. Other specified malignant bone tumors" + description: >- + Other specified malignant bone tumors including giant cell tumor + of bone, malignant and adamantinoma. + meaning: NCIT:C4882 + annotations: + main_group: VIII + VIIIe_UNSPECIFIED_BONE: + title: "VIIIe. Unspecified malignant bone tumors" + description: Malignant bone tumors, NOS. + meaning: NCIT:C4882 + annotations: + main_group: VIII + + # ===== Group IX: Soft tissue sarcomas ===== + IXa_RHABDOMYOSARCOMAS: + title: "IXa. Rhabdomyosarcomas" + description: >- + Rhabdomyosarcoma, NOS; embryonal rhabdomyosarcoma; alveolar + rhabdomyosarcoma; and other rhabdomyosarcomas. + meaning: NCIT:C3359 + annotations: + main_group: IX + icdo3_codes: "8900-8905, 8910, 8912, 8920" + IXb_FIBROSARCOMAS: + title: "IXb. Fibrosarcomas, peripheral nerve sheath tumors, and other fibrous neoplasms" + description: >- + Fibrosarcoma, NOS; infantile fibrosarcoma; dermatofibrosarcoma; + and malignant peripheral nerve sheath tumor. + meaning: NCIT:C3043 + annotations: + main_group: IX + icdo3_codes: "8810-8815, 8820-8823, 8830, 8832-8833, 9540, 9560-9561" + IXc_KAPOSI_SARCOMA: + title: "IXc. Kaposi sarcoma" + description: Kaposi sarcoma. + meaning: NCIT:C9087 + annotations: + main_group: IX + icdo3_codes: "9140" + IXd_OTHER_SOFT_TISSUE: + title: "IXd. Other specified soft tissue sarcomas" + description: >- + Includes liposarcoma, leiomyosarcoma, synovial sarcoma, + hemangiosarcoma, and other specified soft tissue sarcomas. + meaning: NCIT:C9306 + annotations: + main_group: IX + IXe_UNSPECIFIED_SOFT_TISSUE: + title: "IXe. Unspecified soft tissue sarcomas" + description: Soft tissue sarcomas, NOS. + meaning: NCIT:C9306 + annotations: + main_group: IX + + # ===== Group X: Germ cell tumors ===== + Xa_INTRACRANIAL_GERM_CELL: + title: "Xa. Intracranial and intraspinal germ cell tumors" + description: >- + CNS germ cell tumors including germinoma, teratoma, and + nongerminomatous germ cell tumors. + meaning: NCIT:C6286 + annotations: + main_group: X + icdo3_codes: "9060-9102" + Xb_EXTRACRANIAL_EXTRAGONADAL_GERM_CELL: + title: "Xb. Malignant extracranial and extragonadal germ cell tumors" + description: >- + Extracranial germ cell tumors not involving the gonads including + sacrococcygeal, retroperitoneal, and mediastinal germ cell tumors. + meaning: NCIT:C6545 + annotations: + main_group: X + Xc_GONADAL_GERM_CELL: + title: "Xc. Malignant gonadal germ cell tumors" + description: >- + Germ cell tumors of the ovary and testis including dysgerminoma, + yolk sac tumor, embryonal carcinoma, and mixed germ cell tumors. + meaning: NCIT:C3708 + annotations: + main_group: X + Xd_GONADAL_CARCINOMAS: + title: "Xd. Gonadal carcinomas" + description: Carcinomas arising in the ovary and testis. + meaning: NCIT:C3709 + annotations: + main_group: X + Xe_OTHER_GONADAL: + title: "Xe. Other and unspecified malignant gonadal tumors" + description: Other specified and unspecified gonadal tumors. + meaning: NCIT:C3708 + annotations: + main_group: X + + # ===== Group XI: Epithelial neoplasms and melanomas ===== + XIa_ADRENOCORTICAL_CARCINOMAS: + title: "XIa. Adrenocortical carcinomas" + description: Adrenocortical carcinoma. + meaning: NCIT:C9325 + annotations: + main_group: XI + icdo3_codes: "8370" + XIb_THYROID_CARCINOMAS: + title: "XIb. Thyroid carcinomas" + description: >- + Papillary thyroid carcinoma, follicular thyroid carcinoma, + and medullary thyroid carcinoma. + meaning: NCIT:C7510 + annotations: + main_group: XI + XIc_NASOPHARYNGEAL_CARCINOMAS: + title: "XIc. Nasopharyngeal carcinomas" + description: Nasopharyngeal carcinoma and related carcinomas. + meaning: NCIT:C3871 + annotations: + main_group: XI + XId_MALIGNANT_MELANOMAS: + title: "XId. Malignant melanomas" + description: Cutaneous and non-cutaneous malignant melanomas. + meaning: NCIT:C3224 + annotations: + main_group: XI + XIe_SKIN_CARCINOMAS: + title: "XIe. Skin carcinomas" + description: >- + Basal cell carcinoma, squamous cell carcinoma of skin, and + other skin carcinomas. + meaning: NCIT:C3372 + annotations: + main_group: XI + XIf_OTHER_CARCINOMAS: + title: "XIf. Other and unspecified carcinomas" + description: >- + Carcinomas at other sites and carcinomas, NOS. + meaning: NCIT:C3709 + annotations: + main_group: XI + + # ===== Group XII: Other and unspecified ===== + XIIa_OTHER_SPECIFIED: + title: "XIIa. Other specified malignant tumors" + description: >- + Malignant tumors not classifiable in groups I-XI but with + specified histology. + meaning: NCIT:C3262 + annotations: + main_group: XII + XIIb_OTHER_UNSPECIFIED: + title: "XIIb. Other unspecified malignant tumors" + description: Malignant tumors, NOS not classifiable in groups I-XI. + meaning: NCIT:C3262 + annotations: + main_group: XII diff --git a/src/valuesets/schema/medical/pediatric_oncology/staging/neuroblastoma.yaml b/src/valuesets/schema/medical/pediatric_oncology/staging/neuroblastoma.yaml new file mode 100644 index 00000000..8cee35a4 --- /dev/null +++ b/src/valuesets/schema/medical/pediatric_oncology/staging/neuroblastoma.yaml @@ -0,0 +1,312 @@ +name: neuroblastoma_staging +title: Neuroblastoma Staging Value Sets +description: >- + Staging systems for neuroblastoma including the International Neuroblastoma + Risk Group Staging System (INRGSS) and International Neuroblastoma Staging + System (INSS). INRGSS is the current standard (effective 2024+) based on + imaging and image-defined risk factors. INSS is the legacy surgical staging + system still used for historical data. +id: https://w3id.org/linkml/valuesets/medical/pediatric_oncology/staging/neuroblastoma +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + valuesets: https://w3id.org/valuesets/ + NCIT: http://purl.obolibrary.org/obo/NCIT_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ + seer: https://seer.cancer.gov/ +default_prefix: valuesets +enums: + INRGSSStage: + title: INRGSS Stage + description: >- + International Neuroblastoma Risk Group Staging System (INRGSS) stages. + A clinical staging system based on imaging and image-defined risk factors + (IDRFs), effective for diagnosis years 2024+. Allows staging before any + treatment, unlike the surgical INSS system. + status: RELEASED + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://staging.seer.cancer.gov/pediatric/input/1.0/neuroblastoma/inrgss/ + - https://pmc.ncbi.nlm.nih.gov/articles/PMC2650389/ + annotations: + source: SEER/INRG Task Force + effective_year: 2024 + staging_basis: imaging + permissible_values: + L1: + title: "L1 - Localized, no IDRFs" + description: >- + Localized tumor not involving vital structures as defined by the + list of image-defined risk factors and confined to one body + compartment (neck, chest, abdomen, or pelvis). + meaning: NCIT:C133427 + annotations: + localized: true + idrfs_present: false + L2: + title: "L2 - Localized, with IDRFs" + description: >- + Locoregional tumor with presence of one or more image-defined + risk factors. The tumor has not spread far from where it started + but has at least one IDRF. + meaning: NCIT:C133428 + annotations: + localized: true + idrfs_present: true + M: + title: "M - Metastatic" + description: >- + Distant metastatic disease (except as defined for MS). The tumor + has spread (metastasized) to distant parts of the body. + meaning: NCIT:C133429 + annotations: + metastatic: true + MS: + title: "MS - Metastatic special" + description: >- + Metastatic disease in children younger than 18 months with + metastases confined to skin, liver, and/or bone marrow (bone + marrow involvement limited to <10% tumor cells). This stage + has a favorable prognosis despite metastatic disease. + meaning: NCIT:C133430 + aliases: + - Stage 4S equivalent + annotations: + metastatic: true + special_category: true + age_restriction: "<18 months" + favorable_prognosis: true + + INSSStage: + title: INSS Stage + description: >- + International Neuroblastoma Staging System (INSS) stages. A post-surgical + staging system based on extent of tumor resection, lymph node involvement, + and metastatic spread. This is the legacy system; INRGSS is now preferred + for diagnosis years 2024+. + status: RELEASED + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.ncbi.nlm.nih.gov/books/NBK65747.5/table/CDR0000062786__725/ + - https://www.cancer.org/cancer/types/neuroblastoma/detection-diagnosis-staging/staging.html + annotations: + source: INSS Consensus Conference + staging_basis: surgical + legacy_system: true + permissible_values: + STAGE_1: + title: "Stage 1" + description: >- + Localized tumor with complete gross excision, with or without + microscopic residual disease; representative ipsilateral lymph + nodes negative for tumor microscopically. + meaning: NCIT:C6639 + annotations: + localized: true + resection: complete + STAGE_2A: + title: "Stage 2A" + description: >- + Localized tumor with incomplete gross excision; representative + ipsilateral nonadherent lymph nodes negative for tumor microscopically. + meaning: NCIT:C6640 + annotations: + localized: true + resection: incomplete + lymph_nodes: negative + STAGE_2B: + title: "Stage 2B" + description: >- + Localized tumor with or without complete gross excision, with + ipsilateral nonadherent lymph nodes positive for tumor. + Enlarged contralateral lymph nodes must be negative microscopically. + meaning: NCIT:C6641 + annotations: + localized: true + lymph_nodes: ipsilateral_positive + STAGE_3: + title: "Stage 3" + description: >- + Unresectable unilateral tumor infiltrating across the midline, + with or without regional lymph node involvement; or localized + unilateral tumor with contralateral regional lymph node involvement; + or midline tumor with bilateral extension by infiltration + (unresectable) or by lymph node involvement. + meaning: NCIT:C6642 + annotations: + localized: false + crosses_midline: true + STAGE_4: + title: "Stage 4" + description: >- + Any primary tumor with dissemination to distant lymph nodes, + bone, bone marrow, liver, skin, and/or other organs (except as + defined for stage 4S). + meaning: NCIT:C6643 + annotations: + metastatic: true + STAGE_4S: + title: "Stage 4S" + description: >- + Localized primary tumor (as defined for stage 1, 2A, or 2B) + with dissemination limited to skin, liver, and/or bone marrow + (limited to infants <1 year of age). Marrow involvement should + be minimal (<10% of total nucleated cells). + meaning: NCIT:C6644 + aliases: + - Special stage 4 + annotations: + metastatic: true + special_category: true + age_restriction: "<12 months" + favorable_prognosis: true + + NeuroblastomaRiskGroup: + title: Neuroblastoma Risk Group + description: >- + International Neuroblastoma Risk Group (INRG) pretreatment risk + classification groups. Combines INRGSS stage with tumor histology, + MYCN status, ploidy, and other prognostic factors. + status: RELEASED + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://pmc.ncbi.nlm.nih.gov/articles/PMC2650388/ + annotations: + source: INRG Task Force + permissible_values: + VERY_LOW: + title: Very Low Risk + description: >- + Very low risk neuroblastoma with excellent prognosis. Typically + includes L1 tumors and MS without MYCN amplification. + meaning: NCIT:C103236 + annotations: + expected_efs: ">85%" + LOW: + title: Low Risk + description: >- + Low risk neuroblastoma with favorable prognosis. Treatment + may include surgery alone or observation. + meaning: NCIT:C103237 + annotations: + expected_efs: ">75%" + INTERMEDIATE: + title: Intermediate Risk + description: >- + Intermediate risk neuroblastoma requiring multimodal treatment + including chemotherapy. + meaning: NCIT:C103238 + annotations: + expected_efs: "50-75%" + HIGH: + title: High Risk + description: >- + High risk neuroblastoma with poor prognosis. Requires intensive + multimodal therapy including high-dose chemotherapy with + autologous stem cell rescue, surgery, radiation, and + immunotherapy. + meaning: NCIT:C103239 + annotations: + expected_efs: "<50%" + mycn_amplified: often + + ImageDefinedRiskFactor: + title: Image-Defined Risk Factor + description: >- + Image-defined risk factors (IDRFs) used in INRGSS staging to determine + surgical risk. Presence of any IDRF upgrades a tumor from L1 to L2. + status: RELEASED + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://pmc.ncbi.nlm.nih.gov/articles/PMC2650389/ + annotations: + source: INRG Task Force + permissible_values: + IPSILATERAL_TUMOR_EXTENSION_TO_BODY_CAVITIES: + title: Ipsilateral tumor extension within two body compartments + description: >- + Tumor extension from neck to chest, chest to abdomen, + or abdomen to pelvis. + NECK_ENCASING_CAROTID_OR_VERTEBRAL: + title: Neck - Tumor encasing carotid and/or vertebral artery + description: Tumor encasing carotid artery and/or vertebral artery. + NECK_ENCASING_JUGULAR: + title: Neck - Tumor encasing internal jugular vein + description: Tumor encasing internal jugular vein. + NECK_EXTENDING_TO_SKULL_BASE: + title: Neck - Tumor extending to base of skull + description: Tumor extending to base of skull. + NECK_COMPRESSING_TRACHEA: + title: Neck - Tumor compressing trachea + description: Tumor compressing the trachea. + CERVICOTHORACIC_ENCASING_BRACHIAL_PLEXUS: + title: Cervico-thoracic junction - Tumor encasing brachial plexus roots + description: Tumor encasing brachial plexus roots (C5-T1). + CERVICOTHORACIC_ENCASING_SUBCLAVIAN: + title: Cervico-thoracic junction - Tumor encasing subclavian vessels + description: >- + Tumor encasing subclavian vessels and/or vertebral artery + and/or carotid artery. + CERVICOTHORACIC_COMPRESSING_TRACHEA: + title: Cervico-thoracic junction - Tumor compressing trachea + description: Tumor compressing the trachea. + THORAX_ENCASING_AORTA: + title: Thorax - Tumor encasing aorta and/or major branches + description: Tumor encasing aorta and/or major branches. + THORAX_COMPRESSING_TRACHEA_BRONCHI: + title: Thorax - Tumor compressing trachea and/or principal bronchi + description: Tumor compressing trachea and/or principal bronchi. + THORAX_LOWER_MEDIASTINUM_INFILTRATING: + title: Thorax - Lower mediastinal tumor infiltrating costo-vertebral junction + description: >- + Lower mediastinal tumor infiltrating the costo-vertebral junction + between T9 and T12. + THORACOABDOMINAL_ENCASING_AORTA_CELIAC: + title: Thoraco-abdominal - Tumor encasing aorta and/or vena cava + description: Tumor encasing the aorta and/or vena cava. + ABDOMEN_PELVIS_ENCASING_CELIAC_SMA: + title: Abdomen/pelvis - Tumor encasing celiac axis and/or SMA + description: >- + Tumor encasing celiac axis and/or superior mesenteric artery. + ABDOMEN_PELVIS_ENCASING_RENAL_VESSELS: + title: Abdomen/pelvis - Tumor encasing origin of renal vessels + description: Tumor encasing origin of renal vessels. + ABDOMEN_PELVIS_ENCASING_AORTA_IVC: + title: Abdomen/pelvis - Tumor encasing aorta and/or IVC + description: Tumor encasing aorta and/or inferior vena cava. + ABDOMEN_PELVIS_ENCASING_ILIAC_VESSELS: + title: Abdomen/pelvis - Tumor encasing iliac vessels + description: Tumor encasing iliac vessels. + ABDOMEN_PELVIS_PELVIC_CROSSING_SCIATIC_NOTCH: + title: Abdomen/pelvis - Pelvic tumor crossing sciatic notch + description: Pelvic tumor crossing the sciatic notch. + INTRASPINAL_EXTENSION: + title: Intraspinal tumor extension + description: >- + Intraspinal tumor extension provided that more than one third + of the spinal canal in the axial plane is invaded and/or the + perimedullary leptomeningeal spaces are not visible and/or + spinal cord signal is abnormal. + ADJACENT_ORGAN_INFILTRATION: + title: Infiltration of adjacent organs/structures + description: >- + Infiltration of adjacent organs/structures such as pericardium, + diaphragm, kidney, liver, duodeno-pancreatic block, and mesentery. diff --git a/src/valuesets/schema/units/quantity_kinds.yaml b/src/valuesets/schema/units/quantity_kinds.yaml new file mode 100644 index 00000000..8e1dd9ec --- /dev/null +++ b/src/valuesets/schema/units/quantity_kinds.yaml @@ -0,0 +1,419 @@ +name: quantity_kinds +title: QUDT Quantity Kinds Value Set +description: >- + Value set for physical quantity kinds based on QUDT (Quantities, Units, Dimensions and Types). + Quantity kinds represent the abstract type of a physical quantity, independent of its units. + For example, "length" is a quantity kind that can be measured in meters, feet, etc. +id: https://w3id.org/valuesets/units/quantity_kinds +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + valuesets: https://w3id.org/valuesets/ + quantitykind: http://qudt.org/vocab/quantitykind/ + PATO: http://purl.obolibrary.org/obo/PATO_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ +default_prefix: valuesets +slots: + quantity_kind: + description: The type of physical quantity being measured + range: QuantityKindEnum +enums: + QuantityKindEnum: + title: Quantity Kind + description: >- + Physical quantity kinds based on QUDT. These represent abstract types of + physical quantities independent of the units used to measure them. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + see_also: + - https://www.qudt.org/doc/DOC_VOCAB-QUANTITY-KINDS.html + permissible_values: + # SI Base Quantity Kinds + LENGTH: + title: length + description: A 1-D extent quality representing distance between two points + meaning: quantitykind:Length + exact_mappings: + - PATO:0000122 + annotations: + si_base: 'true' + dimension: L + MASS: + title: mass + description: The amount of matter in an object + meaning: quantitykind:Mass + exact_mappings: + - PATO:0000125 + annotations: + si_base: 'true' + dimension: M + TIME: + title: time + description: Duration or temporal extent + meaning: quantitykind:Time + exact_mappings: + - PATO:0001309 + annotations: + si_base: 'true' + dimension: T + pato_label: duration + THERMODYNAMIC_TEMPERATURE: + title: thermodynamic temperature + description: The thermal energy of a system + meaning: quantitykind:ThermodynamicTemperature + exact_mappings: + - PATO:0000146 + annotations: + si_base: 'true' + dimension: Θ + pato_label: temperature + AMOUNT_OF_SUBSTANCE: + title: amount of substance + description: The number of elementary entities (atoms, molecules, etc.) + meaning: quantitykind:AmountOfSubstance + close_mappings: + - PATO:0000070 + annotations: + si_base: 'true' + dimension: N + pato_label: amount + ELECTRIC_CURRENT: + title: electric current + description: Flow of electric charge per unit time + meaning: quantitykind:ElectricCurrent + annotations: + si_base: 'true' + dimension: I + LUMINOUS_INTENSITY: + title: luminous intensity + description: Luminous power per unit solid angle emitted by a point light source + meaning: quantitykind:LuminousIntensity + close_mappings: + - PATO:0001718 + annotations: + si_base: 'true' + dimension: J + pato_label: luminance + + # Derived Geometric Quantity Kinds + AREA: + title: area + description: A 2-D extent representing the size of a surface + meaning: quantitykind:Area + exact_mappings: + - PATO:0001323 + annotations: + dimension: L² + VOLUME: + title: volume + description: A 3-D extent representing the amount of space occupied + meaning: quantitykind:Volume + exact_mappings: + - PATO:0000918 + annotations: + dimension: L³ + ANGLE: + title: plane angle + description: The figure formed by two rays sharing a common endpoint + meaning: quantitykind:Angle + exact_mappings: + - PATO:0002326 + annotations: + dimension: dimensionless + SOLID_ANGLE: + title: solid angle + description: A 3-D angular measure + meaning: quantitykind:SolidAngle + annotations: + dimension: dimensionless + + # Mechanical Quantity Kinds + VELOCITY: + title: velocity + description: Rate of change of position with direction + meaning: quantitykind:Velocity + exact_mappings: + - PATO:0002242 + annotations: + dimension: L·T⁻¹ + SPEED: + title: speed + description: Scalar rate of change of position + meaning: quantitykind:Speed + exact_mappings: + - PATO:0000008 + annotations: + dimension: L·T⁻¹ + ACCELERATION: + title: acceleration + description: Rate of change of velocity + meaning: quantitykind:Acceleration + exact_mappings: + - PATO:0001028 + annotations: + dimension: L·T⁻² + FORCE: + title: force + description: Rate of change of momentum + meaning: quantitykind:Force + exact_mappings: + - PATO:0001035 + annotations: + dimension: M·L·T⁻² + PRESSURE: + title: pressure + description: Force per unit area + meaning: quantitykind:Pressure + exact_mappings: + - PATO:0001025 + annotations: + dimension: M·L⁻¹·T⁻² + ENERGY: + title: energy + description: Capacity to do work + meaning: quantitykind:Energy + exact_mappings: + - PATO:0001021 + annotations: + dimension: M·L²·T⁻² + WORK: + title: work + description: Energy transferred by a force + meaning: quantitykind:Work + exact_mappings: + - PATO:0001026 + annotations: + dimension: M·L²·T⁻² + POWER: + title: power + description: Rate of doing work or transferring energy + meaning: quantitykind:Power + exact_mappings: + - PATO:0001024 + annotations: + dimension: M·L²·T⁻³ + MOMENTUM: + title: momentum + description: Product of mass and velocity + meaning: quantitykind:Momentum + exact_mappings: + - PATO:0001023 + annotations: + dimension: M·L·T⁻¹ + TORQUE: + title: torque + description: Rotational force or moment of force + meaning: quantitykind:Torque + annotations: + dimension: M·L²·T⁻² + ANGULAR_VELOCITY: + title: angular velocity + description: Rate of change of angular position + meaning: quantitykind:AngularVelocity + annotations: + dimension: T⁻¹ + ANGULAR_ACCELERATION: + title: angular acceleration + description: Rate of change of angular velocity + meaning: quantitykind:AngularAcceleration + exact_mappings: + - PATO:0001350 + annotations: + dimension: T⁻² + + # Material Property Quantity Kinds + DENSITY: + title: density + description: Mass per unit volume + meaning: quantitykind:Density + exact_mappings: + - PATO:0001019 + annotations: + dimension: M·L⁻³ + pato_label: mass density + VISCOSITY: + title: dynamic viscosity + description: Internal resistance to flow + meaning: quantitykind:DynamicViscosity + exact_mappings: + - PATO:0000992 + annotations: + dimension: M·L⁻¹·T⁻¹ + KINEMATIC_VISCOSITY: + title: kinematic viscosity + description: Dynamic viscosity divided by density + meaning: quantitykind:KinematicViscosity + annotations: + dimension: L²·T⁻¹ + + # Frequency and Time-Related Quantity Kinds + FREQUENCY: + title: frequency + description: Number of repetitive events per unit time + meaning: quantitykind:Frequency + exact_mappings: + - PATO:0000044 + annotations: + dimension: T⁻¹ + + # Concentration Quantity Kinds + MASS_CONCENTRATION: + title: mass concentration + description: Mass of a substance per unit volume + meaning: quantitykind:MassConcentration + exact_mappings: + - PATO:0000033 + annotations: + dimension: M·L⁻³ + pato_label: concentration of + AMOUNT_CONCENTRATION: + title: amount concentration + description: Amount of substance per unit volume (molarity) + meaning: quantitykind:AmountConcentration + close_mappings: + - PATO:0000033 + annotations: + dimension: N·L⁻³ + + # Electromagnetic Quantity Kinds + ELECTRIC_CHARGE: + title: electric charge + description: Fundamental property of matter causing electromagnetic interaction + meaning: quantitykind:ElectricCharge + exact_mappings: + - PATO:0002193 + annotations: + dimension: I·T + ELECTRIC_POTENTIAL: + title: electric potential + description: Potential energy per unit charge (voltage) + meaning: quantitykind:ElectricPotential + exact_mappings: + - PATO:0001464 + aliases: + - voltage + annotations: + dimension: M·L²·T⁻³·I⁻¹ + ELECTRIC_RESISTANCE: + title: electric resistance + description: Opposition to electric current flow + meaning: quantitykind:Resistance + annotations: + dimension: M·L²·T⁻³·I⁻² + ELECTRICAL_CONDUCTIVITY: + title: electrical conductivity + description: Ability to conduct electric current + meaning: quantitykind:Conductivity + exact_mappings: + - PATO:0001757 + annotations: + dimension: I²·T³·M⁻¹·L⁻³ + CAPACITANCE: + title: capacitance + description: Ability to store electric charge + meaning: quantitykind:Capacitance + annotations: + dimension: I²·T⁴·M⁻¹·L⁻² + INDUCTANCE: + title: inductance + description: Property relating magnetic flux to electric current + meaning: quantitykind:Inductance + annotations: + dimension: M·L²·T⁻²·I⁻² + MAGNETIC_FLUX: + title: magnetic flux + description: Measure of total magnetic field passing through a surface + meaning: quantitykind:MagneticFlux + annotations: + dimension: M·L²·T⁻²·I⁻¹ + MAGNETIC_FLUX_DENSITY: + title: magnetic flux density + description: Magnetic flux per unit area + meaning: quantitykind:MagneticFluxDensity + annotations: + dimension: M·T⁻²·I⁻¹ + + # Thermal Quantity Kinds + HEAT_CAPACITY: + title: heat capacity + description: Heat required to raise temperature by one unit + meaning: quantitykind:HeatCapacity + annotations: + dimension: M·L²·T⁻²·Θ⁻¹ + SPECIFIC_HEAT_CAPACITY: + title: specific heat capacity + description: Heat capacity per unit mass + meaning: quantitykind:SpecificHeatCapacity + annotations: + dimension: L²·T⁻²·Θ⁻¹ + THERMAL_CONDUCTIVITY: + title: thermal conductivity + description: Ability to conduct heat + meaning: quantitykind:ThermalConductivity + exact_mappings: + - PATO:0001756 + annotations: + dimension: M·L·T⁻³·Θ⁻¹ + pato_label: heat conductivity + + # Optical Quantity Kinds + LUMINOUS_FLUX: + title: luminous flux + description: Total perceived light power emitted + meaning: quantitykind:LuminousFlux + exact_mappings: + - PATO:0001296 + annotations: + dimension: J + ILLUMINANCE: + title: illuminance + description: Luminous flux per unit area + meaning: quantitykind:Illuminance + annotations: + dimension: J·L⁻² + RADIANT_INTENSITY: + title: radiant intensity + description: Radiant power per unit solid angle + meaning: quantitykind:RadiantIntensity + annotations: + dimension: M·L²·T⁻³ + + # Radioactivity Quantity Kinds + ACTIVITY: + title: activity (radioactivity) + description: Number of nuclear disintegrations per unit time + meaning: quantitykind:Activity + annotations: + dimension: T⁻¹ + ABSORBED_DOSE: + title: absorbed dose + description: Energy deposited per unit mass by ionizing radiation + meaning: quantitykind:AbsorbedDose + annotations: + dimension: L²·T⁻² + DOSE_EQUIVALENT: + title: dose equivalent + description: Absorbed dose weighted by radiation type + meaning: quantitykind:DoseEquivalent + annotations: + dimension: L²·T⁻² + + # Information Quantity Kinds + INFORMATION_ENTROPY: + title: information entropy + description: Measure of information content or uncertainty + meaning: quantitykind:InformationEntropy + annotations: + dimension: dimensionless + DATA_RATE: + title: data rate + description: Amount of data transferred per unit time + meaning: quantitykind:DataRate + annotations: + dimension: T⁻¹ diff --git a/src/valuesets/schema/valuesets.yaml b/src/valuesets/schema/valuesets.yaml index 7f920d62..067a4534 100644 --- a/src/valuesets/schema/valuesets.yaml +++ b/src/valuesets/schema/valuesets.yaml @@ -83,10 +83,14 @@ imports: - medical/clinical - medical/neuroimaging - medical/family_history +- medical/pediatric_oncology/diagnosis_categories +- medical/pediatric_oncology/iccc3 +- medical/pediatric_oncology/staging/neuroblastoma - clinical/nih_demographics - clinical/phenopackets - bioprocessing/scale_up - units/measurements +- units/quantity_kinds - computing/file_formats - computing/maturity_levels - computing/ontologies