Merge pull request #39 from linkml/add-qudt-quantity-kinds

Add QUDT QuantityKinds value set

Author: dragon-ai-agent

src/valuesets/enums/medical/oncology/__init__.py

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+"""Auto-generated package."""

src/valuesets/enums/medical/oncology/icdo.py

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+"""
+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",
+]

src/valuesets/enums/medical/pediatric_oncology/__init__.py

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+"""Auto-generated package."""