uberon mappings and labels

src/fetch_tissue_data/run_breast.py

@@ -6,16 +6,18 @@
 
 table_importer: CdaTableImporter = configure_cda_table_importer()
 
-Tsite = Q('primary_diagnosis_site = "%breast%"', )
-cohort_name = 'Breast'
-p = table_importer.get_ga4gh_phenopackets(Tsite, cohort_name=cohort_name)
+Tsite_breast = Q('primary_diagnosis_site = "%breast%"')
+cohort_name_breast = 'Breast'
+p_breast = table_importer.get_ga4gh_phenopackets(Tsite_breast, cohort_name=cohort_name_breast)
 
-result_dir = os.path.abspath(os.path.join('phenopackets', cohort_name))
-os.makedirs(result_dir, exist_ok=True)
 
-print(f'Writing {len(p)} phenopackets to {result_dir}')
-for pp in p:
-    file_path = os.path.join(result_dir, f'{pp.id}.json')
+result_dir_breast = os.path.abspath(os.path.join('phenopackets', cohort_name_breast))
+os.makedirs(result_dir_breast, exist_ok=True)
+
+# Writing phenopackets for Breast tissue
+print(f'Writing {len(p_breast)} phenopackets to {result_dir_breast}')
+for pp in p_breast:
+    file_path = os.path.join(result_dir_breast, f'{pp.id}.json')
     with open(file_path, 'w') as fh:
         json = MessageToJson(pp)
         fh.write(json)

src/oncoexporter/cda/mapper/op_uberon_mapper.py

@@ -22,7 +22,19 @@ def __init__(self):
             "uterine cervix": "UBERON:0000002",
             "uterus": "UBERON:0000995",
             "body of uterus": "UBERON:0009853",
-            "lower respiratory tract": "UBERON:0001558"
+            "lower respiratory tract": "UBERON:0001558",
+            'breast': 'UBERON:0000310',
+            'bone marrow': 'UBERON:0002371',
+            'bone': 'UBERON:0002481',
+            'brain': 'UBERON:0000955',
+            'colon': 'UBERON:0001155',
+            'heart': 'UBERON:0000948',
+            'kidney': 'UBERON:0002113',
+            'adrenal gland': 'UBERON:0002369',
+            'liver': 'UBERON:0002107',
+            'pancreas': 'UBERON:0001264',
+            'skin': 'UBERON:0002097',
+            'thyroid gland': 'UBERON:0002046'
         }
         self._site_to_uberon_label_d = {
             "Lung": "lung",
@@ -39,6 +51,66 @@ def __init__(self):
             "Bronchus and lung": "lower respiratory tract",
             "Lung/Bronchus": "lower respiratory tract",
             "Lung/Bronchus, Unknown": "lower respiratory tract",
+            "Breast": "breast", 
+            "Breast, NOS": "breast",
+            "Breast, Unknown": "breast",
+            "Bone marrow": "bone marrow", 
+            "Bone Marrow": "bone marrow",
+            "Bones, joints and articular cartilage of other and unspecified sites": "bone",
+            "Bones, joints and articular cartilage of limbs": "bone",
+            "Bones of skull and face and associated joints (excludes mandible C41.1)": "bone",
+            "Long bones of lower limb and associated joints": "bone",
+            "Long bones of upper limb, scapula and  associated joints": 'bone',
+            "Pelvic bones, sacrum, coccyx and associated joints": "bone",
+            "Bone, NOS" : 'bone',
+            "Bone": "bone",
+            "Bones": "bone",
+            "Brain": "brain",
+            "Brain, NOS": "brain",
+            "Brain, Unknown": "brain",
+            "Overlapping lesion of brain and central nervous system": "brain",
+            "Overlapping lesion of brain": "brain",
+            "Brain stem": "brain",
+            "Colon": "colon",
+            "Colon, NOS": "colon",
+            "Colon, Unknown": "colon",
+            "Heart, mediastinum, and pleura": "heart",
+            "Connective, subcutaneous and other soft tissues of thorax (excludes thymus C37.9, heart and mediastinum C38._)": "heart",
+            "Kidney": "kidney",
+            "Kidney, NOS": "kidney",
+            "Kidney, Unknown": "kidney",
+            "Renal pelvis": "kidney",
+            "Renal Pelvis": "kidney",
+            "Adrenal gland": "adrenal gland",
+            "Adrenal Gland": "adrenal gland",
+            "Adrenal gland, NOS": "adrenal gland",
+            "Adrenal gland, Unknown": "adrenal gland",
+            "Liver and intrahepatic bile ducts": "liver",
+            "Liver": "liver",
+            "Intrahepatic bile ducts": "liver",
+            "Pancreas": "pancreas",
+            "Pancreas, NOS": "pancreas",
+            "Pancreas, Unknown": "pancreas",
+            "Pancreatic duct": "pancreas",
+            "Skin": "skin",
+            "Skin, NOS": "skin",
+            "Skin, Unknown": "skin",
+            "Connective, subcutaneous and other soft tissues": "skin",
+            "Connective, subcutaneous and other soft tissues of pelvis": "skin",
+            "Connective, subcutaneous and other soft tissues of lower limb and hip": "skin",
+            "Connective, subcutaneous and other soft tissues, NOS": "skin",
+            "Connective, subcutaneous and other soft tissues of upper limb and shoulder": "skin",
+            "Connective, subcutaneous and other soft tissues of head, face, and neck (excludes connective tissue of orbit C69.6 and nasal cartilage C30.0)": "skin",
+            "Skin of scalp and neck": "skin",
+            "Skin of lower limb and hip": "skin",
+            "Connective, subcutaneous and other soft tissues of abdomen": "skin",
+            "Connective, subcutaneous and other soft tissues of trunk, NOS": "skin",
+            "Skin, NOS (excludes skin of labia majora C51.0, skin of vulva C51.9, skin of penis C60.9 and skin of scrotum C63.2)": "skin",
+            "Thyroid gland": "thyroid gland",
+            "Thyroid Gland": "thyroid gland",
+            "Thyroid gland, NOS": "thyroid gland",
+            "Thyroid gland, Unknown": "thyroid gland",
+            "Thyroid Gland, Unknown": "thyroid gland",
         }
 
     def get_ontology_term(self, row: pd.Series) -> Optional[PPkt.OntologyClass]:
@@ -54,4 +126,3 @@ def get_ontology_term(self, row: pd.Series) -> Optional[PPkt.OntologyClass]:
         else:
             # TODO -- more robust error handling in final release, but for development fail early
             raise ValueError(f"Could not find UBERON term for primary_site=\"{primary_site}\"")
-