Merge pull request #419 from ncihtan/392-update-permissible-value-lis…

…t-for-clinical-tier-1-diagnosis-precancerous-condition-type

Add Precancerous Condition Type valid values

HTAN.model.csv

@@ -667,7 +667,7 @@ Tumor Extranodal Extension Indicator,The indicator to determine extranodal invol
 Satellite Metastasis Present Indicator,A yes/no indicator to ask if intransit metastases or satellite lesions are present.,"Yes, No, unknown",,,FALSE,Diagnosis,,,
 Other Biopsy Resection Site,A description of the location on or within the human body where the surgical biopsy/resection procedure was performed (Not covered under HTAN Clinical Data Tier 1),,,,FALSE,Diagnosis,,,
 Extent of Tumor Resection,"The degree to which the lesion has been cut out, or resected.","Gross Total Resection, Open Biopsy, Subtotal Resection, Extensive Subtotal, Minor, Optimal debulking, Other, Partial debulking, Segmental, Suboptimal, Suboptimal debulking, NTR, unknown, Not Reported, Not Applicable      ",,,FALSE,Diagnosis,,,
-Precancerous Condition Type,The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).,"Ductal Carcinoma In Situ,Pancreatic Intraductal Papillary-Mucinous Neoplasm,Atypical Adenomatous Lung Hyperplasia,Other,Pancreatic Intraepithelial Neoplasia,Prostatic Intraepithelial Neoplasia,Melanocytic hyperplasia,Atypical melanocytic proliferation,Melanoma in situ,Superficial spreading,Melanoma in situ,Lentigo maligna type,Melanoma in situ,Acral-lentiginous,Melanoma in situ arising in a giant congenital nevus,Persistent melanoma in situ,Melanoma in situ not otherwise classified,Scar - no residual melanoma,Invasive melanoma - superficial spreading,Invasive melanoma - nodular type,Invasive melanoma - lentigo maligna,Invasive melanoma - acral lentiginous,Invasive melanoma - desmoplastic,Invasive melanoma - nevoid,Invasive melanoma,Normal WDA,Reserve cell hyperplasia,Squamous metaplasia - mature,Squamous metaplasia - immature,Mild dysplasia,Moderate dysplasia,Severe dysplasia,Atypical adenomatous hyperplasia,Adenocarcinoma in situ - non mucinous,Adenocarcinoma in situ - mucinous,Benign tumor NOS,Hamartoma,Carcinoma NOS,No diagnosis possible, Not Applicable",,,FALSE,Diagnosis,,,
+Precancerous Condition Type,The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).,"Ductal Carcinoma In Situ,Pancreatic Intraductal Papillary-Mucinous Neoplasm,Atypical Adenomatous Lung Hyperplasia,Other,Pancreatic Intraepithelial Neoplasia,Prostatic Intraepithelial Neoplasia,Melanocytic hyperplasia,Atypical melanocytic proliferation,Melanoma in situ,Superficial spreading,Melanoma in situ,Lentigo maligna type,Melanoma in situ,Acral-lentiginous,Melanoma in situ arising in a giant congenital nevus,Persistent melanoma in situ,Melanoma in situ not otherwise classified,Scar - no residual melanoma,Invasive melanoma - superficial spreading,Invasive melanoma - nodular type,Invasive melanoma - lentigo maligna,Invasive melanoma - acral lentiginous,Invasive melanoma - desmoplastic,Invasive melanoma - nevoid,Invasive melanoma,Normal WDA,Reserve cell hyperplasia,Squamous metaplasia - mature,Squamous metaplasia - immature,Mild dysplasia,Moderate dysplasia,Severe dysplasia,Atypical adenomatous hyperplasia,Adenocarcinoma in situ - non mucinous,Adenocarcinoma in situ - mucinous,Benign tumor NOS,Hamartoma,Carcinoma NOS, Normal, Squamous carcinoma in situ, Neuroendocrine cell hyperplasia, No diagnosis possible, Not Applicable",,,FALSE,Diagnosis,,,
 Prior Sites of Radiation,The anatomic location to which radiation treatment was administered to a patient prior to enrollment on a protocol.,"Abdomen total,Abdominal Wall,Acetabulum,Adenoid,Adipose,Adrenal,Alveolar Ridge,Amniotic Fluid,Ampulla of Vater,Anal Sphincter,Ankle,Anorectum,Antecubital Fossa,Antrum,Anus,Aorta,Aortic Body,Appendix,Aqueous Fluid,Arm,Artery,Ascending Colon,Ascending Colon Hepatic Flexure,Ascites,Auditory Canal,Autonomic Nervous System,Axilla,Back,Bile Duct,Bladder,Blood,Blood Vessel,Body total,Bone,Bone Marrow,Bone non-spine,Bowel,Brain,Brain Stem,Breast,Broad Ligament,Bronchiole,Bronchus,Brow,Buccal Cavity,Buccal Mucosa,Buttock,Calf,Capillary,Cardia,Carina,Carotid Artery,Carotid Body,Cartilage,Cecum,Cell-Line,Central Nervous System,Cerebellum,Cerebral Cortex,Cerebrospinal Fluid,Cerebrum,Cervical Spine,Cervix,Chest,Chest Wall,Chin,Clavicle,Clitoris,Colon,Colon Mucosa Only,Common Duct,Conjunctiva,Connective Tissue,Dermal,Descending Colon,Diaphragm,Distant Site,Duodenum,Ear,Ear Canal,Ear Pinna (External),Elbow,Endocrine Gland,Epididymis,Epidural Space,Epitrochlear,Esophagogastric Junction,Esophagus,Esophagus Mucosa Only,Eye,Fallopian Tube,Femoral Artery,Femoral Vein,Femur,Fibroblasts,Fibula,Finger,Floor of Mouth,Fluid,Foot,Forearm,Forehead,Foreskin,Frontal Cortex,Frontal Lobe,Fundus of Stomach,Gallbladder,Ganglia,Gastroesophageal Junction,Gastrointestinal Tract,Gastrointestinal Intestine,Genitourinary NOS,Groin,Gum,Hand,Hard Palate,Head Face Or Neck Nos,Head and Neck,Heart,Hepatic,Hepatic Duct,Hepatic Vein,Hilar,Hip,Hippocampus,Humerus,Hypopharynx,Ileocecal Valve,Ileum,Ilium,Index Finger,Ischium,Islet Cells,Jaw,Jejunum,Joint,Kidney,Knee,Lacrimal Gland,Large Bowel,Laryngopharynx,Larynx,Leg,Leptomeninges,Ligament,Lip,Liver,Lumbar Spine,Lung,Lymph Node,Lymph Node(s) Axilla,Lymph Node(s) Cervical,Lymph Node(s) Distant,Lymph Node(s) Epitrochlear,Lymph Node(s) Femoral,Lymph Node(s) Hilar,Lymph Node(s) Iliac-Common,Lymph Node(s) Iliac-External,Lymph Node(s) Inguinal,Lymph Node(s) Internal Mammary,Lymph Node(s) Mammary,Lymph Node(s) Mediastinal,Lymph Node(s) Mesenteric,Lymph Node(s) Occipital,Lymph Node(s) Paraaortic,Lymph Node(s) Parotid,Lymph Node(s) Pelvic,Lymph Node(s) Popliteal,Lymph Node(s) Regional,Lymph Node(s) Retroperitoneal,Lymph Node(s) Scalene,Lymph Node(s) Splenic,Lymph Node(s) Subclavicular,Lymph Node(s) Submandibular,Lymph Node(s) Supraclavicular,Mandible,Mantle,Maxilla,Mediastinal Soft Tissue,Mediastinum,Mesentery,Mesothelium,Middle Finger,Mitochondria,Muscle,Nails,Nasal Cavity,Nasal Soft Tissue,Nasopharynx,Neck,Nerve,Nerve(s) Cranial,Occipital Cortex,Ocular Orbits,Omentum,Oral Cavity,Oral Cavity Mucosa Only,Oropharynx,Other,Ovary,Palate,Pancreas,Parametrium,Paraspinal Ganglion,Parathyroid,Parotid Gland,Patella,Pelvis,Penis,Pericardium,Periorbital Soft Tissue,Peritoneal Cavity,Peritoneum,Pharynx,Pineal,Pineal Gland,Pituitary Gland,Placenta,Pleura,Popliteal Fossa,Pouch,Primary Tumor Field,Primary tumor site,Prostate,Prostate Bed,Prostate Seminal Vesicles and Lymph Nodes,Pylorus,Rectosigmoid Junction,Rectum,Regional Site,Retina,Retro-Orbital Region,Retroperitoneum,Rib,Ring Finger,Round Ligament,Sacrum,Salivary Gland,Scalp,Scapula,Sciatic Nerve,Scrotum,Seminal Vesicle,Shoulder,Sigmoid Colon,Sinus,Sinus(es) Maxillary,Skeletal Muscle,Skin,Skin lower extremity local,Skin total,Skin trunk local,Skin upper extremity local,Skull,Small Bowel,Small Bowel Mucosa Only,Small Finger,Soft Tissue,Spinal Column,Spinal Cord,Spine,Spleen,Splenic Flexure,Sternum,Stomach,Stomach Mucosa Only,Subcutaneous Tissue,Synovium,Temporal Cortex,Tendon,Testis,Thigh,Thoracic Spine,Thorax,Throat,Thumb,Thymus,Thyroid,Tibia,Tongue,Tonsil,Tonsil (Pharyngeal),Trachea / Major Bronchi,Transverse Colon,Trunk,Umbilical Cord,unknown,Ureter,Urethra,Urinary Tract,Uterus,Uvula,Vagina,Vas Deferens,Vein,Venous,Vertebra,Vulva,White Blood Cells,Wrist,Not Reported",,,FALSE,Therapy,,,
 Immunosuppression,The indicator that describes whether or not immunosuppressive therapy was administered.,"Yes, No, unknown, Not Applicable, Not Done",,,FALSE,Therapy,,,
 Concomitant Medication Received Type,An enumerated list of the type of concomitant medication received by the patient.,"Anticoagulant agents,Anticonvulsant,Antifungal,Antiplatelet agents,Antidepressants-Moderate CYP2D6 inhibitors,Antidepressants-Strong CYP2D6 inhibitors,Antidepressants-weak CYP2D2 inhibitors or non-inhibitors,Anxiolytics or sedatives,Aspirin,Bisphosphonates for treatment/prevention of bone loss,Corticosteroid,COX-2 inhibitor,Decadron,Diabetes-Insulin,Diabetes-Metformin containing agents,Growth factor,Intravaginal estrogen preparations,Lipid-lowering drugs,Non-prescription supplements for memory,Non-prescription supplements for relief of hot flashes,Non-steroidal anti-inflammatory agents,Opioids,Other,Prescription medications for memory,Prescription medications for relief of hot flashes,Prophylactic antiplatelet therapy,Tricyclic antidepressants,Not Applicable,unknown,Not Reported",,,FALSE,Therapy,,,

HTAN.model.jsonld

@@ -26784,6 +26784,15 @@
                 {
                     "@id": "bts:CarcinomaNOS"
                 },
+                {
+                    "@id": "bts:Normal"
+                },
+                {
+                    "@id": "bts:Squamouscarcinomainsitu"
+                },
+                {
+                    "@id": "bts:Neuroendocrinecellhyperplasia"
+                },
                 {
                     "@id": "bts:Nodiagnosispossible"
                 },
@@ -61359,6 +61368,9 @@
                 },
                 {
                     "@id": "bts:TestResult"
+                },
+                {
+                    "@id": "bts:PrecancerousConditionType"
                 }
             ],
             "schema:isPartOf": {
@@ -106028,6 +106040,40 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:Squamouscarcinomainsitu",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "Squamouscarcinomainsitu",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:PrecancerousConditionType"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Squamous carcinoma in situ",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:Neuroendocrinecellhyperplasia",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "Neuroendocrinecellhyperplasia",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:PrecancerousConditionType"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Neuroendocrine cell hyperplasia",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:Abdomentotal",
             "@type": "rdfs:Class",