bwalsh
commented
7 years ago We are having trouble match the following Primary Tumor type values in the disease ontology.
For example, should entries separated by semi-colons (ex: Liposarcoma;Lymphoma;Any cancer type) be read as (Liposarcoma OR Lymphoma OR Any cancer type) ?
| association.phenotype.description.keyword: Descending | Count |
|---|---|
| Any cancer type | 142 |
| Non-small cell lung | 66 |
| Gastrointestinal stromal | 60 |
| Ovary | 29 |
| Malignant peripheral nerve sheat tumor | 18 |
| Lung squamous cell | 17 |
| Renal | 16 |
| Thyroid | 12 |
| Bladder BLCA | 10 |
| Head an neck | 8 |
| Myelodisplasic proliferative syndrome | 8 |
| Breast;Any cancer type | 7 |
| Head an neck squamous | 7 |
| Thymic | 7 |
| Billiary tract | 6 |
| Glioma;Any cancer type | 6 |
| Non-small cell lung;Lagerhans cell histiocytosis;Erdheim-Chester histiocytosis | 6 |
| Prostate adenocarcinoma PRAD | 6 |
| Hepatic carcinoma | 5 |
| Chronic myeloid leukemia;Acute lymphoblastic leukemia | 4 |
| Liposarcoma;Lymphoma;Any cancer type | 4 |
| Malignant rhabdoid tumor | 4 |
| Mesothelioma | 4 |
| B cell lymphoma | 3 |
| Hematologic malignancies | 3 |
| Megakaryoblastic leukemia | 3 |
| Glioma;Leukemia | 2 |
| Glioma;Malignant peripheral nerve sheat tumor;Leukemia | 2 |
| Head an neck;Salivary glands | 2 |
| Malignant astrocytoma | 2 |
| Mesothelioma;Ovary | 2 |
| Myelodisplasic syndrome;Myelodisplasic proliferative syndrome | 2 |
| Non-small cell lung;Lung adenocarcinoma | 2 |
| Ovary;Any cancer type | 2 |
| Plexiform neurofibroma;Malignant peripheral nerve sheat tumor | 2 |
| Renal;Any cancer type | 2 |
| Schwannoma;Meningioma | 2 |
| Schwannoma;Neurofibroma | 2 |
| Stomach;Gastroesophageal junction adenocarcinoma | 2 |
| Thyroid;Glioma;Lung;Ovary;Breast;Any cancer type;Endometrium | 2 |
| Acute myeloid leukemia;Acute lymphoblastic leukemia;Myelodisplasic syndrome | 1 |
| Acute myeloid leukemia;Cervix;Ovary | 1 |
| Acute myeloid leukemia;Lung adenocarcinoma;Acute lymphoblastic leukemia | 1 |
| Acute myeloid leukemia;Myelodisplasic proliferative syndrome | 1 |
| Angiosarcoma;Renal | 1 |
| Basal cell carcinoma;Medulloblastoma | 1 |
| Bladder;Head an neck;Lung | 1 |
| Breast;Lung adenocarcinoma | 1 |
| Breast;Ovary;Cervix squamous cell;Endometrium | 1 |
| Breast;Stomach | 1 |
| Cervix | 1 |
| Cervix squamous cell | 1 |
| Colorectal adenocarcinoma COREAD | 1 |
| Colorectal adenocarcinoma;Inflammatory myofibroblastic | 1 |
| Cutaneous melanoma;Lung adenocarcinoma;Prostate adenocarcinoma | 1 |
| Cutaneous melanoma;Renal;Any cancer type BLCA | 1 |
| Cutaneous melanoma;Thyroid | 1 |
| Endometrium;Lung | 1 |
| Endometrium;Myeloma | 1 |
| Female germ cell tumor;Male germ cell tumor | 1 |
| Gastrointestinal stromal;Myelodisplasic syndrome;Myelodisplasic proliferative syndrome;Hyper eosinophilic advanced snydrome;Eosinophilic chronic leukemia;Chronic myeloid leukemia;Acute lymphoblastic leukemia;Systemic mastocytosis | 1 |
| Giant cell astrocytoma | 1 |
| Glioma;Thyroid carcinoma | 1 |
| Hyper eosinophilic advanced snydrome | 1 |
| Hyper eosinophilic advanced snydrome;Eosinophilic chronic leukemia | 1 |
| Inflammatory myofibroblastic | 1 |
| Inflammatory myofibroblastic;Thyroid carcinoma | 1 |
| Lung adenocarcinoma;Cutaneous melanoma;Prostate adenocarcinoma | 1 |
| Lung adenocarcinoma;Hairy-Cell leukemia;Myeloma | 1 |
| Lung adenocarcinoma;Stomach | 1 |
| Lung adenocarcinoma;Thyroid | 1 |
| Lung;Billiary tract | 1 |
| Lung;Colorectal adenocarcinoma | 1 |
| Lymphoma;Glioblastoma | 1 |
| Male germ cell tumor | 1 |
| Mantle cell lymphoma;Chronic lymphocytic leukemia | 1 |
| Myeloma;Neuroblastoma | 1 |
| Non-small cell lung;Colorectal adenocarcinoma | 1 |
| Pediatric glioma | 1 |
| Prostate adenocarcinoma PR | 1 |
| Prostate adenocarcinoma;Any cancer type | 1 |
| Prostate adenocarcinoma;Pancreas adenocarcinoma | 1 |
| Renal R | 1 |
| Renal angiomyolipoma RA | 1 |
| Renal angiomyolipoma;Giant cell astrocytoma RA | 1 |
| Sarcoma;Stomach | 1 |
| Solid tumors | 1 |
| Stomach;Adrenal gland | 1 |
| Stomach;Prostate adenocarcinoma | 1 |
| Urinary tract carcinoma | 1 |
DavidTamborero
Currently, CGI uses abbreviations that are not recognized by our normalization routines as phenotypes, which leads to high normalization failure rates.
Contact David Tamborero for mappings.