| """Populated extractions for each record type's extracted dictionary (#237, Phase B). |
| |
| A record type's *extracted dictionary* is the set of fields that source supplies. This module holds a |
| committed, de-identified sample of that dictionary per record type, each value carrying the evidence that |
| supports it (invariant 2: no value without its evidence). The samples were assembled in-conversation, not |
| through the extraction API, so the seed is reproducible from the committed data alone: |
| |
| - `pathology_extraction`: twenty-five fields read from twenty TCGA-UCEC pathology reports (eight checklist |
| fields plus seventeen further report fields: IHC, tumour size, adnexal/ovarian, lymph-node detail); evidence |
| is the verbatim report snippet. |
| - `clinical_join`: outcome, follow-up, and treatment fields derived from the real GDC longitudinal join; |
| evidence names the GDC record. |
| - `registry_join` / `local_research`: small illustrative samples, since those external sources are not part |
| of the open TCGA-UCEC corpus; evidence says so. |
| |
| `coverage.seed_extractions` loads every record type into the `record_type_extractions` table. The raw |
| quantity is stored (invariant 1), and a field the source does not supply carries a coded absence |
| (`not_stated`) with null evidence. |
| """ |
|
|
| from __future__ import annotations |
|
|
| from endopath import coverage_data |
|
|
| PROJECT_ID = coverage_data.PROJECT_ID |
|
|
| |
| RECORD_TYPE_EXTRACTIONS: dict[str, dict[str, dict[str, tuple[str, str | None]]]] = { |
| 'pathology_extraction': { |
| 'TCGA-D1-A15W': { |
| 'histologic_type': ('endometrioid', 'endometrial adenocarcinoma, endometrioid type'), |
| 'histologic_grade': ('1', 'FIGO grade I (of III)'), |
| 'myometrial_invasion_percent': ('0.7 cm of 1.8 cm', 'invading 0.7 cm into the 1.8 cm myometrial thickness'), |
| 'cervical_stromal_invasion': ('absent', 'The cervix is uninvolved'), |
| 'lymphovascular_space_invasion': ('not_stated', None), |
| 'regional_lymph_node_status': ('positive', 'is positive for metastatic adenocarcinoma'), |
| 'pathologic_stage': ('not_stated', None), |
| 'molecular_classification': ('not_stated', None), |
| 'date_biopsy_reported': ('not_stated', None), |
| 'msh6_staining_biopsy': ('not_stated', None), |
| 'pms2_staining_biopsy': ('not_stated', None), |
| 'msh2_staining_biopsy': ('not_stated', None), |
| 'mlh1_staining_biopsy': ('not_stated', None), |
| 'p53_staining_biopsy': ('not_stated', None), |
| 'mlh1meth_testing_ans': ('not_stated', None), |
| 'tumor_size': ('8.5', 'forming a mass (8.5 x 2.6 x 1.1 cm) invading 0.7 cm into the 1.8 cm myometrial thickness'), |
| 'omentum': ('not_stated', None), |
| 'adnexal': ('No', 'Ovary, left, oophorectomy: Without diagnostic abnormality.'), |
| 'seoc': ('No', 'Ovary, right, oophorectomy: Focus of endometriosis.'), |
| 'perit_wash': ('not_stated', None), |
| 'lymph_node_sampling': ('Full-pelvic node sampling performed | Full para-aortic', 'right and left pelvic lymph nodes and left para-aortic nodes'), |
| 'check_lymphnodes_w_metas': ('not_stated', None), |
| 'lymph_node_itc': ('not_stated', None), |
| 'lymph_node_micrometastases': ('not_stated', None), |
| 'lymph_node_macrometastases': ('not_stated', None), |
| }, |
| 'TCGA-AP-A1E0': { |
| 'histologic_type': ('endometrioid', 'Adenocarcinoma, endometrioid type'), |
| 'histologic_grade': ('2', 'FIGO Grade (For Endometrioid Types only): Grade 2'), |
| 'myometrial_invasion_percent': ('9 mm of 26 mm', 'Measures 9mm in maximum depth. Myometrium thickness measures 26mm in the area of maximal tumor invasion.'), |
| 'cervical_stromal_invasion': ('absent', 'Endocervical Invasion: Not identified.'), |
| 'lymphovascular_space_invasion': ('constrained', 'Lymphovascular invasion: Identified.'), |
| 'regional_lymph_node_status': ('positive', 'Metastatic adenocarcinoma in one of four lymph nodes (1/4)'), |
| 'pathologic_stage': ('not_stated', None), |
| 'molecular_classification': ('not_stated', None), |
| 'date_biopsy_reported': ('not_stated', None), |
| 'msh6_staining_biopsy': ('not_stated', None), |
| 'pms2_staining_biopsy': ('not_stated', None), |
| 'msh2_staining_biopsy': ('not_stated', None), |
| 'mlh1_staining_biopsy': ('not_stated', None), |
| 'p53_staining_biopsy': ('not_stated', None), |
| 'mlh1meth_testing_ans': ('not_stated', None), |
| 'tumor_size': ('not_stated', None), |
| 'omentum': ('not_stated', None), |
| 'adnexal': ('No', 'Benign ovaries and fallopian tubes'), |
| 'seoc': ('No', 'Benign ovaries and fallopian tubes'), |
| 'perit_wash': ('not_stated', None), |
| 'lymph_node_sampling': ('Sentinel nodes performed (pelvic +/- para-aortic) | Full para-aortic', 'SP: Right external iliac sentinel lymph node ... SP: Right para-sortic lymph nodes; dissection'), |
| 'check_lymphnodes_w_metas': ('not_stated', None), |
| 'lymph_node_itc': ('not_stated', None), |
| 'lymph_node_micrometastases': ('not_stated', None), |
| 'lymph_node_macrometastases': ('not_stated', None), |
| }, |
| 'TCGA-AP-A0LV': { |
| 'histologic_type': ('endometrioid', 'Tumor Type: Adenocarcinoma, endometrioid type.'), |
| 'histologic_grade': ('1', 'FIGO Grade (For Endometrioid Types only): Grade 1.'), |
| 'myometrial_invasion_percent': ('10 mm of 28 mm', 'Myometrial Invasion: (=<50%). Measures 10mm in maximum depth. Myometrium thickness measures 28mm in the area of maximal tumor.'), |
| 'cervical_stromal_invasion': ('absent', 'Endocervical Invasion: Not identified.'), |
| 'lymphovascular_space_invasion': ('not_identified', 'Lymphovascular invasion: Not identified.'), |
| 'regional_lymph_node_status': ('negative', 'One benign lymph node (0/1).'), |
| 'pathologic_stage': ('not_stated', None), |
| 'molecular_classification': ('not_stated', None), |
| 'date_biopsy_reported': ('not_stated', None), |
| 'msh6_staining_biopsy': ('not_stated', None), |
| 'pms2_staining_biopsy': ('not_stated', None), |
| 'msh2_staining_biopsy': ('not_stated', None), |
| 'mlh1_staining_biopsy': ('not_stated', None), |
| 'p53_staining_biopsy': ('not_stated', None), |
| 'mlh1meth_testing_ans': ('not_stated', None), |
| 'tumor_size': ('not_stated', None), |
| 'omentum': ('not_stated', None), |
| 'adnexal': ('No', 'Ovary with numerous cystic follicles and stromal hyperplasia. Benign fallopian tube with paratubal cysts.'), |
| 'seoc': ('No', 'Ovary with numerous cystic follicles and stromal hyperplasia.'), |
| 'perit_wash': ('not_stated', None), |
| 'lymph_node_sampling': ('Debulking (selected enlarged nodes)', '4: SP: Enlarged left external iliac lymph node'), |
| 'check_lymphnodes_w_metas': ('not_applicable', None), |
| 'lymph_node_itc': ('not_applicable', None), |
| 'lymph_node_micrometastases': ('not_applicable', None), |
| 'lymph_node_macrometastases': ('not_applicable', None), |
| }, |
| 'TCGA-AP-A059': { |
| 'histologic_type': ('endometrioid', 'ADENOCARCINOMA OF ENDOMETRIUM, ENDOMETRIOID TYPE'), |
| 'histologic_grade': ('3', 'FIGO GRADE III'), |
| 'myometrial_invasion_percent': ('3 mm of 25 mm', 'THE MAXIMAL THICKNESS OF MYOMETRIAL INVASION IS 3 MM. THE THICKNESS OF THE MYOMETRIUM IN THE AREA OF MAXIMAL TUMOR INVASION IS 25 MM.'), |
| 'cervical_stromal_invasion': ('absent', 'NO ENDOCERVICAL INVASION IS IDENTIFIED'), |
| 'lymphovascular_space_invasion': ('not_identified', 'NO DEFINITE VASCULAR INVASION IS IDENTIFIED'), |
| 'regional_lymph_node_status': ('negative', 'ONE BENIGN LYMPH NODE (0/1)'), |
| 'pathologic_stage': ('not_stated', None), |
| 'molecular_classification': ('mmr_deficient', 'IMMUNOHISTOCHEMICAL STAINS SHOW APPARENT LOSS OF MSH6 PROTEIN'), |
| 'date_biopsy_reported': ('not_stated', None), |
| 'msh6_staining_biopsy': ('not_stated', None), |
| 'pms2_staining_biopsy': ('not_stated', None), |
| 'msh2_staining_biopsy': ('not_stated', None), |
| 'mlh1_staining_biopsy': ('not_stated', None), |
| 'p53_staining_biopsy': ('not_stated', None), |
| 'mlh1meth_testing_ans': ('not_stated', None), |
| 'tumor_size': ('not_stated', None), |
| 'omentum': ('not_stated', None), |
| 'adnexal': ('No', 'ALL ADNEXA ARE UNREMARKABLE.'), |
| 'seoc': ('No', 'ALL ADNEXA ARE UNREMARKABLE.'), |
| 'perit_wash': ('not_stated', None), |
| 'lymph_node_sampling': ('Full-pelvic node sampling performed | Full para-aortic', '2: SP: Left external iliac lymph node 3: SP: Left hypogastric lymph node 4: SP: Left obturator lymph node 5: SP: Right external iliac lymph node 6: SP: Right obturator lymph node 7: SP: Left para-aortic lymph node 8: SP: Right para-aortic lymph nodes'), |
| 'check_lymphnodes_w_metas': ('not_applicable', None), |
| 'lymph_node_itc': ('not_applicable', None), |
| 'lymph_node_micrometastases': ('not_applicable', None), |
| 'lymph_node_macrometastases': ('not_applicable', None), |
| }, |
| 'TCGA-BG-A0LX': { |
| 'histologic_type': ('endometrioid', 'MODERATELY DIFFERENTIATED ENDOMETRIOID ADENOCARCINOMA OF THE ENDOMETRIUM'), |
| 'histologic_grade': ('2', 'Moderately differentiated (FIGO 2)'), |
| 'myometrial_invasion_percent': ('up to 90% of the myometrial uterine wall', 'ENDOMETRIOID CARCINOMA PENETRATES UP TO 90% OF THE MYOMETRIAL UTERINE WALL'), |
| 'cervical_stromal_invasion': ('absent', 'UTERINE CERVIX -CHRONIC CYSTIC CERVICITIS AND SQUAMOUS METAPLASIA FREE OF TUMOR'), |
| 'lymphovascular_space_invasion': ('constrained', 'ANGIOLYMPHATIC INVASION IDENTIFIED'), |
| 'regional_lymph_node_status': ('negative', 'N STAGE, PATHOLOGIC: pNO'), |
| 'pathologic_stage': ('IB', 'FIGO STAGE: IB'), |
| 'molecular_classification': ('not_stated', None), |
| 'date_biopsy_reported': ('not_stated', None), |
| 'msh6_staining_biopsy': ('not_stated', None), |
| 'pms2_staining_biopsy': ('not_stated', None), |
| 'msh2_staining_biopsy': ('not_stated', None), |
| 'mlh1_staining_biopsy': ('not_stated', None), |
| 'p53_staining_biopsy': ('not_stated', None), |
| 'mlh1meth_testing_ans': ('not_stated', None), |
| 'tumor_size': ('7.5', 'TUMOR SIZE: Maximum dimension: 7.5 mm'), |
| 'omentum': ('not_stated', None), |
| 'adnexal': ('No', 'LEFT OVARY WITH FOCI OF HEMOSIDERIN LADEN MACROPHAGES, ENDOMETRIOSIS, PHYSIOLOGIC CHANGES AND FOCAL MICROCALCIFICATIONS. ... RIGHT OVARY WITH EPITHELIAL INCLUSION, MICROCALCIFICATIONS AND PHYSIOLOGICAL CHANGES.'), |
| 'seoc': ('No', 'RIGHT OVARY WITH EPITHELIAL INCLUSION, MICROCALCIFICATIONS AND PHYSIOLOGICAL CHANGES.'), |
| 'perit_wash': ('not_stated', None), |
| 'lymph_node_sampling': ('Full-pelvic node sampling performed | Full para-aortic', 'PART 2: LEFT PELVIC LYMPH NODES - SEVEN (7) LEFT PELVIC LYMPH NODES, FREE OF TUMOR (0/7). ... PART 5: RIGHT PERIAORTIC LYMPH NODES - THREE (3) RIGHT PERIAORTIC LYMPH NODES, FREE OF TUMOR (0/3).'), |
| 'check_lymphnodes_w_metas': ('not_applicable', None), |
| 'lymph_node_itc': ('not_applicable', None), |
| 'lymph_node_micrometastases': ('not_applicable', None), |
| 'lymph_node_macrometastases': ('not_applicable', None), |
| }, |
| 'TCGA-BG-A0M0': { |
| 'histologic_type': ('endometrioid', 'ENDOMETRIAL ADENOCARCINOMA, ENDOMETRIOID TYPE'), |
| 'histologic_grade': ('1', 'Well differentiated (FIGO 1)'), |
| 'myometrial_invasion_percent': ('0.1 cm of 1.5 cm myometrium (6%)', 'TUMOR INVADES 0.1 CM OF 1.5 CM MYOMETRIUM (6%)'), |
| 'cervical_stromal_invasion': ('absent', 'CERVIX FREE OF TUMOR.'), |
| 'lymphovascular_space_invasion': ('not_identified', 'LYMPHOVASCULAR INVASION IS NOT IDENTIFIED.'), |
| 'regional_lymph_node_status': ('negative', 'ONE LYMPH NODE, NEGATIVE FOR METASTATIC CARCINOMA (0/1)'), |
| 'pathologic_stage': ('IA', 'FIGO - IA (current classification)'), |
| 'molecular_classification': ('not_stated', None), |
| 'date_biopsy_reported': ('not_stated', None), |
| 'msh6_staining_biopsy': ('not_stated', None), |
| 'pms2_staining_biopsy': ('not_stated', None), |
| 'msh2_staining_biopsy': ('not_stated', None), |
| 'mlh1_staining_biopsy': ('not_stated', None), |
| 'p53_staining_biopsy': ('not_stated', None), |
| 'mlh1meth_testing_ans': ('not_stated', None), |
| 'tumor_size': ('5.2', 'INVASIVE WELL DIFFERENTIATED ENDOMETRIAL ADENOCARCINOMA, ENDOMETRIOID TYPE, FIGO GRADE 1, NUCLEAR GRADE 1, 5.2 CM (GROSS)'), |
| 'omentum': ('not_stated', None), |
| 'adnexal': ('No', 'BILATERAL ADNEXA, FREE OF TUMOR.'), |
| 'seoc': ('No', 'BILATERAL OVARIES WITH SURFACE EPITHELIAL INCLUSIONS.'), |
| 'perit_wash': ('Negative', 'PELVIC WASH – NEGATIVE.'), |
| 'lymph_node_sampling': ('Full-pelvic node sampling performed', 'PART 2: LYMPH NODES, RIGHT EXTERNAL ILIAC, DISSECTIONS – ONE LYMPH NODE, NEGATIVE FOR METASTATIC CARCINOMA (0/1). PART 3: LYMPH NODES, LEFT EXTERNAL ILIAC, DISSECTION– BENIGN FIBROFATTY TISSUE, NO LYMPH NODE IDENTIFIED.'), |
| 'check_lymphnodes_w_metas': ('not_applicable', None), |
| 'lymph_node_itc': ('not_applicable', None), |
| 'lymph_node_micrometastases': ('not_applicable', None), |
| 'lymph_node_macrometastases': ('not_applicable', None), |
| }, |
| 'TCGA-BG-A0MH': { |
| 'histologic_type': ('endometrioid', 'MODERATELY DIFFERENTIATED ENDOMETRIOID ADENOCARCINOMA (GRADE 2)'), |
| 'histologic_grade': ('2', 'Moderately differentiated (FIGO 2)'), |
| 'myometrial_invasion_percent': ('up to 80% of myometrial thickness', 'PENETRATING UP TO 80% OF MYOMETRIAL THICKNESS'), |
| 'cervical_stromal_invasion': ('absent', 'T STAGE, PATHOLOGIC: pT1c'), |
| 'lymphovascular_space_invasion': ('not_stated', None), |
| 'regional_lymph_node_status': ('negative', 'Number of lymph nodes positive:: 0'), |
| 'pathologic_stage': ('IC', 'FIGO STAGE: IC'), |
| 'molecular_classification': ('not_stated', None), |
| 'date_biopsy_reported': ('not_stated', None), |
| 'msh6_staining_biopsy': ('not_stated', None), |
| 'pms2_staining_biopsy': ('not_stated', None), |
| 'msh2_staining_biopsy': ('not_stated', None), |
| 'mlh1_staining_biopsy': ('not_stated', None), |
| 'p53_staining_biopsy': ('not_stated', None), |
| 'mlh1meth_testing_ans': ('not_stated', None), |
| 'tumor_size': ('4.5', 'TUMOR SIZE: Maximum dimension: 4.5 cm'), |
| 'omentum': ('not_stated', None), |
| 'adnexal': ('No', 'OVARY WITH MATURE CYSTIC TERATOMA, NO ADENOCARCINOMA IS SEEN ... LEFT OVARY WITH MICROSCOPIC MATURE CYSTIC TERATOMA AND SEROSAL ADHESIONS, NO ADENOCARCINOMA IS SEEN'), |
| 'seoc': ('Yes', 'OVARY WITH MATURE CYSTIC TERATOMA, NO ADENOCARCINOMA IS SEEN'), |
| 'perit_wash': ('Negative', 'The peritoneal cytology is negative.'), |
| 'lymph_node_sampling': ('Full-pelvic node sampling performed; Full para-aortic', 'PART 3: LYMPH NODES, LEFT PELVIC, BIOPSY; PART 4: LYMPH NODES, LEFT PERIAORTIC, BIOPSY; PART 5: LYMPH NODES, RIGHT PELVIC, BIOPSY; PART 6: LYMPH NODES, RIGHT PERIAORTIC, BIOPSY'), |
| 'check_lymphnodes_w_metas': ('not_applicable', None), |
| 'lymph_node_itc': ('not_applicable', None), |
| 'lymph_node_micrometastases': ('not_applicable', None), |
| 'lymph_node_macrometastases': ('not_applicable', None), |
| }, |
| 'TCGA-BG-A0MO': { |
| 'histologic_type': ('endometrioid', 'ENDOMETRIOID ADENOCARCINOMA OF THE ENDOMETRIUM'), |
| 'histologic_grade': ('1', 'FIGO GRADE 1'), |
| 'myometrial_invasion_percent': ('0.5 cm of 1.4 cm', '0.5 CM INVASION INTO 1.4 CM. TOTAL MYOMETRIAL WALL THICKNESS'), |
| 'cervical_stromal_invasion': ('absent', 'CERVIX, NEGATIVE FOR NEOPLASM'), |
| 'lymphovascular_space_invasion': ('not_identified', 'NO LYMPHOVASCULAR INVASION IS IDENTIFIED'), |
| 'regional_lymph_node_status': ('negative', 'Number of lymph nodes positive:: 0'), |
| 'pathologic_stage': ('IB', 'FIGO STAGE: IB'), |
| 'molecular_classification': ('not_stated', None), |
| 'date_biopsy_reported': ('not_stated', None), |
| 'msh6_staining_biopsy': ('not_stated', None), |
| 'pms2_staining_biopsy': ('not_stated', None), |
| 'msh2_staining_biopsy': ('not_stated', None), |
| 'mlh1_staining_biopsy': ('not_stated', None), |
| 'p53_staining_biopsy': ('not_stated', None), |
| 'mlh1meth_testing_ans': ('not_stated', None), |
| 'tumor_size': ('2.5', 'TUMOR SIZE: Maximum dimension: 2.5 cm'), |
| 'omentum': ('not_stated', None), |
| 'adnexal': ('No', 'RIGHT AND LEFT OVARIES WITH ENDOSALPINGIOSIS AND BENIGN SURFACE FIBROMAS, NEGATIVE FOR NEOPLASM.'), |
| 'seoc': ('No', 'RIGHT AND LEFT OVARIES WITH ENDOSALPINGIOSIS AND BENIGN SURFACE FIBROMAS, NEGATIVE FOR NEOPLASM.'), |
| 'perit_wash': ('not_stated', None), |
| 'lymph_node_sampling': ('Full-pelvic node sampling performed, Full para-aortic', 'PART 2: RIGHT PELVIC LYMPH NODES, BIOPSY... PART 4: RIGHT OBTURATOR LYMPH NODES, BIOPSY... PART 5: RIGHT COMMON AND PERIAORTIC LYMPH NODES, BIOPSY... PART 7: LEFT PELVIC BICIRCUMFLEX LYMPH NODES, BIOPSY... PART 9: LEFT OBTURATOR LYMPH NODES, BIOPSY'), |
| 'check_lymphnodes_w_metas': ('not_applicable', None), |
| 'lymph_node_itc': ('not_applicable', None), |
| 'lymph_node_micrometastases': ('not_applicable', None), |
| 'lymph_node_macrometastases': ('not_applicable', None), |
| }, |
| 'TCGA-BG-A0VV': { |
| 'histologic_type': ('endometrioid', 'Endometroid adenocarcinoma, NOS'), |
| 'histologic_grade': ('1', 'Well differentiated (FIGO 1)'), |
| 'myometrial_invasion_percent': ('Less than 1/2 thickness of myometrium', 'Less than 1/2 thickness of myometrium'), |
| 'cervical_stromal_invasion': ('not_stated', None), |
| 'lymphovascular_space_invasion': ('not_stated', None), |
| 'regional_lymph_node_status': ('negative', 'Number of lymph nodes positive:: 0. LYMPH NODES EXAMINED: Total number of lymph nodes examined: 9'), |
| 'pathologic_stage': ('IA', 'FIGO STAGE: IA'), |
| 'molecular_classification': ('not_stated', None), |
| 'date_biopsy_reported': ('not_stated', None), |
| 'msh6_staining_biopsy': ('not_stated', None), |
| 'pms2_staining_biopsy': ('not_stated', None), |
| 'msh2_staining_biopsy': ('not_stated', None), |
| 'mlh1_staining_biopsy': ('not_stated', None), |
| 'p53_staining_biopsy': ('not_stated', None), |
| 'mlh1meth_testing_ans': ('not_stated', None), |
| 'tumor_size': ('2.5', 'Maximum dimension: 25 mm'), |
| 'omentum': ('not_stated', None), |
| 'adnexal': ('not_stated', None), |
| 'seoc': ('not_stated', None), |
| 'perit_wash': ('not_stated', None), |
| 'lymph_node_sampling': ('Full-pelvic node sampling performed | Full para-aortic', 'pelvic and periaortic lymph node dissection'), |
| 'check_lymphnodes_w_metas': ('not_applicable', None), |
| 'lymph_node_itc': ('not_applicable', None), |
| 'lymph_node_micrometastases': ('not_applicable', None), |
| 'lymph_node_macrometastases': ('not_applicable', None), |
| }, |
| 'TCGA-BG-A3PP': { |
| 'histologic_type': ('serous', 'TUMOR TYPE: Serous adenocarcinoma'), |
| 'histologic_grade': ('3', 'Poorly differentiated (FIGO) 3)'), |
| 'myometrial_invasion_percent': ('approximately 85%', 'INVADING APPROXIMAYELY 85% OF MYOMETRIUM'), |
| 'cervical_stromal_invasion': ('present', 'ADENOCARCINOMA INVADES ENDOCERVICAL GLANDS AND CERVICAL STROMA'), |
| 'lymphovascular_space_invasion': ('constrained', 'MULTIFOCAL LYMPHOVASCULAR INVASION IDENTIFIED'), |
| 'regional_lymph_node_status': ('negative', 'N STAGE, PATHOLOGIC: pNO'), |
| 'pathologic_stage': ('II', 'FIGO STAGE: II'), |
| 'molecular_classification': ('not_stated', None), |
| 'date_biopsy_reported': ('not_stated', None), |
| 'msh6_staining_biopsy': ('not_stated', None), |
| 'pms2_staining_biopsy': ('not_stated', None), |
| 'msh2_staining_biopsy': ('not_stated', None), |
| 'mlh1_staining_biopsy': ('not_stated', None), |
| 'p53_staining_biopsy': ('not_stated', None), |
| 'mlh1meth_testing_ans': ('not_stated', None), |
| 'tumor_size': ('4.3', 'TUMOR SIZE: Maximum dimension: 43 mm'), |
| 'omentum': ('No', 'PART 6: OMENTUM, OMENTECTOMY - A. NEGATIVE FOR TUMOR.'), |
| 'adnexal': ('No', 'BILATERAL OVARIES NEGATIVE FOR TUMOR, WITH PHYSIOLOGIC CHANGES AND EPITHELIAL INCLUSIONS.'), |
| 'seoc': ('No', 'BILATERAL OVARIES NEGATIVE FOR TUMOR, WITH PHYSIOLOGIC CHANGES AND EPITHELIAL INCLUSIONS.'), |
| 'perit_wash': ('Positive', 'Pelvic cytology ... is suspicious for malignant cells.'), |
| 'lymph_node_sampling': ('Full-pelvic node sampling performed | Full para-aortic', 'PART 2: LYMPH NODES, LEFT PELVIC, DISSECTION; PART 3: LYMPH NODES, LEFT PERIAORTIC, DISSECTION; PART 4: LYMPH NODES, RIGHT PELVIC, DISSECTION; PART 5: LYMPH NODES, RIGHT PERIAORTIC, DISSECTION'), |
| 'check_lymphnodes_w_metas': ('not_applicable', None), |
| 'lymph_node_itc': ('not_applicable', None), |
| 'lymph_node_micrometastases': ('not_applicable', None), |
| 'lymph_node_macrometastases': ('not_applicable', None), |
| }, |
| 'TCGA-D1-A16O': { |
| 'histologic_type': ('endometrioid', 'endometrioid type'), |
| 'histologic_grade': ('1', 'FIGO grade I (of III)'), |
| 'myometrial_invasion_percent': ('0.1 to 0.2 cm of 1.6 cm', 'The tumor invades superficially (0.1 to 0.2 cm) into the myometrium (total wall thickness, 1.6 cm)'), |
| 'cervical_stromal_invasion': ('absent', 'The tumor does not involve the endocervix.'), |
| 'lymphovascular_space_invasion': ('constrained', 'Lymphovascular space invasion is identified.'), |
| 'regional_lymph_node_status': ('not_stated', None), |
| 'pathologic_stage': ('not_stated', None), |
| 'molecular_classification': ('not_stated', None), |
| 'date_biopsy_reported': ('not_stated', None), |
| 'msh6_staining_biopsy': ('not_stated', None), |
| 'pms2_staining_biopsy': ('not_stated', None), |
| 'msh2_staining_biopsy': ('not_stated', None), |
| 'mlh1_staining_biopsy': ('not_stated', None), |
| 'p53_staining_biopsy': ('not_stated', None), |
| 'mlh1meth_testing_ans': ('not_stated', None), |
| 'tumor_size': (5.0, 'polypoid mass (5.0 x 3.8 x 1.5 cm) circumferentially involving the endometrium'), |
| 'omentum': ('not_stated', None), |
| 'adnexal': ('No', 'The ovaries show bilateral corpus luteal cysts (right--1.7 cm in greatest dimension; left--1.3 cm in greatest dimension). The bilateral fallopian tubes are not identified.'), |
| 'seoc': ('No', 'The ovaries show bilateral corpus luteal cysts (right--1.7 cm in greatest dimension; left--1.3 cm in greatest dimension)'), |
| 'perit_wash': ('not_stated', None), |
| 'lymph_node_sampling': ('not_stated', None), |
| 'check_lymphnodes_w_metas': ('not_applicable', None), |
| 'lymph_node_itc': ('not_applicable', None), |
| 'lymph_node_micrometastases': ('not_applicable', None), |
| 'lymph_node_macrometastases': ('not_applicable', None), |
| }, |
| 'TCGA-SL-A6JA': { |
| 'histologic_type': ('endometrioid', 'Histologic Type: Endometrioid andenocarcinoma'), |
| 'histologic_grade': ('3', 'FIGO grade 3 (architectural grade 2, cytologic grade 3)'), |
| 'myometrial_invasion_percent': ('1.1 cm of 1.8 cm', 'Maximal depth of invasion is 1.1cm in total thickness of 1.8cm'), |
| 'cervical_stromal_invasion': ('present', 'Endocervical stromal invasion is seen'), |
| 'lymphovascular_space_invasion': ('constrained', 'Lymphatic invasion is seen with a D240'), |
| 'regional_lymph_node_status': ('negative', 'pNO'), |
| 'pathologic_stage': ('not_stated', None), |
| 'molecular_classification': ('not_stated', None), |
| 'date_biopsy_reported': ('not_stated', None), |
| 'msh6_staining_biopsy': ('not_stated', None), |
| 'pms2_staining_biopsy': ('not_stated', None), |
| 'msh2_staining_biopsy': ('not_stated', None), |
| 'mlh1_staining_biopsy': ('not_stated', None), |
| 'p53_staining_biopsy': ('not_stated', None), |
| 'mlh1meth_testing_ans': ('not_stated', None), |
| 'tumor_size': ('not_stated', None), |
| 'omentum': ('not_stated', None), |
| 'adnexal': ('No', 'The bilateral ovaries and fallopian tubes are uninvolved by tumor and demonstrate atrophic features.'), |
| 'seoc': ('No', 'The bilateral ovaries and fallopian tubes are uninvolved by tumor and demonstrate atrophic features.'), |
| 'perit_wash': ('not_stated', None), |
| 'lymph_node_sampling': ('not_stated', None), |
| 'check_lymphnodes_w_metas': ('not_applicable', None), |
| 'lymph_node_itc': ('not_applicable', None), |
| 'lymph_node_micrometastases': ('not_applicable', None), |
| 'lymph_node_macrometastases': ('not_applicable', None), |
| }, |
| 'TCGA-AJ-A5DV': { |
| 'histologic_type': ('endometrioid', 'Endometrioid adenocarcinoma'), |
| 'histologic_grade': ('2', 'Histologic grade 2/3'), |
| 'myometrial_invasion_percent': ('0.5 cm depth of invasion of 1.5 cm total myometrial thickness', 'Depth of invasion: 0.5 cm (total myometrial thickness 1.5 cm; tumor. predominantly exophytic; 0.5 cm)'), |
| 'cervical_stromal_invasion': ('absent', 'Upper portion of endocervical glands involved with no. stromal invasion identified'), |
| 'lymphovascular_space_invasion': ('not_identified', 'Lymphovascular invasion: Not identified'), |
| 'regional_lymph_node_status': ('negative', 'Right pelvic lymph node: One (1) negative lymph node'), |
| 'pathologic_stage': ('pT1a,pN0', 'AJCC pathologic stage: pT1a,pNo.'), |
| 'molecular_classification': ('not_stated', None), |
| 'date_biopsy_reported': ('not_stated', None), |
| 'msh6_staining_biopsy': ('not_stated', None), |
| 'pms2_staining_biopsy': ('not_stated', None), |
| 'msh2_staining_biopsy': ('not_stated', None), |
| 'mlh1_staining_biopsy': ('not_stated', None), |
| 'p53_staining_biopsy': ('not_stated', None), |
| 'mlh1meth_testing_ans': ('not_stated', None), |
| 'tumor_size': (4.8, 'Maximum tumor size: 4.8 cm.'), |
| 'omentum': ('not_stated', None), |
| 'adnexal': ('No', 'Left and right adnexa with physiologic changes.'), |
| 'seoc': ('No', 'Left and right adnexa with physiologic changes.'), |
| 'perit_wash': ('not_stated', None), |
| 'lymph_node_sampling': ('not_stated', None), |
| 'check_lymphnodes_w_metas': ('not_applicable', None), |
| 'lymph_node_itc': ('not_applicable', None), |
| 'lymph_node_micrometastases': ('not_applicable', None), |
| 'lymph_node_macrometastases': ('not_applicable', None), |
| }, |
| 'TCGA-AX-A3FS': { |
| 'histologic_type': ('endometrioid', 'HIGH GRADE ENDOMETRIOID ADENOCARCINOMA'), |
| 'histologic_grade': ('3', 'HISTOLOGIC GRADE: FIGO grade 3'), |
| 'myometrial_invasion_percent': ('5 mm depth of invasion, 25 mm myometrial thickness', 'Depth of invasion: 5 mm. Myometrial thickness: 25 mm.'), |
| 'cervical_stromal_invasion': ('absent', 'INVOLVEMENT OF CERVIX: Not involved.'), |
| 'lymphovascular_space_invasion': ('focal', 'FOCAL VASCULAR SPACE INVASION'), |
| 'regional_lymph_node_status': ('negative', 'pNO: No regional lymph node metastasis.'), |
| 'pathologic_stage': ('IA', 'pTla(IA]'), |
| 'molecular_classification': ('not_stated', None), |
| 'date_biopsy_reported': ('not_stated', None), |
| 'msh6_staining_biopsy': ('not_stated', None), |
| 'pms2_staining_biopsy': ('not_stated', None), |
| 'msh2_staining_biopsy': ('not_stated', None), |
| 'mlh1_staining_biopsy': ('not_stated', None), |
| 'p53_staining_biopsy': ('not_stated', None), |
| 'mlh1meth_testing_ans': ('not_stated', None), |
| 'tumor_size': ('4', 'TUMOR SIZE: Greatest dimension: 4'), |
| 'omentum': ('not_stated', None), |
| 'adnexal': ('No', 'BILATERAL OVARIES AND FALLOPIAN TUBES PHYSIOLOGICAL CHANGES NO TUMOR IDENTIFIED'), |
| 'seoc': ('No', 'BILATERAL OVARIES AND FALLOPIAN TUBES PHYSIOLOGICAL CHANGES NO TUMOR IDENTIFIED'), |
| 'perit_wash': ('Negative', '*PERITONEAL ASCITIC FLUID: *Negative for malignancy/normal/benign'), |
| 'lymph_node_sampling': ('Full-pelvic node sampling performed', 'LYMPH NODE SAMPLING: Performed Pelvic lymph nodes'), |
| 'check_lymphnodes_w_metas': ('not_applicable', None), |
| 'lymph_node_itc': ('not_applicable', None), |
| 'lymph_node_micrometastases': ('not_applicable', None), |
| 'lymph_node_macrometastases': ('not_applicable', None), |
| }, |
| 'TCGA-BG-A222': { |
| 'histologic_type': ('endometrioid', 'TUMOR TYPE: Endometroid adenocarcinoma, NOS.'), |
| 'histologic_grade': ('3', 'Poorly differentiated (FIGO 3).'), |
| 'myometrial_invasion_percent': ('approximately 35%', 'INVADING APPROXIMATELY 35%. OF MYOMETRIUM'), |
| 'cervical_stromal_invasion': ('absent', 'CHRONIC CERVICITIS, SQUAMOUS METAPLASIA, REACTIVE CHANGES AND MICROGLANDULAR'), |
| 'lymphovascular_space_invasion': ('focal', 'FOCAL LYMPHOVASCULAR INVASION IDENTIFIED.'), |
| 'regional_lymph_node_status': ('negative', 'Number of lymph nodes positive:: 0.'), |
| 'pathologic_stage': ('IA', 'FIGO STAGE: IA.'), |
| 'molecular_classification': ('not_stated', None), |
| 'date_biopsy_reported': ('not_stated', None), |
| 'msh6_staining_biopsy': ('not_stated', None), |
| 'pms2_staining_biopsy': ('not_stated', None), |
| 'msh2_staining_biopsy': ('not_stated', None), |
| 'mlh1_staining_biopsy': ('not_stated', None), |
| 'p53_staining_biopsy': ('not_stated', None), |
| 'mlh1meth_testing_ans': ('not_stated', None), |
| 'tumor_size': ('7.0', 'TUMOR SIZE: Maximum dimension: 70 mm'), |
| 'omentum': ('not_stated', None), |
| 'adnexal': ('No', 'BILATERAL OVARIES AND FALLOPIAN TUBES, NEGATIVE FOR TUMOR.'), |
| 'seoc': ('No', 'BILATERAL OVARIES AND FALLOPIAN TUBES, NEGATIVE FOR TUMOR.'), |
| 'perit_wash': ('Negative', 'Pelvic cytology (...) is negative for malignant cells.'), |
| 'lymph_node_sampling': ('Full-pelvic node sampling performed | Full para-aortic', 'PROCEDURE: ... pelvic and periaortic lymph node dissection.'), |
| 'check_lymphnodes_w_metas': ('not_applicable', None), |
| 'lymph_node_itc': ('not_applicable', None), |
| 'lymph_node_micrometastases': ('not_applicable', None), |
| 'lymph_node_macrometastases': ('not_applicable', None), |
| }, |
| 'TCGA-D1-A0ZQ': { |
| 'histologic_type': ('endometrioid', 'endometrial adenocarcinoma, endometrioid. type with. mucinous differentiation'), |
| 'histologic_grade': ('2', 'FIGO. grade 2 (of 3) endometrial adenocarcinoma'), |
| 'myometrial_invasion_percent': ('1.2 cm of 2.0 cm total wall thickness', 'The tumor invades 1.2 cm into the myometrium (total wall. thickness, 2.0. cm)'), |
| 'cervical_stromal_invasion': ('absent', 'The tumor does not involve the endocervix.'), |
| 'lymphovascular_space_invasion': ('not_identified', 'Lymphovascular. space invasion is not identified.'), |
| 'regional_lymph_node_status': ('not_examined', '[AJCCpT1cNxMx]'), |
| 'pathologic_stage': ('not_stated', None), |
| 'molecular_classification': ('not_stated', None), |
| 'date_biopsy_reported': ('not_stated', None), |
| 'msh6_staining_biopsy': ('not_stated', None), |
| 'pms2_staining_biopsy': ('not_stated', None), |
| 'msh2_staining_biopsy': ('not_stated', None), |
| 'mlh1_staining_biopsy': ('not_stated', None), |
| 'p53_staining_biopsy': ('not_stated', None), |
| 'mlh1meth_testing_ans': ('not_stated', None), |
| 'tumor_size': ('2.7', 'mass (2.7 x 2.6 x 0.7 cm)'), |
| 'omentum': ('not_stated', None), |
| 'adnexal': ('No', 'The right ovary shows a peritoneal inclusion cyst. The left ovary shows a serous cystadenoma. Both fallopian tubes are unremarkable.'), |
| 'seoc': ('Yes', 'The left ovary shows a serous cystadenoma.'), |
| 'perit_wash': ('not_stated', None), |
| 'lymph_node_sampling': ('not_applicable', None), |
| 'check_lymphnodes_w_metas': ('not_applicable', None), |
| 'lymph_node_itc': ('not_applicable', None), |
| 'lymph_node_micrometastases': ('not_applicable', None), |
| 'lymph_node_macrometastases': ('not_applicable', None), |
| }, |
| 'TCGA-D1-A16F': { |
| 'histologic_type': ('endometrioid', 'Endometrial adenocarcinoma,. endometrioid. type'), |
| 'histologic_grade': ('2', 'FIGO grade II (of III)'), |
| 'myometrial_invasion_percent': ('0.5 cm (2.0 cm total myometrial thickness)', 'invades the myometrium to a. maximal depth. of 0.5 cm (2.0 cm total myometrial thickness)'), |
| 'cervical_stromal_invasion': ('absent', 'The cervix is uninvolved.'), |
| 'lymphovascular_space_invasion': ('not_stated', None), |
| 'regional_lymph_node_status': ('negative', 'right. pelvic lymph nodes are negative for tumor'), |
| 'pathologic_stage': ('not_stated', None), |
| 'molecular_classification': ('not_stated', None), |
| 'date_biopsy_reported': ('not_stated', None), |
| 'msh6_staining_biopsy': ('not_stated', None), |
| 'pms2_staining_biopsy': ('not_stated', None), |
| 'msh2_staining_biopsy': ('not_stated', None), |
| 'mlh1_staining_biopsy': ('not_stated', None), |
| 'p53_staining_biopsy': ('not_stated', None), |
| 'mlh1meth_testing_ans': ('not_stated', None), |
| 'tumor_size': ('7.5', 'forming a polypoid mass (7.5 x 2.5 x 1.3 cm)'), |
| 'omentum': ('not_stated', None), |
| 'adnexal': ('No', 'Ovary and fallopian tube, right salpingo-oophorectomy: No diagnostic abnormalities.'), |
| 'seoc': ('No', 'Ovary and fallopian tube, right salpingo-oophorectomy: No diagnostic abnormalities.'), |
| 'perit_wash': ('not_stated', None), |
| 'lymph_node_sampling': ('Full-pelvic node sampling performed | Full para-aortic', 'right and left pelvic lymph nodes (laparoscopically), right and left para-aortic lymph nodes above and below the inferior mesenteric artery (laparoscopically)'), |
| 'check_lymphnodes_w_metas': ('not_applicable', None), |
| 'lymph_node_itc': ('not_applicable', None), |
| 'lymph_node_micrometastases': ('not_applicable', None), |
| 'lymph_node_macrometastases': ('not_applicable', None), |
| }, |
| 'TCGA-D1-A2G5': { |
| 'histologic_type': ('endometrioid', 'endometrial. adenocarcinoma, endometrioid type'), |
| 'histologic_grade': ('3', 'FIGO grade III (of III)'), |
| 'myometrial_invasion_percent': ('0.4 cm of 2.0 cm total myometrial thickness', '0.4 cm into the myometrium (total myometrial thickness,. 2.0 cm)'), |
| 'cervical_stromal_invasion': ('absent', 'The cervix is uninvolved by tumor'), |
| 'lymphovascular_space_invasion': ('not_identified', 'Angiolymphatic invasion is not identified'), |
| 'regional_lymph_node_status': ('positive', 'is positive for a microscopic. focus of. metastatic adenocarcinoma'), |
| 'pathologic_stage': ('not_stated', None), |
| 'molecular_classification': ('not_stated', None), |
| 'date_biopsy_reported': ('not_stated', None), |
| 'msh6_staining_biopsy': ('not_stated', None), |
| 'pms2_staining_biopsy': ('not_stated', None), |
| 'msh2_staining_biopsy': ('not_stated', None), |
| 'mlh1_staining_biopsy': ('not_stated', None), |
| 'p53_staining_biopsy': ('not_stated', None), |
| 'mlh1meth_testing_ans': ('not_stated', None), |
| 'tumor_size': ('8.4', 'forming an 8.4 x 3.5 x 2.4 cm polypoid mass filling the endometrial cavity'), |
| 'omentum': ('not_stated', None), |
| 'adnexal': ('No', 'Ovary and fallopian tube, right and left, salpingo-oophorectomy: Without diagnostic abnormality.'), |
| 'seoc': ('No', 'Ovary and fallopian tube, right and left, salpingo-oophorectomy: Without diagnostic abnormality.'), |
| 'perit_wash': ('not_stated', None), |
| 'lymph_node_sampling': ('Full-pelvic node sampling performed | Full para-aortic', 'Lymph nodes, left pelvic, excision: Multiple left pelvic lymph nodes (4 external iliac, 2 internal iliac, 5 common iliac, 7 obturator) are negative for tumor. Lymph nodes, right and left para-aortic, lymphadenectomy: Multiple para-aortic lymph nodes above the inferior mesenteric artery (5 right, 5 left) are negative for tumor.'), |
| 'check_lymphnodes_w_metas': ('not_stated', None), |
| 'lymph_node_itc': ('not_stated', None), |
| 'lymph_node_micrometastases': ('not_stated', None), |
| 'lymph_node_macrometastases': ('not_stated', None), |
| }, |
| 'TCGA-EY-A1GI': { |
| 'histologic_type': ('endometrioid', 'Moderately differentiated endometrioid adenocarcinoma'), |
| 'histologic_grade': ('2', 'overall FIGO grade 2'), |
| 'myometrial_invasion_percent': ('1.3 cm of 1.7 cm (76%)', 'Tumor invades into the outer half of the myometrial wall to 1.3 cm out of 1.7 cm in total myometrial wall thickness. (76%)'), |
| 'cervical_stromal_invasion': ('absent', 'Cervix. - No tumor seen.'), |
| 'lymphovascular_space_invasion': ('focal', 'Focal lymphovascular space invasion present'), |
| 'regional_lymph_node_status': ('negative', 'Sixteen lymph nodes, no tumor seen (0/16)'), |
| 'pathologic_stage': ('IB', 'FIGO stage grouping: IB.'), |
| 'molecular_classification': ('not_stated', None), |
| 'date_biopsy_reported': ('not_stated', None), |
| 'msh6_staining_biopsy': ('not_stated', None), |
| 'pms2_staining_biopsy': ('not_stated', None), |
| 'msh2_staining_biopsy': ('not_stated', None), |
| 'mlh1_staining_biopsy': ('not_stated', None), |
| 'p53_staining_biopsy': ('not_stated', None), |
| 'mlh1meth_testing_ans': ('not_stated', None), |
| 'tumor_size': ('6.0', 'Tumor is roughly circumferential and measures approximately 6 cm from cervical to fundic and approximately 3.3 cm in width'), |
| 'omentum': ('Unknown (not sampled)', 'Received are three appropriately labeled containers.'), |
| 'adnexal': ('not_stated', None), |
| 'seoc': ('not_stated', None), |
| 'perit_wash': ('not_stated', None), |
| 'lymph_node_sampling': ('Full-pelvic node sampling performed', 'undergoing a radical hysterectomy, bilateral salpingo-oophorectomy and bilateral pelvic lymphadenectomy.'), |
| 'check_lymphnodes_w_metas': ('not_applicable', None), |
| 'lymph_node_itc': ('not_applicable', None), |
| 'lymph_node_micrometastases': ('not_applicable', None), |
| 'lymph_node_macrometastases': ('not_applicable', None), |
| }, |
| 'TCGA-KP-A3W1': { |
| 'histologic_type': ('serous', 'High-grade endometrial serous carcinoma'), |
| 'histologic_grade': ('3', 'Figo grade 3/3'), |
| 'myometrial_invasion_percent': ('inner half of myometrium (superficial); invasion depth 0.5 cm, least thickness of uninvolved myometrium 1.3 cm', 'Only superficial invasion of inner half of myometrium'), |
| 'cervical_stromal_invasion': ('absent', 'does not involve the endocervix'), |
| 'lymphovascular_space_invasion': ('not_identified', 'No lymphovascular invasion'), |
| 'regional_lymph_node_status': ('negative', 'Three benign lymph nodes, negative. for metastasis'), |
| 'pathologic_stage': ('pT1aN0', 'pTlaNO'), |
| 'molecular_classification': ('not_stated', None), |
| 'date_biopsy_reported': ('not_stated', None), |
| 'msh6_staining_biopsy': ('not_stated', None), |
| 'pms2_staining_biopsy': ('not_stated', None), |
| 'msh2_staining_biopsy': ('not_stated', None), |
| 'mlh1_staining_biopsy': ('not_stated', None), |
| 'p53_staining_biopsy': ('not_stated', None), |
| 'mlh1meth_testing_ans': ('not_stated', None), |
| 'tumor_size': ('4.5', 'the endometrium is involved by tumor, 4.5 cm in greatest dimension'), |
| 'omentum': ('not_stated', None), |
| 'adnexal': ('No', 'Histologically unremarkable ovaries and fallopian tubes.'), |
| 'seoc': ('No', 'Histologically unremarkable ovaries and fallopian tubes.'), |
| 'perit_wash': ('Negative', 'Pelvic washings: Benign mesothelial cells and chronic inflammatory cells.'), |
| 'lymph_node_sampling': ('not_stated', None), |
| 'check_lymphnodes_w_metas': ('not_applicable', None), |
| 'lymph_node_itc': ('not_applicable', None), |
| 'lymph_node_micrometastases': ('not_applicable', None), |
| 'lymph_node_macrometastases': ('not_applicable', None), |
| }, |
| }, |
| 'clinical_join': { |
| 'TCGA-D1-A15W': { |
| 'vital_status': ('Alive', 'GDC demographic record: vital_status = Alive'), |
| 'disease_response': ('TF-Tumor Free', 'GDC follow-up record: disease_response = TF-Tumor Free'), |
| 'days_to_last_follow_up': ('915', 'GDC last-follow-up record: days_to_last_follow_up = 915'), |
| 'chemotherapy': ('administered', 'GDC treatment record: chemotherapy'), |
| 'radiation_therapy': ('administered', 'GDC treatment record: radiation, implants'), |
| 'hormone_therapy': ('not_stated', None), |
| }, |
| 'TCGA-AP-A1E0': { |
| 'vital_status': ('Alive', 'GDC demographic record: vital_status = Alive'), |
| 'disease_response': ('TF-Tumor Free', 'GDC follow-up record: disease_response = TF-Tumor Free'), |
| 'days_to_last_follow_up': ('1832', 'GDC last-follow-up record: days_to_last_follow_up = 1832'), |
| 'chemotherapy': ('administered', 'GDC treatment record: chemotherapy'), |
| 'radiation_therapy': ('administered', 'GDC treatment record: radiation therapy, nos'), |
| 'hormone_therapy': ('not_stated', None), |
| }, |
| 'TCGA-AP-A0LV': { |
| 'vital_status': ('Alive', 'GDC demographic record: vital_status = Alive'), |
| 'disease_response': ('TF-Tumor Free', 'GDC follow-up record: disease_response = TF-Tumor Free'), |
| 'days_to_last_follow_up': ('763', 'GDC last-follow-up record: days_to_last_follow_up = 763'), |
| 'chemotherapy': ('administered', 'GDC treatment record: pharmaceutical therapy, nos'), |
| 'radiation_therapy': ('administered', 'GDC treatment record: radiation therapy, nos'), |
| 'hormone_therapy': ('not_stated', None), |
| }, |
| 'TCGA-AP-A059': { |
| 'vital_status': ('Alive', 'GDC demographic record: vital_status = Alive'), |
| 'disease_response': ('TF-Tumor Free', 'GDC follow-up record: disease_response = TF-Tumor Free'), |
| 'days_to_last_follow_up': ('1461', 'GDC last-follow-up record: days_to_last_follow_up = 1461'), |
| 'chemotherapy': ('administered', 'GDC treatment record: pharmaceutical therapy, nos'), |
| 'radiation_therapy': ('administered', 'GDC treatment record: radiation, implants'), |
| 'hormone_therapy': ('not_stated', None), |
| }, |
| 'TCGA-BG-A0LX': { |
| 'vital_status': ('Alive', 'GDC demographic record: vital_status = Alive'), |
| 'disease_response': ('TF-Tumor Free', 'GDC follow-up record: disease_response = TF-Tumor Free'), |
| 'days_to_last_follow_up': ('614', 'GDC last-follow-up record: days_to_last_follow_up = 614'), |
| 'chemotherapy': ('administered', 'GDC treatment record: pharmaceutical therapy, nos'), |
| 'radiation_therapy': ('administered', 'GDC treatment record: radiation, implants'), |
| 'hormone_therapy': ('not_stated', None), |
| }, |
| 'TCGA-BG-A0M0': { |
| 'vital_status': ('Alive', 'GDC demographic record: vital_status = Alive'), |
| 'disease_response': ('TF-Tumor Free', 'GDC follow-up record: disease_response = TF-Tumor Free'), |
| 'days_to_last_follow_up': ('588', 'GDC last-follow-up record: days_to_last_follow_up = 588'), |
| 'chemotherapy': ('administered', 'GDC treatment record: pharmaceutical therapy, nos'), |
| 'radiation_therapy': ('administered', 'GDC treatment record: radiation therapy, nos'), |
| 'hormone_therapy': ('not_stated', None), |
| }, |
| 'TCGA-BG-A0MH': { |
| 'vital_status': ('Alive', 'GDC demographic record: vital_status = Alive'), |
| 'disease_response': ('TF-Tumor Free', 'GDC follow-up record: disease_response = TF-Tumor Free'), |
| 'days_to_last_follow_up': ('1930', 'GDC last-follow-up record: days_to_last_follow_up = 1930'), |
| 'chemotherapy': ('administered', 'GDC treatment record: pharmaceutical therapy, nos'), |
| 'radiation_therapy': ('administered', 'GDC treatment record: radiation, external beam'), |
| 'hormone_therapy': ('not_stated', None), |
| }, |
| 'TCGA-BG-A0MO': { |
| 'vital_status': ('Alive', 'GDC demographic record: vital_status = Alive'), |
| 'disease_response': ('TF-Tumor Free', 'GDC follow-up record: disease_response = TF-Tumor Free'), |
| 'days_to_last_follow_up': ('1309', 'GDC last-follow-up record: days_to_last_follow_up = 1309'), |
| 'chemotherapy': ('administered', 'GDC treatment record: pharmaceutical therapy, nos'), |
| 'radiation_therapy': ('administered', 'GDC treatment record: radiation, implants'), |
| 'hormone_therapy': ('not_stated', None), |
| }, |
| 'TCGA-BG-A0VV': { |
| 'vital_status': ('Alive', 'GDC demographic record: vital_status = Alive'), |
| 'disease_response': ('TF-Tumor Free', 'GDC follow-up record: disease_response = TF-Tumor Free'), |
| 'days_to_last_follow_up': ('1553', 'GDC last-follow-up record: days_to_last_follow_up = 1553'), |
| 'chemotherapy': ('administered', 'GDC treatment record: pharmaceutical therapy, nos'), |
| 'radiation_therapy': ('administered', 'GDC treatment record: radiation therapy, nos'), |
| 'hormone_therapy': ('not_stated', None), |
| }, |
| 'TCGA-BG-A3PP': { |
| 'vital_status': ('Alive', 'GDC demographic record: vital_status = Alive'), |
| 'disease_response': ('WT-With Tumor', 'GDC follow-up record: disease_response = WT-With Tumor'), |
| 'days_to_last_follow_up': ('681', 'GDC last-follow-up record: days_to_last_follow_up = 681'), |
| 'chemotherapy': ('administered', 'GDC treatment record: chemotherapy'), |
| 'radiation_therapy': ('administered', 'GDC treatment record: radiation, external beam'), |
| 'hormone_therapy': ('not_stated', None), |
| }, |
| 'TCGA-D1-A16O': { |
| 'vital_status': ('Alive', 'GDC demographic record: vital_status = Alive'), |
| 'disease_response': ('TF-Tumor Free', 'GDC follow-up record: disease_response = TF-Tumor Free'), |
| 'days_to_last_follow_up': ('1023', 'GDC last-follow-up record: days_to_last_follow_up = 1023'), |
| 'chemotherapy': ('administered', 'GDC treatment record: pharmaceutical therapy, nos'), |
| 'radiation_therapy': ('administered', 'GDC treatment record: radiation therapy, nos'), |
| 'hormone_therapy': ('not_stated', None), |
| }, |
| 'TCGA-SL-A6JA': { |
| 'vital_status': ('Alive', 'GDC demographic record: vital_status = Alive'), |
| 'disease_response': ('TF-Tumor Free', 'GDC follow-up record: disease_response = TF-Tumor Free'), |
| 'days_to_last_follow_up': ('7', 'GDC last-follow-up record: days_to_last_follow_up = 7'), |
| 'chemotherapy': ('administered', 'GDC treatment record: pharmaceutical therapy, nos'), |
| 'radiation_therapy': ('administered', 'GDC treatment record: radiation therapy, nos'), |
| 'hormone_therapy': ('not_stated', None), |
| }, |
| 'TCGA-AJ-A5DV': { |
| 'vital_status': ('Alive', 'GDC demographic record: vital_status = Alive'), |
| 'disease_response': ('TF-Tumor Free', 'GDC follow-up record: disease_response = TF-Tumor Free'), |
| 'days_to_last_follow_up': ('679', 'GDC last-follow-up record: days_to_last_follow_up = 679'), |
| 'chemotherapy': ('administered', 'GDC treatment record: pharmaceutical therapy, nos'), |
| 'radiation_therapy': ('administered', 'GDC treatment record: radiation therapy, nos'), |
| 'hormone_therapy': ('not_stated', None), |
| }, |
| 'TCGA-AX-A3FS': { |
| 'vital_status': ('Alive', 'GDC demographic record: vital_status = Alive'), |
| 'disease_response': ('not_stated', None), |
| 'days_to_last_follow_up': ('7', 'GDC last-follow-up record: days_to_last_follow_up = 7'), |
| 'chemotherapy': ('administered', 'GDC treatment record: pharmaceutical therapy, nos'), |
| 'radiation_therapy': ('administered', 'GDC treatment record: radiation therapy, nos'), |
| 'hormone_therapy': ('not_stated', None), |
| }, |
| 'TCGA-BG-A222': { |
| 'vital_status': ('Alive', 'GDC demographic record: vital_status = Alive'), |
| 'disease_response': ('TF-Tumor Free', 'GDC follow-up record: disease_response = TF-Tumor Free'), |
| 'days_to_last_follow_up': ('291', 'GDC last-follow-up record: days_to_last_follow_up = 291'), |
| 'chemotherapy': ('administered', 'GDC treatment record: pharmaceutical therapy, nos'), |
| 'radiation_therapy': ('administered', 'GDC treatment record: radiation therapy, nos'), |
| 'hormone_therapy': ('not_stated', None), |
| }, |
| 'TCGA-D1-A0ZQ': { |
| 'vital_status': ('Alive', 'GDC demographic record: vital_status = Alive'), |
| 'disease_response': ('TF-Tumor Free', 'GDC follow-up record: disease_response = TF-Tumor Free'), |
| 'days_to_last_follow_up': ('0', 'GDC last-follow-up record: days_to_last_follow_up = 0'), |
| 'chemotherapy': ('administered', 'GDC treatment record: pharmaceutical therapy, nos'), |
| 'radiation_therapy': ('administered', 'GDC treatment record: radiation therapy, nos'), |
| 'hormone_therapy': ('not_stated', None), |
| }, |
| 'TCGA-D1-A16F': { |
| 'vital_status': ('Alive', 'GDC demographic record: vital_status = Alive'), |
| 'disease_response': ('TF-Tumor Free', 'GDC follow-up record: disease_response = TF-Tumor Free'), |
| 'days_to_last_follow_up': ('80', 'GDC last-follow-up record: days_to_last_follow_up = 80'), |
| 'chemotherapy': ('administered', 'GDC treatment record: pharmaceutical therapy, nos'), |
| 'radiation_therapy': ('administered', 'GDC treatment record: radiation therapy, nos'), |
| 'hormone_therapy': ('not_stated', None), |
| }, |
| 'TCGA-D1-A2G5': { |
| 'vital_status': ('Alive', 'GDC demographic record: vital_status = Alive'), |
| 'disease_response': ('Unknown', 'GDC follow-up record: disease_response = Unknown'), |
| 'days_to_last_follow_up': ('1455', 'GDC last-follow-up record: days_to_last_follow_up = 1455'), |
| 'chemotherapy': ('administered', 'GDC treatment record: pharmaceutical therapy, nos'), |
| 'radiation_therapy': ('administered', 'GDC treatment record: radiation therapy, nos'), |
| 'hormone_therapy': ('not_stated', None), |
| }, |
| 'TCGA-EY-A1GI': { |
| 'vital_status': ('Alive', 'GDC demographic record: vital_status = Alive'), |
| 'disease_response': ('TF-Tumor Free', 'GDC follow-up record: disease_response = TF-Tumor Free'), |
| 'days_to_last_follow_up': ('710', 'GDC last-follow-up record: days_to_last_follow_up = 710'), |
| 'chemotherapy': ('administered', 'GDC treatment record: pharmaceutical therapy, nos'), |
| 'radiation_therapy': ('administered', 'GDC treatment record: brachytherapy, high dose'), |
| 'hormone_therapy': ('not_stated', None), |
| }, |
| 'TCGA-KP-A3W1': { |
| 'vital_status': ('Alive', 'GDC demographic record: vital_status = Alive'), |
| 'disease_response': ('TF-Tumor Free', 'GDC follow-up record: disease_response = TF-Tumor Free'), |
| 'days_to_last_follow_up': ('288', 'GDC last-follow-up record: days_to_last_follow_up = 288'), |
| 'chemotherapy': ('administered', 'GDC treatment record: pharmaceutical therapy, nos'), |
| 'radiation_therapy': ('administered', 'GDC treatment record: radiation therapy, nos'), |
| 'hormone_therapy': ('not_stated', None), |
| }, |
| }, |
| 'registry_join': { |
| 'TCGA-D1-A15W': { |
| 'cause_of_death': ('not_applicable', None), |
| 'second_primary_cancer': ('none reported', 'Illustrative example; this source is not part of the open TCGA-UCEC corpus.'), |
| }, |
| 'TCGA-BG-A3PP': { |
| 'cause_of_death': ('not_stated', None), |
| 'second_primary_cancer': ('none reported', 'Illustrative example; this source is not part of the open TCGA-UCEC corpus.'), |
| }, |
| }, |
| 'local_research': { |
| 'TCGA-AP-A059': { |
| 'tumor_board_reviewed': ('yes', 'Illustrative example; this source is not part of the open TCGA-UCEC corpus.'), |
| 'trial_enrollment': ('not enrolled', 'Illustrative example; this source is not part of the open TCGA-UCEC corpus.'), |
| }, |
| 'TCGA-SL-A6JA': { |
| 'tumor_board_reviewed': ('yes', 'Illustrative example; this source is not part of the open TCGA-UCEC corpus.'), |
| 'trial_enrollment': ('not enrolled', 'Illustrative example; this source is not part of the open TCGA-UCEC corpus.'), |
| }, |
| }, |
| } |
|
|
