cdapython 2.0.12__tar.gz → 2.0.14__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {cdapython-2.0.12 → cdapython-2.0.14}/CHANGELOG.md +4 -0
- {cdapython-2.0.12 → cdapython-2.0.14}/PKG-INFO +1 -1
- {cdapython-2.0.12 → cdapython-2.0.14}/cdapython/get_data.py +634 -6
- {cdapython-2.0.12 → cdapython-2.0.14}/pyproject.toml +1 -1
- {cdapython-2.0.12 → cdapython-2.0.14}/LICENSE +0 -0
- {cdapython-2.0.12 → cdapython-2.0.14}/README.md +0 -0
- {cdapython-2.0.12 → cdapython-2.0.14}/cdapython/__init__.py +0 -0
- {cdapython-2.0.12 → cdapython-2.0.14}/cdapython/application_utilities.py +0 -0
- {cdapython-2.0.12 → cdapython-2.0.14}/cdapython/config/__init__.py +0 -0
- {cdapython-2.0.12 → cdapython-2.0.14}/cdapython/config/logger_default_config.yml +0 -0
- {cdapython-2.0.12 → cdapython-2.0.14}/cdapython/discover.py +0 -0
- {cdapython-2.0.12 → cdapython-2.0.14}/cdapython/logging_wrappers.py +0 -0
- {cdapython-2.0.12 → cdapython-2.0.14}/cdapython/summarize.py +0 -0
- {cdapython-2.0.12 → cdapython-2.0.14}/cdapython/validation.py +0 -0
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@@ -1,3 +1,7 @@
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2025-12-09: 2.0.14: add sort postproc to POC disease\_slims return column
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2025-12-09: 2.0.13: add POC `include\_disease\_slims` Boolean flag to get\_data()
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2025-10-31: 2.0.12: standardize debug-layer SQL echo; adjust column\_values() to handle known pathologies
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2025-10-27: 2.0.11: _cough_ bugfix for previous
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@@ -43,7 +43,8 @@ def get_file_data(
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exclude_columns=None,
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collate_results=False,
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return_data_as='dataframe',
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output_file=''
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output_file='',
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include_disease_slims=False
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):
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"""
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Get CDA file rows ('result rows') that match user-specified criteria.
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@@ -141,7 +142,7 @@ def get_file_data(
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"""
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return get_data( table='file', match_all=match_all, match_any=match_any, match_from_file=match_from_file, data_source=data_source, add_columns=add_columns, exclude_columns=exclude_columns, collate_results=collate_results, include_external_refs=False, return_data_as=return_data_as, output_file=output_file )
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return get_data( table='file', match_all=match_all, match_any=match_any, match_from_file=match_from_file, data_source=data_source, add_columns=add_columns, exclude_columns=exclude_columns, collate_results=collate_results, include_external_refs=False, return_data_as=return_data_as, output_file=output_file, include_disease_slims=include_disease_slims )
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#############################################################################################################################
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#
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@@ -160,7 +161,8 @@ def get_subject_data(
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collate_results=False,
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include_external_refs=False,
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return_data_as='dataframe',
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output_file=''
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output_file='',
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include_disease_slims=False
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):
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"""
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Get CDA subject rows ('result rows') that match user-specified criteria.
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"""
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return get_data( table='subject', match_all=match_all, match_any=match_any, match_from_file=match_from_file, data_source=data_source, add_columns=add_columns, exclude_columns=exclude_columns, collate_results=collate_results, include_external_refs=include_external_refs, return_data_as=return_data_as, output_file=output_file )
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return get_data( table='subject', match_all=match_all, match_any=match_any, match_from_file=match_from_file, data_source=data_source, add_columns=add_columns, exclude_columns=exclude_columns, collate_results=collate_results, include_external_refs=include_external_refs, return_data_as=return_data_as, output_file=output_file, include_disease_slims=include_disease_slims )
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#############################################################################################################################
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#
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collate_results=False,
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include_external_refs=False,
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return_data_as='dataframe',
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output_file=''
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output_file='',
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include_disease_slims=False
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):
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"""
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Get CDA data rows ('result rows') from `table` that match user-specified criteria.
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@@ -858,6 +861,631 @@ def get_data(
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if result_record[ f"{table}_data_at_{upstream_data_source.lower()}" ] == True:
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result_dataframe['data_source'].iloc[row_index].append( upstream_data_source )
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# BEGIN :: REMOVE ME AFTER SLIM DB INFRASTRUCTURE UPDATE
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disease_slim_map = {
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866
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'Abdominal fibromatosis': 'Fibromatous neoplasms',
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867
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'Acinar cell adenoma': 'Acinar cell neoplasms',
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868
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+
'Acinar cell carcinoma': 'Acinar cell neoplasms',
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869
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+
'Acinar cell tumor': 'Acinar cell neoplasms',
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870
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'Acral melanoma': 'Nevi and melanomas',
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871
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'Acute erythroid leukemia': 'Leukemias',
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872
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+
'Acute leukemia, NOS': 'Leukemias',
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873
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+
'Acute megakaryoblastic leukemia': 'Leukemias',
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874
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+
'Acute monocytic leukemia': 'Leukemias',
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875
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+
'Acute myeloid leukemia with abnormal marrow eosinophils': 'Leukemias',
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876
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'Acute myeloid leukemia with biallelic mutation of CEBPA': 'Leukemias',
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877
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+
'Acute myeloid leukemia with inv(3)(q21;q26.2) or t(3;3)(q21;q26.2); RPN1-EVI1': 'Leukemias',
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878
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'Acute myeloid leukemia with maturation': 'Leukemias',
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879
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+
'Acute myeloid leukemia with mutated NPM1': 'Leukemias',
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880
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+
'Acute myeloid leukemia with myelodysplasia-related changes': 'Leukemias',
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881
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+
'Acute myeloid leukemia with t(6;9)(p23;q34); DEK-NUP214': 'Leukemias',
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882
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+
'Acute myeloid leukemia without maturation': 'Leukemias',
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883
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+
'Acute myeloid leukemia, 11q23 abnormalities': 'Leukemias',
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884
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+
'Acute myeloid leukemia, NOS': 'Leukemias',
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885
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'Acute myeloid leukemia, minimal differentiation': 'Leukemias',
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886
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+
'Acute myeloid leukemia, t(8;21)(q22;q22)': 'Leukemias',
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887
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+
'Acute myelomonocytic leukemia, NOS': 'Leukemias',
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888
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+
'Acute promyelocytic leukemia, t(15;17)(q22;q11-12)': 'Leukemias',
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889
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'Adenocarcinoma in adenomatous polyposis coli': 'Adenomas and adenocarcinomas',
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890
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+
'Adenocarcinoma in situ in adenomatous polyp': 'Adenomas and adenocarcinomas',
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891
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'Adenocarcinoma in situ, NOS': 'Adenomas and adenocarcinomas',
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892
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'Adenocarcinoma in tubulovillous adenoma': 'Adenomas and adenocarcinomas',
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893
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'Adenocarcinoma in villous adenoma': 'Adenomas and adenocarcinomas',
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894
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'Adenocarcinoma of anal glands': 'Adenomas and adenocarcinomas',
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895
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'Adenocarcinoma of the lung, mucinous': 'Adenomas and adenocarcinomas',
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896
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'Adenocarcinoma with mixed subtypes': 'Adenomas and adenocarcinomas',
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897
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'Adenocarcinoma with neuroendocrine differentiation': 'Complex epithelial neoplasms',
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898
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'Adenocarcinoma, NOS': 'Adenomas and adenocarcinomas',
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899
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'Adenocarcinoma, endocervical type': 'Adenomas and adenocarcinomas',
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900
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'Adenocarcinoma, intestinal type': 'Adenomas and adenocarcinomas',
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901
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'Adenocarcinoma, metastatic, NOS': 'Adenomas and adenocarcinomas',
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902
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'Adenoid basal carcinoma': 'Basal cell neoplasms',
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903
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'Adenoid cystic carcinoma': 'Adenomas and adenocarcinomas',
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904
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'Adenoma, NOS': 'Adenomas and adenocarcinomas',
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905
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'Adenomatous polyp, NOS': 'Adenomas and adenocarcinomas',
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906
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'Adenomatous polyposis coli': 'Adenomas and adenocarcinomas',
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907
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'Adenomyoepithelioma, NOS': 'Complex mixed and stromal neoplasms',
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908
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'Adenosarcoma': 'Complex mixed and stromal neoplasms',
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909
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'Adenosquamous carcinoma': 'Complex epithelial neoplasms',
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910
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'Adnexal adenocarcinoma, NOS': 'Adnexal and skin appendage neoplasms',
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911
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'Adnexal and skin appendage neoplasms': 'Adnexal and skin appendage neoplasms',
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912
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'Adrenal cortical adenoma, NOS': 'Adenomas and adenocarcinomas',
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913
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'Adrenal cortical carcinoma': 'Adenomas and adenocarcinomas',
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914
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'Adult T-cell leukemia/lymphoma (HTLV-1 positive)': 'Leukemias',
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915
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'Adult granulosa cell tumor of ovary': 'Specialized gonadal neoplasms',
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916
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'Adult granulosa cell tumor of testis': 'Specialized gonadal neoplasms',
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917
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'Aggressive fibromatosis': 'Fibromatous neoplasms',
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918
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'Alveolar rhabdomyosarcoma': 'Myomatous neoplasms',
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919
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'Alveolar soft part sarcoma': 'Granular cell tumors and alveolar soft part sarcomas',
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920
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'Amelanotic melanoma': 'Nevi and melanomas',
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'Anaplastic large cell lymphoma, T-cell and Null-cell type': 'Hodgkin and non-Hodgkin lymphomas',
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922
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'Angiocentric glioma': 'Gliomas',
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923
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'Angioimmunoblastic T-cell lymphoma': 'Hodgkin and non-Hodgkin lymphomas',
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924
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'Angiomatoid fibrous histiocytoma': 'Fibromatous neoplasms',
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925
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'Angiomyofibroblastoma': 'Fibromatous neoplasms',
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'Angiomyolipoma': 'Lipomatous neoplasms',
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'Angiomyosarcoma': 'Myomatous neoplasms',
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'Aortic body tumor': 'Paragangliomas and glomus tumors',
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'Apocrine adenocarcinoma': 'Adnexal and skin appendage neoplasms',
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930
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'Astroblastoma': 'Gliomas',
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'Astrocytoma, NOS': 'Gliomas',
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'Astrocytoma, anaplastic': 'Gliomas',
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'Atypical adenoma': 'Adenomas and adenocarcinomas',
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'Atypical choroid plexus papilloma': 'Gliomas',
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'Atypical chronic myeloid leukemia, BCR/ABL negative': 'Leukemias',
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'Atypical meningioma': 'Meningiomas',
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937
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'Atypical teratoid/rhabdoid tumor': 'Neuroepitheliomatous neoplasms',
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'B lymphoblastic leukemia/lymphoma with hyperdiploidy': 'Leukemias',
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'B lymphoblastic leukemia/lymphoma with hypodiploidy(Hypodiploid ALL)': 'Leukemias',
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'B lymphoblastic leukemia/lymphoma with t(12;21)(p13;q22); TEL-AML1(ETV6-RUNX1)': 'Leukemias',
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'B lymphoblastic leukemia/lymphoma with t(1;19)(q23;p13.3); E2A-PBX1(TCF3-PBX1)': 'Leukemias',
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'B lymphoblastic leukemia/lymphoma with t(9;22)(q34;q11.2); BCR-ABL1': 'Leukemias',
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'B lymphoblastic leukemia/lymphoma with t(v;11q23); MLL rearranged': 'Leukemias',
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'B lymphoblastic leukemia/lymphoma, NOS': 'Leukemias',
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'B-cell chronic lymphocytic leukemia/small lymphocytic lymphoma': 'Leukemias',
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'Basal cell adenocarcinoma': 'Adenomas and adenocarcinomas',
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'Basal cell carcinoma, NOS': 'Basal cell neoplasms',
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948
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'Basal cell carcinoma, nodular': 'Basal cell neoplasms',
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949
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'Basal cell neoplasms': 'Basal cell neoplasms',
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950
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'Basaloid carcinoma': 'Transitional cell papillomas and carcinomas',
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951
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'Basaloid squamous cell carcinoma': 'Squamous cell neoplasms',
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952
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'Benign cystic nephroma': 'Complex mixed and stromal neoplasms',
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953
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'Blood vessel tumors': 'Blood vessel tumors',
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954
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'Blue nevus, malignant': 'Nevi and melanomas',
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955
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'Borderline Intraductal carcinoma and lobular': 'Ductal and lobular neoplasms',
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956
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'Brenner tumor, NOS': 'Fibroepithelial neoplasms',
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957
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'Bronchiolo-alveolar carcinoma, non-mucinous': 'Adenomas and adenocarcinomas',
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958
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'Burkitt lymphoma, NOS': 'Hodgkin and non-Hodgkin lymphomas',
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959
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'CNS embryonal tumor, NOS': 'Gliomas',
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960
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'Carcinoma in situ, NOS': 'Epithelial neoplasms',
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961
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'Carcinoma with osteoclast-like giant cells': 'Epithelial neoplasms',
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962
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'Carcinoma, NOS': 'Epithelial neoplasms',
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963
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'Carcinoma, anaplastic, NOS': 'Epithelial neoplasms',
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964
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'Carcinoma, diffuse type': 'Adenomas and adenocarcinomas',
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965
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'Carcinoma, metastatic, NOS': 'Epithelial neoplasms',
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966
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'Carcinoma, undifferentiated, NOS': 'Epithelial neoplasms',
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967
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'Carcinosarcoma, NOS': 'Complex mixed and stromal neoplasms',
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968
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'Cavernous hemangioma': 'Blood vessel tumors',
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969
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'Central neurocytoma': 'Neuroepitheliomatous neoplasms',
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970
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'Central osteosarcoma, NOS': 'Osseous and chondromatous neoplasms',
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971
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'Cholangiocarcinoma': 'Adenomas and adenocarcinomas',
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972
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'Chondroblastic osteosarcoma': 'Osseous and chondromatous neoplasms',
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973
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'Chondroblastoma, NOS': 'Osseous and chondromatous neoplasms',
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974
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'Chondroid chordoma': 'Miscellaneous tumors',
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975
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'Chondrosarcoma, NOS': 'Osseous and chondromatous neoplasms',
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976
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'Chordoma, NOS': 'Miscellaneous tumors',
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977
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'Choriocarcinoma combined with other germ cell elements': 'Trophoblastic neoplasms',
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978
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'Choriocarcinoma, NOS': 'Trophoblastic neoplasms',
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979
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'Choroid plexus carcinoma': 'Gliomas',
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980
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'Choroid plexus papilloma, NOS': 'Gliomas',
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981
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'Chronic eosinophilic leukemia': 'Chronic myeloproliferative disorders',
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982
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'Chronic myelogenous leukemia, BCR/ABL positive': 'Leukemias',
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983
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'Chronic myeloid leukemia, NOS': 'Leukemias',
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984
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'Chronic myelomonocytic leukemia, NOS': 'Leukemias',
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985
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'Chronic neutrophilic leukemia': 'Chronic myeloproliferative disorders',
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986
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'Clear cell adenocarcinoma, NOS': 'Adenomas and adenocarcinomas',
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987
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'Clear cell adenoma': 'Adenomas and adenocarcinomas',
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988
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'Clear cell meningioma': 'Meningiomas',
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989
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'Clear cell odontogenic carcinoma': 'Odontogenic tumors',
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990
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'Clear cell sarcoma of kidney': 'Complex mixed and stromal neoplasms',
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991
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'Clear cell sarcoma, NOS': 'Synovial-like neoplasms',
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992
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'Collecting duct carcinoma': 'Adenomas and adenocarcinomas',
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993
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'Combined hepatocellular carcinoma and cholangiocarcinoma': 'Adenomas and adenocarcinomas',
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994
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'Combined small cell carcinoma': 'Epithelial neoplasms',
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995
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'Comedocarcinoma, noninfiltrating': 'Ductal and lobular neoplasms',
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996
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'Complex epithelial neoplasms': 'Complex epithelial neoplasms',
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997
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'Complex mixed and stromal neoplasms': 'Complex mixed and stromal neoplasms',
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998
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'Composite Hodgkin and non-Hodgkin lymphoma': 'Hodgkin and non-Hodgkin lymphomas',
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999
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'Craniopharyngioma': 'Miscellaneous tumors',
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1000
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'Craniopharyngioma, adamantinomatous': 'Miscellaneous tumors',
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1001
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'Craniopharyngioma, papillary': 'Miscellaneous tumors',
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1002
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'Cribriform carcinoma, NOS': 'Adenomas and adenocarcinomas',
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1003
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'Cutaneous T-cell lymphoma, NOS': 'Hodgkin and non-Hodgkin lymphomas',
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1004
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'Cystadenocarcinoma, NOS': 'Cystic, mucinous and serous neoplasms',
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1005
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'Cystic, mucinous and serous neoplasms': 'Cystic, mucinous and serous neoplasms',
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1006
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'Dedifferentiated chondrosarcoma': 'Osseous and chondromatous neoplasms',
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1007
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'Dedifferentiated liposarcoma': 'Lipomatous neoplasms',
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1008
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'Dermatofibroma, NOS': 'Fibromatous neoplasms',
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1009
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'Dermatofibrosarcoma protuberans, NOS': 'Fibromatous neoplasms',
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1010
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'Dermatofibrosarcoma protuberans, fibrosarcomatous': 'Fibromatous neoplasms',
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1011
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'Dermoid cyst, NOS': 'Germ cell neoplasms',
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1012
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'Desmoplastic infantile astrocytoma': 'Gliomas',
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1013
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'Desmoplastic melanoma': 'Nevi and melanomas',
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1014
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'Desmoplastic nodular medulloblastoma': 'Gliomas',
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1015
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'Desmoplastic small round cell tumor': 'Soft tissue tumors and sarcomas',
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1016
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'Diffuse large B-cell lymphoma, NOS': 'Hodgkin and non-Hodgkin lymphomas',
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1017
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'Diffuse midline glioma, H3 K27M-mutant': 'Gliomas',
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1018
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'Ductal and lobular neoplasms': 'Ductal and lobular neoplasms',
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1019
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'Dysembryoplastic neuroepithelial tumor': 'Gliomas',
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1020
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'Dysgerminoma': 'Germ cell neoplasms',
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1021
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'Embryonal carcinoma, NOS': 'Germ cell neoplasms',
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1022
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'Embryonal rhabdomyosarcoma, NOS': 'Myomatous neoplasms',
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1023
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'Embryonal sarcoma': 'Complex mixed and stromal neoplasms',
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1024
|
+
'Embryonal tumor with multilayered rosettes with C19MC alteration': 'Gliomas',
|
|
1025
|
+
'Endometrial stromal sarcoma, NOS': 'Complex mixed and stromal neoplasms',
|
|
1026
|
+
'Endometrial stromal sarcoma, low grade': 'Complex mixed and stromal neoplasms',
|
|
1027
|
+
'Endometrioid adenocarcinoma, NOS': 'Adenomas and adenocarcinomas',
|
|
1028
|
+
'Endometrioid adenocarcinoma, secretory variant': 'Adenomas and adenocarcinomas',
|
|
1029
|
+
'Endometrioid adenoma, borderline malignancy': 'Adenomas and adenocarcinomas',
|
|
1030
|
+
'Ependymoma, NOS': 'Gliomas',
|
|
1031
|
+
'Ependymoma, RELA fusion-positive': 'Gliomas',
|
|
1032
|
+
'Ependymoma, anaplastic': 'Gliomas',
|
|
1033
|
+
'Epithelial tumor, benign': 'Epithelial neoplasms',
|
|
1034
|
+
'Epithelial-myoepithelial carcinoma': 'Complex epithelial neoplasms',
|
|
1035
|
+
'Epithelioid cell melanoma': 'Nevi and melanomas',
|
|
1036
|
+
'Epithelioid cell nevus': 'Nevi and melanomas',
|
|
1037
|
+
'Epithelioid hemangioendothelioma, NOS': 'Blood vessel tumors',
|
|
1038
|
+
'Epithelioid leiomyosarcoma': 'Myomatous neoplasms',
|
|
1039
|
+
'Epithelioid mesothelioma, malignant': 'Mesothelial neoplasms',
|
|
1040
|
+
'Epithelioid sarcoma': 'Soft tissue tumors and sarcomas',
|
|
1041
|
+
'Essential thrombocythemia': 'Chronic myeloproliferative disorders',
|
|
1042
|
+
'Ewing sarcoma': 'Miscellaneous tumors',
|
|
1043
|
+
'Extra-adrenal paraganglioma, NOS': 'Paragangliomas and glomus tumors',
|
|
1044
|
+
'Fibrillary astrocytoma': 'Gliomas',
|
|
1045
|
+
'Fibroblastic osteosarcoma': 'Osseous and chondromatous neoplasms',
|
|
1046
|
+
'Fibroepithelial neoplasms': 'Fibroepithelial neoplasms',
|
|
1047
|
+
'Fibrolipoma': 'Lipomatous neoplasms',
|
|
1048
|
+
'Fibroma, NOS': 'Fibromatous neoplasms',
|
|
1049
|
+
'Fibromatous neoplasms': 'Fibromatous neoplasms',
|
|
1050
|
+
'Fibrosarcoma, NOS': 'Fibromatous neoplasms',
|
|
1051
|
+
'Fibrous mesothelioma, malignant': 'Mesothelial neoplasms',
|
|
1052
|
+
'Follicular adenocarcinoma, well differentiated': 'Adenomas and adenocarcinomas',
|
|
1053
|
+
'Follicular carcinoma, NOS': 'Adenomas and adenocarcinomas',
|
|
1054
|
+
'Follicular carcinoma, minimally invasive': 'Adenomas and adenocarcinomas',
|
|
1055
|
+
'Follicular dendritic cell sarcoma': 'Neoplasms of histiocytes and accessory lymphoid cells',
|
|
1056
|
+
'Follicular lymphoma, NOS': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1057
|
+
'Gangliocytoma, NOS': 'Neuroepitheliomatous neoplasms',
|
|
1058
|
+
'Ganglioglioma, NOS': 'Neuroepitheliomatous neoplasms',
|
|
1059
|
+
'Ganglioglioma, anaplastic': 'Neuroepitheliomatous neoplasms',
|
|
1060
|
+
'Ganglioneuroblastoma': 'Neuroepitheliomatous neoplasms',
|
|
1061
|
+
'Ganglioneuroma': 'Neuroepitheliomatous neoplasms',
|
|
1062
|
+
'Gastrointestinal stromal tumor': 'Complex mixed and stromal neoplasms',
|
|
1063
|
+
'Gastrointestinal stromal tumor, NOS': 'Complex mixed and stromal neoplasms',
|
|
1064
|
+
'Gastrointestinal stromal tumor, benign': 'Complex mixed and stromal neoplasms',
|
|
1065
|
+
'Genital rhabdomyoma': 'Myomatous neoplasms',
|
|
1066
|
+
'Germ cell neoplasms': 'Germ cell neoplasms',
|
|
1067
|
+
'Germ cell tumor, nonseminomatous': 'Germ cell neoplasms',
|
|
1068
|
+
'Germinoma': 'Germ cell neoplasms',
|
|
1069
|
+
'Giant cell carcinoma': 'Epithelial neoplasms',
|
|
1070
|
+
'Giant cell glioblastoma': 'Gliomas',
|
|
1071
|
+
'Giant cell sarcoma': 'Soft tissue tumors and sarcomas',
|
|
1072
|
+
'Giant cell tumor of bone, NOS': 'Giant cell tumors',
|
|
1073
|
+
'Giant cell tumor of bone, malignant': 'Giant cell tumors',
|
|
1074
|
+
'Giant cell tumor of soft parts, NOS': 'Giant cell tumors',
|
|
1075
|
+
'Giant pigmented nevus, NOS': 'Nevi and melanomas',
|
|
1076
|
+
'Glassy cell carcinoma': 'Epithelial neoplasms',
|
|
1077
|
+
'Glioblastoma, IDH-mutant': 'Gliomas',
|
|
1078
|
+
'Glioblastoma, NOS': 'Gliomas',
|
|
1079
|
+
'Glioma, malignant': 'Gliomas',
|
|
1080
|
+
'Gliomatosis cerebri': 'Gliomas',
|
|
1081
|
+
'Gliosarcoma': 'Gliomas',
|
|
1082
|
+
'Glomangiosarcoma': 'Paragangliomas and glomus tumors',
|
|
1083
|
+
'Glomus tumor, NOS': 'Paragangliomas and glomus tumors',
|
|
1084
|
+
'Glomus tumor, malignant': 'Paragangliomas and glomus tumors',
|
|
1085
|
+
'Goblet cell carcinoid': 'Adenomas and adenocarcinomas',
|
|
1086
|
+
'Granular cell tumor, NOS': 'Granular cell tumors and alveolar soft part sarcomas',
|
|
1087
|
+
'Granulosa cell tumor, juvenile': 'Specialized gonadal neoplasms',
|
|
1088
|
+
'HHV8-positive diffuse large B-cell lymphoma': 'Plasma Cell Tumors',
|
|
1089
|
+
'Hairy cell leukemia, NOS': 'Leukemias',
|
|
1090
|
+
'Hemangioblastoma': 'Blood vessel tumors',
|
|
1091
|
+
'Hemangioendothelioma, NOS': 'Blood vessel tumors',
|
|
1092
|
+
'Hemangioendothelioma, malignant': 'Blood vessel tumors',
|
|
1093
|
+
'Hemangioma, NOS': 'Blood vessel tumors',
|
|
1094
|
+
'Hemangiosarcoma': 'Blood vessel tumors',
|
|
1095
|
+
'Hepatoblastoma, NOS': 'Complex mixed and stromal neoplasms',
|
|
1096
|
+
'Hepatocellular carcinoma, NOS': 'Adenomas and adenocarcinomas',
|
|
1097
|
+
'Hepatocellular carcinoma, clear cell type': 'Adenomas and adenocarcinomas',
|
|
1098
|
+
'Hepatocellular carcinoma, fibrolamellar': 'Adenomas and adenocarcinomas',
|
|
1099
|
+
'Hepatocellular carcinoma, spindle cell variant': 'Adenomas and adenocarcinomas',
|
|
1100
|
+
'Hepatoid adenocarcinoma': 'Complex epithelial neoplasms',
|
|
1101
|
+
'Hepatosplenic T-cell lymphoma': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1102
|
+
'Hereditary leiomyomatosis and renal cell carcinoma (HRCC)-associated renal cell carcinoma': 'Adenomas and adenocarcinomas',
|
|
1103
|
+
'Hibernoma': 'Lipomatous neoplasms',
|
|
1104
|
+
'High grade serous carcinoma': 'Cystic, mucinous and serous neoplasms',
|
|
1105
|
+
'High grade surface osteosarcoma': 'Osseous and chondromatous neoplasms',
|
|
1106
|
+
'Histiocytic sarcoma': 'Neoplasms of histiocytes and accessory lymphoid cells',
|
|
1107
|
+
'Hodgkin lymphoma, NOS': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1108
|
+
'Hodgkin lymphoma, nodular lymphocyte predominant': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1109
|
+
'Hodgkin lymphoma, nodular sclerosis, NOS': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1110
|
+
'Hyalinizing trabecular tumor': 'Adenomas and adenocarcinomas',
|
|
1111
|
+
'Hydatidiform mole, NOS': 'Trophoblastic neoplasms',
|
|
1112
|
+
'Indolent systemic mastocytosis': 'Mast Cell Tumors',
|
|
1113
|
+
'Infantile fibrosarcoma': 'Fibromatous neoplasms',
|
|
1114
|
+
'Infiltrating duct and lobular carcinoma': 'Ductal and lobular neoplasms',
|
|
1115
|
+
'Infiltrating duct carcinoma, NOS': 'Ductal and lobular neoplasms',
|
|
1116
|
+
'Infiltrating duct mixed with other types of carcinoma': 'Ductal and lobular neoplasms',
|
|
1117
|
+
'Infiltrating ductular carcinoma': 'Ductal and lobular neoplasms',
|
|
1118
|
+
'Infiltrating ductular carcinoma, borderline malignancy': 'Ductal and lobular neoplasms',
|
|
1119
|
+
'Infiltrating lobular mixed with other types of carcinoma': 'Ductal and lobular neoplasms',
|
|
1120
|
+
'Inflammatory carcinoma': 'Ductal and lobular neoplasms',
|
|
1121
|
+
'Interdigitating dendritic cell sarcoma': 'Neoplasms of histiocytes and accessory lymphoid cells',
|
|
1122
|
+
'Intimal sarcoma': 'Blood vessel tumors',
|
|
1123
|
+
'Intraductal Papillary mucinous adenoma': 'Cystic, mucinous and serous neoplasms',
|
|
1124
|
+
'Intraductal Papillary mucinous neoplasm with an associated invasive carcinoma': 'Cystic, mucinous and serous neoplasms',
|
|
1125
|
+
'Intraductal Papillary mucinous neoplasm with high grade dysplasia': 'Cystic, mucinous and serous neoplasms',
|
|
1126
|
+
'Intraductal carcinoma, noninfiltrating, NOS': 'Ductal and lobular neoplasms',
|
|
1127
|
+
'Intraductal micropapillary carcinoma': 'Ductal and lobular neoplasms',
|
|
1128
|
+
'Intraductal papillary adenocarcinoma with invasion': 'Ductal and lobular neoplasms',
|
|
1129
|
+
'Intravascular large B-cell lymphoma': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1130
|
+
'Invasive micropapillary carcinoma of breast': 'Ductal and lobular neoplasms',
|
|
1131
|
+
'Juvenile myelomonocytic leukemia, NOS': 'Leukemias',
|
|
1132
|
+
'Kaposi sarcoma': 'Blood vessel tumors',
|
|
1133
|
+
'Kupffer cell sarcoma': 'Blood vessel tumors',
|
|
1134
|
+
'Lactotroph adenoma': 'Adenomas and adenocarcinomas',
|
|
1135
|
+
'Langerhans cell histiocytosis, NOS': 'Neoplasms of histiocytes and accessory lymphoid cells',
|
|
1136
|
+
'Langerhans cell histiocytosis, disseminated': 'Neoplasms of histiocytes and accessory lymphoid cells',
|
|
1137
|
+
'Large cell carcinoma, NOS': 'Epithelial neoplasms',
|
|
1138
|
+
'Large cell medulloblastoma': 'Gliomas',
|
|
1139
|
+
'Large cell neuroendocrine carcinoma': 'Epithelial neoplasms',
|
|
1140
|
+
'Leiomyoma, NOS': 'Myomatous neoplasms',
|
|
1141
|
+
'Leiomyosarcoma, NOS': 'Myomatous neoplasms',
|
|
1142
|
+
'Lentiginous melanocytic nevus': 'Nevi and melanomas',
|
|
1143
|
+
'Lentigo maligna': 'Nevi and melanomas',
|
|
1144
|
+
'Lentigo maligna melanoma': 'Nevi and melanomas',
|
|
1145
|
+
'Lepidic adenocarcinoma': 'Adenomas and adenocarcinomas',
|
|
1146
|
+
'Leukemia, NOS': 'Leukemias',
|
|
1147
|
+
'Leydig cell tumor of the ovary, NOS': 'Specialized gonadal neoplasms',
|
|
1148
|
+
'Leydig cell tumor of the testis, NOS': 'Specialized gonadal neoplasms',
|
|
1149
|
+
'Lipid cell tumor of ovary': 'Specialized gonadal neoplasms',
|
|
1150
|
+
'Lipoblastomatosis': 'Lipomatous neoplasms',
|
|
1151
|
+
'Lipoma, NOS': 'Lipomatous neoplasms',
|
|
1152
|
+
'Liposarcoma, NOS': 'Lipomatous neoplasms',
|
|
1153
|
+
'Liposarcoma, well differentiated, NOS': 'Lipomatous neoplasms',
|
|
1154
|
+
'Lobular carcinoma in situ, NOS': 'Ductal and lobular neoplasms',
|
|
1155
|
+
'Lobular carcinoma, NOS': 'Ductal and lobular neoplasms',
|
|
1156
|
+
'Low cumulative sun damage melanoma': 'Nevi and melanomas',
|
|
1157
|
+
'Low grade central osteosarcoma': 'Osseous and chondromatous neoplasms',
|
|
1158
|
+
'Low grade serous carcinoma': 'Cystic, mucinous and serous neoplasms',
|
|
1159
|
+
'Lymphangioleiomyomatosis': 'Lymphatic vessel tumors',
|
|
1160
|
+
'Lymphangioma, NOS': 'Lymphatic vessel tumors',
|
|
1161
|
+
'Lymphoepithelial carcinoma': 'Squamous cell neoplasms',
|
|
1162
|
+
'Lymphoid leukemia, NOS': 'Leukemias',
|
|
1163
|
+
'Lymphoproliferative disorder, NOS': 'Other hematologic disorders',
|
|
1164
|
+
'Malignant Spitz tumor': 'Nevi and melanomas',
|
|
1165
|
+
'Malignant fibrous histiocytoma': 'Fibromatous neoplasms',
|
|
1166
|
+
'Malignant histiocytosis': 'Neoplasms of histiocytes and accessory lymphoid cells',
|
|
1167
|
+
'Malignant lymphoma, NOS': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1168
|
+
'Malignant lymphoma, non-Hodgkin, NOS': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1169
|
+
'Malignant lymphoma, small B lymphocytic, NOS': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1170
|
+
'Malignant mastocytosis': 'Mast Cell Tumors',
|
|
1171
|
+
'Malignant melanoma, NOS': 'Nevi and melanomas',
|
|
1172
|
+
'Malignant peripheral nerve sheath tumor with rhabdomyoblastic differentiation': 'Nerve sheath tumors',
|
|
1173
|
+
'Malignant peripheral nerve sheath tumor, NOS': 'Nerve sheath tumors',
|
|
1174
|
+
'Malignant tumor, small cell type': 'Neoplasms',
|
|
1175
|
+
'Malignant tumor, spindle cell type': 'Neoplasms',
|
|
1176
|
+
'Mantle cell lymphoma': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1177
|
+
'Marginal zone B-cell lymphoma, NOS': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1178
|
+
'Mast cell leukemia': 'Mast Cell Tumors',
|
|
1179
|
+
'Mastocytoma, NOS': 'Mast Cell Tumors',
|
|
1180
|
+
'Mature B-cell lymphomas': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1181
|
+
'Mature T- and NK-cell lymphomas': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1182
|
+
'Mature T-cell lymphoma, NOS': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1183
|
+
'Mediastinal large B-cell lymphoma': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1184
|
+
'Medullary carcinoma, NOS': 'Ductal and lobular neoplasms',
|
|
1185
|
+
'Medulloblastoma, NOS': 'Gliomas',
|
|
1186
|
+
'Medulloblastoma, non-WNT/non-SHH': 'Gliomas',
|
|
1187
|
+
'Medulloepithelioma, NOS': 'Neuroepitheliomatous neoplasms',
|
|
1188
|
+
'Melanoma in situ': 'Nevi and melanomas',
|
|
1189
|
+
'Melanotic neuroectodermal tumor': 'Miscellaneous tumors',
|
|
1190
|
+
'Melanotic schwannoma': 'Nerve sheath tumors',
|
|
1191
|
+
'Meningeal melanocytoma': 'Nevi and melanomas',
|
|
1192
|
+
'Meningeal melanocytosis': 'Nevi and melanomas',
|
|
1193
|
+
'Meningeal melanomatosis': 'Nevi and melanomas',
|
|
1194
|
+
'Meningioma, NOS': 'Meningiomas',
|
|
1195
|
+
'Meningioma, malignant': 'Meningiomas',
|
|
1196
|
+
'Meningiomatosis, NOS': 'Meningiomas',
|
|
1197
|
+
'Meningothelial meningioma': 'Meningiomas',
|
|
1198
|
+
'Merkel cell carcinoma': 'Adenomas and adenocarcinomas',
|
|
1199
|
+
'Mesenchymal chondrosarcoma': 'Osseous and chondromatous neoplasms',
|
|
1200
|
+
'Mesenchymoma, NOS': 'Complex mixed and stromal neoplasms',
|
|
1201
|
+
'Mesenchymoma, malignant': 'Complex mixed and stromal neoplasms',
|
|
1202
|
+
'Mesoblastic nephroma': 'Complex mixed and stromal neoplasms',
|
|
1203
|
+
'Mesodermal mixed tumor': 'Complex mixed and stromal neoplasms',
|
|
1204
|
+
'Mesonephroma, malignant': 'Mesonephromas',
|
|
1205
|
+
'Mesothelioma, biphasic, malignant': 'Mesothelial neoplasms',
|
|
1206
|
+
'Mesothelioma, malignant': 'Mesothelial neoplasms',
|
|
1207
|
+
'Metaplastic carcinoma, NOS': 'Complex epithelial neoplasms',
|
|
1208
|
+
'Metastatic Atypical carcinoid tumor': 'Adenomas and adenocarcinomas',
|
|
1209
|
+
'Metastatic Alveolar rhabdomyosarcoma': 'Myomatous neoplasms',
|
|
1210
|
+
'Metastatic Epithelioid sarcoma': 'Soft tissue tumors and sarcomas',
|
|
1211
|
+
'Metastatic Infiltrating duct carcinoma': 'Ductal and lobular neoplasms',
|
|
1212
|
+
'Metastatic Malignant melanoma': 'Nevi and melanomas',
|
|
1213
|
+
'Metastatic Mullerian mixed tumor': 'Complex mixed and stromal neoplasms',
|
|
1214
|
+
'Metastatic Neuroendocrine carcinoma': 'Adenomas and adenocarcinomas',
|
|
1215
|
+
'Metastatic Serous cystadenocarcinoma': 'Cystic, mucinous and serous neoplasms',
|
|
1216
|
+
'Metastatic Serous surface papilloma': 'Cystic, mucinous and serous neoplasms',
|
|
1217
|
+
'Metastatic Spindle cell sarcoma': 'Soft tissue tumors and sarcomas',
|
|
1218
|
+
'Metastatic Tubular adenocarcinoma': 'Adenomas and adenocarcinomas',
|
|
1219
|
+
'Metastatic carcinoma': 'Epithelial neoplasms',
|
|
1220
|
+
'Metastatic signet ring cell carcinoma': 'Cystic, mucinous and serous neoplasms',
|
|
1221
|
+
'Metastatic small cell carcinoma': 'Epithelial neoplasms',
|
|
1222
|
+
'Micronodular thymoma with lymphoid stroma': 'Thymic epithelial neoplasms',
|
|
1223
|
+
'Micropapillary carcinoma, NOS': 'Adenomas and adenocarcinomas',
|
|
1224
|
+
'Mixed germ cell tumor': 'Germ cell neoplasms',
|
|
1225
|
+
'Mixed phenotype acute leukemia with t(9;22)(q34;q11.2); BCR-ABL1': 'Leukemias',
|
|
1226
|
+
'Mixed phenotype acute leukemia with t(v;11q23); MLL rearranged': 'Leukemias',
|
|
1227
|
+
'Mixed phenotype acute leukemia, B/myeloid, NOS': 'Leukemias',
|
|
1228
|
+
'Mixed phenotype acute leukemia, T/myeloid, NOS': 'Leukemias',
|
|
1229
|
+
'Mixed type rhabdomyosarcoma': 'Myomatous neoplasms',
|
|
1230
|
+
'Mucin-producing adenocarcinoma': 'Cystic, mucinous and serous neoplasms',
|
|
1231
|
+
'Mucinous adenocarcinoma': 'Cystic, mucinous and serous neoplasms',
|
|
1232
|
+
'Mucinous carcinoma, gastric type': 'Cystic, mucinous and serous neoplasms',
|
|
1233
|
+
'Mucinous cystadenoma, NOS': 'Cystic, mucinous and serous neoplasms',
|
|
1234
|
+
'Mucinous cystic neoplasm with high grade dysplasia': 'Cystic, mucinous and serous neoplasms',
|
|
1235
|
+
'Mucinous cystic tumor of borderline malignancy': 'Cystic, mucinous and serous neoplasms',
|
|
1236
|
+
'Mucoepidermoid carcinoma': 'Mucoepidermoid neoplasms',
|
|
1237
|
+
'Mucosal lentiginous melanoma': 'Nevi and melanomas',
|
|
1238
|
+
'Mullerian mixed tumor': 'Complex mixed and stromal neoplasms',
|
|
1239
|
+
'Mycosis fungoides': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1240
|
+
'Myelodysplastic syndrome with excess blasts': 'Myelodysplastic syndromes',
|
|
1241
|
+
'Myelodysplastic syndrome with isolated del (5q)': 'Myelodysplastic syndromes',
|
|
1242
|
+
'Myelodysplastic syndrome with multilineage dysplasia': 'Myelodysplastic syndromes',
|
|
1243
|
+
'Myelodysplastic syndrome with ring sideroblasts and multilineage dysplasia': 'Myelodysplastic syndromes',
|
|
1244
|
+
'Myelodysplastic syndrome with ring sideroblasts and single lineage dysplasia': 'Myelodysplastic syndromes',
|
|
1245
|
+
'Myelodysplastic syndrome with single lineage dysplasia': 'Myelodysplastic syndromes',
|
|
1246
|
+
'Myelodysplastic syndrome, NOS': 'Myelodysplastic syndromes',
|
|
1247
|
+
'Myeloid leukemia associated with Down syndrome': 'Leukemias',
|
|
1248
|
+
'Myeloid leukemia, NOS': 'Leukemias',
|
|
1249
|
+
'Myeloid or lymphoid neoplasm with PDGFRA rearrangement': 'Chronic myeloproliferative disorders',
|
|
1250
|
+
'Myeloid sarcoma': 'Leukemias',
|
|
1251
|
+
'Myeloproliferative neoplasm, NOS': 'Chronic myeloproliferative disorders',
|
|
1252
|
+
'Myeloproliferative neoplasm, unclassifiable': 'Other hematologic disorders',
|
|
1253
|
+
'Myoepithelial carcinoma': 'Complex mixed and stromal neoplasms',
|
|
1254
|
+
'Myofibroblastic tumor, NOS': 'Fibromatous neoplasms',
|
|
1255
|
+
'Myofibroblastic tumor, peribronchial': 'Fibromatous neoplasms',
|
|
1256
|
+
'Myofibroma': 'Fibromatous neoplasms',
|
|
1257
|
+
'Myofibromatosis': 'Fibromatous neoplasms',
|
|
1258
|
+
'Myxofibrosarcoma': 'Fibromatous neoplasms',
|
|
1259
|
+
'Myxoid chondrosarcoma': 'Osseous and chondromatous neoplasms',
|
|
1260
|
+
'Myxoid leiomyosarcoma': 'Myomatous neoplasms',
|
|
1261
|
+
'Myxoid liposarcoma': 'Lipomatous neoplasms',
|
|
1262
|
+
'Myxoma, NOS': 'Myxomatous neoplasms',
|
|
1263
|
+
'Myxopapillary ependymoma': 'Gliomas',
|
|
1264
|
+
'Myxosarcoma': 'Myxomatous neoplasms',
|
|
1265
|
+
'Neoplasm, benign': 'Neoplasms',
|
|
1266
|
+
'Neoplasm, malignant': 'Neoplasms',
|
|
1267
|
+
'Neoplasm, metastatic': 'Neoplasms',
|
|
1268
|
+
'Neoplasm, uncertain whether benign or malignant': 'Neoplasms',
|
|
1269
|
+
'Nephroblastoma, NOS': 'Complex mixed and stromal neoplasms',
|
|
1270
|
+
'Nerve sheath tumors': 'Nerve sheath tumors',
|
|
1271
|
+
'Neuroblastoma, NOS': 'Neuroepitheliomatous neoplasms',
|
|
1272
|
+
'Neuroendocrine carcinoma, NOS': 'Adenomas and adenocarcinomas',
|
|
1273
|
+
'Neuroendocrine tumor, NOS': 'Adenomas and adenocarcinomas',
|
|
1274
|
+
'Neuroendocrine tumor, grade 2': 'Adenomas and adenocarcinomas',
|
|
1275
|
+
'Neuroepithelioma, NOS': 'Neuroepitheliomatous neoplasms',
|
|
1276
|
+
'Neurofibroma, NOS': 'Nerve sheath tumors',
|
|
1277
|
+
'Neuroma, NOS': 'Nerve sheath tumors',
|
|
1278
|
+
'Nevi and melanomas': 'Nevi and melanomas',
|
|
1279
|
+
'Nodular melanoma': 'Nevi and melanomas',
|
|
1280
|
+
'Non-small cell carcinoma': 'Epithelial neoplasms',
|
|
1281
|
+
'Nonencapsulated sclerosing carcinoma': 'Adenomas and adenocarcinomas',
|
|
1282
|
+
'Noninfiltrating intraductal papillary adenocarcinoma': 'Ductal and lobular neoplasms',
|
|
1283
|
+
'Nuclear protein in testis (NUT) associated carcinoma': 'Epithelial neoplasms',
|
|
1284
|
+
'Oat cell carcinoma': 'Epithelial neoplasms',
|
|
1285
|
+
'Odontogenic carcinosarcoma': 'Odontogenic tumors',
|
|
1286
|
+
'Odontogenic tumor, malignant': 'Odontogenic tumors',
|
|
1287
|
+
'Olfactory neuroblastoma': 'Neuroepitheliomatous neoplasms',
|
|
1288
|
+
'Olfactory neurocytoma': 'Neuroepitheliomatous neoplasms',
|
|
1289
|
+
'Oligoastrocytoma, NOS': 'Gliomas',
|
|
1290
|
+
'Oligodendroglioma, NOS': 'Gliomas',
|
|
1291
|
+
'Oligodendroglioma, anaplastic, NOS': 'Gliomas',
|
|
1292
|
+
'Osseous and chondromatous neoplasms': 'Osseous and chondromatous neoplasms',
|
|
1293
|
+
'Ossifying fibroma': 'Miscellaneous bone tumors',
|
|
1294
|
+
'Ossifying fibromyxoid tumor, NOS': 'Myxomatous neoplasms',
|
|
1295
|
+
'Osteoblastoma, NOS': 'Osseous and chondromatous neoplasms',
|
|
1296
|
+
'Osteoma, NOS': 'Osseous and chondromatous neoplasms',
|
|
1297
|
+
'Osteosarcoma in Paget disease of bone': 'Osseous and chondromatous neoplasms',
|
|
1298
|
+
'Osteosarcoma, NOS': 'Osseous and chondromatous neoplasms',
|
|
1299
|
+
'Oxyphilic adenocarcinoma': 'Adenomas and adenocarcinomas',
|
|
1300
|
+
'Oxyphilic adenoma': 'Adenomas and adenocarcinomas',
|
|
1301
|
+
'Paget disease and infiltrating duct carcinoma of breast': 'Ductal and lobular neoplasms',
|
|
1302
|
+
'Paget disease, extramammary': 'Ductal and lobular neoplasms',
|
|
1303
|
+
'Paget disease, mammary': 'Ductal and lobular neoplasms',
|
|
1304
|
+
'Pancreatic endocrine tumor, NOS': 'Adenomas and adenocarcinomas',
|
|
1305
|
+
'Pancreatic neuroendocrine tumor, nonfunctioning': 'Adenomas and adenocarcinomas',
|
|
1306
|
+
'Pancreatobiliary type carcinoma': 'Adenomas and adenocarcinomas',
|
|
1307
|
+
'Pancreatoblastoma': 'Complex mixed and stromal neoplasms',
|
|
1308
|
+
'Papillary adenocarcinoma, NOS': 'Adenomas and adenocarcinomas',
|
|
1309
|
+
'Papillary carcinoma, NOS': 'Squamous cell neoplasms',
|
|
1310
|
+
'Papillary carcinoma, columnar cell': 'Adenomas and adenocarcinomas',
|
|
1311
|
+
'Papillary carcinoma, follicular variant': 'Adenomas and adenocarcinomas',
|
|
1312
|
+
'Papillary carcinoma, oncocytic variant': 'Adenomas and adenocarcinomas',
|
|
1313
|
+
'Papillary glioneuronal tumor': 'Neuroepitheliomatous neoplasms',
|
|
1314
|
+
'Papillary intralymphatic angioendothelioma': 'Blood vessel tumors',
|
|
1315
|
+
'Papillary meningioma': 'Meningiomas',
|
|
1316
|
+
'Papillary microcarcinoma': 'Adenomas and adenocarcinomas',
|
|
1317
|
+
'Papillary squamous cell carcinoma': 'Squamous cell neoplasms',
|
|
1318
|
+
'Papillary transitional cell carcinoma': 'Transitional cell papillomas and carcinomas',
|
|
1319
|
+
'Papillary tumor of the pineal region': 'Gliomas',
|
|
1320
|
+
'Papillary urothelial carcinoma, non-invasive': 'Transitional cell papillomas and carcinomas',
|
|
1321
|
+
'Papilloma, NOS': 'Squamous cell neoplasms',
|
|
1322
|
+
'Paraganglioma, NOS': 'Paragangliomas and glomus tumors',
|
|
1323
|
+
'Paragangliomas and glomus tumors': 'Paragangliomas and glomus tumors',
|
|
1324
|
+
'Parosteal osteosarcoma': 'Osseous and chondromatous neoplasms',
|
|
1325
|
+
'Perineurioma, NOS': 'Nerve sheath tumors',
|
|
1326
|
+
'Periosteal osteosarcoma': 'Osseous and chondromatous neoplasms',
|
|
1327
|
+
'Perivascular epithelioid tumor, malignant': 'Paragangliomas and glomus tumors',
|
|
1328
|
+
'Pheochromocytoma, NOS': 'Paragangliomas and glomus tumors',
|
|
1329
|
+
'Phyllodes tumor, borderline': 'Fibroepithelial neoplasms',
|
|
1330
|
+
'Phyllodes tumor, malignant': 'Fibroepithelial neoplasms',
|
|
1331
|
+
'Pigmented dermatofibrosarcoma protuberans': 'Fibromatous neoplasms',
|
|
1332
|
+
'Pigmented nevus, NOS': 'Nevi and melanomas',
|
|
1333
|
+
'Pilocytic astrocytoma': 'Gliomas',
|
|
1334
|
+
'Pilomyxoid astrocytoma': 'Gliomas',
|
|
1335
|
+
'Pinealoma': 'Miscellaneous tumors',
|
|
1336
|
+
'Pineoblastoma': 'Miscellaneous tumors',
|
|
1337
|
+
'Pituicytoma': 'Gliomas',
|
|
1338
|
+
'Pituitary adenoma, NOS': 'Adenomas and adenocarcinomas',
|
|
1339
|
+
'Pituitary carcinoma, NOS': 'Adenomas and adenocarcinomas',
|
|
1340
|
+
'Plasma cell myeloma': 'Plasma Cell Tumors',
|
|
1341
|
+
'Plasmacytoma, NOS': 'Plasma Cell Tumors',
|
|
1342
|
+
'Plasmacytoma, extramedullary': 'Plasma Cell Tumors',
|
|
1343
|
+
'Pleomorphic adenoma': 'Complex mixed and stromal neoplasms',
|
|
1344
|
+
'Pleomorphic carcinoma': 'Epithelial neoplasms',
|
|
1345
|
+
'Pleomorphic liposarcoma': 'Lipomatous neoplasms',
|
|
1346
|
+
'Pleomorphic rhabdomyosarcoma, adult type': 'Myomatous neoplasms',
|
|
1347
|
+
'Pleomorphic xanthoastrocytoma': 'Gliomas',
|
|
1348
|
+
'Pleuropulmonary blastoma': 'Complex mixed and stromal neoplasms',
|
|
1349
|
+
'Plexiform fibrohistiocytic tumor': 'Fibromatous neoplasms',
|
|
1350
|
+
'Plexiform neurofibroma': 'Nerve sheath tumors',
|
|
1351
|
+
'Polycythemia vera': 'Chronic myeloproliferative disorders',
|
|
1352
|
+
'Poorly differentiated thyroid carcinoma': 'Adenomas and adenocarcinomas',
|
|
1353
|
+
'Porocarcinoma, NOS': 'Adnexal and skin appendage neoplasms',
|
|
1354
|
+
'Precursor T-cell lymphoblastic leukemia': 'Leukemias',
|
|
1355
|
+
'Precursor cell lymphoblastic leukemia, NOS': 'Leukemias',
|
|
1356
|
+
'Precursor cell lymphoblastic lymphoma, NOS': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1357
|
+
'Primary cutaneous anaplastic large cell lymphoma': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1358
|
+
'Primary cutaneous follicle centre lymphoma': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1359
|
+
'Primary effusion lymphoma': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1360
|
+
'Primary myelofibrosis': 'Chronic myeloproliferative disorders',
|
|
1361
|
+
'Proliferative dermal lesion in congenital nevus': 'Nevi and melanomas',
|
|
1362
|
+
'Prolymphocytic leukemia, T-cell type': 'Leukemias',
|
|
1363
|
+
'Psammomatous meningioma': 'Meningiomas',
|
|
1364
|
+
'Pseudomyogenic (epithelioid sarcoma-like) hemangioendothelioma': 'Blood vessel tumors',
|
|
1365
|
+
'Pseudomyxoma peritonei': 'Cystic, mucinous and serous neoplasms',
|
|
1366
|
+
'Pseudosarcomatous carcinoma': 'Epithelial neoplasms',
|
|
1367
|
+
'Racemose hemangioma': 'Blood vessel tumors',
|
|
1368
|
+
'Renal cell carcinoma, NOS': 'Adenomas and adenocarcinomas',
|
|
1369
|
+
'Renal cell carcinoma, chromophobe type': 'Adenomas and adenocarcinomas',
|
|
1370
|
+
'Renal cell carcinoma, sarcomatoid': 'Adenomas and adenocarcinomas',
|
|
1371
|
+
'Retinoblastoma, NOS': 'Neuroepitheliomatous neoplasms',
|
|
1372
|
+
'Retinoblastoma, differentiated': 'Neuroepitheliomatous neoplasms',
|
|
1373
|
+
'Retinoblastoma, undifferentiated': 'Neuroepitheliomatous neoplasms',
|
|
1374
|
+
'Rhabdoid tumor, NOS': 'Complex mixed and stromal neoplasms',
|
|
1375
|
+
'Rhabdomyoma, NOS': 'Myomatous neoplasms',
|
|
1376
|
+
'Rhabdomyosarcoma, NOS': 'Myomatous neoplasms',
|
|
1377
|
+
'Sarcoma, NOS': 'Soft tissue tumors and sarcomas',
|
|
1378
|
+
'Schneiderian carcinoma': 'Transitional cell papillomas and carcinomas',
|
|
1379
|
+
'Schwannoma, NOS': 'Nerve sheath tumors',
|
|
1380
|
+
'Sclerosing stromal tumor': 'Specialized gonadal neoplasms',
|
|
1381
|
+
'Sclerotic fibroma': 'Fibromatous neoplasms',
|
|
1382
|
+
'Sebaceoma': 'Adnexal and skin appendage neoplasms',
|
|
1383
|
+
'Sebaceous carcinoma': 'Adnexal and skin appendage neoplasms',
|
|
1384
|
+
'Secretory carcinoma': 'Ductal and lobular neoplasms',
|
|
1385
|
+
'Seminoma, NOS': 'Germ cell neoplasms',
|
|
1386
|
+
'Seromucinous carcinoma': 'Cystic, mucinous and serous neoplasms',
|
|
1387
|
+
'Serous borderline tumor, NOS': 'Cystic, mucinous and serous neoplasms',
|
|
1388
|
+
'Serous carcinoma, NOS': 'Cystic, mucinous and serous neoplasms',
|
|
1389
|
+
'Serous cystadenoma, NOS': 'Cystic, mucinous and serous neoplasms',
|
|
1390
|
+
'Serrated adenoma, NOS': 'Adenomas and adenocarcinomas',
|
|
1391
|
+
'Sertoli-Leydig cell tumor of intermediate differentiation': 'Specialized gonadal neoplasms',
|
|
1392
|
+
'Sertoli-Leydig cell tumor, intermediate differentiation, with heterologous elements': 'Specialized gonadal neoplasms',
|
|
1393
|
+
'Sertoli-Leydig cell tumor, poorly differentiated': 'Specialized gonadal neoplasms',
|
|
1394
|
+
'Sertoli-Leydig cell tumor, poorly differentiated, with heterologous elements': 'Specialized gonadal neoplasms',
|
|
1395
|
+
'Sex cord-gonadal stromal tumor, NOS': 'Specialized gonadal neoplasms',
|
|
1396
|
+
'Sex cord-gonadal stromal tumor, incompletely differentiated': 'Specialized gonadal neoplasms',
|
|
1397
|
+
'Sex cord-gonadal stromal tumor, mixed forms': 'Specialized gonadal neoplasms',
|
|
1398
|
+
'Sezary syndrome': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1399
|
+
'Signet ring cell carcinoma': 'Cystic, mucinous and serous neoplasms',
|
|
1400
|
+
'Sinonasal papilloma, inverted': 'Transitional cell papillomas and carcinomas',
|
|
1401
|
+
'Small cell carcinoma, NOS': 'Epithelial neoplasms',
|
|
1402
|
+
'Small cell osteosarcoma': 'Osseous and chondromatous neoplasms',
|
|
1403
|
+
'Small cell sarcoma': 'Soft tissue tumors and sarcomas',
|
|
1404
|
+
'Smooth muscle tumor of uncertain malignant potential': 'Myomatous neoplasms',
|
|
1405
|
+
'Soft tissue tumor, benign': 'Soft tissue tumors and sarcomas',
|
|
1406
|
+
'Soft tissue tumors and sarcomas, NOS': 'Soft tissue tumors and sarcomas',
|
|
1407
|
+
'Solid carcinoma, NOS': 'Adenomas and adenocarcinomas',
|
|
1408
|
+
'Solid pseudopapillary neoplasm of the pancreas': 'Cystic, mucinous and serous neoplasms',
|
|
1409
|
+
'Solid pseudopapillary tumor of ovary': 'Cystic, mucinous and serous neoplasms',
|
|
1410
|
+
'Solitary fibrous tumor, NOS': 'Fibromatous neoplasms',
|
|
1411
|
+
'Solitary fibrous tumor/Hemangiopericytoma, grade 1': 'Fibromatous neoplasms',
|
|
1412
|
+
'Specialized gonadal neoplasms': 'Specialized gonadal neoplasms',
|
|
1413
|
+
'Spindle cell carcinoma, NOS': 'Epithelial neoplasms',
|
|
1414
|
+
'Spindle cell melanoma, NOS': 'Nevi and melanomas',
|
|
1415
|
+
'Spindle cell melanoma, type B': 'Nevi and melanomas',
|
|
1416
|
+
'Spindle cell nevus, NOS': 'Nevi and melanomas',
|
|
1417
|
+
'Spindle cell rhabdomyosarcoma': 'Myomatous neoplasms',
|
|
1418
|
+
'Spindle cell sarcoma': 'Soft tissue tumors and sarcomas',
|
|
1419
|
+
'Spiradenoma, NOS': 'Adnexal and skin appendage neoplasms',
|
|
1420
|
+
'Squamous cell carcinoma in situ, NOS': 'Squamous cell neoplasms',
|
|
1421
|
+
'Squamous cell carcinoma, NOS': 'Squamous cell neoplasms',
|
|
1422
|
+
'Squamous cell carcinoma, adenoid': 'Squamous cell neoplasms',
|
|
1423
|
+
'Squamous cell carcinoma, clear cell type': 'Squamous cell neoplasms',
|
|
1424
|
+
'Squamous cell carcinoma, keratinizing, NOS': 'Squamous cell neoplasms',
|
|
1425
|
+
'Squamous cell carcinoma, large cell, nonkeratinizing, NOS': 'Squamous cell neoplasms',
|
|
1426
|
+
'Squamous cell carcinoma, metastatic, NOS': 'Squamous cell neoplasms',
|
|
1427
|
+
'Squamous cell carcinoma, small cell, nonkeratinizing': 'Squamous cell neoplasms',
|
|
1428
|
+
'Squamous cell carcinoma, spindle cell': 'Squamous cell neoplasms',
|
|
1429
|
+
'Squamous cell neoplasms': 'Squamous cell neoplasms',
|
|
1430
|
+
'Subcutaneous panniculitis-like T-cell lymphoma': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1431
|
+
'Subependymal giant cell astrocytoma': 'Gliomas',
|
|
1432
|
+
'Subependymoma': 'Gliomas',
|
|
1433
|
+
'Sweat gland adenocarcinoma': 'Adnexal and skin appendage neoplasms',
|
|
1434
|
+
'Synovial sarcoma, NOS': 'Synovial-like neoplasms',
|
|
1435
|
+
'Synovial sarcoma, biphasic': 'Synovial-like neoplasms',
|
|
1436
|
+
'Synovial sarcoma, spindle cell': 'Synovial-like neoplasms',
|
|
1437
|
+
'T-cell large granular lymphocytic leukemia': 'Leukemias',
|
|
1438
|
+
'T-cell/histiocyte rich large B-cell lymphoma': 'Hodgkin and non-Hodgkin lymphomas',
|
|
1439
|
+
'Telangiectatic osteosarcoma': 'Osseous and chondromatous neoplasms',
|
|
1440
|
+
'Tenosynovial giant cell tumor, NOS': 'Giant cell tumors',
|
|
1441
|
+
'Teratocarcinoma': 'Germ cell neoplasms',
|
|
1442
|
+
'Teratoma with malignant transformation': 'Germ cell neoplasms',
|
|
1443
|
+
'Teratoma, NOS': 'Germ cell neoplasms',
|
|
1444
|
+
'Teratoma, benign': 'Germ cell neoplasms',
|
|
1445
|
+
'Teratoma, malignant, NOS': 'Germ cell neoplasms',
|
|
1446
|
+
'Thecoma, NOS': 'Specialized gonadal neoplasms',
|
|
1447
|
+
'Therapy-related myelodysplastic syndrome, NOS': 'Myelodysplastic syndromes',
|
|
1448
|
+
'Therapy-related myeloid neoplasm': 'Leukemias',
|
|
1449
|
+
'Thymic carcinoma, NOS': 'Thymic epithelial neoplasms',
|
|
1450
|
+
'Thymic epithelial neoplasms': 'Thymic epithelial neoplasms',
|
|
1451
|
+
'Thymoma, NOS': 'Thymic epithelial neoplasms',
|
|
1452
|
+
'Thymoma, type A': 'Thymic epithelial neoplasms',
|
|
1453
|
+
'Thymoma, type AB': 'Thymic epithelial neoplasms',
|
|
1454
|
+
'Thymoma, type B1': 'Thymic epithelial neoplasms',
|
|
1455
|
+
'Thymoma, type B2': 'Thymic epithelial neoplasms',
|
|
1456
|
+
'Thymoma, type B3': 'Thymic epithelial neoplasms',
|
|
1457
|
+
'Trabecular adenocarcinoma': 'Adenomas and adenocarcinomas',
|
|
1458
|
+
'Transient abnormal myelopoiesis': 'Leukemias',
|
|
1459
|
+
'Transitional cell carcinoma, NOS': 'Transitional cell papillomas and carcinomas',
|
|
1460
|
+
'Transitional cell papillomas and carcinomas': 'Transitional cell papillomas and carcinomas',
|
|
1461
|
+
'Trophoblastic tumor, epithelioid': 'Trophoblastic neoplasms',
|
|
1462
|
+
'Tubular adenocarcinoma': 'Adenomas and adenocarcinomas',
|
|
1463
|
+
'Tubular adenoma, NOS': 'Adenomas and adenocarcinomas',
|
|
1464
|
+
'Tubulovillous adenoma, NOS': 'Adenomas and adenocarcinomas',
|
|
1465
|
+
'Tumor cells, benign': 'Neoplasms',
|
|
1466
|
+
'Tumor cells, malignant': 'Neoplasms',
|
|
1467
|
+
'Tumor cells, uncertain whether benign or malignant': 'Neoplasms',
|
|
1468
|
+
'Undifferentiated sarcoma': 'Soft tissue tumors and sarcomas',
|
|
1469
|
+
'Urothelial carcinoma in situ': 'Transitional cell papillomas and carcinomas',
|
|
1470
|
+
'Verrucous carcinoma, NOS': 'Squamous cell neoplasms',
|
|
1471
|
+
'Villous adenocarcinoma': 'Adenomas and adenocarcinomas',
|
|
1472
|
+
'Waldenstrom macroglobulinemia': 'Immunoproliferative diseases',
|
|
1473
|
+
'Yolk sac tumor, NOS': 'Germ cell neoplasms',
|
|
1474
|
+
'metastatic neuroblastoma': 'Neuroepitheliomatous neoplasms',
|
|
1475
|
+
'myomatous neoplasm': 'myomatous neoplasm',
|
|
1476
|
+
}
|
|
1477
|
+
if include_disease_slims and not collate_results and ( 'diagnosis' in result_dataframe or 'morphology' in result_dataframe ):
|
|
1478
|
+
# Make a new column called 'disease_slims', populated with slim terms corresponding to any mapped terms from `observation.diagnosis` or `observation.morphology`.
|
|
1479
|
+
result_dataframe['disease_slims'] = [ set() for _ in range( len( result_dataframe ) ) ]
|
|
1480
|
+
column_data_types['disease_slims'] = 'text'
|
|
1481
|
+
for row_index, result_record in result_dataframe.iterrows():
|
|
1482
|
+
for disease_column in [ 'diagnosis', 'morphology' ]:
|
|
1483
|
+
if disease_column in result_dataframe:
|
|
1484
|
+
for term in result_dataframe.loc[row_index, disease_column]:
|
|
1485
|
+
if term in disease_slim_map and term != '':
|
|
1486
|
+
result_dataframe.loc[row_index, 'disease_slims'].add( disease_slim_map[term] )
|
|
1487
|
+
# END :: REMOVE ME AFTER SLIM DB INFRASTRUCTURE UPDATE
|
|
1488
|
+
|
|
861
1489
|
# Ensure the contents and ordering of the set of default columns for this endpoint
|
|
862
1490
|
# is the same whether or not additional column data (e.g. from other tables) has
|
|
863
1491
|
# been requested. Also make sure non-user-facing columns (e.g. `subject_data_at_gdc`)
|
|
@@ -1089,7 +1717,7 @@ def get_data(
|
|
|
1089
1717
|
# We have a nonzero-length list of non-null data values.
|
|
1090
1718
|
processed_cell_value = list()
|
|
1091
1719
|
|
|
1092
|
-
for list_element in current_cell_value:
|
|
1720
|
+
for list_element in sorted( current_cell_value ):
|
|
1093
1721
|
|
|
1094
1722
|
processed_list_element = list_element
|
|
1095
1723
|
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|