| { |
| "passages": [ |
| { |
| "id": "breast-normal", |
| "datasets": [ |
| "bracs-fine", |
| "bracs-coarse" |
| ], |
| "entities": [ |
| "breast:N" |
| ], |
| "topic": "definition", |
| "he_observable": true, |
| "text": "Normal mammary glandular tissue has two epithelial cell types (the luminal layer and the basal myoepithelial layer) and two stromal types (interlobular and intralobular stroma). Unlike the pathological benign category, the ratio of epithelial component to stroma is preserved.", |
| "source_id": "bracs-paper", |
| "locator": "Subtype annotations, Normal Tissue (N)", |
| "quote_type": "paraphrase", |
| "facts": [ |
| { |
| "s": "breast:N", |
| "r": "has_feature", |
| "o": "breast:preserved-epithelium-stroma-ratio", |
| "he_observable": true |
| }, |
| { |
| "s": "breast:N", |
| "r": "has_feature", |
| "o": "breast:two-layer-epithelium", |
| "he_observable": true |
| } |
| ] |
| }, |
| { |
| "id": "breast-pb", |
| "datasets": [ |
| "bracs-fine", |
| "bracs-coarse" |
| ], |
| "entities": [ |
| "breast:PB" |
| ], |
| "topic": "definition", |
| "he_observable": true, |
| "text": "In BRACS the pathological benign category holds non-proliferative and proliferative benign lesions other than UDH, FEA and ADH, which are separate subtypes. It includes cyst, apocrine metaplasia, ductal ectasia, squamous metaplasia, atrophy, stromal fibrosis, mastitis, sclerosing adenosis, papilloma, radial scar, and simple and complex fibroadenoma.", |
| "source_id": "bracs-paper", |
| "locator": "Subtype annotations, Pathological Benign (PB)", |
| "quote_type": "paraphrase", |
| "facts": [ |
| { |
| "s": "breast:PB", |
| "r": "has_feature", |
| "o": "breast:altered-epithelium-stroma-ratio", |
| "he_observable": true |
| }, |
| { |
| "s": "breast:PB", |
| "r": "distinguished_from", |
| "o": "breast:N", |
| "feature": "breast:preserved-epithelium-stroma-ratio", |
| "he_observable": true |
| } |
| ] |
| }, |
| { |
| "id": "breast-udh", |
| "datasets": [ |
| "bracs-fine", |
| "bracs-coarse" |
| ], |
| "entities": [ |
| "breast:UDH" |
| ], |
| "topic": "definition", |
| "he_observable": true, |
| "text": "Usual ductal hyperplasia is an increase in the epithelial layers: a cohesive proliferation of disorderly distributed but oriented cells. Its architecture can be solid, fenestrated or micropapillary. It shares some architectural features with ADH and DCIS but shows no atypia.", |
| "source_id": "bracs-paper", |
| "locator": "Subtype annotations, Usual Ductal Hyperplasia (UDH)", |
| "quote_type": "paraphrase", |
| "facts": [ |
| { |
| "s": "breast:UDH", |
| "r": "has_feature", |
| "o": "breast:epithelial-hyperplasia", |
| "he_observable": true |
| }, |
| { |
| "s": "breast:UDH", |
| "r": "lacks_feature", |
| "o": "breast:cytologic-atypia", |
| "he_observable": true |
| }, |
| { |
| "s": "breast:ADH", |
| "r": "distinguished_from", |
| "o": "breast:UDH", |
| "feature": "breast:cytologic-atypia", |
| "he_observable": true |
| }, |
| { |
| "s": "breast:DCIS", |
| "r": "distinguished_from", |
| "o": "breast:UDH", |
| "feature": "breast:cytologic-atypia", |
| "he_observable": true |
| } |
| ] |
| }, |
| { |
| "id": "breast-fea", |
| "datasets": [ |
| "bracs-fine", |
| "bracs-coarse" |
| ], |
| "entities": [ |
| "breast:FEA" |
| ], |
| "topic": "definition", |
| "he_observable": true, |
| "text": "Flat epithelial atypia is a proliferative lesion with low-grade cytologic atypia, cell monomorphism, loss of polarity and orientation relative to the basement membrane, apical snouts, endoluminal secretion and frequent calcifications.", |
| "source_id": "bracs-paper", |
| "locator": "Subtype annotations, Flat Epithelial Atypia (FEA)", |
| "quote_type": "paraphrase", |
| "facts": [ |
| { |
| "s": "breast:FEA", |
| "r": "has_feature", |
| "o": "breast:cytologic-atypia", |
| "he_observable": true |
| }, |
| { |
| "s": "breast:FEA", |
| "r": "has_feature", |
| "o": "breast:apical-snouts", |
| "he_observable": true |
| }, |
| { |
| "s": "breast:FEA", |
| "r": "has_feature", |
| "o": "breast:calcifications", |
| "he_observable": true |
| }, |
| { |
| "s": "breast:FEA", |
| "r": "has_feature", |
| "o": "breast:monomorphic-cells", |
| "he_observable": true |
| } |
| ] |
| }, |
| { |
| "id": "breast-adh-bracs", |
| "datasets": [ |
| "bracs-fine", |
| "bracs-coarse" |
| ], |
| "entities": [ |
| "breast:ADH" |
| ], |
| "topic": "definition", |
| "he_observable": true, |
| "text": "Atypical ductal hyperplasia is a proliferation of monomorphic cells that only partially fill the ductal spaces. Its architecture can be solid, cribriform or papillary. The cytologic atypia is similar to low-grade DCIS, but the lesion spans no more than 2 mm or has insufficient architectural atypia, involving ducts or lobules only partially.", |
| "source_id": "bracs-paper", |
| "locator": "Subtype annotations, Atypical Ductal Hyperplasia (ADH)", |
| "quote_type": "paraphrase", |
| "facts": [ |
| { |
| "s": "breast:ADH", |
| "r": "has_feature", |
| "o": "breast:cytologic-atypia", |
| "he_observable": true |
| }, |
| { |
| "s": "breast:ADH", |
| "r": "has_feature", |
| "o": "breast:monomorphic-cells", |
| "he_observable": true |
| }, |
| { |
| "s": "breast:ADH", |
| "r": "has_feature", |
| "o": "breast:partial-duct-involvement", |
| "he_observable": true |
| }, |
| { |
| "s": "breast:ADH", |
| "r": "has_feature", |
| "o": "breast:cribriform-pattern", |
| "he_observable": true |
| } |
| ] |
| }, |
| { |
| "id": "breast-adh-khoury", |
| "datasets": [ |
| "bracs-fine", |
| "bracs-coarse" |
| ], |
| "entities": [ |
| "breast:ADH" |
| ], |
| "topic": "cytomorphology", |
| "he_observable": true, |
| "text": "ADH is an intraductal neoplastic epithelial proliferation in terminal duct lobular units. The cells are small, round and monomorphic with well-defined borders, in complex patterns that are solid, cribriform or micropapillary. In the cribriform pattern the cells are polarized around lumens. In the micropapillary pattern the tips of the micropapillae are broader than the bases. Part of the involved ducts can show usual ductal hyperplasia.", |
| "source_id": "pmc8833401", |
| "locator": "section on ADH histology", |
| "quote_type": "paraphrase", |
| "facts": [ |
| { |
| "s": "breast:ADH", |
| "r": "has_feature", |
| "o": "breast:micropapillary-pattern", |
| "he_observable": true |
| }, |
| { |
| "s": "breast:ADH", |
| "r": "has_feature", |
| "o": "breast:polarization-around-lumens", |
| "he_observable": true |
| } |
| ] |
| }, |
| { |
| "id": "breast-dcis-bracs", |
| "datasets": [ |
| "bracs-fine", |
| "bracs-coarse" |
| ], |
| "entities": [ |
| "breast:DCIS" |
| ], |
| "topic": "definition", |
| "he_observable": true, |
| "text": "Ductal carcinoma in situ is a malignant proliferation of epithelial cells that fills the entire duct without evidence of stromal invasion. It typically involves several adjacent ductal spaces and can be cribriform, solid, papillary or micropapillary.", |
| "source_id": "bracs-paper", |
| "locator": "Subtype annotations, Ductal Carcinoma in Situ (DCIS)", |
| "quote_type": "paraphrase", |
| "facts": [ |
| { |
| "s": "breast:DCIS", |
| "r": "has_feature", |
| "o": "breast:complete-duct-filling", |
| "he_observable": true |
| }, |
| { |
| "s": "breast:DCIS", |
| "r": "has_feature", |
| "o": "breast:multiple-adjacent-ducts", |
| "he_observable": true |
| }, |
| { |
| "s": "breast:DCIS", |
| "r": "lacks_feature", |
| "o": "breast:stromal-invasion", |
| "he_observable": true |
| }, |
| { |
| "s": "breast:DCIS", |
| "r": "distinguished_from", |
| "o": "breast:ADH", |
| "feature": "breast:complete-duct-filling", |
| "he_observable": true |
| } |
| ] |
| }, |
| { |
| "id": "breast-dcis-grades", |
| "datasets": [ |
| "bracs-fine", |
| "bracs-coarse" |
| ], |
| "entities": [ |
| "breast:DCIS" |
| ], |
| "topic": "grading", |
| "he_observable": true, |
| "text": "The WHO grades DCIS as low, intermediate or high. Low grade has small monomorphic cells in a complex pattern (cribriform, micropapillary, less often solid), uniform nuclei 1 to 1.5 times the size of an erythrocyte, rare mitoses, and involves more than two complete spaces or more than 2 mm. Intermediate grade shows moderate variability in size, shape and polarization, coarse chromatin, sometimes prominent nucleoli, and focal or comedo necrosis. High grade has large atypical cells with minimal polarization around lumens, large pleomorphic nuclei more than 2.5 times an erythrocyte, frequent mitoses and usually central comedonecrosis, most often in a solid pattern.", |
| "source_id": "pmc8833401", |
| "locator": "section on DCIS morphology and grading", |
| "quote_type": "paraphrase", |
| "facts": [ |
| { |
| "s": "breast:DCIS", |
| "r": "has_feature", |
| "o": "breast:comedonecrosis", |
| "he_observable": true |
| }, |
| { |
| "s": "breast:DCIS", |
| "r": "has_feature", |
| "o": "breast:nuclear-pleomorphism", |
| "he_observable": true |
| } |
| ] |
| }, |
| { |
| "id": "breast-ic", |
| "datasets": [ |
| "bracs-fine", |
| "bracs-coarse" |
| ], |
| "entities": [ |
| "breast:IC" |
| ], |
| "topic": "definition", |
| "he_observable": true, |
| "text": "Invasive carcinoma is tumour cells infiltrating the breast stroma with loss of the peripheral myoepithelial cells. The presence of the myoepithelial layer is the key distinction of DCIS from invasive carcinoma.", |
| "source_id": "bracs-paper", |
| "locator": "Subtype annotations, Invasive Carcinoma (IC)", |
| "quote_type": "paraphrase", |
| "facts": [ |
| { |
| "s": "breast:IC", |
| "r": "has_feature", |
| "o": "breast:stromal-invasion", |
| "he_observable": true |
| }, |
| { |
| "s": "breast:IC", |
| "r": "lacks_feature", |
| "o": "breast:myoepithelial-layer", |
| "he_observable": true |
| }, |
| { |
| "s": "breast:IC", |
| "r": "distinguished_from", |
| "o": "breast:DCIS", |
| "feature": "breast:stromal-invasion", |
| "he_observable": true |
| }, |
| { |
| "s": "breast:IC", |
| "r": "distinguished_from", |
| "o": "breast:DCIS", |
| "feature": "breast:myoepithelial-layer", |
| "he_observable": true |
| } |
| ] |
| }, |
| { |
| "id": "breast-adh-vs-dcis", |
| "datasets": [ |
| "bracs-fine", |
| "bracs-coarse" |
| ], |
| "entities": [ |
| "breast:ADH", |
| "breast:DCIS" |
| ], |
| "topic": "differential", |
| "he_observable": true, |
| "text": "ADH and low-grade DCIS have similar histomorphology and differ mainly in extent. Page defined low-grade DCIS as atypical cells involving at least two spaces, and Tavassoli and Norris proposed more than 2 mm. When spaces are only partially involved by atypical cells the diagnosis is ADH regardless of extent. Applying the cutoffs is hard because extent is difficult to measure, nuclear grade has high interobserver variability, and grades can be mixed. The author accepts lesions of 3 to 4 mm with mixed low and intermediate nuclei as severe ADH bordering on DCIS. This is one author's view.", |
| "source_id": "pmc8833401", |
| "locator": "section 3.3, severe ADH bordering on DCIS", |
| "quote_type": "paraphrase", |
| "facts": [ |
| { |
| "s": "breast:DCIS", |
| "r": "distinguished_from", |
| "o": "breast:ADH", |
| "feature": "breast:lesion-extent", |
| "he_observable": true |
| } |
| ] |
| }, |
| { |
| "id": "breast-hard-boundaries", |
| "datasets": [ |
| "bracs-fine", |
| "bracs-coarse" |
| ], |
| "entities": [ |
| "breast:UDH", |
| "breast:ADH", |
| "breast:DCIS" |
| ], |
| "topic": "differential", |
| "he_observable": true, |
| "text": "Some morphological patterns are shared between classes. ADH resembles DCIS and may include all DCIS features while being limited in size. UDH, ADH and DCIS all show intraductal growth, which makes them hard to tell apart on H&E, especially when a pathologist cannot use WSI-level context.", |
| "source_id": "bracs-paper", |
| "locator": "end of subtype annotations", |
| "quote_type": "paraphrase", |
| "facts": [] |
| }, |
| { |
| "id": "breast-atypical-significance", |
| "datasets": [ |
| "bracs-fine", |
| "bracs-coarse" |
| ], |
| "entities": [ |
| "breast:FEA", |
| "breast:ADH" |
| ], |
| "topic": "clinical", |
| "he_observable": false, |
| "text": "The atypical lesions FEA and ADH matter because they can indicate abnormality in neighbouring tissue that goes undetected in small samples, or a high risk of later DCIS or invasive carcinoma. They cannot be found by mammography or clinical examination. When found in a core biopsy, closer imaging follow-up and often surgical excision are recommended.", |
| "source_id": "bracs-paper", |
| "locator": "Subtype annotations, atypical lesions", |
| "quote_type": "paraphrase", |
| "facts": [] |
| }, |
| { |
| "id": "breast-wsi-label-rule", |
| "datasets": [ |
| "bracs-fine", |
| "bracs-coarse" |
| ], |
| "entities": [], |
| "topic": "labeling_note", |
| "he_observable": false, |
| "text": "In BRACS the label of a whole slide is defined as the most aggressive tumour subtype annotated anywhere in the image, so a slide labelled with a serious class can contain large areas of milder tissue. Retrieved neighbours with the same label may therefore differ in what most of the slide shows.", |
| "source_id": "bracs-paper", |
| "locator": "dataset construction, WSI-level labels", |
| "quote_type": "paraphrase", |
| "facts": [] |
| } |
| ] |
| } |
|
|
