From 503c414a04547cc29efb6e8fc4fcef5d027a3d67 Mon Sep 17 00:00:00 2001 From: jmvera255 <56414911+jmvera255@users.noreply.github.com> Date: Mon, 24 Jun 2024 09:52:52 -0500 Subject: [PATCH 1/2] update description of Histologic Morphology Code as described in issue #429 --- HTAN.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/HTAN.model.csv b/HTAN.model.csv index 5dac056b..7e9938ee 100644 --- a/HTAN.model.csv +++ b/HTAN.model.csv @@ -487,7 +487,7 @@ Portion Weight,"Numeric value that represents the sample portion weight, measure Total Volume,Numeric value for the total amount of sample or specimen,,Total Volume Unit,,FALSE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3005019&version=1.0, Total Volume Unit,Unit of measurement used for the total amount of sample or specimen,"mL,cubic millimeter,square centimeter",,,FALSE,Biospecimen,,, Tumor Tissue Type,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints),"Additional Primary, Local recurrence, Metastatic, Premalignant, Primary, Recurrent, Normal, Normal adjacent, Normal distant, Post therapy, Post therapy neoadjuvant, Post therapy adjuvant, Not Otherwise Specified, Premalignant - in situ, Atypia - hyperplasia, Not analyzed",,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3288124&version=1.0, -Histologic Morphology Code,"Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510",,,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3226275&version=1.0, +Histologic Morphology Code,"The microscopic anatomy of normal and abnormal cells and tissues of the specimen as captured in the morphology codes of the International Classification of Diseases for Oncology, 3rd Edition (ICD-O-3). Example - 8010/0",,,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3226275&version=1.0, Preinvasive Morphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN","Melanocytic hyperplasia, Atypical melanocytic proliferation, Melanoma in situ - superficial spreading, Melanoma in situ - lentigo maligna type, Melanoma in situ - acral-lentiginous, Melanoma in situ - arising in a giant congenital nevus, Persistent melanoma in situ, Melanoma in situ - not otherwise classified, Scar - no residual melanoma, Invasive melanoma - superficial spreading, Invasive melanoma - nodular type, Invasive melanoma - lentigo maligna, Invasive melanoma - acral lentiginous, Invasive melanoma - desmoplastic, Invasive melanoma - nevoid, Invasive melanoma - other, Normal WDA, Reserve cell hyperplasia, Squamous metaplasia - mature, Squamous metaplasia - immature, Mild dysplasia, Moderate dysplasia, Severe dysplasia, Squamous Carcinoma in situ, Atypical adenomatous hyperplasia, Adenocarcinoma in situ - non mucinous, Adenocarcinoma in situ - mucinous, Benign tumor NOS, Hamartoma, Carcinoma NOS, No diagnosis possible",,,FALSE,Biospecimen,,, Slide Charge Type,A description of the charge on the glass slide.,"Uncharged, Charged, Coverslip, Not applicable, Other",,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5227611&version=1.0, Section Thickness Value,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).",,,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=3024951&version=1.0, From 6a2f71753d2d9c798d9669a7b169d476f5337035 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 24 Jun 2024 15:06:17 +0000 Subject: [PATCH 2/2] GitHub Action: convert *.model.csv to *.model.jsonld --- HTAN.model.jsonld | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld index 4788368d..c8b09fc7 100644 --- a/HTAN.model.jsonld +++ b/HTAN.model.jsonld @@ -33420,7 +33420,7 @@ { "@id": "bts:HistologicMorphologyCode", "@type": "rdfs:Class", - "rdfs:comment": "Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510", + "rdfs:comment": "The microscopic anatomy of normal and abnormal cells and tissues of the specimen as captured in the morphology codes of the International Classification of Diseases for Oncology, 3rd Edition (ICD-O-3). Example - 8010/0", "rdfs:label": "HistologicMorphologyCode", "rdfs:subClassOf": [ {