{"id":46325,"date":"2023-11-20T06:07:24","date_gmt":"2023-11-20T12:07:24","guid":{"rendered":"https:\/\/stage.cancerimagingarchive.net\/analysis-result\/cptac-pda-tumor-annotations\/"},"modified":"2025-03-20T13:35:08","modified_gmt":"2025-03-20T18:35:08","slug":"cptac-pda-tumor-annotations","status":"publish","type":"tcia_analysis_result","link":"https:\/\/stage.cancerimagingarchive.net\/analysis-result\/cptac-pda-tumor-annotations\/","title":{"rendered":"CPTAC-PDA-TUMOR-ANNOTATIONS"},"featured_media":0,"template":"","class_list":["post-46325","tcia_analysis_result","type-tcia_analysis_result","status-publish"],"cancer_types":["Ductal Adenocarcinoma"],"citations":[46315,9225],"result_doi":"10.7937\/BW9V-BX61","result_download_info":"","result_downloads":[46317,46319],"version_change_log_archived":"Version 1 (Current): Updated 2023\/07\/24\r\n\r\nData TypeDownload all or Query\/FilterLicenseCPTAC-PDA Annotations - Segmentations, Seed Points, and Negative Findings Assessments\u00a0 (DICOM, 0.01 GB)\r\n Download\u00a0\r\n\r\n Search\u00a0\r\n(Download requires NBIA Data Retriever)CC BY 4.0CPTAC-PDA Annotation Metadata (CSV)\r\n Download\u00a0\r\nCC BY 4.0Original CPTAC-PDA Images used to create Segmentations and Seed Points (DICOM, 18.0 GB)\r\n Download\u00a0\r\n(Download requires NBIA Data Retriever)CC BY 4.0Original CPTAC-PDA Images used to create Negative Assessment reports (DICOM, 1.54 GB)\r\n Download\u00a0\r\n(Download requires NBIA Data Retriever)CC BY 4.0","versions":false,"additional_resources":"<ul>\r\n \t<li>The NCI Cancer Research Data Commons (CRDC) provides access to proteomic, genomic and clinical data related to these subjects.\r\n<ul>\r\n \t<li><a href=\"https:\/\/portal.imaging.datacommons.cancer.gov\/explore\/filters\/?collection_id=cptac_pda\">Imaging Data Commons (IDC)<\/a>\u00a0(Imaging Data)<\/li>\r\n \t<li><a href=\"https:\/\/pdc.cancer.gov\/pdc\/browse\/filters\/study_name:CPTAC%20PDA%20Discovery%20Study%20-%20Proteome%7CCPTAC%20PDA%20Discovery%20Study%20-%20Phosphoproteome%7CCPTAC%20PDA%20Discovery%20Study%20-%20Intact%20Glycoproteome\">Proteomic Data Commons (PDC)<\/a>\u00a0(Proteomic &amp; Clinical Data)<\/li>\r\n \t<li><a href=\"https:\/\/portal.gdc.cancer.gov\/exploration?filters=%7B%22op%22%3A%22AND%22%2C%22content%22%3A%5B%7B%22op%22%3A%22IN%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%22CPTAC-3%22%7D%7D%2C%7B%22op%22%3A%22IN%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22pancreas%22%5D%7D%7D%5D%7D&amp;searchTableTab=cases\">Genomic Data Commons (GDC)<\/a>\u00a0(Genomic &amp; Clinical Data)<\/li>\r\n<\/ul>\r\n<\/li>\r\n \t<li><a href=\"https:\/\/github.com\/kirbyju\/TCIA_Notebooks\/blob\/main\/CPTAC\/CPTAC.ipynb\">Jupyter notebook<\/a>\u00a0demonstrating how to use the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/NBIA+Data+Retriever+Command-Line+Interface+Guide\">NBIA Data Retriever Command-Line Interface<\/a>\u00a0application and\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/Public\/NBIA+Search+with+Authentication+REST+API+Guide\">REST API<\/a>\u00a0to access these data<\/li>\r\n \t<li>Instructions for\u00a0<a href=\"https:\/\/github.com\/QIICR\/TCIABrowser\/raw\/master\/User%20Guide%20for%203D%20Slicer%20TCIA%20Browser.pptx\">Visualizing these data in 3D Slicer<\/a><\/li>\r\n<\/ul>","cancer_locations":["Pancreas"],"publications_related":"","result_page_accessibility":"Public","detailed_description":"","publications_using":"TCIA maintains\u00a0<a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\">a list of publications<\/a> which leverage TCIA data. If you have a manuscript you'd like to add please<a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\"> contact the TCIA Helpdesk<\/a>.","result_title":"Annotations for The Clinical Proteomic Tumor Analysis Consortium Pancreatic Ductal Adenocarcinoma Collection","species":["Human"],"version_number":"1","date_updated":"2023-07-24","related_collections":[45161],"result_short_title":"CPTAC-PDA-Tumor-Annotations","subjects":"103","related_analysis_results":false,"result_browse_title":"Annotations for The Clinical Proteomic Tumor Analysis Consortium Pancreatic Ductal Adenocarcinoma Collection (CPTAC-PDA-Tumor-Annotations)","supporting_data":false,"version_change_log":"","collections":"Below is a list of the Collections used in these analyses:\r\n<table><colgroup> <col \/> <col \/> <col \/><\/colgroup>\r\n<tbody>\r\n<tr>\r\n<th scope=\"col\">Source Data Type<\/th>\r\n<th scope=\"col\">Download<\/th>\r\n<th scope=\"col\">License<\/th>\r\n<\/tr>\r\n<tr>\r\n<td>Original <a href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2018.SC20FO18\">CPTAC-PDA<\/a> Images used to create Segmentations and Seed Points (DICOM, 18.0 GB)<\/td>\r\n<td>\r\n<div>\r\n\r\n<a href=\"\/wp-content\/uploads\/CPTAC-PDA_SourceImages_SEGSandSeedpoints-manifest-07-05-2023.tcia\" download=\"CPTAC-PDA_SourceImages_SEGSandSeedpoints-manifest-07-05-2023.tcia\"><button><i><\/i> Download<\/button><\/a>\r\n(Download requires <a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\">NBIA Data Retriever<\/a>)\r\n\r\n<\/div><\/td>\r\n<td>\r\n<div>\r\n\r\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/4.0\/\">CC BY 4.0<\/a>\r\n\r\n<\/div><\/td>\r\n<\/tr>\r\n<tr>\r\n<td>Original <a href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2018.SC20FO18\">CPTAC-PDA<\/a> Images used to create Negative Assessment reports (DICOM, 1.54 GB)<\/td>\r\n<td>\r\n<div>\r\n\r\n<a href=\"\/wp-content\/uploads\/CPTAC-PDA_SourceImages_NegativeAssessments-manifest-07-05-2023.tcia\" download=\"CPTAC-PDA_SourceImages_NegativeAssessments-manifest-07-05-2023.tcia\"><button><i><\/i> Download<\/button><\/a>\r\n(Download requires <a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\">NBIA Data Retriever<\/a>)\r\n\r\n<\/div><\/td>\r\n<td>\r\n<div>\r\n\r\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/4.0\/\">CC BY 4.0<\/a>\r\n\r\n<\/div><\/td>\r\n<\/tr>\r\n<\/tbody>\r\n<\/table>\r\n<ul>\r\n \t<li><a href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2018.SC20FO18\">The Clinical Proteomic Tumor Analysis Consortium Pancreatic Ductal Adenocarcinoma Collection (CPTAC-PDA)<\/a><\/li>\r\n<\/ul>","result_summary":"This dataset contains image annotations derived from \"<a href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2018.SC20FO18\">The Clinical Proteomic Tumor Analysis Consortium Pancreatic Ductal Adenocarcinoma Collection (CPTAC-PDA)<\/a>\u201d.\u00a0 This dataset was generated as part of a National Cancer Institute project to augment images from The Cancer Imaging Archive with tumor annotations that will improve their value for cancer researchers and artificial intelligence experts.\r\n<h3><strong>Annotation Protocol<\/strong><\/h3>\r\nFor each patient, all scans were reviewed to identify and annotate the clinically relevant time points and sequences\/series. Scans were initially annotated by an international team of radiologists holding MBBS degrees or higher, which were then reviewed by US-based board-certified radiologists to ensure accuracy. In a typical patient all available time points were annotated. The following annotation rules were followed:\r\n<ol>\r\n \t<li>PERCIST criteria was followed for PET imaging. Specifically, the lesions estimated to have the most elevated SUVmax were annotated.<\/li>\r\n \t<li>RECIST 1.1 was otherwise generally followed for MR and CT imaging. A maximum of 5 lesions were annotated per patient scan (timepoint); no more than 2 per organ. The same 5 lesions were annotated at each time point. Lymph nodes were annotated if &gt;1 cm in short axis. Other lesions were annotated if &gt;1 cm. If the primary lesion measures &lt; 1 cm, it was still annotated.<\/li>\r\n \t<li>Three-dimensional segmentations of lesions were created in the axial plane. If no axial plane was available, lesions were annotated in the coronal plane.<\/li>\r\n \t<li>MRIs were annotated using axial T1-weighted post contrast sequences that best demonstrated the tumor.<\/li>\r\n \t<li>CTs were annotated using all axial post contrast series. If not available, the axial non-contrast series were annotated.<\/li>\r\n \t<li>PET\/CTs were annotated on the CT and attenuation corrected PET images, unless there was a diagnostic CT from the same time point, in which case the CT portion of the PET\/CT was not annotated.<\/li>\r\n \t<li>Lesions were labeled separately.<\/li>\r\n \t<li>Seed points were automatically generated, but reviewed by a radiologist.<\/li>\r\n \t<li>A \u201cnegative\u201d annotation was created for any exam without findings.<\/li>\r\n<\/ol>\r\nAt each time point:\r\n<ol>\r\n \t<li>Volume calculations were performed for each segmented structure. \u00a0These calculations are provided in the Annotation Metadata CSV.<\/li>\r\n \t<li>A seed point (kernel) was created for each segmented structure. The seed points for each segmentation are provided in a separate DICOM RTSTRUCT file.<\/li>\r\n \t<li>SNOMED-CT \u201cAnatomic Region Sequence\u201d and \u201cSegmented Property Category Code Sequence\u201d and codes were inserted for all segmented structures.<\/li>\r\n \t<li>Imaging time point codes were inserted to help identify each annotation in the context of the clinical trial assessment protocol.\r\n<ol>\r\n \t<li>\u201cClinical Trial Time Point ID\u201d was used to encode time point type using one of the following strings as applicable: \u201cpre-dose\u201d or \u201cpost-chemotherapy\u201d.<\/li>\r\n \t<li>Content Item in \u201cAcquisition Context Sequence\u201d was added containing \"Time Point Type\" using Concept Code Sequence (0040,A168) selected from:\r\n<ol>\r\n \t<li>(255235001, SCT, \u201cPre-dose\u201d)<\/li>\r\n \t<li>(719864002, SCT, \"Post-cancer treatment monitoring\")<\/li>\r\n<\/ol>\r\n<\/li>\r\n<\/ol>\r\n<\/li>\r\n<\/ol>\r\n<h3>Important supplementary information and sample code<\/h3>\r\n<ol>\r\n \t<li>A spreadsheet containing key details about the annotations is available in the\u00a0<strong>Data Access<\/strong>\u00a0section below.<\/li>\r\n \t<li>A\u00a0Jupyter notebook demonstrating how to use the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/NBIA+Data+Retriever+Command-Line+Interface+Guide\">NBIA Data Retriever Command-Line Interface<\/a>\u00a0application and the\u00a0<a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/Public\/NBIA+Search+REST+API+Guide\">REST API<\/a>\u00a0to access these data can be found in the\u00a0<strong>Additional Resources<\/strong>\u00a0section below.<\/li>\r\n<\/ol>","collection_downloads":[46321,46323],"result_featured_image":false,"result_acknowledgements":"","hide_from_browse_table":"0","program":["CPTAC"],"_links":{"self":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/analysis-results\/46325","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/analysis-results"}],"about":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/types\/tcia_analysis_result"}],"version-history":[{"count":1,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/analysis-results\/46325\/revisions"}],"predecessor-version":[{"id":47481,"href":"https:\/\/stage.cancerimagingarchive.net\/api\/v1\/analysis-results\/46325\/revisions\/47481"}],"wp:attachment":[{"href":"https:\/\/stage.cancerimagingarchive.net\/api\/wp\/v2\/media?parent=46325"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}