SDTM datasets of clinical data and measurements for selected cancer collections to TCIA

The Data Integration & Imaging Informatics (DI-Cubed) project explored the issue of lack of standardized data capture at the point of data creation, as reflected in the non-image data accompanying 4 TCIA breast cancer collections (<a href="https://cancerimagingarchive.net/collection/ispy1/" target="_blank" rel="noopener">Multi-center breast DCE-MRI data and segmentations from patients in the I-SPY 1/ACRIN 6657 trials (ISPY1)</a>, <a href="https://cancerimagingarchive.net/collection/breast-diagnosis/" target="_blank" rel="noopener">BREAST-DIAGNOSIS</a>, <a href="https://cancerimagingarchive.net/collection/breast-mri-nact-pilot/" target="_blank" rel="noopener">Single site breast DCE-MRI data and segmentations from patients undergoing neoadjuvant chemotherapy (Breast-MRI-NACT-Pilot)</a>, <a href="https://cancerimagingarchive.net/collection/tcga-brca/" target="_blank" rel="noopener">The Cancer Genome Atlas Breast Invasive Carcinoma Collection (TCGA-BRCA)</a>) and the <a href="https://cancerimagingarchive.net/collection/ivygap/" target="_blank" rel="noopener">Ivy Glioblastoma Atlas Project (IvyGAP)</a> brain cancer collection. The work addressed the desire for semantic interoperability between various NCI initiatives by aligning on common clinical metadata elements and supporting use cases that connect clinical, imaging, and genomics data. Accordingly, clinical and measurement data imported into I2B2 were cross-mapped to industry standard concepts for names and values including those derived from BRIDG, CDISC SDTM, DICOM Structured Reporting models and using NCI Thesaurus, SNOMED CT and LOINC controlled terminology.A subset of the standardized data was then exported from I2B2 in SDTM compliant SAS transport files.  The SDTM data was derived from data taken from both the curated TCIA spreadsheets as well as tumor measurements and dates from the TCIA Restful API.  Due to the nature of the available data not all SDTM conformance rules were applicable or adhered to.These Study Data Tabulation Model format (SDTM) datasets were validated using Pinnacle 21 CDISC validation software. The validation software reviews datasets according to their degree of conformance to rules developed for the purposes of FDA submissions of electronic data.  Iterative refinements were made to the datasets based upon group discussions and feedback from the validation tool.Export datasets for the following SDTM domains were generated:<ul><li>DM (Demographics)</li><li>DS (Disposition)</li><li>MI (Microscopic Findings)</li><li>PR (Procedures)</li><li>SS (Subject Status)</li><li>TU (Tumor/Lesion Identification)</li><li>TR (Tumor/Lesion Results)</li></ul>

数据集成与成像信息学（DI-Cubed）项目深入探讨了数据创建阶段标准化数据采集缺失的问题，这一问题在伴随四组TCIA乳腺癌集合的非图像数据中得以体现，包括来自I-SPY 1/ACRIN 6657试验（ISPY1）的多中心乳腺癌DCE-MRI数据和分割、BREAST-DIAGNOSIS、接受新辅助化疗的患者单中心乳腺癌DCE-MRI数据和分割（Breast-MRI-NACT-Pilot）、癌症基因组图谱乳腺癌侵袭性癌集合（TCGA-BRCA）以及Ivy Glioblastoma Atlas Project（IvyGAP）脑癌集合。该项目旨在通过统一临床元数据元素，并支持连接临床、成像和基因组数据的用例，以满足各NCI（美国国家癌症研究所）倡议间语义互操作性的需求。因此，导入I2B2的临床和测量数据被跨映射至行业标准的概念名称和值，包括源自BRIDG、CDISC SDTM、DICOM结构化报告模型以及使用NCI术语表、SNOMED CT和LOINC受控术语的值。随后，一组标准化数据从I2B2中导出，并以符合SDTM（研究数据表格模型）规范的SAS传输文件格式。SDTM数据来源于经过精心编制的TCIA电子表格中的数据以及从TCIA Restful API获取的肿瘤测量和日期。鉴于可用数据的性质，并非所有SDTM合规性规则均适用或得到遵守。这些SDTM格式数据集通过Pinnacle 21 CDISC验证软件进行了验证。验证软件根据其符合为FDA电子数据提交目的而制定的规则的程度来审查数据集。根据小组讨论和验证工具的反馈，对数据集进行了迭代优化。生成了以下SDTM领域的导出数据集：
<ul>
<li>DM（人口统计学）
</li>
<li>DS（处置）
</li>
<li>MI（显微镜检查发现）
</li>
<li>PR（程序）
</li>
<li>SS（受试者状态）
</li>
<li>TU（肿瘤/病变识别）
</li>
<li>TR（肿瘤/病变结果）
</li>
</ul>