DeepPhe-CR: Natural Language Processing Software Services for Cancer Registrar Case Abstraction.
| العنوان: | DeepPhe-CR: Natural Language Processing Software Services for Cancer Registrar Case Abstraction. |
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| المؤلفون: | Hochheiser H; Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA.; Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, USA., Finan S; Boston Childrens' Hospital, Boston, MA, USA and Harvard Medical School, Boston, MA, USA., Yuan Z; Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA., Durbin EB; Kentucky Cancer Registry, Markey Cancer Center, Lexington, KY, USA.; Division of Biomedical Informatics, College of Medicine, University of Kentucky, Lexington, KY, USA., Jeong JC; Division of Biomedical Informatics, College of Medicine, University of Kentucky, Lexington, KY, USA., Hands I; Kentucky Cancer Registry, Markey Cancer Center, Lexington, KY, USA.; Division of Biomedical Informatics, College of Medicine, University of Kentucky, Lexington, KY, USA., Rust D; Kentucky Cancer Registry, Markey Cancer Center, Lexington, KY, USA., Kavuluru R; Division of Biomedical Informatics, College of Medicine, University of Kentucky, Lexington, KY, USA., Wu XC; Louisiana Cancer Registry, New Orleans, LA, USA., Warner JL; Lifespan Health System, Providence, RI, USA.; Legorreta Cancer Center at Brown University, Providence, RI, USA., Savova G; Boston Childrens' Hospital, Boston, MA, USA and Harvard Medical School, Boston, MA, USA. |
| المصدر: | MedRxiv : the preprint server for health sciences [medRxiv] 2023 Oct 26. Date of Electronic Publication: 2023 Oct 26. |
| نوع المنشور: | Preprint |
| اللغة: | English |
| بيانات الدورية: | Country of Publication: United States NLM ID: 101767986 Publication Model: Electronic Cited Medium: Internet NLM ISO Abbreviation: medRxiv Subsets: PubMed not MEDLINE |
| مستخلص: | Objective: The manual extraction of case details from patient records for cancer surveillance efforts is a resource-intensive task. Natural Language Processing (NLP) techniques have been proposed for automating the identification of key details in clinical notes. Our goal was to develop NLP application programming interfaces (APIs) for integration into cancer registry data abstraction tools in a computer-assisted abstraction setting. Methods: We used cancer registry manual abstraction processes to guide the design of DeepPhe-CR, a web-based NLP service API. The coding of key variables was done through NLP methods validated using established workflows. A container-based implementation including the NLP wasdeveloped. Existing registry data abstraction software was modified to include results from DeepPhe-CR. An initial usability study with data registrars provided early validation of the feasibility of the DeepPhe-CR tools. Results: API calls support submission of single documents and summarization of cases across multiple documents. The container-based implementation uses a REST router to handle requests and support a graph database for storing results. NLP modules extract topography, histology, behavior, laterality, and grade at 0.79-1.00 F1 across common and rare cancer types (breast, prostate, lung, colorectal, ovary and pediatric brain) on data from two cancer registries. Usability study participants were able to use the tool effectively and expressed interest in adopting the tool. Discussion: Our DeepPhe-CR system provides a flexible architecture for building cancer-specific NLP tools directly into registrar workflows in a computer-assisted abstraction setting. Improving user interactions in client tools, may be needed to realize the potential of these approaches. DeepPhe-CR: https://deepphe.github.io/. |
| التعليقات: | Update in: JCO Clin Cancer Inform. 2023 Sep;7:e2300156. doi: 10.1200/CCI.23.00156. (PMID: 38113411) |
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| معلومات مُعتمدة: | HHSN261201800013I United States CA NCI NIH HHS; P30 CA177558 United States CA NCI NIH HHS; U24 CA248010 United States CA NCI NIH HHS; UH3 CA243120 United States CA NCI NIH HHS |
| فهرسة مساهمة: | Keywords: Application Programming Interfaces; Cancer Informatics; Cancer Registry; Data Abstraction; Natural Language Processing |
| تواريخ الأحداث: | Date Created: 20230519 Latest Revision: 20240603 |
| رمز التحديث: | 20240604 |
| مُعرف محوري في PubMed: | PMC10187451 |
| DOI: | 10.1101/2023.05.05.23289524 |
| PMID: | 37205575 |
| قاعدة البيانات: | MEDLINE |
| DOI: | 10.1101/2023.05.05.23289524 |
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