A multipurpose TNM stage ontology for cancer registries.

IF 2 3区工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY

Journal of Biomedical Semantics Pub Date : 2022-02-22 DOI:10.1186/s13326-022-00260-w

Nicholas Charles Nicholson, Francesco Giusti, Manola Bettio, Raquel Negrao Carvalho, Nadya Dimitrova, Tadeusz Dyba, Manuela Flego, Luciana Neamtiu, Giorgia Randi, Carmen Martos

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引用次数: 1

Abstract

Background: Population-based cancer registries are a critical reference source for the surveillance and control of cancer. Cancer registries work extensively with the internationally recognised TNM classification system used to stage solid tumours, but the system is complex and compounded by the different TNM editions in concurrent use. TNM ontologies exist but the design requirements are different for the needs of the clinical and cancer-registry domains. Two TNM ontologies developed specifically for cancer registries were designed for different purposes and have limitations for serving wider application. A unified ontology is proposed to serve the various cancer registry TNM-related tasks and reduce the multiplication effects of different ontologies serving specific tasks. The ontology is comprehensive of the rules for TNM edition 7 as required by cancer registries and designed on a modular basis to allow extension to other TNM editions.

Results: A unified ontology was developed building on the experience and design of the existing ontologies. It follows a modular approach allowing plug in of components dependent upon any particular TNM edition. A Java front-end was developed to interface with the ontology via the Web Ontology Language application programme interface and enables batch validation or classification of cancer registry records. The programme also allows the means of automated error correction in some instances. Initial tests verified the design concept by correctly inferring TNM stage and successfully handling the TNM-related validation checks on a number of cancer case records, with a performance similar to that of an existing ontology dedicated to the task.

Conclusions: The unified ontology provides a multi-purpose tool for TNM-related tasks in a cancer registry and is scalable for different editions of TNM. It offers a convenient way of quickly checking validity of cancer case stage information and for batch processing of multi-record data via a dedicated front-end programme. The ontology is adaptable to many uses, either as a standalone TNM module or as a component in applications of wider focus. It provides a first step towards a single, unified TNM ontology for cancer registries.

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用于癌症登记的多用途TNM阶段本体。

背景:基于人群的癌症登记是癌症监测和控制的重要参考来源。癌症登记处与国际公认的TNM分类系统广泛合作，用于分期实体肿瘤，但该系统很复杂，并且同时使用不同的TNM版本。TNM本体是存在的，但设计要求因临床和癌症注册域的需要而有所不同。专门为癌症登记处开发的两种TNM本体是为不同的目的而设计的，并且在服务于更广泛的应用方面存在局限性。提出了一个统一的本体来服务于各种癌症注册tnm相关的任务，并减少了服务于特定任务的不同本体的倍增效应。本体论综合了癌症登记处要求的TNM第7版规则，并以模块化为基础进行设计，以允许扩展到其他TNM版本。结果:基于现有本体的经验和设计，开发了统一的本体。它遵循模块化方法，允许插件依赖于任何特定TNM版本的组件。开发了Java前端，通过Web ontology Language应用程序编程接口与本体进行接口，实现对癌症注册记录的批量验证或分类。该程序还允许在某些情况下采用自动纠错的手段。初始测试通过正确推断TNM阶段并成功地处理与TNM相关的癌症病例记录的验证检查来验证设计概念，其性能与专门用于该任务的现有本体相似。结论:统一本体为癌症注册中TNM相关任务提供了一个多用途工具，并且可扩展到不同版本的TNM。它提供了一种方便的方法，快速检查癌症病例阶段信息的有效性，并通过专用的前端程序批量处理多记录数据。本体适用于多种用途，既可以作为独立的TNM模块，也可以作为更广泛应用程序中的组件。它为癌症注册提供了一个单一的、统一的TNM本体的第一步。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Biomedical Semantics MATHEMATICAL & COMPUTATIONAL BIOLOGY-

CiteScore

4.20

自引率

5.30%

发文量

审稿时长

30 weeks

期刊介绍： Journal of Biomedical Semantics addresses issues of semantic enrichment and semantic processing in the biomedical domain. The scope of the journal covers two main areas: Infrastructure for biomedical semantics: focusing on semantic resources and repositories, meta-data management and resource description, knowledge representation and semantic frameworks, the Biomedical Semantic Web, and semantic interoperability. Semantic mining, annotation, and analysis: focusing on approaches and applications of semantic resources; and tools for investigation, reasoning, prediction, and discoveries in biomedicine.