The ACGT Master Ontology and its applications – Towards an ontology-driven cancer research and management system

Abstract

Objective This paper introduces the objectives, methods and results of ontology development in the EU co-funded project Advancing Clinico-genomic Trials on Cancer – Open Grid Services for Improving Medical Knowledge Discovery (ACGT). While the available data in the life sciences has recently grown both in amount and quality, the full exploitation of it is being hindered by the use of different underlying technologies, coding systems, category schemes and reporting methods on the part of different research groups. The goal of the ACGT project is to contribute to the resolution of these problems by developing an ontology-driven, semantic grid services infrastructure that will enable efficient execution of discovery-driven scientific workflows in the context of multi-centric, post-genomic clinical trials. The focus of the present paper is the ACGT Master Ontology (MO). Methods ACGT project researchers undertook a systematic review of existing domain and upper-level ontologies, as well as of existing ontology design software, implementation methods, and end-user interfaces. This included the careful study of best practices, design principles and evaluation methods for ontology design, maintenance, implementation, and versioning, as well as for use on the part of domain experts and clinicians. Results To date, the results of the ACGT project include (i) the development of a master ontology (the ACGT-MO) based on clearly defined principles of ontology development and evaluation; (ii) the development of a technical infra-structure (the ACGT Platform) that implements the ACGT-MO utilizing independent tools, components and resources that have been developed based on open architectural standards, and which includes an application updating and evolving the ontology efficiently in response to end-user needs; and (iii) the development of an Ontology-based Trial Management Application (ObTiMA) that integrates the ACGT-MO into the design process of clinical trials in order to guarantee automatic semantic integration without the need to perform a separate mapping process.

A comparison between ontologies related to cancer: the interoperability of these ontologies with Ontocancro

“…Nas pesquisas em respeito ao câncer, são utilizadas ferramentas de alto rendimento que resultam em uma "explosão" de informações e conhecimento sobre os diversos tipos de câncer e seu tratamento [Brochhausen et al 2011]. …”

“…Na mesma linha da Ontocancro, pode ser encontrada a ACGT Master Ontology [Brochhausen et al 2011] que busca um formato padrão de conceitos para o câncer de mama, além de dados técnicos e clínicos para tratamentos. Também podemos encontrar na rede, ontologias para estudos biológicos e ferramentas que auxiliam na comparação de ontologias, como é o exemplo do SBO (Systems Biology Ontology) [Courtot & Juty 2011], TEDDY (TErminology for the Description of Dynamics) [Courtot & Juty 2011] e AgreementMaker v0.23 [Cruz et.…”

Towards an environment for data mining based analysis processes in bioinformatics and personalized medicine

“…Comprehensive meta-data describing the semantics of the heterogeneous and complex data are needed to leverage it for further research (Weiler et al 2007). To address this issue, efforts exist for describing the data in a comprehensive way by domainspecific ontologies (Brochhausen et al 2011).…”

The Challenges of Defining Oral Cancer: Analysis of an Ontological Approach

“…As a comprehensive ontology of human anatomy, the FMA includes terms that represent the structural organization of the human body from the macromolecular to macroscopic levels. The types of malignant neoplasms found in the mouth region can be linked through FMA to other comprehensive terminologies related to cancer such as Mouse Pathology [47], and Cancer Research and Management ACGT Master Ontology [48]. Currently, we are developing a standardized vocabulary for the surgical pathology domain and we are planning to link the mouth region cancer terminologies to that vocabulary.…”