Data Access and Management in ACGT: Tools to Solve Syntactic and Semantic Heterogeneities Between Clinical and Image Databases

Martín, Luiz A. B. San; Bonsma, Erwin; Anguita, Alberto; Vrijnsen, Jeroen; García-Remesal, Miguel; Crespo, José; Tsiknakis, Manolis; Maojo, Víctor

doi:10.1007/978-3-540-76292-8_4

Cited by 8 publications

(16 citation statements)

References 6 publications

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“…We have tested our system with a range of heterogeneous databases of the biomedical domain. Previous experiments, including image (DICOM) and relational sources, with preliminary versions of the system were performed and documented [27]. To achieve this goal, we have classified the different types of conflicts that can be present at different levels.…”

Section: Experiments and Resultsmentioning

confidence: 99%

Enabling Cross Constraint Satisfaction in RDF-Based Heterogeneous Database Integration

Martín

Anguita

Jimenez

et al. 2008

2008 20th IEEE International Conference on Tools With Artificial Intelligence

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Section: Experiments and Resultsmentioning

confidence: 99%

Enabling Cross Constraint Satisfaction in RDF-Based Heterogeneous Database Integration

Martín

Anguita

Jimenez

et al. 2008

2008 20th IEEE International Conference on Tools With Artificial Intelligence

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“…The process of finding the best query rewriting using local views can be an NP-hard problem. This issue has been approached in several projects [52,53], but the problem of scalability is still difficult to overcome. To this end, we propose to constrain the queries that can be formulated by a single user, creating a personalized profile based on requirements gathered using examples.…”

Section: Exploitation Of the Mo In The Acgt Projectmentioning

confidence: 99%

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

Brochhausen

Spear

Cocos

et al. 2011

Journal of Biomedical Informatics

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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.

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“…This software system has been tested with clinical relational and image databases [31], obtaining promising results. Currently the consortium is developing a final user query tool, with the aim of helping non technical users in the processes of building and launching queries.…”

Section: Database Integration Processmentioning

confidence: 99%

Applications of the ACGT Master Ontology on Cancer

Brochhausen

Weiler

Martín

et al. 2008

On the Move to Meaningful Internet Systems: OTM 2008 Workshops

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Abstract. In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology within the ACGT project thus far.

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Data Access and Management in ACGT: Tools to Solve Syntactic and Semantic Heterogeneities Between Clinical and Image Databases

Cited by 8 publications

References 6 publications

Enabling Cross Constraint Satisfaction in RDF-Based Heterogeneous Database Integration

Enabling Cross Constraint Satisfaction in RDF-Based Heterogeneous Database Integration

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

Applications of the ACGT Master Ontology on Cancer

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