RT Journal Article
T1 Querying phenotype-genotype relationships on patient datasets using semantic web technology: the example of cerebrotendinous xanthomatosis
A1 Taboada Iglesias, María Jesús
A1 Martínez Hernández, Diego
A1 Pilo, Belén
A1 Jiménez Escrig, Adriano
A1 Robinson, Peter N.
A1 Sobrido Gómez, María Jesús
K1 Cerebrotendinous xanthomatos
K1 Phenotype-genotype relationships
K1 Semantic web technology
AB Background: Semantic Web technology can considerably catalyze translational genetics and genomics research in medicine, where the interchange of information between basic research and clinical levels becomes crucial.This exchange involves mapping abstract phenotype descriptions from research resources, such as knowledge databases and catalogs, to unstructured datasets produced through experimental methods and clinical practice.This is especially true for the construction of mutation databases. This paper presents a way of harmonizing abstract phenotype descriptions with patient data from clinical practice, and querying this dataset about relationships between phenotypes and genetic variants, at different levels of abstraction.Methods: Due to the current availability of ontological and terminological resources that have already reached some consensus in biomedicine, a reuse-based ontology engineering approach was followed. The proposed approach uses the Ontology Web Language (OWL) to represent the phenotype ontology and the patient model, the Semantic Web Rule Language (SWRL) to bridge the gap between phenotype descriptions and clinical data, andthe Semantic Query Web Rule Language (SQWRL) to query relevant phenotype-genotype bidirectional relationships.The work tests the use of semantic web technology in the biomedical research domain named cerebrotendinous xanthomatosis (CTX), using a real dataset and ontologies.Results: A framework to query relevant phenotype-genotype bidirectional relationships is provided. Phenotype descriptions and patient data were harmonized by defining 28 Horn-like rules in terms of the OWL concepts.In total, 24 patterns of SWQRL queries were designed following the initial list of competency questions. As the approach is based on OWL, the semantic of the framework adapts the standard logical model of an open world assumption.Conclusions: This work demonstrates how semantic web technologies can be used to support flexible representation and computational inference mechanisms required to query patient datasets at different levels of abstraction. The open world assumption is especially good for describing only partially known phenotype-genotype relationships, in a way that is easily extensible. In future, this type of approach could offer researchers a valuable resource to infer new data from patient data for statistical analysis in translational research. In conclusion, phenotype description formalization and mapping to clinical data are two key elements for interchanging knowledge between basic and clinical research.
PB BMC
YR 2012
FD 2012
LK http://hdl.handle.net/10347/21389
UL http://hdl.handle.net/10347/21389
LA eng
NO Taboada, M., Martínez, D., Pilo, B. et al. Querying phenotype-genotype relationships on patient datasets using semantic web technology: the example of cerebrotendinous xanthomatosis. BMC Med Inform Decis Mak 12, 78 (2012). https://doi.org/10.1186/1472-6947-12-78
NO The work presented in this paper has been developed in the funded national project Gestión de Terminologías Médicas para Arquetipos (TIN2009-14159-C05-05) by the Ministerio de Educación y Ciencia. This work was partly supported by the network REGENPSI (2009/019) from the Program of Consolidation and Structure of Competitive Units, Consellería de Educación e Ordenación Universitaria, Xunta de Galicia, and by FEDER funds for regional development. PNR was supported by a grant from the Deutsche Forschungsgemeinschaft (DFGRO2005/4-2)
DS Minerva
RD 23 abr 2026