PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-2 (2)
 

Clipboard (0)
None

Select a Filter Below

Journals
Authors
Year of Publication
Document Types
1.  Querying phenotype-genotype relationships on patient datasets using semantic web technology: the example of cerebrotendinous xanthomatosis 
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, and the 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.
doi:10.1186/1472-6947-12-78
PMCID: PMC3444309  PMID: 22849591
2.  Geometric Stability and Lens Decentering in Compact Digital Cameras 
Sensors (Basel, Switzerland)  2010;10(3):1553-1572.
A study on the geometric stability and decentering present in sensor-lens systems of six identical compact digital cameras has been conducted. With regard to geometrical stability, the variation of internal geometry parameters (principal distance, principal point position and distortion parameters) was considered. With regard to lens decentering, the amount of radial and tangential displacement resulting from decentering distortion was related with the precision of the camera and with the offset of the principal point from the geometric center of the sensor. The study was conducted with data obtained after 372 calibration processes (62 per camera). The tests were performed for each camera in three situations: during continuous use of the cameras, after camera power off/on and after the full extension and retraction of the zoom-lens. Additionally, 360 new calibrations were performed in order to study the variation of the internal geometry when the camera is rotated. The aim of this study was to relate the level of stability and decentering in a camera with the precision and quality that can be obtained. An additional goal was to provide practical recommendations about photogrammetric use of such cameras.
doi:10.3390/s100301553
PMCID: PMC3264438  PMID: 22294886
geometric stability; digital camera; photogrammetry; lens decentering

Results 1-2 (2)