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Epigenomic annotation-based interpretation of genomic data: from enrichment analysis to machine learning.

Bioinformatics (Oxford, England)
MOTIVATION: One of the goals of functional genomics is to understand the regulatory implications of experimentally obtained genomic regions of interest (ROIs). Most sequencing technologies now generate ROIs distributed across the whole genome. The in...

Tool-supported Interactive Correction and Semantic Annotation of Narrative Clinical Reports.

Methods of information in medicine
OBJECTIVES: Our main objective is to design a method of, and supporting software for, interactive correction and semantic annotation of narrative clinical reports, which would allow for their easier and less erroneous processing outside their origina...

Structuring Legacy Pathology Reports by openEHR Archetypes to Enable Semantic Querying.

Methods of information in medicine
BACKGROUND: Clinical information is often stored as free text, e.g. in discharge summaries or pathology reports. These documents are semi-structured using section headers, numbered lists, items and classification strings. However, it is still challen...

ProvCaRe Semantic Provenance Knowledgebase: Evaluating Scientific Reproducibility of Research Studies.

AMIA ... Annual Symposium proceedings. AMIA Symposium
Scientific reproducibility is critical for biomedical research as it enables us to advance science by building on previous results, helps ensure the success of increasingly expensive drug trials, and allows funding agencies to make informed decisions...

Personalized Guideline-Based Treatment Recommendations Using Natural Language Processing Techniques.

Studies in health technology and informatics
Clinical guidelines and clinical pathways are accepted and proven instruments for quality assurance and process optimization. Today, electronic representation of clinical guidelines exists as unstructured text, but is not well-integrated with patient...

Natural Language Understanding Performance & Use Considerations in Virtual Medical Encounters.

Studies in health technology and informatics
A virtual standardized patient (VSP) prototype was tested for natural language understanding (NLU) performance. The conversational VSP was evaluated in a controlled 61 subject study over four repetitions of a patient case. The prototype achieved more...

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

Journal of integrative bioinformatics
The number, size and complexity of computational models of biological systems are growing at an ever increasing pace. It is imperative to build on existing studies by reusing and adapting existing models and parts thereof. The description of the stru...

The CellML Metadata Framework 2.0 Specification.

Journal of integrative bioinformatics
The CellML Metadata Framework 2.0 is a modular framework that describes how semantic annotations should be made about mathematical models encoded in the CellML (www.cellml.org) format, and their elements. In addition to the Core specification, there ...

[Development of a Knowledge-based Application Utilizing Ontologies for the Continuing Site-specific JJ1017 Master Maintenance].

Nihon Hoshasen Gijutsu Gakkai zasshi
The purpose of this study was to develop the JJ1017 Knowledge-based Application (JKA) to support the continuing maintenance of a site-specific JJ1017 master defined by the JJ1017 guideline as a standard radiologic procedure master for medical informa...