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Biological Ontologies

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Ontology mapping for semantically enabled applications.

Drug discovery today
In this review, we provide a summary of recent progress in ontology mapping (OM) at a crucial time when biomedical research is under a deluge of an increasing amount and variety of data. This is particularly important for realising the full potential...

Ontology-based specification and generation of search queries for post-market surveillance.

Journal of biomedical semantics
BACKGROUND: The vigilant observation of medical devices during post-market surveillance (PMS) for identifying safety-relevant incidents is a non-trivial task. A wide range of sources has to be monitored in order to integrate all accessible data about...

Towards the automated economic assessment of newborn screening for rare diseases.

Journal of biomedical informatics
OBJECTIVE: Economic assessments of newborn screening programs for rare diseases involve the use of models and require huge efforts to synthesize information from different sources. Sharing and automatically or semi-automatically reusing this informat...

A mobile health monitoring-and-treatment system based on integration of the SSN sensor ontology and the HL7 FHIR standard.

BMC medical informatics and decision making
BACKGROUND: Mobile health (MH) technologies including clinical decision support systems (CDSS) provide an efficient method for patient monitoring and treatment. A mobile CDSS is based on real-time sensor data and historical electronic health record (...

Reporting and connecting cell type names and gating definitions through ontologies.

BMC bioinformatics
BACKGROUND: Human immunology studies often rely on the isolation and quantification of cell populations from an input sample based on flow cytometry and related techniques. Such techniques classify cells into populations based on the detection of a p...

OSCI: standardized stem cell ontology representation and use cases for stem cell investigation.

BMC bioinformatics
BACKGROUND: Stem cells and stem cell lines are widely used in biomedical research. The Cell Ontology (CL) and Cell Line Ontology (CLO) are two community-based OBO Foundry ontologies in the domains of in vivo cells and in vitro cell line cells, respec...

Cells in ExperimentaL Life Sciences (CELLS-2018): capturing the knowledge of normal and diseased cells with ontologies.

BMC bioinformatics
Cell cultures and cell lines are widely used in life science experiments. In conjunction with the 2018 International Conference on Biomedical Ontology (ICBO-2018), the 2nd International Workshop on Cells in ExperimentaL Life Science (CELLS-2018) focu...

An ontology for representing hematologic malignancies: the cancer cell ontology.

BMC bioinformatics
BACKGROUND: Within the cancer domain, ontologies play an important role in the integration and annotation of data in order to support numerous biomedical tools and applications. This work seeks to leverage existing standards in immunophenotyping cell...

The cell line ontology-based representation, integration and analysis of cell lines used in China.

BMC bioinformatics
BACKGROUND: The Chinese National Infrastructure of Cell Line stores and distributes cell lines for biomedical research in China. This study aims to represent and integrate the information of NICR cell lines into the community-based Cell Line Ontology...