Journal of biomedical semantics
Jan 18, 2018
BACKGROUND: The biodiversity domain, and in particular biological taxonomy, is moving in the direction of semantization of its research outputs. The present work introduces OpenBiodiv-O, the ontology that serves as the basis of the OpenBiodiv Knowled...
Journal of biomedical semantics
Jan 18, 2018
BACKGROUND: Creation and use of ontologies has become a mainstream activity in many disciplines, in particular, the biomedical domain. Ontology developers often disseminate information about these ontologies in peer-reviewed ontology description repo...
Journal of biomedical semantics
Jan 15, 2018
BACKGROUND: Biomedical ontologies pose several challenges to ontology matching due both to the complexity of the biomedical domain and to the characteristics of the ontologies themselves. The biomedical tracks in the Ontology Matching Evaluation Init...
Journal of biomedical semantics
Jan 12, 2018
Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ...
Journal of biomedical semantics
Jan 10, 2018
BACKGROUND: Traditionally text mention normalization corpora have normalized concepts to single ontology identifiers ("pre-coordinated concepts"). Less frequently, normalization corpora have used concepts with multiple identifiers ("post-coordinated ...
Journal of biomedical semantics
Jan 9, 2018
BACKGROUND: Ontologies are commonly used to annotate and help process life sciences data. Although their original goal is to facilitate integration and interoperability among heterogeneous data sources, when these sources are annotated with distinct ...
Journal of biomedical semantics
Dec 19, 2017
BACKGROUND: Integration and analysis of phenotype data from humans and model organisms is a key challenge in building our understanding of normal biology and pathophysiology. However, the range of phenotypes and anatomical details being captured in c...
Journal of biomedical semantics
Dec 6, 2017
BACKGROUND: One important type of information contained in biomedical research literature is the newly discovered relationships between phenotypes and genotypes. Because of the large quantity of literature, a reliable automatic system to identify thi...
Journal of biomedical semantics
Dec 4, 2017
BACKGROUND: One of the longest running tracks in the Ontology Alignment Evaluation Initiative is the Anatomy track which focuses on aligning two anatomy ontologies. The Anatomy track was started in 2005. In 2005 and 2006 the task in this track was to...
Journal of biomedical semantics
Dec 2, 2017
BACKGROUND: The disease and phenotype track was designed to evaluate the relative performance of ontology matching systems that generate mappings between source ontologies. Disease and phenotype ontologies are important for applications such as data ...