International Conference on Biomedical Ontology 2005

Pain Assessment Terminology in the NCBO BioPortal: Evaluation and Recommendations

The 5th International Conference on Biomedical Ontology brought together ontologists, researchers who use ontologies for their work, clinicians, students, and individuals interested in how ontology might benefit their work to hear and present the latest findings on the benefits of ontology. This volume contains the proceedings of the conference. It comprises six scientific papers, six early-car...

International Conference on Biomedical Ontology

The Ontology-Epistemology Divide: A Case Study in Medical Terminology.

Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain both by practitioners and also in the course of biomedical research. In addition to serving as labels for biomedical classes, these names reflect the organizational principles of biomedical vocabularies and ontologies. Some names represent invariant features (classes, universals) of bi...

Gene ontology annotation by density and gravitation models.

Gene Ontology (GO) is developed to provide standard vocabularies of gene products in different databases. The process of annotating GO terms to genes requires curators to read through lengthy articles. Methods for speeding up or automating the annotation process are thus of great importance. We propose a GO annotation approach using full-text biomedical documents for directing more relevant pap...

What's in a 'nym'? Synonyms in Biomedical Ontology Matching

To bring the Life Sciences domain closer to a Semantic Web realization it is fundamental to establish meaningful relations between biomedical ontologies. The successful application of ontology matching techniques is strongly tied to an effective exploration of the complex and diverse biomedical terminology contained in biomedical ontologies. In this paper, we present an overview of the lexical ...

Reconstruction of phylogenetic relationships from metabolic pathways based on the enzyme hierarchy and the gene ontology.

There has been much interest in the structural comparison and alignment of metabolic pathways. Several techniques have been conceived to assess the similarity of metabolic pathways of different organisms. In this paper, we show that the combination of a new heuristic algorithm for the comparison of metabolic pathways together with any of three enzyme similarity measures (hierarchical, informati...