ABSTRACT This paper presents a new method to measure semantic relatedness between concepts of an ... more ABSTRACT This paper presents a new method to measure semantic relatedness between concepts of an ontology with a rich set of relationship types, and preforms a preliminary assessment of its validity. The measure was designed to be applicable to all biomedical ontologies, and to be flexible enough as to allow for different applications to address their own requirements by tuning, for example, the weight of each relationship type. We focus on the fact that we measure relatedness instead of similarity, which measures not simple likeness between concepts but also other interactions like articulation of cartilage and bones. We applied the measure to the Foundational Model of Anatomy, an ontology of human anatomy, and showed that it can be used to differentiate between related pairs of anatomical concepts and unrelated ones with higher performance than a custom similarity measure would. This work has shown positive preliminary analysis of the generic measure developed, which is a step forward to implementing tools to process the information contained in the increasing amount of biomedical ontologies.
The AgreementMaker system was the leading system in the anatomy task of the Ontology Alignment Ev... more The AgreementMaker system was the leading system in the anatomy task of the Ontology Alignment Evaluation Initiative (OAEI) competition in 2011. While AgreementMaker did not compete in OAEI 2012, here we report on its performance in the 2012 anatomy task, using the same configurations of AgreementMaker submitted to OAEI 2011. Additionally, we also test AgreementMaker using an updated version of the UBERON ontology as a mediating ontology, and otherwise identical configurations. AgreementMaker achieved an F-measure of 91.8% with the 2011 configurations, and an F-measure of 92.2% with the updated UBERON ontology. Thus, AgreementMaker would have been the second best system had it competed in the anatomy task of OAEI 2012, and only 0.1% below the F-measure of the best system.
ABSTRACT This paper presents a new method to measure semantic relatedness between concepts of an ... more ABSTRACT This paper presents a new method to measure semantic relatedness between concepts of an ontology with a rich set of relationship types, and preforms a preliminary assessment of its validity. The measure was designed to be applicable to all biomedical ontologies, and to be flexible enough as to allow for different applications to address their own requirements by tuning, for example, the weight of each relationship type. We focus on the fact that we measure relatedness instead of similarity, which measures not simple likeness between concepts but also other interactions like articulation of cartilage and bones. We applied the measure to the Foundational Model of Anatomy, an ontology of human anatomy, and showed that it can be used to differentiate between related pairs of anatomical concepts and unrelated ones with higher performance than a custom similarity measure would. This work has shown positive preliminary analysis of the generic measure developed, which is a step forward to implementing tools to process the information contained in the increasing amount of biomedical ontologies.
The AgreementMaker system was the leading system in the anatomy task of the Ontology Alignment Ev... more The AgreementMaker system was the leading system in the anatomy task of the Ontology Alignment Evaluation Initiative (OAEI) competition in 2011. While AgreementMaker did not compete in OAEI 2012, here we report on its performance in the 2012 anatomy task, using the same configurations of AgreementMaker submitted to OAEI 2011. Additionally, we also test AgreementMaker using an updated version of the UBERON ontology as a mediating ontology, and otherwise identical configurations. AgreementMaker achieved an F-measure of 91.8% with the 2011 configurations, and an F-measure of 92.2% with the updated UBERON ontology. Thus, AgreementMaker would have been the second best system had it competed in the anatomy task of OAEI 2012, and only 0.1% below the F-measure of the best system.
Uploads
Papers by Francisco Couto