Abstract. BioPortal is a repository for biomedical ontologies that also includes mappings between them from various sources. Considered as a whole, these mappings may cause logical errors, due to incompatibilities between the ontologies or even erroneous mappings. We have performed an automatic evaluation of BioPortal mappings between 19 ontology pairs using the mapping repair systems of LogMap and AgreementMakerLight. We found logical errors in 11 of these pairs, which on average involved 22% of the mappings between each pair. Furthermore, we conducted a manual evaluation of the repair results to identify the actual sources of error, verifying that erroneous mappings were behind over 60% of the repairs. Given the results of our analysis, we believe that annotating BioPortal mappings with information about their logical conflicts with other mappings would improve their usability for semantic web applications and facilitate the identification of erroneous mappings. In future work, we aim to collaborate with BioPortal developers in extending BioPortal with these annotations. Despite some community efforts to ensure a coordinated development of biomedical ontologies [38], many ontologies are being developed independently by different groups of experts and, as a result, they often cover the same or related subjects, but follow different modeling principles and use different entity naming schemes. Thus, to integrate data among applications, it is crucial to establish correspondences (called mappings) between the entities of the ontologies they use.In the last ten years, the semantic web and bioinformatics research communities have extensively investigated the problem of (semi-)automatically computing correspondences between independently developed ontologies, which is usually referred to as the ontology matching problem. Resulting from this effort are the growing number of ontology matching systems in development [8,7,37] and the large mapping repositories that have been created (e.g., [2,10]).