NCBO BioPortal Version 4 Ray W. Fergerson, Paul R. Alexander, Michael Dorf, Rafael S. Gonçalves, Manuel Salvadores, Alex Skrenchuk, Jennifer Vendetti, and Mark A. Musen Stanford  Center  for  Biomedical  Informatics  Research   Stanford  University,  USA     ABSTRACT new system for visualizing mappings between sets of The BioPortal web application of the National Center for ontologies. Biomedical Ontology is a resource that provides access to Resource Index: The Resource Index is a pre-compiled set more than 600 biomedical ontologies. BioPortal users can of annotations for all ontologies in BioPortal over the browse ontologies with any web browser and search for contents of a publicly available resource (such as PubMed terms across all the ontologies. Users may also access all abstracts). We have re-engineered the Resource Index to ontology content and metadata through a Web services improve its scalability, now allowing us to index all years of interface; many users have taken advantage of this feature to PubMed and about 50 other biomedical resources. build applications on top of BioPortal. We present here the Ontology Recommender: The Ontology Recommender is a most recent updates to the system, featured in version 4 of system that helps users identifying ontologies of interest in a the BioPortal software – roughly corresponding to the past particular domain; it accepts text and returns ontologies that year, as well as planned extensions to BioPortal. are most relevant for annotating this text. We have re- engineered this tool to provide better recommendations, and NEW FEATURES AND UPDATES have provided mechanisms for users to fine-tune the ranking In the version 4 release of BioPortal, we have introduced a system to better suit their needs. series of changes and new features to make it easier both to Usage Metrics: We now make usage metrics for ontologies use the web interface to explore ontologies, and to access available in the UI for ontology authors, and others to view. the system through web services. We summarize these These metrics include the number of views of all ontologies changes below. in the previous month, and a graph of the number of views Search: The search system allows a user to search for a for a given ontology in the previous 18 months. We make class in all of the ontologies in BioPortal. We have revised these and other ontology access metrics available via the this system to fetch matches not only according to class programmatic API. names and synonyms, but also on other fields such as CSV and RDF Downloads: We now allow users to UMLS CUI and ID. Additionally, we have reworked the download ontologies in both CSV and RDF formats. These search results display to highlight the distinction between features make it easier for users to manipulate ontologies in ontologies that define a class and those that simply reuse or a spreadsheet (CSV) and/or to load them into a triple-store import a class. (RDF). Annotation: The annotator allows a user to submit text to API Improvements: We have completely revised the API the system and have the system return classes that match to be consistent across all of the functionality in BioPortal. concepts in the submitted text. We have revised the We also now provide a number of API parameters that annotation system so that new ontologies, and revisions of allow a user to specify exactly which fields to return. This existing ontologies, are available for annotation within feature can greatly speed up processing since the system hours of their being loaded into the system. Previously this does not have to look up and transfer unnecessary fields process took weeks or months. back to the client, only to then have the client discard them. Mappings: The mappings system records relationships between classes in different ontologies. These relationships FUTURE PLANS can be generated manually (by users) or automatically (by In the coming year we have plans for additional the system). We have revised the mappings system to enhancements to BioPortal that will be outlined in the significantly reduce the resources required, and to presentation. substantially speed up their retrieval. Moreover, our collaborators at the University of Victoria have generated a 1 Copyright c 2015 for this paper by its authors. Copying permitted for private and academic purposes Fergerson et al. ACKNOWLEDGEMENTS The NCBO is one of the National Centers for Biomedical Computing supported by the NHGRI, the NHLBI, and the NIH Common Fund under grant U54-HG004028 REFERENCES Musen, M. A., Noy, N. F., Shah, N. H., Whetzel, P. L., Chute, C. G., Story, M. A., Smith, B., and the NCBO team. The National Center for Biomedical Ontology. Journal of the American Medical Informatics Association. 2012 Mar-Apr; 19(2):190-5. Whetzel, P. L., Noy, N. F., Shah, N. H., Alexander, P. R., Nyulas, C., Tudorache, T., and Musen, M. A. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Research. 2011 Jul; 39 (Web Server issue):W541-5. Salvadores, M., Horridge, M., Alexander, P. R., Fergerson, R. W., Musen, M. A., and Noy, N. F. Using SPARQL to Query BioPortal Ontologies and Metadata. In Proceedings of the International Semantic Web Conference (ISWC), 2012. 2 Copyright c 2015 for this paper by its authors. Copying permitted for private and academic purposes