AVAILABLE DATA Ontologies BioPortal contains ontologies that range in subject matter such as anatomy, phenotype, experimental conditions, imaging, chemistry, and health. In March 2008, the repos- itory included 72 ontologies (300 000 total classes) and has almost doubled in the last year to 134 ontologies (680 000 total classes). Metadata collected for each ontology include keyword terms, text descriptions, version informa- tion, release date, ontology author contact information and links to documentation. Ontology content and meta- data can be updated automatically or by user submission. Prior ontology versions are able to be accessed through both the Web services and Web interface and are available for download. Notes Users can add notes to all ontology classes in BioPortal, discussing the rationale for modeling decisions, pointing out problems with deﬁnitions and requesting changes from ontology authors. Notes are RSS-enabled to provide timely updates when new notes are added. The content of the notes can be exported and used in context with ontology editing software to incorporate changes to the ontology. Reviews BioPortal also supports peer reviews of ontologies. When a user is evaluating an ontology for use in a project, a key piece of information is what other projects have used the ontology and the suitability of the ontology for the tasks of the project. Users can submit descriptions of their ontology-based projects to BioPortal and link these descriptions to BioPortal ontologies. They can provide comments on the ontology along several diﬀerent dimen- sions, such as degree of formality, documentation and support, usability, domain coverage, quality of content. Mappings BioPortal also represents mappings between terms in dif- ferent ontologies. Users can browse the mappings, create new point-to-point mappings, upload mappings created with other tools, and download the mappings. They can add notes on existing mappings and carry out discussions about the mappings. Each mapping has its own set of metadata that describes who created the mapping and when, which algorithm was used to produce the mapping, application context in which the mapping might be valid, the speciﬁc mapping relationship, and other properties. At the time of this writing, BioPortal contains more than 30 000 mappings created by biomedical researchers in diﬀerent contexts. Mappings among ontologies consti- tute a key component that enables the use of the ontolo- gies for data and information integration. In the future, we plan to include the ability to access the mapping data via the BioPortal Web services. Nucleic Acids Research, 2009, Vol. 37, Web Server issue W171 Open biomedical repository The Open Biomedical Resources (OBR) component automatically indexes the metadata for important biomed- ical data sets available online (e.g. entries in GEO, ArrayExpress, ClinicalTrials.gov), and links the underly- ing data sets to the terms in the ontologies in BioPortal and UMLS. The annotation of these resources takes advantage of the semantic relationships in the ontology, including subsumption relationships among ontology terms and mappings among ontologies (3). OBR allows biomedical investigators to use the terms in the BioPortal ontologies to enhance their ability to search for relevant online data in a manner that is not possible with conven- tional keyword search strategies. These resources can be accessed through the Resources tab when users navigate the ontology (Figure 1), via a dedicated search mechanism or programmatically through Web services. User interface enhancements We have added functionality to the BioPortal user inter- face to facilitate the human computer interaction. Users can ﬁlter ontologies by group, such as all OBO Foundry ontologies (4) or caBIG ontologies (e.g. http:// bioportal.bioontology.org/?ﬁlter=OBOFoundry). Users can also ﬁlter by domain or relevant organism. The full listing of ontologies available from BioPortal can be viewed at http://bioportal.bioontology.org/ontologies. RSS feeds provide alerts of changed content, notes, mappings, new ontology versions, and new ontology submissions. Architecture Ontologies in BioPortal may be represented in OWL, RDF, OBO format or the Prote´ g e´ frame language. BioPortal uses the Mayo Clinic’s LexGrid system (http://informatics.mayo.edu/LexGrid) to store ontologies in OBO format and to access standard biomedical ter- minologies, such as UMLS. Prote´ g e´ (http://protege. stanford.edu) serves as the backend for OWL, RDF and Prote´ g e´ frames ontologies. BioPortal adopts a layered architecture approach (Figure 2), which decouples the logic and domain object models between each layer. The Presentation Tier delivers the BioPortal user interface, which currently uses Ruby- on-Rails technology. The Interface Tier consists of RESTful Web services that present all BioPortal capabil- ities to the upper tiers (e.g., browse, search, ontology con- cept display, visualization, etc.). The Presentation Tier is driven solely by the RESTful Web services. The Business Logic Tier provides API access to the ontologies and the resource index. Web services The BioPortal Web services are RESTful services. REST architecture consists of four verbs (GET, POST, PUT and DELETE) and nouns, which are URIs for the resources being accessed. Similar to SOAP services, RESTful Web services are language and platform inde- pendent. However, RESTful Web services have additional