Ontohub is a repository engine for managing distributed heterogeneous ontologies. The distributed nature enables communities to share and exchange their contributions easily. The heterogeneous nature makes it possible to integrate ontologies written in various ontology languages. Ontohub supports a wide range of formal logical and ontology languages, as well as various structuring and modularity constructs and inter-theory (concept) mappings, building on the OMG-standardized DOL language. Ontohub repositories are organised as Git repositories, thus inheriting all features of this popular version control system. Moreover, Ontohub is the first repository engine meeting a substantial amount of the requirements formulated in the context of the Open Ontology Repository (OOR) initiative, including an API for federation as well as support for logical inference and axiom selection.
 We describe an extension of the description logic underlying OWL-DL, SHOIN, with a number of expressive means that we believe will make it more useful in practice. Roughly speaking, we extend SHOIN with all expressive means that were suggested to us by ontology developers as useful additions to OWL-DL, and which, additionally, do not affect its decidability and practicability. We consider complex role inclusion axioms of the form R o S ⊑ R or S o R ⊑ R to express propagation of one property along another one, which have proven useful in medical terminologies. Furthermore, we extend SHOIN with reflexive, antisymmetric, and irreflexive roles, disjoint roles, a universal role, and constructs ∃R. Self, allowing, for instance, the definition of concepts such as a "narcist". Finally, we consider negated role assertions in Aboxes and qualified number restrictions. The resulting logic is called SROIQ. We present a rather elegant tableau-based reasoning algorithm: it combines the use of automata to keep track of universal value restrictions with the techniques developed for SHOIQ. The logic SROIQ has been adopted as the logical basis for the next iteration of OWL, OWL 1.1. Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing and decision support. BioPortal (http: bioportal.bioontology.org) is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protege frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content by providing features to add notes to ontology terms, mappings between terms and ontology reviews based on criteria such as usability, domain coverage, quality of content, and documentation and support. BioPortal also enables integrated search of biomedical data resources such as the Gene Expression Omnibus (GEO), ClinicalTrials.gov, and ArrayExpress, through the annotation and indexing of these resources with ontologies in BioPortal. Thus, BioPortal not only provides investigators, clinicians, and developers ‘one-stop shopping’ to programmatically access biomedical ontologies, but also provides support to integrate data from a variety of biomedical resources. Ontologies are considered a key technology enabling semantic interoperability and integration of data and processes. We are now entering a phase of knowledge system development, in which ontologies are produced in larger numbers and exhibit greater complexity. Also we have witnessed an increasing need for technologies that enable the reuse of existing (Semantic) Web resources from within the ontology engineering environment itself. In the NeOn project we aim at advancing the state of the art in using ontologies for large-scale semantic applications. This is realized by providing an infrastructure for networked ontology management and engineering capable of suiting the community’s needs [1]. The heart of this infrastructure is the NeOn Toolkit for engineering contextualized networked ontologies and semantic applications. The shift from closed semantic applications, characterized by a monolithic corporate ontology, to open semantic applications, characterized by networks of ontologies, implies that a number of other aspects like dealing with context, collaboration or data and web integration become crucial. The NeOn Toolkit was built with the web-centric elements of semantic technologies in mind: much like Web 2.0 environments emphasize distributed content production, the NeOn Toolkit features methods and tools for managing knowledge that is distributed, heterogeneous, contextualized, and developed collaboratively. The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or 'ontologies'. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium is pursuing a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing coordinated reform, and new ontologies are being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality. We describe this OBO Foundry initiative and provide guidelines for those who might wish to become involved.