Michel Dumontier

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The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in structured formats, but there is an increasing need to provide an additional semantic layer. Semantic information adds meaning to components of structured(More)
There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that(More)
SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally-hosted environment. SeqHound is based on the National Center for Biotechnology Information data model and programming tools. It offers daily updated(More)
Bio2RDF currently provides the largest network of Linked Data for the Life Sciences. Here, we describe a significant update to increase the overall quality of RDFized datasets generated from open scripts powered by an API to generate registry-validated IRIs, dataset provenance and metrics, SPARQL endpoints, downloadable RDF and database files. We(More)
The identification and annotation of protein domains provides a critical step in the accurate determination of molecular function. Both computational and experimental methods of protein structure determination may be deterred by large multi-domain proteins or flexible linker regions. Knowledge of domains and their boundaries may reduce the experimental cost(More)
BACKGROUND Translational medicine requires the integration of knowledge using heterogeneous data from health care to the life sciences. Here, we describe a collaborative effort to produce a prototype Translational Medicine Knowledge Base (TMKB) capable of answering questions relating to clinical practice and pharmaceutical drug discovery. RESULTS We(More)
The Semanticscience Integrated Ontology (SIO) is an ontology to facilitate biomedical knowledge discovery. SIO features a simple upper level comprised of essential types and relations for the rich description of arbitrary (real, hypothesized, virtual, fictional) objects, processes and their attributes. SIO specifies simple design patterns to describe and(More)
Although pictorial renditions of statistical data are ubiquitous, few techniques and standards exist to exchange, search and query these graphical representations. We present several improvements to human-graph interaction including i) a new approach to manage statistical graph knowledge by semantic annotation of graphs that bridges the gap between Web 2.0(More)
Ontologies are now pervasive in biomedicine, where they serve as a means to standardize terminology, to enable access to domain knowledge, to verify data consistency and to facilitate integrative analyses over heterogeneous biomedical data. For this purpose, research on biomedical ontologies applies theories and methods from diverse disciplines such as(More)
Most biomedical ontologies are represented in the OBO Flatfile Format, which is an easy-to-use graph-based ontology language. The semantics of the OBO Flatfile Format 1.2 enforces a strict predetermined interpretation of relationship statements between classes. It does not allow flexible specifications that provide better approximations of the intuitive(More)