Andra Waagmeester

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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)
WikiPathways (http://www.wikipathways.org) is an open, collaborative platform for capturing and disseminating models of biological pathways for data visualization and analysis. Since our last NAR update, 4 years ago, WikiPathways has experienced massive growth in content, which continues to be contributed by hundreds of individuals each year. New aspects of(More)
Mycobacterium smegmatis is a saprophytic species that has been used for 15 years as a model to perform heterologous regulation and virulence studies of Mycobacterium tuberculosis. Members of the extracytoplasmic sigma factors family, which are required for adaptive responses to various environmental stresses, are responsible for some of the virulence traits(More)
Biological pathways are abstract and functional visual representations of existing biological knowledge. By mapping high-throughput data on these representations, changes and patterns in biological systems on the genetic, metabolic and protein level are instantly assessable. Many public domain repositories exist for storing biological pathways, each(More)
Carotenoid metabolism is relevant to the prevention of various diseases. Although the main actors in this metabolic pathway are known, our understanding of the pathway is still incomplete. The information on the carotenoids is scattered in the large and growing body of scientific literature. We designed a text-mining work flow to enrich existing pathways.(More)
Wikidata is an open, Semantic Web-compatible database that anyone can edit. This ‘data commons’ provides structured data for Wikipedia articles and other applications. Every article on Wikipedia has a hyperlink to an editable item in this database. This unique connection to the world’s largest community of volunteer knowledge editors could help make(More)
Core to the success of applying Semantic Web technologies (SWT) towards supporting Life Sciences research is the availability of tools that lower the entry barrier for adoption by biomedical researchers. Researchers need to easily and intuitively exploit and query the wealth of data that is available behind as SPARQL endpoints. Here, we present SemScape, a(More)
Natural language understanding systems have to exploit various kinds of knowledge to be able to represent the meaning behind texts. Getting this knowledge in place is often such a huge enterprise that it is tempting to look for systems that can discover such knowledge automatically. In this paper, we describe how the distinction between conceptual and(More)
BACKGROUND Making data available as Linked Data using Resource Description Framework (RDF) promotes integration with other web resources. RDF documents can natively link to related data, and others can link back using Uniform Resource Identifiers (URIs). RDF makes the data machine-readable and uses extensible vocabularies for additional information, making(More)
The discovery of new medicines requires pharmacologists to interact with a number of information sources ranging from tabular data to scientific papers, and other specialized formats. In this application report, we describe a linked data platform for integrating multiple pharmacology datasets that form the basis for several drug discovery applications. The(More)