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Register a new userChem2Bio2RDF: A Linked Open Data Portal for Chemical Biology
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Bin Chen
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The Chem2Bio2RDF portal is a Linked Open Data (LOD) portal for systems chemical biology aiming for facilitating drug discovery. It converts around 25 different datasets on genes, compounds, drugs, pathways, side effects, diseases, and MEDLINE/PubMed documents into RDF triples and links them to other LOD bubbles, such as Bio2RDF, LODD and DBPedia. The portal is based on D2R server and provides a SPARQL endpoint, but adds on few unique features like RDF faceted browser, user-friendly SPARQL query generator, MEDLINE/PubMed cross validation service, and Cytoscape visualization plugin. Three use cases demonstrate the functionality and usability of this portal.
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Invited contribution to Quantum Aspects of Life, D. Abbott Ed. (World Scientific, Singapore, 2007).
Though it goes without saying that linear algebra is fundamental to mathematical biology, polynomial algebra is less visible. In this article, we will give a brief tour of four diverse biological problems where multivariate polynomials play a central role -- a subfield that is sometimes called algebraic biology. Namely, these topics include biochemical reaction networks, Boolean models of gene regulatory networks, algebraic statistics and genomics, and place fields in neuroscience. After that, we will summarize the history of discrete and algebraic structures in mathematical biology, from their early appearances in the late 1960s to the current day. Finally, we will discuss the role of algebraic biology in the modern classroom and curriculum, including resources in the literature and relevant software. Our goal is to make this article widely accessible, reaching the mathematical biologist who knows no algebra, the algebraist who knows no biology, and especially the interested student who is curious about the synergy between these two seemingly unrelated fields.
In the Open Data Portal Germany (OPAL) project, a pipeline of the following data refinement steps has been developed: requirements analysis, data acquisition, analysis, conversion, integration and selection. 800,000 datasets in DCAT format have been produced.
Linked Open Data (LOD) is the publicly available RDF data in the Web. Each LOD entity is identfied by a URI and accessible via HTTP. LOD encodes globalscale knowledge potentially available to any human as well as artificial intelligence that may want to benefit from it as background knowledge for supporting their tasks. LOD has emerged as the backbone of applications in diverse fields such as Natural Language Processing, Information Retrieval, Computer Vision, Speech Recognition, and many more. Nevertheless, regardless of the specific tasks that LOD-based tools aim to address, the reuse of such knowledge may be challenging for diverse reasons, e.g. semantic heterogeneity, provenance, and data quality. As aptly stated by Heath et al. Linked Data might be outdated, imprecise, or simply wrong: there arouses a necessity to investigate the problem of linked data validity. This work reports a collaborative effort performed by nine teams of students, guided by an equal number of senior researchers, attending the International Semantic Web Research School (ISWS 2018) towards addressing such investigation from different perspectives coupled with different approaches to tackle the issue.
In this work we discuss the related challenges and describe an approach towards the fusion of state-of-the-art technologies from the Spoken Dialogue Systems (SDS) and the Semantic Web and Information Retrieval domains. We envision a dialogue system named LD-SDS that will support advanced, expressive, and engaging user requests, over multiple, complex, rich, and open-domain data sources that will leverage the wealth of the available Linked Data. Specifically, we focus on: a) improving the identification, disambiguation and linking of entities occurring in data sources and user input; b) offering advanced query services for exploiting the semantics of the data, with reasoning and exploratory capabilities; and c) expanding the typical information seeking dialogue model (slot filling) to better reflect real-world conversational search scenarios.
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