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Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange(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)
BACKGROUND Over the past several centuries, chemistry has permeated virtually every facet of human lifestyle, enriching fields as diverse as medicine, agriculture, manufacturing, warfare, and electronics, among numerous others. Unfortunately, application-specific, incompatible chemical information formats and representation strategies have emerged as a(More)
BACKGROUND The diversity and the largely independent nature of chemical research efforts over the past half century are, most likely, the major contributors to the current poor state of chemical computational resource and database interoperability. While open software for chemical format interconversion and database entry cross-linking have partially(More)
BACKGROUND The development of high-throughput experimentation has led to astronomical growth in biologically relevant lipids and lipid derivatives identified, screened, and deposited in numerous online databases. Unfortunately, efforts to annotate, classify, and analyze these chemical entities have largely remained in the hands of human curators using(More)
The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while(More)
Industrial and regulatory evaluation of chemical toxicity is often done via statistical analysis of chemical features focusing on chemical structure and function. One popular method to characterize chemical toxicity involves the development of decision trees based on large sets of empirical toxicological data where chemicals are assigned toxicity or(More)
In this paper we examine a series of hydrocarbons with structural features which cause a weakening of the C-H bond. We use theoretical calculations to explore whether the carbon-centered radicals R(*) which are created after breaking the bond can be stabilized enough so that they resist the addition of molecular oxygen, i.e. where the reaction R(*) + O(2)(More)
Over the past decade, we have witnessed Semantic Web Technologies in a tremendous range of applications, from representation and integration of knowledge to enable rich, multi-domain queries to automation of computational workflows using a range of Semantic Web Service platforms. By the virtue of its design, the Semantic Automated Discovery and Integration(More)
BACKGROUND Scientists have long been driven by the desire to describe, organize, classify, and compare objects using taxonomies and/or ontologies. In contrast to biology, geology, and many other scientific disciplines, the world of chemistry still lacks a standardized chemical ontology or taxonomy. Several attempts at chemical classification have been made;(More)
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