ChemSpider: An Online Chemical Information Resource

Journal of chemical education (Impact Factor: 1.11). 08/2010; 87(11). DOI: 10.1021/ed100697w


ChemSpider is a free, online chemical database offering access to physical and chemical properties, molecular structure, spectral data, synthetic methods, safety information, and nomenclature for almost 25 million unique chemical compounds sourced and linked to almost 400 separate data sources on the Web. ChemSpider is quickly becoming the primary chemistry Internet portal and it can be very useful for both chemical teaching and research.


Available from: Antony John Williams
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    • "Such data have been captured in computerized databases since the 1970s [24]. In addition to compilations of experimental data [30] [27], there are extensive efforts to create repositories of computed properties, such as crystal structure parameters and formation enthalpies for binary alloys [14]; the many data collected in the the Computational Materials Repository [20] [23], Materials Project [16] [18], [10]; and the NIST repositories [1]. "
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    ABSTRACT: Advances in both sensor and computing technologies promise new approaches to discovery in materials science and engineering. For example, it appears possible to integrate theoretical modeling and experiment in new ways, test existing models with unprecedented rigor, and infer entirely new models from first principles. But, before these new approaches can become useful in practice, practitioners must be able to work with petabytes and petaflops as intuitively and interactively as they do with gigabytes and gigaflops today. The Discovery Engines for Big Data project at Argonne National Laboratory is tackling key bottlenecks along the end-to-end discovery path, focusing in particular on opportunities at Argonne's Advanced Photon Source. Here, we describe results relating to data acquisition, management, and analysis. For acquisition, we describe automated pipelines based on Globus services that link instruments, computations, and people for rapid and reliable data exchange. For management, we describe digital asset management solutions that enable the capture, management, sharing, publication, and discovery of large quantities of complex and diverse data, along with associated metadata and programs. For analysis, we describe the use of 100K+ supercomputer cores to enable new research modalities based on near-real-time processing and feedback, and the use of Swift parallel scripting to facilitate authoring, understanding, and reuse of data generation, transformation, and analysis software.
    Advances in Parallel Computing 01/2015; 26. DOI:10.3233/978-1-61499-583-8-117
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    • "From this spectrum, approximately 30 individual compounds can be reliably identified and quantified. The initial signal assignment was performed with the use of literature data (Fris and Midelfart, 2007; Fris et al., 2006; Risa et al., 2004; Midelfart et al., 1996) and online databases (Wishart et al., 2013; Pence and Williams, 2010), and then the identification was confirmed by the addition of standard samples into the lens extract solutions. "
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    ABSTRACT: This work is the first comprehensive report on the quantitative metabolomic composition of the rat lens. Quantitative metabolomic profiles of lenses were acquired with the combined use of high-frequency nuclear magnetic resonance (NMR) and high-performance liquid chromatography with high-resolution mass-spectrometric detection (LC-MS) methods. More than forty low molecular weight compounds found in the lens have been reliably identified and quantified. The most abundant metabolites in the 3-month-old Wistar rat lens are taurine, hypotaurine, lactate, phosphocholine and reduced glutathione. The analysis of age-related changes in the lens metabolomic composition shows a gradual decrease of the content of most metabolites. This decrease is the most pronounced between 1 and 3 months, which probably corresponds to the completion of the lens maturation in one-month-old rats and to the high rate of the young lens growth. The enhanced levels of tryptophan, tyrosine, carnitine, glycerolphosphate, GSH and GSSG were found in lenses of senescence-accelerated OXYS rats; for some metabolites, this effect may probably be attributed to the compensatory response to oxidative stress.
    Experimental Eye Research 06/2014; 125. DOI:10.1016/j.exer.2014.05.016 · 2.71 Impact Factor
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    • "“1”, “2”, “3”, …). Another way is to reuse identifiers assigned by external identification systems such as PubChem [31] and ChemSpider [32] database identifiers. "
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    ABSTRACT: Background Research efforts in the field of descriptive and predictive Quantitative Structure-Activity Relationships or Quantitative Structure–Property Relationships produce around one thousand scientific publications annually. All the materials and results are mainly communicated using printed media. The printed media in its present form have obvious limitations when they come to effectively representing mathematical models, including complex and non-linear, and large bodies of associated numerical chemical data. It is not supportive of secondary information extraction or reuse efforts while in silico studies poses additional requirements for accessibility, transparency and reproducibility of the research. This gap can and should be bridged by introducing domain-specific digital data exchange standards and tools. The current publication presents a formal specification of the quantitative structure-activity relationship data organization and archival format called the QSAR DataBank (QsarDB for shorter, or QDB for shortest). Results The article describes QsarDB data schema, which formalizes QSAR concepts (objects and relationships between them) and QsarDB data format, which formalizes their presentation for computer systems. The utility and benefits of QsarDB have been thoroughly tested by solving everyday QSAR and predictive modeling problems, with examples in the field of predictive toxicology, and can be applied for a wide variety of other endpoints. The work is accompanied with open source reference implementation and tools. Conclusions The proposed open data, open source, and open standards design is open to public and proprietary extensions on many levels. Selected use cases exemplify the benefits of the proposed QsarDB data format. General ideas for future development are discussed.
    Journal of Cheminformatics 05/2014; 6(1):25. DOI:10.1186/1758-2946-6-25 · 4.55 Impact Factor
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