ChemSpider

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ChemSpider is a free chemical compound search system maintained by the Royal Society of Chemistry that has indexed chemical structures by "reading" images in patents and other documents throughout the web. It then "tags" the chemical structure data with a number of chemical identifiers and chemical properties. ChemSpider relies on both open access sources (such as regulatory lists) and closed, for-profit commercial sources for the data it indexes. One of its partners for patent content is the SureChem database. A list of all sources that allow ChemSpider to index their chemical data is available here.

ChemSpider provides free chemical structure and even sub-structure searches, as well as searches by other identifiers such as IUPAC chemical name, SMILES codes, and InChI codes. Available options for search forms include:

  • Simple Search - Search by Systematic Name, Synonym, Trade Name, Registry Number, SMILES, InChI or CSID. Additional filter options available (Sinlge/Multi-component, Isotopically Labeled, Additional Filters)
  • Structure Search - Convert identifier to structure, load structure, or draw structure in structure-drawing tool. Search options include Exact, Substructure, or Similarity, with additional options available depending on selected search type. Additional filter options available (Sinlge/Multi-component, Isotopically Labeled, Additional Filters)
  • Advanced Search - Search by Structure, Identifier, Elements, Properties, Calculated Properties, Data Source/Type/Focused Library, LASSO Similarity. Additional filter options available (Sinlge/Multi-component, Isotopically Labeled, Additional Filters)
  • Ligand screening (available in Advanced Search options)
  • Chemical elements (available in Advanced Search options)
  • Intrinsic properties (available in Advanced Search options)
  • Predicted properties (available in Advanced Search options)
  • Data slice (available in Advanced Search options)

Because ChemSpider relies on automated data-gathering, and collects both highly-curated and lower-quality data, the search is not the most reliable source of chemical information, but as a free service to the public, it is still a valuable resource.

After being acquired by the Royal Society of Chemistry (RSC), ChemSpider planned to re-launch its search engine at the American Chemical Society's 2009 Annual Meeting.[1]

Use

The ChemSpider blog lists a number of methods for searching on the site:[2]

  • Search by name – systematic name, synonym, trade name
  • Search by chemical identifier – InChI, InChIKey, SMILES
  • Search by database identifier – registry number
  • Search by exact structure drawn, substructure, similarity – exact match, all tautomers, same skeleton (including/excluding H), all isomers
  • Draw an exact structure – in one of several structure drawers
  • Load from mol, sdf, skc, cdx files
  • Load from an image of the structure – gif, png, jpg, tiff – to get an editable/correctable structure for search
  • Convert an identifier or name to a structure, to use or amend in the structure search
  • Search for compound with/without a particular element or elements
  • Search by properties – molecular formula, mol wt, nominal mass, average mass, monoisotopic mass. Exact match or within a range
  • Search by calculated properties range – ACD/LogP, ACD/LogD (pH 5.5), ACD/LogD (pH 7.4), Rule Of 5, Number of Hydrogen Bond Acceptors, Number of Hydrogen Bond Donors, Number of Freely Rotatable Bonds, Polar Surface Area, Polar Surface Area, Molar Volume, Refractive Index, Boiling Point, Flash Point, Density, Surface Tension
  • Search by data sources – select one or many individual data sources (from the 400 we hold), one or many data source types from Available Chemicals Databases, Biological Properties, Chemical Reactions, Chemical Safety Data, Drugs or Compounds in Development, Imaging Agents, Information Aggregators, Journal Publishers via MeSH, Ligand/binding/crystal Structure Databases, Metabolic Pathways, Molecular Libraries Screening Center Network, Natural Products, NIH Substance Repository, Patents, Personal Collections, Physical Properties (including SAR/QSAR databases), Protein 3D Structures, Publication or Magazine Article, Spectroscopy Databases, Substance Vendors, Theoretical Properties, Toxicology/Environmental Databases, Virtual Library, Web-based Article (blog or commentary)
  • Search by focused library – Building Blocks, Screening Compounds, Building Stock, D-EXP014, Acetylcholinesterase (AChE), cAMP dependent protein kinase (PKA), Estrogen Receptor (Alpha), Phospholipase A2 (PLA(2)), Test Set for DILI modelling, Test Set for DILI modelling, Training Set for DILI modelling
  • Search by ligand screening – LASSO (Ligand Activity in Surface Similarity Order) similarity
  • Combine search to look for Single or multi-component structures
  • Combine search to look for, or disregard, isotopically labelled structures
  • Filter results with analytical data


Recent Updates

Summer 2011 - According to a recent blog post from RSC Publishing, chemical compound names have been extracted from all journal publications from 2008-2010 (over 30,000 articles), and these compounds are available via text or structure searching in ChemSpider. The ChemSpider record for the compound will list the relevant references from the RSC journal articles.[3]

The article records on both the HTML version of RSC's Publishing Platform and the PDF version on the Utopia Documents reader will include highlighting and links of the chemical compounds to the compound records on ChemSpider.[3] According to the post, "the project will run routinely on all new journal articles published by RSC and be extended further back into the RSC’s 170-year archive."[3]


Sources

  1. "ChemSpider re-launching search engine for chemists." AltSearchEngines blog. Posted August 14th, 2009. http://www.altsearchengines.com/2009/08/14/chemspider-re-launching-search-engine-for-chemists/ (link no longer available). Accessed on August 14, 2009.
  2. Weblog entry. Richard. "How many ways to search ChemSpider?" ChemSpider Blog. ChemSpider. Posted September 16, 2011. http://www.chemspider.com/blog/how-many-ways-to-search-chemspider.html. Accessed October 6, 2011.
  3. 3.0 3.1 3.2 Kidd, Richard."Utopia Documents highlights RSC Publishing’s semantic chemistry." RSC Publishing Blogs. Posted June 21, 2011. http://blogs.rsc.org/technical/2011/06/21/utopia-documents-highlights-rsc-publishings-semantic-chemistry/. Accessed August 18, 2011.

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