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An overview of the types of searches available on ChemSpider for MS Spectrometrists and how MS scientists can derive value from the ChemSpider database
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ChemSpider for Mass Spectrometrists ChemSpider for Mass Spectrometrists
Antony WilliamsAntony Williams
Building a Structure Centric Community for Chemists
ChemSpider - A Search Engine for ChemistsChemSpider - A Search Engine for Chemists
Questions a chemist might ask…Questions a chemist might ask… What is the melting point of n-butanol? What is the melting point of n-butanol? What is the chemical structure of Xanax?What is the chemical structure of Xanax? Chemically, what is phenolphthalein?Chemically, what is phenolphthalein? What are the stereocenters of cholesterol?What are the stereocenters of cholesterol? Where can I find publications about xylene?Where can I find publications about xylene? What are the different trade names for Ketoconazole?What are the different trade names for Ketoconazole? What is the NMR spectrum of Aspirin?What is the NMR spectrum of Aspirin? What are the safety handling issues for Thymol Blue?What are the safety handling issues for Thymol Blue?
ChemSpider can answer all of these questionsChemSpider can answer all of these questions
Building a Structure Centric Community for Chemists
ChemSpider Data ContentChemSpider Data Content
Over 21.5 million unique chemical structures from ca. Over 21.5 million unique chemical structures from ca. 150 data sources150 data sources Online Databases –PubChem, Drugbank, HMDB, WikipediaOnline Databases –PubChem, Drugbank, HMDB, Wikipedia Chemical Vendors – over 40 different vendors and growingChemical Vendors – over 40 different vendors and growing Personal Depositions – individual contributionsPersonal Depositions – individual contributions Journal Publishers Journal Publishers Content database vendorsContent database vendors Analytical data collectionsAnalytical data collections Patents (9 MILLION Structures being deposited nowPatents (9 MILLION Structures being deposited now)) Web scrapingWeb scraping
Content is generally linked back to the original data sourcesContent is generally linked back to the original data sources
Building a Structure Centric Community for Chemists
ChemSpider for MS SpectrometristsChemSpider for MS Spectrometrists
What would an MS spectrometrist want to do?What would an MS spectrometrist want to do? Search the database based on mass (various forms)Search the database based on mass (various forms) Search selected subsets of the database based on massSearch selected subsets of the database based on mass Search based on mass and substructure(s)Search based on mass and substructure(s) Search for structure based on name(s) or database IDsSearch for structure based on name(s) or database IDs Search for structures based on elements/not elementsSearch for structures based on elements/not elements Download the structure/structures in standard formatDownload the structure/structures in standard format Search literature for informationSearch literature for information Identify related data sources – chemical vendors, pathway Identify related data sources – chemical vendors, pathway
databases, etcdatabases, etc
Building a Structure Centric Community for Chemists
Tell me about AspirinTell me about Aspirin
Building a Structure Centric Community for Chemists
Tell me about AspirinTell me about Aspirin
Building a Structure Centric Community for Chemists
Link outsLink outs
Building a Structure Centric Community for Chemists
Tell me about AspirinTell me about Aspirin
Building a Structure Centric Community for Chemists
Tell me About AspirinTell me About Aspirin
Building a Structure Centric Community for Chemists
ChemSpider for MS SpectrometristsChemSpider for MS Spectrometrists
What would an MS spectrometrist want to do?What would an MS spectrometrist want to do? Search the database based on mass (various forms)Search the database based on mass (various forms) Search selected subsets of the database based on massSearch selected subsets of the database based on mass Search based on mass and substructure(s)Search based on mass and substructure(s) Search for structure based on name(s) or database IDsSearch for structure based on name(s) or database IDs Search for structures based on elements/not elementsSearch for structures based on elements/not elements Download the structure/structures in standard formatDownload the structure/structures in standard format Search literature for informationSearch literature for information Identify related data sources – chemical vendors, pathway Identify related data sources – chemical vendors, pathway
databases, etcdatabases, etc
Building a Structure Centric Community for Chemists
Search Database Based on MassSearch Database Based on Mass
Building a Structure Centric Community for Chemists
Search 309.08+/- 0.001Search 309.08+/- 0.001527 hits out of 21.5 MILLION Structures 527 hits out of 21.5 MILLION Structures
in 2 secondsin 2 seconds
Building a Structure Centric Community for Chemists
Include/Exclude Elements During a SearchInclude/Exclude Elements During a Search
Building a Structure Centric Community for Chemists
Search based on Data SourcesSearch based on Data Sources
Building a Structure Centric Community for Chemists
Combined SearchesCombined Searches
Search for a particular mass ANDSearch for a particular mass AND Search a series of data sources only ANDSearch a series of data sources only AND Search inclusion/exclusion lists of elements ANDSearch inclusion/exclusion lists of elements AND Search a particular substructureSearch a particular substructure
Building a Structure Centric Community for Chemists
Structure SearchingStructure Searching
Building a Structure Centric Community for Chemists
Substructure SearchingSubstructure Searching
Building a Structure Centric Community for Chemists
Outlinks – to vendors and other databasesOutlinks – to vendors and other databases
Example databases of interest to MS Spectrometrists:Example databases of interest to MS Spectrometrists: HMDB – Human Metabolome DatabaseHMDB – Human Metabolome Database
KEGG – Kyoto Encyclopedia of Genes and GenomesKEGG – Kyoto Encyclopedia of Genes and Genomes
BioCyc - collection of Pathway/Genome DatabasesBioCyc - collection of Pathway/Genome Databases
Uni. Minnesota Biodegradation DB - information on Uni. Minnesota Biodegradation DB - information on microbial biocatalytic reactions and biodegradation pathways microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds for primarily xenobiotic, chemical compounds
WikiPathways – new initiative to build crowdsourced WikiPathways – new initiative to build crowdsourced pathway data managementpathway data management
Building a Structure Centric Community for Chemists
Links out to KEGGLinks out to KEGGKyoto Encyclopedia of Genes and Genomes Kyoto Encyclopedia of Genes and Genomes
Building a Structure Centric Community for Chemists
WikiPathways LinkWikiPathways Link
Building a Structure Centric Community for Chemists
Download Structure(s)Download Structure(s)
Download individual record – molfileDownload individual record – molfile
Download SDF file (group of structures)Download SDF file (group of structures)
Building a Structure Centric Community for Chemists
Search LiteratureSearch Literature
Text indexing of >1/2 million Open Access ArticlesText indexing of >1/2 million Open Access Articles Searching of Pubmed via the NCBI Entrez SystemSearching of Pubmed via the NCBI Entrez System
Potential directions include extension to focused Potential directions include extension to focused searching- LCMS only, HPLC only etc. We can index searching- LCMS only, HPLC only etc. We can index based on Title and Abstracts and on chemical namesbased on Title and Abstracts and on chemical names
Building a Structure Centric Community for Chemists
Building a Structure Centric Community for Chemists
MassSpec API Web ServicesMassSpec API Web Services
http://http://www.chemspider.com/MassSpecAPI.asmxwww.chemspider.com/MassSpecAPI.asmx
Building a Structure Centric Community for Chemists
Web ServicesWeb Services
Building a Structure Centric Community for Chemists
Test Web Services for MassSpecTest Web Services for MassSpec
http://http://www.chemspider.com/WebServices/WSMassSpecAPIDemo.aspxwww.chemspider.com/WebServices/WSMassSpecAPIDemo.aspx
Building a Structure Centric Community for Chemists
Test resultsTest results
Building a Structure Centric Community for Chemists
Waters IntegrationWaters Integration
Building a Structure Centric Community for Chemists
Waters IntegrationWaters Integration
Building a Structure Centric Community for Chemists
Outlinks from TableOutlinks from Table
