ChemSpider for Mass Spectrometrists  Antony Williams
ChemSpider - A Search Engine for Chemists <ul><li>Questions a chemist might ask… </li></ul><ul><ul><li>What is the melting...
ChemSpider Data Content <ul><li>Over 21.5 million unique chemical structures from ca. 150 data sources </li></ul><ul><ul><...
ChemSpider for MS Spectrometrists <ul><li>What would an MS spectrometrist want to do? </li></ul><ul><ul><li>Search the dat...
Tell me about Aspirin
Tell me about Aspirin
Link outs
Tell me about Aspirin
Tell me About Aspirin
ChemSpider for MS Spectrometrists <ul><li>What would an MS spectrometrist want to do? </li></ul><ul><ul><li>Search the dat...
Search Database Based on Mass
Search 309.08+/- 0.001 527 hits out of 21.5 MILLION Structures  in 2 seconds
Include/Exclude Elements During a Search
Search based on Data Sources
Combined Searches <ul><li>Search for a particular mass AND </li></ul><ul><ul><li>Search a series of data sources only AND ...
Structure Searching
Substructure Searching
Outlinks – to vendors and other databases <ul><li>Example databases of interest to MS Spectrometrists: </li></ul><ul><ul><...
Links out to KEGG Kyoto Encyclopedia of Genes and Genomes
WikiPathways Link
Download Structure(s) <ul><li>Download individual record – molfile </li></ul><ul><li>Download SDF file (group of structure...
Search Literature <ul><li>Text indexing of >1/2 million Open Access Articles </li></ul><ul><li>Searching of Pubmed via the...
 
MassSpec API Web Services <ul><li>http:// www.chemspider.com/MassSpecAPI.asmx   </li></ul>
Web Services
Test Web Services for MassSpec <ul><li>http:// www.chemspider.com/WebServices/WSMassSpecAPIDemo.aspx   </li></ul>
Test results
Waters Integration
Waters Integration
Outlinks from Table
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Chemspider For Mass Spectrometrists Public Version

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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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  • This Powerpoint provides an overview of how MS spectrometrists can derive value from ChemSpider
  • Chemspider For Mass Spectrometrists Public Version

    1. 1. ChemSpider for Mass Spectrometrists Antony Williams
    2. 2. ChemSpider - A Search Engine for Chemists <ul><li>Questions a chemist might ask… </li></ul><ul><ul><li>What is the melting point of n-butanol? </li></ul></ul><ul><ul><li>What is the chemical structure of Xanax? </li></ul></ul><ul><ul><li>Chemically, what is phenolphthalein? </li></ul></ul><ul><ul><li>What are the stereocenters of cholesterol? </li></ul></ul><ul><ul><li>Where can I find publications about xylene? </li></ul></ul><ul><ul><li>What are the different trade names for Ketoconazole? </li></ul></ul><ul><ul><li>What is the NMR spectrum of Aspirin? </li></ul></ul><ul><ul><li>What are the safety handling issues for Thymol Blue? </li></ul></ul><ul><ul><li>ChemSpider can answer all of these questions </li></ul></ul>
    3. 3. ChemSpider Data Content <ul><li>Over 21.5 million unique chemical structures from ca. 150 data sources </li></ul><ul><ul><li>Online Databases –PubChem, Drugbank, HMDB, Wikipedia </li></ul></ul><ul><ul><li>Chemical Vendors – over 40 different vendors and growing </li></ul></ul><ul><ul><li>Personal Depositions – individual contributions </li></ul></ul><ul><ul><li>Journal Publishers </li></ul></ul><ul><ul><li>Content database vendors </li></ul></ul><ul><ul><li>Analytical data collections </li></ul></ul><ul><ul><li>Patents (9 MILLION Structures being deposited now ) </li></ul></ul><ul><ul><li>Web scraping </li></ul></ul><ul><ul><li>Content is generally linked back to the original data sources </li></ul></ul>
    4. 4. ChemSpider for MS Spectrometrists <ul><li>What would an MS spectrometrist want to do? </li></ul><ul><ul><li>Search the database based on mass (various forms) </li></ul></ul><ul><ul><li>Search selected subsets of the database based on mass </li></ul></ul><ul><ul><li>Search based on mass and substructure(s) </li></ul></ul><ul><ul><li>Search for structure based on name(s) or database IDs </li></ul></ul><ul><ul><li>Search for structures based on elements/not elements </li></ul></ul><ul><ul><li>Download the structure/structures in standard format </li></ul></ul><ul><ul><li>Search literature for information </li></ul></ul><ul><ul><li>Identify related data sources – chemical vendors, pathway databases, etc </li></ul></ul>
    5. 5. Tell me about Aspirin
    6. 6. Tell me about Aspirin
    7. 7. Link outs
    8. 8. Tell me about Aspirin
    9. 9. Tell me About Aspirin
    10. 10. ChemSpider for MS Spectrometrists <ul><li>What would an MS spectrometrist want to do? </li></ul><ul><ul><li>Search the database based on mass (various forms) </li></ul></ul><ul><ul><li>Search selected subsets of the database based on mass </li></ul></ul><ul><ul><li>Search based on mass and substructure(s) </li></ul></ul><ul><ul><li>Search for structure based on name(s) or database IDs </li></ul></ul><ul><ul><li>Search for structures based on elements/not elements </li></ul></ul><ul><ul><li>Download the structure/structures in standard format </li></ul></ul><ul><ul><li>Search literature for information </li></ul></ul><ul><ul><li>Identify related data sources – chemical vendors, pathway databases, etc </li></ul></ul>
    11. 11. Search Database Based on Mass
    12. 12. Search 309.08+/- 0.001 527 hits out of 21.5 MILLION Structures in 2 seconds
    13. 13. Include/Exclude Elements During a Search
    14. 14. Search based on Data Sources
    15. 15. Combined Searches <ul><li>Search for a particular mass AND </li></ul><ul><ul><li>Search a series of data sources only AND </li></ul></ul><ul><ul><li>Search inclusion/exclusion lists of elements AND </li></ul></ul><ul><ul><li>Search a particular substructure </li></ul></ul>
    16. 16. Structure Searching
    17. 17. Substructure Searching
    18. 18. Outlinks – to vendors and other databases <ul><li>Example databases of interest to MS Spectrometrists: </li></ul><ul><ul><li>HMDB – Human Metabolome Database </li></ul></ul><ul><ul><li>KEGG – Kyoto Encyclopedia of Genes and Genomes </li></ul></ul><ul><ul><li>BioCyc - collection of Pathway/Genome Databases </li></ul></ul><ul><ul><li>Uni. Minnesota Biodegradation DB - information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds </li></ul></ul><ul><ul><li>WikiPathways – new initiative to build crowdsourced pathway data management </li></ul></ul>
    19. 19. Links out to KEGG Kyoto Encyclopedia of Genes and Genomes
    20. 20. WikiPathways Link
    21. 21. Download Structure(s) <ul><li>Download individual record – molfile </li></ul><ul><li>Download SDF file (group of structures) </li></ul>
    22. 22. Search Literature <ul><li>Text indexing of >1/2 million Open Access Articles </li></ul><ul><li>Searching of Pubmed via the NCBI Entrez System </li></ul><ul><li>Potential directions include extension to focused searching- LCMS only, HPLC only etc. We can index based on Title and Abstracts and on chemical names </li></ul>
    23. 24. MassSpec API Web Services <ul><li>http:// www.chemspider.com/MassSpecAPI.asmx </li></ul>
    24. 25. Web Services
    25. 26. Test Web Services for MassSpec <ul><li>http:// www.chemspider.com/WebServices/WSMassSpecAPIDemo.aspx </li></ul>
    26. 27. Test results
    27. 28. Waters Integration
    28. 29. Waters Integration
    29. 30. Outlinks from Table
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