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How an Online Resource for Chemistry Can Change Our World
 

How an Online Resource for Chemistry Can Change Our World

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This is a presentation given at the Triangle Chromatography Discussion Group with a focus on Mass Spectrometry and associated web services and what is possible for chromatographers

This is a presentation given at the Triangle Chromatography Discussion Group with a focus on Mass Spectrometry and associated web services and what is possible for chromatographers

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  • This is a list of some of the things an MS scientist might want to do and some of the queries we have already experienced

How an Online Resource for Chemistry Can Change Our World How an Online Resource for Chemistry Can Change Our World Presentation Transcript

  • How an Online Chemistry Resource Could Change Our World Antony Williams Triangle Chromatography Discussion Group, Raleigh, NC, May 2009
  • Imagine a time when ….  The internet is searchable by chemical structure and substructure (e.g.Wikipedia, Google Scholar)  When there is an online database of NMR, IR, MS spectra and chromatography methods built by available to the community  Chemistry articles are indexed and searchable by “chemistry”  The web is linked together through the “language of chemistry”  Publicly funded research data can be shared and discussed in the Open, maybe as Open Notebook Science  Cheminformatics has as much of a public face and success as bioinformatics (Protein DataBank, Genbank, etc) Building a Structure Centric Community for Chemists
  • The Language of Chemistry  My language…. Building a Structure Centric Community for Chemists
  • And its dialects…. Building a Structure Centric Community for Chemists
  • As a chemist…  I look for information about chemicals/chemistry  What is a particular structure ?  What alternative names/identifiers?  Reaction synthesis?  Physical properties?  Analytical data?  Purchase?  Tell me more?  Similar stuff – what other compounds are “like” mine? Building a Structure Centric Community for Chemists
  • Linked Data Cloud Building a Structure Centric Community for Chemists
  • Chemistry on the Internet  Much of the information online is User Beware!  The Quality of information is “diverse”  Technologies can “link and connect” information but validation and curation is key to providing quality  The LinkedData web is of less value when the data linked are “wrong” Building a Structure Centric Community for Chemists
  • “Good Stuff” TotallySynthetic.com Building a Structure Centric Community for Chemists
  • PubChem Building a Structure Centric Community for Chemists
  •  Questions a chemist might ask…  What is the melting point of n-butanol?  What is the chemical structure of Xanax?  Chemically, what is phenolphthalein?  What are the stereocenters of cholesterol?  Where can I find publications about xylene?  What are the different trade names for Ketoconazole?  What is the NMR spectrum of Aspirin?  What are the safety handling issues for Thymol Blue? Building a Structure Centric Community for Chemists
  • Search Cholesterol Building a Structure Centric Community for Chemists
  • Search Cholesterol Building a Structure Centric Community for Chemists
  • Search Cholesterol Building a Structure Centric Community for Chemists
  • Search Cholesterol Building a Structure Centric Community for Chemists
  • Search Cholesterol Building a Structure Centric Community for Chemists
  • Link outs Building a Structure Centric Community for Chemists
  • Complex Data and Information Building a Structure Centric Community for Chemists
  • Online Analytical Data Building a Structure Centric Community for Chemists
  • Various Searches  Structure searching  Substructure searching  Subset searching – choose from 200 data sources  Property searching  Value for Mass Spectrometrists and Chromatographers? Building a Structure Centric Community for Chemists
  • ChemSpider for MS Spectrometrists  What would an MS spectrometrist want to do?  Search the database based on mass (various forms)  Search selected subsets of the database based on mass  Search based on mass and substructure(s)  Search for structure based on name(s) or database IDs  Search for structures based on elements/not elements  Download the structure/structures in standard format  Search literature for information  Identify related data sources – chemical vendors, pathway databases, etc Building a Structure Centric Community for Chemists
  • Search Database Based on Mass Building a Structure Centric Community for Chemists
  • Mass Based Searches?  What compounds have a mass of 300+/-0.001? Building a Structure Centric Community for Chemists
  • 59 hits/1.3 seconds from 21.5 MILLION Building a Structure Centric Community for Chemists
  • Substructure and Property Building a Structure Centric Community for Chemists
  • Building a Structure Centric Community for Chemists
  • Elemental Constraints Building a Structure Centric Community for Chemists
  • Search based on Data Sources Building a Structure Centric Community for Chemists
  • Outlinks – to vendors and other databases  Example databases of interest to MS Spectrometrists:  HMDB – Human Metabolome Database  KEGG – Kyoto Encyclopedia of Genes and Genomes  BioCyc - collection of Pathway/Genome Databases  Uni. Minnesota Biodegradation DB - information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds  WikiPathways – new initiative to build crowdsourced pathway data management Building a Structure Centric Community for Chemists
  • Links out to KEGG Kyoto Encyclopedia of Genes and Genomes Building a Structure Centric Community for Chemists
  • WikiPathways Link Building a Structure Centric Community for Chemists
  • Download Structure(s)  Download individual record – molfile  Download SDF file (group of structures) Building a Structure Centric Community for Chemists
  • Web Service Integration  ChemSpider integration presently integrated to Bruker, Waters and Thermo – more vendors coming…  Direct integration to vendor data processing tools Building a Structure Centric Community for Chemists
  • MassSpec API Web Services  http://www.chemspider.com/MassSpecAPI.asmx Building a Structure Centric Community for Chemists
  • Web Services Building a Structure Centric Community for Chemists
  • Test Web Services for MassSpec  http:// www.chemspider.com/WebServices/WSMassSpecAPIDem Building a Structure Centric Community for Chemists
  • Test results Building a Structure Centric Community for Chemists
  • Waters Integration Building a Structure Centric Community for Chemists
  • Waters Integration Building a Structure Centric Community for Chemists
  • Outlinks from Table Building a Structure Centric Community for Chemists
  • For Chromatographers?  “Structure-based methods” being linked  Structure-centric searching of methods  We can host chromatograms for display  LogPs and LogDs (pH5.5 and 7.4) calculated for >21 million compounds using ACD/Labs software  We’d love to host collections from the column vendors! tony@chemspider.com Building a Structure Centric Community for Chemists
  • From 21.5 MILLION molecules…  Data are gathered/deposited from >200 data sources  Government databases  Chemical vendors  Wikipedia  There are “imperfections” in all online data sources  How bad can it get???? Building a Structure Centric Community for Chemists
  • What is “wrong”? Building a Structure Centric Community for Chemists
  • Quality is a Major Issue- Search Butanol OLD EXAMPLE..now fixed Building a Structure Centric Community for Chemists
  • Vancomycin  Who will curate?  PubChem is not resourced to clean these errors   How would you clean such a large dataset? Building a Structure Centric Community for Chemists
  • Wikipedia, C&E News, PubChem C&E News (from ACS) Building a Structure Centric Community for Chemists
  • Building a Structure Centric Community for Chemists
  • Does one stereocenter matter? Thalidomide Building a Structure Centric Community for Chemists
  • Question Everything www.dhmo.org Building a Structure Centric Community for Chemists
  • DailyMed “DailyMed provides high quality information about marketed drugs. This information includes FDA approved labels (package inserts).” Building a Structure Centric Community for Chemists
  • The FDA’s DailyMed Building a Structure Centric Community for Chemists
  • Structures on DailyMed Poor Representations Building a Structure Centric Community for Chemists
  • Incorrect Structures Scanning (?) Issues Building a Structure Centric Community for Chemists
  • Incorrect Structures Building a Structure Centric Community for Chemists
  • Wikis for Science  Who in the room hasn’t used Wikipedia?  Is it trustworthy?  What are the advantages and disadvantages of the Wiki environment?  How suitable is it for Chemistry? Building a Structure Centric Community for Chemists
  • Collaborative Knowledge Management for Chemists Building a Structure Centric Community for Chemists
  • Wikipedia Curation  Looking for self-consistency across a Wikipedia Page  Primary key is the article TITLE  The chemical shown needs to match the title  Cyclic self-consistency – and decisions must get made Building a Structure Centric Community for Chemists
  • Taxol on PubChem Building a Structure Centric Community for Chemists
  • When are things “wrong”?  Structures have a timeline….. Building a Structure Centric Community for Chemists
  • Building a Structure Centric Community for Chemists
  • Building a Structure Centric Community for Chemists
  • Building a Structure Centric Community for Chemists
  • Creating a trusted source…  Small databases can be curated by the hosts – EPA’s DSSTox, Wikipedia, etc.  Who will curate an enormous database? Building a Structure Centric Community for Chemists
  • Crowdsourcing Building a Structure Centric Community for Chemists
  • Curating ChemSpider  Anyone can “Post Comments” associated with a structure. To curate data we require login to track Building a Structure Centric Community for Chemists
  • Multi-level Curation and Approval Building a Structure Centric Community for Chemists
  • ChemMantis  Chemical Markup And Nomenclature Transformation Integrated System Building a Structure Centric Community for Chemists
  • On the fly conversion Building a Structure Centric Community for Chemists
  • Nature Publications Building a Structure Centric Community for Chemists
  • Integrations Out to Other Sources Building a Structure Centric Community for Chemists
  • Reactions Building a Structure Centric Community for Chemists
  • ChemSpider Everywhere RSC Compounds Building a Structure Centric Community for Chemists
  • ChemSpider Everywhere Nature Chemistry Nature Chemistry articles are annotated to identify all of the chemical compounds mentioned throughout the text. Those compounds are linked out to other information resources including PubChem and ChemSpider. Building a Structure Centric Community for Chemists
  • ChemSpider Everywhere ChemMobi Building a Structure Centric Community for Chemists
  • Building a Structure Centric Community for Chemists
  • It Happened in a Basement!!  Homebuilt servers  Cable internet  Software donations  Lots of hard work  >8000 users per day  >80,000 transactions per day Building a Structure Centric Community for Chemists
  • And now…  The Royal Society of Chemistry announced on May 11th that it has acquired ChemSpider, heralding a breakthrough investment for the organisation and for the Chemistry Community. This acquisition reflects RSC's commitment to providing access to rich resources of chemistry data and information. Building a Structure Centric Community for Chemists