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Web Crawling Chemistry
 

Web Crawling Chemistry

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    Web Crawling Chemistry Web Crawling Chemistry Presentation Transcript

    • Weaving a New Web for Chemistry Antony Williams
    • Structure-Enabled Articles
    • Searching from the Structure Balloon
    • Imagine a time when ….
      • The internet is searchable by chemical structure and substructure
      • Chemistry articles are indexed and searchable by a free online service
      • Publicly funded research data can be shared and discussed in the Open
      • Cheminformatics has as much of a public face as bioinformatics
    • ChemSpider - A Search Engine 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?
        • ChemSpider can answer all of these questions
    • ChemSpider Data Content
      • Over 21.5 million unique chemical structures from ca. 150 data sources
        • Online Databases –PubChem, Drugbank, HMDB, Wikipedia
        • Chemical Vendors – over 40 different vendors and growing
        • Personal Depositions – individual contributions
        • Journal Publishers
        • Content database vendors
        • Analytical data collections
        • Patents (9 MILLION Structures being deposited now )
        • Web scraping
        • Content is generally linked back to the original data sources
    • Tell me about Aspirin
    • Tell me about Aspirin
    • Link outs
    • Links out to KEGG Kyoto Encyclopedia of Genes and Genomes
    • Tell me about Aspirin
    • Tell me About Aspirin
    • Tell me about Aspirin
    • Tell me about Aspirin
    • Tell me about Aspirin
    • Text- Indexing and ChemSpider?
      • ChemSpider text-indexes almost 500,000 Open Access and Free Access articles
      • Collection is growing weekly and more publishers have already agreed
    • Open Access Literature Search
    • Search PubMed – ChemSpider
    • Other Searches
      • What compounds have a mass of 300+/-0.001?
      • or search a combination of intrinsic/predicted properties
    • Other Searches
    • Complex Search
    • The Quality of Data Online…
      • Aggregating data opens up quality issues
      • Structure-identifier associations are “dirty”
      • Structures are COMMONLY incorrect – stereochem issues
      • Manual curation of small databases is enough work – what about millions of structures?
      • Structures are far from perfect. What is a “correct structure”?
        • Full stereochemistry?
        • Historical timeline of structure?
        • Who is the authority?
    • Who holds THE Quality Authority?
      • Chemical Abstracts Service is the structural authority today. 1400 (?) employees, world standard in chemistry information
      • 101 years of knowledge, process and expertise. MANUAL curation is key. Robotic curation is enabling
      • How can an online, free access system peacefully co-exist with the authority?
    • Quality is a Major Issue- Search Butanol
    • Wikipedia – Crowdsourcing Chemistry
    • Wikipedia Chemistry Curation project
      • Only ca. 5000 organic structures, 7000 total structures
      • MONTHS of work so far for a team of 6 people
      • Many errors removed in the process. Curation process is a daily event for users/depositors
      • Slow and torturous process for stereo molecules.
    • Thymol Blue on ChemSpider
      • Data online includes:
        • UV-vis spectrum
        • Measured experimental properties
        • Link to Wikipedia article
        • Links to chromatography details
        • Multiple identifiers/trade names etc.
        • Links to vendors/suppliers/other databases
        • Safety information
    • Differences between ChemSpider/Wikipedia No Analytical Data Active editors – about 50 (?) Active depositors/curators – 30 No Prediction of properties ???? 5000 people/day; 1100 registered Detailed compound monographs Compound monographs linked Text Complex queries – Properties, Text, structure/substructure, OA publishers, Data Sources, … ~5000 organics, 2000 others >21 million unique structures Wikipedia ChemSpider
    • Differences between Wikipedia/ChemSpider Growing reputation as focused on quality Worldwide reputation as quality source Chemistry is the focus of ‘Spider Chemistry is a subset of the ‘Pedia Mixed “licensing” GFL licensing for everything Growing team of WP:Chem advocates, curators and admins Strong team of WP:Chem advocates, curators and admins “ Out of a basement” on three servers and 5 volunteers Established infrastructure and Wikipedia Foundation Team Primarily Microsoft .NET technologies with OS components Supported by tried and tested Media-Wiki platform. ChemSpider Wikipedia
    • Crowd-sourcing Curation
      • How to curate data for millions of structures?
      • Robot processes can clean up depositions
        • Search for Chloride and check molecular formula for Cl
        • Check for stereochemistry and remove names with stereo
      • Provide a simple-to-use platform to curate, annotate and tag data
      • Provide curator administration to prevent vandalism (Veropedia)
    • Multi-level Curation and Approval
    • Post Comments
      • Anyone can “Post Comments” associated with a structure. To curate data we require login to track
    • Crowd-sourcing Chemistry
      • Crowd-sourced curation: identify and tag errors, edit names, synonyms, identify records for deprecation
      • ALSO
      • Crowd-sourced deposition: anyone can deposit data (structures, text, images, analytical data)
    • But, when registered and logged in…
      • Ability to curate and add to the database
        • Add structures
        • “ Clean” structures
        • Add data (spectra, CIFs, images)
        • Add links to other pages (URLs)
        • Add publication details
    • Adding to the Database - Structure
    • Adding New Text Data Add Publication Add Identifier Add URL
    • Adding Supplementary Info to a Structure
    • ChemSpider TouchGraph
    • Structure-Centric
      • We want to search Open-Access articles by structure, substructure, similarity of structure
      • Standard approaches would be:
        • Identify chemical names “entity extraction”
        • Convert chemical names to structures and index
      • ChemSpider has a validated dictionary of structure-name pairs
      • Use name extraction, name-conversion and dictionary look-up. THEN curate.
    • “Entity Extraction”
      • Rule-based recognition of systematic names:
        • Use a lexeme of name fragments
        • Rules for identifying bounds of a name
      • Look-up dictionary:
        • Drug Names
        • Trivial Names
        • Numbers : Registry IDs, EINECS/ELINCS/Beilstein IDs
    • Name Recognition
      • Azo aldehyde 2   was  synthesized according to a reported  method [17]. To  a stirred  solution  of azo aldehyde 2   (1.08 g, 3.76 mmol )  in  dry CH2Cl2  (30.00 mL) at  0 oC  were  successively  added (3,4-diaminophenyl)phenyl methanone 1 (0.40 g, 1.88 mmol) and a excces of anhydrous MgSO4 (2.00 g,16.67 mmol) . The resulting  mixture  was  stirred  for  6 hours  at room temperature [18]. The mixture was  filtered and washed with dichloromethane . Then the solvent was  evaporated under reduced pressure to  give azo Schiff base 3   as a red solid which was recrystalized from ethanol 95%    (1.28 g, 91 %)
    • Name Recognition
      • Azo aldehyde 2   was  synthesized according to a reported  method [17]. To  a stirred  solution  of azo aldehyde 2   (1.08 g, 3.76 mmol )  in  dry CH2Cl2   (30.00 mL) at  0 oC  were  successively  added  (3,4-diaminophenyl)phenyl methanone 1 (0.40 g, 1.88 mmol) and a excess of anhydrous MgSO 4 (2.00 g,16.67 mmol) .
      • The resulting  mixture  was  stirred  for  6 hours  at room temperature [18]. The mixture was  filtered and washed with dichloromethane . Then the solvent was  evaporated under reduced pressure to  give azo Schiff base 3   as a red solid which was recrystalized from ethanol 95%    (1.28 g, 91 %)
    • How Many Chemical Names?
      • “ She had the drive to derive success in any venture and was well versed in Karate. When the man in the tartan shirt approached her with a dagger in his hand she spat in his face, took the stance of a commando and took advantage of his shock to release the dagger from his grip and causing him to recoil. He went home and took an aspirin after the beating.”
    • How Many Chemical Names?
      • “ She had the drive to derive success in any venture and was well versed in Karate . When the man in the tartan shirt approached her with a dagger in his hand she spat in his face, took the stance of a commando and took advantage of his shock to release the dagger from his grip and causing him to recoil . He went home and took an aspirin after the beating.”
    • Making Open Access Articles Searchable Proof of Concept
      • Can we HOST Chemistry Open Access articles on ChemSpider and add-value
      • Can we identify chemical names in Open Access articles in a user-friendly manner
      • Can we convert names to structures in Open-Access articles and expand ChemSpider and provide structure searching of Open Access chemistry articles?
      • Can we provide an environment for chemists to mark-up their own articles and crowd-source markup of an archive?
    • Document markup
      • ChemSpider now hosting Open Access articles from MDPI, Molecular Diversity Preservation International
      • Hosting the Molbank collection at present
    • A Standard for Document Markup?
      • NLM-DTD: National Library of Medicine; Document Type Definition
      • Approved markup definitions to apply to journal articles – extended as necessary for our purposes
    • NLM/DTD markup
    • Chemistry and Biology
    • Chemistry and Biology
      • Menus can be extended as necessary
    • Document markup
    • Searching from the Structure Balloon
    • A Platform for Markup
      • Can we provide a platform for document markup for chemists?
      • Workflow:
        • Upload word docs, RTF files or point to HTML and load
        • Apply entity extraction, convert names to structures, mark-up automatically and ask for user participation
        • Publish final version with NLM-DTD markup
        • Deposit all structures on ChemSpider under embargo and wait for article DOI to release
    • Online Markup
    • Automated markup
    • Name to Structure Conversion
    • Conversion of Structure Images
      • Not all compounds have a “name”
      • Structure images can be converted to connection tables
    • Cryptomisrine
    • Structure Conversion from Images-CLiDE
      • Conversion dependent on zoom-factor can give perfect conversion!
    • Supports Word .DOC, HTML, RTF
    • Extensible Markup Process
      • Markup process is easily extendable
      • Configurable from one XML file
      • NLM/DTD is incorporated but is easy to extend
    • Tipping Point
      • Tipping point - the point at which a slow gradual change becomes irreversible and then proceeds with gathering pace
    • Our Challenges
      • There are “no employees”
      • ChemSpider is non-funded
      • System is hyper-dependent on ISP, power and limited compute power
      • We are upsetting some people – specifically “closed” data content providers
    • What’s Coming?
      • Agreement with Royal Society of Chemistry that we can add their structure-based RSS feeds to ChemSpider
      • Agreement with Nature Publishing Group to add their Nature Chemical Biology structure collections to ChemSpider as they issue
      • Presently indexing Acta Chemica Scandanavica, 1947-1999 PDF backfile – our first foray into OCR
      • Presently indexing PLoS journals directly
      • More publishers have agreed…
    • Conclusions
      • The quality of structure-based data online should always be questioned – that includes ChemSpider
      • Robots and software algorithms can help but eyeballs are necessary
      • Data on ChemSpider are being added and curated on a daily basis but we need more eyeballs helping always
      • ChemSpider now has a large validated structure-name dictionary
    • Further reading
      • www.chemspider.com/blog
      • Internet-based tools for communication and collaboration in chemistry, Drug Discovery Today, Volume 13, Numbers 11/12, June 2008 502-506, doi:10.1016/j.drudis.2008.03.015
      • A perspective of publicly accessible/open-access chemistry databases, Drug Discovery Today, Volume 13, Numbers 11/12, June 2008, 495-501, doi:10.1016/j.drudis.2008.03.017
    • ChemSpider Forums/Blogs
      • Forum.chemspider.com
      • www.chemspider.com/blog
    • Acknowledgments
      • The ChemSpider team of volunteer developers
      • ChemSpider Advisory Group
      • Our curators, depositors and users
      • Suppliers of commercial software – Microsoft, ACD/Labs, OpenEye, ChemAxon, SimBioSys
      • SureChem – Structure Based Online Patent Searching