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II-SDV 2015, 20 - 21 April, in Nice

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II-SDV 2015, 20 - 21 April, in Nice

  1. 1. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 1 / 29 Interlinking scientific information by means of chemical semantic enrichment Valentina Eigner-Pitto, Josef Eiblmaier, Hans Kraut, Heinz Saller, Peter Loew InfoChem GmbH, Landsberger Strasse 408, Munich, 81241, Germany
  2. 2. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 2 / 29 Outline • Introduction o Role of chemical structure searching o Where do I perform structure searches? o Cost implications • Setting the scene: chemical structures as common denominator? o Publishers efforts  Creation of chemical content  Semantic enrichment of journal articles • Case Studies: o Wiley The Smart Article o Springer Chemistry Demonstrator http://www.bubblews.com/news/2372700-tips-to-be-a-professional-content-writer
  3. 3. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 3 / 29 Why structure searching? • CICAG (RSC) survey by Neil Stutchbury, May 20, 2009 Chemical Information Mining: Possibilities and Pitfalls (http://www.rsc.org/images/ChemInfoMining_tcm18-153536.pdf) 65 responses from pharma, academia, vendors, and publishers “Search documents by chemical structure or substructure”?
  4. 4. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 4 / 29 Diazepam OR Valium OR Ansiolisina OR Diazemuls OR Relanium OR Stesolid OR Apaurin OR Faustan OR Seduxen OR Sibazon OR Methyldiazepinone OR Calmocitene OR Neurolytril OR Bialzepam OR Ceregulart OR Condition OR Diazetard OR Liberetas OR Relaminal OR Serenamin OR Tranquirit OR Ansiolin OR Apozepam OR Atensine OR Bensedin OR Calmpose OR Diacepan OR Diazepan OR Dipezona OR Domalium OR Kiatrium OR Paranten OR Quetinil OR Quiatril OR Quievita OR Renborin OR Ruhsitus OR Seduksen OR Serenack OR Serenzin OR Stesolin OR Tensopam OR Horizon OR Lembrol OR Morosan OR Saromet OR Sedipam OR Setonil Anxionil OR Benzopin OR Calmaven OR Chuansuan OR Desconet OR Desloneg OR Diaceplex OR Diazepin OR Gewacalm OR Jinpanfan OR Mentalium OR Metamidol OR Nixtensyn OR Novodipam OR Pacitran OR Paralium OR Prozepam OR Psychopax OR Radizepam OR Simasedan OR Trankinon OR Trazepam OR Valaxona OR Valiquid OR Valuzepam OR Vanconin OR Antenex OR Arzepam OR Betapam OR Diapine OR Diaquel OR 7-Chloro- 1,3-dihydro-1-methyl-5-phenyl-2H-1,4-benzodiazepin-2-one OR NCGC00178168-01 OR WLN: T67 GNV JN IHJ CG G1 KR OR 2H-1,4-Benzodiazepin-2-one, 7-chloro-1,3- dihydro-1-methyl-5-phenyl- OR CPD000058398 OR SAM001246536 OR SMR000058398 OR 439-14-5 OR 7-Chloro-1-methyl-5-phenyl-3H-1,4-benzodiazepin- 2(1H)-one OR 7-Chloro-1-methyl-2-oxo-5-phenyl-3H-1,4-benzodiazepine OR 7-Chloro- 1-methyl-5-phenyl-2H-1,4-benzodiazepin-2-one OR C06948 OR D00293 OR 5-24-04- 00300 OR D003975 OR A3662/0155188 OR I06-0194 OR 1-Methyl-5-phenyl-7-chloro- 1,3-dihydro-2H-1,4-benzodiazepin-2-one OR 7-Chloro-1-methyl-5-3H-1,4- benzodiazepin-2(1H)-one OR 7-chloro-1-methyl-5-phenyl-3H-1,4-benzodiazepin-2-one OR DZP OR Dap OR Pax OR 11100-37-1 OR 53320-84-6 OR InChI=1/C16H13ClN2O/c1-19-14-8-7-12(17)9-13(14)16(18-10-15(19)20)11-5-3-2-4-6- 11/h2-9H,10H2,1H ... (343 Synonyms!) „Full text searching is sufficient!“ WLN SMILES SMARTS ROSDAL Connection Table Molfile SDfile CML InChI InChI Key http://us.cdn4.123rf.com/168nwm/baz777/baz7771101/baz777110100 058/8576422-cartoon-scienziato-isolato-su-sfondo-bianco.jpg
  5. 5. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 5 / 29 Where am I able to perform structure searches?
  6. 6. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 6 / 29 Manuscript submission Publishing Cost implications Manual Indexing Database production http://premium.wpmudev.org/blog/tutorial- how-to-add-authors-images-to-your- wordpress-blog/
  7. 7. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 7 / 29 • Automatic production of chemical content: o chemical named entity recognition o automatic CDX work-up • Semantic enrichment of journal articles o RSC: RSC Semantic Publishing (Project Prospect) o NPG: sematically enriched PDF o Elsevier: Article of the future o Wiley: The Smart Article • Structure search on web-pages (partly) • Automatic production of chemical content: o chemical named entity recognition o automatic CDX work-up • Semantic enrichment of journal articles o RSC: RSC Semantic Publishing (Project Prospect) o NPG: sematically enriched PDF o Elsevier: Article of the future o Wiley: The Smart Article • Structure search on web-pages (partly) Publishers efforts
  8. 8. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 8 / 29 Automatic production of chemical content Manual IndexingPublishing
  9. 9. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 9 / 29 http://manuelo-pro.deviantart.com/art/Disclaimer-281316501 • Automatic production of chemical content: o chemical named entity recognition o automatic CDX work-up • Semantic enrichment of journal articles o RSC: RSC Semantic Publishing (Project Prospect) o NPG: sematically enriched PDF o Elsevier: Article of the future o Wiley: The Smart Article • Structure search on web-pages (partly) • Automatic production of chemical content: o chemical named entity recognition o automatic CDX work-up • Semantic enrichment of journal articles o RSC: RSC Semantic Publishing (Project Prospect) o NPG: sematically enriched PDF o Elsevier: Article of the future o Wiley: The Smart Article • Structure search on web-pages (partly) Publishers efforts
  10. 10. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 10 / 29 • Pioneer work: Project Prospect (2007) • Online since 2011 • Extraction of chemical names from over 30,000 journal articles • Integration of compounds into ChemSpider • Approach integrated within routine publication processes • Features: o Highlighting of:  Compounds  Chemical terms  Biomedical terms o Link to compounds in ChemSpider o Structure search only in ChemSpider RSC: Semantic Publishing
  11. 11. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 11 / 29 • XMP-embedded PDFs available online since 2008 • Entity specific annotation service: o SureChem for chemical compounds o LuXiD for genes/proteins o … • Mix between automated services and editorial QA • Features: o Figures and compound browser o Links to:  Web of Science  PubMed  CAS Reference Linking o No structure search Nature Publishing Group: Semantically enriched PDF
  12. 12. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 12 / 29 • Launched 2012 • Guiding principals: o readability o discoverability o extensibility • Supplementary content, features and external databases info presented in right sidebar • Features: o 3-pane presentation layout:  navigation bar  main content area  right sidebar o Links to:  NCBI  Reaxys  … (depending on subject) o No structure search Elsevier: Article of the Future
  13. 13. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 13 / 29 Wiley: The Smart Article • Launched in 2012 • Goal: providing quick information on chemical compounds featured in an article, chemical terms in the text, and other key parts of the chemistry within the article • Live for following journals and major reference works: o Chemistry: An Asian Journal o Chirality o Applied Organometallic Chemistry o Journal of Physical Organic Chemistry o Journal of Heterocyclic Chemistry o eEros o Organic Synthesis o Organic Reactions • Features: o Compound browser o Chemistry term highlighter o Compound index o Enhanced abstract page o Compound record o Chemistry structure search
  14. 14. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 14 / 29 Structure as common denominator: 2 use cases Chemistry Demonstrator
  15. 15. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 15 / 29 The challenge* *Reinhard Neudert: Enhancing the User Experience for Wiley Chemistry Content, ICIC 2012 14. – 17. October, Berlin
  16. 16. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 16 / 29 Text annotation: Chemistry enrichment workflow* *Reinhard Neudert: Enhancing the User Experience for Wiley Chemistry Content, ICIC 2012 14. – 17. October, Berlin
  17. 17. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 17 / 29 Text annotation: ICANNOTATOR
  18. 18. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 18 / 29 CDX scheme enumeration: Chemistry enrichment workflow* *Reinhard Neudert: Enhancing the User Experience for Wiley Chemistry Content, ICIC 2012 14. – 17. October, Berlin
  19. 19. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 19 / 29 Author‘s CDX file CDX template Templating CDX-Templating Guidelines (Structures) *Reinhard Neudert: Enhancing the User Experience for Wiley Chemistry Content, ICIC 2012 14. – 17. October, Berlin CDX scheme enumeration: Templating*
  20. 20. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 20 / 29 CDX scheme enumeration: Template* *Reinhard Neudert: Enhancing the User Experience for Wiley Chemistry Content, ICIC 2012 14. – 17. October, Berlin
  21. 21. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 21 / 29 CDX scheme enumeration: ICSchemeProcessor Chemical structures (SD files) ICSchemeProcessor Reactions (RD files) Source: Thieme Pharmaceutical Substances, Ticagrelor (in production) Reagent Solvent Catalyst SOCl2 LiOH H2O, THF Pd(OAc)2 Cl-Co2Et, Et3N Acetone, H2O Conditions (RD files)
  22. 22. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 22 / 29 Examples
  23. 23. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 23 / 29 Chemistry Demonstrator The challenge • Chemical annotation of > 6 mio SpringerLink documents • Interlink different data repositories via chemical structure • Create one search interface • Data aggregation / results consolidation
  24. 24. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 24 / 29 Document display The demonstrator Springer Chemistry Demonstrator Structure search Display servers Client computers Contains: • master index of all structures • basic molecule attributes • links to the source page/document Internet/Intranet HTTP(S)
  25. 25. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 25 / 29
  26. 26. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 26 / 29 Example
  27. 27. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 27 / 29 Summary • Importance of structure searching and cost implications • Publisher efforts o Automatic generation of chemical content o Semantic enrichment • Case studies where structure is common denominator o Generation of chemical content for Wiley o Springer study: “Chemistry Demonstrator”  Proof of concept  Demonstrator http://writing.phillipmartin.info/la_summary.htm
  28. 28. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 28 / 29 Conclusions • Starting middle 2000 chemical structure gains significance by publishers • Publishers recognize importance of structure searching • Chemical content is generated to a greater extent with automatic processes The chemical structure is an extremely efficient entity to be used for effective retrieval as well as linking of different sources http://www.nedarc.org/emsDataSystems/lessonslearned.html
  29. 29. InfoChem GmbH © 2015 Dr. Valentina Eigner PittoII-SDV, Nice, April 21, 2015 29 / 29 Acknowledgments • Reinhard Neudert (Wiley) • Wendy Warr • InfoChem Team http://www.wien2k.at/pictures/pa2005/pa/Thank%20you%20for%20your%20attention%2001.html http://www.allenschool.edu/blog-online/questions-medical-billing-job-offered/2681/

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