The document discusses capturing chemistry data using XML and Chemical Markup Language (CML) to enhance data validity and reusability. It outlines methods for machine parsing of structured, semi-structured, and unstructured data in chemistry, alongside case studies and applications in computational chemistry. The document emphasizes the development of tools for high-throughput data extraction and error checking in chemical research publications.

1. Capturing Chemistry in XML/CML J. A. Townsend * , S. E. Adams * , J. M. Goodman * , P. Murray-Rust * , C. A. Waudby * Capturing Chemistry in XML/CML ACS March 2004 * Unilever Centre for Molecular Informatics, University of Cambridge

2. The Agony Of Publication - Loss Capturing Chemistry in XML/CML ACS March 2004 The World

3. The Agony Of Publication - Loss Capturing Chemistry in XML/CML ACS March 2004 The World Sad The Scientist The Lab Journals Web Pages

4. The Vision-1 Capturing Chemistry in XML/CML ACS March 2004 < scalar dictRef =“ ccml:mp ” units =“units:c” minValue =“65” maxValue =“66” /> mp 65-66  C Human-readable Machine-readable

5. The Vision-2 Chemists can carry on doing what they want Capturing Chemistry in XML/CML ACS March 2004 Reuse chemistry Archive data Ensure validity of data Create new sources of data / molecules But also

6. Our Approach Let chemists use familiar programs … … and document templates Focus on Journal Articles, Theses, CompChem Create data for knowledge-based discovery Let computers do the work Evolution… Capturing Chemistry in XML/CML ACS March 2004

7. Machine Parsing of Chemistry Capturing Chemistry in XML/CML ACS March 2004 Structured (CompChem) Semi-Structured (Articles) Unstructured (Discussion) Structured documents and data in XML MACHINE PARSING ?

8. How? Abstract Discussion Experimental Capturing Chemistry in XML/CML ACS March 2004 Article semi- structured Add Structure Parse with Regular Expressions Legacy to CML converters

9. Regular Expressions Capturing Chemistry in XML/CML ACS March 2004 [Mm]\.?p\p{Punct}?\s+>?\s?\d*\.?\d?\s?-\s?\d*?\.?\d?\s°?\s?C Maybe ‘.’ Any punctuation 0 or more digits Capital ‘ C’ Melting point: two possible syntaxes Capital or lowercase ‘m’ Lowercase ‘ p’ Maybe whitespace Maybe degrees sign m.p. > 23.5 °C mp 23.5 – 25 °C

10. CML - XML For Chemistry Based on W3C XML Schemas 300+ components Customisable Extensible through dictionaries Openly available software Capturing Chemistry in XML/CML ACS March 2004 J. Chem. Inf. Comp. Sci., 2003 , 43 , 757

11. The CML Family Controlled XMLNamespaces: CMLCore – compounds and properties CMLReact – reactions CMLSpect – spectra * CMLComp – compChem CMLCryst – crystallography and condensed matter Interoperates with HTML, MathML, SVG, * AniML + , * ThermoML $ , etc. Capturing Chemistry in XML/CML ACS March 2004 + spectra: ANSI/JCAMP $ thermochemistry: NIST J. Chem. Inf. Comp. Sci., 2003 , 43 , 757

12. Case Studies Parsing output from 750,000 MOPAC jobs High-throughput parsing of journals Capturing Chemistry in XML/CML ACS March 2004

13. CompChem Logs Capturing Chemistry in XML/CML ACS March 2004 Coordinates Molecular Formula Calculation Type Point Group Dipole Total Energy

14. Loss From CompChem Capturing Chemistry in XML/CML ACS March 2004 Coordinates Molecular Formula Calculation Type Dipole Total Energy Ionisation Potential

15. Loss From CompChem Capturing Chemistry in XML/CML ACS March 2004 Coordinates Molecular Formula Calculation Type Dipole Total Energy Ionisation Potential

16. Parsing Data CompChem Output Capturing Chemistry in XML/CML ACS March 2004 Coordinates Energy Levels Vibrations Coordinates Energy Level Vibration CML File CMLCore CMLCore CMLComp CMLSpect Input/jobControl General Parsers

17. Display Process 1 Capturing Chemistry in XML/CML ACS March 2004 CompChem Log Xindice CML XSLT

18. Display Process 2 Capturing Chemistry in XML/CML ACS March 2004 CML File CMLCore CMLCore CMLComp CMLSpect compChem Output 3D structure, electronic properties Coordinates Energy Levels Vibrations Input/jobControl XSLT Display Normal modes 2D structure, thermodynamic properties

19. Parsing Data Capturing Chemistry in XML/CML ACS March 2004 Dictionary Entry: The pointgroup of a molecule ... The Schoenflies convention is normally used, but Hermann Mauguin is also allowed. D [debye] ParentSI: c.m Multiplier: 3.335641E-30 CGS units for electric dipole

20. Dictionaries Capturing Chemistry in XML/CML ACS March 2004 < scalar dictRef =“ ccml:mp ” units =“units:c” minValue =“65” maxValue =“66” /> Linked to CML schema Accesses CCML namespace Units dictionary id =&quot;celsius&quot; name =&quot;Celsius&quot; parentSI =&quot;k&quot; multiplierToSI =&quot;1&quot; constantToSI =&quot;273.15&quot; abbreviation =&quot;C&quot; unitType =&quot;temp&quot; id =&quot;meltrange&quot; term =&quot;Melting range&quot; definition =&quot;Minimum and maximum values of melting range in degrees Celsius&quot;

21. OSCAR Open Source Chemistry Analysis Routines Capturing Chemistry in XML/CML ACS March 2004 Sponsored by the Royal Society of Chemistry (Cambridge) Mounted on http://www.rsc.org/

22. Article Structure Capturing Chemistry in XML/CML ACS March 2004 Front Matter Abstract Introduction Discussion Experimental References Results Article

23. Article Structure Capturing Chemistry in XML/CML ACS March 2004 Front Matter Abstract Introduction Discussion Experimental References Results Article

24. Article Structure Capturing Chemistry in XML/CML ACS March 2004 Front Matter Abstract Introduction Discussion Experimental References Results Article

25. Article Structure Capturing Chemistry in XML/CML ACS March 2004 Front Matter Abstract Introduction Discussion Experimental References Results Article

26. Article Structure Capturing Chemistry in XML/CML ACS March 2004 Front Matter Abstract Introduction Discussion Experimental References Results Article

27. Article Structure Capturing Chemistry in XML/CML ACS March 2004 Front Matter Abstract Introduction Discussion Experimental References Results Synthesis Set up Analysis Compound Name Article Experimental

28. Information Checked / Extracted Capturing Chemistry in XML/CML ACS March 2004 Chemical name Yield Boiling / Melting point Carbon NMR Hydrogen NMR Infra Red spectrometry Mass spectrometry Elemental Analysis Optical Rotation Refractive Index R f value Ultra Violet spectrometry Nature (colour, state, modifiers, description, etc.)

29. OSCAR Parsing Data Capturing Chemistry in XML/CML ACS March 2004 H NMR Nature HRMS

30. OSCAR Parsing Data Capturing Chemistry in XML/CML ACS March 2004

31. OSCAR Data Found Capturing Chemistry in XML/CML ACS March 2004 Results from one paper

32. OSCAR Error Checking Capturing Chemistry in XML/CML ACS March 2004 Serious Error Warning Type 1 Warning Type 2

33. OSCAR Error Checking Capturing Chemistry in XML/CML ACS March 2004 ~30 errors / warnings searched for This article has: 4 errors 2 warnings (type 1) 30 warnings (type 2) Elemental analysis, incorrect – calculations are for a different molecular formula

34. OSCAR Data Presentation Capturing Chemistry in XML/CML ACS March 2004

35. OSCAR Speed Capturing Chemistry in XML/CML ACS March 2004 A typical paper contains ca. 20 compounds JOC (Feb 2004) contains ~600 compounds OSCAR could extract and tabulate in under 5 minutes OBC (Feb 2004) contains ~300 compounds OSCAR could extract and tabulate in under 3 minutes High throughput, high precision

36. OSCAR Accuracy Capturing Chemistry in XML/CML ACS March 2004 92 % of Data Correctly Identified 3 % incorrect author entry 5 % missed 437 items, ~10,000 data fields in test set, working with current Regular Expressions False-positives: 3 %

37. XML-CML Databases Capturing Chemistry in XML/CML ACS March 2004 CML Journals Theses CompChem XMLDb can support > 250,000 molecules Millisecond retrieval on INChI, properties Xindice

38. Capturing Molecules Capturing Chemistry in XML/CML ACS March 2004 Autogenerate IUPAC INChI universal identifier Embed MDLMol or Chemdraw files in MSWord Autoconvert to CML connection table Next phase: Parse chemical names into CML using modern NLP + Learning-machine rather than rule-based + Natural Language Processing Encourage chemists to

39. NLP & Parsing Names Capturing Chemistry in XML/CML ACS March 2004 KEY: Locant Characteristic Group Mono valent parent hydride Multiplier Heterocyclic parent hydride

40. Thank You Unilever RSC Jonathan Goodman Sam Adams Fraser Norton Chris Waudby Yong Zhang Capturing Chemistry in XML/CML ACS March 2004