Extraction of structural information from ChemDraw CDX files: easy, or an underestimated, difficult challenge?
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1 1 / 23 Extraction of structural information from ChemDraw CDX files: easy, or an underestimated, difficult challenge? Josef Eiblmaier, Hans Kraut, Sascha Hausberg, Peter Loew
2 Outline 2 / 23» ChemDraw files: Relevance and the Challenge» Approach» Projects» InfoChem ChemProspector» Wiley Smart Article cora / PIXELIO, Thieme Science of Synthesis Update / Pharmaceutical Substances» Conclusion / Outlook
3 3 / 23 Patents, Journal Articles and MRW s: a Buried Treasure? Chemical structures (images) Chemical names/fragments (text) Markush structures (text, images, CDX) Chemical structures (CDX files) Reactions (CDX files)
4 4 / 23 Manuscript Article Database Publishing Manuscript submission Manual Indexing Database production e.g. SciFinder, Reaxys, SPRESI eeros,...
5 5 / 23 CDX Scheme vs. Database Record ChemDraw file Purpose: presentation / publishing no search Unstructured Structures: no strict rules General rules: none Database Purpose: search / retrieval Structured Structures: strict rules Database rules: strict Reactant Product Reagent Solvent Catalyst SOCl 2 LiOH H 2 O, THF Pd(OAc) 2 Cl-Co2Et, Et 3 Acetone, H 2 O Source: Thieme Pharmaceutical Substances, Ticagrelor (in production)
6 6 / 23 CDX Scheme Processing, what does that mean? Chemical structures (SD files) Reactions (RD files) ICSchemeProcessor Conditions (RD files) Reagent Solvent Catalyst Source: Thieme Pharmaceutical Substances, Ticagrelor (in production) SOCl 2 LiOH H 2 O, THF Pd(OAc) 2 Cl-Co2Et, Et 3 Acetone, H 2 O
7 7 / 23 But: CDX files, often an optical illusion! Authors are very inventive for a perfect layout! Appearences are deceiving!» Usage of graphical symbols Polymer supports Heteroatoms C Grid:
8 8 / 23 Optical illusions 2» Unresolvable labels Labels not defined Element symbols used as R-group labels Ambiguous fragment labels (e.g. molecular formula)
9 9 / 23 Optical illusions 3» Variable points of attachment
10 10 / 23 Optical illusions 4» Reaction arrows / forked arrows / brackets
11 11 / 23 Approach Gerd Altmann / PIXELIO,
12 12 / 23 Approach» The algorithmic approach: Application of a set of rules in the software (generic, project unspecific). Software should recognize all cases that might occur! project (title-) specific rules (drawing conventions must not change), otherwise further development necessary manual post correction required (cost/time intensive) problem is infinite, unprecedented issues can not be handled» The templating approach: software is developed to recognize a defined set of problems (PS) all content must be manually pre-templated (cost intensive) according to the capabilities of the software» The hybrid approach: depending on the source the focus can be laid on either approach
13 13 / 23 Templating» Templating: Guidelines for authors and typesetters Syntax definitions for tables, R-groups etc. Syntax rules for captions Reaction arrangement, forked arrows Rules for reaction conditions (reactants, catalysts, solvents, yields, temperature)
14 14 / 23 Examples:» Algorithmic detection of features» Resolution of repeating groups» Enumeration of R-groups» Resolution of aliases/labels source specific alias databases continuously extended» Table Enumeration compound enumeration reaction factual data: Caption/Yield» Variable points of attachment» Forked arrows
15 15 / 23 Projects
16 16 / 23 Sucessful Application of CDX Processing: Chemistry Enrichment Workflow*, (Wiley Smart Article) *Reinhard eudert: Enhancing the User Experience for Wiley Chemistry Content, ICIC October, Berlin
17 17 / 23 Templating* Author s CDX File CDX Template Enumerated structures Templating ICSchemeProcessor CDX-Templating Guidelines (Structures) *Reinhard eudert: Enhancing the User Experience for Wiley Chemistry Content, ICIC October, Berlin
18 18 / 23 Workflow Science of Synthesis Update R 5 O H 2 HO H + HO R 5 H2O OH H R 5 H O H 2 HO H + HO H2O OH H R 5 O H R 5 H H 3 R 5 2 HO H R 5 2 O H 2O O R 5 H H 3 R 5 2 HO H R 5 2 O H 2O R 5 H R 5 H ICSchemeProcessor CDX- Templating Guidelines (Reactions) Correct / extend process R 5 O H 2 + OH H HO HO Scheme R H Error 4 Report R 5 H H2O O R 5 H 2 39 R 5 HO H 2 40 H 3 R 5 O H 2O Scheme correction not possible R 5 H Manual data entry
19 19 / 23 Sample Pharmaceutical Substances Update Source: Thieme Pharmaceutical Substances, Abiraterone
20 20 / 23 Conclusion» As much as possible algorithmic processing desirable generic: can be applied to other contents as well cheaper (humans cost!)» 100% conversion (without human interaction) never possible» Solutions are project / source specific» Relevance of automatic extraction will continuously increase» Authors / Publishers play an essential role in a successful conversion
21 21 / 23 Acknowledgements» Wiley Michael Forster Reinhard eudert» Thieme Guido Herrmann Rolf Hoppe Klaus Köberlein» InfoChem Hans Kraut, Sascha Hausberg, Thomas Menke, Manuela Rauh Fanny Irlinger, Huyen gyen, Dagmar Kunzmann
22 22 / 23 Thank you! Thomas Link / Flickr
23 23 / 23 Questions?
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