EUGM 2013 - David Deng, Daniel Bonniot (ChemAxon) - What’s New with Naming
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ChemAxon’s Naming provides reliable English name and chemical structure conversion. It is the underlying technology utilized in ChemAxon’s chemical text mining tool D2S (Document-to-Structure), JChem for SharePoint, and Chemicalize.org. In this presentation, the latest enhancement will be highlighted, including: Chinese chemical name recognition to accommodate the fast grouping Chinese scientific literature, Custom corporate ID to structure conversion using a webservice, Database indexing of structures from document repositories.
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EUGM 2013 - David Deng, Daniel Bonniot (ChemAxon) - What’s New with Naming
- 1. What’s New with Naming? Wei Deng (David), Daniel Bonniot ChemAxon European UGM May 2013
- 2. 2 Naming Structure to Name Name to Structure Document to Structure Document to Database JChem for SharePoint
- 3. Structure to “Name" 3 S2N • 2-(acetyloxy) benzoic acid • Aspirin
- 4. Structure to “Name" 4 S2N • 2-(acetyloxy) benzoic acid • Aspirin • 50-78-2 11126-35-5 11126-37-7 2349-94-2 26914-13-6 98201-60-6
- 5. “Name” to Structure 5 • 2-(acetyloxy) benzoic acid • Aspirin • Acetylsalicylate • Easprin … • 50-78-2 N2S
- 6. Document to Structure 6 D2S • O=C(Oc1ccccc1C(= O)O)C • InChI=1S/C9H8O4/ c1-6(10)13-8-5-3-2- 4-7(8)9(11)12/h2- 5H,1H3,(H,11,12) • 2-(acetyloxy) benzoic acid • Aspirin • Acetylsalicylate • Easprin … • 50-78-2
- 7. Document to Structure • Extract chemical information from documents – Names, SMILES, InChI, CAS number … – Embedded objects – Structure images Support: OSRA currently Multiple OSR engines (CLiDE, Imago…) in 6.1 – Works with scanned non-searchable PDF – Returns structures and their locations in the document – Correct OCR errors – Supported formats: PDF, text, XML, HTML, MS Office document (doc, docx, ppt, pptx, xls, xlsx), OpenOffice 7 Non-searchable chemical patent Documents Structure (text + image) + location D2S
- 10. Document to Structure Demo 10
- 12. JChem for SharePoint • SharePoint 2010 and 2007 – Sketch, Import/export, store structures – Structure search – Calculate properties and naming – Filtering and Sorting • New improvement – Index and search chemical information in documents • Text • Embedded structure object – Connect SharePoint to your chemical database
- 13. Free Online Service Chemicalize.org • Extract • Interactively display • Calculate • Search 13 Recently reviewed in J. Chem. Inf. Model., 2012, 52 (2), pp 613–615
- 15. PDF File - Chemicalized
- 16. Growing IP Filing in China 16The Economist, Dec 2012
- 17. Name to Structure 17 • 2-（乙酰氧基）苯甲 酸 • 阿司匹林 • 2-(acetyloxy) benzoic acid • Aspirin • Acetylsalicylate • Easprin … • 50-78-2 N2S Chinese
- 18. In Fact, Even without CN2S… 18 • 阿司匹林 N2S CN2S Customized Dictionary
- 19. Customized Dictionary • A SMILES file “custom_names.smi” • Default location ChemAxon DIR e.g. in Windows 7 C:UsersUSERNAMEchemaxon • Format SMILES Tab ANY text string 19 c1ccccc1 CXN000001
- 21. Customized Dictionary • A SMILES file “custom_names.smi” • Default location ChemAxon DIR e.g. in Windows 7 C:UsersUSERNAMEchemaxon • Format SMILES Tab ANY text string • From Version 6.0, a custom web service can also be used 21 c1ccccc1 CXN000001
- 22. Naming Web Service Demo 22
- 23. Dictionary is Limited 23 N2S Customized Dictionary • 2-（乙酰氧基） 苯甲酸
- 24. The Real CN2S 24 • 2-(acetyloxy) benzoic acid • 2-（乙酰氧基） 苯甲酸 CN2S CN2S
- 25. Mapping Chinese Names to English 中文 English 中文 English 甲 meth- 苯 benzene 乙 eth- 吲哚 indole 丙 prop- 硝基 nitro- 丁 buta- 盐 salt 氧 oxy- 环 cyclo- 氢 hydrogen- 二 bi- 硫 thio- 三 tri- 酸 acid 顺 cis- 醇 -ol 反 trans- 酯 ester 异 iso- 25
- 26. The Real CN2S 26 2-（乙酰 氧基） 苯甲酸 2-(acetyl oxy ) benzoic acid
- 27. The Challenges 1. Chinese texts have no spaces 2. Ester & Salt 乙酸乙酯 Ethyl Acetate 27
- 28. The Challenges 3. English: name alterations 丁烷 buta + ane butane 4. Chinese: many Characters have different meanings 盐 = salt 酸 = acid 盐酸 = hydrochloric acid 28
- 29. The Challenges 5. Chinese names are usually abbreviated 苯 = benzene 苯基 = phenyl There are many other challenges, overall solution: Make our N2S more tolerant to mistakes 29
- 30. Accuracy Result • Test set: 38,600 Chinese names + CAS number • Contains unusual, incorrect, ambiguous names, radicals, inorganic salts, • Conversion rate = 58 – 78 % • Accuracy = 91% • Look for another test set from Chinese patents 30
- 31. Version History 31 N2S D2S: Text only D2S: Text + Image D2S: OCR + Image English 5.1 5.2.5 5.6 5.8 Chinese 5.12 5.12 5.12 6.x
- 33. Chinese Patent Document <p id="d66" num="067">将0.76g(2.9mmol)5-乙氧基-4-甲基-2-苯氧基羰基-2，4- <br/>二氢-3H-1，2，4-三唑-3-酮溶于40ml乙腈中，在室温(约20℃)、搅 <br/>拌下，以每次少量的方式与0.75g(3.2mmol)4-甲氧基羰基-2-甲 <br/>基噻吩-3-磺酰胺和0.49g(3.2mmol)1，8-二氮杂二环[5.4.0]十 <br/>一碳-7-烯(DBU)混合。将该反应混合物在室温搅拌12小时，然后减 <br/>压浓缩。将残余物置于二氯甲烷中，依次用1N盐酸和水洗涤，用硫 <br/>酸钠干燥，并过滤。将滤液在水泵真空下浓缩，将残余物用异丙醇蒸 <br/>煮，通过抽滤分离出所得结晶产物。 <br/> </p>
- 34. Upcoming in 6.1: Chinese D2S <p id="d66" num="067">将0.76g(2.9mmol)5-乙氧基-4-甲基-2-苯氧基羰基-2，4- <br/>二氢-3H-1，2，4-三唑-3-酮溶于40ml乙腈中，在室温(约20℃)、搅 <br/>拌下，以每次少量的方式与0.75g(3.2mmol)4-甲氧基羰基-2-甲 <br/>基噻吩-3-磺酰胺和0.49g(3.2mmol)1，8-二氮杂二环[5.4.0]十 <br/>一碳-7-烯(DBU)混合。将该反应混合物在室温搅拌12小时，然后减 <br/>压浓缩。将残余物置于二氯甲烷中，依次用1N盐酸和水洗涤，用硫 <br/>酸钠干燥，并过滤。将滤液在水泵真空下浓缩，将残余物用异丙醇蒸 <br/>煮，通过抽滤分离出所得结晶产物。 <br/> </p>
- 35. CN2S on Chinese Patents Demo 35
- 36. One Door Many Other Doors 36 Ácido 2-(acetiloxi)-benzoico 2-Acetoxybenzoesäure Acide 2-acétyloxybenzoïque 2-（乙酰氧基）苯甲酸 2-アセトキシ安息香酸 2-아세톡시-벤조산 2-ацетилоксибензойная кислота CN2S JN2S KN2S RN2S FN2S GN2S SN2S
- 38. But English and Chinese Names are Different, Really (1S,3S)-1-bromo-1-chloro-3- ethyl-3-methylcyclohexane Fundamental Organic Chemistry I, Qiyi Xing et. al., Ed. 3, Page 44 38 (1S,3S)-1-甲基-1-乙基-3-氯-3-溴环己 烷 基础有机化学（上），邢其毅等，第 三版，第44页
- 39. Acknowledgement Daniel Bonniot 邓巍 Wei Deng (David) 39 N2S
- 40. Please Help US Make it Better Evaluators Welcome 40