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.

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

8. OCR Error Correction
8
(2R)-2-rnethylsulfany1-3-hydr0xybutanedi0ate
(2R)-2-methylsulfanyl-3-hydroxybutanedioate
Λr-benzyl-Λr-[3-(lH-tetrazol-5-
yl)phenyl]propanamide
?-benzyl-?-[3-(?H-tetrazol-5-
yl)phenyl]propanamide

9. OCR Error Correction
9
(2R)-2-rnethylsulfany1-3-hydr0xybutanedi0ate
(2R)-2-methylsulfanyl-3-hydroxybutanedioate
Λr-benzyl-Λr-[3-(lH-tetrazol-5-
yl)phenyl]propanamide
N-benzyl-N-[3-(1H-tetrazol-5-
yl)phenyl]propanamide

10. Document to Structure Demo
10

11. Document to Database
11

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

14. 14
Webpage - Chemicalized

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

20. Custom Dictionary Demo
20

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

32. Chinese D2S Demo
32

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

37. The Other Half
37
2-（乙酰氧基）苯甲酸CS2N

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