Banville DL "Mining chemical structural information from the drug literature" Drug Discovery Today, 11(1-2): 35-42, January 2006.

[Eugene Garfield]

E-Mail:
debra.banville at astrazeneca.com

FOR PDF FILE COPY ENTIRE URL BELOW (FOLLOWING 4 LINES)AND PASTE
IN "ADDRESS" IN YOUR BROWSER:
http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6T64-4J853YK-6-
1&_cdi=5020&_user=10&_orig=browse&_coverDate=01%2F31%
2F2006&_sk=999889998&view=c&wchp=dGLzVlz-
zSkzV&md5=b150085f11d435e7ee8dacc7c77a2b1f&ie=/sdarticle.pdf

AUTHOR : Debra L. Banville,  debra.banville at astrazeneca.com

TITLE :  Mining chemical structural information from the drug literature
         (Review)

SOURCE:  Drug Discovery Today, Volume 11, Issues 1-2, January 2006, P.35-
42.

ADDRESS:  AstraZeneca Pharmaceuticals, 1800 Concord Pike, Wilmington,
          DE 19850, USA

Available online 13 February 2006.

It is easier to find too many documents on a life science topic than to
find the right information inside these documents. With the application of
text data mining to biological documents, it is no surprise that
researchers are starting to look at applications that mine out chemical
information. The mining of chemical entities – names and structures –
brings with it some unique challenges, which commercial and academic
efforts are beginning to address. Ultimately, life science text data
mining applications need to focus on the marriage of biological and
chemical information.



Addresses: Banville DL (reprint author), AstraZeneca Pharmaceut, 1800
Concord Pike, Wilmington, DE 19850 USA
AstraZeneca Pharmaceut, Wilmington, DE 19850 USA

E-mail Addresses: Debra.Banville at AstraZeneca.com

Publisher: ELSEVIER SCI LTD, THE BOULEVARD, LANGFORD LANE, KIDLINGTON,
OXFORD OX5 1GB, OXON, ENGLAND
Subject Category: PHARMACOLOGY & PHARMACY
IDS Number: 005LJ
ISSN: 1359-6446


CITED REFERENCES :
AI CS
EXTRACTION OF CHEMICAL-REACTION INFORMATION FROM PRIMARY JOURNAL TEXT
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 30 : 163 1990

BORKENT JH
CHEMICAL-REACTION SEARCHING COMPARED IN REACCS, SYNLIB, AND ORAC
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 28 : 148 1988

BRECHER J
Name=Struct: A practical approach to the sorry state of real-life chemical
nomenclature
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 39 : 943 1999

BRUEGGEMANN R
CHEMOSPHERE 31 : 3585 1995

CALDWELL GW
CURR TOP MED CHEM 1 : 353 2001

CHOWDHURY GG
AUTOMATIC INTERPRETATION OF THE TEXTS OF CHEMICAL PATENT ABSTRACTS .1.
LEXICAL ANALYSIS AND CATEGORIZATION
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 32 : 463 1992

CHOWDHURY GG
AUTOMATIC INTERPRETATION OF THE TEXTS OF CHEMICAL PATENT ABSTRACTS .2.
PROCESSING AND RESULTS
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 32 : 468 1992

CLAUS BL
Discovery informatics: its evolving role in drug discovery
DRUG DISCOVERY TODAY 7 : 957 2002

COOKEFOX DI
J CHEM INF COMP SCI 31 : 153 1991

COOKEFOX DI
COMPUTER TRANSLATION OF IUPAC SYSTEMATIC ORGANIC-CHEMICAL NOMENCLATURE .4.
CONCISE CONNECTION TABLES TO STRUCTURE DIAGRAMS
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 30 : 122 1990

COOKEFOX DI
COMPUTER TRANSLATION OF IUPAC SYSTEMATIC ORGANIC-CHEMICAL NOMENCLATURE .5.
STEROID NOMENCLATURE
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 30 : 128 1990

COOKEFOX DI
COMPUTER TRANSLATION OF IUPAC SYSTEMATIC ORGANIC CHEMICAL NOMENCLATURE .1.
INTRODUCTION AND BACKGROUND TO A GRAMMAR-BASED APPROACH
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 29 : 101 1989

COOKEFOX DI
COMPUTER TRANSLATION OF IUPAC SYSTEMATIC ORGANIC CHEMICAL NOMENCLATURE .2.
DEVELOPMENT OF A FORMAL GRAMMAR
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 29 : 106 1989

COOKEFOX DI
COMPUTER TRANSLATION OF IUPAC SYSTEMATIC ORGANIC CHEMICAL NOMENCLATURE .3.
SYNTAX ANALYSIS AND SEMANTIC PROCESSING
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 29 : 112 1989

COOPER JW
229 ACN NAT M 13 17 : 2005

DORLAND L
J CHEM EDUC 79 : 778 2002

GARFIELD E
AN ALGORITHM FOR TRANSLATING CHEMICAL NAMES TO MOLECULAR FORMULAS
JOURNAL OF CHEMICAL DOCUMENTATION 2 : 177 1962

GARFIELD E
>From laboratory to information explosions ... the evolution of chemical
information services at ISI
JOURNAL OF INFORMATION SCIENCE 27 : 119 2001

GOLDFARB C
SGML HDB : 1990

HAHN U
PAC S BIOCOMPUT 7 : 338 2002

HAUSER WC
217 ACS NAT M 21 25 : 1999

HEARLE EM
P MONTREUX INT CHEM : 84 1993

HELMA C
Data quality in predictive toxicology: Identification of chemical
structures and calculation of chemical properties
ENVIRONMENTAL HEALTH PERSPECTIVES 108 : 1029 2000

HODGE GM
ACS APR 1989 : 197 1989

HODGE GM
ACS AUG 1989 : 202 1989

IBISON P
CHEMICAL LITERATURE DATA EXTRACTION - THE CLIDE PROJECT
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 33 : 338 1993

JACKSON P
NATURAL LANGUAGE PRO : 2002

JONCKHEERE C
P INT CHEM INF C 19 : 63 1997

KEMP N
J CHEM INF COMP SCI 38 : S44 1998
 KONTOSTATHIS A
SURVEY TEXT MINING C : CH9 2003

KRALLINGER M
Text mining approaches in molecular biology and biomedicine
DRUG DISCOVERY TODAY 10 : 439 2005

LAKINGS DB
NEW DRUG APPROV 100 : 17 2000

MACK R
Text-based knowledge discovery: search and mining of life-sciences
documents
DRUG DISCOVERY TODAY 7 : S89 2002

MACK R
Text analytics for life science using the unstructured information
management architecture
IBM SYSTEMS JOURNAL 43 : 490 2004

MCDANIEL JR
KEKULE - OCR OPTICAL CHEMICAL (STRUCTURE) RECOGNITION
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 32 : 373 1992

POSTEMA PTE
DIGESTION S 1 : 36 1996

REDMOND L
EUROMAP 1217 : 2002

RICHARD AM
226 ACS NAT M 7 11 S : 2003

ROVNER SL
C E NEWS 0516 : 40 2005

RUSSELL J
BIOL IT WORLD 0204 : 2005

RZHETSKY A
A knowledge model for analysis and simulation of regulatory networks
BIOINFORMATICS 16 : 1120 2000

SHABRANG M
226 ACS NAT M 7 11 S : 2003

SIMON A
Recent advances in the CLiDE project: Logical layout analysis of chemical
documents
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 37 : 109 1997

SINGH SB
Text Influenced Molecular Indexing (TIMI): A literature database mining
approach that handles text and chemistry
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 43 : 743 2003

SMEATON AF
PROGRESS IN THE APPLICATION OF NATURAL-LANGUAGE PROCESSING TO INFORMATION-
RETRIEVAL TASKS
COMPUTER JOURNAL 35 : 268 1992

STENSOMO M
1110 INF

SWANSON DR
2 MEDICAL LITERATURES THAT ARE LOGICALLY BUT NOT BIBLIOGRAPHICALLY
CONNECTED
JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE 38 : 228 1987

SWANSON DR
FISH OIL, RAYNAUDS SYNDROME, AND UNDISCOVERED PUBLIC KNOWLEDGE
PERSPECTIVES IN BIOLOGY AND MEDICINE 30 : 7 1986

TANABE L
MedMiner: An Internet text-mining tool for biomedical information, with
application to gene expression profiling
BIOTECHNIQUES 27 : 1210 1999

THOMSON MA
215 ACS NAT M MARCH : 1998

VANDERSTOUW GG
PROCEDURES FOR CONVERTING SYSTEMATIC NAMES OF ORGANIC COMPOUNDS INTO ATOM-
BOND CONNECTION TABLES
JOURNAL OF CHEMICAL DOCUMENTATION 7 : 165 1967

WEBER M
J AM SOC INF SCI TEC 52 : 548 2001

WEININGER D
SPECIAL PUBLICATION 142 : 67 1994

WILBUR WJ
P AMIA S : 176 1999

WISNIEWSKI JL
AUTONOM CHEM DREAM S 2 : 55 1993

WOLPERT AJ
229 ACS NAT M 13 17 : 2005

ZAMORA EM
EXTRACTION OF CHEMICAL-REACTION INFORMATION FROM PRIMARY JOURNAL TEXT
USING COMPUTATIONAL-LINGUISTICS TECHNIQUES .1. LEXICAL AND SYNTACTIC PHASES
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 24 : 176 1984

ZAMORA EM
EXTRACTION OF CHEMICAL-REACTION INFORMATION FROM PRIMARY JOURNAL TEXT
USING COMPUTATIONAL-LINGUISTICS TECHNIQUES .2. SEMANTIC PHASE
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 24 : 181 1984