Transcript Recent Developments in Chemical Database Searching Gary Wiggins E-mail: [email protected] Indiana University School of Informatics ACS Wabash Valley Section November 4, 2004

Recent Developments in
Chemical Database Searching
Gary Wiggins
E-mail: [email protected]
Indiana University
School of Informatics
ACS Wabash Valley Section
November 4, 2004
The Current Database Environment
• Interdisciplinary science
• Consolidation of the Scientific-TechnicalMedical (STM) publishing world
• Databases covering different formats:
encyclopedias, treatises,review serials
• Influence of the Web
– Move to open access journals
– Different cultures in the chemistry publishing
environment compared to that in biology
Huge Size of the Chemical
Literature
•
•
•
•
•
~ 50 million chemical substances
~ 6 million reagents
~ 7 million published reactions
~16,000 protein crystal structures
~250,000 small molecule x-ray structures
--Robert Glen and Susan Aldridge (2002)
Growth of Articles in CA
Year
1907
1945
1960
1970
1980
1990
2000
Articles Abstracted
7,994
22,824
104,484
230,902
407,342
394,945
573,469
Source: http://www.cas.org/EO/casstats.pdf
Vendors and Publishers
• Partnership between commercial vendors
and abstracting/indexing services (and to
some extent with journal publishers)
– Most activity in online searching started in the
1970s
– Comparatively little change in the vendors’
search systems until relatively recently
• Aggregation of databases
• Cross-file searching
• Command-driven access
Vendors of Chemical Databases
• STN International (http://info.cas.org/stn.html)
– SciFinder and SciFinder Scholar (http://www.cas.org/)
• ISI Thomson (http://www.isinet.com)
• QuestelOrbit (http://www.questel.orbit.com/index.htm)
– Merged Markush Service
•
•
•
•
•
•
•
•
Dialog (http://www.dialog.com/)
MDL (http://www.mdl.com/)
US National Library of Medicine (http://www.nlm.nih.gov/)
Ovid Technologies (http://www.ovid.com/)
CSA (Cambridge Scientific Abstracts) (http://www.csa.com/)
Chemical Information System (http://www.nisc.com/cis/qcis1.asp)
knovel (http://www.knovel.com/)
Technical Database Services (http://www.tdsonline.com/)
STN International
• Partnership among Chemical Abstracts
Service, FIZ Chemie, and the Japan
Science and Technology Corporation
• Has over 200 STM databases
– STN Database Summary Sheets:
http://info.cas.org/ONLINE/DBSS/dbsslist.html
– Includes some databases also available free
through other venues (e.g., Medline,
GenBank)
Features in Commercial Systems
•
•
Special Boolean operators (proximity, adjacency, etc.)
Truncation (wild cards and left-hand or right-hand
truncation)
Controlled vocabulary tools (MeSH, CAS’s Index
Guide, CA Lexicon)
Classification of the documents
•
•
–
–
•
•
•
•
PACS (Physics and Astronomy Classification Scheme)
CA Sections/Subsections
Structure searching (usually range from exact to full
substructure search)
Numeric and other data that is searchable
Data analysis tools
Current awareness options
Command Language Systems
• Allow field-directed searches
• Incorporate sophisticated Boolean
relationships
– AND, OR, NOT
– Adjacency, Proximity, Logical linking to the
same field or sub-field of a record
• Numbers of intervening words can be specified
• Drawback: User must learn the commands
User-Oriented Software
• Front-end systems to mask command
language
– STN’s SciFinder (&SF Scholar)
– STN on the Web, STNEasy, STN Express
– CrossFire Commander and MDL
DiscoveryGate
– Questel-ORBIT’s QWeb and Imagination
SciFinder and SciFinder Scholar
• Access to the CAplus, Registry, CHEMCATS,
CHEMLIST files, plus Medline (1957-) and links
to the Web
• Easy structure searching capabilities + 3D
visualization (with ViewerLite)
• Integrated with ChemPort for easy access to the
primary journal and other literature
• Citation searching (from 1998)
• SFS pricing tied to number of seats
• Industrial version permits customized usage and
other features not found in SFS
Limitations in SciFinder Scholar
• OK for organic compounds, author and
orientational topic searches, many reactions
• PROBLEMATIC for some organometallics and
most inorganics
• NOT REALLY FEASIBLE (use STN) for:
–
–
–
–
–
polymers
most sequences/subsequences
all materials
some reactions (AutoFix imposes limits!)
"comprehensive" topic searches
--Bert Zass, CHMINF-L, 11/4/2004
Saving Records in SFS
• Download limit of 100 records
DiscoveryGate for Academics
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
CrossFire Beilstein
CrossFire Gmelin
MDL® Available Chemicals Directory
MDL® Screening Compounds Directory
MDL® Reference Library of Synthetic Methodology
MDL® Solid-Phase Organic Reactions
ORGSYN (Organic Syntheses) Database
Encyclopedia of Reagents for Organic Synthesis
Comprehensive Organic Functional Group Transformations
Comprehensive Asymmetric Catalysis
MDL® Comprehensive Medicinal Chemistry
MDL® Drug Data Report
MDL® Metabolite Database
MDL® Toxicity Database
ChemInform Reaction Library
Current Synthetic Methodology
Derwent Journal of Synthetic Methods
National Cancer Institute Database
http://www.mdl.com/solutions/solutions_for/academics/dg_academics.jsp
Main Chemical Databases
•
•
•
•
•
Chemical Abstracts
Beilstein/Gmelin
Cambridge Structural Database
Protein Data Bank
Many other relevant databases
CAS DBs: CA File
• CA File, a bibliographic database covering
journal articles (from ~8000 journals), technical
reports, conference proceedings, dissertations,
patents and other literature
• 1907 to the present; full indexing has been added for all
records retrospectively
• Linked through the Registry Number to compound data
• CAplus File, includes CA File data plus ejournals, some preprints, and all articles from
~1500 key chemical journals within one week of
receipt
Relative Contributions of Literature
Types to CA
Used with the permission of Chemical Abstracts Service (CAS),
a division of the American Chemical Society, from:
http://www.cas.org/casdb.html
Old References Recently Added to
CA Database
The boiling-point curve for mixtures of ethyl alcohol and water.
Noyes, William A.; Warfel, R. R. Rose Polytechnic Institute, Terre
Haute, Journal of the American Chemical Society (1901), 23(7),
463-8. CODEN: JACSAT ISSN: 0002-7863. Journal written in
English. CAN 0:1311 AN 1906:1311 CAPLUS (Copyright
2004 ACS on SciFinder (R))
Abstract
In the determination with small amounts of alcohol, the readings of the
thermometer were taken when the vapors first entered the
condenser, as after boiling for a few minutes a relatively large
proportion of the alcohol present would be found in the upper layers
and in the condenser. The thermometer under these conditions
registered about 0.3 higher. An examination of the table and curve
revealed that the minimum boiling point is for alcohol of 96% by
weight. The curve was steeper on the side toward absolute alcohol.
Alcohol of 90.7% had the same boiling point as absolute alcohol.
Special Fields in the CA File
• In addition to the standard bibliographic
citation data, have:
– Controlled Terms (CT)
– Classification Codes (CC: the 80 section codes
into which the content of the paper CA is divided:
http://www.cas.org/PRINTED/sects.html)
– Document type (DT)
– Language Code (LA)
– Role (RL)
CAS DBs: Registry File
• “Authority” file that lets indexers and
searchers definitively identify a substance
as new or find a previous entry
• Contains all types of chemical substances,
including biomolecules
• Best file for chemical names
• Many physical properties being added
• Linked to CA and other files through the
Registry Number (RN)
CAS Registry Number
• Serves as the accession number in the
Registry File
• RN has no meaning
– Example: Isatin is 91-56-5
Registry File Contents
• Includes synonyms, molecular formulas,
alloy composition tables, classes for
polymers, nucleic acid and protein
sequences, ring analysis data, and
structure diagrams
• Also: experimental and calculated property
data from various sources as well as super
roles and document type information from
CAplus
Registry File Contents
• 72,297,557substances have a RN in the
Registry File as of 9/26/2004
• All substances in CAS files plus others
• Many physical constants now added to the
records, most of them calculated
– Lipinski Rule of Five values
– BP, MP, Density, Optical Rotatory Power,
Refractive Index
– Data for 3D visualization
Traumatic Acid
Registry File Record
Traumatic Acid: SFS  eScience
Size of the Registry File
Date
Sunday, 9/26/2004
Count
24,205,177 organic and
inorganic substances
48,092,380 sequences
CAS Registry Number
751481-24-0 is the most
recent CAS Registry
Number
CAS DBs: CASReact
• Derived from journal and patent
documents from 1840 to date
• Contains both single-step and multistep
reactions
• Structure searchable
• Contains yield data, reaction conditions,
etc.
CAS Databases: Other
• CHEMCATS--information about commercially
available chemicals and their worldwide
suppliers
• CHEMLIST--contains chemical substances on
national inventories
• MARPAT--more than 500,000 Markush structure
records for patents found in the CA File with
patent publication year 1988 to the present
• TOXCENTER--covers the pharmacological,
biochemical, physiological, and toxicological
effects of drugs and other chemicals
Beilstein Database
•
•
•
•
•
Covers organic chemistry back to 1771
Includes many physical properties
Includes reaction information
Structure searchable
Available on the CrossFire Commander
system for academic institutions
• Available on STN and Dialog vendor
systems
Gmelin Database
• Covers inorganic and organometallic
chemistry back to 1772
• Includes many physical and chemical
properties
• Not searchable for reactions
• Accessible through the CrossFire
Commander system for academic
institutions
Reaction Databases
• CASReact
• SPRESI
• Organic Syntheses
– Free version:
http://chemfinder.cambridgesoft.com/reactions/orgsyn.asp
• ISI’s Index Chemicus
• e-EROS (Encyclopedia of Reagents for Organic
Synthesis)
• MDL’s Integrated Major Reference Works
– Reactions indexed with InfoChem’s Reaction Classification
Code, based on the degree of specificity around the reacting
center:
– http://www.infochem.de/eng/index.htm
Cross-Product Approaches
• MDL/InfoChem’s Integrated Major Reference
Works
– Thieme’s Science of Synthesis (successor to
Houben–Weyl)
– Springer’s Comprehensive Asymmetric Synthesis and
their Glycoscience
– Elsevier Science’s Comprehensive Organic
Functional Group Transformations
– Wiley’s Encyclopedia of Reagents for Organic
Synthesis
– Links to primary journal literature.
Physical Property Databases
•
•
•
•
Beilstein & Gmelin
CRC Handbook (CHEMnetBASE)
Ei ChemVillage
knovel
– Perry’s Chemical Engineers’ Handbook
– Lange’s Handbook of Chemistry
• Landolt-Börnstein
Spectral Databases
•
•
•
•
Bio-Rad
Aldrich
NIST Chemical WebBook
Some high-quality free databases on the
Web, e.g.,
• SDBS, Integrated Spectral Data System
for Organic Compounds
– http://www.aist.go.jp/RIODB/SDBS/menu-e.html
SDBS IR Spectrum for
Traumatic Acid
CCDC
Cambridge Structural Database
• Bibliographic, chemical and crystallographic
information for:
– organic molecules
– metal-organic compounds
• 3D structures have been determined using:
– X-ray diffraction
– neutron diffraction
• The CSD records results of:
• 3D atomic coordinate data for at least all non-H
atoms
CSD components
• ConQuest: search and information
retrieval
• Mercury: structure visualization
• Vista: numerical analysis
• PreQuest: database creation
Isatin on the CSD
Other Structural Databases
• Protein Data Bank for polypeptides and
polysaccharides having more than 24 units
FREE http://www.rcsb.org/pdb/
• Nucleic Acids Data Bank for oligonucleotides
FREE http://ndbserver.rutgers.edu/
• Inorganic Crystal Structure Database
http://www.fizinformationsdienste.de/en/DB/icsd/
• CRYSTMET® for metals and alloys
http://www.tothcanada.com/
Materials Chemistry Databases
• TDS specializes in chemical engineering
data. Includes:
– American Institute of Chemical Engineers’
DIPPR Pure Component Data
• 29 fixed-value properties and 13 temperaturedependent properties for about 1600 industrial
chemicals
• http://www.tdsonline.com/
Patent Databases
•
•
•
•
Derwent World Patents Index
USPATFULL
PCTFULL (WIPO/PCT Patents Full Text)
INPADOC (INternational PAtent
DOcumentation Center)
• IFIPAT
• CA and CAplus
Chemical Information System
• 34 environmental databases
– Originally developed by the US National Institutes of
Health and the Environmental Protection Agency
• Covers over 515,000 compounds
–
–
–
–
–
–
Toxicological and/or carcinogenic research data
information on handling hazardous materials
chemical/physical property information
Regulations
safety and health effects information
pharmaceutical data
• http://www.nisc.com/cis/qcis1.asp
Hybrid Links to the Web
• STN’s eScience
– http://www.escience.org/
• Elsevier Science’s Scirus
– http://www.scirus.com/srsapp/
Electronic Journals
• Coverage in some cases back to the 17th
century
• Most major publishers’ backfiles are now online
• DOI: http://www.doi.org/
– Turn a DOI into a URL by appending http://dx.doi.org/
to the front of it
• SFX: http://www.exlibrisgroup.com/sfx.htm
• MDL’s Litlink
• CrossRef: http://www.crossref.org/
CrossRef Search
• CrossRef Search
http://www.crossref.org/crossrefsearch.html
• Pilot initiative running in 2004 in collaboration
with Google
• Includes the content of 29 publishers (out of the
650 CrossRef publishers and societies)
• Now covers approximately 3.4 million research
articles.
Shift from Ownership to Licensing
of Journals
• IUB Chemistry Library e-journals
– http://www.indiana.edu/~libchem/402ejrnl.html
• Archival issues
– Publisher archives (usually 2-3 locations)
– LOCKSS: http://lockss.stanford.edu/
– Libraries often have no archival rights
Single Publisher Databases
• Elsevier’s ScienceDirect and their
encyclopedia DBs
– Scirus: http://www.scirus.com/srsapp/
• Wiley’s journal, book, and encyclopedia
DBs: http://www3.interscience.wiley.com/
• American Chemical Society journals
– http://pubs.acs.org/
Getting at the Data
• STN’s Information Keep & Share Program
– http://info.cas.org/copyright/index.html
• SciFinder Scholar download restrictions:
100 items at a time
Data Analysis Tools
• STN’s Analyze and Tabulate feature
• STN Express with Discover! (Analysis
Edition)
• Limited access because of A&I publishers’
reluctance to turn loose of the data
Free Services
• ChemFinder
– http://chemfinder.cambridgesoft.com/
• ChemIDplus
– http://chemfinder.cambridgesoft.com/
• Frederick/Bethesda Data and Online Services
– http://cactus.nci.nih.gov/
• PubMed
– http://www.ncbi.nlm.nih.gov/entrez/query.fcgi
• DOE’s STI Information Bridge
– http://www.osti.gov/bridge/
Budapest Open Access Initiative
• Based on:
– Self archiving by authors
– Open Access journals, e.g., BioMed Central
• http://www.soros.org/openaccess/
Open Access
• Institute of Physics: most papers free for 30 days
after publication
– http://www.iop.org/EJ/ and
http://www.iop.org/EJ/journal/NJP
• Public Library of Science
– http://www.publiclibraryofscience.org
• Highwire Press
– http://www.highwire.org/
• PubMed Central
– http://www.pubmedcentral.nih.gov/
Opposition to Open Access
• Reacting to NIH’s proposed policy on open
access, C&EN Editor Rudy Baum says:
“[This] action will inflict long-term damage on
the communication of scientific results and
on maintenance of the archive of scientific
knowledge.”
-- C&EN, September 20, 2004, p. 7
Open Access + Semantic Web
• "Almost all of an author's output (compounds,
spectra, reactions, properties, etc.) is nowadays
computerised and in principle redistributable to
the community for re-use. Few journals actively
validate the primary data (e.g. spectra) involved
in a publication (chemical crystallography being
a clear exception where data are intensively
reviewed by machine). We reassert that
chemists must now move towards publishing
their collective knowledge in a systematic and
easily accessible form for re-use and
innovation....
Open Access + Semantic Web
• We urge that authors, funders, editors,
publishers and readers move further towards the
following protocol:
[1] All information should be ultimately machineunderstandable in XML....
[2] Machine-understandable information for a compound
should include a connection table, the IUPAC unique
identifier (INChI) which guarantees that the
connection table can be checked and regenerated,
and a name....
[3] Rights metadata.”
-- Murray-Rust, Rzepa, Tyrrella, Zhanga (2004)
Future
• XML and metadata
– Dymond (DYnamic Metadata ON Demand)
• Virtual journals (Virtual Journal of Nanoscale
Science and Technology)
• Copyright question and open access resolution
• Legal protection of databases
• Impact of INCHi and CML
• Demise of Abstracting and Indexing Services?
Conclusion
• “The main challenge is for chemists to
recognise the value of making their data
machine-understandable, rather than
destroying it with traditional paper or slidefocused publication and dissemination
processes.”
-- Murray-Rust, Rzepa, Tyrrella, Zhanga (2004)
Parting words . . .
If you're not part of the solution, you're part
of the precipitate!
Searches
•
•
•
•
Isatin (91-56-5)
Moronic Acid (RN 6713-27-5)
Traumatic Acid (RN 6402-36-4)
Others:
http://www.chm.bris.ac.uk/sillymolecules/sillymols.htm
Beilstein Structure Search
R1=O or S
R2=H, OH, OMe, CH3, or CO2H
X = any halogen
? = any bond value
Beilstein Property Search
• Find the compounds in the Beilstein
CrossFire database that have structure
keyword "stereo compound" and
molecular formula C29H36O8 and melting
points in the range 258-271 Celsius.
Bibliography
• Culp, F. Bartow. "Ten or so things that every chemistry librarian
absolutely, positively has to have to keep from being an absolute
plonk." Sci-Tech News, February 2004, 58(1), 9. also published as:
SLA Chemistry Division E-Newsletter Winter 2004, 18(3), 19-20).
http://www.sla.org/division/dche/Newsletters/Feb_2004.pdf
• Gasaway, Laura. “The open archives movement.” Information
Outlook October 2004, 8(10), 36, 39-40.
• Glen, Robert; Aldridge, Susan. “Developing tools and standards in
molecular informatics.” Chemical Communications 2002, (23), 27452747. DOI: 10.1039/b207793k
http://xlink.rsc.org/?DOI=b207793k
Bibliography
•
Huber, C.; Porter, K. “Cheap tricks.”
http://www.indiana.edu/~cheminfo/workshop/cheap.html
•
McLeland, Le-Nhung. What every chemist should know about patents.
http://www.chemistry.org/portal/resources/?id=1b41692a6cf811d6f8dd6ed9fe800100
•
Murray-Rust, Peter; Rzepa, Henry S.; Tyrrella, Simon M.; Zhanga, Y.
“Representation and use of chemistry in the global electronic age.”
forthcoming article in: Organic & Biomolecular Chemistry.
http://www.ch.ic.ac.uk/rzepa/obc/ (preprint)
•
Wagner, A. Ben. "Finding physical properties of chemicals: A practical guide
for scientists, engineers, and librarians.” Science & Technology Libraries
2001, 21(3/4), 27-45. (published Fall 2003)
Text for personal and professional use available at:
http://ublib.buffalo.edu/libraries/asl/staff/documents/wagner_phys_prop_stl_art.pdf
Bibliography
• Wiggins, Gary. “Overview of databases/data sources.” in Gasteiger,
Johannes, ed. Handbook of Chemoinformatics: From Data to
Knowledge in 4 Volumes. Wiley-VCH: 2003, v. 2, pp. 496-506.
http://www.indiana.edu/~cheminfo/C571/wiggins_chapter_2003.pdf
• Wiggins, Gary. “Teaching chemical literature, databases, and
chemical informatics.” CPT; Committee on Professional Training
[newsletter] Spring 2004, 4(1), 1-2.
http://www.chemistry.org/portal/resources/ACS/ACSContent/education/
cpt/nl_cpt_spring2004.pdf