commercial vendors & databases gary wiggins i571 fall 2006
DESCRIPTION
Size of the Chemical Literature: 2002 Estimate ~ 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)TRANSCRIPT
Commercial Vendors & Databases
Gary WigginsI571
Fall 2006
Factors in the Current Environment
• Interdisciplinary science• Consolidation of the Scientific-Technical-
Medical (STM) publishing world• Different cultures in the chemistry
publishing environment compared to that in biology
• Move to open access journals and data• Influence of the Web
Size of the Chemical Literature: 2002 Estimate
• ~ 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)
Size of the Chemical Literature: 2006
• ~ 88 million chemical substances• ~ ? million reagents• ~ ? million published reactions• ~ 39,000 protein crystal structures• ~ 367,000 small molecule x-ray structures
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
early 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/)• Thomson Scientific (http://www.isinet.com) (ISI)• Questel (http://www.questel.orbit.com/index.htm) (Orbit)
– Merged Markush Service• Thomson Dialog (http://www.dialog.com/)• Elsevier Scopus (http://www.info.scopus.com/) • Elsevier 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• Concept of the Basic Index
– Default field; in bibliographic databases often limited to keywords from titles, abstracts, and index terms
• 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
Vocabulary Control
• “The entities we deal with, such as genes, sequences, and chemical data, and manipulate and analyze in the context of bioinformatics and biomedical research have not always been properly defined. There are no control vocabularies, no standards for much of the data, and no unified way to refer to them.”
--Pablo Tamayo, senior computational biologist and manager, cancer genomics informatics, MIT Broad Institute, quoted in Drug Discovery & Development August 2004, 7(8), 52.
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• 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– Elsevier MDL’s CrossFire Commander and
DiscoveryGate– Questel’s QWeb and Imagination
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 ~9500 journals), technical reports, conference proceedings, dissertations, patents and other literature
• 1907 to the present (and some earlier); full indexing was added retrospectively for all records
• Linked through the Registry Number to compound data
• CAplus File, includes CA File data plus e-journals, some preprints, and all articles from ~1500 key chemical journals within one week of receipt
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))
AbstractIn 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.
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
Growth of Articles in CA
Year Articles Abstracted1907 7,994 1945 22,824 1960 104,484 1970 230,902 1980 407,342 1990 394,945 2000 573,469 2005 737,480
Source: http://www.cas.org/EO/casstats.pdf
Basic Index from the CA FileField Name |Examples
Basic Index: single words | S 50-21-5 from title (TI), supplementary | S ?FLUOROCARBON? term (ST), index term (IT), | S (WATER(S)OIL)/BI and abstract field (AB), as | S transgenic cottonwell as CAS Registry Numbers.
Special Fields in the CA File
• In addition to the standard bibliographic citation data, have:– Controlled Terms (CT) or (IT)– 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 Roles• Used in conjunction with chemical substance searches• Seven super roles, e.g., ANST, BIOL, CMBI, FORM,
OCCU, PREP, PROC, RACT, USES• Over 60 more specific role descriptors, e.g., with PREP:
– BMF Bioindustrial manufacture – BPN Biosynthetic preparation – BYP Byproduct– Combinatorial preparation – IMF Industrial manufacture – PNU Preparation, unclassified– PUR Purification or recovery– SPN Synthetic preparation
• Also two roles not up-posted to super roles: PRP (Properties) and MSC (Miscellaneous)
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
• 87,711,955 substances have a RN in the Registry File as of 9/8/2006
• 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
Size of the Registry File
Date Friday, 9/8/2006
Count 29,884,228 organic and inorganic substances 57,827,727 sequences
CAS Registry Number
Source:
906063-52-3 most recent CAS RN http://www.cas.org/cgi-bin/regreport.pl
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
SciFinder and SciFinder Scholar
• Includes access to the CA, Registry, CHEMCATS, CHEMLIST files, plus Medline (1957-)
• Easy structure searching capabilities• Integrated with ChemPort for easy access
to the primary literature• Download page for SFS:
– http://www.libraries.iub.edu/index.php?pageId=2114
SciFinder Scholar Under the Hood
• A. Ben Wagner’s look at what really underlies the apparent simplicity of SFS searches
• http://ublib.buffalo.edu/libraries/e-resources/SciFinder/SciFinder200dpi.pdf
PubChem: A Threat to CAS?
• PubChem, part of the NIH Roadmap plan under the Molecular Libraries and Imaging Initiative
• Several million compounds already in the database
• To be linked to assay data from High Throughput Screening analyses
• http://pubchem.ncbi.nlm.nih.gov/
InChI: Another Threat?• IUPAC-NIST Chemical Identifier• a unique label which would be a non-proprietary
identifier for chemical substances that could be used in printed and electronic data sources thus enabling easier linking of diverse data compilations
• latest version handles:– organic, covalent structures– inorganic and organometallic compounds
• http://chemdata.nist.gov/IChI/INChIv11b.zip
Beilstein Database
• Covers organic chemistry back to 1771• Includes many physical properties• Includes reaction information• Structure searchable• Available on the CrossFire Commander
system (and direct from MDL via DiscoveryGate) for academic institutions
Gmelin Database
• Covers inorganic and organometallic chemistry back to 1771
• Includes many physical and chemical properties
• Not searchable for reactions• Accessible through the CrossFire
Commander system (and direct from MDL via DiscoveryGate) for academic institutions
MDL’s CrossFire Commander
• Download page for Commander at IU:– http://www.libraries.iub.edu/index.php?pageId=2114
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
Reaction Databases• CASReact• SPRESI
– http://www.spresi.com/• 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 CLASSIFY Reaction Classification Code, based on the degree of specificity around the reacting center:
– http://www.infochem.de/content/downloads/classify.pdf
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• CAS Registry File
Spectral Databases
• Bio-Rad• Aldrich• NIST Chemical WebBook• Some high-quality free databases on the
Web, e.g.,• SDBS, Spectral Database for Organic
Compounds– http://www.aist.go.jp/RIODB/SDBS/menu-e.html
SDBS IR Spectrum for Traumatic Acid
CCDC
Isatin on the CSD
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
Accessing the CSD at IUB
• Download the Citrix Metaframe client at:– http://
www.citrix.com/site/SS/downloads/downloads.asp?dID=2755
• Connect to IUB via VPN and link to:– http://www.libraries.iub.edu/scripts/
countResources.php?resourceId=1399945– For IUPUI, ask Kelsey Forsythe
Other Structural Databases• Protein Data Bank for polypeptides and
polysaccharides having more than 24 units http://www.rcsb.org/pdb/
• Nucleic Acids Database for oligonucleotides http://ndbserver.rutgers.edu/
• Inorganic Crystal Structure Database http://www.fiz-informationsdienste.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 temperature-
dependent properties for about 1600 industrial chemicals
Patent Databases
• Derwent World Patents Index• USPATFULL• PCTFULL (WIPO/PCT Patents Full Text)• INPADOC (INternational PAtent
DOcumentation Center)• IFIPAT• CA and CAplus• MDL Patent Chemistry Database
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
Hybrid Links to the Web• STN’s eScience
– http://www.escience.org/• Elsevier Science’s Scirus
– http://www.scirus.com/srsapp/• Elsevier Science’s Scopus (includes Scirus)
– http://www.info.scopus.com– 15,000 titles going back to the mid 1960s– More than 500,000 records link to the Beilstein
database on either CrossFire or DiscoveryGate– 250 million web sources
Traumatic Acid: SFS eScience
Electronic Journals
• Coverage in some cases back to the 17th century
• Most major publishers’ backfiles are now online
• CrossRef• DOI• SFX
Shift from Ownership to Licensing of Journals
• IUB Chemistry Library e-journals– http://www.indiana.edu/~libchem/ejournals.html
• Shift away from ownership• Archival issues
– Publisher archives (usually 2-3 locations)– LOCKSS and other proposals– Libraries often have no archival rights
Archival Issues
• “Given their transitory nature, are commercial and even society publishers the parties to which we want to entrust the task of keeping and preserving human knowledge?”
William W. Armstrong, Chemistry Librarian, Louisiana State University, C&EN 10 October 2005, 83(41), 53
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/
CrossRef
• CrossRef Search http://www.crossref.org/crossrefsearch.html
• Pilot initiative running in 2004 in collaboration with Google
• Includes the content of 45 publishers (out of the 1488 CrossRef publishers and societies)
• Now covers approximately 6.5 million research articles
• Allows XML searching
Getting at the Data
• New CAS Information Use Policies– http://www.cas.org/infopolicy.html
• 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)• STN AnaVist
– http://www.cas.org/stnanavist/prices.html– Flat fee cost based on size of the answer set
analyzed (ranges from $230 for up to 1,000 to $850 for up to 20,000)
• Limited access to records because of A&I publishers’ fear of data piracy
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/
Budapest Open Access Initiative
• Based on:– Self archiving by authors– Open Access journals, e.g., BioMed Central
• http://www.soros.org/openaccess/
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 machine-
understandable 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)
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
Recent Legislative Action
• In the US, Senators Cornyn and Lieberman introduced S. 2696 (109th Congress, 2nd session).– Federal Research Public Access Act of 2006
• In the UK, half of the Research Councils UK and the Wellcome trust have endorsed open access.– http://www.rcuk.ac.uk/access/index.asp – http://www.wellcome.ac.uk/doc_WTD002766.html
Free Services• ChemFinder
– http://chemfinder.cambridgesoft.com/• ChemIDplus
– http://chem.sis.nlm.nih.gov/chemidplus/• 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/• CICC guide to free chemistry databases
– http://www.chembiogrid.org/related/resources/databases.html
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 slide-focused publication and dissemination processes.”-- Murray-Rust, Rzepa, Tyrrella, Zhanga (2004)
What is Citation Indexing?• Utilizes a known relevant document regardless
of when published to find newer journal articles that have cited that document
• Assumption: Authors who are citing the document must be writing on a related topic– Citation indexing lets you find newer articles from an
older reference– Found on other tools, e.g., SciFinder Scholar,
SCOPUS, but citation indexing doesn’t go as far back as does SCI
• Gets around the problems of doing a subject search when you aren’t sure of the words to use
Source Journal Coverage
• SCIE: 5700 titles• SSCI: 1735 titles*• A&HCI: 1145 titles*
*also includes selected articles from SCIE• Weekly updates
– Lag time: 2-3 weeks• Journal List: http://www.isinet.com/journals/
Web of Science Search Screen
Search Example: Cited Reference Searching
• Use the Full General Search and Cited Reference Search Option
• Find publications that have cited the works of Donald E. Linn.– Dots before his name indicates he is not the
first listed author on the publication.– Links are to ISI source journals.– Unlinked items may be incorrect forms of the
reference.
SCI Cited Ref Search for DE Linn
Lookup Results for DE Linn Search
DE Linn’s 2003 JACS Article
Newer Articles Citing the 2003 JACS Article by DE Linn et al.
Analysis of All Authors Citing DE Linn
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
Bibliography• Kaufman-Wills Group LLC. The Facts About Open Access. Association of
Learned and Professional Societies, 2005. ISBN 0-907341-29-2
• 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), 2745-2747. 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.” Organic & Biomolecular Chemistry 2004, 2, 3192-3203.
http://www.ch.ic.ac.uk/rzepa/obc/ (preprint)
Bibliography• 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
• 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://acswebcontent.acs.org/PDF/cpt/nl_cpt_spring2004.pdf