Introduction to Chemistry & Life Sciences Databases Gary Wiggins I533 Spring 2006

Introduction to Chemistry & Life Sciences Databases

Gary Wiggins

I533

Spring 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

• Influence of the Web

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

Commercial Database Vendors

• 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/)• Scopus (http://www.scopus.com/scopus/home.url)• 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/)• Google Scholar (http://scholar.google.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.

Main Life Sciences Databases

• BIOSIS

• Medline and PubMed

• Many public domain databases, including:– Protein Data Bank– GenBank– Many others:

• Nucleic Acids Research Database issue (First issue of each calendar year) http://nar.oupjournals.org/content/vol34/suppl_1/

Main Chemical Databases

• Chemical Abstracts

• Beilstein/Gmelin

• Cambridge Structural Database

• Protein Data Bank

• Many other relevant databases, including some free databases:– Chemistry Databases on the Web

• http://www.indiana.edu/~cheminfo/cicc/databases.html

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 (and now even earlier!); full indexing has been added for all records retrospectively

• 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 Abstracted

1907 7,994

1945 22,824

1960 104,484

1970 230,902

1980 407,342

1990 394,945

2000 573,469 Source: http://www.cas.org/EO/casstats.pdf

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 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

• 83,654,922 substances have a RN in the Registry File as of 10/16/2004

• 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

Size of the Registry File

Date Thursday, 10/16/2005

Count 26,818,300 organic and inorganic substances

56,836,622 sequences

CAS Registry Number

Source:

865347-39-3 most recent CAS RN http://www.cas.org/cgi-bin/regreport.pl

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/

PubChem Tools by I571 Students

• PubChemSR (Search and Retrieve) Tool (Junguk Hur; download zip file from the Tools section, 452 KB)

• Accessing PubChem Through SOAP (Yue Wang Webster)

• PubChem search page (Joel L. Duerksen) • PubChem frontend (Fred Soltanshahi; zip file,

60.5 MB) • PubChem 2-D structure search (Christopher

Kibbey; zip file, 6.5 MB)

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

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

• 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

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

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 for academic institutions

MDL’s CrossFire Commander

• Download page for Commander at IU:– http://www.libraries.iub.edu/index.php?pageId=2114

• Likely to be replaced soon by Discovery Gate

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 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, 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://bl-libg-wind.ads.iu.edu/ICAS/conquest.ica

– 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– 14,000 titles going back to the mid 1960s– More than 500,000 records link to the Beilstein

database on either CrossFire or DiscoveryGate

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

• 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

– Software free through 12/31/05:• http://www.cas.org/stnanavist/prices.html• Flat fee cost based on size of the answer set analyzed

(ranges from $190 for up to 1,000 to $690 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

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/

• PubChem– http://pubchem.ncbi.nlm.nih.gov/

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: Autors 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://www.chemistry.org/portal/resources/ACS/ACSContent/education/cpt/nl_cpt_spring2004.pdf