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Robin Reid  (library subject specialist) | U of U  Biology | Harold F. Hirth (Department Representative)

Biology Indexes and Databases

Library Databases:

Biomedical Reference Collection: Basic
Provides doctors, research scientists, students, clinical specialists and managers with access to 100 full text journals covering such disciplines as clinical medicine, nursing, dentistry, veterinary medicine, the health care system and the preclinical sciences. All 100 full text journals contained in the database are also indexed in MEDLINE.

BioMed Central
This independent publishing house, is committed to providing free access to peer-reviewed biomedical research results and has made a permanent committment to open access, regardless more than 50 online journals covering biology, medicine, and the life sciences. Links to information about BioMed Central, the Faculty of 1000, and work published by researchers at the University of Utah

BioOne
BioOne is an aggregation/gateway of high impact bioscience research journals. BioOne provides integrated access to a thoroughly linked information resource of interrelated full text journals focused on the biological, ecological and environmental sciences from small scientific society presses.

Chemical Abstracts via SciFinder Scholar
Requires a one-time installation of the Citrix client. Maximum of 3 simultaneous users. Help Sheet for Chemical Abstracts.

CogNet
MIT CogNet Library offers a core repository of digitized text, featuring major reference works, along with a customized netLibrary collection of MIT Press cognitive and brain science titles, select Publisher Collections, material from a range of leading journals, and other related materials.

Dr. Duke's Phytochemical and Ethnobotanical Databases (Agricultural Research Service, U.S. Department of Agriculture)

National Genetic Resources Program (Agricultural Research Service, U.S. Department of Agriculture)
Covers the following areas; Plants, Animals, Microbes and Invertebrates.

Science Citation Index 1980-2002 (max. of 5 users)
Science Citation Index 1997-present (now known as Web of Science) (max. of 10 users)
Covers thousands of international science and technology journals in over 100 disciplines, though no field in depth. Uniquely valuable for ability to track who has subsequently cited a known paper.

Web of Knowledge/Web of Science
Consolidated searching of Science Citation Index, Social Science Citation Index, and Arts & Humanities Citation Index, multidisciplinary databases listing articles in 8500 major scholarly journals. Especially useful for finding articles which have cited a known article or given author in their bibliography. Search by topic, author, journal title, author's institution, cited author, cited work, cited year. 1997 - present (articles may be earlier if they were CITED from 1997 on). Use Science Citation Index in this database list for 1980 -. Printed indexes (1955- ) in Science Reference and General Reference. Please logout when finished.

Zoological Record (1978-Present)
Covers virtually every aspect of zoology, including biochemistry, behavior, ecology, evolution, genetics, etc. Over 6,500 serials plus approximately 1,500 non-serial publications are covered including professional journals, magazines, newsletters, monographs, books, dissertations, and conference proceedings. The subjects related to animals used for human subject research is not covered in the Zoological Record database

Cambridge Medical and Biological Collection
Covers the biological, medical, and agricultural sciences. Over 6,000 journals, books,conference proceedings, monographs, and reports from 21 CSA abstract journals are reviewed for inclusion in LSC.

AGRICOLA (1970-Current)
Database consisting of literature citations for journal articles, monographs, proceedings, theses, patents, translations, audiovisual materials, computer software, and technical reports pertaining to all aspects of agriculture from the National Library of Agriculture.

Biological Sciences (see the subfiles of this database) 1982-Current
Indexes the world's literature on biology and applied life sciences: especially useful for biochemistry, genetics, and virology. Citations from thousands of journals and conferences.

Biology Digest (1989-Current)
Citations from about 190 magazines and journals which have articles suitable for underclass research in biology and the health sciences. The University of Utah owns most of the journals indexed

Conference Papers Index (1982-Current)
Citations to papers and posters from thousands of scientific conferences held around the world. Since 1995 this index has focused on the life sciences; between 1982 and 1994 it also covered physics and engineering conferences.

JSTOR
Provides image and full-text online access to back issues of selected scholarly
journals. There are 3 JSTOR collections: the Arts & Sciences I Collection which
includes 117 titles, the Ecology & Botany Collection which includes 29 titles, and the
General Science Collection with 7 titles. Help sheets for JSTOR databases are available for the following areas, Botany and Ecology.

MEDLINE (1993-Current)
This version of MEDLINE contains over 4 million citations and abstracts to worldwide biomedical literature.

NTIS (National Technical Information Service - U.S. Department of Commerce, 1964-Current)
The NTIS Database produced by the National Technical Information Service, is the preeminent resource for accessing the latest U.S. government-sponsored research and worldwide scientific, technical, engineering, and business-related information. NTIS is the central source for the sale of unclassified and publicly available information from research reports, journal articles, data files, computer programs and audio visual products from Federal sources.

Physical Education Index (1970-Current)
Scholarly and trade literature ranging from physical education curricula, to sports medicine, to dance. Other coverage includes sport law, kinesiology, motor learning,
recreation, standardized fitness tests, sports equipment, business and marketing, coaching and training, sport sociology/psychology, health education and physical
therapy.

Plant Science (1994-Current)
Focuses on all plant scientific aspects, especially on pathology, symbiosis, biochemistry, genetics, biotechnology, techniques and environmental biology.

TOXLINE (1994-Current)
Indexes literature on toxicology: chemicals, pharmaceuticals, pollutants. Citations to journal articles, conference papers, technical reports and theses.

Databases from the National Library of Medicine and the NIH

A series of articles from the NLM Technical Bulletin, on searching databases from the National Library of Medicine

AIDSinfo (U.S. Department of Health and Human Services (DHHS))
A central resource for current information on federally and privately funded clinical trials for AIDS patients and others infected with HIV. AIDS clinical trials evaluate experimental drugs and other therapies for adults and children at all stages of HIV infection -- from patients who are HIV positive with no symptoms to those with various symptoms of AIDS.

MEDLINE/PUBMED (Medical Literature, Analysis, and Retrieval System Online) is the U.S. National Library of Medicine's (NLM) premier bibliographic database that contains over 12 million references to journal articles in life sciences with a concentration on biomedicine, coverage from 1966 to the present. A helpsheet for Medline is available.

OLDMEDLINE contains journal citations published in the 1957 through 1965

PROW (National Cancer Inst.)
PROW (Protein Reviews On the Web) is an online resource that features PROW Guides, authoritative short, structured reviews on proteins and protein families. The Guides provide approximately 20 standardized categories of information (abstract, biochemical function, ligands, references, etc.) for each protein.

The Visible Human Project® (The National Library of Medicine)
The creation of complete, anatomically detailed, three-dimensional representations of the normal male and female human bodies. Acquisition of transverse CT, MR and cryosection images of representative male and female cadavers has been completed.

Entez databases, Nucleotide databases and Molecular databases- National Center for Biotechnology Information (U.S. National Library of Medicine)
Entrez is a search and retrieval system that integrates information from databases at NCBI. Formal instruction in the use of the Entez and other NLM databases is available from the Eccles Health Sciences Library (Division of Education & Instruction Services).

Nucleotide Sequences (The Entrez Nucleotides database is a collection of sequences from several sources, including GenBank, RefSeq, and PDB. The number of bases grows at an exponential rate)

Protein Sequences (The protein entries in the Entrez search and retrieval system have been compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq)

Macromolecular Structure (The Molecular Modelling Database (MMDB) contains 3-D macromolecular structures, including proteins and polynucleotides. MMDB contains over 10,000 structures and is linked to the rest of the NCBI databases, including sequences, bibliographic citations, taxonomic classifications, and sequence and structure neighbors)

Popset (a set of DNA sequences that have been collected to analyse the evolutionary relatedness of a population)

Online Mendelian Inheritance in Man (also know as OMIM, this database is a catalog of human genes and genetic disorders)

NCBI taxonomy database (contains the names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence),

ProbeSet (ProbeSet is a "by experiment" view of NCBI's Gene Expression Omnibus gene expression and hybridization array repository)

3D Domains ( The Molecular Modelling Database (MMDB) contains 3-D macromolecular structures, including proteins and polynucleotides. MMDB contains over 10,000 structures and is linked to the rest of the NCBI databases, including sequences, bibliographic citations, taxonomic classifications, and sequence and structure neighbors)

UniSTS (a NCBI resource that reports information about markers, or Sequence Tagged Sites (STS))

SNP (Single Nucleotide Polymorphism)

CDD (A Conserved Domain Database and Search Service; Proteins often contain several modules or domains, each with a distinct
evolutionary origin and function)

UniGene (An experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented
clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in
which the gene has been expressed and map location)

Nucleotide databases:

GenBank (The NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank (at NCBI), together with the DNA DataBank of Japan (DDBJ) and the European Molecular Biology Laboratory (EMBL) comprise the International Nucleotide Sequence Database Collaboration. These three organizations exchange data on a daily basis. GenBank grows at an exponential rate, with the number of nucleotide bases doubling approximately every 14 months. Currently, GenBank contains more than 17 billion bases from over 100,000 species)

dbEST (Expressed Sequence tags)

dbGSS (Genome Survey Sequences database; The GSS division of GenBank is similar to the EST division, except that its
sequences are genomic in origin, rather than cDNA (mRNA). The GSS division contains (but is not limited to) the following types of data: random "single pass read" genome survey sequences. cosmid/BAC/YAC end sequences, exon trapped genomic sequences and Alu PCR sequences)

dbSTS (An NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites)

Molecular databases:

RefSeq ( Reference Sequence collection aims to provide a comprehensive, integrated, non-redundant set of sequences,including genomic DNA, transcript (RNA), and protein products, for major research organisms. RefSeq standards serve as the basis for medical, functional, and diversity studies; they provide a stable reference for gene identification and characterization, mutation analysis, expression studies, polymorphism discovery, and comparative analyses.RefSeqs are used as a reagent for the functional annotation of some genome sequencing projects, including those of human and mouse)

GEO (Gene Expression Omnibus supports the public use and dissemination of gene expression data.. GEO is a gene expression and hybridization array data repository, as well as an online resource for the retrieval of gene expression data from any organism or artificial source)

BLAST (Basic Local Alignment Search Tool, is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA). An Online BLAST tutorial is available.

The Gray Herbarium Index of New World Plant Names (Harvard University)

Botanists (Authors of plant names, collectors of botanical specimens, and authors of botanical publications)

Publications (Titles and abbreviations of botanical publications with authors, dates of publication and BPH and TL2 references)

Specimens (Specimen records, primarily type specimens from the Harvard University Herbaria and New England Botanical Club)

The Gray Index (in part) is now incorporated into the International Plant Names Index (IPNI), a joint project with the Royal Botanic Gardens, Kew and the Australian National Herbaria to provide an online database of the names and associated basic bibliographical details of all vascular plants.

Interdisciplinary Indexes and Databases

Belsteins Hanbook of Organic Chemisty see: Crossfire

CRC Handbook of Chemistry and Physics
Since the first volume in 1913, the Handbook of Chemistry and Physics has been revised annually except for a few wartime years and has grown steadily, in both size and diversity of information, to become the most widely used source of data for chemists, physicists, and professionals in related fields of science.

Crossfire
Electronic edition of "Beilsteins Handbuch der organischenChemie", a complete chemical information system comprising of the Beilstein Database, the CrossFire search and retrieval server software and the Beilstein Commander client.

Digital Dissertations aka Dissertation Abstracts
IMPORTANT NOTE: ProQuest Digital Dissertations provides full text access to University of Utah, Utah State University and Brigham Young University Dissertations published from 1997 and forward, and citations only to dissertations before that date. Because of the size of the files, dissertations cannot be downloaded to floppy disks. In order to access them patrons must have an e-mail account and a hardrive to download the file to. The database also provides access to the first 24 pages of other school dissertations that have been published since 1997

Environmental Universe (1975 - present. Lexix/Nexis)
Indexes journals, meetings, reports, newspapers, books and publications covering research on the impact of humankind on the environment.

EPADoc (1996 - present)
Contains a variety of EPA documents of general interest.. Requires a one-time installation of the Citrix client to your web browser.

Electronic Companion to Biochemistry
Requires a one-time installation of the Citrix client to your web browser.

Electronic Companion to Complete Nutrition
Requires a one-time installation of the Citrix client to your web browser.

Electronic Companion to Essential Nutrition
Requires a one-time installation of the Citrix client to your web browser.

Family & Society Studies Worldwide
The world's most comprehensive, systematic, and non-evaluative resource of research, policy, and practice literature in the fields of Family Science, Human Ecology, and Human Development.

Federal Register (GPO Access - U.S. Government Printing Office ; 1995-Present)
The Federal Register is the official daily publication for Rules, Proposed Rules, and Notices of Federal agencies and organizations, as well as Executive Orders and other Presidential Documents.

HazMat (NLM)
Information on Hazardous Chemicals and Occupational Diseases.

GPO Monthly Catalog (U.S. Government Printing Office)
Over 380,000 records on all subjects of interest to the U.S. government. 1994 to the present. Among the items of interest to those individuals studying biological sciences are publications (print & electronic) published by the Departments of Health & Human Services, The U.S. Public Health Service, the medical branches of the U.S. Armed Services, The Department of Agriculture, U.S. Forest Service, Department of the Interior, National Park Service, and the Bureau of Land Management, among others.

Materials Safety Data Sheets MSDS
The MSDS Database, produced by The Canadian Centre for Occupational Health and Safety, is a comprehensive full text database containing over 70,000 Material Safety Data Sheets (MSDSs) for chemical products sold or manufactured in North America. There are 500+ contributors (manufacturers/suppliers/distributors).

MSDS, Material Safety Data Sheets (Produced by The Canadian Centre for Occupational Health and Safety)
MSDS is a comprehensive full text database containing over 70,000 Material Safety Data Sheets for chemical products sold or manufactured in North America. There are 500+ contributors (manufacturers/suppliers/distributors).

Nutrition abstracts and reviews. Series A: human and experimental
Includes international coverage of analytical methods, foods, physiology and biochemistry, human health and nutrition, nutritional disorders and therapeutic nutrition.

Optics.org
Physics, astronomy, geophysics, optics, and photonics resources for scientists and engineers. Citations & abstracts, standards, jobs, products.

POPLINE® (Johns Hopkins Center for Communication Programs)
World's largest bibliographic database on population, family planning, and related health issues. POPLINE® provides citations with abstracts for 300,000 records representing published and unpublished literature in the field.

Wisconsin Primate Research Center-National Primate Research Centers Program (University of Wisconsin-Madison)

United States Patent & Trademark
The Web Patent Full-Text Database (PatFT) contains the full-text of over 3,000,000 patents from 1976 to the present, plus limited bibliographic data for over 4,000,000 patents from 1790 to 1975. It provides links to the Web Patent Full-Page Images Database (PatImg), which contains over 70,000,000 images, including every page of over 7,000,000 patents from 1790 to the most recent issue week. Among the patents of interest to biologists are full-text AIDS-related patents and images and the publication site for issued and patented sequences (PSIPS).

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