This alphabetical list describes and provides access to databases that are used frequently by faculty, staff, and students in the biological sciences. KEY SITE designates the most frequently used of these. Following the list are annotations on each database. Many of these databases, along with other resources, are grouped by subject area in the RESEARCH GUIDES. A more complete list of science and engineering databases is available at Databases at Stanford.
Academic Search Premier
AGRICOLA
AGRIS
Arctic & Antarctic Regions
ASFA: Aquatic Sciences and Fisheries Abstracts
Bacteriology Abstracts (Microbiology B)
BIOBASE Knowledge Library (BKL)
BioOne
BIOSIS KEY SITE
CAB Abstracts KEY SITE
CSA Illumina
Dissertations & Theses @ Stanford University
Dissertations & Theses, A&I
Ecology Abstracts
EIS: Digests of Environmental Impact Statements
Entrez
Environment Index
Environmental Engineering Abstracts
Environmental Fate Database
Environmental Sciences and Pollution Management Databases
Global Population Dynamics Database
Hazardous Substances Data Bank (HSDB)
Health & Safety Sciences Abstracts
Industrial & Applied Microbiology Abstracts (Microbiology A)
Journal Citation Reports (JCR)
Material Safety Data Sheets (MSDS)
Metabolite
Metalloprotein Database and Browser
Oceanic Abstracts
Pollution Abstracts
POPLINE
Protein Databank in Europe (PDBe)
PubMed KEY SITE
Research portfolio online reporting tool (RePORT) Expenditures and Results (RePORTER)
Registry of Toxic Effects of Chemical Substances (RTECS)
Toxicology Abstracts
TOXLINE
TOXNET
Web of Science KEY SITE
xSearch KEY SITE
Zoological Record KEY SITE
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Academic Search Premier is a multidisciplinary database that includes scholarly journals as well as newspapers and popular magazines. It indexes well over 8,000 journal titles, including more than 4,700 full text journals. Most of the journals covered in Academic Search Premier are peer-reviewed. Subject coverage spans biology, chemistry, education, engineering, humanities, physics, psychology, religion & theology, sociology, and many other disciplines. The database is updated daily.
AGRICOLA serves as the catalog and index to the collections of the National Agricultural Library. The records describe publications and resources encompassing all aspects of agriculture and allied disciplines, including animal and veterinary sciences, entomology, plant sciences, forestry, aquaculture and fisheries, farming and farming systems, agricultural economics, extension and education, food and human nutrition, and earth and environmental sciences. AGRICOLA is organized into two data sets. The NAL Public Access Catalog contains citations to books, audiovisuals, serials, and other materials. The Article Citation Database contains citations, many with abstracts, to journal articles, book chapters, reports, and reprints.
AGRIS is an international, multilingual bibliographic database covering all aspects of agriculture. It is compiled from contributions of more than 160 national and international centers.
"Arctic & Antarctic Regions (AAR) is the world's largest collection of international polar databases. Coverage is multidisciplinary. A wide variety of sources are indexed including: scientific periodicals, monographs, proceedings of conferences and symposia, government reports, theses, dissertations, and books. Many are indexed only in AAR -- the best resource for research on cold regions anywhere, from temperate regions with cold winters to the Himalayas of Tibet."--NISC product factsheet
ASFA (Aquatic Sciences and Fisheries Abstracts) indexes literature in the field of aquatic resources, including aquaculture, aquatic pollution, brackish water environments, fisheries, marine biology, and oceanography. Input to ASFA is provided by an international network of information centers monitoring over 5,000 serial publications, books, reports, conference proceedings, translations and limited distribution literature.
Bacteriology Abstracts (Microbiology B) indexes journal articles in bacteriology. Over 400 journals are monitored for inclusion in this database, and years of coverage are 1982 to the present. With topics ranging from bacterial immunology and vaccinations to diseases of man and animals, the database provides access to clinical findings as well as pure bacteriology, biochemistry, and genetics. Major areas of coverage include: aggressins and toxins, animal bacteriology, antibacterial agents, cell structure and function, ecology and distribution, genetics and evolution, immunology, microbial symbiosis, plasmids, and bacterial taxonomy.
BIOBASE Knowledge Library (BKL), combining the PROTEOME and TRANSFAC suites of databases, offers rich, high quality content and integrated analysis tools spanning gene regulation and pathways to fully annotated genomes. These database products offer a combination of computational and experimental data. PROTEOME is a comprehensive knowledge resource for the complete known proteomes of selected species, including humans. TRANSFAC compiles data on transcription factors, their experimentally-proven binding sites, and regulated genes.
BioOne is a full-text aggregation of bioscience research journals. Most are published by small societies and other not-for-profit organizations. Subjects covered by BioOne journals include ecology, evolution, environmental science, natural history, taxonomy, and systematics.
BIOSIS KEY SITE
Also known as BIOSIS Previews, BIOSIS indexes the worldwide literature of research in the biological and biomedical sciences. The database covers the entire field of life sciences including original research reports and reviews in field, laboratory, clinical, experimental, and theoretical work. BIOSIS indexes journals, technical reports, meeting proceedings, United States patents, and books in biology, biomedicine, and related areas. The database indexes literature published from 1926 to the present. Over 500,000 journal articles and other documents from over 6,000 journals and other sources are indexed each year. The database is available to Stanford users via Web of Knowledge.
CAB Abstracts, 1910-present KEY SITE
CAB Abstracts indexes journal articles in the applied life sciences. It covers the fields of agriculture, forestry, animal and veterinary sciences, human health and communicable diseases, human nutrition, food science, animal health and welfare, microbiology and parasitology, leisure and tourism, plant science and crop science, and the management and conservation of natural resources. The database indexes literature published from 1910 to the present. Over 9,000 serials representing 125 countries are indexed in full or in part.
CSA Illumina provides access to more than 100 full-text and bibliographic databases published by CSA and its publishing partners. CSA Illumina's databases cover major areas of research, including materials science, environmental sciences and pollution management, biological sciences, aquatic sciences and fisheries, biotechnology, engineering, computer science, sociology, art history, and linguistics.
Dissertations & Theses @ Stanford University, also known as Stanford Dissertations, provides full PDF versions of Stanford dissertations from 1989 onward. Some earlier dissertations are available.
Dissertations & Theses, A&I is a searchable database of Ph. D. dissertations and selected master’s theses with abstracts from 1861 to the present.
Ecology Abstracts indexes journal articles in ecology and environmental science. Nearly 700 journals are indexed in full or in part, and the database indexes literature published from 1982 to the present. Coverage includes habitats, food chains, erosion, land reclamation, resource and ecosystems management, modeling, climate, water resources, soil, and pollution.
EIS: Digests of Environmental Impact Statements indexes the hundreds of environmental impact statements issued by United States government agencies each year. For each environmental impact statement indexed in the database, an abstract includes a concise description of the project, sections on positive impact and negative consequences, and a list of legal mandates. The database indexes statements published from 1985 to the present.
Entrez searches the National Center for Biotechnology Information (NCBI) databases to provide integrated access to nucleotide and protein sequence data from over 160,000 species, along with three-dimensional protein structures, genomic mapping information, PubMed MEDLINE, and more. Sequence data are combined from various sources, including GenBank, EMBL, DDBJ, RefSeq, PIR-International, PRF, Swiss-Prot, and PDB. Entrez can be searched with a wide variety of text terms such as author name, journal name, gene or protein name, organism, unique identifier (e.g., accession number, sequence ID, PubMed ID), and other terms, depending on the database being searched.
Environment Index offers deep coverage in applicable areas of agriculture, ecosystem ecology, energy, natural resources, marine & freshwater science, geography, pollution & waste management, environmental technology, environmental law, public policy, social impacts, urban planning, and more. Environment Index contains more than 1,590,000 records from 1,500 domestic and international titles going back to the 1950s (including 960 active core titles) as well as 100 monographs. Environment Index also features an in-depth thesaurus, and author profiles are provided for 3,000 authors in environmental science.
Environmental Engineering Abstracts covers the world literature pertaining to technological and engineering aspects of air and water quality, environmental safety, and energy production. Updated monthly, it includes more than 700 indexed primary journals and 2,500 relevant monographs and conference proceedings.
Environmental Fate Database, also known as Environmental Issues and Policy Index, provides access to the following databases: DATALOG, which contains 18 types of environmental fate data; BIOLOG, or the Microbial degradation/toxicity file, which provides sources of microbial toxicity and biodegradation data; CHEMFATE, a data file containing 25 categories of environmental fate and physical/chemical property information on commercially important chemical compounds; BIODEG, which contains experimental values relating to biodegradation subjects; and BIODEG summary, which provides summary evaluation and reliability codes for different test methods, as well as summaries for biodegradability under aerobic and anaerobic conditions.
Environmental Sciences and Pollution Management. This database collection, produced by CSA, has 13 subfiles that can be searched individually or as a single database. It offers abstracts for the worldwide literature covering the environmental sciences, including air, land, water and noise pollution, bacteriology, ecology, toxicology, risk assessment, environmental biotechnology and engineering, waste management, water resources, policies and regulations, and U.S. federal environmental impact statements.
The Global Population Dynamics Database is the largest collection of animal and plant population data in the world, bringing together nearly five thousand time series in one database. Sources of data vary enormously, from annual counts of mammals or birds at individual sampling sites, to weekly counts of zooplankton and other marine fauna.
Hazardous Substances Data Bank (HSDB) is a toxicology data file on the National Library of Medicine’s (NLM) Toxicology Data Network (TOXNET). It focuses on the toxicology of potentially hazardous chemicals. It is enhanced with information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, and related areas. All data are referenced and derived from a core set of books, government documents, technical reports and selected primary journal literature. HSDB is peer-reviewed by the Scientific Review Panel (SRP), a committee of experts in the major subject areas within the data bank's scope. HSDB is organized into individual chemical records, and contains over 5000 such records. Users can search by chemical or other name, chemical name fragment, Chemical Abstracts Service Registry Number (RN), and/or subject terms.
Health & Safety Sciences Abstracts provides a survey of recent work relating to public health, safety, and industrial hygiene. Cited studies are geared to help individuals identify, evaluate, and eliminate or control risks and hazards across the spectrum of environmental and occupational situations. The database provides perspectives on topics of widespread concern such as aviation and aerospace safety, environmental safety, nuclear safety, medical safety occupational safety, and ergonomics. Health and safety related aspects of pollution, waste disposal, radiation, pesticides, epidemics, and other phenomena having the potential to threaten the public, the environment, or the workplace itself are indexed here. The database indexes government reports as well as journal articles, conference proceedings, books, and other publications.
Industrial & Applied Microbiology Abstracts (Microbiology A) indexes journal articles that report significant findings and practical applications in agricultural, food and beverage, chemical, and pharmaceutical industries. Over 360 journals are indexed and the database indexes literature published from 1982 to the present. Specific topics include antibiotic and antimicrobial agents; contamination; ripening and fermentation processes for foods, wines and beer; soil microbiology; plant diseases; biodegradation; and isolation and identification of microorganisms.
Journal Citation Reports (JCR) allows users to evaluate and compare journals using citation data drawn from over 7,500 scholarly and technical journals from more than 3,300 publishers in over 60 countries. It covers virtually all areas of science, technology, and social sciences. JCR can be used to identify the most frequently cited journals in a field, the journals with the highest impact in a field, or the largest journals in a field.
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Material Safety Data Sheets (MSDS), available from Stanford Environmental Health & Safety, is a searchable database of chemical substances. For each substance, its data sheet provides chemical and safety information. Included is information on risks resulting from exposure, flammability, recommended procedures for safe handling and transportation, and legislation and regulations. Another version of MSDS is available from the Canadian Centre for Occupational Health and Safety (CCOHS).
Metabolite is a complete metabolism information system that includes key information about metabolic transformations of xenobiotic compounds from the literature and a registration system to input proprietary metabolism studies. Information in the database is abstracted from Biotransformations of Drugs (1977-1983), Pharmacokinetics (1986-1990), and original metabolism literature (1990 onwards). The database indexes path and scheme information, even across studies and literature citations. In addition to the chemical structures of the parent compound and the metabolites, the database includes: species, route of administration and excretion, analytical methodology, parent compound class, physiological activity and literature references. Note : MDL Information Systems, Inc.
TSRI's Metalloprotein Database and Browser (MDB) site contains quantitative information on all the metal-containing sites available from structures in the PDB distribution. This database contains geometrical and molecular information that allows the classification and search of particular combinations of site characteristics.
Oceanic Abstracts indexes the worldwide technical literature pertaining to the marine and brackish-water environment. Over 600 journals are indexed and literature published from 1981 to the present is covered. The database focuses on marine biology and physical oceanography, fisheries, aquaculture, non-living resources, meteorology and geology, plus environmental, technological, and legislative topics. It covers living and non-living resources, meteorology and geology, plus environmental, technological, and legislative topics.
Pollution Abstracts indexes material from conference proceedings and hard-to-find documents, in addition to journal articles. Over 1,000 journals are indexed and literature published from 1981 to the present is covered. Topics in pollution and its management are extensively covered from the standpoints of atmosphere, emissions, mathematical models, effects on people and animals, and environmental action. Major areas of coverage include: air pollution, marine pollution, freshwater pollution, sewage and wastewater treatment, waste management, land pollution, toxicology and health, noise, and radiation.
POPLINE (POPulation information onLINE) contains citations with abstracts to scientific articles, reports, books, and unpublished reports in the field of reproductive health, population, family planning, and related health issues. POPLINE is maintained by the INFO Project at the Johns Hopkins Bloomberg School of Public Health/Center for Communication Programs and is funded by the United States Agency for International Development. (USAID). POPLINE contains nearly 360,000 records. The majority of items are published from 1970 to the present, however, there are selected citations dating back to 1827. In addition to free text searching, the database can be searched by keywords from the POPLINE Thesaurus , a controlled vocabulary of 2,400+ terms used to index documents in the database.
The Protein Databank in Europe (PDBe), the European project for the collection, management and distribution of data about macromolecular structures, is derived in part from the Protein Data Bank (PDB). MSD presents primarily data for macromolecular structures associated with the metabolism of living organisms, that is, the atomic coordinates of proteins, nucleic acids and molecules that bind with these. The database also offers links to protein sequence information, textual information from scientific publications and a number of derived properties that augment the macromolecular structure information.
PubMed KEY SITE
Developed by the National Center for Biotechnology Information (NCBI), Pubmed is a free version of MEDLINE that offers links to GenBank records, other molecular sequence data, and other resources. MEDLINE, produced by the National Library of Medicine, is an index to journal articles in medicine, nursing, dentistry, veterinary medicine, the health care system, and the preclinical sciences, including both basic biomedical sciences and clinical practice. It indexes over 4,000 journals. The database contains citations from 1950 to the present with some older citations. An important feature of MEDLINE is the use of Medical Subject Headings (MeSH), a powerful tool for searching specific topics or for comprehensive general searches. MEDLINE is also available to Stanford users via EBSCO, ISI Web of Knowledge, NLM Gateway, OCLC ,and Ovid.
Registry of Toxic Effects of Chemical Substances (RTECS) is a compendium of data extracted from the scientific literature. For each chemical substance indexed in RTECS, six types of toxicity data are included: (1) primary irritation; (2) mutagenic effects; (3) reproductive effects; (4) tumorigenic effects; (5) acute toxicity; and (6) other multiple dose toxicity. Specific numeric toxicity values such as LD50, LC50, TDLo, and TCLo are noted as well as species studied and route of administration used. For each citation, the bibliographic source is listed thereby enabling the user to access the actual studies cited.
Research portfolio online reporting tool (RePORT) Expenditures and Results (RePORTER) is an upgraded version of CRISP that provides enhanced searching capabilities and access to the results (publications and patents) of both intramural and extramural projects funded by the National Institutes of Health (NIH). It also links to related information in other databases such as the National Library of Medicine’s Medline. RePORTER provides access to records of projects funded each year from fiscal year 1985 to the present.
Toxicology Abstracts indexes journal articles in toxicology and related areas. Over 300 journals are indexed from 1981 to the present. The database covers social poisons, substance abuse, natural toxins, legislation and recommended standards, environmental issues, industrial and agricultural chemicals, household products, pharmaceuticals, the effects of alcohol and smoking, drug abuse, hydrocarbon studies, nitrosamines, radiation and radioactive materials, toxicity testing methods and analytical procedures for toxic substances.
TOXLINE, available via CSA, is the National Library of Medicine's (NLM) bibliographic database for toxicology. TOXLINE records provide bibliographic information covering the biochemical, pharmacological, physiological, and toxicological effects of drugs and other chemicals. Most records include abstracts and/or indexing terms and CAS Registry Numbers. TOXLINE references are drawn from various sources organized into component subfiles which are searched together but which may be used to limit searches as well. TOXLINE is also available via NLM’s TOXNET.
TOXNET is a system of files oriented to toxicology and related areas. It is managed by the National Library of Medicine's Toxicology and Environmental Health Information Program (TEHIP). TOXNET is an integrated system containing modules for building and reviewing records as well as providing sophisticated search and retrieval features for NLM online users. Components of TOXNET are: CCRIS (Chemical carcinogenesis research information system); ChemIDplus Lite (available for name and RN searching without the need for plugins or applets); ChemIDplus Advanced (web based chemical identification and structure search database); DART (Developmental and reproductive toxicology); Gene-Tox (Genetic toxicology); Haz-Map (database linking chemicals, jobs and diseases); Household Products (potential health effects of chemicals in 5,000 common household products); HSDB (hazardous substances data bank); IRIS (Integrated risk information system); ITER (International toxicity estimates for risk); LactMed (database of drugs and other chemicals to which breastfeeding mothers may be exposed); TOXLINE (Toxicology information online); TOXMAP (Environmental health e-maps); and TRI (Toxic chemical release inventory).
Web of Science KEY SITE
The Web of Science service, available via ISI Web of Knowledge, includes three core component databases: the expanded version of Science Citation Index (SciSearch), Social Sciences Citation Index, and Arts & Humanities Citation Index. The Science Citation Index provides access to current and retrospective bibliographic information, author abstracts, and cited references found in the world's leading scholarly science and technical journals covering over 100 disciplines from 1900 to the present. An important feature of SciSearch is the ability to perform cited reference searching to find recent articles that cite an earlier work.
xSearch KEY SITE
xSearch, developed through the Stanford University Libraries' partnership with Deep Web Technologies, provides Stanford researchers and students with a single search option for multiple online resources. Searches may be limited to specific databases, or all available sources may be searched simultaneously. Search results are merged into one relevance ranked list, and are clustered by topic, author, source publication, publisher, and date. Custom searches using any selection of available databases can be created and re-used. Users may also create alerts in order to be informed automatically of new items that match search criteria.
Zoological Record KEY SITE indexes the world's zoological and animal science literature, covering all research from biochemistry to veterinary medicine. The database provides a collection of references from over 4,500 international serial publications, plus books, meetings, reviews and other no- serial literature from over 100 countries. It is the oldest continuing database of animal biology, indexing literature published from 1864 to the present. Zoological Record has long been recognized as the "unofficial register" for taxonomy and systematics, but other topics in animal biology are also covered.