Selected Resources for: Bioinformatics

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Subject Librarian:

Josh Bishoff

jbishoff@umn.edu

The application of mathematics, computer science, and information technology to biological problems, especially problems in molecular biology and biochemistry. The broad goals of bioinformatics are to gather and organize large data sets generated from biological experiments, and to allow flexible retrieval and analysis of that data to form new biological insights.


Article Databases and Indexes

* Premier Resources *

Provides comprehensive coverage of scholarly literature in the fields of physics and astrophysics, electrical engineering, electronics, computing and control, and information technology. Indexed are primarily journal articles and conference papers, with some books,technical reports, and dissertations. The database provides bibliographic citations plus abstracts.

The major national resource for molecular biology information; NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information. Includes bibliographic and data resources such as PubMed, GenBank, OMIM, and many more.

Primary source of journal article access for the health sciences - the campus version provides full text access to all MEDLINE e-journals subscribed to by the University of Minnesota TC Libraries.

An abstract and citation database with a single search platform searching content from ScienceDirect, Scopus, SciTopics, and relevant Web content.

Indexes over 11,000 international journals in the sciences, social sciences, and arts and humanities. Titles of the print equivalent are: Arts and Humanities Citation Index, Book Citation, Science Citation Index, and Social Sciences Citation Index. Coverage runs from 1975 to the present. Basic truncation symbol is the asterisk(*).


Academic or Scholarly Articles Subject Indexes

Full text of most ACM journals and proceedings since 1950; also includes publications of affiliated organization.

NO LONGER CURRENT. Due to budget pressures, we have canceled our subscription to BIOSIS Previews. Although you will continue to be able to access the database, no new articles will be added after January 2011.

Covers the biological and medical sciences, including biochemistry, biophysics, biotechnology, botany, environment, microbiology, and zoology. Provides citations and abstracts to articles, conference papers, technical reports and chapters of books from over 5000 publications.

The Libraries' subscription to this resource allows for 10 users at any one time. If you get a busy signal, please wait a few minutes and try accessing the site again.

CAB Abstracts covers agriculture in its broadest sense, including crop production, forestry, environment, animal health and nutrition, veterinary science, agricultural engineering, biotechnology, soil and water, agricultural economics, recreation and tourism, rural sociology, and human nutrition and health. Indexes journal articles, monographs, conferences, and other primary literature.

Provides extensive indexing of scholarly and technical periodicals, conference proceedings, and report literature in all engineering disciplines including applied physics, electronics, materials science, and related fields in science and management. Indexes nearly 3000 sources worldwide.

Connect to Google Scholar through the Libraries' web site to gain off-campus access to all the articles and journals in full text in the Libraries. Use Google Scholar to find articles from a wide variety of academic publishers, professional societies, preprint repositories and universities, as well as scholarly articles available across the web. To connect to the full text, click "FindIt@U of M Twin Cities" in your Google Scholar search results. Learn more: Google Scholar FAQ

Alternative interface to the MEDLINE/PubMed health and biological sciences database. Provides a number of powerful features not included in PubMed (e.g., direct export of citations to your RefWorks account), and retains many advanced functionalities of PubMed (e.g., ability to use PubMed's syntax to refine your searches).

Full-text access to the transactions, journals, magazines and conference proceedings of the Institute of Electrical and Electronics Engineers. Includes all current IEEE Standards.
Remote access available for University of Minnesota -- Twin Cities students, staff and faculty

Provides access to drug information resources, including DRUGDEX; POISINDEX; Martindale, the Extra Pharmacopoeia; Index Nominum; and Physician's Desk Reference.

The Neuroscience Information Framework is a dynamic inventory of Web-based neuroscience resources that includes data, materials, and tools. An initiative of the NIH Blueprint for Neuroscience Research, NIF advances neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment.

OVID, like PubMed, is an interface to search the MEDLINE database. It includes citations from the fields of medicine, public health, nursing, dentistry, veterinary medicine, and the basic biomedical sciences. MEDLINE is the National Library of Medicine's bibliographic database/article index that contains over 17 million references to journal articles. Coverage is from 1949 to the present. Over 5200 journals worldwide in over 37 languages are indexed.

SciFinder is the best database for chemistry-related topics. Registration is required, and you must download VPN and then log in to it for off-campus access.


SciFinder includes journal and patent references,chemical regulatory data, and supplier, reaction, and substance information. SciFinder Mobile is best for quick searches. It has no IP access restrictions but limited functionality, and it requires a SciFinder account.


General Indexes to Magazine, Journal & Newspaper Articles

The world's largest academic multi-disciplinary database, Academic Search Premier provides full text for thousands of scholarly (peer-reviewed) publications.

Lists citations to health-related articles reported in the Star Tribune - Newspaper of the Twin Cities [Minneapolis Edition].


Catalogs and Bibliographies

Catalogs

Search with MNCAT to find books, journals, etc. owned by the library. Search by keyword, subject, title, or author for materials on your topic.


General Reference Sources

Biographical Sources

Provides brief factual information on approximately 130,000 living scientists in biology, physical sciences, public health, mathematics, statistics, and computer science. Includes birthdate, education, professional career, and honors received.

Focuses particularly on contemporary scientists and includes selected bibliographies, chronologies, tables of scientific discoveries, and quotations.


Chemical Compounds

ChemIDplus indexes more than 368,000 records for chemical substances cited in the National Library of Medicine (NLM) databases. It is searchable by Name, Synonym, CAS Registry Number, Molecular Formula, Classification Code, Locator Code, and Structure (requires Chime plug-in or ISIS/Draw). The records contain information on structure, names and synonyms, formulas, registry numbers, and some physical properties in addition to toxicity information and links to NLM-indexed articles which cite the substances.

Database of descriptive & numerical data on chemical, physical & biological properties of compounds; systematic & common names; literature references; & structures. Contains all compounds included in: Dictionary of Organic Compounds (255,000 records) Dictionary of Natural Products (170,000) ; Dictionary of Inorganic and Organometallic Compounds (101,000) ; Dictionary of Drugs (40,000+) ; Dictionary of Analytical Reagents (14,000)


Dictionaries

Dictionary of Cell and Molecular Biology

Dictionary of Gene Technology Terms

Dictionary of Gene Technology: Genomics, Transcriptomics, Proteomics

Dictionary of Microbiology and Molecular Biology

Dorland's Illustrated Medical Dictionary

Facts on File Dictionary of Biotechnology and Genetic Engineering

FOLDOC is a searchable dictionary of acronyms, jargon, programming languages, tools, architecture, operating systems, networking, theory, conventions, standards, mathematics, telecoms, electronics, institutions, companies, projects, products, history, in fact anything to do with computing. The dictionary has been growing since 1985 and now contains over 13000 definitions

Gives technical and descriptive data for common substances and phenomena. Identifies thousands of chemicals by name, physical properties, source of occurrence, shipping regulations, CAS number, hazards, derivations, synonyms and applications. Available online through Knovel as well as in print.

Illustrated Dictionary of Immunology

Defines over 6,500 terms associated with biochemistry, biotechnology, botany, cellular biology and genetics, as well as chemistry, ecology, medicine, pharmacology and toxicology terms. Both words and definitions can be searched.

Provides "over 10,000 definitions to technology terms and concepts," With an emphasis on computer-related subjects.


Directories

Global information resource listing over 8,000 organizations, product and service providers in the biotechnology industry.


Encyclopedias

Encyclopedia of Analytical Science

A ten-volume set describing the theory and applications of various analytical techniques. The index has more individual compounds than that of the Encyclopedia of Analytical Chemistry.

Covers all areas of biochemistry including aspects related to molecular biology, cell biology, genetics, and biophysics. Intended for a cross-disciplinary audience.

Encyclopedia of Evolution

This is a comprehensive and concise guide to evolutionary biology, from the origins of species to the selfish gene and beyond.

Encyclopedia of Genetics

Encyclopedia of Immunology

A comprehensive reference source of current immunological knowledge. Includes information for experimental and clinical immunologists and scientists and physicians from related fields.

Encyclopedia of Molecular Biology and Molecular Medicine

Frontiers of Life

Four-volume encyclopedia of the life sciences containing articles that are well illustrated with photographs, sketches, and graphs; each article ends with a comprehensive bibliography and there is an extensive subject index at the end of the fourth volume.


Handbooks and Manuals

Bergey's Manual of Systematic Bacteriology

Standard guide to the classification of bacteria. (Second Edition is currently in production, with volumes 1 and 2 released and volume 3 currently in preparation.)

Computer Science and Engineering Handbook

Annually published reference source for chemical & physical property data, nomenclature, structure, & composition of substances. Includes physical constants of organic & inorganic compounds, conversion factors, & much more.

Series of standard, authoritative guides to research laboratory methods in the life sciences; the U of M subscribes to 5 Current Protocols titles: Bioinformatics, Microbiology, Molecular Biology,Protein Science and Toxicology. Limited access to articles published through 2011 for Cell Biology, Human Genetics, Immunology and Neuroscience.

Lange's Handbook of Chemistry

Classic reference covering the entire field of chemistry, with up-to-date facts, figures, numerical values, tables, and formulas.

Classic reference source for chemists; contains over 10,000 entries on drugs and pharmaceuticals, common organic chemicals and laboratory reagents. The entries include data such as chemical names, molecular formula, chemical structure, physical data, literature references, and more.

Nature Protocols is an online resource for experimental protocols, primarily in biology and chemistry, including authoritative, peer-reviewed 'Nature Protocols' and an interactive 'Protocols Network'. The two create a dynamic forum for scientists to upload and comment on protocols.

Extensive online catalog of human genes and genetic disorders, with detailed monographs on mechanistic and clinical aspects of the genes, disease states, and variations.

Practical Handbook of Biochemistry and Molecular Biology

Tables of physical and chemical data on molecules of biological significance.

Springer Handbook of Enzymes


Internet Resources

Electronic Texts

Books24x7 is a web-based, searchable, e-book site that provides users access to the complete contents of nearly 3,000 titles covering a broad range of engineering and technology topics. Contributing publishers include: Cambridge University Press, The MIT Press, IEEE Press, John Wiley & Sons, McGraw-Hill, Microsoft Press, Sybex, Wrox Press and many others.

Growing collection of online, open access biomedical books; full text can be searched directly from this interface.

A collection of IT-related electronic books from several publishers, most notably O'Reilly. The Libraries has licensed 320 titles from among Safari's offering. This content covers Database, Java, Linux/Unix, Networking, Perl, Programming, and Web technologies generally. The titles we have licensed are all listed in MnCat.


Gateways & Megasites


Web Sites

This resource provides a convenient Google-based search tool for 31 bioinformatics journals. The Journals can be searched either indivdually or collectively, and impact factor data is provided for most of the 31 titles. Article titles in the journal current issues can be quickly viewed with one click, and RSS feeds are provided for automatic article updates. The site has a three-part knowledgebase (biology, bioinformatics, informatics) with glossary-style definitions and links to relevant datatabases (such as Entrez Gene, EMBL-EBI, Cambridge Structural Database, etc.; note that not all the databases are free). There is also a bioinformatics conference list and a forum for user questions and suggestions.

A comprehensive index, with abstracts, to the research literature of mathematics. Corresponds to the print indexes Mathematical Reviews (MR) and Current Mathematical Publications (CMP). Published by the American Mathematical Society.


Statistics and Data

Data Resources

Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between biological sequences; the program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

Public-domain archive of simple genetic polymorphisms in a variety of model eukaryotes, including single-base nucleotide substitutions (SNPs) as well as small-scale multi-base deletions or insertions, and retroposable element insertions and microsatellite repeat variations. Each dbSNP entry includes the sequence context of the polymorphism (i.e., the surrounding sequence), the occurrence frequency of the polymorphism (by population or individual), and the experimental method(s), protocols, and conditions used to assay the variation.

Provides data sets resulting from an automated genome analysis and annotation process for selected eukaryotic (primarily vertebrate) genomes. The Ensemble software system aims to provide accurate, automatic analysis of genome data; analysis and annotation maintained on the current data; presentation of the analysis to all via the web; and means of distribution of the analysis to users. Data can be accessed through text search and genome/chromosome browser functions. Through a data upload and distributed annotation system, Ensembl offers users the ability to display their own data sets in the genome browser framework; users may also share data with others.

Overviews and allows text-based searches of over 25 of the bibliographic databases and biomolecular data resources held at NCBI (the National Center for Biotechnology Information), including PubMed, OMIM, Entrez Gene, and Entrez Taxonomy; this site performs a simultaneous search of the various databases and reports back the number of hits in each -- you can then select an individual database to view detailed search results.

Searchable database of genes from a wide range of organisms, supplying key connections to other databases providing map, sequence, expression, structure, function, citation, and homology data; a good starting point for investigating the structure and role of a particular gene.

Collection of nucleotide (DNA and RNA) sequences from several primary database sources, including GenBank, RefSeq, and PDB; text-searchable through Entrez Nucleotide; sequences are similarity-searchable through BLAST. The number of bases in these databases continues to grow at an exponential rate. As of April 2006, there are over 130 billion bases in GenBank and RefSeq alone.

Access point for prokayotic genome information and the prok genome browser on NCBI web site. The RefSeq (NC_) records lead to a browseable and searchable chromosomal view of the sequenced genomes.

Provides text-based searching of records in the Molecular Modeling Database (MMDB), containing 3D macromolecular structures of proteins and polynucleotides; links to the Cn3D structure viewer program (download required). MMDB contains over 28,000 structures and is linked to other NCBI databases including sequences, bibliographic citations, taxonomic classifications, and sequence and structure neighbors.

ExPASy (Expert Protein Analysis System) proteomics server is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE; includes the UniProt Knowledgebase (Swiss-Prot and TrEMBL) Protein knowledgebase; the PROSITE - Protein families and domains database; SWISS-2DPAGE - Two-dimensional polyacrylamide gel electrophoresis database; ENZYME - Enzyme nomenclature database; and SWISS-MODEL Repository - Automatically generated protein models. Site also provides a number of analysis and prediction tools.

GenBank is the National Institutes of Health genetic sequence database, an annotated collection of all publicly available DNA sequences. Sequence data in GenBank is searchable through sequence similarity algorithms such as NCBI BLAST, and textual annotation of GenBank sequence records is searchable through the NCBI's Entrez Nucleotide search tool.

Suite of databases and associated software, integrating current knowledge on the function and utility of biological systems (PATHWAY and BRITE databases), information about genes and proteins (GENES database), and chemical compounds and reactions (LIGAND database). KEGG is especially noted for its metabolic pathway database.

The major national resource for molecular biology information; NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information. Includes bibliographic and data resources such as PubMed, GenBank, OMIM, and many more.

The Map Viewer provides special browsing capabilities for a subset of organisms in Entrez Genomes. Map Viewer allows you to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. The number and types of available maps vary by organism, and are described in the "data and search tips" file for each organism. If multiple maps are available for a chromosome, it displays them aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system.

Provides many protein sequence databases and analysis tools, including the Protein Sequence Database and its successor, UniProt, functional analysis tools, protein classification and ontology systems.

PDB is the single worldwide repository for the processing and distribution of 3-D structure data of large molecules of proteins and nucleic acids; the site provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease.

PubChem provides information on the biological activities of small molecules. It is organized as three linked databases within the NCBI's Entrez information retrieval system. These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides a fast chemical structure similarity search tool. Links from PubChem's chemical structure records to other Entrez databases provide information on biological properties.

The Genome Browser provides a visual display of chromosomal informaiton, allowing zoom and scroll over chromosomal and DNA sequence, showing the work of annotators worldwide. Other tools included on the site provide other means of accessing genomic and proteomic data: Gene Sorter shows expression, homology and other information on groups of genes that can be related in many ways; Blat quickly maps your sequence to the genome; Table Browser provides convenient access to the underlying database; VisiGene lets you browse through a large collection of in situ mouse and frog images to examine expression patterns. The site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides a portal to the ENCODE genome annotation project.


Style Manuals and Writing Guides

Bibliography Software

RefWorks is a web-based citation manager that allows you to create your own databases of citations by importing references from MNCAT and other databases, and then in seconds automatically generate bibliographies in all major styles (MLA, APA, Turabian, Chicago, etc.).


Style Manuals

Includes recommended citation format styles for journals, books, conference publications, patents, audio visuals, electronic information, maps, legal materials, newspaper articles, bibliographies, dissertations, and scientific reports. "Internet formats" supplement available at http://www.nlm.nih.gov/pubs/formats/internet.pdf

Electronic Styles : A Handbook for Citing Electronic Information

Useful tool for finding the full title of a journal in biomedicine, if you only have an abbreviation, or for determining from the full title what the official NLM and ISO abbreviations of the title are (e.g., for preparing a reference list).

Publication Manual of the American Psychological Association

The Publication Manual of the American Psychological Association (6th edition) is the style manual of choice for writers, editors, students, educators, and professionals in psychology, sociology, business, economics, nursing, social work, and justice administration.


Writing Guides

How to Write and Publish a Scientific Paper.

Pt. I. Some preliminaries. What is scientific writing? -- Historical perspectives -- Approaching a writing project -- What is a scientific paper? -- Ethics in scientific publishing -- Where to submit your manuscript -- Pt. II. Preparing the text. How to prepare the title -- How to list the authors and addresses -- How to prepare the abstract - How to write the introduction -- How to write the materials and methods section --How to write the results -- How to write the discussion -- How to state the acknowledgments -- How to cite the references -- Pt. III. Preparing the tables and figures. How to design effective tables -- How to prepare effective graphs -- How to prepare effective photographys -- Pt. IV. Publishing the paper. Rights and permissions -- How to submit the manuscript -- The review process (how to deal with editors) -- The publishing process (how to deal with proofs) -- Pt. V. Doing other writing for publication. How to write a review paper -- How to write opinion (book reviews, editorials, and letters to the editor) -- How to write a book chapter or a book -- How to write for the public -- Pt. VI. conference communications. How to present a paper orally -- How to prepare a poster -- How to write a conference report -- Pt. VII. Scientific style. Use and misuse of English -- Avoiding jargon -- How and when to use abbreviations -- Writing clearly across cultures and media -- How to write science in English as a foreign language -- Pt. VIII. Other topics in scientific communication. How to write a thesis -- How to prepare a curriculum vitae -- How to prepare grant proposals and progress reports -- How to write a recommendation letter - and how to ask for one -- How to work with the media -- How to provide peer review -- How to seek a scientific-communication career.

Covers guidelines for the format of manuscripts submitted to biomedical journals. In addition, discusses retraction of research findings, order of authorship, definition of a peer-reviewed journal, and conflict of interest


Library Information

Magrath Library

1984 Buford Avenue
St. Paul Campus
Circulation: (612) 624-2233; Reference: (612) 624-1212
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Science and Engineering Library

Walter Library
East Bank, Minneapolis Campus
Circulation: (612) 624-3366; Reference: (612) 624-0224
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