Selected Resources for: Biology, Cell and Molecular

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Subject Librarian:

Josh Bishoff

jbishoff@umn.edu

This subject covers: the organization, composition, function and assembly of cells and cellular components, and the molecular basis of living things.


Article Databases and Indexes

* Premier Resources *

MNCAT Article Discovery is the Library's powerful new tool that simultaneously searches hundreds of databases, including popular ones such as JSTOR, Project MUSE and Medline. This is the automatic choice when you search from the "Articles and Databases" tab.

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

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.

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

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.

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.


Catalogs and Bibliographies

Catalogs

Search for books, conference proceedings, journals, maps, videos, and other items in our collection.


General Reference Sources

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

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.

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.


Directories

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


Encyclopedias


Handbooks and Manuals

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.


Internet Resources

Electronic Texts

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


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.

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

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).


Writing Guides

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

Bio-Medical Library

Diehl Hall, 505 Essex St. S.E.
East Bank, Minneapolis Campus
Reference: 612-626-3260; Circulation: 612-626-4045
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Magrath Library

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