Table of Contents
Article resources
BIOSIS Citation Index 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.
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 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.
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.
Web resources
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between 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.
BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models present in BioModels Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc.
BiosciRegister.com is a manual compilation of biotechnology and life sciences suppliers enabling buyers to easily identify manufacturers of biotechnology equipment and reagents for cell biology, cell culture, genomics, proteomics and more. The site includes new projects, free magazines and trade publications, jobs, news and events.
Cell and Molecular Biology Online is an informational resource for cell and molecular biologists. Links to online publications, protocols and current research are also included.
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.
CiteAb is an antibody search engine that helps scientists find commercial and academic sources of antibodies. Over 100 suppliers are included, and CiteAb provides a simple citation-ranked search engine that finds antibodies.
CiteXplore combines literature searches of MEDLINE/PubMed and full-text databases such as PubMedCentral and patents with text mining tools for biology. Search results are cross referenced to EBI applications based on publication identifiers. Links to full text versions are provided where available.
CMS Molecular Biology Resource has a large collection of electronic and Internet tools for a wide variety of subjects. Some of the subjects included are protein analysis, DNA analysis, Biomolecular modeling and Bioinformatics.
Cold Spring Harbor Protocols is an interdisciplinary digital journal providing a definitive source of research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging. Each monthly issue details multiple essential methods—a mix of cutting-edge and well-established techniques. Newly commissioned protocols and unsolicited submissions are supplemented with articles based on Cold Spring Harbor Laboratory’s courses and manuals.
Horst Ibelgaufts' COPE is the updated and revised internet version of the "Dictionary of Cytokines" that appeared in print in 1995. This book itself was an updated version of the German "Lexikon Zytokine" published in 1992.
DAVID, maintained by the National Institute of Allergy and Infectious Diseases (NIAID), provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind a large list of genes.
The Entrez Cross-database Search Page lists, describes, and provides a link to each NCBI database. On this page, all NCBI databases can be searched simultaneously.
The European Molecular Biology Laboratory (EMBL) is dedicated to basic research in the molecular life sciences.
This E-Book is broken down into chapters based on subjects in Molecular Biology. The chapters are cells and viruses, protein structure and function, various genetics topics, biotechnology and bioinformatics, and diseases. Links to free articles are also available.
The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.
PDBe is the EBI Protein Structure Database in Europe, a project for the collection, management and distribution of data about macromolecular structures, derived from the Protein Data Bank (PDB).
Protocol-Online provides access to protocols for various subjects such as biochemistry, bioinformatics, genetics and genomics, molecular biology. Also listed are a large amount of protocols for model organisms.
Rhea is a freely available, manually annotated database of chemical reactions created by EMBL-EBI in collaboration with the Swiss Institute of Bioinformatics (SIB).
Scitable is a free science library and personal learning tool brought to you by Nature Publishing Group. Scitable currently concentrates on genetics and cell biology, which include the topics of evolution, gene expression, and cellular processes. The site also offers resources for effective science communication and career paths.
The SeekProducts site is hosted by SeekQuence and allows you to search and filter commercially available antibodies by validated publications, research area, and vendor information. SeekProducts also allows you to compare multiple antibodies next to each other and link directly to a supplier page for product purchase.
The Universal Protein Resource (UniProt), maintained by EMBL-EBI, is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc). The UniProt Metagenomic and Environmental Sequences (UniMES) database is a repository specifically developed for metagenomic and environmental data.
Encyclopedias
Supports the development and use of statistical methods for addressing the problems and critical issues that confront scientists, practitioners and policy makers engaged in the life and medical sciences.
Features over 4,900 specially commissioned, peer-reviewed and citable articles spanning the entire spectrum of the life sciences.
Molecular data
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between 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.
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.
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.
The BioSystems database contains records that group together molecules that interact in biological systems. One type of biosystem is a biological pathway, which can consist of interacting genes, proteins, and small molecules. Another type of biosystem is a disease, which can involve components such as genes, biomarkers, and drugs.
In collaboration with authors and publishers, the National Center for Biotechnology Information (NCBI) is adapting biomedical Books for the web.
CDD currently contains domains derived from two popular collections, Smart and Pfam, plus contributions from colleagues at NCBI, such as COG. The source databases also provide descriptions and links to citations. Since conserved domains correspond to compact structural units, CDs contain links to 3D-structure via Cn3D whenever possible.
The database of genotype and phenotype (dbGaP) stores phenotype and genotype data, as well as the associations between them. Studies generating data for dbGaP will include genome-wide association studies, medical sequencing, and molecular diagnostic assays. Summaries of phenotype and genotype data as well as study documents and association analyses (when available) will be found on the public site. Authorized access may be required for downloading coded individual-level phenotypes genotypes and pedigrees.
The EST database contains all records found within the Expressed Sequence Tag (EST) division of GenBank. EST records contain first-pass single-read cDNA sequences and include no annotated biological features.
Gene organizes information about the characteristics and defining sequences of genes from species in Genome, RefSeq, and other model organisms.
The whole Genomes of over 1000 viruses and over 100 microbes can be found in Entrez Genome. The genomes represent both completely sequenced organisms and those for which sequencing is in progress. All three main domains of life - bacteria, archaea, and eukaryota - are represented, as well as many viruses and organelles.
Genome Project is a collection of complete and incomplete large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. The database is organized into organism-specific overviews that function as portals from which all projects in the database pertaining to that organism can be browsed and retrieved.
Comparable experimental sample sets assembled from the Gene Expression Omnibus (GEO) repository. Entrez GDS queries all GEO DataSet annotation, allowing identification of experiments of interest.
Individual gene expression and molecular abundance profiles assembled from the Gene Expression Omnibus (GEO) repository. Entrez GEO Profiles queries annotation and pre-computed profile characteristics, allowing identification of specific genes, and molecular abundance profiles of interest.
The GSS database contains all records found within the Genome Survey Sequence (GSS) division of GenBank. GSS records contain first-pass single-read genomic sequences and rarely include annotated biological features.
HomoloGene is an automated system for detecting homologs among the annotated genes of several completely sequenced eukaryotic genomes.
The Entrez Journals database searches for a journal and has links to records for that journal in the databases. The Journals database can be searched using the journal title, MEDLINE abbreviation, NLM ID, ISO abbreviation, or ISSN. The database includes the journals in all Entrez databases, e.g., PubMed, Nucleotide, Protein.
MeSH is NLM's controlled vocabulary used for indexing articles in PubMed. MeSH terminology provides a consistent way to retrieve information that may use different terminology for the same concepts. Use the MeSH database to build a PubMed search strategy.
The Nucleotide database contains records for all Entrez Nucleotide sequences that are not found within the Expressed Sequence Tag (EST) or Genome Survey Sequence (GSS) divisions of GenBank. These include sequences from all remaining divisions of GenBank, NCBI Reference Sequences (RefSeqs), Whole Genome Shotgun (WGS) sequences, Third Party Annotation (TPA) sequences, and sequences imported from the Entrez Structure database.
Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in animal species (other than human and mouse) authored by Professor Frank Nicholas of the University of Sydney, Australia, with help from many people over the years. The database contains textual information and references, as well as links to other relevant records.
Online Mendelian Inheritance in Man (OMIM) is a catalog of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases. It is based on the book, Mendelian Inheritance in Man. The online version is updated daily. The OMIM FAQs provide additional information about the book and the online database.
PopSet is a set of DNA sequences that have been collected to analyse the evolutionary relatedness of a population. The population could originate from different members of the same species, or from organisms from different species. They are submitted to GenBank via Sequin, often as a sequence alignment.
The Probe Database is a public registry of sequence-specific reagents designed for use in a wide variety of biomedical research applications, together with information on reagent availability, experimental protocols, probe effectiveness, and computed sequence similarities.
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.
Protein Clusters is a collection of related protein sequences (clusters). Currently it consists of Reference Sequence proteins encoded by complete prokaryotic and chloroplast genomes and plasmids. This database contains both curated and non-curated clusters.
SNP is NCBI’s database of Single Nucleotide Polymorphisms.
SRA is a database of raw sequence data from sequencing instruments.
Structure: The Molecular Modeling Database (MMDB) contains 3-D macromolecular structures, including proteins and polynucleotides. MMDB contains over 20,000 structures and is linked to the rest of the NCBI databases, including sequences, bibliographic citations, taxonomic classifications, and sequence and structure neighbors.
UniGene is 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.
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. If multiple maps are available for a chromosome, Map Viewer 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.
The NCBI Taxonomy database contains the names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence.
PubChem BioAssay contains the results of biological activity screening from a variety of public sources. It provides searchable descriptions of each bioassay, including descriptions of the conditions and readouts specific to that screening procedure. PubChem BioAssay results are linked to PubChem Substance, and in turn to PubChem Compound, whenever chemical structures are known. Screening results may be browsed via a web interface and also downloaded for further cheminformatics analysis.
PubChem Compound contains chemical structure information drawn from a variety of public sources. Compounds may be searched by chemical properties and are pre-clustered into identity and similarity groups by structure comparison. Whenever possible, compounds are linked via PubChem Substance to information on their biological activities. Available links include PubMed citations, protein 3D structures and links to biological screening results available in PubChem BioAssay.
PubChem Substance contains descriptions of chemical samples, from a variety of public sources, and links to information on their biological activities. The description includes links to PubChem Compound in cases where the chemical structures of compounds in the sample are known. Links providing information on biological activity include links to PubMed citations, protein 3D structures, and to biological screening results available in PubChem BioAssay.
PubMed Central (PMC) is the U.S. National Library of Medicine's digital archive of life sciences journal literature. Access to the full text of articles in PMC is free, except where a journal requires a subscription for access to recent articles.
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