Entrez
Encyclopedia
Federated search
Federated search is an information retrieval technology that allows the simultaneous search of multiple searchable resources. A user makes a single query request which is distributed to the search engines participating in the federation...
engine, or web portal
Web portal
A web portal or links page is a web site that functions as a point of access to information in the World Wide Web. A portal presents information from diverse sources in a unified way....
that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information
National Center for Biotechnology Information
The National Center for Biotechnology Information is part of the United States National Library of Medicine , a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper...
(NCBI) website. The NCBI is a part of the National Library of Medicine
United States National Library of Medicine
The United States National Library of Medicine , operated by the United States federal government, is the world's largest medical library. Located in Bethesda, Maryland, the NLM is a division of the National Institutes of Health...
(NLM), which is itself a department of the National Institutes of Health
National Institutes of Health
The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...
(NIH), which in turn is a part of the United States Department of Health and Human Services
United States Department of Health and Human Services
The United States Department of Health and Human Services is a Cabinet department of the United States government with the goal of protecting the health of all Americans and providing essential human services. Its motto is "Improving the health, safety, and well-being of America"...
. "Entrez" also happens to be the second person plural (or formal) form of the French verb "entrer (to enter)", meaning the invitation "Come in!".
Entrez Global Query is an integrated search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Entrez can efficiently retrieve related sequences
Primary structure
The primary structure of peptides and proteins refers to the linear sequence of its amino acid structural units. The term "primary structure" was first coined by Linderstrøm-Lang in 1951...
, structures
Tertiary structure
In biochemistry and molecular biology, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.-Relationship to primary structure:...
, and references. The Entrez system can provide views of gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
and protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
sequences and chromosome
Chromosome
A chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.Chromosomes...
maps. Some textbooks are also available online through the Entrez system.
Features
The Entrez front page provides, by default, access to the global query. All databases indexed by Entrez can be searched via a single query string, supporting boolean operators and search term tags to limit parts of the search statement to particular fields. This returns a unified results page, that shows the number of hits for the search in each of the databases, which are also links to actual search results for that particular database.Entrez also provides a similar interface for searching each particular database and for refining search results. The Limits feature allows the user to narrow a search a web forms interface. The History feature gives a numbered list of recently performed queries. Results of previous queries can be referred to by number and combined via boolean operators. Search results can be saved temporarily in a Clipboard. Users with a MyNCBI account can save queries indefinitely and also choose to have updates with new search results e-mailed for saved queries of most databases. It is widely used in the field of biotechnology to enhance the knowledge of students worldwide.
Databases
Entrez searches the following databases:- PubMedPubMedPubMed is a free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez information retrieval system...
: biomedical literature citations and abstracts, including MedlineMEDLINEMEDLINE is a bibliographic database of life sciences and biomedical information. It includes bibliographic information for articles from academic journals covering medicine, nursing, pharmacy, dentistry, veterinary medicine, and health care...
- articles from (mainly medicalMedical journalA public health journal is a scientific journal devoted to the field of public health, including epidemiology, biostatistics, and health care . Public health journals, like most scientific journals, are peer-reviewed...
) journalsScientific journalIn academic publishing, a scientific journal is a periodical publication intended to further the progress of science, usually by reporting new research. There are thousands of scientific journals in publication, and many more have been published at various points in the past...
, often including abstracts. Links to PubMed CentralPubMed CentralPubMed Central is a free digital database of full-text scientific literature in biomedical and life sciences. It grew from the online Entrez PubMed biomedical literature search system. PubMed Central was developed by the U.S. National Library of Medicine as an online archive of biomedical journal...
and other full-text resources are provided to articles from the 1990s. - PubMed CentralPubMed CentralPubMed Central is a free digital database of full-text scientific literature in biomedical and life sciences. It grew from the online Entrez PubMed biomedical literature search system. PubMed Central was developed by the U.S. National Library of Medicine as an online archive of biomedical journal...
: free, full text journal articles - Site Search: NCBI web and FTP web sites
- Books: online books
- OMIM: online Mendelian Inheritance in Man
- OMIAOmiaOmia may refer to:* Omia District, Peru* In biology, OMIA stands for Online Mendelian Inheritance in Animals, an online database of animal phenotypes...
: online Mendelian Inheritance in Animals - Nucleotide: sequence database (GenBankGenBankThe GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information as part of the International Nucleotide Sequence...
) - Protein: sequence database
- Genome: whole genome sequences and MappingHuman Genome ProjectThe Human Genome Project is an international scientific research project with a primary goal of determining the sequence of chemical base pairs which make up DNA, and of identifying and mapping the approximately 20,000–25,000 genes of the human genome from both a physical and functional...
- Structure: three-dimensional macromolecular structures
- Taxonomy: organisms in GenBank Taxonomy
- SNP: single nucleotide polymorphism
- Gene: gene-centered information
- HomoloGene: eukaryotic homology groups
- PubChemPubChemPubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information , a component of the National Library of Medicine, which is part of the United States National Institutes of Health . PubChem can...
Compound: unique small molecule chemical structures - PubChemPubChemPubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information , a component of the National Library of Medicine, which is part of the United States National Institutes of Health . PubChem can...
Substance: deposited chemical substance records - Genome ProjectGenome projectGenome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism and to annotate protein-coding genes and other important genome-encoded features...
: genome project information - UniGeneUniGeneUniGene is an NCBI database of the transcriptome and thus, despite the name, not primarily a database for genes. Each entry is a set of transcripts that appear to stem from the same transcription locus...
: gene-oriented clusters of transcript sequences - CDDConserved domain databaseThe Conserved Domain Database is a database of well-annotated multiple sequence alignment models and derived database search models, for ancient domains and full-length proteins.-Philosophy:...
: conserved protein domain database - UniSTS: markers and mapping data
- PopSet: population study data sets (epidemiologyEpidemiologyEpidemiology is the study of health-event, health-characteristic, or health-determinant patterns in a population. It is the cornerstone method of public health research, and helps inform policy decisions and evidence-based medicine by identifying risk factors for disease and targets for preventive...
) - GEO Profiles: expression and molecular abundance profiles
- GEO DataSets: experimental sets of GEO data
- Sequence read archive: high-throughput sequencing data
- Cancer Chromosomes: cytogenetic databases
- PubChem BioAssay: bioactivity screens of chemical substances
- GENSAT: gene expression atlas of mouse central nervous system
- Probe: sequence-specific reagents
- NLM Catalog: NLM bibliographic data for over 1.2 million journals, books, audiovisuals, computer software, electronic resources, and other materials resident in LocatorPlus (updated every weekday).
Accessing Entrez
In addition to using the search engine forms to query the data in Entrez, NCBINational Center for Biotechnology Information
The National Center for Biotechnology Information is part of the United States National Library of Medicine , a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper...
provides the Entrez Programming Utilities (eUtils) for more direct access to query results. The eUtils are accessed by posting specially formed URLs to the NCBI server, and parsing the XML response. There is also an eUtils SOAP interface.