Skip HSL Header
Return to Home Page
Need Help? Ask a Librarian

NCBI Entrez Global Search Portal

The National Center for Biotechnology Information and the National Library of Medicine maintain a portal to search and access two dozen databases and related products available via the Entrez system. This portal page enables you to find information on a topic, including a gene, disease, or other biomedical topic, by searching all 24 databases at once rather than each individually. To get to the Entrez Portal it is best to first access PubMed via a UNC-sponsored link, then to click the word "Entrez" in the black navigation bar at the top of the screen. This will allow you to access full-text articles via the PubMed LinkOut service.

PubMed: Literature database for biomedical information from 1955-present. Includes MEDLINE and affiliated databases as well as publisher-submitted citations, totaling more than 14 million articles. Use a UNC-sponsored link to get to full-text articles.
PubMed Central: Repository of more than 75 free full-text journals in HTML and PDF format. Many are new, online-only journals (ex: BioMedCentral titles); others are historically print journals (ex: BMJ). Print journals may not have complete back issues or most recent issue available.
Books: "Online bookshelf" of 30 titles (as of November 2003) covering a range of subjects in biomedicine, including Genes and Disease, Human Molecular Genetics, and Molecular Biology of the Cell. Most are included as e-books in the UNC Catalog.
OMIM: Online Mendelian Inheritance in Man provides curated and interlinked reviews of genetic diseases and conditions. OMIM links to PubMed records for each article cited, to other OMIM articles, and to sequence and genetic mapping data. Some links go to external (non-NCBI) databases, including JAX.
Nucleotide: This section allows simultaneous searching of the major nucleotide (DNA & RNA) databases available from the NCBI, including GenBank (updated nightly with records from EMBL and DDBJ), RefSeq (the curated sequence database), and PDB. Records in RefSeq include brief notes for gene function, polymorphisms/SNPs, conserved regions, functional regions, chromosomal locus, and literature references.
Protein: Search many major protein/amino acid sequence databases as once, including Protein Data Bank (PDB), SwissProt, Protein Information Resource (PIR), and annotated sequence records from GenBank and RefSeq.
Genome: NCBI has [approximately] whole genome data for a growing number of species, viruses, and plasmids located here. Tools available in this section include the MapViewer (contiged sequence maps with annotations and links to other databases internal and external to NCBI), TaxPlot, COGs, and whole genome BLAST. NOTE: This section is still under development!
Structure: The main component of this database is the Molecular Modelling Database, which contains 20,000 3D macromolecular structures for proteins and polynucleotides. Some are available for VAST (Vector Alignment Search Tool) and PDBeast (taxonomy by structure) research.
Taxonomy: Any biological species represented by at least one sequence in GenBank is classified here based on cladistic analysis of genetic divergence from other species either in the complete tree or selected by the researcher. The species-specific page has nice links to external taxonomy databases as well as a complete (estimated) lineage for the species.
SNP: AKA dbSNP, this database collects information about single nucleotide polymorphisms for genes in RefSeq and GenBank. Data includes frequency, location, and effect. SNPs can be searched by gene, function, chromosome, weight, and detection method.
Gene: This database is still under development. It allows you to search for genes by sequence and/or in the Map Viewer. Results are presented in a clear graphical and mapped fashion, with data pulled from a number of other databases. Similar to, and may eventually replace, LocusLink.
UniGene: This database clusters related genes to represent the uniqueness or stability of a gene across multiple species. Computations are done (in advance) using BLAST comparisons. Records include related information such as expression in tissues, chromosomal locus, and links to SAGE Genie.
CDD: The Conserved Domain Database draws data from a variety of derivative protein databases, including Pfam, Smart, and COG. Computations are done (in advance) using BLAST to determine conserved regions of protein sequence, which can then be compared visually using the CN3D viewer. This databases also uses CDART (the Conserved Domain Architecture Retrieval Tool) to compare possible conserved domains to determine function.
3D Domains: This database is part of the Molecular Modelling Database that is searchable in the Structure section. It provides information about compact structural domains of proteins that can be compared using VAST.
UniSTS: Known primers (based on Sequence Tagged Sites, or STS's) are cataloged and annotated in this database. Included in each record are the 5' and 3' primer sequences, estimated product size and base pair location, mapping information, and links to other NCBI sites about the gene sequence in question.
PopSet: This database uses DNA sequences to analyze the evolutionary relatedness of a population. This is helpful both for taxonomic research and epidemiology (ex: the "evolution" of SARS). Some sets are aligned using BLAST but many are not.
GEO: The Gene Expression Omnibus provides molecular abundance profiles based on expression microarrays using tissue samples.
GEO DataSets: This is the curated version of GEO, where sets of related records from that database have been combined into meta-expression analyses. The datasets do not always follow expected groupings.
Homologene: A system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic geneomes.
Cancer Chromosomes: Three databases, the NCI/NCBI SKY/M-FISH & CGH Database, the NCI Mitelman Database of Chromosome Aberrations in Cancer, and the NCI Recurrent Aberrations in Cancer, are now integrated into NCBI's Entrez system as Cancer Chromosomes. Search for cytogenetic, clinical, and/or reference information.
PubChem Substance: This database contains descriptions of chemical samples, from a variety of sources, and links to PubMed citations, protein 3D structures, and biological screening results that are available in PubChem BioAssay. If the contents of a chemical sample are known, the description includes links to PubChem Compound.
PubChem Compound: This database contains validated chemical depiction information provided to describe substances in PubChem Substance. Structures stored within PubChem Compounds are pre-clustered and cross-referenced by identity and similarity groups. Additionally, calculated properties and descriptors are available for searching and filtering of chemical structures.
PubChem BioAssay: Contains bioactivity screens of chemical substances described in PubChem Substance. It provides searchable descriptions of each bioassay, including descriptions of the conditions and readouts specific to that screening procedure.