BioProject

The BioProject database is a searchable collection of complete and incomplete (in-progress) large-scale molecular projects including genome sequencing and assembly, transcriptome, metagenomic, annotation, expression, and mapping projects. BioProject provides a central point to link to all data associated with a project in the NCBI molecular and literature databases.

BioSample

BioSample contains descriptions of biological source materials used in studies that have data in other NCBI molecular databases such as Nucleotide and SRA.

Bookshelf

The NCBI Bookshelf contains a collection of full-text books that can be searched online and that are linked to PubMed records through research paper citations within the text. The collection includes biomedical textbooks, other scientific titles, and NCBI help manuals.

ClinVar

ClinVar is a public archive of submitted reports of clinically relevant human genetic variants and their relationships to phenotypes, with supporting evidence. ClinVar provides standardized nomenclature for variants and phenotypes, a review status for variants, and links to related NCBI literature and molecular databases.

Conserved Domains

Conserved Domains is a database of protein domains represented by sequence alignments and profiles for protein domains conserved in molecular evolution. It also includes alignments of the domains to known three-dimensional protein structures in the MMDB database. The source databases for Conserved Domains include Pfam, Smart, and COG.

dbGaP

dbGaP (Database of Genotypes and Phenotypes) provides the results of studies that have investigated the interaction of genotype and phenotype including genome-wide association studies, medical sequencing, molecular diagnostic assays, as well as association between genotype and non-clinical traits.

dbVAR

dbVAR (Database of Genomic Structural Variation) contains information about large-scale genomic variation, including large insertions, deletions, translocations, and inversions. dbVar also provides associations of defined variants with phenotype information.

Gene

Gene is a searchable database of genes, focusing on genomes that have been completely sequenced and that have an active research community to contribute gene-specific data. Information in Gene records includes nomenclature, chromosomal localization, gene products and their attributes (e.g., protein interactions), associated markers, phenotypes, interactions, and links to citations, sequences, variation details, maps, expression reports, homologs, protein domain content, and external databases.

GEO Datasets

GEO Datasets stores curated gene expression and molecular abundance data sets assembled by NCBI from the Gene Expression Omnibus (GEO) repository of microarray data.

GEO Profiles

GEO Profiles stores individual gene expression and molecular abundance profiles assembled from the Gene Expression Omnibus (GEO) repository of microarray data.

GTR

The Genetic Testing Registry (GTR) is a repository for voluntary submissions of genetic test information by providers. The scope includes the purpose of the test, methodology, validity, evidence of the usefulness of the test, and laboratory contacts and credentials. GTR includes information from and links to NCBI resources such as Gene, ClinVar and MedGen as well as many resources from outside the NIH.

MedGen

MedGen is a portal to information about human disorders and other phenotypes having a genetic component. MedGen aggregates the wide variety of terms used for disorders into a specific concept. Each concept may have associated clinical findings, causative genetic variants and the genes in which they occur, available clinical and research tests, molecular resources, professional guidelines, original and review literature, consumer resources, clinical trials, and links to other related NCBI molecular and literature databases as well as non-NCBI resources.

MeSH

MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary and classification system (ontology) used for indexing articles in PubMed. MeSH terminology provides a consistent way to retrieve information that may use different terminology for the same concepts. Searches in the Entrez MeSH database provide synonymous MeSH terms that can provide more useful results in PubMed. The MeSH database records show subheadings access the MeSH browser showing related concepts and hierarchical relationships among MeSH terms.

NLM Catalog

The NLM Catalog contains records for books, journals, audiovisuals, computer software, electronic resources, and other materials in the National Library of Medicine (NLM) collections. The old Journals database was merged into the NLM Catalog database, and the information once retrieved via Journals, is provided by the NLM Catalog. This includes data such as journal title, MEDLINE abbreviation, NLM ID, ISO abbreviation, or ISSN.

Nucleotide

The Nucleotide database contains all the sequence data from GenBank, EMBL, and DDBJ, the members of the International Nucleotide Sequence Databases Collaboration (INSDC). Nucleotide also includes NCBI-curated Reference Sequences (RefSeqs), submitted assemblies and annotations from the Third Party Annotation (TPA) database, and nucleotide sequences extracted from structure records from the Protein Databank (PDB).

OMIM

The OMIM (Online Mendelian Inheritance in Man) database allows searches of OMIM articles about human genes, genetic disorders, and other inherited traits. OMIM articles provide links to associated literature references, sequence records, maps, and related databases. The NCBI service provides searching capabilities. OMIM records are hosted and served by the independent OMIM site (www.omim.org).

Protein

The Protein database contains amino acid sequences created from the translations of coding regions provided on nucleotide records in GenBank, EMBL, and DDBJ, the members of the International Nucleotide Sequence Databases Collaboration (INSDC) as well as those from coding regions on NCBI Reference Sequences and the Third Party Annotation (TPA) database records. Protein records are also imported from the outside protein-only data sources Protein Information Resource (PIR), UniProtKB/Swiss-Prot, Protein Research Foundation (PRF). Protein sequences are also extracted from structure records from the Protein Data Bank (PDB).

Protein Clusters

Protein Clusters is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins that are encoded by complete prokaryotic genomes as well those encoded eukaryotic organelle plasmids and genomes. The database provides easy access to annotation information, publications, domains, structures, external links, and analysis tools.

PubChem BioAssay

PubChem BioAssay is a database that 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.

PubChem Compound

The PubChem Compound database contains unique, validated chemical structures (small molecules) that can be searched using names, synonyms or keywords. The compound records may link to more than one PubChem Substance record if different depositors supplied the same structure. Structures in 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. Compound records are linked to related PubChem Substance Records, PubMed citations, protein 3D structures, and biological screening results that are available in PubChem BioAssay.

PubChem Substance

The PubChem Substance database contains information on chemical substances including mixtures electronically submitted to PubChem by depositors. This includes any chemical structure information submitted, as well as chemical names, comments, and links to the depositor's web site.

PubMed

PubMed is database of citations and abstracts for biomedical literature from MEDLINE and additional life science journals. Links are provided when full text versions of the articles are available through PubMed Central or other websites.

PubMed Central

PubMed Central (PMC) is the U.S. National Library of Medicine's digital archive of life sciences journal literature. PMC contains full-text manuscripts deposited by authors and articles provided by the publisher.

SNP

The SNP (Single Nucleotide Polymorphism) database is a central repository for single nucleotide polymorphisms, microsatellites, and small-scale insertions and deletions. Both submitted SNPs and NCBI-produced non-redundant reference records (RefSNPs) that cluster reports of the same polymorphism from different sources are available. SNP also contains population-specific frequency and genotype data, experimental conditions, molecular context, and mapping information for both neutral polymorphisms and clinical mutations.

SRA

The SRA (Sequence Read Archive) contains sequencing data from the next generation sequencing platforms. SRA accepts and presents data from all current next-generation sequencing platforms.

Structure

The Structure or Molecular Modeling Database (MMDB) contains experimental data from crystallographic and NMR structure determinations. The data for MMDB are obtained from the Protein Data Bank (PDB). Structure records link to bibliographic information, the sequence databases, and to the NCBI taxonomy. iCn3D, the web based NCBI 3D structure viewer, allows for easy interactive visualization of molecular structures from Entrez.

Taxonomy

The Taxonomy database contains the names and phylogenetic lineages of the organisms that have molecular data in the NCBI databases. New taxa are added to the Taxonomy database as data are deposited for them. The taxonomy records include links to all molecular data for the organism or group as well as links to outside classification resources. Taxonomy names provide the major controlled vocabulary for classifying molecular data across the Entrez system.

Using Boolean Operators

Boolean operators provide a way of generating precise queries that produce well-defined sets of results. The Boolean operators used in Entrez and how they work are as follows.

AND: Finds documents that contain terms on both sides of the operator terms, the intersection of both searches.

OR: Finds documents that contain either term, the union of both searches.

NOT: Finds documents that contain the term on the left but not the term on the right of the operator, the subtraction of the right-hand search from the one on the left.

Entrez requires the Boolean operator AND to be entered in uppercase. This is not required in all databases for the other two operators, but it is simplest to enter all of them in uppercase:

promoters OR response elements NOT human AND mammals

Entrez processes all Boolean operators in a left-to-right sequence. Enclosing individual concepts in parentheses changes this priority. The terms inside the parentheses are processed first as a unit and then incorporated into the overall strategy. For example, in the following search statement, the union of response element and promoter results is generated first and then is intersected with the result of the g1p3 search.

g1p3 AND (response element OR promoter)

Indexed Fields, Query Translation, and Automatic Term Mapping

To facilitate searching, various indices are created for each Entrez database. These indices include information extracted from aspects of the record known as fields. Some of these fields contain essentially free text while other such as those for database identifiers (Accession, PMID), MeSH, and Organism are tightly controlled. Default searches in Entrez are All Fields searches. This usually results in the largest number of returned records but can produce unwanted results. For example, a search in any of the molecular databases with the term horse finds all records that contain this word in a variety of contexts, and many have nothing to do with that animal. If the goal is to find records specifically associated with that species, restricting the search to a particular field produces a more useful set of results. The available Fields and their indexed terms in any Entrez database can be explored on the Advanced Search page as part of the Search Builder. The Advanced Search interface, described in a separate section below, is linked beneath the search box of any page in an Entrez database as shown below for Nucleotide.

After a search there is also a Create alert option above the Search box that allows saving a search strategy in a My NCBI account. My NCBI provides the ability to schedule saved searches to be run automatically. The My NCBI help manual has more information on Saved searches and the other features of My NCBI mentioned in this document.

The Entrez Gene Advanced Search Page is shown in Figure 1 with the index for the Organism field expanded. The term horse is in the Organism index for Gene. Selecting the Organism field before the search finds only Gene records for the horse (Equus caballus) while the default All Fields search finds records for other species as well. Field restricted searching can be performed using the Search Builder. Restricted searches may also be entered manually by following the term with the name of the field in square brackets “[ ]”, as shown in the following examples:

Figure 1.

The Entrez Gene Advanced Search page showing the Search Builder with the Index for the Organism Field expanded.

                          horse[Organism]
                          neoplasms[MeSH Terms]
                          prolactin[Protein Name]
                          srcdb_refseq[Properties]
                          2010/06[Publication Date]

Dates and Other Ranges

Certain fields can accept ranges of values. Common examples are Publication Date, Modification Date, Accession, Molecular Weight, and Sequence Length. In these cases, the low and high numbers of the range are separated by a colon “:” as the range operator between them followed by the field:

                          110:500[Sequence Length]
                          2015/3/1:2016/4/30[Publication Date]

Facet Filters

Many of useful restrictions including some of the search terms described above can be applied to searches through the faceted filter links on the left-hand column of the Entrez search page. Figure 2 shows a PubMed search page with several facets selected. Selecting any of the facet filters intersects the current search with the corresponding filter terms. Facet filters may restrict to certain types of records or exclude undesired ones.

Figure 2.

A PubMed search results page with several facet filters selected: Free full text, Review, Publication date from 2020/01/01 to 2024/05/31. The results page reports in the line with the checkbox the fact that the search was filtered with a link (Clear all) (more...)

Controlled Vocabulary Fields and Query Mapping

The indexed MeSH (Medical Subject Headings) and Organism fields have special roles in the PubMed and the traditional biomolecular databases respectively. Both MeSH and the Organism fields are tightly controlled vocabularies that are also hierarchical classification systems for the database records in PubMed and molecular databases. Every PubMed record is assigned sets of MeSH terms that add important information about the subject matter of the original paper. Records in the small molecule databases that are component PubChem are also associated with MeSH terms for the chemical components. The PubMed help document gives more details on the importance of the MeSH system. In a similar manner nearly all the biomolecular database records are attached to the source organism and its phylogenetic classification in the NCBI Taxonomy database. The MeSH Browser and the Taxonomy Browser are useful ways of exploring these systems and their associated records. Because of the importance of these two systems, queries are automatically mapped to these vocabularies whenever possible. The search terms may be expanded and translated as well. In certain databases other fields are involved in this mapping as well. The query horse dopamine receptor D2 becomes the more complex search statements in the PubMed and Protein Entrez search systems as shown in the box immediately below.

PubMed: ("horse s"[All Fields] OR "horses"[MeSH Terms] OR "horses"[All Fields] OR "horse"[All Fields]) AND ("receptors, dopamine"[MeSH Terms] OR ("receptors"[All Fields] AND "dopamine"[All Fields]) OR "dopamine receptors"[All Fields] OR ("dopamine"[All Fields] AND "receptor"[All Fields]) OR "dopamine receptor"[All Fields]) AND "D2"[All Fields]

Protein: ("Equus caballus"[Organism] OR horse[All Fields]) AND (dopamine 
receptor D2[Protein Name] OR (dopamine[All Fields] AND receptor[All Fields]
 AND D2[All Fields]))

Using Wild Cards or Query Truncation

Entrez allows searching with single word stems where the ending of the term is replaced by an asterisk “*” to represent any character. This is often called truncation searching. For example, the search term hors* in the Protein database finds records with the terms hors, hors4, horse, horse's, horseradish, horst, and many more. Truncation is supported in fielded as well as All Fields searches and is helpful if the spelling of a word is uncertain. It can also help gather ranges of identifiers. For example, the following search statement in the Entrez Nucleotide database will find records for all human chromosomes:

NC_0000*[Accession] AND Human[Organism]

Because truncation searches use the only first 600 variations of a search term indexed for a particular field, poorly determined terms, for example cat* in PubMed, will give incomplete results.

Search Details Shows Query Interpretation

In some cases, it is useful to see how Entrez interpreted, expanded, or mapped the query as described above. In most databases, this information is provided in the Search Details in the Search details box in the right-hand column of search results. The Search details box below shows how the following search is interpreted in Protein.

Lee Y cytochrome oxidase 1 in the catfishes

The words “in” and “the” are stopwords ignored by Entrez; “Lee Y” is mapped to an author search; and the term catfishes is expanded and mapped to the Organism vocabulary. The protein name “Cytochrome oxidase 1” is searched both as a phrase and as individual tokens.

Note: In PubMed the Search details are available on the Advanced Search page in the Search History.

Using the Advanced Search Page to Construct Complex Search Statements

The Advanced Search page for each Entrez database is useful for constructing complex and highly precise queries. Figure 3 shows the Advanced Search page for Entrez protein. The page functions as an independent search interface that allows formulation of complex queries. The Search Builder in combination with Search History facilitates the construction of more precise queries.

Figure 3.

The Protein Advanced Search interface showing the Search Builder and Search History. Entries from the Search Builder and the Search History can be combined in the Search Box to construct complex queries. Clicking on the numbered entries in the Search (more...)

The pull-down list in the Search Builder shows all of the fields indexed for a particular database. The Show Index link opens an alphabetical list of terms for the selected field. When a term is entered in the Search Builder, the index will open to the closest match in the index. The Add to Search Box button puts the field-restricted queries into the Search Box. These may be run using the Search button or may be added to the Search History using the Preview button.

The Search History is maintained separately for each Entrez database and keeps track of all searches until the Web browser is closed or the history is deleted. Histories are automatically deleted after eight hours of inactivity. Entries in the Search History may be combined to create new searches that give precise results. The example in Figure 3 combines searches for frogs (#28), RefSeq proteins (#26), with a protein name search for prolactin to obtain the prolactin protein record for Xenopus tropicalis, NP_001093699.

About the Clipboard and My Collections

The Clipboard is a temporary place on the NCBI website to save records. Each Entrez database has its own independent Clipboard that is limited to 500 items. Items saved to the clipboard are lost after eight hours of inactivity. When there are items in the clipboard, a link to access the clipboard appears in the upper right of any Entrez page for that database. The Clipboard behaves in the same way as any other page view in the database with equivalent Display Settings, Send to menus, and other features of that database. Records can be removed from the Clipboard through the link next to each item or by selecting the items using the check box and clicking the Remove Selected Items link at the top of the page. This link also functions to clear the Clipboard when no records are selected.

My Collections that is a part of the My NCBI service is a more permanent place to save records.

Access to Related Data

The Discovery Column

Easy access to related data is available on the individual records through the Links menu, the list of hypertext links available in the All links from this record section in the right-hand column of the full-record display. This right-hand column known as the Discovery Column contains additional access to related data and, in some cases, analysis tools. Many components in the Discovery column function as advertisements for related data providing more details about what information is available. The Discovery Column also functions in the search results providing additional options for searching and navigating including alternative search strategies as well as the Search details and Recent activity components described in the Entrez Searching section of this document. The Discovery Column on search results and other multiple record displays also provides access to related data through the Find related data component shown immediately below set for PubMed to Protein RefSeq. This follows the corresponding link for all records in the display when the Find items button is clicked.

In some databases, certain links to related data are also available from the individual summaries in search results, for example Identical Proteins in the Protein databases. Optionally, a preferences setting in My NCBI allows all links to be displayed in the summaries.

Recent Activity

An additional component that appears at the bottom of the Discovery Column is the Recent Activity list. While the Search History described previously in this document as part of the Advanced Search page, can be used to navigate to previous search results in the same database, it does not allow cross-database access. The Recent Activity component, present on many Entrez searches and record views, provides navigation to searches and record views in other databases. Only links to the last five searches and record views are listed by default, but activity for the past six months is available through a My NCBI account, where these searches can be saved and records can be added to collections.

Database Homepages, Advanced Search, Limits

The base URL alone retrieves the homepage for the resource. The Advanced Search and Limits pages may also be addressed directly.

Linking Directly to Records Using an Identifier

The base URL for the database followed by a valid unique identifier for the database retrieves the record in the default single record view format. The summary format is displayed by default for more than one record. Most valid unique identifiers are purely numeric such as PubMed IDs, gene ids, and gi numbers for sequences. For the sequence databases accession numbers or accession.version numbers may also be used to address specific records. The report and format display options may be specified following the identifiers. The options available for report vary depending on the database and are listed on the Display settings menu for record views in that database. The NCBI Help Manual sections on individual Entrez databases have more information on available report formats. The format option may be used to retrieve text rather than the default HTML format.

Linking to Search Results

Links to search results in Entrez databases may be created by adding a term to the URL. Report options and the maximum number of records to display per page may also be specified.