NCBI and Entrez Database Searching

Vocabulary flashcards covering NCBI resources, Entrez database retrieval systems, PubMed, MEDLINE, search query construction, and My NCBI tools.

Entrez

The primary molecular biology and literature search and retrieval system hosted by the NCBI that provides integrated access across multiple biomedical databases.

National Center for Biotechnology Information (NCBI)

A center within the National Library of Medicine (NLM) at the NIH that advances science and health by providing access to biomedical and genomic information and analysis tools.

Assembly Database

An NCBI database that provides detailed information on the structure of assembled genomes, assembly names, metadata, statistical reports, and direct links to genomic sequence data.

BioProject

An NCBI collection (formerly named Genome Project) describing the scope, material, and objectives of genomics, functional genomics, and genetics studies, providing unified access to their resulting datasets.

Database of Genomic Structural Variation (dbVar)

An NCBI repository designed to archive large-scale genomic variation—such as large insertions, deletions, translocations, and inversions—as well as associations between defined variants and phenotypes.

Genome Database (NCBI)

An NCBI database containing sequence and map data from the whole genomes of completely sequenced and ongoing organisms across bacteria, archaea, eukaryota, viruses, phages, viroids, plasmids, and organelles.

Genome Data Viewer (GDV)

An interactive NCBI genome visualization tool providing an ideogram/karyotype view to explore genome assemblies, gene models, transcript annotations, dbSNP variations, and RNA-seq coverage tracks.

PubMed

A free biomedical literature database containing more than $40\text{ million}$ citations and abstracts from MEDLINE, life science journals, and online books.

MEDLINE

The premier bibliographic database of the U.S. National Library of Medicine (NLM) containing citations and abstracts for biomedical and life sciences journals worldwide.

PubMed Identifier (PMID)

A unique numerical identifier assigned to each individual article or citation record indexed in PubMed.

Boolean Operators (Entrez)

The logical operators AND, OR, and NOT used in Entrez searches, which must be capitalized and can be grouped using parentheses/brackets to specify order of operations.

[auth] / [AU]

The search field qualifier in Entrez used in brackets after a term to restrict the search specifically to an author's name.

[jour] / [TA]

The search field qualifier in Entrez used to restrict a query term specifically to the journal title or journal abbreviation.

Range Operator ($:$)

An Entrez search syntax operator placed between two values (e.g., $x : y\,[SLEN]$) to search a bounded range for sequence lengths, publication dates, molecular weights, or accession numbers.

[SLEN]

The Entrez search field qualifier used to filter sequence results according to sequence length.

Medical Subject Headings (MeSH)

The controlled vocabulary thesaurus used by NLM to index articles in MEDLINE/PubMed, which PubMed uses to generate related article recommendations.

LinkOut

An NCBI service that directs users from database records to external sources, including full-text articles on publishers' websites and specialized biological databases (e.g., FlyBase).

My NCBI

A personalized tool that retains user preferences, saves searches, automates email updates, organizes bibliographies for NIH public access compliance, and stores search activity for $6\text{ months}$.

SciENcv

The Science Experts Network Curriculum Vitae tool in My NCBI used by researchers to create, maintain, and export formatted biosketches (such as the NIH BioSketch) for grant applications.

PUBmed Entrez search fields (picture)