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Lecture 4-Entrez-Biological Information Repository.

Entrez is a federated search engine by NCBI that allows users to search multiple health science databases simultaneously with a single query. It provides features such as refined search results, temporary saving of results, and a My NCBI account for saving queries. NCBI hosts various databases including PubMed, GenBank, and others, offering extensive resources for biomedical research.

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9 views10 pages

Lecture 4-Entrez-Biological Information Repository.

Entrez is a federated search engine by NCBI that allows users to search multiple health science databases simultaneously with a single query. It provides features such as refined search results, temporary saving of results, and a My NCBI account for saving queries. NCBI hosts various databases including PubMed, GenBank, and others, offering extensive resources for biomedical research.

Uploaded by

Its Zainu
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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Entrez (NCBI)-Biological

Information Repository

Ishtiaq Ahmad
What is Entrez?
• A French word meaning ‘To come in’ or
‘To enter’.
• A federated search Engine, which
simultaneously searches multiple online
databases of health sciences at NCBI
website with a single query string and user
interface.
• NCBI is a component of NLM, a
department of NIH by US government.
Entrez (NCBI)-Features
• The Entrez front page provides access to
all databases indexed by it through a
single query search.
• The out put of the search results in a list of
all relevant entries in unified format.
• The search results can be refined through
specific search queries.
• Additionally, the search for a specific data
can also be performed.
Entrez (NCBI)-Features Contd.
• The search results can be temporarily
saved to clip board.
• History of the recent search can be viewed
by a numbered list
• My NCBI account feature provides us with
the feature of saving as many queries as
possible.
NCBI
• NCBI is a part of NLM containing in house
genome data in GenBank.

• Also contain an index of biomedical


research articles as PubMed Central and
PubMed.
NCBI-Features
In addition to GenBank, NCBI provides
• Online Mendelian Inheritance in Man
• The Molecular Modeling Database (3D protein
structures),
• dbSNP a database of Single Nucleotide
Polymorphisms,
• A Gene Map of the Human genome.
• A Taxonomy Browser
And coordinates with the National Cancer
Institute to provide the Cancer Genome
Anatomy Project. The NCBI assigns a unique
identifier (Taxonomy ID number) to each
species of organism
Databases Searched by Entrez
(NCBI)
• PubMed: biomedical literature citations and
abstracts, including Medline - articles from
(mainly medical) journals, often including
abstracts. Links to PubMed Central and other
full-text resources are provided to articles from
the 1990s.
• PubMed Central: free, full text journal articles
• Books: online books
• OMIM: online Mendelian Inheritance in Man
• OMIA: online Mendelian Inheritance in Animals
Databases Searched by Entrez
(NCBI)
• Nucleotide: sequence database (GenBank)
• Protein: sequence database
• Genome: whole genome sequences and
Mapping
• Structure: three-dimensional macromolecular
structures
• Taxonomy: organisms in GenBank Taxonomy
• SNP: single nucleotide polymorphism
• Gene: gene-centered information
• HomoloGene: eukaryotic homology groups
Databases Searched by Entrez
(NCBI)
• PubChem Compound: unique small molecule
chemical structures
• PubChem Substance: deposited chemical
substance records
• Genome Project: genome project information
• UniGene: gene-oriented clusters of transcript
sequences
• CDD: conserved protein domain database
• 3D Domains: domains from Entrez Structure
Databases Searched by Entrez
(NCBI)
• UniSTS: markers and mapping data
• PopSet: population study data sets (epidemiology)
• GEO Profiles: expression and molecular abundance
profiles
• GEO DataSets: experimental sets of GEO 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

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