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This page is a continuation
of discussing NCBI databases. Previous page is here
The Entrez retrieval system
Please, open ENTREZ PubMed homepage in a new window by clicking
here. The black navigation bar lists all Entrez data bases
available at NCBI. Currently, you can do an Entrez (word)
search against the following databases:
- PubMed for scientific literature
- Nucleotide (GenBank) for nucleotide sequences
- Protein for amino acid sequences
- Genomes for organisms or organelles sequenced completely.
That means for example, that complete mitochondrial sequences
will also be retreived.
- Structure for information on 3D structure of proteins.
- PopSet for information on genetic similarity among populations
or higher taxa
- Taxonomy for information on species or higher taxa
- OMIM (Online Mendalian Inheritance in Man) for genes or
suspected genes affecting characters in humans
The data bases are interconnected. Connections among sets
of data are shown in the figure (downloaded from NCBI tutorial).
Even though search should be limited to one of such databases,
the information retreived will contain links to related items
within and among databases.
Entrez integrates
- the scientific literature,
- DNA and protein sequence databases,
- 3-D protein structure data,
- population study data sets,
- taxonomic information
- assemblies of complete genomes
- and more
into a tightly coupled system. Thus when you retreive a specific
sequence in GenBank, you also get links to protein sequence,
taxonomy of the organism, scientific articles, function, and
much more. Similarly, when you hit a scientific paper in PubMed,
nucleotid or protein sequences used in that research will
be linked to the abstract.
Search with words: Entrez is a retreival system which
can be used to match "words". You type in words
like
- English or scientific name of any taxa (species, family,
order, etc.)
- gene or protein name
- GenBank accession number
- PubMed accession number
- molecular weight
- or other
and Entrez retreives you information on your querry in any
database you select. You may enter one or more terms (e.g.,
bird, evolution) in the query box and they will be automatically
combined together. Words can be combined by Boolean operators
AND, OR, NOT, which must be in upper case.
In each data base there are further options for narrowing
or focusing your search. We will review them briefly. If you
need more, you may want to go through one of the tutorials
available at NCBI later
Next: we'll do some searches in some of the database
at NCBI. Please, follow the link of your interest (Links #1,
#2 and #7 are important for the course.) Some of the links
will lead you to NCBI help pages.
- PubMed for scientific literature
- Nucleotide (GenBank) for nucleotide sequences
- Protein for amino acid sequences
- Genomes for organisms or organelles sequenced completely.
That means for example, that complete mitochondrial sequences
will also be retreived.
- Structure for information on 3D structure of proteins.
- PopSet for information on genetic similarity among populations
or higher taxa
- Taxonomy for information on species or higher taxa
- OMIM (Online Mendalian Inheritance in Man) for genes or
suspected genes affecting characters in humans
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