Introduction to the
NCBI Data Bases and ENTREZ
e-mail
us questions, comments or suggestions!
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REVIEW:
Boolean Logic
The National
Center for Biotechnology Information (NCBI)
What
is a Data Base?
The NCBI
Data Bases
ENTREZ and a few
of the most commonly used NCBI Databases
Data Mining:
Sickle Cell anemia
POSTER PROJECT
![](ncbi_logo.gif) |
The National Center for Biotechnology Information (NCBI) was established
in 1988 under the National Library of Medicine (NLM), which is a subdivision
of the National Institutes of Health (NIH). It is a national resource for
molecular biology information, NCBI creates public databases, conducts
research in computational biology, develops software tools for analyzing
genomic, proteomic and transcriptomic data, and disseminates biomedical
information - all for the better understanding of molecular processes affecting
human health and disease. See About
NCBI.
Click on the image to see what the NCBI Home Page looks like or go
directly to it. |
The NCBI offers many data bases and
tools. Some of them are indicated below.
ALPHABETICAL
LIST |
BankIt |
GenBank sample record |
Plant Genomes |
BLAST |
GeneMap'99 |
Proteins Sequences |
Books |
Genes and Disease |
PROW |
CCAP |
Genomes and Maps |
PubMed |
CDD |
GEO |
PubMed Central |
CGAP |
HTGs |
RefSeq |
Clone Registry |
HomoloGene |
Research at NCBI |
Cn3D |
Human Genome Resources |
Retroviruses |
Coffee Break |
Human Genome Sequencing |
SAGEmap |
COGs |
Human-Mouse Homology Maps |
Seminars |
|
LocusLink |
Sequin |
DART |
Malaria |
Site
Search |
dbEST |
Map Viewer |
SKY/CGH |
dbGSS |
MGC |
Structures |
dbSNP |
Microbial Genomes |
Taxonomy |
dbSTS |
MMDB |
Trace Archive |
Education |
Mutation Databases |
UniGene |
E-mail servers |
NCBI
Home |
UniSTS |
E-PCR |
NCBI News |
VAST |
ENTREZ |
Nucleotide Sequences |
VecScreen |
FTP |
OMIM |
What's New |
GenBank |
ORF Finder |
|
Tools and data bases have
been color coded as follows: white = general; cerulean = protein
resources; red = genome and map resources; pink = nucleotide
resources; lime = biochemical and phenotype resources.
The search and retrieval system used
for the NCBI data bases is known as ENTREZ.
This software not only searches all the databases, but links the data bases
together. There are at least two great advantages to ENTREZ:
-
It provides a single search engine, with
the same features and controls for searching all data bases.
-
The "hits" from a search of any data base
can be linked directly to the same, or related, records, in other relevant
data bases.
Click
on the image
to see
full-size! |
The graphic to the left shows a highly
simplified representation of the various databases, and how they are searched
and linked together by ENTREZ. The Data Bases covered in the following
tutorials are indicated with arrows. Click on
the thumbnail to see it full-size.
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A Data Mining Strategy
for Information on Human Genetic Disease:
Poster Project:
The final project for this module is a Poster and presentation
to the rest of the class. This will be worth 1/3 of your
grade for this module.
The topic is any human genetic disease or condition of your choice.
A list of suggested phenotypes
is provided. Since knowledge of human biology is still fragmentary and
incomplete however, you should check with the Instructor before choosing
a topic which is not on this list.
Each poster should incorporate a discussion of the following aspect
of the phenotype:
-
Clinical Features / Genotype / Phenotype.
-
Molecular Genetics / Gene Function.
-
Protein Function / Biochemistry / Allelic Variants.
-
An explanation*+of
the structure and function of the relevant protein.
-
A 3-D visualization of the protein which explains its structure and function.
-
An description of the changes in primary, secondary and tertiary structure
of the protein which result in aberrant function.
-
An explanation of how and why
the structure of the variant changes the function of the protein.
-
An explanation of how and why
the defective function of the variant results in the aberrant phenotype.
-
A bibliography of resources you have used.
*
NOTE: An explanation is
not simply a statement of what!
An explanation discusses how and why!
+
NOTE: An explanation is
not simply a paraphrase or a quote
from a reference! It reflects your own understanding!
GRADING CRITERIA: The Poster will
be graded by your Instructor using the following
criteria. Alternatively, your Instructor may choose different criteria
of her/his own.
Go to the top of the page.
RETURN to INDEX
for Entrez
RETURN to the SITE
MAP
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