Introduction to the NCBI Data Bases and ENTREZ

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

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. A more complete diagram of the links between each data base. See a brief description of a few of the most commonly used databases.

A Data Mining Strategy for Information on Human Genetic Disease:
 

Click on the image  to see full-size!	Introduction. This page! An introduction to the concept of databases. The NCBI databases. The ENTREZ search and retrieval system for bioinformatics data mining.
	Bookshelf. Using Entrez to search full-text books online.
	OMIM. Using Entrez to search "Online Mendelian Inheritance in Man" the phenotypes and clinical aspect of human genetic diseases and syndromes.
	PubMed. Using Entrez to search the published literature for primary references and reviews. Building a bibliography with the clipboard.
	Gene Database. Summaries of available information on genes.
	Nucleotide Database (Genbank). Using Entrez to search for nucleotide sequences and annotations.
	Protein Database. Using Entrez to search for protein sequences and annotations.
	Structure Database. Visualization of 3D structure of macromolecules and relation to function.

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.