Lecture 4 - Biological sequence database: National Center for Biotechnology Information (PART 1) | Bioinformatics - Botany PDF Download

 Page 1


Biological sequence database: NCBI 
 0 
 
 
 
 
 
 
 
 
 
 
Subject : Bioinformatics 
Lesson : Biological sequence database: National Center for Biotechnology 
Information (NCBI ) 
Lesson Developer : Sandip Das 
College/ Department: Department of Botany, University of Delhi 
 
 
 
 
 
 
 
 
 
 
Page 2


Biological sequence database: NCBI 
 0 
 
 
 
 
 
 
 
 
 
 
Subject : Bioinformatics 
Lesson : Biological sequence database: National Center for Biotechnology 
Information (NCBI ) 
Lesson Developer : Sandip Das 
College/ Department: Department of Botany, University of Delhi 
 
 
 
 
 
 
 
 
 
 
Biological sequence database: NCBI 
 1 
Table of Contents 
Chapter: Biological sequence database: National Center for 
Biotechnology Information (NCBI)  
? Introduction  
? Databases at NCBI 
? Literature 
? Bookshelf 
? Pubmed 
? Nucleic Acid 
? dbEST 
? dbGSS 
? dbGSS 
? Popset 
? dbGaP 
? dbVar 
o Genome 
o Taxonomy 
o PubChem 
o Expression analysis 
o Protein 
 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
National Center for Biotechnology Information (NCBI) 
NCBI has emerged as the primary free-to-access source of data and analysis tools in the 
field of computational biology.  The free-access nature of NCBI is possible as the policy of 
funding and publication in most countries dictates that the researcher mandatorily deposits 
the information generated using public-fund into a free-to-access central repository. In 
return, the repository (such as NCBI or EMBL) assigns a unique identification number, often 
termed as accession number, to the data that also can be used to identify the depositor and 
Page 3


Biological sequence database: NCBI 
 0 
 
 
 
 
 
 
 
 
 
 
Subject : Bioinformatics 
Lesson : Biological sequence database: National Center for Biotechnology 
Information (NCBI ) 
Lesson Developer : Sandip Das 
College/ Department: Department of Botany, University of Delhi 
 
 
 
 
 
 
 
 
 
 
Biological sequence database: NCBI 
 1 
Table of Contents 
Chapter: Biological sequence database: National Center for 
Biotechnology Information (NCBI)  
? Introduction  
? Databases at NCBI 
? Literature 
? Bookshelf 
? Pubmed 
? Nucleic Acid 
? dbEST 
? dbGSS 
? dbGSS 
? Popset 
? dbGaP 
? dbVar 
o Genome 
o Taxonomy 
o PubChem 
o Expression analysis 
o Protein 
 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
National Center for Biotechnology Information (NCBI) 
NCBI has emerged as the primary free-to-access source of data and analysis tools in the 
field of computational biology.  The free-access nature of NCBI is possible as the policy of 
funding and publication in most countries dictates that the researcher mandatorily deposits 
the information generated using public-fund into a free-to-access central repository. In 
return, the repository (such as NCBI or EMBL) assigns a unique identification number, often 
termed as accession number, to the data that also can be used to identify the depositor and 
Biological sequence database: NCBI 
 2 
several other features.  The following section will introduce you to a variety of databases 
dealing with a wide range of disciplines. Please do note that although the data may be 
organized separately for the sake of simplicity and clarity, in reality, all the databases are 
inter-linked and can be navigated from one to the other. The databases are also associated 
with their appropriate analysis tools. 
The following section lists some of the databases that have been created at NCBI. For the 
sake of simplicity, the databases in this lesson have been divided into three sections-section 
I dealing with publication, literature and small scale DNA/RNA sequencing projects; section 
II-dealing with whole genome, epigenome, maps of genomes, taxonomy and chemical 
structures; and section III dealing with resources for RNA and protein that are required for 
“functional genomics” . These sections marked as I, II and III will be dealt in their 
respective chapters. 
 
 
Databases-I: 
Literature (PubMed, PubMed Central; NCBI Bookshelf): 
 DNA and RNA (Refseq, nucleotide, EST, GSS, WGS, PopSet, trace archive, SRA): 
Databases-II: 
Genomes (Map Viewer, Genome workbench, Plant Genome Central, Genome 
Reference Consortium, Epigenomics, Genomics Structural variation): 
Maps: 
Taxonomy: 
PubChem Substance:  
Databases-III: 
Expression analysis-GEO 
Proteins (Reference sequences, GenPept, UniProt/SwissProt, PRF, PDB, Protein 
clusters, Structure, UniGene, CDD): 
 
Entrez is the single point database search and retrieval system that allows a user to 
perform the search and retrieve action against “all” or a “specific” database in an 
interlinked manner. 
 
Page 4


Biological sequence database: NCBI 
 0 
 
 
 
 
 
 
 
 
 
 
Subject : Bioinformatics 
Lesson : Biological sequence database: National Center for Biotechnology 
Information (NCBI ) 
Lesson Developer : Sandip Das 
College/ Department: Department of Botany, University of Delhi 
 
 
 
 
 
 
 
 
 
 
Biological sequence database: NCBI 
 1 
Table of Contents 
Chapter: Biological sequence database: National Center for 
Biotechnology Information (NCBI)  
? Introduction  
? Databases at NCBI 
? Literature 
? Bookshelf 
? Pubmed 
? Nucleic Acid 
? dbEST 
? dbGSS 
? dbGSS 
? Popset 
? dbGaP 
? dbVar 
o Genome 
o Taxonomy 
o PubChem 
o Expression analysis 
o Protein 
 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
National Center for Biotechnology Information (NCBI) 
NCBI has emerged as the primary free-to-access source of data and analysis tools in the 
field of computational biology.  The free-access nature of NCBI is possible as the policy of 
funding and publication in most countries dictates that the researcher mandatorily deposits 
the information generated using public-fund into a free-to-access central repository. In 
return, the repository (such as NCBI or EMBL) assigns a unique identification number, often 
termed as accession number, to the data that also can be used to identify the depositor and 
Biological sequence database: NCBI 
 2 
several other features.  The following section will introduce you to a variety of databases 
dealing with a wide range of disciplines. Please do note that although the data may be 
organized separately for the sake of simplicity and clarity, in reality, all the databases are 
inter-linked and can be navigated from one to the other. The databases are also associated 
with their appropriate analysis tools. 
The following section lists some of the databases that have been created at NCBI. For the 
sake of simplicity, the databases in this lesson have been divided into three sections-section 
I dealing with publication, literature and small scale DNA/RNA sequencing projects; section 
II-dealing with whole genome, epigenome, maps of genomes, taxonomy and chemical 
structures; and section III dealing with resources for RNA and protein that are required for 
“functional genomics” . These sections marked as I, II and III will be dealt in their 
respective chapters. 
 
 
Databases-I: 
Literature (PubMed, PubMed Central; NCBI Bookshelf): 
 DNA and RNA (Refseq, nucleotide, EST, GSS, WGS, PopSet, trace archive, SRA): 
Databases-II: 
Genomes (Map Viewer, Genome workbench, Plant Genome Central, Genome 
Reference Consortium, Epigenomics, Genomics Structural variation): 
Maps: 
Taxonomy: 
PubChem Substance:  
Databases-III: 
Expression analysis-GEO 
Proteins (Reference sequences, GenPept, UniProt/SwissProt, PRF, PDB, Protein 
clusters, Structure, UniGene, CDD): 
 
Entrez is the single point database search and retrieval system that allows a user to 
perform the search and retrieve action against “all” or a “specific” database in an 
interlinked manner. 
 
Biological sequence database: NCBI 
 3 
 
 
 
Figure : Various databases at NCBI can be accessed through the Entrez portal 
Source: http://www.ncbi.nlm.nih.gov/sites/gquery 
 
The National Center for Biotechnology Center (NCBI) site is conveniently organized into 
four major domains and these domains are interlinked :  
1. Databases,  
2. Tools,  
3. Data submission and  
4. Education  
 
The following figure depicts the interlinked nature of these domains and can be reached 
by 
1. Open the ncbi page by typing in www.ncbi.nlm.nih.gov in  the web browser 
2. Click the “search” button on the home page without enetering any keyword . 
3. On the  top left hand corner of the webpage, click on the “site map” to reach the 
page. 
Page 5


Biological sequence database: NCBI 
 0 
 
 
 
 
 
 
 
 
 
 
Subject : Bioinformatics 
Lesson : Biological sequence database: National Center for Biotechnology 
Information (NCBI ) 
Lesson Developer : Sandip Das 
College/ Department: Department of Botany, University of Delhi 
 
 
 
 
 
 
 
 
 
 
Biological sequence database: NCBI 
 1 
Table of Contents 
Chapter: Biological sequence database: National Center for 
Biotechnology Information (NCBI)  
? Introduction  
? Databases at NCBI 
? Literature 
? Bookshelf 
? Pubmed 
? Nucleic Acid 
? dbEST 
? dbGSS 
? dbGSS 
? Popset 
? dbGaP 
? dbVar 
o Genome 
o Taxonomy 
o PubChem 
o Expression analysis 
o Protein 
 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
National Center for Biotechnology Information (NCBI) 
NCBI has emerged as the primary free-to-access source of data and analysis tools in the 
field of computational biology.  The free-access nature of NCBI is possible as the policy of 
funding and publication in most countries dictates that the researcher mandatorily deposits 
the information generated using public-fund into a free-to-access central repository. In 
return, the repository (such as NCBI or EMBL) assigns a unique identification number, often 
termed as accession number, to the data that also can be used to identify the depositor and 
Biological sequence database: NCBI 
 2 
several other features.  The following section will introduce you to a variety of databases 
dealing with a wide range of disciplines. Please do note that although the data may be 
organized separately for the sake of simplicity and clarity, in reality, all the databases are 
inter-linked and can be navigated from one to the other. The databases are also associated 
with their appropriate analysis tools. 
The following section lists some of the databases that have been created at NCBI. For the 
sake of simplicity, the databases in this lesson have been divided into three sections-section 
I dealing with publication, literature and small scale DNA/RNA sequencing projects; section 
II-dealing with whole genome, epigenome, maps of genomes, taxonomy and chemical 
structures; and section III dealing with resources for RNA and protein that are required for 
“functional genomics” . These sections marked as I, II and III will be dealt in their 
respective chapters. 
 
 
Databases-I: 
Literature (PubMed, PubMed Central; NCBI Bookshelf): 
 DNA and RNA (Refseq, nucleotide, EST, GSS, WGS, PopSet, trace archive, SRA): 
Databases-II: 
Genomes (Map Viewer, Genome workbench, Plant Genome Central, Genome 
Reference Consortium, Epigenomics, Genomics Structural variation): 
Maps: 
Taxonomy: 
PubChem Substance:  
Databases-III: 
Expression analysis-GEO 
Proteins (Reference sequences, GenPept, UniProt/SwissProt, PRF, PDB, Protein 
clusters, Structure, UniGene, CDD): 
 
Entrez is the single point database search and retrieval system that allows a user to 
perform the search and retrieve action against “all” or a “specific” database in an 
interlinked manner. 
 
Biological sequence database: NCBI 
 3 
 
 
 
Figure : Various databases at NCBI can be accessed through the Entrez portal 
Source: http://www.ncbi.nlm.nih.gov/sites/gquery 
 
The National Center for Biotechnology Center (NCBI) site is conveniently organized into 
four major domains and these domains are interlinked :  
1. Databases,  
2. Tools,  
3. Data submission and  
4. Education  
 
The following figure depicts the interlinked nature of these domains and can be reached 
by 
1. Open the ncbi page by typing in www.ncbi.nlm.nih.gov in  the web browser 
2. Click the “search” button on the home page without enetering any keyword . 
3. On the  top left hand corner of the webpage, click on the “site map” to reach the 
page. 
Biological sequence database: NCBI 
 4 
 
 Figure: Various databases are organized into four major domains and are interlinked 
Source: http://www.ncbi.nlm.nih.gov/guide/sitemap/ 
 
 
Databases of NCBI 
The following section introduces you to some of the following databases at NCBI 
Databases-I: 
Literature (PubMed, PubMed Central; NCBI Bookshelf): 
 DNA and RNA (Refseq, nucleotide, EST, GSS, WGS, PopSet, trace archive, SRA): 
 
Literature:  
? Bookshelf provides free access and allows users to browse and retrieve a wealth of 
information in life sciences and healthcare. The information may be in the form of 
books documents and policy information from various government agencies and 
publishers. The bookshelf titles are organized subject-wise, by Type or by Publisher 
in a searchable or browsable format.