Lecture 6 - NCBI : Data Submission | Bioinformatics - Botany PDF Download

 Page 1


NCBI: Data Submission 
Institute of Life Long Learning 0 
 
 
 
 
 
Subject: Bioinformatics 
Lesson: NCBI: Data Submission 
Lesson Developer: Sandip Das 
College/Department: Department of Botany, University of Delhi 
 
Page 2


NCBI: Data Submission 
Institute of Life Long Learning 0 
 
 
 
 
 
Subject: Bioinformatics 
Lesson: NCBI: Data Submission 
Lesson Developer: Sandip Das 
College/Department: Department of Botany, University of Delhi 
 
NCBI: Data Submission 
Institute of Life Long Learning 1 
Table of Contents  
? Chapter : NCBI: Data Submission Introduction  
o NCBI 
? Roles and Goals of NCBI 
?  Resources at NCBI 
o Data Submission at NCBI 
?  Submission of Sequence data 
 BankIt 
Sequin 
Barcode 
Batch Submission 
Genome Sequence data 
? Submission of non-sequence data 
GEO 
dbGaP 
PubChem 
o Growth of NCBI 
? Summary 
? Exercises 
? Glossary  
? References  
 
 
 
 
 
 
 
 
 
Page 3


NCBI: Data Submission 
Institute of Life Long Learning 0 
 
 
 
 
 
Subject: Bioinformatics 
Lesson: NCBI: Data Submission 
Lesson Developer: Sandip Das 
College/Department: Department of Botany, University of Delhi 
 
NCBI: Data Submission 
Institute of Life Long Learning 1 
Table of Contents  
? Chapter : NCBI: Data Submission Introduction  
o NCBI 
? Roles and Goals of NCBI 
?  Resources at NCBI 
o Data Submission at NCBI 
?  Submission of Sequence data 
 BankIt 
Sequin 
Barcode 
Batch Submission 
Genome Sequence data 
? Submission of non-sequence data 
GEO 
dbGaP 
PubChem 
o Growth of NCBI 
? Summary 
? Exercises 
? Glossary  
? References  
 
 
 
 
 
 
 
 
 
NCBI: Data Submission 
Institute of Life Long Learning 2 
 
Introduction 
The National Center for Biotechnology Information was established in 1988 at the National 
Institute of Health (NIH) as part of the National Library of Medicine (NLM) and is located at 
Bethedsa, Maryland, USA. This association of NCBI with NIH and NLM is reflected in its web-
address (www.ncbi.nlm.nih.gov). NCBI was set up to collate information, create databases 
and conduct research in the field of molecular biology especially for biomedical data, and 
develop computational tools. Since then, the database and computational tools have 
expanded to include diverse organisms including plants so as to encompass not only data 
from biomedical field but also include agriculture, food and other plant derived resources. 
NCBI has now emerged as the primary source of free public-access data encompassing a 
wide range of disciplines ranging from literature, sequence information, expression profile 
data, protein sequence and structure, chemical structure and bioassays, taxonomy; in 
addition, NCBI has developed a variety of analysis tools that are available for free download 
and use. 
 
 
Figure: Webpage of NCBI 
Source: http://www.ncbi.nlm.nih.gov 
www.ncbi.nlm.nih.gov 
Page 4


NCBI: Data Submission 
Institute of Life Long Learning 0 
 
 
 
 
 
Subject: Bioinformatics 
Lesson: NCBI: Data Submission 
Lesson Developer: Sandip Das 
College/Department: Department of Botany, University of Delhi 
 
NCBI: Data Submission 
Institute of Life Long Learning 1 
Table of Contents  
? Chapter : NCBI: Data Submission Introduction  
o NCBI 
? Roles and Goals of NCBI 
?  Resources at NCBI 
o Data Submission at NCBI 
?  Submission of Sequence data 
 BankIt 
Sequin 
Barcode 
Batch Submission 
Genome Sequence data 
? Submission of non-sequence data 
GEO 
dbGaP 
PubChem 
o Growth of NCBI 
? Summary 
? Exercises 
? Glossary  
? References  
 
 
 
 
 
 
 
 
 
NCBI: Data Submission 
Institute of Life Long Learning 2 
 
Introduction 
The National Center for Biotechnology Information was established in 1988 at the National 
Institute of Health (NIH) as part of the National Library of Medicine (NLM) and is located at 
Bethedsa, Maryland, USA. This association of NCBI with NIH and NLM is reflected in its web-
address (www.ncbi.nlm.nih.gov). NCBI was set up to collate information, create databases 
and conduct research in the field of molecular biology especially for biomedical data, and 
develop computational tools. Since then, the database and computational tools have 
expanded to include diverse organisms including plants so as to encompass not only data 
from biomedical field but also include agriculture, food and other plant derived resources. 
NCBI has now emerged as the primary source of free public-access data encompassing a 
wide range of disciplines ranging from literature, sequence information, expression profile 
data, protein sequence and structure, chemical structure and bioassays, taxonomy; in 
addition, NCBI has developed a variety of analysis tools that are available for free download 
and use. 
 
 
Figure: Webpage of NCBI 
Source: http://www.ncbi.nlm.nih.gov 
www.ncbi.nlm.nih.gov 
NCBI: Data Submission 
Institute of Life Long Learning 3 
 
 
 
Roles and Goals of NCBI 
The diverse activities of NCBI can be broadly categorized into: 
a. research at molecular level using mathematical and computational tools on 
fundamental problems in biology 
b. formulating uniform standards for generation and deposition of computational data, 
nomenclature or annotation of biological material and information; and facilitating 
exchange of such standards 
c. developing and distributing databases and software 
d. developing and maintaining collaborations with academia, industry and other 
governmental agencies at national and international level through visitors program 
e. fostering scientific communication through sponsoring and organizing meetings, 
workshops and lectures 
f. supporting training program on basic and applied aspects of computational biology 
Resources at NCBI 
The resources at NCBI are categorized into major groups and following are some of the 
broad sets of various databases and tools developed, curated and hosted at NCBI: 
Submissions: 
 Genbank: BankIt 
 Genbank: Barcode 
 Genbank: Sequin 
 GEO Web deposit 
 NIH Manuscript submission (NIHMS) 
 SNP submission 
 PUBChem Deposition gateway 
 BioProject Submission 
Databases: 
 Literature (PubMed, PubMed Central; NCBI Bookshelf): 
 Entrez and Entrez Programming utilities: 
DNA and RNA (Refseq, nucleotide, EST, GSS, WGS, PopSet, trace archive, SRA): 
Proteins (Reference sequences, GenPept, UniProt/SwissProt, PRF, PDB, Protein 
clusters, GEO, Structure, UniGene, CDD): 
Page 5


NCBI: Data Submission 
Institute of Life Long Learning 0 
 
 
 
 
 
Subject: Bioinformatics 
Lesson: NCBI: Data Submission 
Lesson Developer: Sandip Das 
College/Department: Department of Botany, University of Delhi 
 
NCBI: Data Submission 
Institute of Life Long Learning 1 
Table of Contents  
? Chapter : NCBI: Data Submission Introduction  
o NCBI 
? Roles and Goals of NCBI 
?  Resources at NCBI 
o Data Submission at NCBI 
?  Submission of Sequence data 
 BankIt 
Sequin 
Barcode 
Batch Submission 
Genome Sequence data 
? Submission of non-sequence data 
GEO 
dbGaP 
PubChem 
o Growth of NCBI 
? Summary 
? Exercises 
? Glossary  
? References  
 
 
 
 
 
 
 
 
 
NCBI: Data Submission 
Institute of Life Long Learning 2 
 
Introduction 
The National Center for Biotechnology Information was established in 1988 at the National 
Institute of Health (NIH) as part of the National Library of Medicine (NLM) and is located at 
Bethedsa, Maryland, USA. This association of NCBI with NIH and NLM is reflected in its web-
address (www.ncbi.nlm.nih.gov). NCBI was set up to collate information, create databases 
and conduct research in the field of molecular biology especially for biomedical data, and 
develop computational tools. Since then, the database and computational tools have 
expanded to include diverse organisms including plants so as to encompass not only data 
from biomedical field but also include agriculture, food and other plant derived resources. 
NCBI has now emerged as the primary source of free public-access data encompassing a 
wide range of disciplines ranging from literature, sequence information, expression profile 
data, protein sequence and structure, chemical structure and bioassays, taxonomy; in 
addition, NCBI has developed a variety of analysis tools that are available for free download 
and use. 
 
 
Figure: Webpage of NCBI 
Source: http://www.ncbi.nlm.nih.gov 
www.ncbi.nlm.nih.gov 
NCBI: Data Submission 
Institute of Life Long Learning 3 
 
 
 
Roles and Goals of NCBI 
The diverse activities of NCBI can be broadly categorized into: 
a. research at molecular level using mathematical and computational tools on 
fundamental problems in biology 
b. formulating uniform standards for generation and deposition of computational data, 
nomenclature or annotation of biological material and information; and facilitating 
exchange of such standards 
c. developing and distributing databases and software 
d. developing and maintaining collaborations with academia, industry and other 
governmental agencies at national and international level through visitors program 
e. fostering scientific communication through sponsoring and organizing meetings, 
workshops and lectures 
f. supporting training program on basic and applied aspects of computational biology 
Resources at NCBI 
The resources at NCBI are categorized into major groups and following are some of the 
broad sets of various databases and tools developed, curated and hosted at NCBI: 
Submissions: 
 Genbank: BankIt 
 Genbank: Barcode 
 Genbank: Sequin 
 GEO Web deposit 
 NIH Manuscript submission (NIHMS) 
 SNP submission 
 PUBChem Deposition gateway 
 BioProject Submission 
Databases: 
 Literature (PubMed, PubMed Central; NCBI Bookshelf): 
 Entrez and Entrez Programming utilities: 
DNA and RNA (Refseq, nucleotide, EST, GSS, WGS, PopSet, trace archive, SRA): 
Proteins (Reference sequences, GenPept, UniProt/SwissProt, PRF, PDB, Protein 
clusters, GEO, Structure, UniGene, CDD): 
NCBI: Data Submission 
Institute of Life Long Learning 4 
Genomes (Map Viewer, Genome workbench, Plant Genome Central, Genome 
Reference Consortium, Epigenomics, Genomics Structural variation): 
Maps: 
Taxonomy: 
PubChem Substance:  
OMIM: 
Tools: 
 Data mining: 
 Sequence analysis (Vector Screen, BLAST, CDART): 
 Electronic PCR (forward and Reverse) 
 GEO-BLAST: 
 Genetic codes: 
 ORF finder: 
Splign 
3-D structure viewer (Cn3D): 
 3-D structure and similarity searching: 
 1000 Genome Browser: 
Others: 
FTP downloads sites: 
Collaborative cancer research: 
 
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. 
 
Data Submission at NCBI 
NCBI relies on submission of accurately annotated and curated data submitted by the 
research community. The data can be grouped into two major types - sequence and non-
sequence.  The diverse types and categories of data hosted at NCBI require that these are 
deposited into one of the many databases in an appropriate format with annotations. The 
following section will introduce you to the several forms of biological data and the 
submission gateways at NCBI. 
Submission of sequence data: