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The NCBI Handbook
1st
McEntyre
Jo
Ostell
Jim
National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, MD 20892-6510
2002-2009
Copyright and disclaimer
bioinformatics
Table of Contents
Book Information
Part 1 The Databases
Chapter 1 GenBank: The Nucleotide Sequence Database
Ilene Mizrachi
Created: October 9, 2002
Last Update: August 22, 2007
History
International Collaboration
Confidentiality of Data
Direct Submissions
Bulk Submissions: High-Throughput Genomic Sequence (HTGS)
Whole Genome Shotgun Sequences (WGS)
Bulk Submissions: EST, STS, and GSS
Bulk Submissions: HTC and FLIC
Submission Tools
Sequence Data Flow and Processing: From Laboratory to GenBank
Microbial Genomes
Third Party Annotation (TPA) Sequence Database
Appendix: GenBank, RefSeq, TPA and UniProt: What’s in a Name?
References
Chapter 2 PubMed: The Bibliographic Database
Kathi Canese, Jennifer Jentsch, and Carol Myers
Created: October 9, 2002
Last Update: August 13, 2003
Data Sources
Electronic Data Submission
Database Management and Hardware
Indexing
How PubMed Queries Are Processed
Using PubMed
Additional PubMed Features
Results
Links from PubMed
How to Create Hyperlinks to PubMed
Customer Support
Chapter 3 Macromolecular Structure Databases
Eric Sayers and Steve Bryant
Created: October 9, 2002
Last Update: August 13, 2003
Overview
Content of the Molecular Modeling Database (MMDB)
Content of the Conserved Domain Database (CDD)
Finding and Viewing Structures
Finding and Viewing Structure Neighbors
Finding and Viewing Conserved Domains
Finding and Viewing Proteins with Similar Domain Architectures
Links Between Structure and Other Resources
Saving Output from Database Searches
FTP
Frequently Asked Questions
References
Chapter 4 The Taxonomy Project
Scott Federhen
Created: October 9, 2002
Last Update: August 13, 2003
Introduction
Adding to the Taxonomy Database
Using the Taxonomy Browser
The Taxonomy Database: TAXON
Nomenclature Issues
Taxonomy in Entrez: A Quick Tour
The Common Tree Viewer
Indexing Taxonomy in Entrez
The Taxonomy Statistics Page
Other Relevant References
NCBI Taxonomists
Contact Us
Appendix 1. TAXON nametypes
Appendix 2. Functional classes of TAXON scientific names
Appendix 3. Other TAXON data types
Chapter 5 The Single Nucleotide Polymorphism Database (dbSNP) of Nucleotide Sequence Variation
Adrienne Kitts and Stephen Sherry
Created: October 9, 2002
Last Update: November 12, 2009
Introduction
Searching dbSNP
Submitted Content
Computed Content (The dbSNP Build Cycle)
dbSNP Resource Integration
How to Create a Local Copy of dbSNP
Appendix 1. dbSNP report formats.
Appendix 2. Rules and methodology for mapping
Appendix 3 Alignment profiling function
Appendix 4. 3D structure neighbor analysis.
Chapter 6 The Gene Expression Omnibus (GEO): A Gene Expression and Hybridization Repository
Ron Edgar and Alex Lash
Created: October 9, 2002
Last Update: August 13, 2003
Site Description
Design and Implementation
Retrieving Data
Depositing Data
Search and Integration
Example of Retrieving Data
Future Directions
Frequently Asked Questions
Acknowledgments
Contributors
References
Chapter 7 Online Mendelian Inheritance in Man (OMIM): A Directory of Human Genes and Genetic Disorders
Donna Maglott, Joanna S. Amberger, and Ada Hamosh
Created: October 9, 2002
Content and Access
Guide to OMIM Pages
FTP
Legal Statement
References
Chapter 8 The NCBI BookShelf: Searchable Biomedical Books
Bart Trawick, Jeff Beck, and Jo McEntyre
Created: October 9, 2002
Last Update: August 13, 2003
Content Acquisition
How to Use the Books
Technology
The BookShelf Data Flow
NCBI Book DTD
Frequently Asked Questions
Chapter 9 PubMed Central (PMC): An Archive for Literature from Life Sciences Journals
Jeff Beck and Ed Sequeira
Created: October 9, 2002
Last Update: August 13, 2003
A PubMed Central (PMC) Site Guide
Participation in PMC
Links to Other NCBI Resources
PMC Architecture
Data Flow: 1. SGML/XML Processing
Data Flow: 2. Loading the Database
Special Characters
PMC DTD
Frequently Asked Questions
Chapter 10 The SKY/CGH Database for Spectral Karyotyping and Comparative Genomic Hybridization Data
Turid Knutsen, Vasuki Gobu, Rodger Knaus, Thomas Ried, and Karl Sirotkin
Created: October 9, 2002
Last Update: August 13, 2003
Database Content
Data Analysis: Query Tools
Data Integration
Contributors
References
Chapter 11 The Major Histocompatibility Complex Database, dbMHC
Adrienne Kitts, Michael Feolo, and Wolfgang Helmberg
Created: May 27, 2003
Last Update: August 13, 2003
Introduction
dbMHC Resources
Database Content
Integration with Other Resources
References
Part 2 Data Flow and Processing
Chapter 12 Sequin: A Sequence Submission and Editing Tool
Jonathan Kans
Created: October 9, 2002
Last Update: August 13, 2003
Sequin: A Brief Overview
Sequence Submission
Packaging the Submissions
Viewing and Editing the Sequences
Computational Functions of Sequin
Advanced Topics
Conclusion
Chapter 13 The Processing of Biological Sequence Data at NCBI
Karl Sirotkin, Tatiana Tatusova, Eugene Yaschenko, and Mark Cavanaugh
Created: October 9, 2002
Last Update: March 14, 2006
Overview
Data Flow Components
Data Flow Architecture
Chapter 14 Genome Assembly and Annotation Process
Paul Kitts
Created: October 9, 2002
Last Update: August 13, 2003
Overview of the Genome Assembly and Annotation Process
The Input Data
Preparation of the Input Sequences
Alignment of Sequences to the Input Genomic Sequences
Genome Assembly
Annotation of Genes
Annotation of Other Features
Product Data Sets
Production of Maps That Display Genome Features
Public Release of Assembly and Models
Integration with Other Resources
Contributors
References
Part 3 Querying and Linking the Data
Chapter 15 The Entrez Search and Retrieval System
Jim Ostell
Created: October 9, 2002
Last Update: August 13, 2003
Entrez Design Principles
Entrez Is a Discovery System
Entrez Is Growing
How Entrez Works
References
Chapter 16 The BLAST Sequence Analysis Tool
Tom Madden
Created: October 9, 2002
Last Update: August 13, 2003
Introduction
How BLAST Works: The Basics
BLAST Scores and Statistics
BLAST Output: 1. The Traditional Report
BLAST Output: 2. The Hit Table
BLAST Output: 3. Structured Output
BLAST Code
Appendix 1. FASTA identifiers
Appendix 2. Readdb API
Appendix 3. Excerpt from a demonstration program doblast.c
Appendix 4. A function to print a view of a SeqAlign: MySeqAlignPrint
References
Chapter 17 LinkOut: Linking to External Resources from Entrez Databases
Kathy Kwan
Created: October 9, 2002
Last Update: August 13, 2003
How Is LinkOut Represented in Entrez?
How Does LinkOut Work?
Guides for LinkOut Providers
Communicating with LinkOut Providers
Chapter 18 The Reference Sequence (RefSeq) Project
Kim Pruitt, Tatiana Tatusova, and Donna Maglott
Created: October 9, 2002
Last Update: January 3, 2007
Introduction
Database Content: Background
Assembling and Maintaining the RefSeq Collection
Access and Retrieval
Related Reading
Chapter 19 Entrez Gene: A Directory of Genes
Donna Maglott, Kim Pruitt, and Tatiana Tatusova
Created: March 3, 2005
Overview
Maintaining the Data
How to Query Entrez Gene
Display Formats
Content
References
Chapter 20 Using the Map Viewer to Explore Genomes
Susan M. Dombrowski and Donna Maglott
Created: October 9, 2002
Last Update: August 13, 2003
Introduction
Maintenance of Data
Methods of Access
Interpreting the Display
Customizing the Display
Associated Tools
Technical Details
Caveats for Using Evolving Data
References
Chapter 21 UniGene: A Unified View of the Transcriptome
Joan U. Pontius, Lukas Wagner, and Gregory D. Schuler
Created: October 9, 2002
Last Update: August 13, 2003
Expressed Sequence Tags (ESTs)
Sequence Clusters
UniGene Cluster Browser
Protein Similarity Analysis
Digital Differential Display (DDD)
HomoloGene
References
Chapter 22 The Clusters of Orthologous Groups (COGs) Database: Phylogenetic Classification of Proteins from Complete Genomes
Eugene V. Koonin
Created: October 9, 2002
Last Update: August 13, 2003
Introduction
Construction of the COGs
Phyletic Pattern Analysis in COGs
Description of the COGs Website
Future Directions
The COG Team
References
Part 4 User Support
Chapter 23 User Services: Helping You Find Your Way
David Wheeler and Barbara Rapp
Created: October 9, 2002
Last Update: August 13, 2003
The User Services Team
Development of User Support Materials
Outreach
Conclusion
References
Chapter 24 Exercises: Using Map Viewer
David Wheeler, Kim Pruitt, Donna Maglott, Susan Dombrowski, and Andrei Gabrelian
Created: November 4, 2002
Last Update: August 13, 2003
1. How Do I Obtain the Genomic Sequence around My Gene of Interest?
2. If I Have Physical and/or Genetic Mapping Data, How Do I Use the Map Viewer to Find a Candidate Disease Gene in That Region?
3. How Can I Find and Display a Gene with the Map Viewer?
4. How Can I Analyze a Gene Using the Map Viewer?
5. How Can I Create My Own Transcript Models with the Map Viewer?
6. Using the Mouse Map Viewer
7. How Can I Find Members of a Gene Family Using the Map Viewer?
8. How Can I Find Genes Encoding a Protein Domain Using the Map Viewer?
Glossary
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