Database Resources
The National Center for Biotechnology
Information (NCBI)
a primary resource for molecular biology
information
www.ncbi.nih.gov
NCBI Mission
…. to develop new information technologies to aid in the
understanding of fundamental molecular and genetic processes
that control health and disease.
What does this involve ?
• creating automated systems for storing and analyzing
knowledge about molecular biology, biochemistry, and genetics;
• facilitating the use of such databases and software by the
research and medical community;
• coordinating efforts to gather biotechnology information both
nationally and internationally;
• performing research into advanced methods of computer-based
information processing for analyzing the structure and
function of biologically important molecules.
What is a Database ?
• A model or representation of some aspect of the real
world
• An organized collection of data. May contain many
different types of data
• Coherent, consistent and designed for a specific
purpose
• A computational system for managing and querying
the data.
What is a Database ?
• A collection of information organized in such a way that a
computer program can quickly select desired pieces of data.
• An electronic filing system
• Traditional databases are organized by fields, records, and
files.
• A field is a single piece of information;
• a record is one complete set of fields
• a file is a collection of records. For example, a telephone
book is analogous to a file. It contains a list of records,
each of which consists of three fields: name, address, and
telephone number.
What is a Database ?
• To access information from a database, you need a database
management system (DBMS). This is a collection of programs
that enables you to enter, organize, and select data in a
database.
• Most molecular biology databases primarily use relational
database management systems (RDBMS).
Relational Database
• A relational database is like a large spreadsheet. Each field is
a column, each row is an entry. Relational databases use a set
of tables to organize data.
• Each entry must be unambiguously identified
• Names are not reliable e.g. incorrectly assigned gene
function
• Unique IDs (UID)s are used, e.g. in GenBank these are
called accession numbers
UID
Name
Sequence
Quality Value
BU039022
PP_LEa0001A01f
CATACAAAT …
35
BU039057
PP_LEa0001B17f
TACGGCTAC …
28
Relational Database
• Achieving consistency
• Repeated information is stored in a single
place.
• Only one copy needs to be updated
Sequence
UID
Definition
Locus
Accession
Taxonomy ID*
Sequence
Taxonomy
Taxonomy ID*
Genus
Species
Ref Index*
UID
Medline ID
* May be referred
Ref Index
Medline ID
Authors
Title
Journal
* May be referred to indirectly via an index
to by a secondary ID
Relational Database
• Language used is SQL or structured query language
• Easy to understand (essentially English?)
• Relatively consistent across RBDMS
• Supplies a set of commands to define tables, insert data
and make queries
• Queries
• SELECT some fields FROM some table WHERE some
condition is met
• E.g. select accession, sequence FROM sequence
WHERE Accession = BU039022
BU039022 CATACAAATACTGCTACHTAAATC ….
• More complex queries require two or more tables be
joined to produce a result
Relational Database
• Most RDBMS do not allow users to directly query
the database by SQL.
• An ill formed query can overload or crash the
system
• SQL still too complex for biologists?
• Provide a search interface for the user instead
• E.g. user enters a phrase and the database
identifies what part of the database should
be searched.
• The queries that make it through the web interface
have to be translated to SQL
Relational database : Example GenBank Query
What Constitutes a Good Database ?
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Broad coverage of the chosen topic
Up to date information gathering
Curated
Support staff
Commitment to the future
Good query interface
Issues for Molecular Biological Databases ?
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Annotation
Archives
Updates
Redundancy
Issues for Molecular Biological Databases ?
• Annotation
• Adding biological information to genome sequence.
Textual descriptive information
• Correctness
• Many genes are incorrectly annotated. May assign a
function to a novel gene from a similar sequence that
may itself be incorrectly annotated so the error is
propagated throughout the database.
• Routine error
• Quality
• Expert or non expert curation? Who provided the
curation?
• Is there any biological verification?
• What vocabulary is used
• Has their been any peer review ?
Issues for Molecular Biological Databases ?
• Archival Quality
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Is the database archival or curated
Can the same data be recovered later
• Don’t overwrite primary key (each accession numbers)
• The best databases note any changes to the data.
• Updates
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How often is the database updated?
Major databases take direct submissions
• Only the direct submitter can make changes, even if you
can prove its wrong.
When is a sequence finished ?
How is annotation updated as more knowledge is available
• Redundancy
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This is a major issue, how do we deal with it without losing
potentially valuable information.
Also relates to archival quality
NCBI and GenBank
• Genbank is the genetic sequence database of all
publicly available DNA and derived protein
sequences, with annotations describing the
biological information in them.
• GenBank is hosted within NCBI
• Researchers submit their sequences to GenBank
• NCBI provides analysis and retrieval resources for
the data in GenBank (and many other NCBI hosted
databases).
NCBI Databases (http://www.ncbi.nlm.nih.gov/guide/all/#Databases_)
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Nucleotide Database
EST (dbEST)
GSS (dbGSS)
Protein Database
Structure Database
Genome
3D Domains
Conserved Domains
UniSTS
Gene
UniGene
HomoloGene
Reference Sequence
(refseq)
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SNP (dbSNP)
dbVAR – large scale genomic variation
dbGAP – integration of genotype & phenotype
PopSet Database
Taxonomy Database
GEO Profiles
GEO Datasets
Cancer Chromosomes
Epigenomics
PubMed Central
Journals
MeSH
Bookshelf
OMIM Database
Retrieving Data from NCBI using Entrez
• Entrez is a text based retrieval system that integrates all the
information resources available at the NCBI such as;
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Scientific literature
DNA and protein sequence databases
3D protein structure and protein domain data
Population study datasets
Expression data
Assemblies of complete genomes
Taxonomic information
http://www.ncbi.nlm.nih.gov/guide/all/#howto_
Create/login to the myNCBI portal
Understanding GenBank records
Go to http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#ModificationsDateB
Click on the links on the left to get a
description of what the term means,
Copy the description into a word
document and after completed,
save the document on your drupal
web site
Entrez Sequences Help
http://www.ncbi.nlm.nih.gov/books/NBK44864/