Name
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URL
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Short
description
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General-purpose
data resources and Model
collections
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PubMed
|
URL
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PubMed
comprises more than 26 million
citations for biomedical
literature from MEDLINE, life
science journals, and online
books. Citations may include links
to full-text content from PubMed
Central and publisher web sites.
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BioNumbers
|
URL
|
In
BioNumbers we aim to enable you to
find in one minute any useful
molecular biology number that can
be important for your research.
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PathGuide
|
URL
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Pathguide
contains information about 547
biological pathway related
resources and molecular
interaction related resources.
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BioModels
|
URL
|
BioModels
Database is a repository of
computational models of biological
processes. Models described from
literature are manually curated
and enriched with
cross-references.
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Nucleotide
Sequence Databases
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NCBI
|
URL
|
National
Center for Biotechnology
Information (NCBI) advances
science and health by providing
access to biomedical and genomic
information.
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GenBank
|
URL
|
GenBank
is the NIH genetic sequence
database, an annotated collection
of all publicly available DNA
sequences. GenBank is part of the
International Nucleotide Sequence
Database Collaboration, which
comprises the DNA DataBank of
Japan (DDBJ), the European
Molecular Biology Laboratory
(EMBL), and GenBank at NCBI.
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Protein
Databases
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UniProt
|
URL
|
The mission of
UniProt is to provide the
scientific community with a
comprehensive, high-quality and
freely accessible resource of
protein sequence and functional
information.
|
Protein Data
Bank
|
URL |
A
Structural View of Biology. This
resource is powered by the Protein
Data Bank archive-information
about the 3D shapes of proteins,
nucleic acids, and complex
assemblies that helps students and
researchers understand all aspects
of biomedicine and agriculture,
from protein synthesis to health
and disease.
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Pathway
Databases
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KEGG
|
URL |
KEGG
is a database resource for
understanding high-level functions
and utilities of the biological
system, such as the cell, the
organism and the ecosystem, from
molecular-level information,
especially large-scale molecular
datasets generated by genome
sequencing and other
high-throughput experimental
technologies.
|
BioCyc
|
URL
|
BioCyc
is a collection of 7615
Pathway/Genome Databases (PGDBs),
plus software tools for
understanding their data.
|
MetaCyc
|
URL
|
MetaCyc
is a curated database of
experimentally elucidated
metabolic pathways from all
domains of life. MetaCyc contains
2453 pathways from 2788 different
organisms. MetaCyc
contains pathways involved in both
primary and secondary metabolism,
as well as associated metabolites,
reactions, enzymes, and genes. The
goal of MetaCyc is to catalog the
universe of metabolism by storing
a representative sample of each
experimentally elucidated pathway.
|
REACTOME
|
URL |
Reactome
is a free, open-source, curated
and peer reviewed pathway
database. Our goal is to provide
intuitive bioinformatics tools for
the visualization, interpretation
and analysis of pathway knowledge
to support basic research, genome
analysis, modeling, systems
biology and education.
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Enzyme
Reaction Kinetics Databases
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BRENDA
|
URL |
Comprehensive
enzyme information system
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SABIO-RK
|
URL |
SABIO-RK is a
curated database that contains
information about biochemical
reactions, their kinetic rate
equations with parameters and
experimental conditions.
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Transcription
Factor Databases
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JASPAR
|
URL
|
The
high-quality transcription factor
binding profile database
|
TRED
|
URL
|
In
order to understand gene
regulation, accurate and
comprehensive knowledge of
transcriptional regulatory
elements is essential.
Transcriptional Regulatory Element
Database (TRED) has been built in
response to increasing needs of an
integrated repository for both
cis- and trans- regulatory
elements in mammals, and the lack
of such resources at present.
|
Transc Factor
Encyclopedia
|
URL
|
The
long-term goal of TFe is to create
an online encyclopedic collection
of well-studied transcription
factor proteins in the human,
mouse, and rat genomes, combining
a mixture of both expert-curated
and automatically-populated
content to provide users with a
wide set of information relevant
to a transcription factor protein
of their interest.
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Microarray
and Sequencing Databases
|
GEO
|
URL
|
Gene
Expression Omnibus (GEO). GEO is a
public functional genomics data
repository supporting
MIAME-compliant data submissions.
Array- and sequence-based data are
accepted. Tools are provided to
help users query and download
experiments and curated gene
expression profiles.
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Array Express
|
URL
|
ArrayExpress
Archive of Functional Genomics
Data stores data from
high-throughput functional
genomics experiments, and provides
these data for reuse to the
research community.
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Compound and
Drug Databases
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ChEBI
|
URL |
Chemical
Entities of Biological Interest
(ChEBI) is a freely available
dictionary of molecular entities
focused on ‘small’ chemical
compounds.
|
Guide to
Pharmacology
|
URL |
An
expert-driven guide to
pharmacological targets and the
substances that act on them.
|
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Last version
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September 2016
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