Biology Reference
In-Depth Information
Table 1.
Online resources for working with protein-protein networks. This is
a very incomplete collection, listing some representatives of each category only.
For the full list, the reader is referred to the comprehensive Database Summary main-
tained by the journal
Nucleic Acids Research
(http://www3.oup.co.uk/nar/
database/a/). Over 1000 online resources are available there, sorted into categories.
Online Resources
References
Interaction databases
(
primary experimental data
)
IntAct
Maintained at EBI; a driving force of
50
standardization and interconnectivity for
all interaction databases.
DIP
One of the oldest interaction databases;
51
also contains a tool to align networks
(PathBLAST).
BioGRID
Focused on eukaryotic model organisms;
52
contains many genetic interactions.
HPRD
Limited to human proteins, but conducts
53
extensive curation efforts (also invites
curation from the user community).
MINT
Actively curates interactions from the
54
literature; includes projections from
model organisms to humans
(HomoMINT).
Pathway databases
(
interpreted and distilled interaction knowledge
)
KEGG
Main focus is on metabolism; a worldwide
55
reference source for metabolic pathways
that covers many organisms.
Reactome
State-of-the-art data model and visualizations
56
of pathway knowledge; conducts active
curation of knowledge from the literature.
PID
Maintained at the National Cancer Institute
and at
Nature
; integrates and curates
pathway knowledge, focusing on humans.
pid.nci.nih.gov/
Network resources
(
precomputed interaction networks
)
STRING
Main focus is on association networks;
57
combines experimental data, automated
literature searches, and computational
predictions; covers many organisms
and is regularly updated.
(
Continued
)
