Development of human protein reference database as an initial platform for approaching systems biology in humans.
Human Protein Reference Database (HPRD) is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease. Data pertaining to thousands of protein-protein interactions, posttranslational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization were extracted from the literature for a nonredundant set of 2750 human proteins. Almost all the information was obtained manually by biologists who read and interpreted >300,000 published articles during the annotation process. This database, which has an intuitive query interface allowing easy access to all the features of proteins, was built by using open source technologies and will be freely available at http://www.hprd.org to the academic community. This unified bioinformatics platform will be useful in cataloging and mining the large number of proteomic interactions and alterations that will be discovered in the postgenomic era.
Peri
Suraj
S
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21287, USA.
Navarro
J Daniel
JD
Amanchy
Ramars
R
Kristiansen
Troels Z
TZ
Jonnalagadda
Chandra Kiran
CK
Surendranath
Vineeth
V
Niranjan
Vidya
V
Muthusamy
Babylakshmi
B
Gandhi
T K B
TK
Gronborg
Mads
M
Ibarrola
Nieves
N
Deshpande
Nandan
N
Shanker
K
K
Shivashankar
H N
HN
Rashmi
B P
BP
Ramya
M A
MA
Zhao
Zhixing
Z
Chandrika
K N
KN
Padma
N
N
Harsha
H C
HC
Yatish
A J
AJ
Kavitha
M P
MP
Menezes
Minal
M
Choudhury
Dipanwita Roy
DR
Suresh
Shubha
S
Ghosh
Neelanjana
N
Saravana
R
R
Chandran
Sreenath
S
Krishna
Subhalakshmi
S
Joy
Mary
M
Anand
Sanjeev K
SK
Madavan
V
V
Joseph
Ansamma
A
Wong
Guang W
GW
Schiemann
William P
WP
Constantinescu
Stefan N
SN
Huang
Lily
L
Khosravi-Far
Roya
R
Steen
Hanno
H
Tewari
Muneesh
M
Ghaffari
Saghi
S
Blobe
Gerard C
GC
Dang
Chi V
CV
Garcia
Joe G N
JG
Pevsner
Jonathan
J
Jensen
Ole N
ON
Roepstorff
Peter
P
Deshpande
Krishna S
KS
Chinnaiyan
Arul M
AM
Hamosh
Ada
A
Chakravarti
Aravinda
A
Pandey
Akhilesh
A
D019313:BRCA1 Protein / Q000502:physiology; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein / Q000639:trends*; D005826:Genetics, Medical / Q000379:methods; D006801:Humans; D046911:Macromolecular Substances; D025941:Protein Interaction Mapping / Q000639:trends; D011499:Protein Processing, Post-Translational / Q000502:physiology; D020836:Protein Structure, Quaternary / Q000502:physiology; D017434:Protein Structure, Tertiary / Q000502:physiology; D013379:Substrate Specificity / Q000502:physiology
D019313:BRCA1 Protein; D046911:Macromolecular Substances