article Open Access

Development of Human Protein Reference Database as an Initial Platform for Approaching Systems Biology in Humans

Genome Research · 2003 · Vol. 13(10) · pp. 2363–2371

Suraj Peri✉(Johns Hopkins University)J. Daniel Navarro(Johns Hopkins University)Ramars Amanchy(Johns Hopkins University)Troels Zakarias Kristiansen(Johns Hopkins University)Chandra Kiran Jonnalagadda(Johns Hopkins University)Vineeth Surendranath(Institute of Bioinformatics)Vidya Niranjan(Institute of Bioinformatics)Babylakshmi Muthusamy(Institute of Bioinformatics)T. K. B. Gandhi(Institute of Bioinformatics)Mads Grønborg(Johns Hopkins University)Nieves Ibarrola(Johns Hopkins University)Nandan Deshpande(Institute of Bioinformatics)K. Shanker(Institute of Bioinformatics)H N Shivashankar(Institute of Bioinformatics)B.P. Rashmi(Institute of Bioinformatics)Mummadireddy Ramya(Institute of Bioinformatics)Zhixing Zhao(Johns Hopkins University)K.N. Chandrika(Institute of Bioinformatics)Nambisan Padma(Institute of Bioinformatics)Harsha Gowda(Institute of Bioinformatics)A.J. Yatish(Institute of Bioinformatics)M. Kavitha(Institute of Bioinformatics)Minal Menezes(Institute of Bioinformatics)Dipanwita Roy Choudhury(Institute of Bioinformatics)Shubha Suresh(Institute of Bioinformatics)Neelanjana Ghosh(Institute of Bioinformatics)R. Saravana(Institute of Bioinformatics)Sreenath Chandran(Institute of Bioinformatics)Subhalakshmi Krishna(Institute of Bioinformatics)Mary T. Joy(Institute of Bioinformatics)Sanjeev K. Anand(Institute of Bioinformatics)V. Madavan(Institute of Bioinformatics)Ansamma K. Joseph(Institute of Bioinformatics)G. William Wong(Whitehead Institute for Biomedical Research)William P. Schiemann(National Jewish Health)Stefan N. Constantinescu(Ludwig Cancer Research)Lily Huang(Whitehead Institute for Biomedical Research)Roya Khosravi‐Far(Beth Israel Deaconess Medical Center)Hanno Steen(Harvard University Press)Muneesh Tewari(Harvard University)Saghi Ghaffari(Icahn School of Medicine at Mount Sinai)Gerard C. Blobe(Duke University)Chi V. Dang(Johns Hopkins University)Joe G. N. Garcia(Johns Hopkins University)Jonathan Pevsner(Kennedy Krieger Institute)Ole N. Jensen(University of Southern Denmark)Peter Roepstorff(University of Southern Denmark)K. S. Deshpande(Institute of Bioinformatics)Arul M. Chinnaiyan(University of Michigan)Ada Hamosh(Johns Hopkins University)Aravinda Chakravarti(Johns Hopkins University)Akhilesh Pandey(Johns Hopkins University)

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Abstract

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.

Bioinformatics and Genomic Networks Advanced Proteomics Techniques and Applications Genomics and Rare DiseasesAnnotationBiologyHuman proteinsDatabaseFunction (biology)Protein structure databaseComputational biologySet (abstract data type)Object (grammar)Human Protein Atlas

MeSH terms

Genetics, MedicalHumansProtein Processing, Post-TranslationalSubstrate SpecificityProtein Structure, TertiaryComputational BiologyBRCA1 ProteinProtein Structure, QuaternaryProtein Interaction MappingDatabases, ProteinMacromolecular Substances