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Discovery Informatics and Computing Laboratory
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| Databases and Data Services | |
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Databases HAPPI HIP2 Protein Interaction DB Pathway DB NAR DB List |
DATABASES DEVELOPED IN THE LAB A Database of Human Annotated and Predicted Protein Interactions (HAPPI) The database is a free, open-access, and comprehensive database collection of computer annotated human protein-protein interactions from public data sources and computational predictions. The database was developed by exhaustively integrating publicly available human protein interaction data from BIND, OPHID, MINT, IntAct, HPRD, and STRING databases into a data warehouse powered by our Oracle 10g relational database server. In the data warehouse, various types of sequence, structure, pathway, and literature annotation data from established bioinformatics resources such as NCBI, PubMed, UniProt, HUGO, EBI, PDB were also integrated. Our long-term goal is to develop a new type of protein interaction database resource for biomedical scientists, who are interested in evaluating biological significant protein interactions, developing disease pathway models, and identifying disease drug targets or diagnostic biomarkers. Web Site: http://bio.informatics.iupui.edu/HAPPI/ A Database of Healthy Human Individual's Integrated Plasma Proteome (HIP2) HIP2 database provides comprehensive information on plasma proteins detected from the blood of "healthy" or "normal" individuals (defined as healthy human adults without major life-threatening disease, known genetic diseases, HIV, or inflammation at the time of blood drawing), using different tandem mass spectrometry techniques. The HIP2 database provides protein biologists and clinical biomedical researchers with new opportunities to investigate which proteins may be used for future biomarker research, by comparing plasma proteomics results from patients with diseases such as cancer, neurodegenarative diseases, metabolic diseases, and other genetic disorders. The HIP2 provides first such "background" information on which proteins are expected, with ample peptide sequence as evidence, in health individual's plasma. Web Site: http://bio.informatics.iupui.edu/HIP2/ HPD provides comprehensive information on human biological pathways, including metabolic pathways, signal transduction pathways, and gene regulatory pathways, all integrated from publicly accessible sources. While there are more than 300 web-accessible biological pathway and network resources of different coverage and quality as of 2009 according to Pathguide (http://www.pathguide.org/), our knowledge of human pathways is still quite incomplete. Therefore, a one-stop web-based database to search, browse, and compare human pathways is critical. HPD complement other pathway databases such as KEGG and Reactome by providing pathway-protein and pathway-pathway mappings related to user query genes or proteins. It currently contains approximately 1,000 human pathways. Web Site: http://bio.informatics.iupui.edu/HPD/ PUBLIC DATABASES OF SYSTEMS BIOLOGY INTERESTS
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