BACKGROUND: Human protein-protein interaction (PPIs) data are the foundation for 
understanding molecular signalling networks and the functional roles of 
biomolecules. Several human PPI databases have become available; however, 
comparisons of these datasets have suggested limited data coverage and poor data 
quality. Ongoing collection and integration of human PPIs from different 
sources, both experimentally and computationally, can enable disease-specific 
network biology modelling in translational bioinformatics studies.
RESULTS: We developed a new web-based resource, the Human Annotated and 
Predicted Protein Interaction (HAPPI) database, located at 
http://bio.informatics.iupui.edu/HAPPI/. The HAPPI database was created by 
extracting and integrating publicly available protein interaction databases, 
including HPRD, BIND, MINT, STRING, and OPHID, using database integration 
techniques. We designed a unified entity-relationship data model to resolve 
semantic level differences of diverse concepts involved in PPI data integration. 
We applied a unified scoring model to give each PPI a measure of its reliability 
that can place each PPI at one of the five star rank levels from 1 to 5. We 
assessed the quality of PPIs contained in the new HAPPI database, using 
evolutionary conserved co-expression pairs called "MetaGene" pairs to measure 
the extent of MetaGene pair and PPI pair overlaps. While the overall quality of 
the HAPPI database across all star ranks is comparable to the overall qualities 
of HPRD or IntNetDB, the subset of the HAPPI database with star ranks between 3 
and 5 has a much higher average quality than all other human PPI databases. As 
of summer 2008, the database contains 142,956 non-redundant, medium to 
high-confidence level human protein interaction pairs among 10,592 human 
proteins. The HAPPI database web application also provides ..." should be "The 
HAPPI database web application also provides hyperlinked information of genes, 
pathways, protein domains, protein structure displays, and sequence feature maps 
for interactive exploration of PPI data in the database.
CONCLUSION: HAPPI is by far the most comprehensive public compilation of human 
protein interaction information. It enables its users to fully explore PPI data 
with quality measures and annotated information necessary for emerging network 
biology studies.