Exact(5)
For that reason, we only report HAPPI database results with star grades of 3 and above in our database's web user interface.
We used the new HAPPI database instead of other protein interaction databases because of its overall better data quality (comparable or better than data in the HPRD database for quality star grades of 3 and above) and coverage (more than 280,000 human protein interactions with star grades of 3 and above), which was thoroughly described in Chen et al. [ 19].
However, our results show that the HAPPI database, particularly for star grades of 3, 4, and 5, clearly contains much higher true positive PPI interactions than all other known human PPI databases.
The overall quality of the HAPPI database (at all star grades) is comparable to that of the recently published IntNetDB or HPRD (at approximately 13 15 overlaps overall), still better than that of the ProNet [ 50] database (manually curated data set initially made public as the first database for human protein interactions; at approximately 8 overlaps overall).
The overall quality of HAPPI database at all star grades is not as good as the BioGrid (at approximately 19 overlaps) or the OPHID database (at approximately 27 overlaps but with a wide spread), primarily because HAPPI database at one-star quality grade contains many literature mining based co-citation data that do not physically interact.
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For this study, we only use protein interactions in the HAPPI database with star grade of 3 and higher (consisting of more than 280,000 human protein interactions of primarily physical interactions), which are comparable to the overall quality of HPRD, a much smaller reference human protein interaction database commonly used in bioinformatics.
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