What are the differences between HPRD and BIOGRID protein-protein interactions databases?

  • What are their purposes? Why do we need two different databases?
  • How is data collected into each one?
  • How different are they in the interactions they contain?
  • Is one considered more reliable than the other?
  • Which one is more commonly used when benchmarking models?
  • Are there any other commonly used PPI databases?
  • 1
    $\begingroup$ Do you mean in funding or functionality? Your question is very general. Both projects have different purposes. The latter seems to be more specific, interaction repository with data compiled through comprehensive curation efforts, while the former more general about proteins. In some cases HPRD is better, while BIOGRID in other depending on the situation. Reliability again depends on your issue. It is often the case that BIOGRID can be more reliable in its specific cases, while HPRD can provide some overview well. $\endgroup$ Nov 30 '13 at 17:10
  • $\begingroup$ I've added some details to my question. I'm not sure what you mean by more general/specific. $\endgroup$
    – Uri
    Dec 1 '13 at 1:10
  • $\begingroup$ i've covered major differences in my answer, but most importantly HPRD focusses on high-quality manually curated Human data and BIOGRID is for multiple species $\endgroup$ Dec 17 '13 at 2:14

Short Answer

In a nutshell, there are two major differences:

  • Species range: BioGRID integrates multiple species' protein-protein interaction (PPI) data, whereas HPRD focuses mainly on Human data.

  • Functionality: HPRD has some GUI tools that can interact directly with it's database (e.g. BLAST - for searching proteins and their binding partners via sequence alignment) whereas BioGRID is mostly just a database.

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Long Answer

In bold are the unique features of each database.

About HPRD:

The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data. HPRD has been created using an object oriented database in Zope, an open source web application server, that provides versatility in query functions and allows data to be displayed dynamically.

FAQ HPRD: Why did you decide to develop yet another database instead of integrating other existing databases?" We believe that biological databases are still in their early stages and no protein database can be considered as an established standard. We feel that a variety of databases trying to solve problems in diverse ways provide the biologists the possibility of choosing their favorite. Our approach is radically different from existing databases and we want to offer biologists the possibility of choosing instead of imposing one database by default. Besides, most of the databases are automated and ours is manually curated to avoid errors. We are also trying to provide information that few other databases provide.

About Biogrid:

The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans (thebiogrid.org). BioGRID currently holds over 720,000 interactions curated from both high-throughput datasets and individual focused studies, as derived from over 41,000 publications in the primary literature. Complete coverage of the entire literature is maintained for budding yeast (S. cerevisiae), fission yeast (S. pombe) and thale cress (A. thaliana), and efforts to expand curation across multiple metazoan species are underway. Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health. The BioGRID 3.2 web interface contains new search and display features that enable rapid queries across multiple data types and sources. BioGRID provides interaction data to several model organism databases, resources such as Entrez-Gene, SGD, TAIR, FlyBase and other interaction meta-databases. The entire BioGRID 3.2 data collection may be downloaded in multiple file formats, including IMEx compatible PSI MI XML. For developers, BioGRID interactions are also available via a REST based Web Service and Cytoscape plugin. All BioGRID documentation is available online in the BioGRID Wiki.


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