Human Proteinpedia enables sharing of human protein data

Abstract

Proteomic technologies, such as yeast twohybrid, mass spectrometry (MS), protein/peptide arrays and fluorescence microscopy, yield multi-dimensional data sets, which are often quite large and either not published or published as supplementary information that is not easily searchable. Without a system in place for standardizing and sharing data, it is not fruitful for the biomedical community to contribute these types of data to centralized repositories. Even more difficult is the annotation and display of pertinent information in the context of the corresponding proteins. Wikipedia, an online encyclopedia that anyone can edit, has already proven quite successful1 and can be used as a model for sharing biological data. However, the need for experimental evidence, data standardization and ownership of data creates scientific obstacles. Here, we describe Human Proteinpedia (http://www.humanproteinpedia.org/) as a portal that overcomes many of these obstacles to provide an integrated view of the human proteome. Human Proteinpedia also allows users to contribute and edit proteomic data with two significant differences from Wikipedia: first, the contributor is expected to provide experimental evidence for the data annotated; and second, only the original contributor can edit their data. Human Proteinpedia's annotation system provides investigators with multiple options for contributing data including web forms and annotation servers. Although registration is required to contribute data, anyone can freely access the data in the repository. The web forms simplify submission through the use of pull-down menus for certain data fields and pop-up menus for standardized vocabulary terms. Distributed annotation servers using modified protein DAS (distributed annotation system) protocols developed by us (DAS protocols were originally developed for sharing mRNA and DNA data) permit contributing laboratories to maintain protein annotations locally. All protein annotations are visualized in the context of corresponding proteins in the Human Protein Reference Database (HPRD)3. Figure 1 shows tissue expression data for alpha-2-HS glycoprotein derived from three different types of experiments. Our unique effort differs significantly from existing repositories, such as PeptideAtlas and PRIDE5 in several respects. First, most proteomic repositories are restricted to one or two experimental platforms, whereas Human Proteinpedia can accommodate data from diverse platforms, including yeast two-hybrid screens, MS, peptide/protein arrays, immunohistochemistry, western blots, coimmunoprecipitation and fluorescence microscopy-type experiments. Second, Human Proteinpedia allows contributing laboratories to annotate data pertaining to six features of proteins (posttranslational modifications, tissue expression, cell line expression, subcellular localization, enzyme substrates and protein-protein interactions;). No existing repository currently permits annotation of all these features in proteins. Third, all data submitted to Human Proteinpedia...

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