Human Proteinpedia

From Wikipedia, the free encyclopedia

Human Proteinpedia is a portal for sharing and integration of human proteomic data[1]. It allows research laboratories to contribute and maintain protein annotations. Human Protein Reference Database [2],[3] (HPRD) integrates data, that is deposited in Human Proteinpedia along with the existing literature curated information at the context of an individual protein. In essence, researchers can add new data to HPRD by registering to Human Proteinpedia. The data deposited in Human Proteinpedia is freely available for download. Emphasizing the importance of proteomics data disposition to public repositories, Nature Methods recommends Human Proteinpedia in their editorial[4].

Wikipedia, an online encyclopedia that anyone can edit, has already proven quite successful 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. Human Proteinpedia have two significant differeneces 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. More than 70 labs have participated in this unique effort.

Contents

[edit] What data can be shared?

Data pertaining to post-translational modifications, protein-protein interactions, tissue expression, expression in cell lines, subcellular localization and enzyme substrate relationships can be submitted to Human Proteinpedia - Proteomics portal

[edit] Experimental platforms

Protein annotations present in Human Proteinpedia are derived from a number of platforms such as

  1. Co-immunoprecipitation and mass spectrometry-based protein-protein interaction
  2. Co-immunoprecipitation and Western blotting based protein-protein interaction
  3. Fluorescence based experiments
  4. Immunohistochemistry
  5. Mass Spectrometric Analysis
  6. Protein and peptide microarray
  7. Western blotting
  8. Yeast two-hybrid based protein-protein interaction

This portal that allows adding of protein information was developed as a collaborative effort between the laboratory of Dr. Akhilesh Pandey at Johns Hopkins University and the Institute of Bioinformatics

[edit] FAQs

* What are the criteria for contributing data?

Any investigator who fulfills the following criteria can contribute data:

i) provides experimentally derived data, and,

ii) is willing to share data, and,

iii) is willing to be listed as the 'contributor' of the data

* Can I contribute data anonymously?

Anonymous contributions are not allowed. Contributor details should be clearly presented while contributing data.

* Can bioinformatically predicted data be shared through Human Proteinpedia?

Predictions of any type are not allowed. Contributed data should be derived experimentally and should be accompanied with experimental evidence.

* Is the contributed data subjected to peer review?

The data are not subjected to peer review and the actual experimental data (raw or processed) should be provided.

* What will happen to conflicting results from different laboratories?

In cases where a given entry is documented as erroneous, we will consult with the contributing group(s) about deleting the entry.

[edit] External links

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[edit] References

  1. ^ Mathivanan et al. Human Proteinpedia enables sharing of human protein data. Nat Biotechnology. 2008 Feb;26:164-7
  2. ^ Mishra et al. Human protein reference database--2006 update. Nucleic Acids Res. 2006 Jan;34(Database issue):D411-4
  3. ^ Peri et al. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 2003 Oct;13:2363-71.
  4. ^ Editorial. Thou shalt share your data. Nat Mehods. 2008 Mar;5:209