Human Proteinpedia
Encyclopedia
Human Proteinpedia is a portal for sharing and integration of human proteomic data,. It allows research laboratories to contribute and maintain protein annotations. Human Protein Reference Database, (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. More than 70 labs participate in this effort.
and enzyme
substrate relationships can be submitted to Human Proteinpedia - Proteomics
portal
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
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.
HPRD
The Human Protein Reference Database is a protein database accessible through the internet.The HPRD is a result of an international collaborative effort between the in Bangalore, India and the at Johns Hopkins University in Baltimore, USA. HPRD contains manually curated scientific information...
) 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
Proteomics
Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...
data disposition to public repositories, Nature Methods recommends Human Proteinpedia in their editorial. More than 70 labs participate in this effort.
What data can be shared?
Data pertaining to post-translational modifications, protein-protein interactions, tissue expression, expression in cell lines, subcellular localizationSubcellular localization
The cells of eukaryotic organisms are elaborately subdivided into functionally distinct membrane bound compartments. Some major constituents of eukaryotic cells are: extracellular space, cytoplasm, nucleus, mitochondria, Golgi apparatus, endoplasmic reticulum , peroxisome, vacuoles, cytoskeleton,...
and enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
substrate relationships can be submitted to Human Proteinpedia - Proteomics
Proteomics
Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...
portal
Experimental platforms
Protein annotations present in Human Proteinpedia are derived from a number of platforms such as- Co-immunoprecipitation and mass spectrometryMass spectrometryMass spectrometry is an analytical technique that measures the mass-to-charge ratio of charged particles.It is used for determining masses of particles, for determining the elemental composition of a sample or molecule, and for elucidating the chemical structures of molecules, such as peptides and...
-based protein-protein interaction - Co-immunoprecipitation and Western blotting based protein-protein interaction
- FluorescenceFluorescenceFluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation of a different wavelength. It is a form of luminescence. In most cases, emitted light has a longer wavelength, and therefore lower energy, than the absorbed radiation...
based experiments - ImmunohistochemistryImmunohistochemistryImmunohistochemistry or IHC refers to the process of detecting antigens in cells of a tissue section by exploiting the principle of antibodies binding specifically to antigens in biological tissues. IHC takes its name from the roots "immuno," in reference to antibodies used in the procedure, and...
- Mass Spectrometric Analysis
- ProteinProteinProteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
and peptidePeptidePeptides are short polymers of amino acid monomers linked by peptide bonds. They are distinguished from proteins on the basis of size, typically containing less than 50 monomer units. The shortest peptides are dipeptides, consisting of two amino acids joined by a single peptide bond...
microarrayMicroarrayA microarray is a multiplex lab-on-a-chip. It is a 2D array on a solid substrate that assays large amounts of biological material using high-throughput screening methods.Types of microarrays include:... - Western blotWestern blotThe western blot is a widely used analytical technique used to detect specific proteins in the given sample of tissue homogenate or extract. It uses gel electrophoresis to separate native proteins by 3-D structure or denatured proteins by the length of the polypeptide...
ting - 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
Johns Hopkins University
The Johns Hopkins University, commonly referred to as Johns Hopkins, JHU, or simply Hopkins, is a private research university based in Baltimore, Maryland, United States...
and the Institute of Bioinformatics
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
Anonymity
Anonymity is derived from the Greek word ἀνωνυμία, anonymia, meaning "without a name" or "namelessness". In colloquial use, anonymity typically refers to the state of an individual's personal identity, or personally identifiable information, being publicly unknown.There are many reasons why a...
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
Peer review
Peer review is a process of self-regulation by a profession or a process of evaluation involving qualified individuals within the relevant field. Peer review methods are employed to maintain standards, improve performance and provide credibility...
?
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
Erroneous
Erroneous may refer to:* Your Erroneous Zones, a self-help book by Wayne Dyer* Erroneous rendition, in human rights* Erroneous program, a program whose semantics are not well-defined, but where the language implementation is not obligated to signal an error* Erroneous, pseudonym used by bassist...
, we will consult with the contributing group(s) about deleting the entry.