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Related Concept Videos

Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Organization01:13

Protein Organization

Overview
Protein Organization01:13

Protein Organization

Overview
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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A tutorial on protein ontology resources for proteomic studies.

Cecilia N Arighi1

  • 1Department of Computer and Information Sciences, University of Delaware, Newark, DE, USA.

Methods in Molecular Biology (Clifton, N.J.)
|November 18, 2010
PubMed
Summary

The Protein Ontology (PRO) is a formal resource for classifying proteins and their diverse forms, including isoforms and modifications. It aids in precise biological modeling and proteomics research by detailing protein relationships and attributes.

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Area of Science:

  • Biomedical Informatics
  • Proteomics
  • Bioinformatics

Background:

  • The Protein Ontology (PRO) is a formal ontology within the Open Biomedical Ontologies (OBO) Foundry.
  • PRO classifies proteins based on evolutionary relationships and represents various protein forms, including those from alternative splicing, cleavage, post-translational modifications, and complexes.
  • Unlike databases, PRO provides descriptive relationships between protein types.

Purpose of the Study:

  • To introduce the Protein Ontology (PRO) as a resource for detailed protein information.
  • To demonstrate how PRO facilitates the study of protein isoforms, modifications, and their attributes.
  • To guide users on accessing PRO resources and contributing to the ontology.

Main Methods:

  • Manual curation of content derived from scientific literature.
  • Inclusion of annotations with experimental evidence, linked to other ontologies.
  • Development of the RACE-PRO interface for ontology contribution.

Main Results:

  • PRO enables precise definition of protein types, including specific modified forms like phosphorylated proteins.
  • Facilitates detailed representation of biological pathways, complexes, and disease models.
  • Supports proteomics studies requiring differentiation of isoforms and modified forms.

Conclusions:

  • PRO is a valuable, manually curated resource for understanding protein diversity and relationships.
  • Its structured representation enhances biological pathway analysis and disease modeling.
  • PRO supports researchers in proteomics and bioinformatics, with avenues for community contribution.