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J Biomed Semantics. 2016 Jun 4;7(1):33. doi: 10.1186/s13326-016-0078-9.

The Proteasix Ontology.

Author information

1
School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
2
Institut National de la Sante et de la Recherche Medicale (INSERM), U1048, Toulouse, 24105, France.
3
School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK. Robert.Stevens@manchester.ac.uk.

Abstract

BACKGROUND:

The Proteasix Ontology (PxO) is an ontology that supports the Proteasix tool; an open-source peptide-centric tool that can be used to predict automatically and in a large-scale fashion in silico the proteases involved in the generation of proteolytic cleavage fragments (peptides)

METHODS:

The PxO re-uses parts of the Protein Ontology, the three Gene Ontology sub-ontologies, the Chemical Entities of Biological Interest Ontology, the Sequence Ontology and bespoke extensions to the PxO in support of a series of roles: 1. To describe the known proteases and their target cleaveage sites. 2. To enable the description of proteolytic cleaveage fragments as the outputs of observed and predicted proteolysis. 3. To use knowledge about the function, species and cellular location of a protease and protein substrate to support the prioritisation of proteases in observed and predicted proteolysis.

RESULTS:

The PxO is designed to describe the biological underpinnings of the generation of peptides. The peptide-centric PxO seeks to support the Proteasix tool by separating domain knowledge from the operational knowledge used in protease prediction by Proteasix and to support the confirmation of its analyses and results.

AVAILABILITY:

The Proteasix Ontology may be found at: http://bioportal.bioontology.org/ontologies/PXO . This ontology is free and open for use by everyone.

KEYWORDS:

Cleaveage site; Ontology; Open biomedical ontologies; Peptide; Protease prediction; Proteasix

PMID:
27259807
PMCID:
PMC4893253
DOI:
10.1186/s13326-016-0078-9
[Indexed for MEDLINE]
Free PMC Article

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