The Proteasix Ontology View Full Text


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Article Info

DATE

2016-06-04

AUTHORS

Mercedes Arguello Casteleiro, Julie Klein, Robert Stevens

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. More... »

PAGES

33

References to SciGraph publications

  • 2000-05. Gene Ontology: tool for the unification of biology in NATURE GENETICS
  • 2007-11-07. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration in NATURE BIOTECHNOLOGY
  • 2013. Protégé Ontology Editor in ENCYCLOPEDIA OF SYSTEMS BIOLOGY
  • 2008-01-01. Knowledge Patterns in KNOWLEDGE ENGINEERING: PRACTICE AND PATTERNS
  • 2005-04-29. The Sequence Ontology: a tool for the unification of genome annotations in GENOME BIOLOGY
  • 2005-04-28. Relations in biomedical ontologies in GENOME BIOLOGY
  • 2012-12-17. Analysing Syntactic Regularities and Irregularities in SNOMED-CT in JOURNAL OF BIOMEDICAL SEMANTICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13326-016-0078-9

    DOI

    http://dx.doi.org/10.1186/s13326-016-0078-9

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1038195706

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/27259807


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