The Proteasix Knowledge Base

The Proteasix Ontology (PxO)

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).

Body fluids (e.g. serum, urine, cerebrospinal fluid) contain thousands of protein fragments and disease-associated peptides. Information about proteases and their substrates and cleavage sites is scattered across publications and databases, different formats. This knowledge needs to be brought together and exploited to gain insights into the proteases implicated in peptide generation. PxO seeks to support this task; it is built in OWL and JSON-LD following the W3C’s vision of the Web of linked data.

The PxO core is a selection of concepts names; concept expressions; concept definitions; and annotation assertions from the Protein Ontology (PRO), the three Gene Ontology (GO) sub-ontologies, Chemical Entities of Biological Interest Ontology (ChEBI), Phenotypic Quality Ontology (PATO), the Sequence Ontology (SO), GALEN ontology, and Relationship Ontology (RO). The axioms extracted are designed to describe the biological underpinnings of the generation of peptides. These axioms together with axiom patterns, which capture the appropriate peptide-centric knowledge, enable the PxO ontology to support the Proteasix tool.