An ontology-supported approach to predict automatically the proteases involved in the generation of peptides Mercedes Arguello Casteleiro 1, Julie Klein.

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Presentation transcript:

An ontology-supported approach to predict automatically the proteases involved in the generation of peptides Mercedes Arguello Casteleiro 1, Julie Klein 2 and Robert Stevens 1 1 School of Computer Science, University of Manchester, Oxford road, Manchester, United Kingdom. 2 Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Toulouse, France. And Université Toulouse III Paul-Sabatier, Toulouse, France.

Biomedical Background Complex diseases cannot be adequately described by single features: -Interindividual differences -Mechanism multiplicity why omics? Omics: studying “all” molecules collectively

Tools & Applications Peptides represent a new source of very useful biomarkers in kidney and other disease. Peptides can help better understanding the pathophysiological mechanisms : Parental proteins Proteases Protease Parent protein Peptide

Tools & Applications HELP ? Peptides represent a new source of very useful biomarkers in kidney and other disease. Peptides can help better understanding the pathophysiological mechanisms : Parental proteins Proteases

Proteasix Ontology (PxO) reuse ontologies

chemical entity molecular entity Alanine

Proteasix Ontology (PxO) reuse ontologies Human Rat Mouse

Proteasix Ontology (PxO) reuse ontologies molecular_function cellular_component biological_process

Proteasix Ontology (PxO) reuse ontologies Protein amino acid chain proteolytic cleavage product

Current Work: Proteasix Ontology (PxO) UniProt KB proteins (Swiss-prot and TrEMBL)  Organised by Taxons following PRO ontology  Annotated with GO biological_process; GO cellular_component; and GO molecular_function Model cleavage sites patterns for  Exopeptidase activity  Endopeptidase activity

For using Peptides as Biomarkers, we need more data.. and data linkage.. Class: polypeptide_region SubClassOf: biological_region part_of some protein, associated_with some 'proteolytic cleavage product', only_in_taxon some organism OWL (ontologies) OWL (ontologies)

In Swiss-Prot there are proteins annotated with GO: , which is serine-type endopeptidase activity SELECT ?x FROM { ?x rdf:type owl:Class; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty pr:has_function ; owl:someValuesFrom obo:GO_ ]. } SPARQL (queries) SPARQL (queries) For using Peptides as Biomarkers, we need more data.. and data linkage..

Can we retrieve from Swiss-Prot ALL the proteins annotated with any DESCENDANT of Peptidase activity GO_ ? SPARQL (queries) SPARQL (queries) GRAPH {?C rdfs:subClassOf+ obo:GO_ }. For using Peptides as Biomarkers, we need more data.. and data linkage..

Can we retrieve from Swiss-Prot ALL the proteins annotated with any DESCENDANT of Peptidase activity GO_ ? SPARQL (queries) SPARQL (queries) For using Peptides as Biomarkers, we need more data.. and data linkage.. SELECT ?x FROM FROM NAMED { GRAPH {?C rdfs:subClassOf+ obo:GO_ }. { ?x rdf:type owl:Class; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty pr:has_function ; owl:someValuesFrom ?C ]. } }

Concluding remarks TopFIND2 and Proteasix can help to automatically predict modification of protease activity Current work: exploring the benefits of using Proteasix ontology (PxO) in the Semantic-Web version of Proteasix Hard Limits: Prediction always need validation Data available (over-representation of some proteases, other are missing)

 Biomedical background  Comparison of Current Tools & Applications ACKNOWLEDGMENT: to Julie Klein for providing