Supplementary data

Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models

Méziane Aite, Marie Chevallier, Clémence Frioux, Camille Trottier, Jeanne Got, María Paz Cortés, Nicolás Loira, Grégory Carrier, Olivier Dameron, Nicolas Guillaudeux, Mauricio Latorre, Sebastián Mendoza, Gabriel V. Markov, Alejandro Maass and Annne Siegel*

* Contact us : gem-aureme@inria.fr

Data

All the input and output data mentionned in this article

SparqlEndpoint

Service that accepts SPARQL queries and returns results. Here you can explore the reconstructed metabolic network of Tisochrysis lutea
To test the data exploration with SPARQL...

... here is an example query that allows to display all the information on one of the pathways of the Carnosine. It shows the completion ratio of the pathway and the reactions in the pathway. For each of them, it associates the genes and all the information on the origin of the reactions.

Just copy-paste the lines below in the "Query Text" section on "Virtuoso SPARQL Query Editor".

		
		  PREFIX : <http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#>
		  PREFIX displaySetting: <http://www.irisa.fr/dyliss/rdfVisualization/display>
		  PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
		  PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
		  PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
		  PREFIX rdfg: <http://www.w3.org/2004/03/trix/rdfg-1/>
		  PREFIX owl: <http://www.w3.org/2002/07/owl#>
		  PREFIX prov: <http://www.w3.org/ns/prov#>
		  PREFIX dc: <http://purl.org/dc/elements/1.1/>
		  PREFIX foaf: <http://xmlns.com/foaf/0.1/>
		  PREFIX faldo: <http://biohackathon.org/resource/faldo#>
		  SELECT DISTINCT *
		  WHERE {
		  ?URIpathway1 rdf:type <http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#pathway>.
		  ?URIpathway1 rdfs:label "HISTSYN-PWY"^^xsd:string.
		  ?URIpathway1 <http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#RATE> ?RATE1.
		  ?URIrxn_pwy1 rdf:type <http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#rxn_pwy>.
		  ?URIrxn_pwy1 rdfs:label ?rxn_pwy1.
		  ?URIreaction1 rdf:type <http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#reaction>.
		  ?URIreaction1 rdfs:label ?reaction1.
		  ?URIrxn_gene_recData1 rdf:type <http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#rxn_gene_recData>.
		  ?URIrxn_gene_recData1 rdfs:label ?rxn_gene_recData1.
		  ?URIgene1 rdf:type <http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#gene>.
		  ?URIgene1 rdfs:label ?gene1.
		  ?URIreconstructionData1 rdf:type <http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#reconstructionData>.
		  ?URIreconstructionData1 rdfs:label ?reconstructionData1.
		  ?URIrxn_pwy1 <http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#in_included_in> ?URIpathway1.
		  ?URIrxn_pwy1 <http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#concerns> ?URIreaction1.
		  ?URIrxn_gene_recData1 <http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#concerns> ?URIreaction1.
		  ?URIrxn_gene_recData1 <http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#is_linked_to> ?URIgene1.
		  ?URIrxn_gene_recData1 <http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#was_obtained_with> ?URIreconstructionData1.
		  OPTIONAL {
		  ?URIrxn_gene_recData1 <http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#assignment_evidence> ?URICatassignment_evidence1.
		  ?URICatassignment_evidence1 rdfs:label ?assignment_evidence1.
		  }
		  ?URIreconstructionData1 <http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#CATEGORY> ?URICatCATEGORY1.
		  ?URICatCATEGORY1 rdfs:label ?CATEGORY1.
		  ?URIreconstructionData1 <http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#SOURCE> ?URICatSOURCE1.
		  ?URICatSOURCE1 rdfs:label ?SOURCE1.
		  ?URIreconstructionData1 <http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#TOOL> ?URICatTOOL1.
		  ?URICatTOOL1 rdfs:label ?TOOL1.
		  }