public static MiRNA GetMiRNA(string label)
{
// Get the miRNA from the list
MiRNA mirna = mirnas.Find(m => m.Label == label);
// If the miRNA was found
if (mirna != null)
{
// Return the miRNA
return(mirna);
}
String iri = "OMIT_" + omit_iri.ToString("D7");
// Construct the mirna triple
String mirnaTxt =
"obo:" + iri + " rdfs:subClassOf obo:NCRO_0000810 .\r\n" +
"obo:" + iri + " rdfs:label \"" + label + "\"^^xsd:string .\r\n";
// Create an instance of the new miRNA
mirna = new MiRNA(iri, label);
// Add the new miRNA to the miRNA list
mirnas.Add(mirna);
// Increment the OMIT IRI
++omit_iri;
// Write the miRNA to the mirna.owl file
sw1.WriteLine(mirnaTxt);
// Return the miRNA
return(mirna);
}
static void Main(string[] args)
{
// text_data path
string input_path = "text_data/";
// mirna_data.txt should contain the following columns separated by a tab
// Label IRI
//
// Example mirna_data.txt:
// hsa-let-7a-2-3p NCRO_MIMAT0010195
sr1 = new StreamReader(new FileStream(input_path + "mirna_data.txt", FileMode.Open));
// mirdb_data.txt should contain the following columns separated by a tab
// microRNA GeneId GeneSymbol Score
//
// Example mirdb_data.txt:
// hsa-miR-125b-5p 3662 IRF4 100
sr2 = new StreamReader(new FileStream(input_path + "mirdb_data.txt", FileMode.Open));
// targetscan_data.txt should contain the following columns separated by a tab
// microRNA GeneId GeneSymbol Score
//
// Example targetscan_data.txt:
// hsa-miR-125b-5p 3662 IRF4 100
sr3 = new StreamReader(new FileStream(input_path + "targetscan_data.txt", FileMode.Open));
// miranda_data.txt should contain the following columns separated by a tab
// microRNA GeneId GeneSymbol Score
//
// Example miranda_data.txt:
// hsa-miR-125b-5p 3662 IRF4 100
sr4 = new StreamReader(new FileStream(input_path + "miranda_data.txt", FileMode.Open));
// pubmed_data.txt should contain the following columns separated by a tab
// GeneId PubMedId MeSH_Term
//
// Example pubmed_data.txt:
// 3662 19897031 Mutagenesis
sr5 = new StreamReader(new FileStream(input_path + "pubmed_data.txt", FileMode.Open));
// mesh_term_data.txt should contain the following columns separated by a tab
// MeSH_Term OMIT_IRI
//
// Example mesh_term_data.txt:
// Drug resistance OMIT_0000072
sr6 = new StreamReader(new FileStream(input_path + "mesh_term_data.txt", FileMode.Open));
// If the output directory does not exist
if (!Directory.Exists("output"))
{
// Create the directory
Directory.CreateDirectory("output");
}
// rdf_data path
string output_path = "output/";
// Create owl files for writing
sw1 = new StreamWriter(new FileStream(output_path + "mirna.ttl", FileMode.Create));
sw2 = new StreamWriter(new FileStream(output_path + "genes.ttl", FileMode.Create));
sw3 = new StreamWriter(new FileStream(output_path + "mirdb.ttl", FileMode.Create));
sw4 = new StreamWriter(new FileStream(output_path + "targetscan.ttl", FileMode.Create));
sw5 = new StreamWriter(new FileStream(output_path + "miranda.ttl", FileMode.Create));
sw6 = new StreamWriter(new FileStream(output_path + "pubmed.ttl", FileMode.Create));
// Construct RDF Header
string header =
"@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .\r\n" +
"@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .\r\n" +
"@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .\r\n" +
"@prefix obo: <http://purl.obolibrary.org/obo/> .\r\n\r\n";
// Write header to output files
sw1.WriteLine(header);
sw2.WriteLine(header);
sw3.WriteLine(header);
sw4.WriteLine(header);
sw5.WriteLine(header);
sw6.WriteLine(header);
// Show status
Console.WriteLine("Loading miRNAs...");
// While miRNA data is available
while (!sr1.EndOfStream)
{
// Read line and split into Label and IRI
String[] tokens = sr1.ReadLine().Split("\t".ToCharArray());
// Get the Label and IRI
String label = tokens[0];
String iri = tokens[1];
// Add miRNA to list
mirnas.Add(new MiRNA(iri, label));
}
// Show status
Console.WriteLine("Loading MeSH Terms...");
// While MeSH Term data is available
while (!sr6.EndOfStream)
{
// Read line and split into IRI and Label
String[] tokens = sr6.ReadLine().Split("\t".ToCharArray());
// Get the IRI and Label
String iri = tokens[1];
String label = tokens[0];
// Add MeSH Term to list
meshTerms.Add(new MeshTerm(iri, label));
}
// Show status
Console.WriteLine("Generating miRDB Data...");
// While miRDB.org data is available
while (!sr2.EndOfStream)
{
// Read line and split by tab character
String[] ln = sr2.ReadLine().Split("\t".ToCharArray());
// Get the mirna
MiRNA mirna = GetMiRNA(ln[0]);
// Get the gene
Gene gene = GetGene(ln[2], ln[1]);
String iri = "obo:OMIT_" + omit_iri.ToString("D7");
// Construct the miRDB.org triples
String predTxt =
iri + " rdf:type obo:OMIT_0000020 .\r\n" +
iri + " obo:OMIT_0000159 obo:" + mirna.IRI + " .\r\n" +
iri + " obo:OMIT_0000160 obo:" + gene.IRI + " .\r\n" +
iri + " obo:OMIT_0000108 \"" + ln[3] + "\"^^xsd:integer .\r\n";
// Increment the OMIT IRI
++omit_iri;
// Write the Prediction to the mirdb.owl file
sw3.WriteLine(predTxt);
}
// Show status
Console.WriteLine("Generating TargetScan Data...");
// While targetscan.org data is available
while (!sr3.EndOfStream)
{
// Read line and split by tab character
String[] ln = sr3.ReadLine().Split("\t".ToCharArray());
// Get the mirna
MiRNA mirna = GetMiRNA(ln[0]);
// Get the gene
Gene gene = GetGene(ln[2], ln[1]);
String iri = "obo:OMIT_" + omit_iri.ToString("D7");
// Construct the targetscan.org triples
String predTxt =
iri + " rdf:type obo:OMIT_0000019 .\r\n" +
iri + " obo:OMIT_0000159 obo:" + mirna.IRI + " .\r\n" +
iri + " obo:OMIT_0000160 obo:" + gene.IRI + " .\r\n" +
iri + " obo:OMIT_0000108 \"" + ln[3] + "\"^^xsd:integer .\r\n";
// Increment the OMIT IRI
++omit_iri;
// Write the Prediction to the targetscan.owl file
sw4.WriteLine(predTxt);
}
// Show status
Console.WriteLine("Generating miRanda Data...");
// While microRNA.org data is available
while (!sr4.EndOfStream)
{
// Read line and split by tab character
String[] ln = sr4.ReadLine().Split("\t".ToCharArray());
// Get the mirna
MiRNA mirna = GetMiRNA(ln[0]);
// Get the gene
Gene gene = GetGene(ln[2], ln[1]);
String iri = "obo:OMIT_" + omit_iri.ToString("D7");
// Construct the miRanda.org triples
String predTxt =
iri + " rdf:type obo:OMIT_0000021 .\r\n" +
iri + " obo:OMIT_0000159 obo:" + mirna.IRI + " .\r\n" +
iri + " obo:OMIT_0000160 obo:" + gene.IRI + " .\r\n" +
iri + " obo:OMIT_0000108 \"" + ln[3] + "\"^^xsd:decimal .\r\n";
// Increment the OMIT IRI
++omit_iri;
// Write the Prediction to the targetscan.owl file
sw5.WriteLine(predTxt);
}
// Show status
Console.WriteLine("Generating PubMed Data...");
// While pubmed data is available
while (!sr5.EndOfStream)
{
// Read line and split by tab character
String[] ln = sr5.ReadLine().Split("\t".ToCharArray());
// Find the Gene object
Gene gene = genes.Find(g => g.ID == ln[0]);
// Find the MeSH Term object
MeshTerm term = meshTerms.Find(m => m.Label == ln[2]);
// If both were found
if (gene != null && term != null)
{
String iri = "obo:OMIT_" + omit_iri.ToString("D7");
// Construct the PubMed triples
String pmedTxt =
iri + " rdf:type obo:OMIT_0000003 .\r\n" +
iri + " obo:OMIT_0000161 obo:" + term.IRI + " .\r\n" +
iri + " obo:OMIT_0000160 obo:" + gene.IRI + " .\r\n" +
iri + " obo:OMIT_0000151 \"" + ln[1] + "\"^^xsd:string .\r\n";
// Increment the OMIT IRI
++omit_iri;
// Write the PubMed to the pubmed.owl file
sw6.WriteLine(pmedTxt);
}
}
// Close all files
sw1.Close();
sw2.Close();
sw3.Close();
sw4.Close();
sw5.Close();
sw6.Close();
sr1.Close();
sr2.Close();
sr3.Close();
sr4.Close();
sr5.Close();
sr6.Close();
}
