public HMDB_metabolite_multiple_files(string inputFile)
{
Cts_cas = new List <string>();
Cts_kegg = new List <string>();
Cts_chebi = new List <string>();
string tmp_string = "";
XmlReader reader = XmlReader.Create(@"" + inputFile);
XmlReader subTree;
XElement subTreeContent;
#region accession
reader.ReadToFollowing("accession");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Hmdb_accession = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
#endregion
#region secondary_accessions
Hmdb_secondary_accessions = new List <string>();
reader.ReadToFollowing("secondary_accessions");
subTree = reader.ReadSubtree();
subTreeContent = XElement.Load(subTree);
foreach (XElement synonym_content in subTreeContent.Descendants("accession"))
{
if (string.IsNullOrEmpty(synonym_content.Value) || string.IsNullOrWhiteSpace(synonym_content.Value) || synonym_content.Value == "\n")
{
continue;
}
else
{
Hmdb_secondary_accessions.Add(synonym_content.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim());
}
}
#endregion
#region name
reader.ReadToFollowing("name");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Name = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
#endregion
#region description
reader.ReadToFollowing("description");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Description = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
#endregion
#region synonyms
Synonym_names = new List <string>();
reader.ReadToFollowing("synonyms");
subTree = reader.ReadSubtree();
subTreeContent = XElement.Load(subTree);
foreach (XElement synonym_content in subTreeContent.Descendants("synonym"))
{
if (string.IsNullOrEmpty(synonym_content.Value) || string.IsNullOrWhiteSpace(synonym_content.Value) || synonym_content.Value == "\n")
{
continue;
}
else
{
Synonym_names.Add(synonym_content.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim());
}
}
#endregion
#region chemical_formula
reader.ReadToFollowing("chemical_formula");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Formula = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
#endregion
#region average_molecular_weight
reader.ReadToFollowing("average_molecular_weight");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Average_molecular_weight = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? -1 : Convert.ToDouble(tmp_string);
#endregion
#region monisotopic_moleculate_weight
reader.ReadToFollowing("monisotopic_moleculate_weight");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Monisotopic_molecular_weight = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? -1 : Convert.ToDouble(tmp_string);
#endregion
#region iupac_name
reader.ReadToFollowing("iupac_name");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Iupac_name = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
#endregion
#region traditional_iupac
reader.ReadToFollowing("traditional_iupac");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Traditional_iupac = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
#endregion
#region cas_registry_number
reader.ReadToFollowing("cas_registry_number");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Cas_registry_number = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
#endregion
#region smiles
reader.ReadToFollowing("smiles");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Smiles = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
#endregion
#region inchi
reader.ReadToFollowing("inchi");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim().Split('=').Last();
Inchi = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
#endregion
#region inchikey
reader.ReadToFollowing("inchikey");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim().Split('=').Last();
Inchikey = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
#endregion
#region taxonomy
reader.ReadToFollowing("taxonomy");
subTree = reader.ReadSubtree();
subTreeContent = XElement.Load(subTree);
My_taxonomy = new taxonomy()
{
Direct_parent = (string.IsNullOrEmpty(subTreeContent.Descendants("direct_parent").First().Value) ||
string.IsNullOrWhiteSpace(subTreeContent.Descendants("direct_parent").First().Value) || subTreeContent.Descendants("direct_parent").First().Value == "\n") ?
"" : subTreeContent.Descendants("direct_parent").First().Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Kingdom = (string.IsNullOrEmpty(subTreeContent.Descendants("kingdom").First().Value) ||
string.IsNullOrWhiteSpace(subTreeContent.Descendants("kingdom").First().Value) || subTreeContent.Descendants("kingdom").First().Value == "\n") ?
"" : subTreeContent.Descendants("kingdom").First().Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Super_class = (string.IsNullOrEmpty(subTreeContent.Descendants("super_class").First().Value) ||
string.IsNullOrWhiteSpace(subTreeContent.Descendants("super_class").First().Value) || subTreeContent.Descendants("super_class").First().Value == "\n") ?
"" : subTreeContent.Descendants("super_class").First().Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Tclass = (string.IsNullOrEmpty(subTreeContent.Descendants("class").First().Value) ||
string.IsNullOrWhiteSpace(subTreeContent.Descendants("class").First().Value) || subTreeContent.Descendants("class").First().Value == "\n") ?
"" : subTreeContent.Descendants("class").First().Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Substituents = subTreeContent.Descendants("substituents").First().Descendants("substituent").Select(x => x.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim()).ToList(),
Other_descriptors = subTreeContent.Descendants("other_descriptors").First().Descendants("descriptor").Select(x => x.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim()).ToList()
};
#endregion
#region ontology
reader.ReadToFollowing("ontology");
subTree = reader.ReadSubtree();
subTreeContent = XElement.Load(subTree);
My_onotology = new ontology()
{
Status = (string.IsNullOrEmpty(subTreeContent.Descendants("status").First().Value) ||
string.IsNullOrWhiteSpace(subTreeContent.Descendants("status").First().Value) || subTreeContent.Descendants("status").First().Value == "\n") ?
"" : subTreeContent.Descendants("status").First().Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Origins = subTreeContent.Descendants("origins").First().Descendants("origin").Select(x => x.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim()).ToList(),
Biofunctions = subTreeContent.Descendants("biofunctions").First().Descendants("biofunction").Select(x => x.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim()).ToList(),
Applications = subTreeContent.Descendants("applications").First().Descendants("application").Select(x => x.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim()).ToList(),
Cellular_locations = subTreeContent.Descendants("cellular_locations").First().Descendants("cellular_location").Select(x => x.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim()).ToList()
};
#endregion
#region state
reader.ReadToFollowing("state");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
State = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
#endregion
#region biofluid_locations
Biofluid_locations = new List <string>();
reader.ReadToFollowing("biofluid_locations");
subTree = reader.ReadSubtree();
subTreeContent = XElement.Load(subTree);
foreach (XElement synonym_content in subTreeContent.Descendants("biofluid"))
{
if (string.IsNullOrEmpty(synonym_content.Value) || string.IsNullOrWhiteSpace(synonym_content.Value) || synonym_content.Value == "\n")
{
continue;
}
else
{
Biofluid_locations.Add(synonym_content.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim());
}
}
#endregion
#region tissue_locations
Tissue_locations = new List <string>();
reader.ReadToFollowing("tissue_locations");
subTree = reader.ReadSubtree();
subTreeContent = XElement.Load(subTree);
foreach (XElement synonym_content in subTreeContent.Descendants("tissue"))
{
if (string.IsNullOrEmpty(synonym_content.Value) || string.IsNullOrWhiteSpace(synonym_content.Value) || synonym_content.Value == "\n")
{
continue;
}
else
{
Tissue_locations.Add(synonym_content.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim());
}
}
#endregion
#region pathways
List_of_pathways = new List <pathway>();
reader.ReadToFollowing("pathways");
subTree = reader.ReadSubtree();
subTreeContent = XElement.Load(subTree);
string kegg_map_id = "", smpdb_id = "";
pathway ptwy;
foreach (XElement pathway_content in subTreeContent.Descendants("pathway"))
{
kegg_map_id = (string.IsNullOrEmpty(pathway_content.Descendants("kegg_map_id").First().Value) ||
string.IsNullOrWhiteSpace(pathway_content.Descendants("kegg_map_id").First().Value) ||
pathway_content.Descendants("kegg_map_id").First().Value == "\n") ?
"" : pathway_content.Descendants("kegg_map_id").First().Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
smpdb_id = (string.IsNullOrEmpty(pathway_content.Descendants("smpdb_id").First().Value) ||
string.IsNullOrWhiteSpace(pathway_content.Descendants("smpdb_id").First().Value) ||
pathway_content.Descendants("smpdb_id").First().Value == "\n") ?
"" : pathway_content.Descendants("smpdb_id").First().Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
ptwy = new pathway()
{
Kegg_map_id = kegg_map_id,
Smpdb_map_id = smpdb_id
};
ptwy.get_details();
List_of_pathways.Add(ptwy);
}
foreach (SMPDB_pathway smpdb_ptwy in SMPDB_pathways.list_of_smpdb_pathways.Where(x => x.Hmdb_id == Hmdb_accession))
{
if (!List_of_pathways.Any(x => x.Smpdb_map_id == smpdb_ptwy.Id))
{
ptwy = new pathway()
{
Kegg_map_id = "",
Smpdb_map_id = smpdb_ptwy.Id
};
ptwy.get_details();
List_of_pathways.Add(ptwy);
}
}
#endregion
#region drugbank_id
reader.ReadToFollowing("drugbank_id");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Drugbank_id = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
#endregion
#region drugbank_metabolite_id
reader.ReadToFollowing("drugbank_metabolite_id");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Drugbank_metabolite_id = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
#endregion
#region chemspider_id
reader.ReadToFollowing("chemspider_id");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Chemspider_id = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
#endregion
#region kegg_id
Dict_kegg_details = new Dictionary <string, KEGG_entry_details>();
reader.ReadToFollowing("kegg_id");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Kegg_id = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
addKeggDetails((string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string);
#endregion
#region metlin_id
reader.ReadToFollowing("metlin_id");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Metlin_id = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
#endregion
#region pubchem_compound_id
reader.ReadToFollowing("pubchem_compound_id");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Pubchem_compound_id = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
#endregion
#region chebi_id
reader.ReadToFollowing("chebi_id");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Chebi_id = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
#endregion
#region synthesis_reference
reader.ReadToFollowing("synthesis_reference");
tmp_string = reader.ReadElementContentAsString().Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Synthesis_reference = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
#endregion
#region protein_associations
List_of_proteins = new List <protein>();
reader.ReadToFollowing("protein_associations");
subTree = reader.ReadSubtree();
subTreeContent = XElement.Load(subTree);
foreach (XElement pathway_content in subTreeContent.Descendants("protein"))
{
List_of_proteins.Add(new protein()
{
Protein_accession = (string.IsNullOrEmpty(pathway_content.Descendants("protein_accession").First().Value) ||
string.IsNullOrWhiteSpace(pathway_content.Descendants("protein_accession").First().Value) || pathway_content.Descendants("protein_accession").First().Value == "\n") ?
"" : pathway_content.Descendants("protein_accession").First().Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Name = (string.IsNullOrEmpty(pathway_content.Descendants("name").First().Value) ||
string.IsNullOrWhiteSpace(pathway_content.Descendants("name").First().Value) || pathway_content.Descendants("name").First().Value == "\n") ?
"" : pathway_content.Descendants("name").First().Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Uniprot_id = (string.IsNullOrEmpty(pathway_content.Descendants("uniprot_id").First().Value) ||
string.IsNullOrWhiteSpace(pathway_content.Descendants("uniprot_id").First().Value) || pathway_content.Descendants("uniprot_id").First().Value == "\n") ?
"" : pathway_content.Descendants("uniprot_id").First().Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Gene_name = (string.IsNullOrEmpty(pathway_content.Descendants("gene_name").First().Value) ||
string.IsNullOrWhiteSpace(pathway_content.Descendants("gene_name").First().Value) || pathway_content.Descendants("gene_name").First().Value == "\n") ?
"" : pathway_content.Descendants("gene_name").First().Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Protein_type = (string.IsNullOrEmpty(pathway_content.Descendants("protein_type").First().Value) ||
string.IsNullOrWhiteSpace(pathway_content.Descendants("protein_type").First().Value) || pathway_content.Descendants("protein_type").First().Value == "\n") ?
"" : pathway_content.Descendants("protein_type").First().Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim()
});
}
#endregion
}
public HMDB_metabolite_single_file(XElement metaboliteElement)
{
Cts_cas = new List <string>();
Cts_kegg = new List <string>();
Cts_chebi = new List <string>();
string tmp_string = "";
foreach (XElement item in metaboliteElement.Elements())
{
switch (item.Name.LocalName)
{
case "accession":
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Hmdb_accession = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
break;
case "secondary_accessions":
Hmdb_secondary_accessions = new List <string>();
foreach (XElement secondary_accession in item.Elements().Where(x => x.Name.LocalName == "accession"))
{
if (string.IsNullOrEmpty(secondary_accession.Value) || string.IsNullOrWhiteSpace(secondary_accession.Value) || secondary_accession.Value == "\n")
{
continue;
}
else
{
Hmdb_secondary_accessions.Add(secondary_accession.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim());
}
}
break;
case "name":
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Name = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
break;
case "description":
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Description = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
break;
case "synonyms":
Synonym_names = new List <string>();
foreach (XElement synonym_content in item.Elements().Where(x => x.Name.LocalName == "synonym"))
{
if (string.IsNullOrEmpty(synonym_content.Value) || string.IsNullOrWhiteSpace(synonym_content.Value) || synonym_content.Value == "\n")
{
continue;
}
else
{
Synonym_names.Add(synonym_content.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim());
}
}
break;
case "chemical_formula":
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Formula = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
break;
case "average_molecular_weight":
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Average_molecular_weight = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? -1 : Convert.ToDouble(tmp_string);
break;
case "monisotopic_moleculate_weight":
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Monisotopic_molecular_weight = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? -1 : Convert.ToDouble(tmp_string);
break;
case "iupac_name":
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Iupac_name = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
break;
case "traditional_iupac":
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Traditional_iupac = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
break;
case "cas_registry_number":
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Cas_registry_number = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
break;
case "smiles":
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Smiles = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
break;
case "inchi":
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Inchi = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
break;
case "inchikey":
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Inchikey = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
break;
case "taxonomy":
My_taxonomy = new taxonomy()
{
Description = (string.IsNullOrEmpty(item.Elements().First(x => x.Name.LocalName == "description").Value) ||
string.IsNullOrWhiteSpace(item.Elements().First(x => x.Name.LocalName == "description").Value) ||
item.Elements().First(x => x.Name.LocalName == "description").Value == "\n") ?
"" : item.Elements().First(x => x.Name.LocalName == "description").Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Direct_parent = (string.IsNullOrEmpty(item.Elements().First(x => x.Name.LocalName == "direct_parent").Value) ||
string.IsNullOrWhiteSpace(item.Elements().First(x => x.Name.LocalName == "direct_parent").Value) ||
item.Elements().First(x => x.Name.LocalName == "direct_parent").Value == "\n") ?
"" : item.Elements().First(x => x.Name.LocalName == "direct_parent").Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Kingdom = (string.IsNullOrEmpty(item.Elements().First(x => x.Name.LocalName == "kingdom").Value) ||
string.IsNullOrWhiteSpace(item.Elements().First(x => x.Name.LocalName == "kingdom").Value) ||
item.Elements().First(x => x.Name.LocalName == "kingdom").Value == "\n") ?
"" : item.Elements().First(x => x.Name.LocalName == "kingdom").Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Super_class = (string.IsNullOrEmpty(item.Elements().First(x => x.Name.LocalName == "super_class").Value) ||
string.IsNullOrWhiteSpace(item.Elements().First(x => x.Name.LocalName == "super_class").Value) ||
item.Elements().First(x => x.Name.LocalName == "super_class").Value == "\n") ?
"" : item.Elements().First(x => x.Name.LocalName == "super_class").Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Tclass = (string.IsNullOrEmpty(item.Elements().First(x => x.Name.LocalName == "class").Value) ||
string.IsNullOrWhiteSpace(item.Elements().First(x => x.Name.LocalName == "class").Value) ||
item.Elements().First(x => x.Name.LocalName == "class").Value == "\n") ?
"" : item.Elements().First(x => x.Name.LocalName == "class").Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Molecular_framework = (string.IsNullOrEmpty(item.Elements().First(x => x.Name.LocalName == "direct_parent").Value) ||
string.IsNullOrWhiteSpace(item.Elements().First(x => x.Name.LocalName == "direct_parent").Value) ||
item.Elements().First(x => x.Name.LocalName == "direct_parent").Value == "\n") ?
"" : item.Elements().First(x => x.Name.LocalName == "direct_parent").Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Alternative_parents = item.Elements().First(x => x.Name.LocalName == "alternative_parents").Elements().Where(x => x.Name.LocalName == "alternative_parent").
Select(x => x.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim()).ToList(),
Substituents = item.Elements().First(x => x.Name.LocalName == "substituents").Elements().Where(x => x.Name.LocalName == "substituent").
Select(x => x.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim()).ToList()
};
break;
case "ontology":
My_onotology = new ontology()
{
Status = (string.IsNullOrEmpty(item.Elements().First(x => x.Name.LocalName == "status").Value) ||
string.IsNullOrWhiteSpace(item.Elements().First(x => x.Name.LocalName == "status").Value) ||
item.Elements().First(x => x.Name.LocalName == "status").Value == "\n") ?
"" : item.Elements().First(x => x.Name.LocalName == "status").Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Origins = item.Elements().First(x => x.Name.LocalName == "origins").Elements().Where(x => x.Name.LocalName == "origin").
Select(x => x.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim()).ToList(),
Biofunctions = item.Elements().First(x => x.Name.LocalName == "biofunctions").Elements().Where(x => x.Name.LocalName == "biofunction").
Select(x => x.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim()).ToList(),
Applications = item.Elements().First(x => x.Name.LocalName == "applications").Elements().Where(x => x.Name.LocalName == "application").
Select(x => x.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim()).ToList(),
Cellular_locations = item.Elements().First(x => x.Name.LocalName == "cellular_locations").Elements().Where(x => x.Name.LocalName == "cellular_location").
Select(x => x.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim()).ToList()
};
break;
case "state":
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
State = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
break;
case "biofluid_locations":
Biofluid_locations = new List <string>();
foreach (XElement biofluid in item.Elements().Where(x => x.Name.LocalName == "biofluid"))
{
if (string.IsNullOrEmpty(biofluid.Value) || string.IsNullOrWhiteSpace(biofluid.Value) || biofluid.Value == "\n")
{
continue;
}
else
{
Biofluid_locations.Add(biofluid.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim());
}
}
break;
case "tissue_locations":
Tissue_locations = new List <string>();
foreach (XElement tissue in item.Elements().Where(x => x.Name.LocalName == "tissue"))
{
if (string.IsNullOrEmpty(tissue.Value) || string.IsNullOrWhiteSpace(tissue.Value) || tissue.Value == "\n")
{
continue;
}
else
{
Tissue_locations.Add(tissue.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim());
}
}
break;
case "pathways":
List_of_pathways = new List <pathway>();
string kegg_map_id = "", smpdb_id = "";
pathway ptwy;
foreach (XElement cpathway in item.Elements().Where(x => x.Name.LocalName == "pathway"))
{
kegg_map_id = (string.IsNullOrEmpty(cpathway.Elements().First(x => x.Name.LocalName == "kegg_map_id").Value) ||
string.IsNullOrWhiteSpace(cpathway.Elements().First(x => x.Name.LocalName == "kegg_map_id").Value) ||
cpathway.Elements().First(x => x.Name.LocalName == "kegg_map_id").Value == "\n") ?
"" : cpathway.Elements().First(x => x.Name.LocalName == "kegg_map_id").Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
smpdb_id = (string.IsNullOrEmpty(cpathway.Elements().First(x => x.Name.LocalName == "smpdb_id").Value) ||
string.IsNullOrWhiteSpace(cpathway.Elements().First(x => x.Name.LocalName == "smpdb_id").Value) ||
cpathway.Elements().First(x => x.Name.LocalName == "smpdb_id").Value == "\n") ?
"" : cpathway.Elements().First(x => x.Name.LocalName == "smpdb_id").Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
ptwy = new pathway()
{
Kegg_map_id = kegg_map_id,
Smpdb_map_id = smpdb_id
};
ptwy.get_details();
List_of_pathways.Add(ptwy);
}
foreach (SMPDB_pathway smpdb_ptwy in SMPDB_pathways.list_of_smpdb_pathways.Where(x => x.Hmdb_id == Hmdb_accession))
{
if (!List_of_pathways.Any(x => x.Smpdb_map_id == smpdb_ptwy.Id))
{
ptwy = new pathway()
{
Kegg_map_id = "",
Smpdb_map_id = smpdb_ptwy.Id
};
ptwy.get_details();
List_of_pathways.Add(ptwy);
}
}
break;
case "drugbank_id":
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Drugbank_id = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
break;
case "drugbank_metabolite_id":
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Drugbank_metabolite_id = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
break;
case "chemspider_id":
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Chemspider_id = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
break;
case "kegg_id":
Dict_kegg_details = new Dictionary <string, KEGG_entry_details>();
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Kegg_id = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
addKeggDetails((string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string);
break;
case "metlin_id":
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Metlin_id = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
break;
case "pubchem_compound_id":
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Pubchem_compound_id = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
break;
case "chebi_id":
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Chebi_id = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
break;
case "synthesis_reference":
tmp_string = item.Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim();
Synthesis_reference = (string.IsNullOrEmpty(tmp_string) || string.IsNullOrWhiteSpace(tmp_string) || tmp_string == "\n") ? "" : tmp_string;
break;
case "protein_associations":
List_of_proteins = new List <protein>();
foreach (XElement protein in item.Elements().Where(x => x.Name.LocalName == "protein"))
{
List_of_proteins.Add(new protein()
{
Protein_accession = (string.IsNullOrEmpty(protein.Elements().First(x => x.Name.LocalName == "protein_accession").Value) ||
string.IsNullOrWhiteSpace(protein.Elements().First(x => x.Name.LocalName == "protein_accession").Value) ||
protein.Elements().First(x => x.Name.LocalName == "protein_accession").Value == "\n") ?
"" : protein.Elements().First(x => x.Name.LocalName == "protein_accession").Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Name = (string.IsNullOrEmpty(protein.Elements().First(x => x.Name.LocalName == "name").Value) ||
string.IsNullOrWhiteSpace(protein.Elements().First(x => x.Name.LocalName == "name").Value) ||
protein.Elements().First(x => x.Name.LocalName == "name").Value == "\n") ?
"" : protein.Elements().First(x => x.Name.LocalName == "name").Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Uniprot_id = (string.IsNullOrEmpty(protein.Elements().First(x => x.Name.LocalName == "uniprot_id").Value) ||
string.IsNullOrWhiteSpace(protein.Elements().First(x => x.Name.LocalName == "uniprot_id").Value) ||
protein.Elements().First(x => x.Name.LocalName == "uniprot_id").Value == "\n") ?
"" : protein.Elements().First(x => x.Name.LocalName == "uniprot_id").Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Gene_name = (string.IsNullOrEmpty(protein.Elements().First(x => x.Name.LocalName == "gene_name").Value) ||
string.IsNullOrWhiteSpace(protein.Elements().First(x => x.Name.LocalName == "gene_name").Value) ||
protein.Elements().First(x => x.Name.LocalName == "gene_name").Value == "\n") ?
"" : protein.Elements().First(x => x.Name.LocalName == "gene_name").Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Protein_type = (string.IsNullOrEmpty(protein.Elements().First(x => x.Name.LocalName == "protein_type").Value) ||
string.IsNullOrWhiteSpace(protein.Elements().First(x => x.Name.LocalName == "protein_type").Value) ||
protein.Elements().First(x => x.Name.LocalName == "protein_type").Value == "\n") ?
"" : protein.Elements().First(x => x.Name.LocalName == "protein_type").Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim()
});
}
break;
case "diseases":
List_of_diseases = new List <disease>();
disease ds;
foreach (XElement cdisease in item.Elements().Where(x => x.Name.LocalName == "disease"))
{
ds = new disease()
{
Name = (string.IsNullOrEmpty(cdisease.Elements().First(x => x.Name.LocalName == "name").Value) ||
string.IsNullOrWhiteSpace(cdisease.Elements().First(x => x.Name.LocalName == "name").Value) ||
cdisease.Elements().First(x => x.Name.LocalName == "name").Value == "\n") ?
"" : cdisease.Elements().First(x => x.Name.LocalName == "name").Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
Omim_id = (string.IsNullOrEmpty(cdisease.Elements().First(x => x.Name.LocalName == "omim_id").Value) ||
string.IsNullOrWhiteSpace(cdisease.Elements().First(x => x.Name.LocalName == "omim_id").Value) ||
cdisease.Elements().First(x => x.Name.LocalName == "omim_id").Value == "\n") ?
"" : cdisease.Elements().First(x => x.Name.LocalName == "omim_id").Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim(),
List_of_pubmed_ids = new List <string>()
};
foreach (XElement references in cdisease.Elements().Where(x => x.Name.LocalName == "references"))
{
foreach (XElement reference in references.Elements().Where(x => x.Name.LocalName == "reference"))
{
if (reference.Elements().Any(x => x.Name.LocalName == "pubmed_id") &&
!string.IsNullOrEmpty(reference.Elements().First(x => x.Name.LocalName == "pubmed_id").Value) &&
!string.IsNullOrWhiteSpace(reference.Elements().First(x => x.Name.LocalName == "pubmed_id").Value) &&
reference.Elements().First(x => x.Name.LocalName == "pubmed_id").Value != "\n")
{
ds.List_of_pubmed_ids.Add(reference.Elements().First(x => x.Name.LocalName == "pubmed_id").Value.Replace("\r", "").Replace("\n", "").Replace("\t", "").Trim());
}
}
}
List_of_diseases.Add(ds);
}
break;
default:
break;
}
}
}
