public void ToHMDB_metabolite(metabolite db_metabolite)
{
Hmdb_accession = db_metabolite.Hmdb_accession;
Hmdb_secondary_accessions = db_metabolite.Hmdb_secondary_accessions;
Name = db_metabolite.Name;
IsProblematic = db_metabolite.IsProblematic;
Synonym_names = db_metabolite.Synonym_names;
Description = db_metabolite.Description;
Description_chebi = db_metabolite.Description_chebi;
Quality = db_metabolite.Quality;
Comment = db_metabolite.Comment;
Charge = db_metabolite.Charge;
Formula = db_metabolite.Formula;
Formula_chebi = db_metabolite.Formula_chebi;
Average_molecular_weight = db_metabolite.Average_molecular_weight;
Monisotopic_molecular_weight = db_metabolite.Monisotopic_molecular_weight;
Mass = db_metabolite.Mass;
Monoisotopic_mass = db_metabolite.Monoisotopic_mass;
Iupac_name = db_metabolite.Iupac_name;
Traditional_iupac = db_metabolite.Traditional_iupac;
Cas_registry_number = db_metabolite.Cas_registry_number;
Cts_cas = db_metabolite.Cts_cas;
Smiles = db_metabolite.Smiles;
Inchi = db_metabolite.Inchi;
Inchi_chebi = db_metabolite.Inchi_chebi;
Inchikey = db_metabolite.Inchikey;
My_taxonomy = new taxonomy()
{
Direct_parent = db_metabolite.My_taxonomy.Direct_parent,
Kingdom = db_metabolite.My_taxonomy.Kingdom,
Super_class = db_metabolite.My_taxonomy.Super_class,
Tclass = db_metabolite.My_taxonomy.Tclass,
Substituents = db_metabolite.My_taxonomy.Substituents,
Other_descriptors = db_metabolite.My_taxonomy.Other_descriptors
};
My_onotology = new ontology()
{
Status = db_metabolite.My_onotology.Status,
Origins = db_metabolite.My_onotology.Origins,
Biofunctions = db_metabolite.My_onotology.Biofunctions,
Applications = db_metabolite.My_onotology.Applications,
Cellular_locations = db_metabolite.My_onotology.Cellular_locations
};
State = db_metabolite.State;
Biofluid_locations = db_metabolite.Biofluid_locations;
Tissue_locations = db_metabolite.Tissue_locations;
List_of_pathways = db_metabolite.List_of_pathways;
Drugbank_id = db_metabolite.Drugbank_id;
Drugbank_metabolite_id = db_metabolite.Drugbank_metabolite_id;
Chemspider_id = db_metabolite.Chemspider_id;
Kegg_id = db_metabolite.Kegg_id;
Cts_kegg = db_metabolite.Cts_kegg;
Metlin_id = db_metabolite.Metlin_id;
Pubchem_compound_id = db_metabolite.Pubchem_compound_id;
Chebi_id = db_metabolite.Chebi_id;
Cts_chebi = db_metabolite.Cts_chebi;
Synthesis_reference = db_metabolite.Synthesis_reference;
List_of_proteins = db_metabolite.List_of_proteins;
}
/// <summary> </summary>
public void delete(int id)
{
taxonomy tag = ActiveRecordBase <taxonomy> .Find(id);
ActiveRecordMediator <taxonomy> .Delete(tag);
RedirectToReferrer();
}
/// <summary> </summary>
public static taxonomy get_taxonomy(String alias)
{
List <AbstractCriterion> filtering = new List <AbstractCriterion>();
filtering.Add(Expression.Eq("alias", alias));
taxonomy taxonomy = ActiveRecordBase <taxonomy> .FindFirst(filtering.ToArray());
return(taxonomy);
}
public ActionResult DeleteConfirmed(int id, string content_type)
{
ViewBag._content_type = content_type;
taxonomy taxonomy = db.taxonomies.Find(id);
db.taxonomies.Remove(taxonomy);
db.SaveChanges();
return(RedirectToAction("Index", new { content_type }));
}
/// <summary> </summary>
public void mass_delete_taxonomy(int[] ids)
{
foreach (int id in ids)
{
taxonomy tag = ActiveRecordBase <taxonomy> .Find(id);
ActiveRecordMediator <taxonomy> .Delete(tag);
}
RedirectToAction("taxonomy");
}
/// <summary> </summary>
public void massDeleteTags(int[] ids)
{
foreach (int id in ids)
{
taxonomy tag = ActiveRecordBase <taxonomy> .Find(id);
ActiveRecordMediator <taxonomy> .Delete(tag);
}
RedirectToReferrer();
}
/// <summary> </summary>
public void Update(int id, [DataBind("tag")] taxonomy tag)
{
try {
ActiveRecordMediator <taxonomy> .Save(tag);
} catch (Exception ex) {
Flash["error"] = ex.Message;
Flash["tag"] = tag;
}
RedirectToAction("index");
}
/// <summary> </summary>
public void delete_taxonomy(int id)
{
taxonomy taxonomy = ActiveRecordBase <taxonomy> .Find(id);
Flash["message"] = "A taxonomy, <strong>" + taxonomy.name + "</strong>, has been <strong>deleted</strong>.";
ActiveRecordMediator <taxonomy> .Delete(taxonomy);
CancelLayout();
RedirectToAction("taxonomy");
}
/// <summary> </summary>
public void merge_taxonomy(int[] ids, string newname)
{
CancelLayout();
CancelView();
log.Info("starting merge proccess");
if (!String.IsNullOrEmpty(Request.Params["deleteTags"]))
{
mass_delete_taxonomy(ids); return;
}
dynamic items = new List <_base>();
string name = "";
taxonomy_type oldtype = null;
foreach (int id in ids)
{
taxonomy tax = ActiveRecordBase <taxonomy> .Find(id);
oldtype = tax.taxonomy_type;
name = tax.name;
log.Info("found taxonomy" + name);
items.AddRange(tax.get_taxonomy_items(oldtype.alias, tax.alias));
foreach (dynamic p in tax.items)
{
log.Info("removing taxonomy from item " + p.alias);
p.taxonomies.Remove(tax);
ActiveRecordMediator <_base> .Save(p);
}
ActiveRecordMediator <taxonomy> .Delete(tax);
}
taxonomy t = new taxonomy();
name = String.IsNullOrEmpty(newname) ? name : newname;
t.name = name;
String alias = name.Replace(' ', '_').ToLower();
t.alias = alias;
t.taxonomy_type = oldtype;
ActiveRecordMediator <taxonomy> .Save(t);
log.Info("created taxonomy with new name");
foreach (_base p in items)
{
log.Info("appling taxonomy " + oldtype.alias);
PropertyInfo propInfo = p.GetType().GetProperty(oldtype.alias);
propInfo.SetValue(p, alias, new object[] { });
//postingService.get_taxonomy(p.innovator_company).name
p.taxonomies.Add(t);
log.Info("adding new taxonomy back to items");
ActiveRecordMediator <_base> .Save(p);
}
RedirectToAction("taxonomy");
}
/// <summary> </summary>
public void update_taxonomy([ARDataBind("taxonomy", Validate = true, AutoLoad = AutoLoadBehavior.NewRootInstanceIfInvalidKey)] taxonomy taxonomy, Boolean ajax, String oldtax_alias, String oldtax_type_alias)
{
ActiveRecordMediator <taxonomy> .Save(taxonomy);
dynamic items = new List <_base>();
string name = "";
taxonomy_type type = null;
if (!String.IsNullOrWhiteSpace(oldtax_alias) && !String.IsNullOrWhiteSpace(oldtax_type_alias))
{
type = taxonomy.taxonomy_type;
name = taxonomy.name;
ActiveRecordMediator <_base> .Save(taxonomy);
//find old ones and clean them up
taxonomy tax = ActiveRecordBase <taxonomy> .Find(taxonomy.baseid);
try {
IList <_base> taxed = tax.get_taxonomy_items(oldtax_type_alias, oldtax_alias);
if (taxed.Count() > 0)
{
items.AddRange(taxed);
String alias = taxonomy.alias;
foreach (_base p in items)
{
log.Info("appling taxonomy " + type.alias + " to " + p.baseid + "/" + p.alias);
PropertyInfo propInfo = p.GetType().GetProperty(type.alias);
propInfo.SetValue(p, alias, new object[] { });
log.Info("adding new taxonomy back to items");
ActiveRecordMediator <_base> .Save(p);
}
}
} catch {
}
Flash["message"] = "taxonomy has " + items.Count + " items to change from: <b>" + oldtax_type_alias + "/" + oldtax_alias +
"</b> TO <b>" + type.alias + "/" + taxonomy.alias + "</b>";
log.Info("taxonomy has " + items.Count + " items to change to " + oldtax_type_alias + "/" + oldtax_alias);
}
if (ajax)
{
CancelLayout();
Response.ContentType = "application/json; charset=UTF-8";
if (taxonomy.baseid > 0)
{
RenderText("{\"state\":\"true\",\"baseid\":\"" + taxonomy.baseid + "\",\"name\":\"" + taxonomy.name + "\",\"alias\":\"" + taxonomy.alias + "\"}");
}
else
{
RenderText("{\"state\":\"false\"}");
}
return;
}
RedirectToAction("taxonomy");
}
public ActionResult Edit([Bind(Include = "id,title,body,excerpt,content_type,created_by,created_at")] taxonomy taxonomy, string content_type)
{
ViewBag._content_type = content_type;
if (ModelState.IsValid)
{
db.Entry(taxonomy).State = EntityState.Modified;
db.SaveChanges();
return(RedirectToAction("Index", new { content_type }));
}
ViewBag.created_by = new SelectList(db.users, "id", "username", taxonomy.created_by);
return(View(taxonomy));
}
public ActionResult Delete(int?id, string content_type)
{
if (id == null)
{
return(new HttpStatusCodeResult(HttpStatusCode.BadRequest));
}
taxonomy taxonomy = db.taxonomies.Find(id);
if (taxonomy == null)
{
return(HttpNotFound());
}
return(RedirectToAction("Index", new { content_type }));
}
public ActionResult Details(int?id)
{
if (id == null)
{
return(new HttpStatusCodeResult(HttpStatusCode.BadRequest));
}
taxonomy taxonomy = db.taxonomies.Find(id);
if (taxonomy == null)
{
return(HttpNotFound());
}
return(View(taxonomy));
}
public ActionResult ContestDetails(int?id, string type)
{
ViewBag._index_content_type = type;
if (id == null)
{
return(new HttpStatusCodeResult(HttpStatusCode.BadRequest));
}
taxonomy taxonomy = db.taxonomies.Find(id);
if (taxonomy == null)
{
return(HttpNotFound());
}
return(View(taxonomy));
}
public ActionResult Create([Bind(Include = "id,title,body,excerpt,content_type,created_by,created_at")] taxonomy taxonomy, string content_type)
{
if (ModelState.IsValid)
{
ViewBag._content_type = content_type;
taxonomy.created_at = DateTime.Now;
taxonomy.created_by = db.users.Where(u => u.username == User.Identity.Name).FirstOrDefault().id;
db.taxonomies.Add(taxonomy);
db.SaveChanges();
return(RedirectToAction("Index", new { content_type }));
}
ViewBag.created_by = new SelectList(db.users, "id", "username", taxonomy.created_by);
return(View(taxonomy));
}
public ActionResult Edit(int?id)
{
if (id == null)
{
return(new HttpStatusCodeResult(HttpStatusCode.BadRequest));
}
taxonomy taxonomy = db.taxonomies.Find(id);
if (taxonomy == null)
{
return(HttpNotFound());
}
ViewBag.created_by = new SelectList(db.users, "id", "username", taxonomy.created_by);
return(View(taxonomy));
}
/// <summary> </summary>
public static taxonomy get_taxonomy(String prefix, String alias, String taxonomy_type)
{
List <AbstractCriterion> filtering = new List <AbstractCriterion>();
filtering.Add(Expression.Eq("alias", String.IsNullOrWhiteSpace(prefix) ? "" : prefix + "__" + alias));
filtering.Add(Expression.Eq("taxonomy_type", ActiveRecordBase <taxonomy_type> .FindAll(
new List <AbstractCriterion>()
{
Expression.Eq("alias", taxonomy_type)
}.ToArray()
).FirstOrDefault()));
taxonomy taxonomy = ActiveRecordBase <taxonomy> .FindFirst(filtering.ToArray());
if (taxonomy == null)
{
taxonomy = get_taxonomy(alias); //fallback on single
}
return(taxonomy);
}
/// <summary> </summary>
public void edit_taxonomy(string type, int id, Boolean skiplayout)
{
taxonomy taxonomy_type = new taxonomy();
if (id > 0)
{
taxonomy_type = ActiveRecordBase <taxonomy> .Find(id);
}
PropertyBag["item"] = taxonomy_type;
PropertyBag["taxonomy_types"] = ActiveRecordBase <taxonomy_type> .FindAll(Order.Asc("name"));
PropertyBag["action"] = String.IsNullOrWhiteSpace(type)? taxonomy_type.name : type;
PropertyBag["skiplayout"] = skiplayout;
if (skiplayout)
{
CancelLayout();
}
RenderView("../admin/taxonomy/_editor");
}
/// <summary> </summary>
public void merge(int[] ids, string newname)
{
if (!String.IsNullOrEmpty(Request.Params["deleteTags"]))
{
massDeleteTags(ids);
return;
}
dynamic places = new List <_base>();
string name = "";
foreach (int id in ids)
{
taxonomy tag = ActiveRecordBase <taxonomy> .Find(id);
name = tag.name;
places.AddRange(tag.taxonomies);
foreach (dynamic p in tag.items)
{
p.taxonomies.Remove(tag);
ActiveRecordMediator <_base> .Save(p);
}
ActiveRecordMediator <taxonomy> .Delete(tag);
}
taxonomy t = new taxonomy();
t.name = String.IsNullOrEmpty(newname) ? name : newname;
ActiveRecordMediator <taxonomy> .Save(t);
foreach (posting p in places)
{
p.taxonomies.Add(t);
ActiveRecordMediator <posting> .Save(p);
}
RedirectToReferrer();
}
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;
}
}
}
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 void metabolite_from_db(string db_line)
{
List <string> breakAtSep = db_line.Split('\t').ToList();
Hmdb_accession = breakAtSep.First(); //0
Hmdb_secondary_accessions = breakAtSep.ElementAt(1).Split('|').Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x)).ToList(); //1
Name = breakAtSep.ElementAt(2); //2
IsProblematic = Convert.ToBoolean(breakAtSep.ElementAt(3)); //3
Synonym_names = breakAtSep.ElementAt(4).Split('|').Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x)).ToList(); //4
Description = breakAtSep.ElementAt(5); //5
Description_chebi = breakAtSep.ElementAt(6); //6
Quality = breakAtSep.ElementAt(7); //7
Comment = breakAtSep.ElementAt(8); //8
Charge = breakAtSep.ElementAt(9); //9
Formula = breakAtSep.ElementAt(10); //10
Formula_chebi = breakAtSep.ElementAt(11); //11
Average_molecular_weight = Convert.ToDouble(breakAtSep.ElementAt(12)); //12
Monisotopic_molecular_weight = Convert.ToDouble(breakAtSep.ElementAt(13)); //13
Mass = Convert.ToDouble(breakAtSep.ElementAt(14)); //14
Monoisotopic_mass = Convert.ToDouble(breakAtSep.ElementAt(15)); //15
Iupac_name = breakAtSep.ElementAt(16); //16
Traditional_iupac = breakAtSep.ElementAt(17); //17
Cas_registry_number = breakAtSep.ElementAt(18); //18
Cts_cas = breakAtSep.ElementAt(19).Split('|').Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x)).ToList(); //19
Smiles = breakAtSep.ElementAt(20); //20
Inchi = breakAtSep.ElementAt(21); //21
Inchi_chebi = breakAtSep.ElementAt(22); //22
Inchikey = breakAtSep.ElementAt(23); //23
My_taxonomy = new taxonomy()
{
Description = breakAtSep.ElementAt(24), //24
Direct_parent = breakAtSep.ElementAt(25), //25
Kingdom = breakAtSep.ElementAt(26), //26
Super_class = breakAtSep.ElementAt(27), //27
Tclass = breakAtSep.ElementAt(28), //28
Molecular_framework = breakAtSep.ElementAt(29), //29
Alternative_parents = breakAtSep.ElementAt(30).Split('|').Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x)).ToList(), //30
Substituents = breakAtSep.ElementAt(31).Split('|').Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x)).ToList(), //31
Other_descriptors = breakAtSep.ElementAt(32).Split('|').Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x)).ToList() //32
};
My_onotology = new ontology()
{
Status = breakAtSep.ElementAt(33), //33
Origins = breakAtSep.ElementAt(34).Split('|').Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x)).ToList(), //34
Biofunctions = breakAtSep.ElementAt(35).Split('|').Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x)).ToList(), //35
Applications = breakAtSep.ElementAt(36).Split('|').Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x)).ToList(), //36
Cellular_locations = breakAtSep.ElementAt(37).Split('|').Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x)).ToList() //37
};
State = breakAtSep.ElementAt(38); //38
Biofluid_locations = breakAtSep.ElementAt(39).Split('|').Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x)).ToList(); //39
Tissue_locations = breakAtSep.ElementAt(40).Split('|').Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x)).ToList(); //40
List_of_pathways = returnListOfPathways(breakAtSep.GetRange(41, 16)); //41-56
Drugbank_id = breakAtSep.ElementAt(57); //57
Drugbank_metabolite_id = breakAtSep.ElementAt(58); //58
Chemspider_id = breakAtSep.ElementAt(59); //59
Kegg_id = breakAtSep.ElementAt(60); //60
Cts_kegg = breakAtSep.ElementAt(61).Split('|').Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x)).ToList(); //61
Metlin_id = breakAtSep.ElementAt(62); //62
Pubchem_compound_id = breakAtSep.ElementAt(63); //63
Cts_Pubchem = breakAtSep.ElementAt(64).Split('|').Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x)).ToList(); //64
Lipidmaps_id = breakAtSep.ElementAt(65); //65
Cts_Lipidmaps = breakAtSep.ElementAt(66).Split('|').Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x)).ToList(); //66
Chebi_id = breakAtSep.ElementAt(67); //67
Cts_chebi = breakAtSep.ElementAt(68).Split('|').Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x)).ToList(); //68
Synthesis_reference = breakAtSep.ElementAt(69); //69
List_of_proteins = returnListOfProteins(breakAtSep.GetRange(70, 5)); //70-74
List_of_diseases = returnListOfDiseases(breakAtSep.GetRange(75, 3)); //75-77
}
