private IEnumerable <OmimItem> GetOmimItems(EntryRoot entryRoot, IDictionary <int, string> mimToGeneSymbol, IDictionary <int, string> phenotypeDescriptions)
{
foreach (var entry in entryRoot.omim.entryList)
{
var item = entry.entry;
var mimNumber = item.mimNumber;
//skip if not a supported gene symbol
if (!mimToGeneSymbol.TryGetValue(mimNumber, out var geneSymbol))
{
continue;
}
string description = OmimUtilities.ExtractAndProcessItemDescription(item);
string geneName = item.geneMap?.geneName;
var phenotypes = item.geneMap?.phenotypeMapList?.Select(x => OmimUtilities.GetPhenotype(x, phenotypeDescriptions, _jsonSchema.GetSubSchema("phenotypes")))
.ToList() ?? new List <OmimItem.Phenotype>();
yield return(new OmimItem(geneSymbol, geneName, description, mimNumber, phenotypes, _jsonSchema));
}
}
private static IDictionary <int, string> GetPhenotypeDescriptions(EntryRoot entryRoot)
{
IDictionary <int, string> phenotypeToDescription = new Dictionary <int, string>();
foreach (var entry in entryRoot.omim.entryList)
{
var item = entry.entry;
// gene only item
if (item.prefix == '*')
{
continue;
}
var description = OmimUtilities.ExtractAndProcessItemDescription(item);
if (string.IsNullOrEmpty(description))
{
continue;
}
phenotypeToDescription[item.mimNumber] = description;
}
return(phenotypeToDescription);
}
