Extract of no. shared gene names in disease-disease association though API from Disgenet Database

Question

[alirejwan.stars1994]

Hello Everyone, I am trying to extract the shared gene between two diseases (disease-disease association) from the "Disgenet Database". But I only received a number but not the name or symbol of genes between the diseases. When we click the no. given in the "shared gene" column we receive the names. I also tried Disgenet API but received only the no of shared genes not the name or symbol of genes between the two diseases. I am trying to create a database of shared genes between diseases. Could anyone help me download the name or symbol of shared genes of disease related to candidiasis through Disgenet API without repeatedly clicking on the number in the "shared gene" column?

[GenoMax]

Various downloads appear to be available from Disgenet site. Perhaps one of those files will help you. Requires registration for an account.

[alirejwan.stars1994]

I highly appreciate your response.

Yes, I have an account, and download the tab-separated files. but it gives statistical numbers. In "gene association" they provide the no. of disease not the name of the disease associated with the gene. In "Disease association" they provide no of genes associated with it.

All I want is "shared gene names or symbols" between the two diseases.

Answer 1

[Pierre Lindenbaum]

using the sparql endpoint at: http://rdf.disgenet.org/sparql/ (and the schema here: https://www.disgenet.org/static/disgenet_ap1/images/rdf/disgenet_rdf_schema_v7.png )

SELECT DISTINCT ?gene ?geneSymbol  ?disease1 ?disease1Name ?disease2 ?disease2Name
WHERE {

?gene a ncit:C16612 .
?gene sio:SIO_000205 ?geneInfo .
?geneInfo rdfs:label ?geneSymbol .

?gene2disease1 a sio:SIO_000983 .
?gene2disease1 sio:SIO_000628  ?gene .
?gene2disease1 sio:SIO_000628  ?disease1 .
?disease1 a ncit:C7057 .
?disease1 rdfs:label ?disease1Name .


?gene2disease2 a sio:SIO_000983 .
?gene2disease2 sio:SIO_000628  ?gene .
?gene2disease2 sio:SIO_000628  ?disease2 .
?disease2 a ncit:C7057 .
?disease2 rdfs:label ?disease2Name .

FILTER(STR(?disease1) <STR(?disease2))

} LIMIT 100

output:

"gene"  "geneSymbol"    "disease1"  "disease1Name"  "disease2"  "disease2Name"
"http://identifiers.org/ncbigene/153090"    "DAB2IP [hgnc:DAB2IP]"  "http://linkedlifedata.com/resource/umls/id/C0024121"   "Lung Neoplasms [umls:C0024121]"    "http://linkedlifedata.com/resource/umls/id/C0033578""Prostatic Neoplasms [umls:C0033578]"
"http://identifiers.org/ncbigene/6298"  "SAI1 [hgnc:SAI1]"  "http://linkedlifedata.com/resource/umls/id/C0023452"   "Childhood Acute Lymphoblastic Leukemia [umls:C0023452]"    "http://linkedlifedata.com/resource/umls/id/C0242379"   "Malignant neoplasm of lung [umls:C0242379]"
"http://identifiers.org/ncbigene/11102" "RPP14 [hgnc:RPP14]"    "http://linkedlifedata.com/resource/umls/id/C0005684"   "Malignant neoplasm of urinary bladder [umls:C0005684]" "http://linkedlifedata.com/resource/umls/id/C0009324"   "Ulcerative Colitis [umls:C0009324]"
"http://identifiers.org/ncbigene/11102" "RPP14 [hgnc:RPP14]"    "http://linkedlifedata.com/resource/umls/id/C0007873"   "Uterine Cervical Neoplasm [umls:C0007873]" "http://linkedlifedata.com/resource/umls/id/C0009324""Ulcerative Colitis [umls:C0009324]"
"http://identifiers.org/ncbigene/11102" "RPP14 [hgnc:RPP14]"    "http://linkedlifedata.com/resource/umls/id/C0001418"   "Adenocarcinoma [umls:C0001418]"    "http://linkedlifedata.com/resource/umls/id/C0009324"   "Ulcerative Colitis [umls:C0009324]"

use wc to count the rows or use a sparl statement COUNT(*) to count the number of distinct resutls.

[alirejwan.stars1994]

I highly appreciate your response.

According to the output disease1 varies, if I want to constant the disease1 to only "Candidiasis" and try to know all the associated diseases with it (disease2) and shared genes between them with "association type" and "some statistical measures like GDA score" and other statistical measures "between the genes and the disease1 as well as disease2".