Phenotype and organism model references for a large list of genes

Question

[storm1907]

Hi all. I have to generate table for about 3500 genes with following columns:

1) references to each gene; 2) pathological features 3) reference to the organism model, e.g. MGI number for mouse

Are there any databases/softwares, which takes long gene list as input and outputs if not all, then at least one of desired output type (list above)?

I am really frustrated, because doing this manually, gene by gene, is devastating

Thank you in advance!

Answer 1

[Pierre Lindenbaum]

human, using mondo : https://github.com/monarch-initiative/mondo

mkdir -p WORK/apache-jena-4.8.0/
wget -O "WORK/jeter.zip" "https://dlcdn.apache.org/jena/binaries/apache-jena-4.8.0.zip"
(cd /SCRATCH-BIRD/users/lindenbaum-p/work/NEXTFLOW/2023/20230429.hs38me.mondo.rdf.splarql/work && unzip jeter.zip && rm jeter.zip)
wget -O "WORK/mondo.owl" "https://github.com/monarch-initiative/mondo/releases/latest/download/mondo.owl"
WORK/apache-jena-4.8.0/bin/tdbloader --loc=WORK/TDB/ WORK/mondo.owl
WORK/apache-jena-4.8.0/bin/tdbquery --loc=WORK/TDB/ --query=query.sparql  --results=TSV

?gene_name  ?gene   ?property_label ?property   ?entity_label   ?entity
"RIT1"  <http://identifiers.org/hgnc/10023> "has material basis in germline mutation in"    <http://purl.obolibrary.org/obo/RO_0004003> "Noonan syndrome 8" <http://purl.obolibrary.org/obo/MONDO_0014143>
"RYR2"  <http://identifiers.org/hgnc/10484> "has material basis in germline mutation in"    <http://purl.obolibrary.org/obo/RO_0004003> "arrhythmogenic right ventricular dysplasia 2"  <http://purl.obolibrary.org/obo/MONDO_0010975>
"SCN1A" <http://identifiers.org/hgnc/10585> "has material basis in germline mutation in"    <http://purl.obolibrary.org/obo/RO_0004003> "migraine, familial hemiplegic, 3"  <http://purl.obolibrary.org/obo/MONDO_0012320>
"SCN1B" <http://identifiers.org/hgnc/10586> "has material basis in germline mutation in"    <http://purl.obolibrary.org/obo/RO_0004003> "Brugada syndrome 5"    <http://purl.obolibrary.org/obo/MONDO_0013015>
"SCN1B" <http://identifiers.org/hgnc/10586> "has material basis in germline mutation in"    <http://purl.obolibrary.org/obo/RO_0004003> "atrial fibrillation, familial, 13" <http://purl.obolibrary.org/obo/MONDO_0014155>
"SCN2B" <http://identifiers.org/hgnc/10589> "has material basis in germline mutation in"    <http://purl.obolibrary.org/obo/RO_0004003> "atrial fibrillation, familial, 14" <http://purl.obolibrary.org/obo/MONDO_0014156>
"SCN4B" <http://identifiers.org/hgnc/10592> "has material basis in germline mutation in"    <http://purl.obolibrary.org/obo/RO_0004003> "long QT syndrome 10"   <http://purl.obolibrary.org/obo/MONDO_0012737>
"SCN5A" <http://identifiers.org/hgnc/10593> "has material basis in germline mutation in"    <http://purl.obolibrary.org/obo/RO_0004003> "progressive familial heart block, type 1A" <http://purl.obolibrary.org/obo/MONDO_0007240>
"SCN5A" <http://identifiers.org/hgnc/10593> "has material basis in germline mutation in"    <http://purl.obolibrary.org/obo/RO_0004003> "Brugada syndrome 1"    <http://purl.obolibrary.org/obo/MONDO_0011001>

with query.sparql:

    prefix owl: <http://www.w3.org/2002/07/owl#>
    prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
    prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
    prefix mondo: <http://purl.obolibrary.org/obo/mondo#>
    prefix RO: <http://purl.obolibrary.org/obo/RO_>
    PREFIX obo: <http://purl.obolibrary.org/obo/>

    SELECT DISTINCT
        ?gene_name ?gene
        ?property_label ?property
        ?entity_label  ?entity
    WHERE 
    {


      ?entity rdfs:subClassOf [ rdf:type owl:Restriction ;
      owl:onProperty ?property ;
      owl:someValuesFrom ?gene ] . 
      ?entity rdfs:label ?entity_label .


      ?entity rdfs:subClassOf* obo:MONDO_0004995 .


     OPTIONAL {
      ?property rdfs:label ?property_label .
     }

     OPTIONAL {
      ?gene rdfs:label ?gene_name .
     }


    FILTER (isIRI(?entity) && STRSTARTS(str(?entity), "http://purl.obolibrary.org/obo/MONDO_"))
    FILTER (isIRI(?gene) && regex(str(?gene), "hgnc"))
    }

(see also:

and here is the #sparql query ! (thanks @[e-mail] ) #mondohttps://t.co/m9pNSmGxCh

— Pierre Lindenbaum ([e-mail]) (@yokofakun) May 2, 2023

)