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Update 2nd order interact query #288

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merged 2 commits into from
Jul 14, 2020
Merged

Update 2nd order interact query #288

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735eae1
Fix bug in run.py query when output dir doesn't exist
justaddcoffee Jul 14, 2020
5d457db
Add query for 2nd order interactors with SARS-CoV-2 proteins
justaddcoffee Jul 14, 2020
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25 changes: 25 additions & 0 deletions queries/sparql/query-04-sars-cov-2-interactors_2nd_order.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
title:
"Get 2nd order interactors"
description:
"Get human proteins that interact human proteins that interact with SARS-CoV-2 proteins"
endpoint:
"http://kg-hub-rdf.berkeleybop.io/blazegraph/sparql"
query: >
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
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 bl: <https://w3id.org/biolink/vocab/>
SELECT ?covp ?covplab ?humanp ?humanplab ?humanp2 ?humanp2lab
WHERE {
VALUES ?covtaxon {"2697049"^^xsd:string }
VALUES ?humantaxon { "9606"^^xsd:string }
?humanp bl:interacts_with ?covp .
?humanp bl:interacts_with ?humanp2 .
?covp bl:category bl:Protein; <https://www.example.org/UNKNOWN/ncbi_taxid> ?covtaxon .
?humanp bl:category bl:Protein; <https://www.example.org/UNKNOWN/ncbi_taxid> ?humantaxon .
?humanp2 bl:category bl:Protein; <https://www.example.org/UNKNOWN/ncbi_taxid> ?humantaxon .
OPTIONAL { ?covp rdfs:label ?covplab } .
OPTIONAL { ?humanp rdfs:label ?humanplab } .
OPTIONAL { ?humanp2 rdfs:label ?humanp2lab } .
}
2 changes: 2 additions & 0 deletions run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -102,6 +102,8 @@ def query(yaml: str, output_dir: str,
"""
query = parse_query_yaml(yaml)
result_dict = run_query(query=query[query_key], endpoint=query[endpoint_key])
if not os.path.exists(output_dir):
os.makedirs(output_dir)
outfile = os.path.join(output_dir, os.path.splitext(os.path.basename(yaml))[0] +
outfile_ext)
result_dict_to_tsv(result_dict, outfile)
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