diff options
| -rw-r--r-- | doc/INSTALL.md | 1 | ||||
| -rw-r--r-- | scripts/db_enrichment/country_enrichment.py | 29 | ||||
| -rw-r--r-- | scripts/db_enrichment/input_location.csv | 10 | ||||
| -rw-r--r-- | scripts/db_enrichment/readme.md | 12 |
4 files changed, 34 insertions, 18 deletions
diff --git a/doc/INSTALL.md b/doc/INSTALL.md index 45aca0f..367b452 100644 --- a/doc/INSTALL.md +++ b/doc/INSTALL.md @@ -77,6 +77,7 @@ Note: see above on GUIX_PACKAGE_PATH. ## Run country semantic enrichment script cd bh20-seq-resource/scripts/db_enrichment + edit input_location.csv guix environment guix --ad-hoc git python nss-certs python-rdflib -- python3 country_enrichment.py ## Run the tests diff --git a/scripts/db_enrichment/country_enrichment.py b/scripts/db_enrichment/country_enrichment.py index 1f99d42..f62a64e 100644 --- a/scripts/db_enrichment/country_enrichment.py +++ b/scripts/db_enrichment/country_enrichment.py @@ -39,14 +39,36 @@ def callSPARQL(query): g = Graph() +test_query=""" +# Use with https://query.wikidata.org/ +SELECT DISTINCT ?a ?label ?country ?continent ?coor WHERE { + BIND (XXX as ?a) . + OPTIONAL { + ?a wdt:P625 ?coor. + } + ?a rdfs:label ?label . + ?a wdt:P17 ?country. + ?country rdfs:label ?country_label . + OPTIONAL { + ?country wdt:P30 ?continent. + ?continent rdfs:label ?continent_label + FILTER (lang(?continent_label)='en') + } + FILTER (lang(?country_label)='en') + FILTER (lang(?label)='en') +} +""" + +# wdt:P625 are GEO coordinates + query = """ construct { ?a wdt:P625 ?c. ?a rdfs:label ?label . ?a wdt:P17 ?country. ?country rdfs:label ?country_label . - ?country wdt:P30 ?continent. - ?continent rdfs:label ?continent_label + ?country wdt:P30 ?continent . + ?continent rdfs:label ?continent_label . } WHERE { BIND (XXX as ?a) . @@ -59,7 +81,6 @@ construct { FILTER (lang(?continent_label)='en') FILTER (lang(?country_label)='en') FILTER (lang(?label)='en') - } """"" @@ -72,6 +93,8 @@ with open(outputFile, 'r') as csvfile: counter=counter+1 try: + testq = test_query.replace("XXX", "<"+row[0]+">") + print(testq) tmpquery=query.replace("XXX", "<"+row[0]+">") print(tmpquery) diff --git a/scripts/db_enrichment/input_location.csv b/scripts/db_enrichment/input_location.csv index a4246cd..8c3308f 100644 --- a/scripts/db_enrichment/input_location.csv +++ b/scripts/db_enrichment/input_location.csv @@ -1,16 +1,6 @@ http://www.wikidata.org/entity/Q7960498 http://www.wikidata.org/entity/Q692895 -http://www.wikidata.org/entity/Q928 http://www.wikidata.org/entity/Q2722074 http://www.wikidata.org/entity/Q25622187 http://www.wikidata.org/entity/Q27684996 http://www.wikidata.org/entity/Q2757125 -http://www.wikidata.org/entity/Q1922283 -http://www.wikidata.org/entity/Q490 -http://www.wikidata.org/entity/Q677037 -http://www.wikidata.org/entity/Q3037 -http://www.wikidata.org/entity/Q843 -http://www.wikidata.org/entity/Q183 -http://www.wikidata.org/entity/Q29 -http://www.wikidata.org/entity/Q17 -http://www.wikidata.org/entity/Q810 diff --git a/scripts/db_enrichment/readme.md b/scripts/db_enrichment/readme.md index 88e8be5..7539104 100644 --- a/scripts/db_enrichment/readme.md +++ b/scripts/db_enrichment/readme.md @@ -11,11 +11,13 @@ File containing information about the countries in our database. Additional info This SPARQL query (http://sparql.genenetwork.org/sparql/) retrieves all countries (ids) from our database that do not have a label yet: ->SELECT DISTINCT ?geoLocation WHERE ->{ ->?fasta ?x [ <<http://purl.obolibrary.org/obo/GAZ_00000448>> ?geoLocation] . ->FILTER NOT EXISTS {?geoLocation <<http://www.w3.org/2000/01/rdf-schema#label>> ?geoLocation_tmp_label} ->} +```sparql +SELECT DISTINCT ?geoLocation WHERE +{ + ?fasta ?x [ <http://purl.obolibrary.org/obo/GAZ_00000448> ?geoLocation] . + FILTER NOT EXISTS {?geoLocation <http://www.w3.org/2000/01/rdf-schema#label> ?geoLocation_tmp_label} +} +``` [Run query](http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=%0D%0ASELECT+DISTINCT+%3FgeoLocation++WHERE%0D%0A%7B%0D%0A++%3Ffasta+%3Fx+%5B+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGAZ_00000448%3E+%3FgeoLocation%5D+.%0D%0A++FILTER+NOT+EXISTS+%7B%3FgeoLocation+%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23label%3E+%3FgeoLocation_tmp_label%7D%0D%0A%7D&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+) |