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| author | lltommy | 2020-11-11 09:56:12 +0100 |
|---|---|---|
| committer | lltommy | 2020-11-11 09:56:12 +0100 |
| commit | d6aa323b6fc7a82e45cc1df51fc72c2d547146eb (patch) | |
| tree | 6e8b77bde4dc34fab3fa8804906f3cb821f61dae /scripts/db_enrichment/readme.md | |
| parent | c5fe5de7e4c77bfb48b1ae2f662c2d9cc120c06e (diff) | |
| parent | c872248e43c1c66e5fed8ef341f7b4ac21d63e6f (diff) | |
| download | bh20-seq-resource-d6aa323b6fc7a82e45cc1df51fc72c2d547146eb.tar.gz bh20-seq-resource-d6aa323b6fc7a82e45cc1df51fc72c2d547146eb.tar.lz bh20-seq-resource-d6aa323b6fc7a82e45cc1df51fc72c2d547146eb.zip | |
Merge branch 'master' of https://github.com/arvados/bh20-seq-resource
Diffstat (limited to 'scripts/db_enrichment/readme.md')
| -rw-r--r-- | scripts/db_enrichment/readme.md | 14 |
1 files changed, 9 insertions, 5 deletions
diff --git a/scripts/db_enrichment/readme.md b/scripts/db_enrichment/readme.md index 55ec496..7539104 100644 --- a/scripts/db_enrichment/readme.md +++ b/scripts/db_enrichment/readme.md @@ -11,11 +11,15 @@ 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+) - Use the list of identifiers created with the query above as input for the update script *country_enrichment.py*. The script creates a temporary .ttl file in this folder - Merge the output of the script above manually into the file semantic_enrichment/countries.ttl (TODO: Improve script output so manual intervention no longer needed. Currently there are "double entries" for continents in the output) |