diff options
| -rw-r--r-- | scripts/db_enrichment/readme.md | 9 | ||||
| -rw-r--r-- | semantic_enrichment/labels.ttl | 3 |
2 files changed, 6 insertions, 6 deletions
diff --git a/scripts/db_enrichment/readme.md b/scripts/db_enrichment/readme.md index 83297dc..55ec496 100644 --- a/scripts/db_enrichment/readme.md +++ b/scripts/db_enrichment/readme.md @@ -4,16 +4,17 @@ We have two files in the folder *semantic_enrichment* that are used to enrich th Static label about the ontology vocabulary terms we use. This file has to be updated manually. Use the OLS or bioportal to find more information about a used ontology term. ### semantic_enrichment/countries.ttl -File containing information about the countries in our database. Additional information about countries are e.g. the label or GPS coordinates. We enricht the country identifier via wikidata. +File containing information about the countries in our database. Additional information about countries are e.g. the label or GPS coordinates. We enricht the country identifier via wikidata. Please ensure that the .ttl file is valid by e.g. using his online validator (http://ttl.summerofcode.be/). #### Update process - What countries (=wikidata identifier) do we have to enrich? -This query retrieves all countries (ids) from our database that do not have a label yet: +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} +>?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} >} - 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 diff --git a/semantic_enrichment/labels.ttl b/semantic_enrichment/labels.ttl index 7a1db54..42c199e 100644 --- a/semantic_enrichment/labels.ttl +++ b/semantic_enrichment/labels.ttl @@ -22,7 +22,6 @@ <http://semanticscience.org/resource/SIO_001014> <http://www.w3.org/2000/01/rdf-schema#label> "ethnicity" . <http://purl.obolibrary.org/obo/NCIT_C3833> <http://www.w3.org/2000/01/rdf-schema#label> "Asymptomatic" . <http://purl.obolibrary.org/obo/NCIT_C25269> <http://www.w3.org/2000/01/rdf-schema#label> "Symptomatic" . - <http://purl.obolibrary.org/obo/GENEPIO_0002020> <http://www.w3.org/2000/01/rdf-schema#label> "admitted to hospital" . <http://purl.obolibrary.org/obo/GENEPIO_0001849> <http://www.w3.org/2000/01/rdf-schema#label> "discharged from hospital" . <http://purl.obolibrary.org/obo/NCIT_C28554> <http://www.w3.org/2000/01/rdf-schema#label> "Dead" . @@ -35,7 +34,7 @@ <http://www.ebi.ac.uk/efo/EFO_0009173> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina NextSeq 500" . <http://www.ebi.ac.uk/efo/EFO_0008565> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina HiSeq 2500" . <http://www.ebi.ac.uk/efo/EFO_0008566> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina NextSeq 550" . -<http://www.ebi.ac.uk/efo/EFO_0008636> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina MiniSeq" +<http://www.ebi.ac.uk/efo/EFO_0008636> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina MiniSeq" . <http://www.ebi.ac.uk/efo/EFO_0008632> <http://www.w3.org/2000/01/rdf-schema#label> "ONT MinION" . <http://purl.obolibrary.org/obo/NCIT_C146818> <http://www.w3.org/2000/01/rdf-schema#label> "Oxford Nanopore Sequencing" . <http://www.ebi.ac.uk/efo/EFO_0004205> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina MiSeq" . |