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* Reference items should always have DOI as an alias, so it that users can easily check with the search bar if it is already used somewhere in the database | * Reference items should always have DOI as an alias, so it that users can easily check with the search bar if it is already used somewhere in the database | ||
* Environmental origin of the organisms using EnvO terms, use guidelines aligned to MIxS: https://github.com/EnvironmentOntology/envo/wiki/ENVO-annotations-for-MIxS-v5 | * Environmental origin of the organisms using EnvO terms, use guidelines aligned to MIxS: https://github.com/EnvironmentOntology/envo/wiki/ENVO-annotations-for-MIxS-v5 | ||
== Export for Globi == | |||
SPARQL query to export table with fields used by Globi. The output may need to be processed further. | |||
<sparql tryit="1"> | |||
#List all interactions, optionally the localization, interaction type, and references | |||
PREFIX pp: <https://ppsdb.wikibase.cloud/entity/> | |||
PREFIX ppt: <https://ppsdb.wikibase.cloud/prop/direct/> | |||
PREFIX pps: <https://ppsdb.wikibase.cloud/prop/> | |||
PREFIX ppss: <https://ppsdb.wikibase.cloud/prop/statement/> | |||
PREFIX ppsq: <https://ppsdb.wikibase.cloud/prop/qualifier/> | |||
PREFIX ppsr: <https://ppsdb.wikibase.cloud/prop/reference/> | |||
SELECT DISTINCT ?argumentTypeName ?sourceTaxon ?sourceTaxonName ?sourceWdmap ?sourceTaxonId ?typeLabel ?interactionTypeId ?targetTaxon ?targetTaxonName ?targetWdmap ?targetTaxonId ?sourceBodyPartName ?sourceBodyPartId ?referenceDoi ?referenceCitation WHERE { | |||
?sourceTaxon pps:P19 ?interaction. | |||
?interaction ppss:P19 ?targetTaxon. | |||
OPTIONAL { | |||
?interaction ppsq:P20 ?sourceBodyPart. | |||
?sourceBodyPart rdfs:label ?sourceBodyPartName. | |||
OPTIONAL { ?sourceBodyPart ppt:P17 ?sourceBodyPartId. } | |||
OPTIONAL { ?sourceBodyPart ppt:P44 ?sourceBodyPartId. } | |||
} | |||
OPTIONAL { | |||
?interaction ppsq:P26 ?type. | |||
OPTIONAL { ?type ppt:P16 ?interactionTypeId. } | |||
} | |||
OPTIONAL { | |||
?interaction prov:wasDerivedFrom ?refnode. | |||
# OPTIONAL { ?refnode ppsr:P27 ?doi } | |||
OPTIONAL { | |||
?refnode ppsr:P23 ?statedIn. | |||
OPTIONAL { ?statedIn ppt:P13 ?referenceDoi. } | |||
OPTIONAL { ?statedIn ppt:P14 ?referenceCitation. } | |||
BIND (STR("support") AS ?argumentTypeName) | |||
} | |||
OPTIONAL { | |||
?refnode ppsr:P43 ?statedIn. | |||
OPTIONAL { ?statedIn ppt:P13 ?referenceDoi. } | |||
OPTIONAL { ?statedIn ppt:P14 ?referenceCitation. } | |||
BIND (STR("refute") AS ?argumentTypeName) | |||
} | |||
} | |||
OPTIONAL { | |||
?sourceTaxon ppt:P11 ?sourceTaxon_ncbi. | |||
BIND ( CONCAT("NCBI:txid", STR(?sourceTaxon_ncbi)) as ?sourceTaxonId ) | |||
} | |||
OPTIONAL { | |||
?targetTaxon ppt:P11 ?targetTaxon_ncbi. | |||
BIND ( CONCAT("NCBI:txid", STR(?targetTaxon_ncbi)) as ?targetTaxonId ) | |||
} | |||
?sourceTaxon rdfs:label ?sourceTaxonName . | |||
OPTIONAL { ?targetTaxon rdfs:label ?targetTaxonName. } | |||
OPTIONAL { ?sourceTaxon ppt:P2 ?sourceWdmap . } | |||
OPTIONAL { ?targetTaxon ppt:P2 ?targetWdmap . } | |||
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". } | |||
} ORDER BY ?sourceTaxonName ?targetTaxonName | |||
</sparql> | |||