What DBs target mammals? (哺乳類を対象にしたDBを知りたい)
DEFINE input:inference "subClassOf_NCBITaxon" PREFIX dbc: <http://integbio.jp/dbcatalog/meta#> SELECT DISTINCT ?db_name ?db_id ?organism WHERE { ?taxon rdfs:label "Mammalia"^^xsd:string . ?sub rdfs:subClassOf ?taxon . ?db_id dbc:dbcat_taxonomy_id ?sub . ?db_id dbc:dbcat_db_name ?db_name . ?db_id dbc:dbcat_organism ?organism . } ORDER BY ?db_name
What taxa cover organisms containing alpha-Thujene? (α-ツジェンを生体内に含む生物の分類群は?)
DEFINE input:inference "subClassOf_NCBITaxon" PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX kc: <http://togodb.biosciencedbc.jp/ontology/knapsack_core#> SELECT (STR(?label) AS ?name) ?total_super { { SELECT ?super (COUNT(?super) AS ?total_super) WHERE { ?knapsackcore kc:metabolite "alpha-Thujene" . ?knapsackcore kc:organism_uri ?organism . ?organism rdfs:subClassOf ?super . } GROUP BY ?super } ?super rdfs:label ?label . } ORDER BY DESC(?total_super) ?label
What plants contain compounds that cause hypertrophy in rat livers? (ラットを肝細胞肥大させた化合物を含む植物は?)
PREFIX otp: <http://togodb.biosciencedbc.jp/ontology/open_tggates_pathology#> PREFIX otm: <http://togodb.biosciencedbc.jp/ontology/open_tggates_main#> PREFIX kc: <http://togodb.biosciencedbc.jp/ontology/knapsack_core#> SELECT DISTINCT ?organism ?compound_name ?chebi WHERE { ?tggatespatho otp:find_type "Hypertrophy" . ?tggatespatho otp:compound_name ?compound_name . ?tggatesmain otm:compound_name ?compound_name . ?tggatesmain otm:chebi ?chebi . ?knapsackcore kc:chebi ?chebi . ?knapsackcore kc:organism ?organism } ORDER BY ?organism
List up gene pairs on the photosynthesis pathway whose mutants show similar fluorescence time-course in Synechocystis sp. PCC 6803. (Synechocystis sp. PCC 6803 の Photosynthesis のパスウェイ上の遺伝子について,蛍光時系列が似ているもののリストが欲しい)
PREFIX fl: <http://togodb.biosciencedbc.jp/ontology/fluorome_sim#> SELECT ?simid ?orf1 ?orf2 ?product1 ?product2 ?dist_h ?dist_l WHERE { <http://www.kegg.jp/entry/syn00195> <http://www.genome.jp/linkdb/reverse> ?gene1 . BIND( IRI(CONCAT("http://identifiers.org/kegg.genes/syn:", SUBSTR(STR(?gene1), 30))) AS ?orf1 ) ?simid fl:box1_orf ?orf1 . ?simid fl:box2_orf ?orf2 . ?simid fl:box1_product ?product1 . ?simid fl:box2_product ?product2 . OPTIONAL{ ?simid fl:distance_a_high ?dist_h . } ?simid fl:distance_a_low ?dist_l . BIND( IRI(CONCAT("http://www.kegg.jp/entry/syn:", SUBSTR(STR(?orf2), 39))) AS ?gene2 ) FILTER ( ?orf1 != ?orf2 && ?dist_l < 0.2 ) <http://www.kegg.jp/entry/syn00195> <http://www.genome.jp/linkdb/reverse> ?gene2 . }
What proteins are targeted by compounds from Vigna unguiculata? (ササゲに含まれる化合物のターゲットタンパク質を知りたい)
PREFIX kc: <http://togodb.biosciencedbc.jp/ontology/knapsack_core#> PREFIX sio: <http://semanticscience.org/resource/> PREFIX chbl: <http://rdf.ebi.ac.uk/terms/chembl#> SELECT DISTINCT ?compound_name ?target_name ?target WHERE { ?kc_id kc:organism "Vigna unguiculata". ?kc_id kc:inchi ?inchi . ?kc_id kc:metabolite ?compound_name . SERVICE <https://www.ebi.ac.uk/rdf/services/chembl/sparql> { ?molecule sio:SIO_000008 ?attribute . FILTER regex(?attribute, "standard_inchi$") . ?attribute sio:SIO_000300 ?inchi . ?activity chbl:hasMolecule ?molecule . ?activity chbl:hasAssay ?assay . ?assay chbl:hasTarget ?target . ?target rdfs:label ?target_name . } } ORDER BY ?compound_name ?target_name ?target
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