PREFIX rdfs: PREFIX ssb: PREFIX cco_tc: SELECT distinct ?protein ?protein_id WHERE { ?protein_id ssb:has_function ?function_id. ?function_id ssb:is_a cco_tc:CCO_F0000031. ?protein_id ssb:located_in ?location_id. ?location_id ssb:is_a cco_tc:CCO_C0000252. ?protein_id ssb:participates_in ?process_id. ?process_id ssb:is_a cco_tc:CCO_P0000117. ?protein_id rdfs:label ?protein. } PREFIX rdfs: PREFIX ssb: PREFIX term_id: SELECT ?function ?participates_in ?located_in WHERE { { term_id: ssb:has_function ?f. ?f rdfs:label ?function. } UNION { term_id: ssb:participates_in ?p. ?p rdfs:label ?participates_in. } UNION { term_id: ssb:located_in ?l. ?l rdfs:label ?located_in. } } PREFIX rdfs: PREFIX rdf: PREFIX ssb: SELECT distinct ?protein_name ?definition ?interaction_name ?IntAct_id WHERE { ?protein_id rdf:type ssb:protein. ?protein_id ssb:Definition ?Def. ?Def ssb:def ?definition. FILTER regex(?definition, 'Breast cancer', 'i'). ?protein_id rdfs:label ?protein_name. OPTIONAL { ?protein_id ssb:participates_in ?interaction. ?interaction rdf:type ssb:interaction. ?interaction rdfs:label ?interaction_name. ?interaction ssb:xref ?xref. ?xref ssb:acc ?IntAct_id } } PREFIX rdfs: PREFIX ssb: PREFIX cco: SELECT ?description ?transformed_protein_name ?cco_id WHERE { cco:CCO_B0001575 ssb:transforms_into ?cco_id. ?cco_id ssb:Definition ?Def. ?Def ssb:def ?description. ?cco_id rdfs:label ?transformed_protein_name. } PREFIX rdfs: PREFIX ssb: PREFIX cco_S_pombe: SELECT ?prot_label ?biological_process_label WHERE { ?prot ssb:is_a cco_S_pombe:CCO_B0000000 . ?prot rdfs:label ?prot_label . ?prot ssb:participates_in ?biological_process . ?biological_process rdfs:label ?biological_process_label } PREFIX rdfs: SELECT ?term_id ?term_name WHERE { ?term_id rdfs:label ?term_name. filter regex(str(?term_name), 'cell cycle') } PREFIX rdfs: PREFIX ssb: PREFIX cco_S_pombe_tc: SELECT distinct ?protein WHERE { ?protein_id ssb:is_a cco_S_pombe_tc:CCO_B0000000. ?protein_id ssb:located_in ?location_id. ?location_id ssb:is_a cco_S_pombe_tc:CCO_C0000239. ?protein_id rdfs:label ?protein. } PREFIX rdfs: PREFIX ssb: PREFIX cco_A_thaliana: SELECT ?uniprot_name ?AT_code WHERE { ?prot ssb:is_a cco_A_thaliana:CCO_B0000000 . ?prot rdfs:label ?uniprot_name . ?prot ssb:encoded_by ?gene . ?gene ssb:xref ?b . ?b ssb:dbname ?database . ?b ssb:acc ?AT_code . FILTER(?database = 'TAIR') } PREFIX rdfs: PREFIX rdf: PREFIX ssb: PREFIX cco_A_thaliana_tc: SELECT distinct ?protein_name ?function WHERE { ?protein_id rdf:type ssb:protein. ?protein_id ssb:is_a cco_A_thaliana_tc:CCO_B0000000. ?protein_id ssb:has_function ?subfunction_id. ?subfunction_id ssb:is_a ?function_id. ?protein_id ssb:located_in ?location_id. ?location_id ssb:is_a cco_A_thaliana_tc:CCO_C0000324. ?function_id ssb:Definition ?def. ?def ssb:def ?function. ?protein_id rdfs:label ?protein_name. FILTER regex(?function, 'hydrolysis','i'). } PREFIX rdfs: PREFIX ssb: PREFIX cco: SELECT ?term_label WHERE { cco:CCO_P0000003 rdfs:label ?term_label. } PREFIX rdfs: PREFIX term_id: SELECT ?term_as_child ?outwardarrow ?head_name ?tail_name ?inwardarrow ?term_as_parent WHERE { { term_id: ?outwardarrow ?head_id. term_id: rdfs:label ?term_as_child. ?outwardarrow rdfs:label ?outward_arrow. ?head_id rdfs:label ?head_name. } UNION{ ?tail_id ?inwardarrow term_id:. ?tail_id rdfs:label ?tail_name. ?inwardarrow rdfs:label ?inward_arrow. term_id: rdfs:label ?term_as_parent. } } PREFIX rdfs: PREFIX ssb: PREFIX term_id: SELECT distinct ?name ?definition ?db ?nr ?organism ?comment ?synonym ?scope ?syn_db ?syn_nr ?xref_db ?xref_nr ?subnamespace ?alt_id WHERE { {term_id: rdfs:label ?name} UNION{ term_id: ssb:Definition ?a. {?a ssb:def ?definition.} UNION{ OPTIONAL{ ?a ssb:DbXref ?b. ?b ssb:dbname ?db. ?b ssb:acc ?nr. } } } UNION { term_id: ?has_source ?organism_id. ?organism_id a ssb:taxon. ?organism_id rdfs:label ?organism. } UNION {term_id: rdfs:comment ?comment} UNION{ term_id: ssb:synonym ?a. ?a ssb:syn ?synonym. OPTIONAL{?a ssb:scope ?scope.} OPTIONAL{ ?a ssb:DbXref ?b. ?b ssb:dbname ?syn_db. ?b ssb:acc ?syn_nr. } } UNION{ term_id: ssb:xref ?a. ?a ssb:dbname ?xref_db. ?a ssb:acc ?xref_nr. } UNION{ term_id: a ?subnamespace } UNION{ term_id: ssb:hasAlternativeId ?alt_id. } } PREFIX rdfs: PREFIX ssb: PREFIX cco: SELECT ?name ?CCO_id WHERE { ?CCO_id ssb:is_a cco:CCO_P0000160. ?CCO_id rdfs:label ?name. } PREFIX rdfs: PREFIX ssb: PREFIX cco: SELECT ?name_of_parent ?CCO_id WHERE { cco:CCO_F0001848 ssb:is_a ?CCO_id. ?CCO_id rdfs:label ?name_of_parent. } PREFIX rdfs: PREFIX ssb: SELECT ?name ?found_in ?type_of_found_text WHERE { FILTER regex(str(?found_in), 'cell', 'i') FILTER regex(str(?found_in), 'cycle', 'i') ?term_id rdfs:label ?name. { ?term_id ?type_of_found_text ?found_in. ?term_id rdfs:label ?found_in. } UNION { ?term_id ?type_of_found_text ?a. ?term_id ssb:Definition ?a. ?a ssb:def ?found_in. } UNION { ?term_id ?type_of_found_text ?a. ?term_id ssb:synonym ?a. ?a ssb:syn ?found_in. } UNION { ?term_id ?type_of_found_text ?found_in. ?term_id rdfs:comment ?found_in. } } ORDER BY ?term_id PREFIX ssb: PREFIX cco_A_thaliana: SELECT distinct count(?term_id) WHERE { { ?term_id ssb:is_a cco_A_thaliana:CCO_B0000000. } UNION { ?term_id ssb:is_a cco_A_thaliana:CCO_U0000011. } UNION { ?term_id ssb:is_a cco_A_thaliana:CCO_U0000007. } ?term_id ssb:has_source cco_A_thaliana:CCO_T0000034 . } PREFIX ssb: PREFIX cco_S_pombe: SELECT distinct count(?term_id) WHERE { ?term_id ssb:is_a cco_S_pombe:CCO_U0000008. } PREFIX ssb: PREFIX cco: SELECT distinct count(?term_id) WHERE { ?term_id ssb:is_a cco:CCO_U0000008. ?term_id ssb:has_source cco:CCO_T0000017. } PREFIX rdfs: PREFIX rdf: PREFIX ssb: PREFIX cco_A_thaliana: SELECT ?protein ?participates_in_interaction WHERE { ?term_id ssb:has_source cco_A_thaliana:CCO_T0000034 . ?term_id ssb:participates_in ?interaction. ?interaction rdf:type ssb:interaction. ?term_id rdfs:label ?protein. ?interaction rdfs:label ?participates_in_interaction. }