Simple Question (Direct)
Simple Question
Q23454145
P702
Q863908
USER
What encodes tRNA-specific 2-thiouridylase MnmA    BT_3888 ?
(Q23454145,P702,c(Q863908))
action filter_type
action find
entity Q23454145
relation P702
type Q863908
['Q23454145', 'P702', {'concept': 'Q863908'}]
SELECT DISTINCT ?u WHERE { resource:Q23454145 property:P702 ?u . ?u rdf:type ontology:Q863908 }
tRNA-specific 2-thiouridylase MnmA    BT_3888
action filter_type
action find
entity tRNA-specific 2-thiouridylase MnmA    BT_3888
relation encoded by
type nucleic acid sequence
['tRNA-specific 2-thiouridylase MnmA    BT_3888', 'encoded by', {'concept': 'nucleic acid sequence'}]
SELECT DISTINCT ?u WHERE { resource:tRNA-specific_2-thiouridylase_MnmA____BT_3888 property:encoded_by ?u . ?u rdf:type ontology:nucleic_acid_sequence }
[]
nucleic acid sequence
Q23354870
SYSTEM
tRNA-specific 2-thiouridylase MnmA    BT_3888
Q23354870
(Q23454145,P702,c(Q863908))
action filter_type
action find
entity Q23454145
relation P702
type Q863908
TRNA-specific 2-thiouridylase MnmA BT 3888 encodes tRNA-specific 2-thiouridylase MnmA BT_3888
['Q23454145', 'P702', {'concept': 'Q863908'}]
SELECT DISTINCT ?u WHERE { resource:Q23454145 property:P702 ?u . ?u rdf:type ontology:Q863908 }
tRNA-specific 2-thiouridylase MnmA    BT_3888
TRNA-specific 2-thiouridylase MnmA BT 3888 encodes tRNA-specific 2-thiouridylase MnmA BT_3888
tRNA-specific 2-thiouridylase MnmA    BT_3888
action filter_type
action find
entity tRNA-specific 2-thiouridylase MnmA    BT_3888
relation encoded by
type nucleic acid sequence
['tRNA-specific 2-thiouridylase MnmA    BT_3888', 'encoded by', {'concept': 'nucleic acid sequence'}]
SELECT DISTINCT ?u WHERE { resource:tRNA-specific_2-thiouridylase_MnmA____BT_3888 property:encoded_by ?u . ?u rdf:type ontology:nucleic_acid_sequence }
[]
Verification (Boolean) (All)
Verification|3 entities, 2 direct, 2(direct) are query entities, subject is indirect
Q23354870 Q21105195 Q23454145
P688
Q181394
USER
Does that nucleic acid sequence encodes Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit B and tRNA-specific 2-thiouridylase MnmA    BT_3888 ?
(Q23354870,P688,Q21105195) (Q23354870,P688,Q23454145)
action is_in
entity Q23354870
action intersection
action find_reverse
entity Q21105195
relation P688
action find_reverse
entity Q23454145
relation P688
['Q23354870', 'P688', 'Q21105195'] ['Q23354870', 'P688', 'Q23454145']
ASK WHERE { resource:Q23354870 property:P688 resource:Q21105195 . resource:Q23354870 property:P688 resource:Q23454145 }
tRNA-specific 2-thiouridylase MnmA    BT_3888 Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit B tRNA-specific 2-thiouridylase MnmA    BT_3888
action is_in
entity tRNA-specific 2-thiouridylase MnmA    BT_3888
action intersection
action find_reverse
entity Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit B
relation encodes
action find_reverse
entity tRNA-specific 2-thiouridylase MnmA    BT_3888
relation encodes
['tRNA-specific 2-thiouridylase MnmA    BT_3888', 'encodes', 'Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit B'] ['tRNA-specific 2-thiouridylase MnmA    BT_3888', 'encodes', 'tRNA-specific 2-thiouridylase MnmA    BT_3888']
ASK WHERE { resource:tRNA-specific_2-thiouridylase_MnmA____BT_3888 property:encodes resource:Serine/threonine-protein_phosphatase_6_regulatory_ankyrin_repeat_subunit_B . resource:tRNA-specific_2-thiouridylase_MnmA____BT_3888 property:encodes resource:tRNA-specific_2-thiouridylase_MnmA____BT_3888 }
[]
nutrient
SYSTEM
NO and YES respectively
(Q23354870,P688,Q21105195) (Q23354870,P688,Q23454145)
action is_in
entity Q23354870
action intersection
action find_reverse
entity Q21105195
relation P688
action find_reverse
entity Q23454145
relation P688
[ANSWER]
['Q23354870', 'P688', 'Q21105195'] ['Q23354870', 'P688', 'Q23454145']
ASK WHERE { resource:Q23354870 property:P688 resource:Q21105195 . resource:Q23354870 property:P688 resource:Q23454145 }
NO and YES respectively
action is_in
entity tRNA-specific 2-thiouridylase MnmA    BT_3888
action intersection
action find_reverse
entity Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit B
relation encodes
action find_reverse
entity tRNA-specific 2-thiouridylase MnmA    BT_3888
relation encodes
['tRNA-specific 2-thiouridylase MnmA    BT_3888', 'encodes', 'Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit B'] ['tRNA-specific 2-thiouridylase MnmA    BT_3888', 'encodes', 'tRNA-specific 2-thiouridylase MnmA    BT_3888']
ASK WHERE { resource:tRNA-specific_2-thiouridylase_MnmA____BT_3888 property:encodes resource:Serine/threonine-protein_phosphatase_6_regulatory_ankyrin_repeat_subunit_B . resource:tRNA-specific_2-thiouridylase_MnmA____BT_3888 property:encodes resource:tRNA-specific_2-thiouridylase_MnmA____BT_3888 }
[]
Simple Question (Direct)
Simple Question|Single Entity
Q23354870
P703
Q16521
USER
Which taxon is tRNA-specific 2-thiouridylase MnmA    BT_3888 found in ?
(Q23354870,P703,c(Q16521))
action filter_type
action find
entity Q23354870
relation P703
type Q16521
['Q23354870', 'P703', {'concept': 'Q16521'}]
SELECT DISTINCT ?b WHERE { resource:Q23354870 property:P703 ?b . ?b rdf:type ontology:Q16521 }
tRNA-specific 2-thiouridylase MnmA    BT_3888
action filter_type
action find
entity tRNA-specific 2-thiouridylase MnmA    BT_3888
relation found in taxon
type taxon
['tRNA-specific 2-thiouridylase MnmA    BT_3888', 'found in taxon', {'concept': 'taxon'}]
SELECT DISTINCT ?b WHERE { resource:tRNA-specific_2-thiouridylase_MnmA____BT_3888 property:found_in_taxon ?b . ?b rdf:type ontology:taxon }
[]
taxon
Q21397543
SYSTEM
Bacteroides thetaiotaomicron VPI-5482
Q21397543
(Q23354870,P703,c(Q16521))
action filter_type
action find
entity Q23354870
relation P703
type Q16521
[ANSWER] is tRNA-specific 2-thiouridylase MnmA BT_3888 found in
['Q23354870', 'P703', {'concept': 'Q16521'}]
SELECT DISTINCT ?b WHERE { resource:Q23354870 property:P703 ?b . ?b rdf:type ontology:Q16521 }
Bacteroides thetaiotaomicron VPI-5482
Bacteroides thetaiotaomicron VPI-5482 is tRNA-specific 2-thiouridylase MnmA BT_3888 found in
Bacteroides thetaiotaomicron VPI-5482
action filter_type
action find
entity tRNA-specific 2-thiouridylase MnmA    BT_3888
relation found in taxon
type taxon
['tRNA-specific 2-thiouridylase MnmA    BT_3888', 'found in taxon', {'concept': 'taxon'}]
SELECT DISTINCT ?b WHERE { resource:tRNA-specific_2-thiouridylase_MnmA____BT_3888 property:found_in_taxon ?b . ?b rdf:type ontology:taxon }
[]
Logical Reasoning (All)
Logical|Union|Single_Relation
Q22265593 Q21105195
P688
Q863908
USER
Which nucleic acid sequences encodes Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit B or phage associated protein    NGO1099 ?
OR((c(Q863908),P688,Q21105195), (c(Q863908),P688,Q22265593))
action filter_type
action union
action find_reverse
entity Q21105195
relation P688
action find_reverse
entity Q22265593
relation P688
type Q863908
{'OR': [[{'concept': 'Q863908'}, 'P688', 'Q21105195'], [{'concept': 'Q863908'}, 'P688', 'Q22265593']]}
SELECT DISTINCT ?w WHERE { { { ?w property:P688 resource:Q21105195 } UNION { ?w property:P688 resource:Q22265593 } } . ?w rdf:type ontology:Q863908 }
phage associated protein    NGO1099 Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit B
action filter_type
action union
action find_reverse
entity Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit B
relation encodes
action find_reverse
entity phage associated protein    NGO1099
relation encodes
type nucleic acid sequence
{'OR': [[{'concept': 'nucleic acid sequence'}, 'encodes', 'Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit B'], [{'concept': 'nucleic acid sequence'}, 'encodes', 'phage associated protein    NGO1099']]}
SELECT DISTINCT ?w WHERE { { { ?w property:encodes resource:Serine/threonine-protein_phosphatase_6_regulatory_ankyrin_repeat_subunit_B } UNION { ?w property:encodes resource:phage_associated_protein____NGO1099 } } . ?w rdf:type ontology:nucleic_acid_sequence }
[]
nucleic acid sequence
Q18048525 Q22263739
SYSTEM
ANKRD44, phage associated protein    NGO1099
Q18048525 Q22263739
OR((c(Q863908),P688,Q21105195), (c(Q863908),P688,Q22265593))
action filter_type
action union
action find_reverse
entity Q21105195
relation P688
action find_reverse
entity Q22265593
relation P688
type Q863908
[ANSWERS]
{'OR': [[{'concept': 'Q863908'}, 'P688', 'Q21105195'], [{'concept': 'Q863908'}, 'P688', 'Q22265593']]}
SELECT DISTINCT ?w WHERE { { { ?w property:P688 resource:Q21105195 } UNION { ?w property:P688 resource:Q22265593 } } . ?w rdf:type ontology:Q863908 }
ANKRD44 phage associated protein    NGO1099
ANKRD44 and phage associated protein NGO1099 encode Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit B or phage associated protein NGO1099
ANKRD44 phage associated protein    NGO1099
action filter_type
action union
action find_reverse
entity Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit B
relation encodes
action find_reverse
entity phage associated protein    NGO1099
relation encodes
type nucleic acid sequence
{'OR': [[{'concept': 'nucleic acid sequence'}, 'encodes', 'Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit B'], [{'concept': 'nucleic acid sequence'}, 'encodes', 'phage associated protein    NGO1099']]}
SELECT DISTINCT ?w WHERE { { { ?w property:encodes resource:Serine/threonine-protein_phosphatase_6_regulatory_ankyrin_repeat_subunit_B } UNION { ?w property:encodes resource:phage_associated_protein____NGO1099 } } . ?w rdf:type ontology:nucleic_acid_sequence }
[]
Clarification
Simple Question|Single Entity|Indirect
Q18048525
P684
Q863908
USER
Which nucleic acid sequence is that one an orthlogous gene of ?
(c(Q863908),P684,Q18048525)
action filter_type
action find
entity Q18048525
relation P684
type Q863908
[{'concept': 'Q863908'}, 'P684', 'Q18048525']
SELECT DISTINCT ?s WHERE { resource:Q18048525 property:P684 ?s . ?s rdf:type ontology:Q863908 }
ANKRD44
action filter_type
action find
entity ANKRD44
relation ortholog
type nucleic acid sequence
[{'concept': 'nucleic acid sequence'}, 'ortholog', 'ANKRD44']
SELECT DISTINCT ?s WHERE { resource:ANKRD44 property:ortholog ?s . ?s rdf:type ontology:nucleic_acid_sequence }
[]
nucleic acid sequence
Clarification for simple ques.
Q18048525
SYSTEM
Did you mean ANKRD44 ?
Q18048525 Q22263739
(c(Q863908),P684,Q18048525) (c(Q863908),P684,Q22263739)
[ANSWER]
[{'concept': 'Q863908'}, 'P684', 'Q18048525'] [{'concept': 'Q863908'}, 'P684', 'Q22263739']
SELECT DISTINCT ?s WHERE { resource:Q18048525 property:P684 ?s . ?s rdf:type ontology:Q863908 }
ANKRD44 phage associated protein    NGO1099
Did you mean ANKRD44 ?
ANKRD44
[{'concept': 'nucleic acid sequence'}, 'ortholog', 'ANKRD44'] [{'concept': 'nucleic acid sequence'}, 'ortholog', 'phage associated protein    NGO1099']
SELECT DISTINCT ?s WHERE { resource:ANKRD44 property:ortholog ?s . ?s rdf:type ontology:nucleic_acid_sequence }
[]
Simple Question (Coreferenced)
USER
Yes
(c(Q863908),P684,Q18048525)
[{'concept': 'Q863908'}, 'P684', 'Q18048525']
[{'concept': 'nucleic acid sequence'}, 'ortholog', 'ANKRD44']
[]
Q18302548
SYSTEM
Ankrd44
Q18302548
(c(Q863908),P684,Q18048525)
action filter_type
action find
entity Q18048525
relation P684
type Q863908
[ANSWER] is that one an orthlogous gene of
[{'concept': 'Q863908'}, 'P684', 'Q18048525']
SELECT DISTINCT ?s WHERE { resource:Q18048525 property:P684 ?s . ?s rdf:type ontology:Q863908 }
Ankrd44
Ankrd44 is that one an orthlogous gene of
Ankrd44
action filter_type
action find
entity ANKRD44
relation ortholog
type nucleic acid sequence
[{'concept': 'nucleic acid sequence'}, 'ortholog', 'ANKRD44']
SELECT DISTINCT ?s WHERE { resource:ANKRD44 property:ortholog ?s . ?s rdf:type ontology:nucleic_acid_sequence }
[]
Verification (Boolean) (All)
Verification|3 entities, all direct, 2 are query entities
Q18302548 Q21498972 Q23504074
P688
Q181394
USER
Does Ankrd44 encode Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit B and isopentenyl-diphosphate delta-isomerase    HMPREF0351_10222 ?
(Q18302548,P688,Q21498972) (Q18302548,P688,Q23504074)
action is_in
entity Q18302548
action intersection
action find_reverse
entity Q21498972
relation P688
action find_reverse
entity Q23504074
relation P688
['Q18302548', 'P688', 'Q21498972'] ['Q18302548', 'P688', 'Q23504074']
ASK WHERE { resource:Q18302548 property:P688 resource:Q21498972 . resource:Q18302548 property:P688 resource:Q23504074 }
Ankrd44 Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit B isopentenyl-diphosphate delta-isomerase    HMPREF0351_10222
action is_in
entity Ankrd44
action intersection
action find_reverse
entity Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit B
relation encodes
action find_reverse
entity isopentenyl-diphosphate delta-isomerase    HMPREF0351_10222
relation encodes
['Ankrd44', 'encodes', 'Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit B'] ['Ankrd44', 'encodes', 'isopentenyl-diphosphate delta-isomerase    HMPREF0351_10222']
ASK WHERE { resource:Ankrd44 property:encodes resource:Serine/threonine-protein_phosphatase_6_regulatory_ankyrin_repeat_subunit_B . resource:Ankrd44 property:encodes resource:isopentenyl-diphosphate_delta-isomerase____HMPREF0351_10222 }
[]
nutrient
SYSTEM
YES and NO respectively
(Q18302548,P688,Q21498972) (Q18302548,P688,Q23504074)
action is_in
entity Q18302548
action intersection
action find_reverse
entity Q21498972
relation P688
action find_reverse
entity Q23504074
relation P688
[ANSWER]
['Q18302548', 'P688', 'Q21498972'] ['Q18302548', 'P688', 'Q23504074']
ASK WHERE { resource:Q18302548 property:P688 resource:Q21498972 . resource:Q18302548 property:P688 resource:Q23504074 }
YES and NO respectively
action is_in
entity Ankrd44
action intersection
action find_reverse
entity Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit B
relation encodes
action find_reverse
entity isopentenyl-diphosphate delta-isomerase    HMPREF0351_10222
relation encodes
['Ankrd44', 'encodes', 'Serine/threonine-protein phosphatase 6 regulatory ankyrin repeat subunit B'] ['Ankrd44', 'encodes', 'isopentenyl-diphosphate delta-isomerase    HMPREF0351_10222']
ASK WHERE { resource:Ankrd44 property:encodes resource:Serine/threonine-protein_phosphatase_6_regulatory_ankyrin_repeat_subunit_B . resource:Ankrd44 property:encodes resource:isopentenyl-diphosphate_delta-isomerase____HMPREF0351_10222 }
[]
Logical Reasoning (All)
Logical|Union|Single_Relation
Q27108711 Q23354870
P688
Q181394
USER
Which nutrients are tRNA-specific 2-thiouridylase MnmA    BT_3888 or membrane protein    PP_5623 an encoding of ?
OR((Q23354870,P688,c(Q181394)), (Q27108711,P688,c(Q181394)))
action filter_type
action union
action find
entity Q23354870
relation P688
action find
entity Q27108711
relation P688
type Q181394
{'OR': [['Q23354870', 'P688', {'concept': 'Q181394'}], ['Q27108711', 'P688', {'concept': 'Q181394'}]]}
SELECT DISTINCT ?y WHERE { ?y rdf:type ontology:Q181394 . { { resource:Q27108711 property:P688 ?y } UNION { resource:Q23354870 property:P688 ?y } } }
membrane protein    PP_5623 tRNA-specific 2-thiouridylase MnmA    BT_3888
action filter_type
action union
action find
entity tRNA-specific 2-thiouridylase MnmA    BT_3888
relation encodes
action find
entity membrane protein    PP_5623
relation encodes
type nutrient
{'OR': [['tRNA-specific 2-thiouridylase MnmA    BT_3888', 'encodes', {'concept': 'nutrient'}], ['membrane protein    PP_5623', 'encodes', {'concept': 'nutrient'}]]}
SELECT DISTINCT ?y WHERE { ?y rdf:type ontology:nutrient . { { resource:membrane_protein____PP_5623 property:encodes ?y } UNION { resource:tRNA-specific_2-thiouridylase_MnmA____BT_3888 property:encodes ?y } } }
[]
nutrient
Q23454145 Q27171940
SYSTEM
tRNA-specific 2-thiouridylase MnmA    BT_3888, membrane protein    PP_5623
Q23454145 Q27171940
OR((Q23354870,P688,c(Q181394)), (Q27108711,P688,c(Q181394)))
action filter_type
action union
action find
entity Q23354870
relation P688
action find
entity Q27108711
relation P688
type Q181394
[ANSWERS]
{'OR': [['Q23354870', 'P688', {'concept': 'Q181394'}], ['Q27108711', 'P688', {'concept': 'Q181394'}]]}
SELECT DISTINCT ?y WHERE { ?y rdf:type ontology:Q181394 . { { resource:Q27108711 property:P688 ?y } UNION { resource:Q23354870 property:P688 ?y } } }
tRNA-specific 2-thiouridylase MnmA    BT_3888 membrane protein    PP_5623
TRNA-specific 2-thiouridylase MnmA BT 3888 and membrane protein PP 5623 are tRNA-specific 2-thiouridylase MnmA BT_3888 or membrane protein PP_5623 an encoding of
tRNA-specific 2-thiouridylase MnmA    BT_3888 membrane protein    PP_5623
action filter_type
action union
action find
entity tRNA-specific 2-thiouridylase MnmA    BT_3888
relation encodes
action find
entity membrane protein    PP_5623
relation encodes
type nutrient
{'OR': [['tRNA-specific 2-thiouridylase MnmA    BT_3888', 'encodes', {'concept': 'nutrient'}], ['membrane protein    PP_5623', 'encodes', {'concept': 'nutrient'}]]}
SELECT DISTINCT ?y WHERE { ?y rdf:type ontology:nutrient . { { resource:membrane_protein____PP_5623 property:encodes ?y } UNION { resource:tRNA-specific_2-thiouridylase_MnmA____BT_3888 property:encodes ?y } } }
[]