Simple Question (Direct)
Simple Question
Q23489902
P702
Q863908
USER
Which nucleic acid sequence encodes 4'-phosphopantetheinyl transferase    SSUBM407_1687 ?
(Q23489902,P702,c(Q863908))
action filter_type
action find
entity Q23489902
relation P702
type Q863908
['Q23489902', 'P702', {'concept': 'Q863908'}]
SELECT DISTINCT ?d WHERE { resource:Q23489902 property:P702 ?d . ?d rdf:type ontology:Q863908 }
4'-phosphopantetheinyl transferase    SSUBM407_1687
action filter_type
action find
entity 4'-phosphopantetheinyl transferase    SSUBM407_1687
relation encoded by
type nucleic acid sequence
["4'-phosphopantetheinyl transferase    SSUBM407_1687", 'encoded by', {'concept': 'nucleic acid sequence'}]
SELECT DISTINCT ?d WHERE { resource:4'-phosphopantetheinyl_transferase____SSUBM407_1687 property:encoded_by ?d . ?d rdf:type ontology:nucleic_acid_sequence }
[]
nucleic acid sequence
Q23216360
SYSTEM
4'-phosphopantetheinyl transferase    SSUBM407_1687
Q23216360
(Q23489902,P702,c(Q863908))
action filter_type
action find
entity Q23489902
relation P702
type Q863908
4'-phosphopantetheinyl transferase SSUBM407 1687 encodes 4'-phosphopantetheinyl transferase SSUBM407_1687
['Q23489902', 'P702', {'concept': 'Q863908'}]
SELECT DISTINCT ?d WHERE { resource:Q23489902 property:P702 ?d . ?d rdf:type ontology:Q863908 }
4'-phosphopantetheinyl transferase    SSUBM407_1687
4'-phosphopantetheinyl transferase SSUBM407 1687 encodes 4'-phosphopantetheinyl transferase SSUBM407_1687
4'-phosphopantetheinyl transferase    SSUBM407_1687
action filter_type
action find
entity 4'-phosphopantetheinyl transferase    SSUBM407_1687
relation encoded by
type nucleic acid sequence
["4'-phosphopantetheinyl transferase    SSUBM407_1687", 'encoded by', {'concept': 'nucleic acid sequence'}]
SELECT DISTINCT ?d WHERE { resource:4'-phosphopantetheinyl_transferase____SSUBM407_1687 property:encoded_by ?d . ?d rdf:type ontology:nucleic_acid_sequence }
[]
Simple Question (Direct)
Simple Question|Single Entity
Q23489902
P682
Q1057
USER
Which metabolic process is 4'-phosphopantetheinyl transferase    SSUBM407_1687 involved in ?
(Q23489902,P682,c(Q1057))
action filter_type
action find
entity Q23489902
relation P682
type Q1057
['Q23489902', 'P682', {'concept': 'Q1057'}]
SELECT DISTINCT ?w WHERE { resource:Q23489902 property:P682 ?w . ?w rdf:type ontology:Q1057 }
4'-phosphopantetheinyl transferase    SSUBM407_1687
action filter_type
action find
entity 4'-phosphopantetheinyl transferase    SSUBM407_1687
relation biological process
type metabolic process
["4'-phosphopantetheinyl transferase    SSUBM407_1687", 'biological process', {'concept': 'metabolic process'}]
SELECT DISTINCT ?w WHERE { resource:4'-phosphopantetheinyl_transferase____SSUBM407_1687 property:biological_process ?w . ?w rdf:type ontology:metabolic_process }
[]
metabolic process
Q14349667
SYSTEM
lipid metabolic process
Q14349667
(Q23489902,P682,c(Q1057))
action filter_type
action find
entity Q23489902
relation P682
type Q1057
[ANSWER] is 4'-phosphopantetheinyl transferase SSUBM407_1687 involved in
['Q23489902', 'P682', {'concept': 'Q1057'}]
SELECT DISTINCT ?w WHERE { resource:Q23489902 property:P682 ?w . ?w rdf:type ontology:Q1057 }
lipid metabolic process
Lipid metabolic process is 4'-phosphopantetheinyl transferase SSUBM407_1687 involved in
lipid metabolic process
action filter_type
action find
entity 4'-phosphopantetheinyl transferase    SSUBM407_1687
relation biological process
type metabolic process
["4'-phosphopantetheinyl transferase    SSUBM407_1687", 'biological process', {'concept': 'metabolic process'}]
SELECT DISTINCT ?w WHERE { resource:4'-phosphopantetheinyl_transferase____SSUBM407_1687 property:biological_process ?w . ?w rdf:type ontology:metabolic_process }
[]
Simple Question (Direct)
Simple Question|Single Entity
Q23216360
P703
Q631147
USER
Where is 4'-phosphopantetheinyl transferase    SSUBM407_1687 found ?
(Q23216360,P703,c(Q631147))
action filter_type
action find
entity Q23216360
relation P703
type Q631147
['Q23216360', 'P703', {'concept': 'Q631147'}]
SELECT DISTINCT ?k WHERE { ?k rdf:type ontology:Q631147 . resource:Q23216360 property:P703 ?k }
4'-phosphopantetheinyl transferase    SSUBM407_1687
action filter_type
action find
entity 4'-phosphopantetheinyl transferase    SSUBM407_1687
relation found in taxon
type infraspecific name
["4'-phosphopantetheinyl transferase    SSUBM407_1687", 'found in taxon', {'concept': 'infraspecific name'}]
SELECT DISTINCT ?k WHERE { ?k rdf:type ontology:infraspecific_name . resource:4'-phosphopantetheinyl_transferase____SSUBM407_1687 property:found_in_taxon ?k }
[]
infraspecific name
Q21102960
SYSTEM
Streptococcus suis BM407
Q21102960
(Q23216360,P703,c(Q631147))
action filter_type
action find
entity Q23216360
relation P703
type Q631147
4 '- phosphopantetheinyl transferase SSUBM407_1687 is in [ANSWER]
['Q23216360', 'P703', {'concept': 'Q631147'}]
SELECT DISTINCT ?k WHERE { ?k rdf:type ontology:Q631147 . resource:Q23216360 property:P703 ?k }
Streptococcus suis BM407
4 '- phosphopantetheinyl transferase SSUBM407_1687 is in Streptococcus suis BM407
Streptococcus suis BM407
action filter_type
action find
entity 4'-phosphopantetheinyl transferase    SSUBM407_1687
relation found in taxon
type infraspecific name
["4'-phosphopantetheinyl transferase    SSUBM407_1687", 'found in taxon', {'concept': 'infraspecific name'}]
SELECT DISTINCT ?k WHERE { ?k rdf:type ontology:infraspecific_name . resource:4'-phosphopantetheinyl_transferase____SSUBM407_1687 property:found_in_taxon ?k }
[]
Logical Reasoning (All)
Logical|Union|Single_Relation
Q23474563 Q23489902
P688
Q863908
USER
Which nucleic acid sequences encodes 4'-phosphopantetheinyl transferase    SSUBM407_1687 or hypothetical protein    Caur_1372 ?
OR((c(Q863908),P688,Q23489902), (c(Q863908),P688,Q23474563))
action filter_type
action union
action find_reverse
entity Q23489902
relation P688
action find_reverse
entity Q23474563
relation P688
type Q863908
{'OR': [[{'concept': 'Q863908'}, 'P688', 'Q23489902'], [{'concept': 'Q863908'}, 'P688', 'Q23474563']]}
SELECT DISTINCT ?x WHERE { { { ?x property:P688 resource:Q23489902 } UNION { ?x property:P688 resource:Q23474563 } } . ?x rdf:type ontology:Q863908 }
hypothetical protein    Caur_1372 4'-phosphopantetheinyl transferase    SSUBM407_1687
action filter_type
action union
action find_reverse
entity 4'-phosphopantetheinyl transferase    SSUBM407_1687
relation encodes
action find_reverse
entity hypothetical protein    Caur_1372
relation encodes
type nucleic acid sequence
{'OR': [[{'concept': 'nucleic acid sequence'}, 'encodes', "4'-phosphopantetheinyl transferase    SSUBM407_1687"], [{'concept': 'nucleic acid sequence'}, 'encodes', 'hypothetical protein    Caur_1372']]}
SELECT DISTINCT ?x WHERE { { { ?x property:encodes resource:4'-phosphopantetheinyl_transferase____SSUBM407_1687 } UNION { ?x property:encodes resource:hypothetical_protein____Caur_1372 } } . ?x rdf:type ontology:nucleic_acid_sequence }
[]
nucleic acid sequence
Q23216360 Q23394389
SYSTEM
4'-phosphopantetheinyl transferase    SSUBM407_1687, hypothetical protein    Caur_1372
Q23216360 Q23394389
OR((c(Q863908),P688,Q23489902), (c(Q863908),P688,Q23474563))
action filter_type
action union
action find_reverse
entity Q23489902
relation P688
action find_reverse
entity Q23474563
relation P688
type Q863908
[ANSWERS]
{'OR': [[{'concept': 'Q863908'}, 'P688', 'Q23489902'], [{'concept': 'Q863908'}, 'P688', 'Q23474563']]}
SELECT DISTINCT ?x WHERE { { { ?x property:P688 resource:Q23489902 } UNION { ?x property:P688 resource:Q23474563 } } . ?x rdf:type ontology:Q863908 }
4'-phosphopantetheinyl transferase    SSUBM407_1687 hypothetical protein    Caur_1372
4'-phosphopantetheinyl transferase SSUBM407 1687 and hypothetical protein Caur 1372 encode 4'-phosphopantetheinyl transferase SSUBM407_1687 or hypothetical protein Caur_1372
4'-phosphopantetheinyl transferase    SSUBM407_1687 hypothetical protein    Caur_1372
action filter_type
action union
action find_reverse
entity 4'-phosphopantetheinyl transferase    SSUBM407_1687
relation encodes
action find_reverse
entity hypothetical protein    Caur_1372
relation encodes
type nucleic acid sequence
{'OR': [[{'concept': 'nucleic acid sequence'}, 'encodes', "4'-phosphopantetheinyl transferase    SSUBM407_1687"], [{'concept': 'nucleic acid sequence'}, 'encodes', 'hypothetical protein    Caur_1372']]}
SELECT DISTINCT ?x WHERE { { { ?x property:encodes resource:4'-phosphopantetheinyl_transferase____SSUBM407_1687 } UNION { ?x property:encodes resource:hypothetical_protein____Caur_1372 } } . ?x rdf:type ontology:nucleic_acid_sequence }
[]
Clarification
Quantitative|Count|Single entity type|Indirect
P703
Q631147
USER
How many infraspecific names are that nucleic acid sequence a part of ?
(Q23394389,P703,c(Q631147))
['Q23394389', 'P703', {'concept': 'Q631147'}]
SELECT DISTINCT ( COUNT ( ?z ) AS ?y ) WHERE { resource:Q23394389 property:P703 ?z . ?z rdf:type ontology:Q631147 }
['hypothetical protein    Caur_1372', 'found in taxon', {'concept': 'infraspecific name'}]
SELECT DISTINCT ( COUNT ( ?z ) AS ?y ) WHERE { resource:hypothetical_protein____Caur_1372 property:found_in_taxon ?z . ?z rdf:type ontology:infraspecific_name }
[]
infraspecific name
Quantitative|Count|Single entity type|Clarification
Q23216360
SYSTEM
Did you mean 4'-phosphopantetheinyl transferase    SSUBM407_1687 ?
(Q23216360,P703,c(Q631147)) (Q23394389,P703,c(Q631147))
[ANSWER]
['Q23216360', 'P703', {'concept': 'Q631147'}] ['Q23394389', 'P703', {'concept': 'Q631147'}]
SELECT DISTINCT ( COUNT ( ?z ) AS ?y ) WHERE { resource:Q23394389 property:P703 ?z . ?z rdf:type ontology:Q631147 }
Did you mean 4'-phosphopantetheinyl transferase    SSUBM407_1687 ?
4'-phosphopantetheinyl transferase    SSUBM407_1687
["4'-phosphopantetheinyl transferase    SSUBM407_1687", 'found in taxon', {'concept': 'infraspecific name'}] ['hypothetical protein    Caur_1372', 'found in taxon', {'concept': 'infraspecific name'}]
SELECT DISTINCT ( COUNT ( ?z ) AS ?y ) WHERE { resource:hypothetical_protein____Caur_1372 property:found_in_taxon ?z . ?z rdf:type ontology:infraspecific_name }
[]
Quantitative Reasoning (Count) (All)
USER
No, I meant hypothetical protein    Caur_1372. Could you tell me the answer for that?
(Q23394389,P703,c(Q631147))
Q23394389
['Q23394389', 'P703', {'concept': 'Q631147'}]
['hypothetical protein    Caur_1372', 'found in taxon', {'concept': 'infraspecific name'}]
[]
SYSTEM
1
Q21102955
(Q23394389,P703,c(Q631147))
[ANSWER]
['Q23394389', 'P703', {'concept': 'Q631147'}]
SELECT DISTINCT ( COUNT ( ?z ) AS ?y ) WHERE { resource:Q23394389 property:P703 ?z . ?z rdf:type ontology:Q631147 }
Chloroflexus aurantiacus J-10-fl
1
['hypothetical protein    Caur_1372', 'found in taxon', {'concept': 'infraspecific name'}]
SELECT DISTINCT ( COUNT ( ?z ) AS ?y ) WHERE { resource:hypothetical_protein____Caur_1372 property:found_in_taxon ?z . ?z rdf:type ontology:infraspecific_name }
[]
Simple Question (Direct)
Simple Question|Single Entity
Q23489902
P680
Q44424
USER
What represents the molecular function of 4'-phosphopantetheinyl transferase    SSUBM407_1687 ?
(Q23489902,P680,c(Q44424))
action filter_type
action find
entity Q23489902
relation P680
type Q44424
['Q23489902', 'P680', {'concept': 'Q44424'}]
SELECT DISTINCT ?o WHERE { resource:Q23489902 property:P680 ?o . ?o rdf:type ontology:Q44424 }
4'-phosphopantetheinyl transferase    SSUBM407_1687
action filter_type
action find
entity 4'-phosphopantetheinyl transferase    SSUBM407_1687
relation molecular function
type chemical bond
["4'-phosphopantetheinyl transferase    SSUBM407_1687", 'molecular function', {'concept': 'chemical bond'}]
SELECT DISTINCT ?o WHERE { resource:4'-phosphopantetheinyl_transferase____SSUBM407_1687 property:molecular_function ?o . ?o rdf:type ontology:chemical_bond }
[]
chemical bond
Q14860850 Q13667380
SYSTEM
magnesium ion binding, metal ion binding
Q14860850 Q13667380
(Q23489902,P680,c(Q44424))
action filter_type
action find
entity Q23489902
relation P680
type Q44424
[ANSWERS] represent the molecular function of 4'-phosphopantetheinyl transferase SSUBM407_1687
['Q23489902', 'P680', {'concept': 'Q44424'}]
SELECT DISTINCT ?o WHERE { resource:Q23489902 property:P680 ?o . ?o rdf:type ontology:Q44424 }
magnesium ion binding metal ion binding
Magnesium ion binding and metal ion binding represent the molecular function of 4'-phosphopantetheinyl transferase SSUBM407_1687
magnesium ion binding metal ion binding
action filter_type
action find
entity 4'-phosphopantetheinyl transferase    SSUBM407_1687
relation molecular function
type chemical bond
["4'-phosphopantetheinyl transferase    SSUBM407_1687", 'molecular function', {'concept': 'chemical bond'}]
SELECT DISTINCT ?o WHERE { resource:4'-phosphopantetheinyl_transferase____SSUBM407_1687 property:molecular_function ?o . ?o rdf:type ontology:chemical_bond }
[]
Simple Question (Ellipsis)
only subject is changed, parent and predicate remains same
Q27740285
Q44424
USER
And also tell me about hypothetical protein    ML1495?
(Q27740285,P680,c(Q44424))
action filter_type
action find
entity Q27740285
relation P680
type Q44424
['Q27740285', 'P680', {'concept': 'Q44424'}]
SELECT DISTINCT ?i WHERE { resource:Q27740285 property:P680 ?i . ?i rdf:type ontology:Q44424 }
hypothetical protein    ML1495
action filter_type
action find
entity hypothetical protein    ML1495
relation molecular function
type chemical bond
['hypothetical protein    ML1495', 'molecular function', {'concept': 'chemical bond'}]
SELECT DISTINCT ?i WHERE { resource:hypothetical_protein____ML1495 property:molecular_function ?i . ?i rdf:type ontology:chemical_bond }
[]
chemical bond
Q14633865 Q13667380
SYSTEM
zinc ion binding, metal ion binding
Q14633865 Q13667380
(Q27740285,P680,c(Q44424))
action filter_type
action find
entity Q27740285
relation P680
type Q44424
[ANSWERS]
['Q27740285', 'P680', {'concept': 'Q44424'}]
SELECT DISTINCT ?i WHERE { resource:Q27740285 property:P680 ?i . ?i rdf:type ontology:Q44424 }
zinc ion binding metal ion binding
zinc ion binding metal ion binding
action filter_type
action find
entity hypothetical protein    ML1495
relation molecular function
type chemical bond
['hypothetical protein    ML1495', 'molecular function', {'concept': 'chemical bond'}]
SELECT DISTINCT ?i WHERE { resource:hypothetical_protein____ML1495 property:molecular_function ?i . ?i rdf:type ontology:chemical_bond }
[]
Verification (Boolean) (All)
Verification|one entity, multiple entities (as object) referred indirectly
Q23605909
P680
Q181394
USER
Are alanyl-tRNA synthetase    Smed_1521 the gene that have those chemical bonds as the molecular function ?
(Q23605909,P680,Q14633865) (Q23605909,P680,Q13667380)
action is_in
entity prev_answer
action find
entity Q23605909
relation P680
['Q23605909', 'P680', 'Q14633865'] ['Q23605909', 'P680', 'Q13667380']
ASK WHERE { resource:Q23605909 property:P680 ?m . VALUES ( ?m ) { ( resource:Q14633865 ) ( resource:Q13667380 ) } }
alanyl-tRNA synthetase    Smed_1521
action is_in
entity prev_answer
action find
entity alanyl-tRNA synthetase    Smed_1521
relation molecular function
['alanyl-tRNA synthetase    Smed_1521', 'molecular function', 'zinc ion binding'] ['alanyl-tRNA synthetase    Smed_1521', 'molecular function', 'metal ion binding']
ASK WHERE { resource:alanyl-tRNA_synthetase____Smed_1521 property:molecular_function ?m . VALUES ( ?m ) { ( resource:zinc_ion_binding ) ( resource:metal_ion_binding ) } }
[]
nutrient
SYSTEM
YES
(Q23605909,P680,Q14633865) (Q23605909,P680,Q13667380)
action is_in
entity prev_answer
action find
entity Q23605909
relation P680
[ANSWER]
['Q23605909', 'P680', 'Q14633865'] ['Q23605909', 'P680', 'Q13667380']
ASK WHERE { resource:Q23605909 property:P680 ?m . VALUES ( ?m ) { ( resource:Q14633865 ) ( resource:Q13667380 ) } }
Yes
action is_in
entity prev_answer
action find
entity alanyl-tRNA synthetase    Smed_1521
relation molecular function
['alanyl-tRNA synthetase    Smed_1521', 'molecular function', 'zinc ion binding'] ['alanyl-tRNA synthetase    Smed_1521', 'molecular function', 'metal ion binding']
ASK WHERE { resource:alanyl-tRNA_synthetase____Smed_1521 property:molecular_function ?m . VALUES ( ?m ) { ( resource:zinc_ion_binding ) ( resource:metal_ion_binding ) } }
[]
Verification (Boolean) (All)
Verification|2 entities, both direct
Q23394389 Q21102955
P703
Q631147
USER
Does hypothetical protein    Caur_1372 belong to Chloroflexus aurantiacus J-10-fl ?
(Q23394389,P703,Q21102955)
action is_in
entity Q21102955
action find
entity Q23394389
relation P703
['Q23394389', 'P703', 'Q21102955']
ASK WHERE { resource:Q23394389 property:P703 resource:Q21102955 }
hypothetical protein    Caur_1372 Chloroflexus aurantiacus J-10-fl
action is_in
entity Chloroflexus aurantiacus J-10-fl
action find
entity hypothetical protein    Caur_1372
relation found in taxon
['hypothetical protein    Caur_1372', 'found in taxon', 'Chloroflexus aurantiacus J-10-fl']
ASK WHERE { resource:hypothetical_protein____Caur_1372 property:found_in_taxon resource:Chloroflexus_aurantiacus_J-10-fl }
[]
infraspecific name
SYSTEM
YES
(Q23394389,P703,Q21102955)
action is_in
entity Q21102955
action find
entity Q23394389
relation P703
[ANSWER]
['Q23394389', 'P703', 'Q21102955']
ASK WHERE { resource:Q23394389 property:P703 resource:Q21102955 }
Yes
action is_in
entity Chloroflexus aurantiacus J-10-fl
action find
entity hypothetical protein    Caur_1372
relation found in taxon
['hypothetical protein    Caur_1372', 'found in taxon', 'Chloroflexus aurantiacus J-10-fl']
ASK WHERE { resource:hypothetical_protein____Caur_1372 property:found_in_taxon resource:Chloroflexus_aurantiacus_J-10-fl }
[]
Logical Reasoning (All)
Logical|Difference|Single_Relation
Q27547447 Q23605909
P680
Q44424
USER
Which chemical bonds represent molecular function of alanyl-tRNA synthetase    Smed_1521 but not NAD-dependent histone deacetylase HST3 YOR025W ?
AND((Q23605909,P680,c(Q44424)), NOT((Q27547447,P680,c(Q44424))))
action filter_type
action difference
action find
entity Q23605909
relation P680
action find
entity Q27547447
relation P680
type Q44424
{'AND': [['Q23605909', 'P680', {'concept': 'Q44424'}], {'NOT': [['Q27547447', 'P680', {'concept': 'Q44424'}]]}]}
SELECT DISTINCT ?s WHERE { MINUS { resource:Q27547447 property:P680 ?s } . resource:Q23605909 property:P680 ?s . ?s rdf:type ontology:Q44424 }
NAD-dependent histone deacetylase HST3 YOR025W alanyl-tRNA synthetase    Smed_1521
action filter_type
action difference
action find
entity alanyl-tRNA synthetase    Smed_1521
relation molecular function
action find
entity NAD-dependent histone deacetylase HST3 YOR025W
relation molecular function
type chemical bond
{'AND': [['alanyl-tRNA synthetase    Smed_1521', 'molecular function', {'concept': 'chemical bond'}], {'NOT': [['NAD-dependent histone deacetylase HST3 YOR025W', 'molecular function', {'concept': 'chemical bond'}]]}]}
SELECT DISTINCT ?s WHERE { MINUS { resource:NAD-dependent_histone_deacetylase_HST3_YOR025W property:molecular_function ?s } . resource:alanyl-tRNA_synthetase____Smed_1521 property:molecular_function ?s . ?s rdf:type ontology:chemical_bond }
[]
chemical bond
Q14633865
SYSTEM
zinc ion binding
Q14633865
AND((Q23605909,P680,c(Q44424)), NOT((Q27547447,P680,c(Q44424))))
action filter_type
action difference
action find
entity Q23605909
relation P680
action find
entity Q27547447
relation P680
type Q44424
The [ANSWER] represent molecular function of alanyl-tRNA synthetase Smed_1521 but not NAD-dependent histone deacetylase HST3 YOR025W
{'AND': [['Q23605909', 'P680', {'concept': 'Q44424'}], {'NOT': [['Q27547447', 'P680', {'concept': 'Q44424'}]]}]}
SELECT DISTINCT ?s WHERE { MINUS { resource:Q27547447 property:P680 ?s } . resource:Q23605909 property:P680 ?s . ?s rdf:type ontology:Q44424 }
zinc ion binding
The zinc ion binding represent molecular function of alanyl-tRNA synthetase Smed_1521 but not NAD-dependent histone deacetylase HST3 YOR025W
zinc ion binding
action filter_type
action difference
action find
entity alanyl-tRNA synthetase    Smed_1521
relation molecular function
action find
entity NAD-dependent histone deacetylase HST3 YOR025W
relation molecular function
type chemical bond
{'AND': [['alanyl-tRNA synthetase    Smed_1521', 'molecular function', {'concept': 'chemical bond'}], {'NOT': [['NAD-dependent histone deacetylase HST3 YOR025W', 'molecular function', {'concept': 'chemical bond'}]]}]}
SELECT DISTINCT ?s WHERE { MINUS { resource:NAD-dependent_histone_deacetylase_HST3_YOR025W property:molecular_function ?s } . resource:alanyl-tRNA_synthetase____Smed_1521 property:molecular_function ?s . ?s rdf:type ontology:chemical_bond }
[]