Simple Question (Direct)
Simple Question
Q23602568
P681
Q15989253
USER
What is a component of Protein of unknown function YfiC    FP0346 ?
(Q23602568,P681,c(Q15989253))
action filter_type
action find
entity Q23602568
relation P681
type Q15989253
['Q23602568', 'P681', {'concept': 'Q15989253'}]
SELECT DISTINCT ?m WHERE { resource:Q23602568 property:P681 ?m . ?m rdf:type ontology:Q15989253 }
Protein of unknown function YfiC    FP0346
action filter_type
action find
entity Protein of unknown function YfiC    FP0346
relation cell component
type part
['Protein of unknown function YfiC    FP0346', 'cell component', {'concept': 'part'}]
SELECT DISTINCT ?m WHERE { resource:Protein_of_unknown_function_YfiC____FP0346 property:cell_component ?m . ?m rdf:type ontology:part }
[]
part
Q79899
SYSTEM
cytoplasm
Q79899
(Q23602568,P681,c(Q15989253))
action filter_type
action find
entity Q23602568
relation P681
type Q15989253
A component of Protein of unknown function YfiC FP0346 is the [ANSWER]
['Q23602568', 'P681', {'concept': 'Q15989253'}]
SELECT DISTINCT ?m WHERE { resource:Q23602568 property:P681 ?m . ?m rdf:type ontology:Q15989253 }
cytoplasm
A component of Protein of unknown function YfiC FP0346 is the cytoplasm
cytoplasm
action filter_type
action find
entity Protein of unknown function YfiC    FP0346
relation cell component
type part
['Protein of unknown function YfiC    FP0346', 'cell component', {'concept': 'part'}]
SELECT DISTINCT ?m WHERE { resource:Protein_of_unknown_function_YfiC____FP0346 property:cell_component ?m . ?m rdf:type ontology:part }
[]
Simple Question (Coreferenced)
Simple Question|Single Entity|Indirect
Q23602568
P682
Q2996394
USER
Which biological process is that nutrient involved in ?
(Q79899,P682,c(Q2996394))
action filter_type
action find
entity Q23602568
relation P682
type Q2996394
['Q79899', 'P682', {'concept': 'Q2996394'}]
SELECT DISTINCT ?s WHERE { resource:Q23602568 property:P682 ?s . ?s rdf:type ontology:Q2996394 }
Protein of unknown function YfiC    FP0346
action filter_type
action find
entity Protein of unknown function YfiC    FP0346
relation biological process
type biological process
['cytoplasm', 'biological process', {'concept': 'biological process'}]
SELECT DISTINCT ?s WHERE { resource:Protein_of_unknown_function_YfiC____FP0346 property:biological_process ?s . ?s rdf:type ontology:biological_process }
[]
biological process
Q518328
SYSTEM
methylation
Q518328
(Q79899,P682,c(Q2996394))
action filter_type
action find
entity Q23602568
relation P682
type Q2996394
That nutrient is involved in [ANSWER]
['Q79899', 'P682', {'concept': 'Q2996394'}]
SELECT DISTINCT ?s WHERE { resource:Q23602568 property:P682 ?s . ?s rdf:type ontology:Q2996394 }
methylation
That nutrient is involved in methylation
methylation
action filter_type
action find
entity Protein of unknown function YfiC    FP0346
relation biological process
type biological process
['cytoplasm', 'biological process', {'concept': 'biological process'}]
SELECT DISTINCT ?s WHERE { resource:Protein_of_unknown_function_YfiC____FP0346 property:biological_process ?s . ?s rdf:type ontology:biological_process }
[]
Verification (Boolean) (All)
Verification|2 entities, one direct and one indirect, object is indirect
Q518328 Q23430361
P682
Q181394
USER
Is hypothetical protein    AHA_2596 involved in that biological process ?
(Q23430361,P682,Q518328)
action is_in
entity Q23430361
action find
entity Q518328
relation P682
['Q23430361', 'P682', 'Q518328']
ASK WHERE { resource:Q518328 property:P682 resource:Q23430361 }
methylation hypothetical protein    AHA_2596
action is_in
entity hypothetical protein    AHA_2596
action find
entity methylation
relation biological process
['hypothetical protein    AHA_2596', 'biological process', 'methylation']
ASK WHERE { resource:methylation property:biological_process resource:hypothetical_protein____AHA_2596 }
[]
nutrient
SYSTEM
NO
(Q23430361,P682,Q518328)
action is_in
entity Q23430361
action find
entity Q518328
relation P682
[ANSWER]
['Q23430361', 'P682', 'Q518328']
ASK WHERE { resource:Q518328 property:P682 resource:Q23430361 }
No
action is_in
entity hypothetical protein    AHA_2596
action find
entity methylation
relation biological process
['hypothetical protein    AHA_2596', 'biological process', 'methylation']
ASK WHERE { resource:methylation property:biological_process resource:hypothetical_protein____AHA_2596 }
[]
Quantitative Reasoning (Count) (All)
Quantitative|Count over Atleast/ Atmost/ Approx. the same/Equal|Mult. entity type
P361
Q15989253 Q234460 Q5058355
USER
How many parts are exactly 4 texts and cellular components a portion of ?
(c(Q234460)|c(Q5058355),P361,c(Q15989253))
action count
action equal
action union
action find_reverse_tuple_counts
relation P361
type Q15989253
type Q234460
action find_reverse_tuple_counts
relation P361
type Q15989253
type Q5058355
value 4
[[{'concept': 'Q234460'}, {'concept': 'Q5058355'}], 'P361', {'concept': 'Q15989253'}]
SELECT DISTINCT ( COUNT ( ?s ) AS ?x ) WHERE { { SELECT DISTINCT ( COUNT ( ?r ) AS ?y ) ?s WHERE { { ?r property:P361 ?s . ?s rdf:type ontology:Q15989253 . ?r rdf:type ontology:Q234460 } UNION { ?r property:P361 ?s . ?s rdf:type ontology:Q15989253 . ?r rdf:type ontology:Q5058355 } } GROUP BY ?s } . FILTER ( ?y = 4 ) }
action count
action equal
action union
action find_reverse_tuple_counts
relation part of
type part
type text
action find_reverse_tuple_counts
relation part of
type part
type cellular component
value 4
[[{'concept': 'text'}, {'concept': 'cellular component'}], 'part of', {'concept': 'part'}]
SELECT DISTINCT ( COUNT ( ?s ) AS ?x ) WHERE { { SELECT DISTINCT ( COUNT ( ?r ) AS ?y ) ?s WHERE { { ?r property:part_of ?s . ?s rdf:type ontology:part . ?r rdf:type ontology:text } UNION { ?r property:part_of ?s . ?s rdf:type ontology:part . ?r rdf:type ontology:cellular_component } } GROUP BY ?s } . FILTER ( ?y = 4 ) }
[]
part text cellular component
SYSTEM
2
Q187181 Q14645596
(c(Q234460)|c(Q5058355),P361,c(Q15989253))
action count
action equal
action union
action find_reverse_tuple_counts
relation P361
type Q15989253
type Q234460
action find_reverse_tuple_counts
relation P361
type Q15989253
type Q5058355
value 4
[ANSWER]
[[{'concept': 'Q234460'}, {'concept': 'Q5058355'}], 'P361', {'concept': 'Q15989253'}]
SELECT DISTINCT ( COUNT ( ?s ) AS ?x ) WHERE { { SELECT DISTINCT ( COUNT ( ?r ) AS ?y ) ?s WHERE { { ?r property:P361 ?s . ?s rdf:type ontology:Q15989253 . ?r rdf:type ontology:Q234460 } UNION { ?r property:P361 ?s . ?s rdf:type ontology:Q15989253 . ?r rdf:type ontology:Q5058355 } } GROUP BY ?s } . FILTER ( ?y = 4 ) }
synapse extracellular region
2
action count
action equal
action union
action find_reverse_tuple_counts
relation part of
type part
type text
action find_reverse_tuple_counts
relation part of
type part
type cellular component
value 4
[[{'concept': 'text'}, {'concept': 'cellular component'}], 'part of', {'concept': 'part'}]
SELECT DISTINCT ( COUNT ( ?s ) AS ?x ) WHERE { { SELECT DISTINCT ( COUNT ( ?r ) AS ?y ) ?s WHERE { { ?r property:part_of ?s . ?s rdf:type ontology:part . ?r rdf:type ontology:text } UNION { ?r property:part_of ?s . ?s rdf:type ontology:part . ?r rdf:type ontology:cellular_component } } GROUP BY ?s } . FILTER ( ?y = 4 ) }
[]
Quantitative Reasoning (All)
Quantitative|Atleast/ Atmost/ Approx. the same/Equal|Mult. entity type
P361
Q2996394 Q151885 Q2996394
USER
Which biological processes are a component of atleast 1 biological processes or concepts ?
(c(Q2996394),P361,c(Q2996394)|c(Q151885))
action atleast
action union
action find_tuple_counts
relation P361
type Q2996394
type Q2996394
action find_tuple_counts
relation P361
type Q2996394
type Q151885
value 1
[{'concept': 'Q2996394'}, 'P361', [{'concept': 'Q2996394'}, {'concept': 'Q151885'}]]
SELECT DISTINCT ?c WHERE { { SELECT DISTINCT ?c ( COUNT ( ?j ) AS ?n ) WHERE { VALUES ( ?k ) { ( ontology:Q2996394 ) ( ontology:Q151885 ) } . ?j rdf:type ?k } GROUP BY ?c } . FILTER ( ?n >= 1 ) }
action atleast
action union
action find_tuple_counts
relation part of
type biological process
type biological process
action find_tuple_counts
relation part of
type biological process
type concept
value 1
[{'concept': 'biological process'}, 'part of', [{'concept': 'biological process'}, {'concept': 'concept'}]]
SELECT DISTINCT ?c WHERE { { SELECT DISTINCT ?c ( COUNT ( ?j ) AS ?n ) WHERE { VALUES ( ?k ) { ( ontology:biological_process ) ( ontology:concept ) } . ?j rdf:type ?k } GROUP BY ?c } . FILTER ( ?n >= 1 ) }
[]
biological process concept biological process
Q22291145 Q21104832 Q22294591
SYSTEM
establishment of oocyte nucleus localization involved in oocyte dorsal/ventral axis specification, synaptic vesicle exocytosis, mitotic cell cycle arrest in response to pheromone
Q22294591 Q21107328 Q22294585 Q14860198 Q949618 Q14897640 Q21116174 Q14864099 Q22280551 Q21111890 Q22269731 Q22279989 Q27122058 Q14865659 Q14914558 Q21149516 Q22279517 Q22281166 Q22284167 Q22279591 Q15320925 Q22291145 Q22294726 Q22294880 Q21127160 Q22270384 Q21106668 Q22280424 Q14864210 Q22302766 Q22294463 Q14864899 Q14904772 Q14904771 Q21108839 Q22279704 Q21104832 Q22269699 Q14873676 Q21114820
(c(Q2996394),P361,c(Q2996394)|c(Q151885))
action atleast
action union
action find_tuple_counts
relation P361
type Q2996394
type Q2996394
action find_tuple_counts
relation P361
type Q2996394
type Q151885
value 1
The [ANSWERS] are a component of atleast 1 biological processes or concepts
[{'concept': 'Q2996394'}, 'P361', [{'concept': 'Q2996394'}, {'concept': 'Q151885'}]]
SELECT DISTINCT ?c WHERE { { SELECT DISTINCT ?c ( COUNT ( ?j ) AS ?n ) WHERE { VALUES ( ?k ) { ( ontology:Q2996394 ) ( ontology:Q151885 ) } . ?j rdf:type ?k } GROUP BY ?c } . FILTER ( ?n >= 1 ) }
mitotic cell cycle arrest in response to pheromone development involved in symbiotic interaction adaptation of signaling pathway by response to pheromone involved in conjugation with cellular fusion anatomical structure formation involved in morphogenesis Taxis synaptic vesicle docking synaptic vesicle targeting ovulation cycle process gene conversion at mating-type locus, termination of copy-synthesis synaptic vesicle priming movement in environment of other organism involved in symbiotic interaction gene conversion at mating-type locus, DNA double-strand break processing synaptic vesicle tethering involved in synaptic vesicle exocytosis tolerance induction nitrogen compound metabolic process organic substance metabolic process heteroduplex formation involved in gene conversion at mating-type locus gene conversion at mating-type locus, DNA double-strand break formation peptidyl-serine phosphorylation involved in acrosome reaction strand invasion involved in gene conversion at mating-type locus locomotion involved in locomotory behavior establishment of oocyte nucleus localization involved in oocyte dorsal/ventral axis specification DNA recombinase assembly involved in gene conversion at mating-type locus acquisition of nutrients from other organism during symbiotic interaction fertilization, exchange of chromosomal proteins dissemination or transmission of organism from other organism involved in symbiotic interaction synaptic vesicle fusion to presynaptic active zone membrane somatic diversification of immune receptors anatomical structure morphogenesis calcium-dependent activation of synaptic vesicle fusion sperm chromatin decondensation acrosome matrix dispersal spermatogenesis, exchange of chromosomal proteins sperm chromatin condensation adhesion of symbiont to host gene conversion at mating-type locus, DNA repair synthesis synaptic vesicle exocytosis growth involved in symbiotic interaction cell motility spermatid nucleus elongation
The establishment of oocyte nucleus localization involved in oocyte dorsal/ventral axis specification, synaptic vesicle exocytosis and mitotic cell cycle arrest in response to pheromone are a component of atleast 1 biological processes or concepts
establishment of oocyte nucleus localization involved in oocyte dorsal/ventral axis specification synaptic vesicle exocytosis mitotic cell cycle arrest in response to pheromone
action atleast
action union
action find_tuple_counts
relation part of
type biological process
type biological process
action find_tuple_counts
relation part of
type biological process
type concept
value 1
[{'concept': 'biological process'}, 'part of', [{'concept': 'biological process'}, {'concept': 'concept'}]]
SELECT DISTINCT ?c WHERE { { SELECT DISTINCT ?c ( COUNT ( ?j ) AS ?n ) WHERE { VALUES ( ?k ) { ( ontology:biological_process ) ( ontology:concept ) } . ?j rdf:type ?k } GROUP BY ?c } . FILTER ( ?n >= 1 ) }
[]
Clarification
Comparative|More/Less|Single entity type|Indirect
P682
Q2996394 Q181394
USER
Which biological processes are around the same number of nutrients involved in as that biological process ?
(c(Q181394),P682,c(Q2996394))
[{'concept': 'Q181394'}, 'P682', {'concept': 'Q2996394'}]
SELECT DISTINCT ?y WHERE { ?z property:Q2996394 ?y . ?z rdf:type ontology:Q181394 . ?y rdf:type ontology:Q2996394 }
[{'concept': 'nutrient'}, 'biological process', {'concept': 'biological process'}]
SELECT DISTINCT ?y WHERE { ?z property:biological_process ?y . ?z rdf:type ontology:nutrient . ?y rdf:type ontology:biological_process }
[]
biological process nutrient
Comparative|More/Less|Single entity type|Clarification
Q21104832
SYSTEM
Did you mean synaptic vesicle exocytosis ?
(c(Q181394),P682,c(Q2996394))
[ANSWER]
[{'concept': 'Q181394'}, 'P682', {'concept': 'Q2996394'}]
SELECT DISTINCT ?y WHERE { ?z property:Q2996394 ?y . ?z rdf:type ontology:Q181394 . ?y rdf:type ontology:Q2996394 }
Did you mean synaptic vesicle exocytosis ?
synaptic vesicle exocytosis
[{'concept': 'nutrient'}, 'biological process', {'concept': 'biological process'}]
SELECT DISTINCT ?y WHERE { ?z property:biological_process ?y . ?z rdf:type ontology:nutrient . ?y rdf:type ontology:biological_process }
[]
Comparative Reasoning (All)
USER
Yes
(c(Q181394),P682,c(Q2996394))
[{'concept': 'Q181394'}, 'P682', {'concept': 'Q2996394'}]
[{'concept': 'nutrient'}, 'biological process', {'concept': 'biological process'}]
[]
Q14877671 Q21750263 Q21108938
SYSTEM
cartilage condensation, FtsZ-dependent cytokinesis, preantral ovarian follicle growth
Q22294591 Q21172195 Q14862258 Q21107328 Q22295734 Q14860201 Q288322 Q14902079 Q14863388 Q14904219 Q14911711 Q22271492 Q22271494 Q14864899 Q22294585 Q21122953 Q21104659 Q14860196 Q22294349 Q14860198 Q14864005 Q15325345 Q22269626 Q22269531 Q24459941 Q21438150 Q14897640 Q208353 Q21114926 Q14865609 Q21116174 Q14876119 Q14877671 Q22272257 Q21097540 Q14864099 Q21103041 Q21444598 Q21136671 Q21111890 Q22253821 Q21101822 Q14863654 Q21109007 Q22271536 Q22279989 Q21127160 Q14865397 Q15314382 Q14859996 Q14865659 Q22294730 Q21171796 Q14331109 Q21149516 Q21130714 Q2663023 Q21120908 Q189159 Q22271501 Q22281166 Q22299432 Q14908045 Q14863467 Q21105147 Q21123910 Q15320925 Q163261 Q22298156 Q22271697 Q22269715 Q21119405 Q22297692 Q21130764 Q21750263 Q21762806 Q333666 Q21418091 Q14864443 Q14820875 Q21124921 Q21106668 Q14904764 Q21104990 Q14863664 Q22250139 Q14863667 Q21108563 Q21111494 Q14914540 Q17304930 Q21758676 Q22284328 Q21108938 Q21106266 Q14864210 Q14907898 Q21106018 Q22271479 Q22272219 Q14904772 Q14904771 Q14819471 Q14912956 Q21108839 Q22279704 Q14863453 Q14882364 Q14819856 Q21104832 Q21102309 Q22289134 Q14863538 Q22269699 Q14599729 Q22284230 Q14851921 Q21115753 Q24459846 Q22274350 Q21115817 Q14876924 Q14864904 Q14645719 Q14873676 Q21104842 Q21132115 Q21114820
(c(Q181394),P682,c(Q2996394))
[ANSWERS] are around the same number of nutrients involved in as that biological process
[{'concept': 'Q181394'}, 'P682', {'concept': 'Q2996394'}]
SELECT DISTINCT ?y WHERE { ?z property:Q2996394 ?y . ?z rdf:type ontology:Q181394 . ?y rdf:type ontology:Q2996394 }
mitotic cell cycle arrest in response to pheromone positive regulation of growth factor dependent skeletal muscle satellite cell proliferation dopamine uptake involved in synaptic transmission development involved in symbiotic interaction leukocyte activation anatomical structure development autophagy T cell mediated cytotoxicity response to external stimulus developmental process involved in reproduction male meiosis detoxification of zinc ion detoxification of arsenic-containing substance acrosome matrix dispersal adaptation of signaling pathway by response to pheromone involved in conjugation with cellular fusion male pronucleus assembly detoxification of nitrogen compound developmental growth dormancy process anatomical structure formation involved in morphogenesis ovulation cycle pronuclear fusion single-organism developmental process filamentous growth manchette assembly protein activation cascade synaptic vesicle docking circadian rhythm complement-dependent cytotoxicity myeloid cell homeostasis synaptic vesicle targeting antigen processing and presentation cartilage condensation meiosis I DNA methylation involved in gamete generation ovulation cycle process protein unfolding positive regulation of flagellated sperm motility involved in capacitation female pronucleus assembly synaptic vesicle priming regulation of transcription involved in meiotic cell cycle response to redox state multicellular organismal reproductive process developmental induction response to pheromone involved in conjugation with cellular fusion gene conversion at mating-type locus, DNA double-strand break processing fertilization, exchange of chromosomal proteins T cell selection natural killer cell mediated cytotoxicity mesenchymal smoothened signaling pathway involved in prostate gland development tolerance induction karyogamy involved in conjugation with cellular fusion nitric oxide storage receptor localization to synapse organic substance metabolic process catabolic process cytolysis cellular localization cell growth multi-organism cellular process gene conversion at mating-type locus, DNA double-strand break formation nitrogen utilization menstrual cycle phase immune system development single organism reproductive process leukocyte mediated cytotoxicity locomotion involved in locomotory behavior acrosome reaction maintenance of cell number activation of immune response budding cell bud growth single-organism behavior spore germination ultradian rhythm FtsZ-dependent cytokinesis primary metabolic process abscission antibody-dependent cellular cytotoxicity response to inactivity response to activity P granule organization synaptic vesicle fusion to presynaptic active zone membrane primary ovarian follicle growth spermatid nucleus differentiation neurotransmitter secretion meiotic cell cycle process rhythmic behavior cellular response to stimulus activation of meiosis involved in egg activation female meiotic division cell cycle process carbon utilization peptide mating pheromone maturation involved in conjugation with cellular fusion preantral ovarian follicle growth carbohydrate utilization anatomical structure morphogenesis response to other organism cell separation after cytokinesis mycothiol-dependent detoxification detection of stimulus spermatogenesis, exchange of chromosomal proteins sperm chromatin condensation leukocyte migration ovarian cumulus expansion adhesion of symbiont to host gene conversion at mating-type locus, DNA repair synthesis leukocyte homeostasis killing of cells of other organism feeding behavior synaptic vesicle exocytosis response to abiotic stimulus cellular component organization pigmentation growth involved in symbiotic interaction response to estrogen cell wall organization or biogenesis hormone metabolic process behavioral response to nutrient intermicrovillar adhesion phenotypic switching directional locomotion cellular metabolic process response to biotic stimulus locomotory behavior cell motility chromosome localization to nuclear envelope involved in homologous chromosome segregation prevention of polyspermy spermatid nucleus elongation
Cartilage condensation, FtsZ-dependent cytokinesis and preantral ovarian follicle growth are around the same number of nutrients involved in as that biological process
cartilage condensation FtsZ-dependent cytokinesis preantral ovarian follicle growth
[{'concept': 'nutrient'}, 'biological process', {'concept': 'biological process'}]
SELECT DISTINCT ?y WHERE { ?z property:biological_process ?y . ?z rdf:type ontology:nutrient . ?y rdf:type ontology:biological_process }
[]