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Merge pull request #180 from FlyBase/pattern_labels
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Pattern labels
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Clare72 authored Jun 6, 2024
2 parents 94499d5 + cf985f9 commit 607c013
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18 changes: 18 additions & 0 deletions src/ontology/dpo.Makefile
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Expand Up @@ -28,6 +28,24 @@ tmp/remaining_classes.txt: tmp/all_patternised_classes.txt tmp/all_defined_class
tmp/remaining_definitions.owl: $(SRC) tmp/remaining_classes.txt
$(ROBOT) filter -i $< -T tmp/remaining_classes.txt --axioms "equivalent annotation" --trim false -o $@

##########################
##### Pattern labels #####
##########################

# all filenames for pattern tsvs
ALL_DOSDP_TSVs = $(wildcard $(PATTERNDIR)/data/default/*.tsv)

$(TMPDIR)/$(ONT)-merged.db: $(SRC)
$(ROBOT) merge -i $< -o $(TMPDIR)/$(ONT)-merged.owl
semsql make $@

update_pattern_labels: $(TMPDIR)/$(ONT)-merged.db
wget -O $(SCRIPTSDIR)/update_term_labels_in_file.py https://raw.githubusercontent.com/FlyBase/flybase-ontology-scripts/master/update_term_labels_in_file/src/update_term_labels_in_file.py
for file in $(ALL_DOSDP_TSVs) ; do \
python3 $(SCRIPTSDIR)/update_term_labels_in_file.py -f $$file -i auto -c $< ; \
done


##################################
##### Custom mirroring rules #####
##################################
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2 changes: 1 addition & 1 deletion src/patterns/data/default/abnormalAbsenceOfBehavior.tsv
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@@ -1,2 +1,2 @@
defined_class defined_class_label behavior_process behavior_process_label
http://purl.obolibrary.org/obo/FBcv_0000713 jumpless http://purl.obolibrary.org/obo/NBO_0000016 jumping behavior
FBcv:0000713 jumpless NBO:0000016 jumping behavior
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@@ -1,3 +1,3 @@
defined_class defined_class_label biological_process biological_process_label
http://purl.obolibrary.org/obo/FBcv_0000418 flightless http://purl.obolibrary.org/obo/GO_0060361 flight
http://purl.obolibrary.org/obo/FBcv_0000389 paralytic http://purl.obolibrary.org/obo/GO_0050879 multicellular organismal movement
defined_class defined_class_label biological_process biological_process_label
FBcv:0000418 flightless GO:0060361 flight
FBcv:0000389 paralytic GO:0050879 multicellular organismal movement
4 changes: 2 additions & 2 deletions src/patterns/data/default/abnormalAnatomicalEntity.tsv
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@@ -1,2 +1,2 @@
defined_class defined_class_label anatomical_entity anatomical_entity_label
http://purl.obolibrary.org/obo/FBcv_0000435 neuroanatomy defective http://purl.obolibrary.org/obo/FBbt_00005093 nervous system
defined_class defined_class_label anatomical_entity anatomical_entity_label
FBcv:0000435 abnormal neuroanatomy FBbt:00005093 nervous system
62 changes: 31 additions & 31 deletions src/patterns/data/default/abnormalBehavior.tsv
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@@ -1,32 +1,32 @@
defined_class defined_class_label behavior_process behavior_process_label
http://purl.obolibrary.org/obo/FBcv_0000387 behavior defective http://purl.obolibrary.org/obo/GO_0007610 behavior
http://purl.obolibrary.org/obo/FBcv_0000403 chemosensitive behavior defective http://purl.obolibrary.org/obo/GO_0007635 chemosensory behavior
http://purl.obolibrary.org/obo/FBcv_0000679 circadian behavior defective http://purl.obolibrary.org/obo/GO_0048512 circadian behavior
http://purl.obolibrary.org/obo/FBcv_0000396 eclosion rhythm defective http://purl.obolibrary.org/obo/GO_0008062 eclosion rhythm
http://purl.obolibrary.org/obo/FBcv_0000419 feeding behavior defective http://purl.obolibrary.org/obo/GO_0007631 feeding behavior
http://purl.obolibrary.org/obo/FBcv_0000420 grooming behavior defective http://purl.obolibrary.org/obo/GO_0007625 grooming behavior
http://purl.obolibrary.org/obo/FBcv_0000669 hatching behavior defective http://purl.obolibrary.org/obo/GO_0035187 hatching behavior
http://purl.obolibrary.org/obo/FBcv_0000720 jump response defective http://purl.obolibrary.org/obo/GO_0007630 jump response
http://purl.obolibrary.org/obo/FBcv_0000397 learning defective http://purl.obolibrary.org/obo/GO_0007612 learning
http://purl.obolibrary.org/obo/FBcv_0000414 locomotor behavior defective http://purl.obolibrary.org/obo/GO_0007626 locomotory behavior
http://purl.obolibrary.org/obo/FBcv_0000395 locomotor rhythm defective http://purl.obolibrary.org/obo/GO_0045475 locomotor rhythm
http://purl.obolibrary.org/obo/FBcv_0000401 mating rhythm defective http://purl.obolibrary.org/obo/GO_0035648 circadian mating behavior
http://purl.obolibrary.org/obo/FBcv_0000398 memory defective http://purl.obolibrary.org/obo/GO_0007613 memory
http://purl.obolibrary.org/obo/FBcv_0000412 optomotor response defective http://purl.obolibrary.org/obo/GO_0007634 optokinetic behavior
http://purl.obolibrary.org/obo/FBcv_0006004 oviposition defective http://purl.obolibrary.org/obo/GO_0018991 oviposition
http://purl.obolibrary.org/obo/FBcv_0000680 proboscis extension reflex defective http://purl.obolibrary.org/obo/GO_0007637 proboscis extension reflex
http://purl.obolibrary.org/obo/FBcv_0000402 song defective http://purl.obolibrary.org/obo/GO_0045433 "male courtship behavior, veined wing generated song production"
http://purl.obolibrary.org/obo/FBcv_0000411 visual behavior defective http://purl.obolibrary.org/obo/GO_0007632 visual behavior
http://purl.obolibrary.org/obo/FBcv_0000721 mating behavior defective http://purl.obolibrary.org/obo/GO_0007617 mating behavior
http://purl.obolibrary.org/obo/FBcv_0000400 mating defective http://purl.obolibrary.org/obo/GO_0007618 mating
http://purl.obolibrary.org/obo/FBcv_0000399 courtship behavior defective http://purl.obolibrary.org/obo/GO_0007619 courtship behavior
http://purl.obolibrary.org/obo/FBcv_0007500 abnormal anesthesia-resistant memory http://purl.obolibrary.org/obo/GO_0007615 anesthesia-resistant memory
http://purl.obolibrary.org/obo/FBcv_0007501 abnormal short-term memory http://purl.obolibrary.org/obo/GO_0007614 short-term memory
http://purl.obolibrary.org/obo/FBcv_0007502 abnormal medium-term memory http://purl.obolibrary.org/obo/GO_0072375 medium-term memory
http://purl.obolibrary.org/obo/FBcv_0007503 abnormal long-term memory http://purl.obolibrary.org/obo/GO_0007616 long-term memory
http://purl.obolibrary.org/obo/FBcv_0000415 abnormal jumping http://purl.obolibrary.org/obo/NBO_0000016 jumping behavior
http://purl.obolibrary.org/obo/FBcv_0000416 uncoordinated http://purl.obolibrary.org/obo/NBO_0000339 motor coordination
http://purl.obolibrary.org/obo/FBcv_0000421 abnormal touch response http://purl.obolibrary.org/obo/NBO_0000332 touch related behavior
http://purl.obolibrary.org/obo/FBcv_0007527 abnormal adult walking behavior http://purl.obolibrary.org/obo/GO_0007628 adult walking behavior
http://purl.obolibrary.org/obo/FBcv_0007528 abnormal larval locomotory behavior http://purl.obolibrary.org/obo/GO_0008345 larval locomotory behavior
http://purl.obolibrary.org/obo/FBcv_0007529 abnormal adult locomotory behavior http://purl.obolibrary.org/obo/GO_0008344 adult locomotory behavior
FBcv:0000387 abnormal behavior GO:0007610 behavior
FBcv:0000403 abnormal chemosensory behavior GO:0007635 chemosensory behavior
FBcv:0000679 abnormal circadian behavior GO:0048512 circadian behavior
FBcv:0000396 abnormal eclosion rhythm GO:0008062 eclosion rhythm
FBcv:0000419 abnormal feeding behavior GO:0007631 feeding behavior
FBcv:0000420 abnormal grooming behavior GO:0007625 grooming behavior
FBcv:0000669 abnormal hatching behavior GO:0035187 hatching behavior
FBcv:0000720 abnormal jump response GO:0007630 jump response
FBcv:0000397 abnormal learning GO:0007612 learning
FBcv:0000414 abnormal locomotor behavior GO:0007626 locomotory behavior
FBcv:0000395 abnormal locomotor rhythm GO:0045475 locomotor rhythm
FBcv:0000401 abnormal mating rhythm GO:0035648 circadian mating behavior
FBcv:0000398 abnormal memory GO:0007613 memory
FBcv:0000412 abnormal optomotor response GO:0007634 optokinetic behavior
FBcv:0006004 abnormal oviposition GO:0018991 egg-laying behavior
FBcv:0000680 abnormal proboscis extension reflex GO:0007637 proboscis extension reflex
FBcv:0000402 abnormal song GO:0045433 male courtship behavior, veined wing generated song production
FBcv:0000411 abnormal visual behavior GO:0007632 visual behavior
FBcv:0000721 abnormal mating behavior GO:0007617 mating behavior
FBcv:0000400 abnormal mating GO:0007618 mating
FBcv:0000399 abnormal courtship behavior GO:0007619 courtship behavior
FBcv:0007500 abnormal anesthesia-resistant memory GO:0007615 anesthesia-resistant memory
FBcv:0007501 abnormal short-term memory GO:0007614 short-term memory
FBcv:0007502 abnormal medium-term memory GO:0072375 medium-term memory
FBcv:0007503 abnormal long-term memory GO:0007616 long-term memory
FBcv:0000415 abnormal jumping NBO:0000016 jumping behavior
FBcv:0000416 uncoordinated NBO:0000339 motor coordination
FBcv:0000421 abnormal touch response NBO:0000332 touch related behavior
FBcv:0007527 abnormal adult walking behavior GO:0007628 adult walking behavior
FBcv:0007528 abnormal larval locomotory behavior GO:0008345 larval locomotory behavior
FBcv:0007529 abnormal adult locomotory behavior GO:0008344 adult locomotory behavior
84 changes: 42 additions & 42 deletions src/patterns/data/default/abnormalBiologicalProcess.tsv
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@@ -1,43 +1,43 @@
defined_class defined_class_label biological_process biological_process_label
http://purl.obolibrary.org/obo/FBcv_0000384 aging defective http://purl.obolibrary.org/obo/GO_0007568 aging
http://purl.obolibrary.org/obo/FBcv_0000407 auditory perception defective http://purl.obolibrary.org/obo/GO_0007605 sensory perception of sound
http://purl.obolibrary.org/obo/FBcv_0000686 axis specification defective http://purl.obolibrary.org/obo/GO_0009798 axis specification
http://purl.obolibrary.org/obo/FBcv_0000668 cell adhesion defective http://purl.obolibrary.org/obo/GO_0007155 cell adhesion
http://purl.obolibrary.org/obo/FBcv_0000671 cell cycle defective http://purl.obolibrary.org/obo/GO_0007049 cell cycle
http://purl.obolibrary.org/obo/FBcv_0000424 cell death defective http://purl.obolibrary.org/obo/GO_0008219 cell death
http://purl.obolibrary.org/obo/FBcv_0000427 cell growth defective http://purl.obolibrary.org/obo/GO_0016049 cell growth
http://purl.obolibrary.org/obo/FBcv_0000716 cell migration defective http://purl.obolibrary.org/obo/GO_0016477 cell migration
http://purl.obolibrary.org/obo/FBcv_0000394 circadian rhythm defective http://purl.obolibrary.org/obo/GO_0007623 circadian rhythm
http://purl.obolibrary.org/obo/FBcv_0000684 cold stress response defective http://purl.obolibrary.org/obo/GO_0009409 response to cold
http://purl.obolibrary.org/obo/FBcv_0006000 copulation defective http://purl.obolibrary.org/obo/GO_0007620 copulation
http://purl.obolibrary.org/obo/FBcv_0000433 cytokinesis defective http://purl.obolibrary.org/obo/GO_0000910 cytokinesis
http://purl.obolibrary.org/obo/FBcv_0000706 diapause defective http://purl.obolibrary.org/obo/GO_0055115 entry into diapause
http://purl.obolibrary.org/obo/FBcv_0000423 DNA repair defective http://purl.obolibrary.org/obo/GO_0006281 DNA repair
http://purl.obolibrary.org/obo/FBcv_0000324 dorsal/ventral axis specification defective http://purl.obolibrary.org/obo/GO_0009950 dorsal/ventral axis specification
http://purl.obolibrary.org/obo/FBcv_0000670 eclosion defective http://purl.obolibrary.org/obo/GO_0007562 eclosion
http://purl.obolibrary.org/obo/FBcv_0000672 endomitotic cell cycle defective http://purl.obolibrary.org/obo/GO_0007113 endocytosis
http://purl.obolibrary.org/obo/FBcv_0000417 flight defective http://purl.obolibrary.org/obo/GO_0060361 flight
http://purl.obolibrary.org/obo/FBcv_0000388 gravitaxis defective http://purl.obolibrary.org/obo/GO_0048060 negative gravitaxis
http://purl.obolibrary.org/obo/FBcv_0000410 heat stress response defective http://purl.obolibrary.org/obo/GO_0009408 response to heat
http://purl.obolibrary.org/obo/FBcv_0000448 immune response defective http://purl.obolibrary.org/obo/GO_0006955 immune response
http://purl.obolibrary.org/obo/FBcv_0000431 meiotic cell cycle defective http://purl.obolibrary.org/obo/GO_0051321 meiotic cell cycle
http://purl.obolibrary.org/obo/FBcv_0000432 mitotic cell cycle defective http://purl.obolibrary.org/obo/GO_0000278 mitotic cell cycle
http://purl.obolibrary.org/obo/FBcv_0000409 osmotic stress response defective http://purl.obolibrary.org/obo/GO_0006970 response to osmotic stress
http://purl.obolibrary.org/obo/FBcv_0000725 oxidative stress response defective http://purl.obolibrary.org/obo/GO_0006979 response to oxidative stress
http://purl.obolibrary.org/obo/FBcv_0000393 pain response defective http://purl.obolibrary.org/obo/GO_0048265 response to pain
http://purl.obolibrary.org/obo/FBcv_0000422 photoperiod response variant http://purl.obolibrary.org/obo/GO_0043153 entrainment of circadian clock by photoperiod
http://purl.obolibrary.org/obo/FBcv_0000413 phototaxis defective http://purl.obolibrary.org/obo/GO_0042331 phototaxis
http://purl.obolibrary.org/obo/FBcv_0000449 planar polarity defective http://purl.obolibrary.org/obo/GO_0001736 establishment of planar polarity
http://purl.obolibrary.org/obo/FBcv_0000707 reproductive diapause defective http://purl.obolibrary.org/obo/GO_0055116 entry into reproductive diapause
http://purl.obolibrary.org/obo/FBcv_0000681 sensory perception defective http://purl.obolibrary.org/obo/GO_0007600 sensory perception
http://purl.obolibrary.org/obo/FBcv_0000436 sex-determination defective http://purl.obolibrary.org/obo/GO_0007530 sex determination
http://purl.obolibrary.org/obo/FBcv_0000705 sleep defective http://purl.obolibrary.org/obo/GO_0030431 sleep
http://purl.obolibrary.org/obo/FBcv_0000404 smell perception defective http://purl.obolibrary.org/obo/GO_0007608 sensory perception of smell
http://purl.obolibrary.org/obo/FBcv_0000708 starvation stress response defective http://purl.obolibrary.org/obo/GO_0042594 response to starvation
http://purl.obolibrary.org/obo/FBcv_0000408 stress response defective http://purl.obolibrary.org/obo/GO_0006950 response to stress
http://purl.obolibrary.org/obo/FBcv_0000405 taste perception defective http://purl.obolibrary.org/obo/GO_0050909 sensory perception of taste
http://purl.obolibrary.org/obo/FBcv_0000683 temperature response defective http://purl.obolibrary.org/obo/GO_0009266 response to temperature stimulus
http://purl.obolibrary.org/obo/FBcv_0000002 thermotaxis defective http://purl.obolibrary.org/obo/GO_0043052 thermotaxis
http://purl.obolibrary.org/obo/FBcv_0000682 touch perception defective http://purl.obolibrary.org/obo/GO_0050975 sensory perception of touch
http://purl.obolibrary.org/obo/FBcv_0004000 visual perception defective http://purl.obolibrary.org/obo/GO_0050953 response to light stimulus
http://purl.obolibrary.org/obo/FBcv_0000451 wound healing defective http://purl.obolibrary.org/obo/GO_0042060 wound healing
FBcv:0000384 abnormal aging GO:0007568 obsolete aging
FBcv:0000407 abnormal auditory perception GO:0007605 sensory perception of sound
FBcv:0000686 abnormal axis specification GO:0009798 axis specification
FBcv:0000668 abnormal cell adhesion GO:0007155 cell adhesion
FBcv:0000671 abnormal cell cycle GO:0007049 cell cycle
FBcv:0000424 abnormal cell death GO:0008219 cell death
FBcv:0000427 abnormal cell growth GO:0016049 cell growth
FBcv:0000716 abnormal cell migration GO:0016477 cell migration
FBcv:0000394 abnormal circadian rhythm GO:0007623 circadian rhythm
FBcv:0000684 abnormal cold stress response GO:0009409 response to cold
FBcv:0006000 abnormal copulation GO:0007620 copulation
FBcv:0000433 abnormal cytokinesis GO:0000910 cytokinesis
FBcv:0000706 abnormal diapause GO:0055115 entry into diapause
FBcv:0000423 abnormal DNA repair GO:0006281 DNA repair
FBcv:0000324 abnormal dorsal/ventral axis specification GO:0009950 dorsal/ventral axis specification
FBcv:0000670 abnormal eclosion GO:0007562 eclosion
FBcv:0000672 abnormal endomitotic cell cycle GO:0007113 endomitotic cell cycle
FBcv:0000417 abnormal flight GO:0060361 flight
FBcv:0000388 abnormal gravitaxis GO:0048060 negative gravitaxis
FBcv:0000410 abnormal heat stress response GO:0009408 response to heat
FBcv:0000448 abnormal immune response GO:0006955 immune response
FBcv:0000431 abnormal meiotic cell cycle GO:0051321 meiotic cell cycle
FBcv:0000432 abnormal mitotic cell cycle GO:0000278 mitotic cell cycle
FBcv:0000409 abnormal osmotic stress response GO:0006970 response to osmotic stress
FBcv:0000725 abnormal oxidative stress response GO:0006979 response to oxidative stress
FBcv:0000393 abnormal pain response GO:0048265 response to pain
FBcv:0000422 photoperiod response variant GO:0043153 entrainment of circadian clock by photoperiod
FBcv:0000413 abnormal phototaxis GO:0042331 phototaxis
FBcv:0000449 abnormal planar polarity GO:0001736 establishment of planar polarity
FBcv:0000707 abnormal reproductive diapause GO:0055116 entry into reproductive diapause
FBcv:0000681 abnormal sensory perception GO:0007600 sensory perception
FBcv:0000436 abnormal sex-determination GO:0007530 sex determination
FBcv:0000705 abnormal sleep GO:0030431 sleep
FBcv:0000404 abnormal smell perception GO:0007608 sensory perception of smell
FBcv:0000708 abnormal starvation stress response GO:0042594 response to starvation
FBcv:0000408 abnormal stress response GO:0006950 response to stress
FBcv:0000405 abnormal taste perception GO:0050909 sensory perception of taste
FBcv:0000683 abnormal temperature response GO:0009266 response to temperature stimulus
FBcv:0000002 abnormal thermotaxis GO:0043052 thermotaxis
FBcv:0000682 abnormal touch perception GO:0050975 sensory perception of touch
FBcv:0004000 abnormal visual perception GO:0050953 sensory perception of light stimulus
FBcv:0000451 abnormal wound healing GO:0042060 wound healing
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defined_class defined_class_label anatomical_entity anatomical_entity_label
http://purl.obolibrary.org/obo/FBcv_0000709 cell number defective http://purl.obolibrary.org/obo/CL_0000000 cell
FBcv:0000709 abnormal cell number CL:0000000 cell
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@@ -1,3 +1,3 @@
defined_class defined_class_label anatomical_entity anatomical_entity_label
http://purl.obolibrary.org/obo/FBcv_0000356 body color defective http://purl.obolibrary.org/obo/FBbt_00000001 organism
http://purl.obolibrary.org/obo/FBcv_0000355 eye color defective http://purl.obolibrary.org/obo/FBbt_00004508 eye
defined_class defined_class_label anatomical_entity anatomical_entity_label
FBcv:0000356 abnormal body color FBbt:00000001 organism
FBcv:0000355 abnormal eye color FBbt:00004508 eye
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defined_class defined_class_label biological_process stage biological_process_label stage_label
http://purl.obolibrary.org/obo/FBcv_0000450 abnormal developmental rate http://purl.obolibrary.org/obo/GO_0032502 http://purl.obolibrary.org/obo/FBdv_00007026 developmental process mature adult stage
FBcv:0000450 abnormal developmental rate GO:0032502 FBdv:00007026 developmental process mature adult stage
4 changes: 2 additions & 2 deletions src/patterns/data/default/abnormalShapeOfPhysicalEntity.tsv
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@@ -1,2 +1,2 @@
defined_class defined_class_label entity entity_label
http://purl.obolibrary.org/obo/FBcv_0000429 cell shape defective http://purl.obolibrary.org/obo/CL_0000000 cell
defined_class defined_class_label entity entity_label
FBcv:0000429 abnormal cell shape CL:0000000 cell
8 changes: 4 additions & 4 deletions src/patterns/data/default/abnormalSizeOfAnatomicalEntity.tsv
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@@ -1,4 +1,4 @@
defined_class defined_class_label entity entity_label
http://purl.obolibrary.org/obo/FBcv_0000665 body size defective http://purl.obolibrary.org/obo/FBbt_00000001 organism
http://purl.obolibrary.org/obo/FBcv_0000428 cell size defective http://purl.obolibrary.org/obo/CL_0000000 cell
http://purl.obolibrary.org/obo/FBcv_0000357 size defective http://purl.obolibrary.org/obo/FBbt_00007001 anatomical structure
defined_class defined_class_label entity entity_label
FBcv:0000665 abnormal body size FBbt:00000001 organism
FBcv:0000428 abnormal cell size CL:0000000 cell
FBcv:0000357 abnormal size FBbt:00007001 anatomical structure
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defined_class defined_class_label anatomical_entity anatomical_entity_label
http://purl.obolibrary.org/obo/FBcv_0007504 abnormal body weight http://purl.obolibrary.org/obo/FBbt_00000001 organism
FBcv:0007504 abnormal body weight FBbt:00000001 organism
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