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auto-update labels
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@Clare72
Clare72 committed Jun 6, 2024
1 parent afeaa85 commit cf985f9
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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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6 changes: 3 additions & 3 deletions src/patterns/data/default/abnormalAbsenceOfBiologicalProcess.tsv
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defined_class defined_class_label biological_process biological_process_label
FBcv:0000418 flightless GO:0060361 flight
FBcv:0000389 paralytic 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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defined_class defined_class_label anatomical_entity anatomical_entity_label
FBcv:0000435 neuroanatomy defective FBbt:00005093 nervous system
defined_class defined_class_label anatomical_entity anatomical_entity_label
FBcv:0000435 abnormal neuroanatomy FBbt:00005093 nervous system
44 changes: 22 additions & 22 deletions src/patterns/data/default/abnormalBehavior.tsv
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defined_class defined_class_label behavior_process behavior_process_label
FBcv:0000387 behavior defective GO:0007610 behavior
FBcv:0000403 chemosensitive behavior defective GO:0007635 chemosensory behavior
FBcv:0000679 circadian behavior defective GO:0048512 circadian behavior
FBcv:0000396 eclosion rhythm defective GO:0008062 eclosion rhythm
FBcv:0000419 feeding behavior defective GO:0007631 feeding behavior
FBcv:0000420 grooming behavior defective GO:0007625 grooming behavior
FBcv:0000669 hatching behavior defective GO:0035187 hatching behavior
FBcv:0000720 jump response defective GO:0007630 jump response
FBcv:0000397 learning defective GO:0007612 learning
FBcv:0000414 locomotor behavior defective GO:0007626 locomotory behavior
FBcv:0000395 locomotor rhythm defective GO:0045475 locomotor rhythm
FBcv:0000401 mating rhythm defective GO:0035648 circadian mating behavior
FBcv:0000398 memory defective GO:0007613 memory
FBcv:0000412 optomotor response defective GO:0007634 optokinetic behavior
FBcv:0006004 oviposition defective GO:0018991 oviposition
FBcv:0000680 proboscis extension reflex defective GO:0007637 proboscis extension reflex
FBcv:0000402 song defective GO:0045433 "male courtship behavior, veined wing generated song production"
FBcv:0000411 visual behavior defective GO:0007632 visual behavior
FBcv:0000721 mating behavior defective GO:0007617 mating behavior
FBcv:0000400 mating defective GO:0007618 mating
FBcv:0000399 courtship behavior defective GO:0007619 courtship 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
Expand All @@ -29,4 +29,4 @@ 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
FBcv:0007529 abnormal adult locomotory behavior GO:0008344 adult locomotory behavior
82 changes: 41 additions & 41 deletions src/patterns/data/default/abnormalBiologicalProcess.tsv
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defined_class defined_class_label biological_process biological_process_label
FBcv:0000384 aging defective GO:0007568 aging
FBcv:0000407 auditory perception defective GO:0007605 sensory perception of sound
FBcv:0000686 axis specification defective GO:0009798 axis specification
FBcv:0000668 cell adhesion defective GO:0007155 cell adhesion
FBcv:0000671 cell cycle defective GO:0007049 cell cycle
FBcv:0000424 cell death defective GO:0008219 cell death
FBcv:0000427 cell growth defective GO:0016049 cell growth
FBcv:0000716 cell migration defective GO:0016477 cell migration
FBcv:0000394 circadian rhythm defective GO:0007623 circadian rhythm
FBcv:0000684 cold stress response defective GO:0009409 response to cold
FBcv:0006000 copulation defective GO:0007620 copulation
FBcv:0000433 cytokinesis defective GO:0000910 cytokinesis
FBcv:0000706 diapause defective GO:0055115 entry into diapause
FBcv:0000423 DNA repair defective GO:0006281 DNA repair
FBcv:0000324 dorsal/ventral axis specification defective GO:0009950 dorsal/ventral axis specification
FBcv:0000670 eclosion defective GO:0007562 eclosion
FBcv:0000672 endomitotic cell cycle defective GO:0007113 endocytosis
FBcv:0000417 flight defective GO:0060361 flight
FBcv:0000388 gravitaxis defective GO:0048060 negative gravitaxis
FBcv:0000410 heat stress response defective GO:0009408 response to heat
FBcv:0000448 immune response defective GO:0006955 immune response
FBcv:0000431 meiotic cell cycle defective GO:0051321 meiotic cell cycle
FBcv:0000432 mitotic cell cycle defective GO:0000278 mitotic cell cycle
FBcv:0000409 osmotic stress response defective GO:0006970 response to osmotic stress
FBcv:0000725 oxidative stress response defective GO:0006979 response to oxidative stress
FBcv:0000393 pain response defective GO:0048265 response to pain
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 phototaxis defective GO:0042331 phototaxis
FBcv:0000449 planar polarity defective GO:0001736 establishment of planar polarity
FBcv:0000707 reproductive diapause defective GO:0055116 entry into reproductive diapause
FBcv:0000681 sensory perception defective GO:0007600 sensory perception
FBcv:0000436 sex-determination defective GO:0007530 sex determination
FBcv:0000705 sleep defective GO:0030431 sleep
FBcv:0000404 smell perception defective GO:0007608 sensory perception of smell
FBcv:0000708 starvation stress response defective GO:0042594 response to starvation
FBcv:0000408 stress response defective GO:0006950 response to stress
FBcv:0000405 taste perception defective GO:0050909 sensory perception of taste
FBcv:0000683 temperature response defective GO:0009266 response to temperature stimulus
FBcv:0000002 thermotaxis defective GO:0043052 thermotaxis
FBcv:0000682 touch perception defective GO:0050975 sensory perception of touch
FBcv:0004000 visual perception defective GO:0050953 response to light stimulus
FBcv:0000451 wound healing defective GO:0042060 wound healing
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
2 changes: 1 addition & 1 deletion src/patterns/data/default/abnormalNumberOfAnatomicalEntity.tsv
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defined_class defined_class_label anatomical_entity anatomical_entity_label
FBcv:0000709 cell number defective CL:0000000 cell
FBcv:0000709 abnormal cell number CL:0000000 cell
6 changes: 3 additions & 3 deletions src/patterns/data/default/abnormalPigmentationOfAnatomicalEntity.tsv
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defined_class defined_class_label anatomical_entity anatomical_entity_label
FBcv:0000356 body color defective FBbt:00000001 organism
FBcv:0000355 eye color defective 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
4 changes: 2 additions & 2 deletions src/patterns/data/default/abnormalShapeOfPhysicalEntity.tsv
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defined_class defined_class_label entity entity_label
FBcv:0000429 cell shape defective 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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defined_class defined_class_label entity entity_label
FBcv:0000665 body size defective FBbt:00000001 organism
FBcv:0000428 cell size defective CL:0000000 cell
FBcv:0000357 size defective 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
12 changes: 6 additions & 6 deletions src/patterns/data/default/abnormallyDecreasedEfficacyOfBehavior.tsv
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defined_class defined_class_label behavior_process behavior_process_label
FBcv:0007518 decreased memory GO:0007613 memory
FBcv:0007520 decreased short-term memory GO:0007614 short-term memory
FBcv:0007522 decreased long-term memory GO:0007616 long-term memory
FBcv:0007524 decreased anesthesia-resistant memory GO:0007615 anesthesia-resistant memory
FBcv:0007526 decreased medium-term memory GO:0072375 medium-term memory
FBcv:0007531 decreased efficacy of learning GO:0007612 learning
FBcv:0007518 decreased efficacy of memory GO:0007613 memory
FBcv:0007520 decreased efficacy of short-term memory GO:0007614 short-term memory
FBcv:0007522 decreased efficacy of long-term memory GO:0007616 long-term memory
FBcv:0007524 decreased efficacy of anesthesia-resistant memory GO:0007615 anesthesia-resistant memory
FBcv:0007526 decreased efficacy of medium-term memory GO:0072375 medium-term memory
FBcv:0007531 decreased efficacy of learning GO:0007612 learning
2 changes: 1 addition & 1 deletion src/patterns/data/default/abnormallyDecreasedNumberOfAnatomicalEntity.tsv
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defined_class defined_class_label anatomical_entity anatomical_entity_label
FBcv:0000359 decreased cell number CL:0000000 cell
FBcv:0000359 decreased cell number CL:0000000 cell
2 changes: 1 addition & 1 deletion src/patterns/data/default/abnormallyDecreasedOccurrenceOfBiologicalProcess.tsv
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defined_class defined_class_label biological_process biological_process_label
FBcv:0006006 decreased occurrence of cell division GO:0051301 cell division
FBcv:0000425 decreased cell death GO:0008219 cell death
FBcv:0000425 increased cell death GO:0008219 cell death
6 changes: 3 additions & 3 deletions src/patterns/data/default/abnormallyDecreasedRateOfBehavior.tsv
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defined_class defined_class_label behavior_process behavior_process_label
FBcv:0007514 decreased sleep GO:0030431 sleep
FBcv:0007516 decreased feeding behavior GO:0007631 feeding behavior
FBcv:0007544 decreased rate of chemosensory behaviour GO:0007635 chemosensory behaviour
FBcv:0007516 decreased rate of feeding behavior GO:0007631 feeding behavior
FBcv:0007544 decreased rate of chemosensory behavior GO:0007635 chemosensory behavior
FBcv:0007545 decreased rate of proboscis extension reflex GO:0007637 proboscis extension reflex
FBcv:0007546 decreased rate of grooming behavior GO:0007625 grooming behavior
FBcv:0007547 decreased rate of locomotory behavior GO:0007626 locomotory behavior
Expand All @@ -12,4 +12,4 @@ FBcv:0007551 decreased rate of mating behavior GO:0007617 mating behavior
FBcv:0007552 decreased rate of courtship behavior GO:0007619 courtship behavior
FBcv:0007553 decreased rate of flight behavior GO:0007629 flight behavior
FBcv:0007554 decreased rate of jump response GO:0007630 jump response
FBcv:0007555 decreased rate of copulation GO:0007620 copulation
FBcv:0007555 decreased rate of copulation GO:0007620 copulation
6 changes: 3 additions & 3 deletions src/patterns/data/default/abnormallyDecreasedRateOfBiologicalProcess.tsv
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defined_class defined_class_label biological_process biological_process_label
FBcv:0000718 decreased cell growth GO:0016049 cell growth
FBcv:0000390 hypoactive GO:0050879 multicellular organismal movement
FBcv:0000718 decreased cell growth rate GO:0016049 cell growth
FBcv:0000390 decreased rate of movement GO:0050879 multicellular organismal movement
FBcv:0007510 decreased rate of phototaxis GO:0042331 phototaxis
FBcv:0007512 decreased rate of cell adhesion GO:0007155 cell adhesion
FBcv:0007512 decreased rate of cell adhesion GO:0007155 cell adhesion
2 changes: 1 addition & 1 deletion src/patterns/data/default/abnormallyDecreasedRateOfContinuousBiologicalProcess.tsv
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defined_class defined_class_label biological_process biological_process_label
FBcv:0000791 delayed aging GO:0007568 aging
FBcv:0000791 decreased speed of aging GO:0007568 obsolete aging
4 changes: 2 additions & 2 deletions src/patterns/data/default/abnormallyDecreasedResistanceOfWholeOrganismToChemicalEntity.tsv
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defined_class defined_class_label chemical_entity chemical_entity_label
FBcv:0000440 chemical sensitive CHEBI:24431 chemical entity
defined_class defined_class_label chemical_entity chemical_entity_label
FBcv:0000440 chemical sensitive CHEBI:24431 chemical entity
4 changes: 2 additions & 2 deletions src/patterns/data/default/abnormallyDecreasedResistanceOfWholeOrganismToEntity.tsv
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defined_class defined_class_label entity entity_label
FBcv:0000442 radiation sensitive ENVO:01001023 radiation
defined_class defined_class_label entity entity_label
FBcv:0000442 radiation sensitive ENVO:01001023 radiation
12 changes: 6 additions & 6 deletions src/patterns/data/default/abnormallyIncreasedEfficacyOfBehavior.tsv
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defined_class defined_class_label behavior_process behavior_process_label
FBcv:0007517 increased memory GO:0007613 memory
FBcv:0007519 increased short-term memory GO:0007614 short-term memory
FBcv:0007521 increased long-term memory GO:0007616 long-term memory
FBcv:0007523 increased anesthesia-resistant memory GO:0007615 anesthesia-resistant memory
FBcv:0007525 increased medium-term memory GO:0072375 medium-term memory
FBcv:0007530 increased efficacy of learning GO:0007612 learning
FBcv:0007517 increased efficacy of memory GO:0007613 memory
FBcv:0007519 increased efficacy of short-term memory GO:0007614 short-term memory
FBcv:0007521 increased efficacy of long-term memory GO:0007616 long-term memory
FBcv:0007523 increased efficacy of anesthesia-resistant memory GO:0007615 anesthesia-resistant memory
FBcv:0007525 increased efficacy of medium-term memory GO:0072375 medium-term memory
FBcv:0007530 increased efficacy of learning GO:0007612 learning
2 changes: 1 addition & 1 deletion src/patterns/data/default/abnormallyIncreasedOccurrenceOfBiologicalProcess.tsv
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defined_class defined_class_label biological_process biological_process_label
FBcv:0006005 increased occurrence of cell division GO:0051301 cell division
FBcv:0000426 increased cell death GO:0008219 cell death
FBcv:0000426 decreased cell death GO:0008219 cell death
6 changes: 3 additions & 3 deletions src/patterns/data/default/abnormallyIncreasedRateOfBehavior.tsv
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defined_class defined_class_label behavior_process behavior_process_label
FBcv:0007513 increased sleep GO:0030431 sleep
FBcv:0007515 increased feeding behavior GO:0007631 feeding behavior
FBcv:0007532 increased rate of chemosensory behaviour GO:0007635 chemosensory behaviour
FBcv:0007515 increased rate of feeding behavior GO:0007631 feeding behavior
FBcv:0007532 increased rate of chemosensory behavior GO:0007635 chemosensory behavior
FBcv:0007533 increased rate of proboscis extension reflex GO:0007637 proboscis extension reflex
FBcv:0007534 increased rate of grooming behavior GO:0007625 grooming behavior
FBcv:0007535 increased rate of locomotory behavior GO:0007626 locomotory behavior
Expand All @@ -12,4 +12,4 @@ FBcv:0007539 increased rate of mating behavior GO:0007617 mating behavior
FBcv:0007540 increased rate of courtship behavior GO:0007619 courtship behavior
FBcv:0007541 increased rate of flight behavior GO:0007629 flight behavior
FBcv:0007542 increased rate of jump response GO:0007630 jump response
FBcv:0007543 increased rate of copulation GO:0007620 copulation
FBcv:0007543 increased rate of copulation GO:0007620 copulation
6 changes: 3 additions & 3 deletions src/patterns/data/default/abnormallyIncreasedRateOfBiologicalProcess.tsv
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defined_class defined_class_label biological_process biological_process_label
FBcv:0000717 increased cell growth GO:0016049 cell growth
FBcv:0000392 hyperactive GO:0050879 multicellular organismal movement
FBcv:0000717 increased cell growth rate GO:0016049 cell growth
FBcv:0000392 increased rate of movement GO:0050879 multicellular organismal movement
FBcv:0007509 increased rate of phototaxis GO:0042331 phototaxis
FBcv:0007511 increased rate of cell adhesion GO:0007155 cell adhesion
FBcv:0007511 increased rate of cell adhesion GO:0007155 cell adhesion
2 changes: 1 addition & 1 deletion src/patterns/data/default/abnormallyIncreasedRateOfContinuousBiologicalProcess.tsv
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defined_class defined_class_label biological_process biological_process_label
FBcv:0000792 premature aging GO:0007568 aging
FBcv:0000792 increased speed of aging GO:0007568 obsolete aging
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