Open DitchingIt opened 1 year ago
ZP is another important ontology to check with.
@DitchingIt this process will take a while. As long as there is no overlap between the phenotype and behaviour branches of NBO, you don't need to wait for this process to finish to work on processes. Maybe we can in the name or progress start migrating some terms over.
overlap between the phenotype and behaviour branches
I have just done a pull request deleting the one link which was for agoraphobia.
start migrating some terms over
@matentzn What exactly should I do?
May I suggest we start with https://github.com/obo-behavior/behavior-ontology/issues/136, which is much easier to deal with and to practice the curation cycle. After that, you should:
Put this in a google sheet: https://github.com/obo-behavior/behavior-ontology/blob/master/src/ontology/reports/phenotypes.tsv
Reach out to @rays22 on slack and meet him when he has time, and have him explain to you which terms should be in OBA, and which in uPheno. Once we know for each term which should be in OBA and which in uPheno, and perhaps elsewhere, we can make new term requests at these ontologies.
Here is a table of 140 existing OBA trait terms that use NBO process terms in their logical definitions:
entity_attribute.tsv:OBA:2060000 NBO:0000112 aggressive behavior towards inanimate objects PATO:0000161 rate
entity_attribute.tsv:OBA:2060001 NBO:0000223 contextual conditioning behavior PATO:0000161 rate
entity_attribute.tsv:OBA:2060002 NBO:0000339 motor coordination PATO:0000161 rate
entity_attribute.tsv:OBA:2060003 NBO:0000338 kinesthetic behavior PATO:0000161 rate
entity_attribute.tsv:OBA:2060004 NBO:0000224 cued conditioning behavior PATO:0000161 rate
entity_attribute.tsv:OBA:2060005 NBO:0000015 aggressive behavior PATO:0000161 rate
entity_attribute.tsv:OBA:2060006 NBO:0000092 anxiety-related behavior PATO:0000161 rate
entity_attribute.tsv:OBA:2060007 NBO:0000103 coping behavior PATO:0000161 rate
entity_attribute.tsv:OBA:2060008 NBO:0000097 response to novel environment PATO:0000161 rate
entity_attribute.tsv:OBA:2060009 NBO:0000391 startle reflex PATO:0000161 rate
entity_attribute.tsv:OBA:2060010 NBO:0000381 thigmotaxis PATO:0000161 rate
entity_attribute.tsv:OBA:2060011 NBO:0000448 vertical activity PATO:0000161 rate
entity_attribute.tsv:OBA:2060017 NBO:0000013 locomotory behavior PATO:0000161 rate
entity_attribute.tsv:OBA:2060018 NBO:0000332 touch related behavior PATO:0000161 rate
entity_attribute.tsv:OBA:2060019 NBO:0000412 pupillary light reflex PATO:0000161 rate
entity_attribute.tsv:OBA:2060020 NBO:0000578 righting reflex PATO:0000161 rate
entity_attribute.tsv:OBA:2060166 NBO:0000576 pinna reflex PATO:0000070 amount
entity_attribute.tsv:OBA:2060167 NBO:0000391 startle reflex PATO:0000070 amount
entity_attribute.tsv:OBA:2060168 NBO:0000449 spontaneous movement behavior PATO:0000070 amount
entity_attribute.tsv:OBA:2060169 NBO:0000332 touch related behavior PATO:0000070 amount
entity_attribute.tsv:OBA:2060179 body coordination efficacy NBO:0000351 body coordination PATO:0015002 process efficacy
entity_attribute.tsv:OBA:2060180 limb coordination efficacy NBO:0000342 limb coordination PATO:0015002 process efficacy
entity_attribute.tsv:OBA:2060181 upper limb coordination efficacy NBO:0000346 upper limb coordination PATO:0015002 process efficacy
entity_attribute.tsv:OBA:2060182 lower limb coordination efficacy NBO:0000345 lower limb coordination PATO:0015002 process efficacy
entity_attribute.tsv:OBA:2060183 motor coordination efficacy NBO:0000339 motor coordination PATO:0015002 process efficacy
entity_attribute.tsv:OBA:2060191 gross motor coordination efficacy NBO:0000347 gross motor coordination PATO:0015002 process efficacy
entity_attribute.tsv:OBA:2060192 fine motor coordination efficacy NBO:0000348 fine motor coordination PATO:0015002 process efficacy
entity_attribute.tsv:OBA:2060193 eye-hand coordination efficacy NBO:0000341 eye-hand coordination PATO:0015002 process efficacy
entity_attribute_part_of.tsv:OBA:0000018 appetite NBO:0000235 hunger motivation behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000197 NBO:0000444 eye movement PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000219 NBO:0000129 agitation behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000225 NBO:0000018 fear/anxiety related behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000278 NBO:0000604 social inhibition PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000309 NBO:0000416 vestibulo-ocular reflex PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000345 NBO:0000417 physiologic nystagmus PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000369 NBO:0000313 behavior process PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000372 NBO:0000054 suckling behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000376 NBO:0000015 aggressive behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000384 NBO:0000092 anxiety-related behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000400 NBO:0000128 irritability behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000407 NBO:0000011 social behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000443 NBO:0000120 physical aggression behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000464 NBO:0000119 impulsive behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000493 NBO:0000446 visual pursuit PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000539 NBO:0000605 sexual inhibition PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000544 NBO:0000403 voluntary movement behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000588 NBO:0000617 laughing behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000603 NBO:0000003 emotional behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000647 NBO:0000171 associative learning behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000648 NBO:0000333 chemical nociceptive behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000652 NBO:0000555 spatial working memory PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000654 NBO:0000136 saccharin consumption PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000656 NBO:0000450 social grooming PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000657 NBO:0000098 response to novel object PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000664 NBO:0000560 barbering behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000668 NBO:0001571 behavioral response to light PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000678 NBO:0000001 body part movement PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000679 NBO:0001915 cocaine consumption PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000681 NBO:0000570 head bobbing PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000684 NBO:0000013 locomotory behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000685 NBO:0000211 conditioned taste aversion PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000687 NBO:0000152 maternal nurturing behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000690 NBO:0000134 food consumption PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000691 NBO:0000166 circadian rhythm PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000693 NBO:0000334 mechanical nociceptive behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000707 NBO:0000103 coping behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000708 NBO:0000584 clutching reflex PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000711 NBO:0000336 chemically-elicited antinociceptive behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000712 NBO:0000447 locomotor activation behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000713 NBO:0000330 cutaneous sensation behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000717 NBO:0001728 behavioral response to addictive substance PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000718 NBO:0000574 optokinetic reflex PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000723 NBO:0000172 olfactory learning behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000724 NBO:0001679 behavioral response to xenobiotics PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000726 NBO:0000020 head movement PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000729 NBO:0000552 long term object recognition memory PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000731 NBO:0000157 nest building behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000733 NBO:0000097 response to novel environment PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000735 NBO:0000023 head shaking PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000737 NBO:0000576 pinna reflex PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000739 NBO:0000146 mating receptivity PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000741 NBO:0000389 reflexive behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000746 NBO:0000331 nociceptive behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000747 NBO:0000559 maternal grooming PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000748 NBO:0000079 feeding behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000753 NBO:0000150 maternal behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000757 NBO:0000355 posture PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000760 NBO:0000125 submissive behavior towards male mice PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000765 NBO:0000537 circadian regulation of systemic arterial blood pressure PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000767 NBO:0000085 depression behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000768 NBO:0000217 active avoidance learning behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000771 NBO:0000571 mutlidirectional head movement PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000774 NBO:0000581 vestibulocollic reflex PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000775 NBO:0000339 motor coordination PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000779 NBO:0000641 discrimination learning PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000784 NBO:0000357 limb posture PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000786 NBO:0000599 long-term spatial memory PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000788 NBO:0000224 cued conditioning behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000793 NBO:0000412 pupillary light reflex PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000799 NBO:0002362 behavioral response to anesthetic PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000804 NBO:0000175 spatial learning PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000809 NBO:0000014 mating behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000817 NBO:0000222 conditioned place preference behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000819 NBO:0000415 corneal reflex PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000821 NBO:0000358 resting posture PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000830 NBO:0000227 eye blink conditioning behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000837 NBO:0000578 righting reflex PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000838 NBO:0000335 thermal nociceptive behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000839 NBO:0000583 vibrissae reflex PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000840 NBO:0000131 alcohol consumption PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000845 NBO:0000210 avoidance learning behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000856 NBO:0000557 short term spatial memory PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000858 NBO:0000556 spatial memory PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000861 NBO:0000223 contextual conditioning behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000862 NBO:0000551 visual object recognition PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000865 NBO:0000052 huddling behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000869 NBO:0000361 gait PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000871 NBO:0000577 postural reflex PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000874 NBO:0000218 passive avoidance learning behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000879 NBO:0000212 operant conditioning behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000885 NBO:0000388 involuntary movement behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000890 NBO:0000174 motor learning PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000891 NBO:0000086 novelty response behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000893 NBO:0000575 pilomotor reflex PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000895 NBO:0000180 short-term memory PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000903 NBO:0000561 hetero-barbering PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000905 NBO:0000024 sleeping behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000912 NBO:0000538 circadian temperature homeostasis PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000918 NBO:0000391 startle reflex PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000919 NBO:0000073 chewing PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000923 NBO:0000155 offspring retrieval PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000924 NBO:0000445 tail movement PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000928 NBO:0000148 social investigation PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000933 NBO:0000553 short term object recognition memory PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000935 NBO:0000099 response to novel odor PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000937 NBO:0000091 fear-related behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:1000938 NBO:0000332 touch related behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:2050116 smoking behavior trait NBO:0015005 smoking behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:2050117 reproductive behavior trait NBO:0000010 reproductive behavior PATO:0000001 quality
entity_attribute_part_of.tsv:OBA:2050118 helping behavior trait NBO:0000287 helping behavior PATO:0000001 quality
For OBA, we need
NBO:0000770 behavioral control of defecation phenotype behavioral control of excretion phenotype
NBO:0000771 behavioral control of urination phenotype behavioral control of excretion phenotype
NBO:0000774 behavioral control of lacrimation phenotype behavioral control of external secretion phenotype
NBO:0000777 vocalization behavior phenotype behavioral control of production of sound phenotype
NBO:0000775 crying behavior phenotype behavioral control of production of sound phenotype|emotional behavior phenotype
NBO:0000776 mobbing calling phenotype behavioral control of production of sound phenotype|emotional behavior phenotype
NBO:0000266 cognitive behavior phenotype behavioral phenotype
NBO:0000252 dissociative disorders behavioral phenotype
NBO:0000768 emission behavior phenotype behavioral phenotype
NBO:0000601 emotional behavior phenotype behavioral phenotype
NBO:0000270 feeding behavior phenotype behavioral phenotype
NBO:0000568 kinesthetic behavior phenotype behavioral phenotype
NBO:0000256 mood disorder behavioral phenotype
NBO:0000265 personality disorder behavioral phenotype
NBO:0000259 psychotic disorder behavioral phenotype
NBO:0000755 reproductive behavior phenotype behavioral phenotype
NBO:0000473 rhythmic behavior phenotype behavioral phenotype
NBO:0000012 seizures/epilepsy behavioral phenotype
NBO:0000564 social behavior phenotype behavioral phenotype
NBO:0000249 somatoform behavior phenotype behavioral phenotype
NBO:0000661 olfactory behavior phenotype chemosensory behavior phenotype
NBO:0000485 circadian rhythm sleep disorder circadian behavior phenotype|dyssomnia
NBO:0000753 non-rapid eye movement sleep behavior phenotype circadian behavior phenotype|sleeping behavior phenotype
NBO:0000754 rapid eye movement sleep phenotype circadian behavior phenotype|sleeping behavior phenotype
NBO:0000269 amnestic disorder cognitive behavior phenotype
NBO:0000267 delirium cognitive behavior phenotype
NBO:0000603 delusion cognitive behavior phenotype
NBO:0000268 dementia cognitive behavior phenotype
NBO:0000606 forgetfulness cognitive behavior phenotype
NBO:0000765 learning and/or memory behavior phenotype cognitive behavior phenotype
NBO:0000744 perception behavior phenotype cognitive behavior phenotype
NBO:0000572 senility cognitive behavior phenotype
NBO:0000655 sensation behavior phenotype cognitive behavior phenotype
NBO:0000760 female courtship behavior phenotype courtship behavior phenotype
NBO:0000761 male courtship behavior phenotype courtship behavior phenotype
NBO:0000851 increased amount of liquid in a single drinking act drinking behavior phenotype
NBO:0000886 increased amount of liquid in drinking regulation drinking behavior phenotype
NBO:0000133 liquid preference/aversion drinking behavior phenotype
NBO:0000542 polydipsia drinking behavior phenotype
NBO:0000240 anorexia nervosa eating behavior phenotype
NBO:0000544 aphagia eating behavior phenotype
NBO:0000241 bulimia nervosa eating behavior phenotype
NBO:0000135 food preference/aversion eating behavior phenotype
NBO:0000242 obesity eating behavior phenotype
NBO:0000546 polyphagia eating behavior phenotype
NBO:0000769 behavioral control of excretion phenotype emission behavior phenotype
NBO:0000773 behavioral control of external secretion phenotype emission behavior phenotype
NBO:0000772 behavioral control of production of sound phenotype emission behavior phenotype
NBO:0000602 apathy emotional behavior phenotype
NBO:0000244 pathological anxiety emotional behavior phenotype
NBO:0000540 drinking behavior phenotype feeding behavior phenotype
NBO:0000539 eating behavior phenotype feeding behavior phenotype
NBO:0000705 automatism involuntary movement behavior phenotype
NBO:0000645 convulsion involuntary movement behavior phenotype
NBO:0000005 reflexive behavior phenotype involuntary movement behavior phenotype
NBO:0000588 spasm involuntary movement behavior phenotype
NBO:0000589 tremor involuntary movement behavior phenotype
NBO:0000643 involuntary movement behavior phenotype kinesthetic behavior phenotype
NBO:0000644 voluntary movement behavior phenotype kinesthetic behavior phenotype
NBO:0000766 learning behavior phenotype learning and/or memory behavior phenotype
NBO:0000767 memory behavior phenotype learning and/or memory behavior phenotype
NBO:0000028 akinesia locomotory behavior phenotype
NBO:0000029 bradykinesia locomotory behavior phenotype
NBO:0000598 dystonia locomotory behavior phenotype
NBO:0000032 paralysis locomotory behavior phenotype
NBO:0000759 courtship behavior phenotype mating behavior phenotype
NBO:0000144 mating frequency mating behavior phenotype
NBO:0000145 mating preference mating behavior phenotype
NBO:0000762 copulation phenotype mating behavior phenotype|sexual activity phenotype
NBO:0000590 ataxia motor coordination phenotype
NBO:0000592 dysmetria motor coordination phenotype
NBO:0000165 NREM frequency non-rapid eye movement sleep behavior phenotype
NBO:0000164 NREM duration non-rapid eye movement sleep behavior phenotype|sleep duration
NBO:0000563 catalepsy posture phenotype
NBO:0000596 titubation posture phenotype
NBO:0000162 REM duration rapid eye movement sleep phenotype
NBO:0000163 REM frequency rapid eye movement sleep phenotype
NBO:0000579 hyperekplexia reflexive behavior phenotype
NBO:0000756 mating behavior phenotype reproductive behavior phenotype
NBO:0000757 post-mating behavior phenotype reproductive behavior phenotype
NBO:0000758 sexual activity phenotype reproductive behavior phenotype
NBO:0000659 visual behavior phenotype reproductive behavior phenotype|sensation behavior phenotype
NBO:0000474 circadian behavior phenotype rhythmic behavior phenotype
NBO:0000419 sleeping behavior phenotype rhythmic behavior phenotype
NBO:0000658 auditory behavior phenotype sensation behavior phenotype
NBO:0000660 chemosensory behavior phenotype sensation behavior phenotype
NBO:0000656 somatic sensation related behavior phenotype sensation behavior phenotype
NBO:0000763 female sexual activity phenotype sexual activity phenotype
NBO:0000764 male sexual activity phenotype sexual activity phenotype
NBO:0000067 asleep sleeping behavior phenotype
NBO:0000475 dyssomnia sleeping behavior phenotype
NBO:0000493 parasomnia sleeping behavior phenotype
NBO:0000160 sleep duration sleeping behavior phenotype
NBO:0000158 sleep pattern sleeping behavior phenotype
NBO:0000621 selective mutism social behavior phenotype
NBO:0000565 social withdrawal social behavior phenotype
NBO:0000657 cutaneous sensation behavior phenotype somatic sensation related behavior phenotype
NBO:0000229 vestibular behavior phenotype somatic sensation related behavior phenotype
NBO:0000250 conversion disorder somatoform behavior phenotype
NBO:0000251 hypochondriasis somatoform behavior phenotype
NBO:0000591 motor coordination phenotype vestibular behavior phenotype
NBO:0000595 posture phenotype vestibular behavior phenotype
NBO:0000569 fatigue voluntary movement behavior phenotype
NBO:0000030 hyperactivity voluntary movement behavior phenotype
NBO:0000031 hypoactivity voluntary movement behavior phenotype
NBO:0000009 locomotory behavior phenotype voluntary movement behavior phenotype
NBO:0000567 stereotypic behavior voluntary movement behavior phenotype
NBO:0000243 behavioral phenotype
140 existing OBA trait terms that use NBO process terms
Thanks for this. I checked it before and it contains no phenotype branch terms so it's not currently a problem.
Thanks for this. I checked it before and it contains no phenotype branch terms so it's not currently a problem.
@DitchingIt , I am afraid you have checked something else than what I suggested. The goal is to avoid adding duplicate traits to OBA.
For example, converting NBO:0000474 circadian behavior phenotype
to a new OBA trait would duplicate the existing
OBA:1000691 NBO:0000166 circadian rhythm PATO:0000001 quality
.
It is a problem that we want to avoid. You need to find the NBO phenotype and related NBO/GO biological process term pairs, like my 'circadian rhythm' process - 'circadian behaviour phenotype' example: NBO:0000474 and NBO:0000166.
Ah I see now. Sorry.
@rays22 Three questions arising as I'm putting together my review of NBO traits:
@rays22 @matentzn Pending answers to the questions above, I have created a table below:
NBO ID | NBO LABEL | Suggested OBA Label | Existing OBA | Suggested OBA Superclass | Suggested NBO class | Suggested +PATO | Comment |
---|---|---|---|---|---|---|---|
NBO:0000658 | auditory behavior phenotype | auditory behavior quality | sensation behavior quality | NBO:0000316 | PATO:0001530 | ||
NBO:0000770 | behavioral control of defecation phenotype | defecation behavior quality | emission behavior quality | NBO:0000039 | PATO:0001530 | ||
NBO:0000769 | behavioral control of excretion phenotype | N/A | GO ‘do not annotate’ notice https://github.com/geneontology/go-ontology/issues/22368 do-not-annotate notive | ||||
NBO:0000773 | behavioral control of external secretion phenotype | external secretion behavior quality | emission behavior quality | NBO:0000041 | PATO:0001530 | ||
NBO:0000774 | behavioral control of lacrimation phenotype | lacrimation behavior quality | external secretion behavior quality | NBO:0000042 | PATO:0001530 | ||
NBO:0000772 | behavioral control of production of sound phenotype | sound production behavior quality | emission behavior quality | NBO:0000036 | PATO:0001530 | ||
NBO:0000771 | behavioral control of urination phenotype | micturition behavior quality | emission behavior quality | NBO:0000040 | PATO:0001530 | ||
NBO:0000243 | behavioral phenotype | - | behavior trait OBA:VT0010442 | biological process attribute OBA:0100002 | NBO never defined its phenotype branch with reference to its process branch. | ||
NBO:0000660 | chemosensory behavior phenotype | chemosensory behavior quality | sensation behavior quality | NBO:0000322 | PATO:0001530 | ||
NBO:0000474 | circadian behavior phenotype | - | circadian rhythm quality OBA:1000691 | ||||
NBO:0000266 | cognitive behavior phenotype | cognitive behavior quality | behavior process quality OBA:1000369 | NBO:0000607 | PATO:0001530 | ||
NBO:0000762 | copulation phenotype | copulation quality | mating behavior quality OBA:1000809 | NBO:0000060 | PATO:0001530 | ||
NBO:0000759 | courtship behavior phenotype | courtship behavior quality | mating behavior quality OBA:1000809 | NBO:0000077 | PATO:0001530 | ||
NBO:0000775 | crying behavior phenotype | crying behavior quality | emotional behavior quality OBA:1000603 | NBO:0000618 | PATO:0001530 | ||
NBO:0000657 | cutaneous sensation behavior phenotype | - | cutaneous sensation behavior quality OBA:1000713 | ||||
NBO:0000540 | drinking behavior phenotype | liquid consumption quality | feeding behavior quality OBA:1000748 | NBO:0000130 | PATO:0001530 | ||
NBO:0000539 | eating behavior phenotype | - | food consumption quality OBA:1000690 | ||||
NBO:0000768 | emission behavior phenotype | emission behavior quality | behavior process quality OBA:1000369 | NBO:0000035 | PATO:0001530 | ||
NBO:0000601 | emotional behavior phenotype | - | emotional behavior quality OBA:1000603 | ||||
NBO:0000270 | feeding behavior phenotype | - | feeding behavior quality OBA:1000748 | ||||
NBO:0000760 | female courtship behavior phenotype | female courtship behavior quality | courtship behavior quality | NBO:0000638 | PATO:0001530 | ||
NBO:0000763 | female sexual activity phenotype | female sexual activity quality | sexual activity quality | NBO:0000549 | PATO:0001530 | ||
NBO:0000135 | food preference/aversion | food consumption preference | food consumption quality OBA:1000690 | NBO:0000134 | PATO:0000773 | ||
NBO:0000929 | frequency of drinking | liquid consumption frequency | liquid consumption preference | NBO:0000130 | PATO:0000044 | ||
NBO:0000643 | involuntary movement behavior phenotype | - | involuntary movement behavior quality OBA:1000885 | Consider moving OBA:1000678 to be child of kinesthetic behavior quality | |||
NBO:0000568 | kinesthetic behavior phenotype | kinesthetic behavior quality | behavior process quality OBA:1000369 | NBO:0000338 | PATO:0001530 | ||
NBO:0000765 | learning and/or memory behavior phenotype | learning and/or memory behavior quality | cognitive behavior quality | NBO:0000006 | PATO:0001530 | ||
NBO:0000766 | learning behavior phenotype | learning behavior quality | learning and/or memory behavior quality | NBO:0000022 | PATO:0001530 | Consider moving OBA:1000647 to be child of learning behavior quality | |
NBO:0000133 | liquid preference/aversion | liquid consumption preference | liquid consumption quality | NBO:0000130 | PATO:0000773 | ||
NBO:0000009 | locomotory behavior phenotype | - | locomotory behavior quality OBA:1000684 | Consider move to be child of kinesthetic behavior quality | |||
NBO:0000761 | male courtship behavior phenotype | male courtship behavior quality | courtship behavior quality | NBO:0000637 | PATO:0001530 | ||
NBO:0000764 | male sexual activity phenotype | male sexual activity quality | sexual activity quality | NBO:0000548 | PATO:0001530 | ||
NBO:0000756 | mating behavior phenotype | - | mating behavior quality OBA:1000809 | Consider move to be child of sexual activity quality | |||
NBO:0000144 | mating frequency | copulation frequency | mating behavior quality OBA:1000809 | NBO:0000060 | PATO:0000044 | ||
NBO:0000145 | mating preference | mating preference | mating behavior quality OBA:1000809 | NBO:0002948 | PATO:0000773 | ||
NBO:0000767 | memory behavior phenotype | memory behavior quality | learning and/or memory behavior quality | NBO:0000170 | PATO:0001530 | Consider moving OBA:1000895 & OBA:1000858 & OBA:1000862 to be children of memory behavior quality | |
NBO:0000776 | mobbing calling phenotype | mobbing calling quality | sound production behavior quality | NBO:0000632 | PATO:0001530 | ||
NBO:0000591 | motor coordination phenotype | - | motor coordination quality OBA:1000775 | ||||
NBO:0000753 | non-rapid eye movement sleep behavior phenotype | non-rapid eye movement sleep behavior quality | sleeping behavior quality OBA:1000905 | NBO:0000161 | PATO:0001530 | ||
NBO:0000164 | NREM duration | NREM duration | sleeping behavior quality OBA:1000905 | NBO:0000161 | PATO:0001309 | ||
NBO:0000165 | NREM frequency | NREM frequency | sleeping behavior quality OBA:1000905 | NBO:0000161 | PATO:0000044 | ||
NBO:0000661 | olfactory behavior phenotype | olfactory behavior quality | chemosensory behavior quality | NBO:0000323 | PATO:0001530 | ||
NBO:0000744 | perception behavior phenotype | sensation behavior quality | Synonym in NBO | ||||
NBO:0000757 | post-mating behavior phenotype | post-mating behavior quality | mating behavior quality OBA:1000809 | NBO:0000078 | PATO:0001530 | ||
NBO:0000595 | posture phenotype | - | posture quality OBA:1000757 | ||||
NBO:0000754 | rapid eye movement sleep phenotype | rapid eye movement sleep behavior quality | sleeping behavior quality OBA:1000905 | NBO:0000159 | PATO:0001530 | ||
NBO:0000005 | reflexive behavior phenotype | - | reflexive behavior quality OBA:1000741 | ||||
NBO:0000162 | REM duration | REM duration | sleeping behavior quality OBA:1000905 | NBO:0000159 | PATO:0001309 | ||
NBO:0000163 | REM frequency | REM frequency | sleeping behavior quality OBA:1000905 | NBO:0000159 | PATO:0000044 | ||
NBO:0000755 | reproductive behavior phenotype | - | reproductive behavior trait OBA:2050117 | Doesn’t exist on OLS or Ontobee | |||
NBO:0000473 | rhythmic behavior phenotype | - | rhythmic behavior trait OBA:VT0010455 | ||||
NBO:0000655 | sensation behavior phenotype | sensation behavior quality | behavior process quality OBA:1000369 | NBO:0000308 | PATO:0001530 | ||
NBO:0000758 | sexual activity phenotype | sexual activity quality | behavior process quality OBA:1000369 | NBO:0000034 | PATO:0001530 | ||
NBO:0000160 | sleep duration | sleep duration | sleeping behavior quality OBA:1000905 | NBO:0000024 | PATO:0001309 | ||
NBO:0000158 | sleep pattern | ? | sleep pattern PATO:0001309 | Is PATO the best place for the whole trait? | |||
NBO:0000419 | sleeping behavior phenotype | - | sleeping behavior quality OBA:1000905 | ||||
NBO:0000564 | social behavior phenotype | - | social behavior quality OBA:1000407 | ||||
NBO:0000656 | somatic sensation related behavior phenotype | somatic sensation related behavior quality | sensation behavior quality | NBO:0000327 | PATO:0001530 | ||
NBO:0000229 | vestibular behavior phenotype | vestibular behavior quality | somatic sensation related behavior quality | NBO:0000317 | PATO:0001530 | ||
NBO:0000659 | visual behavior phenotype | visual behavior quality | sensation behavior quality | NBO:0000314 | PATO:0001530 | ||
NBO:0000777 | vocalization behavior phenotype | - | vocalization trait OBA:VT0001529 | ||||
NBO:0000644 | voluntary movement behavior phenotype | - | voluntary movement behavior quality OBA:1000544 | Consider moving OBA:1000678 to be child of kinesthetic behavior quality |
NB: PATO subsumed 'aversion' within 'preference' whereas NBO made them siblings. Unless PATO changes, PATO:0000189 'discrimination' may be preferable to PATO:0000773 'preference' in mixed 'preference/aversion' classes above.
In the light of discussion at #115, suggested changes in the lines above have been modified as follows: NBO ID | NBO LABEL | Suggested OBA Label | Existing OBA | Suggested OBA Superclass | Suggested NBO class | Suggested +PATO | Comment |
---|---|---|---|---|---|---|---|
NBO:0000770 | behavioral control of defecation phenotype | defecation behavior quality | excretion behavior quality | NBO:0000039 | PATO:0001530 | ||
NBO:0000769 | behavioral control of excretion phenotype | excretion behavior quality | emission behavior quality | NBO:0000038 | PATO:0001530 | ||
NBO:0000771 | behavioral control of urination phenotype | micturition behavior quality | excretion behavior quality | NBO:0000040 | PATO:0001530 |
The earlier task list items have been moved to their own issues and are now being monitored in the Project Phenotypes view.
This issue is now focused on delivering the task of deprecating Traits to OBA.