search

obo-behavior / behavior-ontology

Neuro Behaviour Ontology: an ontology for human and animal behaviour processes and behaviour phenotypes
25 stars 15 forks source link

Trait deprecations #131

Open DitchingIt opened 1 year ago

DitchingIt commented 1 year ago

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.

matentzn commented 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.

DitchingIt commented 1 year ago

overlap between the phenotype and behaviour branches

I have just done a pull request deleting the one link which was for agoraphobia.

DitchingIt commented 1 year ago

start migrating some terms over

@matentzn What exactly should I do?

matentzn commented 1 year ago

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.

rays22 commented 1 year ago

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
rays22 commented 1 year ago

For OBA, we need

  1. [x] identify the true traits from the terms below,
  2. [x] identify those that would be new to OBA,
  3. [x] find the appropriate process terms (NBO/GO) for the ones identified in step 2.
  4. [x] If no appropriate process term exists, we need to request GO or create NBO process terms.
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
DitchingIt commented 1 year ago

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.

rays22 commented 1 year ago

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.

DitchingIt commented 1 year ago

Ah I see now. Sorry.

DitchingIt commented 1 year ago

@rays22 Three questions arising as I'm putting together my review of NBO traits:

  1. What's the reason for using PATO:0000001 quality instead of PATO:0001530 behavioral quality of a process when constructing previous OBA quality traits (e.g. OBA:1000603 emotional behavior quality), and which should I use when drafting new behavior quality ones?
  2. A handful of what I would consider behavioral traits are not under OBA:VT0010442 behavior trait and I'm not sure why. I'm not proposing they should necessarily be moved, but I'm not sure when I should follow suit with traits I'm drafting to replace deprecated NBO classes. These are:
    • OBA:0003877 defecation rate ( I would understand if it was gut transit rate or faecal production rate, but defecation itself is generally behaviorally controlled to a degree),
    • OBA:VT0001882 lactation trait (if it refers to nursing behaviour quality),
    • OBA:0003641 tear secretion rate (if it refers to crying behavior),
    • OBA:0002326 kinesis amount,
    • OBA:1000368 micturition quality (frequently a profoundly behavioral quality - for example consider when, why, and how much dogs urinate),
    • OBA:VT0001501 sleep behavior trait.
  3. Under OBA:VT0010442 behavior trait, there are a few undivided traits (aside from rhythmic behavior trait) like drinking, eating and grooming behaviors, alongside the large subdivision of OBA:1000369 behavior process qualit(ies). When should I emulate these traits, and when should I position them within the behavior process quality subdivision?
DitchingIt commented 1 year ago

@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
DitchingIt commented 1 year ago

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.

DitchingIt commented 1 year ago
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