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Trait deprecations #131

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DitchingIt opened this issue Feb 18, 2023 · 13 comments
Open

Trait deprecations #131

DitchingIt opened this issue Feb 18, 2023 · 13 comments
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@DitchingIt
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DitchingIt commented Feb 18, 2023 •
edited

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.
@DitchingIt DitchingIt pinned this issue Feb 18, 2023
@matentzn
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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
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overlap between the phenotype and behaviour branches

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

@DitchingIt
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start migrating some terms over

@matentzn What exactly should I do?

@matentzn
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May I suggest we start with #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.

@DitchingIt DitchingIt self-assigned this Feb 22, 2023
@rays22
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rays22 commented Feb 24, 2023 •
edited

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
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rays22 commented Feb 24, 2023 •
edited by DitchingIt

For OBA, we need

  1. identify the true traits from the terms below,
  2. identify those that would be new to OBA,
  3. find the appropriate process terms (NBO/GO) for the ones identified in step 2.
  4. 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
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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
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rays22 commented Feb 24, 2023

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.

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Ah I see now. Sorry.

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@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?

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DitchingIt commented Feb 27, 2023 •
edited

@rays22 @matentzn Pending answers to the questions above, I have created a table below:

  • It lists all the 62 NBO phenotype branch classes which I think are traits (i.e. potentially suitable for OBA).
  • Of 140 Existing OBA trait terms that use NBO process terms in their logical definitions, 18 would be duplicated (2 of which fall into question 3 above).
  • In addition PATO itself duplicates a whole term ('sleep pattern') which could otherwise become part of OBA.
  • Furthermore, GO is obsoleting the term 'excretion' and NBO may also so it may not be worth creating an OBA term.
  • The remaining 42 phenotypes which could become traits have a Suggested OBA Label based mainly on the NBO phenotype label, a Suggested NBO class, and a Suggested +PATO class. (NB: I don't see the need to create any new NBO process terms.)
  • The new classes will introduce more hierarchy to OBA which is addressed in the Comments alongside a handful of other comments.
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 geneontology/go-ontology#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

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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.

@rays22 rays22 mentioned this issue Mar 1, 2023
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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

This was referenced Mar 2, 2023
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@DitchingIt DitchingIt changed the title Phenotype branch retirement Trait deprecations Mar 3, 2023
@DitchingIt DitchingIt unpinned this issue Jul 23, 2023
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