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obophenotype / bio-attribute-ontology

source files for OBA (Ontology of Biological Attributes)
https://obophenotype.github.io/bio-attribute-ontology
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Import VT terms relevant to MPD into OBA #85

Open rays22 opened 2 years ago

rays22 commented 2 years ago

Import VT terms used by the Mouse Phenome Database into OBA.

See email thread Re: Phenotype-disease mapping

This ticket can be closed when all VT terms in https://phenome.jax.org/downloads "ontology mappings" are integrated in VT.

rays22 commented 2 years ago

Table with the list of VT terms that are annotated in MPD to phenotypic traits/measures, but do not show up in OBA -> VT mapping:

id term
VT:1000472 subcutaneous adipose mass
VT:0003945 lymphocyte physiology trait
VT:0010478 blood lipase amount
VT:0001819 immune system cell physiology trait
VT:0010530 cued fear conditioning behavior trait
VT:0003027 blood acidity-alkalinity balance trait
VT:0010435 response to bacterial infection trait
VT:0010917 bile acid amount
VT:0003620 urine output
VT:0008345 gamma-delta T cell quantity
VT:0015008 total fat pad mass
VT:0015078 blood homeostasis trait
VT:0010464 fertility trait
VT:0003107 behavioral response to novelty trait
VT:0010461 excretion behavior trait
VT:0001006 retinal cone cell morphology trait
VT:0002634 sensorimotor gating trait
VT:0002336 pulmonary gas exchange trait
VT:0003135 reticulocyte quantity
VT:0001731 postnatal growth trait
VT:0010481 blood immunoglobulin M amount
VT:0001392 locomotor behavior trait
VT:0001757 urine molecular composition trait
VT:0000261 arterial blood flow trait
VT:0008616 blood interleukin-12 amount
VT:0002607 basophil quantity
VT:0010719 response to methamphetamine trait
VT:0002636 time of vaginal opening
VT:0001777 body temperature regulation trait
VT:1000738 limb conformation trait
VT:0010463 coat/hair pigmentation trait
VT:0007075 heart left ventricle wall thickness
VT:0010482 body fat mass
VT:0000336 mast cell quantity
VT:0010710 milk copper amount
VT:0004762 blood anti-double stranded DNA antibody amount
VT:3000003 fibrin formation trait
VT:0008073 CD4-positive T cell quantity
VT:0003492 involuntary movement trait
VT:0005431 oocyte quantity
VT:1000748 type IIa muscle fiber quantity
VT:0001349 tear production trait
VT:0010480 blood osteocalcin amount
VT:0003830 testis development trait
VT:0010720 response to morphine trait
VT:0010477 blood lactate dehydrogenase amount
VT:0010731 gait trait
VT:0010718 response to cocaine trait
VT:0005102 iris pigmentation trait
VT:0001805 blood immunoglobulin G amount
VT:0010535 erythrocyte ion amount
VT:0010119 skeletal muscle cellular composition trait
VT:0001304 lens clarity trait
VT:0010513 blood ferritin amount
VT:1000189 offspring quantity
VT:0001280 vibrissa retention trait
VT:0005584 enzyme/coenzyme activity trait
VT:0007088 heart right ventricle wall thickness
VT:0001968 tactile sensory behavior trait
VT:0008498 blood immunoglobulin G3 amount
VT:0001289 hyaloid capillary system development trait
VT:0010722 withdrawal response to addictive substance trait
VT:0004262 physical strength trait
VT:0010919 feces bile acid amount
VT:0001553 blood free fatty acid amount
VT:0010600 maternal nurturing trait
VT:0002063 learning/memory/conditioning trait
VT:0001360 social investigation trait
VT:0010808 milk sulfur amount
VT:0000607 hepatocyte morphology trait
VT:0010483 body lean mass
VT:0000199 blood albumin amount
VT:0002327 respiratory function trait
VT:0004244 spontaneous abortion trait
VT:0001516 motor coordination/balance trait
VT:0002329 blood gas amount
VT:0002458 B cell quantity
VT:0002338 pulmonary ventilation trait
VT:0001314 cornea clarity trait
VT:0004271 paw/hand/foot/hoof morphology trait
VT:0003179 platelet quantity
VT:0005225 vertebra development trait
VT:0010249 blood cell physiology trait
VT:0010918 liver bile acid amount
VT:0002161 female fecundity trait
VT:0010532 active avoidance behavior trait
VT:0000217 leukocyte quantity
VT:0010726 wildness behavior trait
VT:0010711 milk iron amount
VT:0010441 parasite quantity
VT:0004972 regulatory T cell quantity
VT:0005567 blood total protein amount
VT:0008043 natural killer cell quantity
VT:0001502 behavioral circadian rhythm trait
VT:0007086 heart ventricle septum thickness
VT:0002492 blood immunoglobulin E amount
VT:0010748 stereotypic behavior trait
VT:0001923 female fertility trait
VT:0010708 sheltering behavior trait
VT:1000747 type I muscle fiber quantity
VT:0010033 complement protein amount
VT:0010459 behavioral response to novel environment trait
VT:0008497 blood immunoglobulin G2b amount
VT:0010531 operant conditioning behavior trait
VT:0001970 pain threshold
VT:0000646 adrenocortical cell morphology trait
VT:0010694 blood fructosamine amount
VT:0005265 blood urea nitrogen amount
VT:0005372 life span trait
VT:0010732 head movement trait
VT:0000366 brainstem auditory evoked potential
VT:0010714 milk zinc content
VT:0010723 conditioned place preference behavior trait
VT:0001573 blood alanine transaminase amount
VT:0001570 blood enzyme amount
VT:0003065 hepatic copper amount
VT:0002423 mast cell physiology trait
VT:0001756 urine production trait
VT:0001807 blood immunoglobulin A amount
VT:0008723 eosinophil recruitment trait
VT:0004263 limb posture trait
VT:0010183 platelet morphology trait
VT:0010462 defecation behavior trait
VT:0000016 hindlimb conformation trait
VT:0010727 spatial reference memory trait
VT:0010545 blood adiponectin amount
VT:0015014 aggression-related behavior trait
VT:0001830 effector T cell quantity
VT:0002424 reticulocyte morphology trait
VT:0005089 double-negative T cell quantity
VT:0000717 lymphocyte quantity
VT:0001388 stationary movement trait
VT:0010715 fear-related behavior trait
VT:0010878 blood bile acid amount
VT:0003656 erythrocyte physiology trait
VT:0010437 response to parasitic infection trait
VT:1000181 viable offspring quantity
VT:0010436 response to fungal infection trait
VT:0008215 immature B cell quantity
VT:0015026 neuron quantity
VT:0000334 granulocyte quantity
VT:0000223 monocyte quantity
VT:0010677 glycated serum protein amount
VT:0002602 eosinophil quantity
VT:0002463 neutrophil physiology trait
VT:0002673 sperm quantity
VT:0002314 respiratory mechanics trait
VT:0005448 energy balance trait
VT:0010716 anxiety-related behavior trait
VT:0010648 muscle glycogen amount
VT:0002332 exercise endurance trait
VT:0005425 macrophage quantity
VT:0010721 response to nicotine trait
VT:0008495 blood immunoglobulin G1 amount
VT:0010534 erythrocyte ion transport trait
VT:0006387 T cell quantity
VT:0008125 dendritic cell quantity
VT:0008077 CD8-positive T cell quantity
VT:0002871 urine albumin amount
VT:0005327 mesangial cell morphology trait
VT:0010440 bacteria quantity
VT:0010585 brain molecular composition trait
VT:2000009 heart pumping trait
VT:0000004 forelimb conformation trait
VT:0002447 erythrocyte morphology trait
VT:0015015 depression-related behavior trait
VT:0001586 erythrocyte quantity
VT:0008713 cytokine amount
VT:1000047 blood creatine kinase amount
VT:1000000 body conformation trait
VT:0010533 passive avoidance behavior trait
VT:0008397 CD4-positive, CD25-positive, alpha-beta regulatory T cell morphology trait
VT:0003671 eyelid aperture
VT:0000222 neutrophil quantity
VT:0010616 blood lactate amount
VT:0010695 blood ghrelin amount
VT:0009340 splenocyte apoptosis trait
VT:0010490 aorta blood flow trait
VT:0008897 blood immunoglobulin G2c amount
VT:0010529 contextual fear conditioning behavior trait
VT:0008721 chemokine amount
VT:0010474 blood non-HDL cholesterol amount
VT:0002001 visual acuity trait
VT:0002206 CNS synaptic transmission trait
VT:0010709 behavioral response to novel object trait
VT:0001661 total life span
VT:0001505 body posture trait
VT:0010439 response to viral infection trait
VT:0002069 consumption behavior trait
VT:0010473 impulsivity behavior trait
VT:0000203 blood aspartate transaminase amount
VT:0002451 macrophage physiology trait
VT:0002095 skin pigmentation trait
VT:0005119 blood thyroid-stimulating hormone amount
VT:0008719 neutrophil recruitment trait
VT:0001412 scratching trait
VT:0010475 blood amylase amount
VT:0003084 skeletal muscle fiber morphology trait
VT:0000231 heart excitatory physiology trait
VT:0010729 olfactory discrimination memory trait
VT:0008038 NK T cell quantity
VT:0010486 cardiac output trait
VT:0008550 blood interferon-beta amount
VT:0008496 blood immunoglobulin G2a amount
VT:0003457 blood ketone body amount
VT:0003725 blood autoantibody amount
VT:0001895 hippocampus physiology trait
VT:1000152 wellness/fitness trait
VT:0010690 pericardial fat pad mass
VT:0010725 startle reflex trait
VT:0001005 retinal rod cell morphology trait
VT:0010476 blood glutamate dehydrogenase amount
VT:0010042 sperm morphology trait
VT:0010479 blood insulin-like growth factor amount
VT:0010540 urine creatinine amount
VT:0001943 respiration trait
rays22 commented 2 years ago

Actually 57 of the 216 VT terms from the table above are included in OBA:

subject_id predicate_id object_id match_type
VT:0004271 skos:exactMatch OBA:VT0004271 HumanCurated
VT:0005327 skos:exactMatch OBA:VT0005327 HumanCurated
VT:0006387 skos:exactMatch OBA:VT0006387 HumanCurated
VT:0001830 skos:exactMatch OBA:VT0001830 HumanCurated
VT:0008043 skos:exactMatch OBA:VT0008043 HumanCurated
VT:0005584 skos:exactMatch OBA:VT0005584 HumanCurated
VT:0010042 skos:exactMatch OBA:VT0010042 HumanCurated
VT:0003135 skos:exactMatch OBA:VT0003135 HumanCurated
VT:0008345 skos:exactMatch OBA:VT0008345 HumanCurated
VT:0001586 skos:exactMatch OBA:VT0001586 HumanCurated
VT:0005425 skos:exactMatch OBA:VT0005425 HumanCurated
VT:0010183 skos:exactMatch OBA:VT0010183 HumanCurated
VT:0008397 skos:exactMatch OBA:VT0008397 HumanCurated
VT:0001005 skos:exactMatch OBA:VT0001005 HumanCurated
VT:0001006 skos:exactMatch OBA:VT0001006 HumanCurated
VT:0002447 skos:exactMatch OBA:VT0002447 HumanCurated
VT:0003084 skos:exactMatch OBA:VT0003084 HumanCurated
VT:0000717 skos:exactMatch OBA:VT0000717 HumanCurated
VT:0002607 skos:exactMatch OBA:VT0002607 HumanCurated
VT:0010464 skos:exactMatch OBA:VT0010464 HumanCurated
VT:0004972 skos:exactMatch OBA:VT0004972 HumanCurated
VT:0002673 skos:exactMatch OBA:VT0002673 HumanCurated
VT:0000336 skos:exactMatch OBA:VT0000336 HumanCurated
VT:0005089 skos:exactMatch OBA:VT0005089 HumanCurated
VT:0003656 skos:exactMatch OBA:VT0003656 HumanCurated
VT:0002602 skos:exactMatch OBA:VT0002602 HumanCurated
VT:0000222 skos:exactMatch OBA:VT0000222 HumanCurated
VT:0000223 skos:exactMatch OBA:VT0000223 HumanCurated
VT:0015026 skos:exactMatch OBA:VT0015026 HumanCurated
VT:0000646 skos:exactMatch OBA:VT0000646 HumanCurated
VT:0002463 skos:exactMatch OBA:VT0002463 HumanCurated
VT:0003945 skos:exactMatch OBA:VT0003945 HumanCurated
VT:0001923 skos:exactMatch OBA:VT0001923 HumanCurated
VT:0002423 skos:exactMatch OBA:VT0002423 HumanCurated
VT:0005431 skos:exactMatch OBA:VT0005431 HumanCurated
VT:0008125 skos:exactMatch OBA:VT0008125 HumanCurated
VT:0002424 skos:exactMatch OBA:VT0002424 HumanCurated
VT:0002458 skos:exactMatch OBA:VT0002458 HumanCurated
VT:0003179 skos:exactMatch OBA:VT0003179 HumanCurated
VT:0000334 skos:exactMatch OBA:VT0000334 HumanCurated
VT:0000217 skos:exactMatch OBA:VT0000217 HumanCurated
VT:0000607 skos:exactMatch OBA:VT0000607 HumanCurated
VT:0008215 skos:exactMatch OBA:VT0008215 HumanCurated
VT:0002451 skos:exactMatch OBA:VT0002451 HumanCurated
VT:1000747 skos:exactMatch OBA:VT1000747 HumanCurated
VT:1000748 skos:exactMatch OBA:VT1000748 HumanCurated
VT:0005372 skos:exactMatch OBA:VT0005372 HumanCurated
VT:0001360 skos:exactMatch OBA:1000928 HumanCurated
VT:0004263 skos:exactMatch OBA:1000784 HumanCurated
VT:0010531 skos:exactMatch OBA:1000879 HumanCurated
VT:0010715 skos:exactMatch OBA:1000937 HumanCurated
VT:0010716 skos:exactMatch OBA:1000384 HumanCurated
VT:0010720 skos:exactMatch OBA:2040012 HumanCurated
VT:0010723 skos:exactMatch OBA:1000817 HumanCurated
VT:0010725 skos:exactMatch OBA:1000918 HumanCurated
VT:0010731 skos:exactMatch OBA:1000869 HumanCurated
VT:0010732 skos:exactMatch OBA:1000726 HumanCurated
matentzn commented 2 years ago

I guess you simply add them? This is great - we must have not refreshed the list after we did the alignment. So less than 150 to go then?

rays22 commented 2 years ago

I guess you simply add them? This is great - we must have not refreshed the list after we did the alignment. So less than 150 to go then?

No, if I understand your question correctly, I do not even need to add the 57 for this ticket, because they have been already added to both OBA and the mapping table https://github.com/obophenotype/bio-attribute-ontology/blob/master/src/mappings/oba-vt.sssom.tsv from the alignment pipeline. I have added a few more though in addition to the 57. Yes, there are about 150 left to do.

rays22 commented 2 years ago

Progress

As of 2022-10-19, 61.1% of the 216 targeted VT terms in the table above have been mapped or imported into OBA. The mapping or importing of the remaining 84 VT terms is in progress.

matentzn commented 1 year ago

We should update the target based on the "ontology mapping" table in https://phenome.jax.org/downloads