uberon
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obophenotype
Avoid logical definitions with two part-ofs as differentia
this is an antipattern:
id: UBERON:0017612
name: cingulum of lower jaw molar
def: "A ridge that girdles the base of a lower molar tooth." [http://en.wiktionary.org/wiki/cingulid]
synonym: "cingulid" BROAD []
synonym: "cingulid of molar tooth" EXACT []
synonym: "tooth cingulid" RELATED []
intersection_of: UBERON:0017295 ! cingulum of tooth
intersection_of: part_of UBERON:0001710 ! lower jaw region
intersection_of: part_of UBERON:0003655 ! molar tooth
Rationale: we have a precoordinated term "lower jaw molar", and this DP and OWL reasoning is insufficient to infer the crucial part-of between these two.
Formally this is the co-reference problem, so I would classify as a co-reference antipattern. Even if we use a method like materialize or RG to materialize A sub R some B, formally we have models in which the MT is not part of the LJR
Hi @wdduncan - given the relation to the other ticket, hope its ok if I assign this to you too, do let me know if you object to this and I'll find someone else. Thanks heaps!
Hi @shawntanzk I am unsure what the action item is for this particular ticket. The topic in #2692 is focused on teeth. This ticket seem broader. Yes? No?
oh, honestly I have no idea too, I thought it was something you and @cmungall discussed in the other ticket lol - might need some clarification from @cmungall
It sounds like we need to prioritize pattern work in uberon and align on language like antipattern
basically including two part-ofs in your differentia is an anti-pattern. This will all fall out in the reporting when we finish setting up dosdp-tools such that we can see all non-conforming logical definitions
A quick way to explore logical definiton structure in the interim is to use the logical-definitions command in OAK, paste in .all or a query for all uberon terms:
uberon logical-definitions i^UBERON -O csv -o /tmp/uberon.ldefs.tsv
e.g.
| definedClassId | genusIds | restrictions | restrictionsPropertyIds | restrictionsFillerIds | definedClassId_label | genusIds_label | restrictionsPropertyIds_label | restrictionsFillerIds_label |
|---|---|---|---|---|---|---|---|---|
| UBERON:0000002 | UBERON:0001560 | BFO:0000050=UBERON:0000995@RO:0002150=UBERON:0000996 | BFO:0000050@RO:0002150 | UBERON:0000995@UBERON:0000996 | uterine cervix | neck of organ | part of@continuous with | uterus@vagina |
| UBERON:0000003 | UBERON:0000161 | BFO:0000050=UBERON:0005725@RO:0002176=UBERON:0001707 | BFO:0000050@RO:0002176 | UBERON:0005725@UBERON:0001707 | naris | orifice | part of@connects | olfactory system@nasal cavity |
| UBERON:0000005 | UBERON:0000020 | RO:0002215=GO:0007606 | RO:0002215 | GO:0007606 | chemosensory organ | sense organ | capable of | sensory perception of chemical stimulus |
| UBERON:0000018 | UBERON:0000970 | RO:0002473=UBERON:0000971 | RO:0002473 | UBERON:0000971 | compound eye | eye | composed primarily of | ommatidium |
| UBERON:0000020 | UBERON:0000062 | RO:0002215=GO:0050906 | RO:0002215 | GO:0050906 | sense organ | organ | capable of | detection of stimulus involved in sensory perception |
there are 103 double-part ofs
| definedClassId | genusIds | restrictions | restrictionsPropertyIds | restrictionsFillerIds | definedClassId_label | genusIds_label | restrictionsPropertyIds_label | restrictionsFillerIds_label |
|---|---|---|---|---|---|---|---|---|
| UBERON:0001848 | UBERON:0034944 | BFO:0000050=UBERON:0001757@BFO:0000050=UBERON:0001867 | BFO:0000050@BFO:0000050 | UBERON:0001757@UBERON:0001867 | auricular cartilage | zone of organ | part of@part of | pinna@cartilage of external ear |
| UBERON:0003299 | UBERON:0000479 | BFO:0000050=UBERON:0001891@BFO:0000050=UBERON:0003054 | BFO:0000050@BFO:0000050 | UBERON:0001891@UBERON:0003054 | roof plate of midbrain | tissue | part of@part of | midbrain@roof plate |
| UBERON:0003300 | UBERON:0000479 | BFO:0000050=UBERON:0001893@BFO:0000050=UBERON:0003054 | BFO:0000050@BFO:0000050 | UBERON:0001893@UBERON:0003054 | roof plate of telencephalon | tissue | part of@part of | telencephalon@roof plate |
| UBERON:0003301 | UBERON:0000479 | BFO:0000050=UBERON:0001894@BFO:0000050=UBERON:0003054 | BFO:0000050@BFO:0000050 | UBERON:0001894@UBERON:0003054 | roof plate of diencephalon | tissue | part of@part of | diencephalon@roof plate |
| UBERON:0003302 | UBERON:0000479 | BFO:0000050=UBERON:0001895@BFO:0000050=UBERON:0003054 | BFO:0000050@BFO:0000050 | UBERON:0001895@UBERON:0003054 | roof plate of metencephalon | tissue | part of@part of | metencephalon@roof plate |
| UBERON:0003303 | UBERON:0000479 | BFO:0000050=UBERON:0001896@BFO:0000050=UBERON:0003054 | BFO:0000050@BFO:0000050 | UBERON:0001896@UBERON:0003054 | roof plate of medulla oblongata | tissue | part of@part of | medulla oblongata@roof plate |
| UBERON:0003306 | UBERON:0000481 | BFO:0000050=UBERON:0001049@BFO:0000050=UBERON:0003079 | BFO:0000050@BFO:0000050 | UBERON:0001049@UBERON:0003079 | floor plate of neural tube | multi-tissue structure | part of@part of | neural tube@floor plate |
| UBERON:0003307 | UBERON:0000481 | BFO:0000050=UBERON:0001891@BFO:0000050=UBERON:0003079 | BFO:0000050@BFO:0000050 | UBERON:0001891@UBERON:0003079 | floor plate of midbrain | multi-tissue structure | part of@part of | midbrain@floor plate |
| UBERON:0003308 | UBERON:0000481 | BFO:0000050=UBERON:0001893@BFO:0000050=UBERON:0003079 | BFO:0000050@BFO:0000050 | UBERON:0001893@UBERON:0003079 | floor plate of telencephalon | multi-tissue structure | part of@part of | telencephalon@floor plate |
| UBERON:0003309 | UBERON:0000481 | BFO:0000050=UBERON:0001894@BFO:0000050=UBERON:0003079 | BFO:0000050@BFO:0000050 | UBERON:0001894@UBERON:0003079 | floor plate of diencephalon | multi-tissue structure | part of@part of | diencephalon@floor plate |
| UBERON:0003310 | UBERON:0000481 | BFO:0000050=UBERON:0001895@BFO:0000050=UBERON:0003079 | BFO:0000050@BFO:0000050 | UBERON:0001895@UBERON:0003079 | floor plate of metencephalon | multi-tissue structure | part of@part of | metencephalon@floor plate |
| UBERON:0003311 | UBERON:0000481 | BFO:0000050=UBERON:0001896@BFO:0000050=UBERON:0003079 | BFO:0000050@BFO:0000050 | UBERON:0001896@UBERON:0003079 | floor plate of medulla oblongata | multi-tissue structure | part of@part of | medulla oblongata@floor plate |
| UBERON:0004203 | UBERON:0013522 | BFO:0000050=UBERON:0001225@BFO:0000050=UBERON:0001232 | BFO:0000050@BFO:0000050 | UBERON:0001225@UBERON:0001232 | cortical collecting duct | subdivision of tube | part of@part of | cortex of kidney@collecting duct of renal tubule |
| UBERON:0004897 | UBERON:0003104 | BFO:0000050=UBERON:0003404@BFO:0000050=UBERON:0004890 | BFO:0000050@BFO:0000050 | UBERON:0003404@UBERON:0004890 | right lung accessory lobe lobar bronchus mesenchyme | mesenchyme | part of@part of | lobar bronchus of right lung@right lung accessory lobe |
| UBERON:0004899 | UBERON:0003104 | BFO:0000050=UBERON:0002170@BFO:0000050=UBERON:0003404 | BFO:0000050@BFO:0000050 | UBERON:0002170@UBERON:0003404 | right lung cranial lobe lobar bronchus mesenchyme | mesenchyme | part of@part of | upper lobe of right lung@lobar bronchus of right lung |
| UBERON:0004900 | UBERON:0003104 | BFO:0000050=UBERON:0002174@BFO:0000050=UBERON:0003404 | BFO:0000050@BFO:0000050 | UBERON:0002174@UBERON:0003404 | right lung middle lobe lobar bronchus mesenchyme | mesenchyme | part of@part of | middle lobe of right lung@lobar bronchus of right lung |
| UBERON:0004901 | UBERON:0003104 | BFO:0000050=UBERON:0002167@BFO:0000050=UBERON:0002183 | BFO:0000050@BFO:0000050 | UBERON:0002167@UBERON:0002183 | right lung lobar bronchus mesenchyme | mesenchyme | part of@part of | right lung@lobar bronchus |
| UBERON:0004913 | UBERON:0000058 | BFO:0000050=UBERON:0001174@BFO:0000050=UBERON:0004914 | BFO:0000050@BFO:0000050 | UBERON:0001174@UBERON:0004914 | hepatopancreatic ampulla | duct | part of@part of | common bile duct@duodenal papilla |
| UBERON:0005185 | UBERON:0013522 | BFO:0000050=UBERON:0000362@BFO:0000050=UBERON:0001232 | BFO:0000050@BFO:0000050 | UBERON:0000362@UBERON:0001232 | renal medulla collecting duct | subdivision of tube | part of@part of | renal medulla@collecting duct of renal tubule |
| UBERON:0005256 | UBERON:0003104 | BFO:0000050=UBERON:0000922@BFO:0000050=UBERON:0002100 | BFO:0000050@BFO:0000050 | UBERON:0000922@UBERON:0002100 | trunk mesenchyme | mesenchyme | part of@part of | embryo@trunk |
| UBERON:0005723 | UBERON:0000481 | BFO:0000050=UBERON:0002240@BFO:0000050=UBERON:0003079 | BFO:0000050@BFO:0000050 | UBERON:0002240@UBERON:0003079 | floor plate spinal cord region | multi-tissue structure | part of@part of | spinal cord@floor plate |
| UBERON:0005724 | UBERON:0000479 | BFO:0000050=UBERON:0002240@BFO:0000050=UBERON:0003054 | BFO:0000050@BFO:0000050 | UBERON:0002240@UBERON:0003054 | roof plate spinal cord region | tissue | part of@part of | spinal cord@roof plate |
| UBERON:0011806 | UBERON:0000479 | BFO:0000050=UBERON:0002067@BFO:0000050=UBERON:0011782 | BFO:0000050@BFO:0000050 | UBERON:0002067@UBERON:0011782 | dermis of feather follicle | tissue | part of@part of | dermis@feather follicle |
| UBERON:0011807 | UBERON:0000479 | BFO:0000050=UBERON:0001003@BFO:0000050=UBERON:0011782 | BFO:0000050@BFO:0000050 | UBERON:0001003@UBERON:0011782 | epidermis of feather follicle | tissue | part of@part of | skin epidermis@feather follicle |
| UBERON:0012281 | UBERON:0001821 | BFO:0000050=UBERON:0011932@BFO:0000050=UBERON:0012336 | BFO:0000050@BFO:0000050 | UBERON:0011932@UBERON:0012336 | perianal sebaceous gland | sebaceous gland | part of@part of | pilosebaceous unit@perianal skin |
| UBERON:0014455 | UBERON:0001013 | BFO:0000050=UBERON:0000916@BFO:0000050=UBERON:0002072 | BFO:0000050@BFO:0000050 | UBERON:0000916@UBERON:0002072 | subcutaneous abdominal adipose tissue | adipose tissue | part of@part of | abdomen@hypodermis |
| UBERON:0014560 | UBERON:0014567 | BFO:0000050=UBERON:0003883@BFO:0000050=UBERON:0007637 | BFO:0000050@BFO:0000050 | UBERON:0003883@UBERON:0007637 | CA3 stratum lucidum | layer of hippocampal field | part of@part of | CA3 field of hippocampus@hippocampus stratum lucidum |
| UBERON:0014647 | UBERON:0002616 | BFO:0000050=UBERON:0002131@BFO:0000050=UBERON:0002245 | BFO:0000050@BFO:0000050 | UBERON:0002131@UBERON:0002245 | hemisphere part of cerebellar anterior lobe | regional part of brain | part of@part of | anterior lobe of cerebellum@cerebellar hemisphere |
| UBERON:0014648 | UBERON:0002616 | BFO:0000050=UBERON:0002245@BFO:0000050=UBERON:0004002 | BFO:0000050@BFO:0000050 | UBERON:0002245@UBERON:0004002 | hemisphere part of cerebellar posterior lobe | regional part of brain | part of@part of | cerebellar hemisphere@posterior lobe of cerebellum |
| UBERON:0016529 | UBERON:0005401 | BFO:0000050=UBERON:0001950@BFO:0000050=UBERON:0016526 | BFO:0000050@BFO:0000050 | UBERON:0001950@UBERON:0016526 | cortex of cerebral lobe | cerebral hemisphere gray matter | part of@part of | neocortex@lobe of cerebral hemisphere |
| UBERON:0016545 | UBERON:0000490 | BFO:0000050=UBERON:0000076@BFO:0000050=UBERON:0001042 | BFO:0000050@BFO:0000050 | UBERON:0000076@UBERON:0001042 | pharyngeal ectoderm | unilaminar epithelium | part of@part of | external ectoderm@chordate pharynx |
| UBERON:0017271 | UBERON:0007120 | BFO:0000050=UBERON:0001709@BFO:0000050=UBERON:0007116 | BFO:0000050@BFO:0000050 | UBERON:0001709@UBERON:0007116 | upper primary premolar tooth | premolar tooth | part of@part of | upper jaw region@primary dentition |
| UBERON:0017272 | UBERON:0007120 | BFO:0000050=UBERON:0001710@BFO:0000050=UBERON:0007116 | BFO:0000050@BFO:0000050 | UBERON:0001710@UBERON:0007116 | lower primary premolar tooth | premolar tooth | part of@part of | lower jaw region@primary dentition |
| UBERON:0017298 | UBERON:0017295 | BFO:0000050=UBERON:0001098@BFO:0000050=UBERON:0001709 | BFO:0000050@BFO:0000050 | UBERON:0001098@UBERON:0001709 | cingulum of upper incisor tooth | cingulum of tooth | part of@part of | incisor tooth@upper jaw region |
| UBERON:0017299 | UBERON:0017295 | BFO:0000050=UBERON:0001098@BFO:0000050=UBERON:0001710 | BFO:0000050@BFO:0000050 | UBERON:0001098@UBERON:0001710 | cingulum of lower incisor tooth | cingulum of tooth | part of@part of | incisor tooth@lower jaw region |
| UBERON:0017612 | UBERON:0017295 | BFO:0000050=UBERON:0001710@BFO:0000050=UBERON:0003655 | BFO:0000050@BFO:0000050 | UBERON:0001710@UBERON:0003655 | cingulum of lower jaw molar | cingulum of tooth | part of@part of | lower jaw region@molar tooth |
| UBERON:0017613 | UBERON:0017295 | BFO:0000050=UBERON:0001709@BFO:0000050=UBERON:0003655 | BFO:0000050@BFO:0000050 | UBERON:0001709@UBERON:0003655 | cingulum of upper jaw molar | cingulum of tooth | part of@part of | upper jaw region@molar tooth |
| UBERON:0018226 | UBERON:0011216 | BFO:0000050=UBERON:0002048@BFO:0000050=UBERON:0006558 | BFO:0000050@BFO:0000050 | UBERON:0002048@UBERON:0006558 | pulmonary part of lymphatic system | organ system subdivision | part of@part of | lung@lymphatic part of lymphoid system |
| UBERON:0018353 | UBERON:0009979 | BFO:0000050=UBERON:0006597@BFO:0000050=UBERON:0011171 | BFO:0000050@BFO:0000050 | UBERON:0006597@UBERON:0011171 | quadrate condyle | condyle | part of@part of | quadrate bone@joint connecting upper and lower jaws |
| UBERON:0018571 | UBERON:0018294 | BFO:0000050=UBERON:0001709@BFO:0000050=UBERON:0007774 | BFO:0000050@BFO:0000050 | UBERON:0001709@UBERON:0007774 | upper first secondary premolar tooth | premolar 1 | part of@part of | upper jaw region@secondary dentition |
| UBERON:0018572 | UBERON:0018640 | BFO:0000050=UBERON:0001709@BFO:0000050=UBERON:0007774 | BFO:0000050@BFO:0000050 | UBERON:0001709@UBERON:0007774 | upper second secondary premolar tooth | premolar 2 | part of@part of | upper jaw region@secondary dentition |
| UBERON:0018573 | UBERON:0018294 | BFO:0000050=UBERON:0001710@BFO:0000050=UBERON:0007774 | BFO:0000050@BFO:0000050 | UBERON:0001710@UBERON:0007774 | lower first secondary premolar tooth | premolar 1 | part of@part of | lower jaw region@secondary dentition |
| UBERON:0018574 | UBERON:0018640 | BFO:0000050=UBERON:0001710@BFO:0000050=UBERON:0007774 | BFO:0000050@BFO:0000050 | UBERON:0001710@UBERON:0007774 | lower second secondary premolar tooth | premolar 2 | part of@part of | lower jaw region@secondary dentition |
| UBERON:0018575 | UBERON:0018376 | BFO:0000050=UBERON:0001709@BFO:0000050=UBERON:0007774 | BFO:0000050@BFO:0000050 | UBERON:0001709@UBERON:0007774 | upper first secondary molar tooth | molar tooth 1 | part of@part of | upper jaw region@secondary dentition |
| UBERON:0018576 | UBERON:0018606 | BFO:0000050=UBERON:0001709@BFO:0000050=UBERON:0007774 | BFO:0000050@BFO:0000050 | UBERON:0001709@UBERON:0007774 | upper second secondary molar tooth | molar tooth 2 | part of@part of | upper jaw region@secondary dentition |
| UBERON:0018577 | UBERON:0018377 | BFO:0000050=UBERON:0001709@BFO:0000050=UBERON:0007774 | BFO:0000050@BFO:0000050 | UBERON:0001709@UBERON:0007774 | upper third secondary molar tooth | molar tooth 3 | part of@part of | upper jaw region@secondary dentition |
| UBERON:0018578 | UBERON:0018376 | BFO:0000050=UBERON:0001710@BFO:0000050=UBERON:0007774 | BFO:0000050@BFO:0000050 | UBERON:0001710@UBERON:0007774 | lower first secondary molar tooth | molar tooth 1 | part of@part of | lower jaw region@secondary dentition |
| UBERON:0018579 | UBERON:0018606 | BFO:0000050=UBERON:0001710@BFO:0000050=UBERON:0007774 | BFO:0000050@BFO:0000050 | UBERON:0001710@UBERON:0007774 | lower second secondary molar tooth | molar tooth 2 | part of@part of | lower jaw region@secondary dentition |
| UBERON:0018580 | UBERON:0018377 | BFO:0000050=UBERON:0001710@BFO:0000050=UBERON:0007774 | BFO:0000050@BFO:0000050 | UBERON:0001710@UBERON:0007774 | lower third secondary molar tooth | molar tooth 3 | part of@part of | lower jaw region@secondary dentition |
| UBERON:0018588 | UBERON:0018376 | BFO:0000050=UBERON:0001709@BFO:0000050=UBERON:0007116 | BFO:0000050@BFO:0000050 | UBERON:0001709@UBERON:0007116 | upper first primary molar tooth | molar tooth 1 | part of@part of | upper jaw region@primary dentition |
| UBERON:0018589 | UBERON:0018376 | BFO:0000050=UBERON:0001710@BFO:0000050=UBERON:0007116 | BFO:0000050@BFO:0000050 | UBERON:0001710@UBERON:0007116 | lower first primary molar tooth | molar tooth 1 | part of@part of | lower jaw region@primary dentition |
| UBERON:0018599 | UBERON:0018606 | BFO:0000050=UBERON:0001709@BFO:0000050=UBERON:0007116 | BFO:0000050@BFO:0000050 | UBERON:0001709@UBERON:0007116 | upper second primary molar tooth | molar tooth 2 | part of@part of | upper jaw region@primary dentition |
| UBERON:0018600 | UBERON:0018606 | BFO:0000050=UBERON:0001710@BFO:0000050=UBERON:0007116 | BFO:0000050@BFO:0000050 | UBERON:0001710@UBERON:0007116 | lower second primary molar tooth | molar tooth 2 | part of@part of | lower jaw region@primary dentition |
| UBERON:0019253 | UBERON:0001098 | BFO:0000050=UBERON:0001709@BFO:0000050=UBERON:0007774 | BFO:0000050@BFO:0000050 | UBERON:0001709@UBERON:0007774 | upper secondary incisor tooth | incisor tooth | part of@part of | upper jaw region@secondary dentition |
| UBERON:0022649 | UBERON:0001019 | BFO:0000050=UBERON:0001894@BFO:0000050=UBERON:0002138 | BFO:0000050@BFO:0000050 | UBERON:0001894@UBERON:0002138 | habenulo-interpeduncular tract of diencephalon | nerve fasciculus | part of@part of | diencephalon@habenulo-interpeduncular tract |
| UBERON:0023740 | UBERON:0001019 | BFO:0000050=UBERON:0001891@BFO:0000050=UBERON:0002138 | BFO:0000050@BFO:0000050 | UBERON:0001891@UBERON:0002138 | habenulo-interpeduncular tract of midbrain | nerve fasciculus | part of@part of | midbrain@habenulo-interpeduncular tract |
| UBERON:0027331 | UBERON:0002616 | BFO:0000050=UBERON:0002245@BFO:0000050=UBERON:0003012 | BFO:0000050@BFO:0000050 | UBERON:0002245@UBERON:0003012 | flocculonodular lobe, hemisphere portion | regional part of brain | part of@part of | cerebellar hemisphere@flocculonodular lobe |
| UBERON:0034798 | UBERON:0014567 | BFO:0000050=UBERON:0007640@BFO:0000050=UBERON:0034780 | BFO:0000050@BFO:0000050 | UBERON:0007640@UBERON:0034780 | stratum lacunosum-moleculare of caudal CA1 | layer of hippocampal field | part of@part of | hippocampus stratum lacunosum moleculare@caudal CA1 |
| UBERON:0034799 | UBERON:0014567 | BFO:0000050=UBERON:0005372@BFO:0000050=UBERON:0034780 | BFO:0000050@BFO:0000050 | UBERON:0005372@UBERON:0034780 | stratum radiatum of caudal CA1 | layer of hippocampal field | part of@part of | hippocampus stratum radiatum@caudal CA1 |
| UBERON:0034800 | UBERON:0014567 | BFO:0000050=UBERON:0002313@BFO:0000050=UBERON:0034780 | BFO:0000050@BFO:0000050 | UBERON:0002313@UBERON:0034780 | stratum pyramidale of caudal CA1 | layer of hippocampal field | part of@part of | hippocampus pyramidal layer@caudal CA1 |
| UBERON:0034801 | UBERON:0014567 | BFO:0000050=UBERON:0005371@BFO:0000050=UBERON:0034780 | BFO:0000050@BFO:0000050 | UBERON:0005371@UBERON:0034780 | stratum oriens of caudal CA1 | layer of hippocampal field | part of@part of | hippocampus stratum oriens@caudal CA1 |
| UBERON:0034803 | UBERON:0014567 | BFO:0000050=UBERON:0007640@BFO:0000050=UBERON:0034781 | BFO:0000050@BFO:0000050 | UBERON:0007640@UBERON:0034781 | stratum lacunosum-moleculare of caudal CA2 | layer of hippocampal field | part of@part of | hippocampus stratum lacunosum moleculare@caudal CA2 |
| UBERON:0034804 | UBERON:0014567 | BFO:0000050=UBERON:0005372@BFO:0000050=UBERON:0034781 | BFO:0000050@BFO:0000050 | UBERON:0005372@UBERON:0034781 | stratum radiatum of caudal CA2 | layer of hippocampal field | part of@part of | hippocampus stratum radiatum@caudal CA2 |
| UBERON:0034805 | UBERON:0014567 | BFO:0000050=UBERON:0002313@BFO:0000050=UBERON:0034781 | BFO:0000050@BFO:0000050 | UBERON:0002313@UBERON:0034781 | stratum pyramidale of caudal CA2 | layer of hippocampal field | part of@part of | hippocampus pyramidal layer@caudal CA2 |
| UBERON:0034806 | UBERON:0014567 | BFO:0000050=UBERON:0005371@BFO:0000050=UBERON:0034781 | BFO:0000050@BFO:0000050 | UBERON:0005371@UBERON:0034781 | stratum oriens of caudal CA2 | layer of hippocampal field | part of@part of | hippocampus stratum oriens@caudal CA2 |
| UBERON:0034808 | UBERON:0014567 | BFO:0000050=UBERON:0007640@BFO:0000050=UBERON:0034782 | BFO:0000050@BFO:0000050 | UBERON:0007640@UBERON:0034782 | stratum lacunosum-moleculare of caudal CA3 | layer of hippocampal field | part of@part of | hippocampus stratum lacunosum moleculare@caudal CA3 |
| UBERON:0034809 | UBERON:0014567 | BFO:0000050=UBERON:0005372@BFO:0000050=UBERON:0034782 | BFO:0000050@BFO:0000050 | UBERON:0005372@UBERON:0034782 | stratum radiatum of caudal CA3 | layer of hippocampal field | part of@part of | hippocampus stratum radiatum@caudal CA3 |
| UBERON:0034810 | UBERON:0014567 | BFO:0000050=UBERON:0007637@BFO:0000050=UBERON:0034782 | BFO:0000050@BFO:0000050 | UBERON:0007637@UBERON:0034782 | stratum lucidum of caudal CA3 | layer of hippocampal field | part of@part of | hippocampus stratum lucidum@caudal CA3 |
| UBERON:0034811 | UBERON:0014567 | BFO:0000050=UBERON:0002313@BFO:0000050=UBERON:0034782 | BFO:0000050@BFO:0000050 | UBERON:0002313@UBERON:0034782 | stratum pyramidale of caudal CA3 | layer of hippocampal field | part of@part of | hippocampus pyramidal layer@caudal CA3 |
| UBERON:0034812 | UBERON:0014567 | BFO:0000050=UBERON:0005371@BFO:0000050=UBERON:0034782 | BFO:0000050@BFO:0000050 | UBERON:0005371@UBERON:0034782 | stratum oriens of caudal CA3 | layer of hippocampal field | part of@part of | hippocampus stratum oriens@caudal CA3 |
| UBERON:0034828 | UBERON:0014567 | BFO:0000050=UBERON:0007640@BFO:0000050=UBERON:0034777 | BFO:0000050@BFO:0000050 | UBERON:0007640@UBERON:0034777 | stratum lacunosum-moleculare of rostral CA1 | layer of hippocampal field | part of@part of | hippocampus stratum lacunosum moleculare@rostral CA1 |
| UBERON:0034829 | UBERON:0014567 | BFO:0000050=UBERON:0005372@BFO:0000050=UBERON:0034777 | BFO:0000050@BFO:0000050 | UBERON:0005372@UBERON:0034777 | stratum radiatum of rostral CA1 | layer of hippocampal field | part of@part of | hippocampus stratum radiatum@rostral CA1 |
| UBERON:0034830 | UBERON:0014567 | BFO:0000050=UBERON:0002313@BFO:0000050=UBERON:0034777 | BFO:0000050@BFO:0000050 | UBERON:0002313@UBERON:0034777 | stratum pyramidale of rostral CA1 | layer of hippocampal field | part of@part of | hippocampus pyramidal layer@rostral CA1 |
| UBERON:0034831 | UBERON:0014567 | BFO:0000050=UBERON:0005371@BFO:0000050=UBERON:0034777 | BFO:0000050@BFO:0000050 | UBERON:0005371@UBERON:0034777 | stratum oriens of rostral CA1 | layer of hippocampal field | part of@part of | hippocampus stratum oriens@rostral CA1 |
| UBERON:0034833 | UBERON:0014567 | BFO:0000050=UBERON:0007640@BFO:0000050=UBERON:0034778 | BFO:0000050@BFO:0000050 | UBERON:0007640@UBERON:0034778 | stratum lacunosum-moleculare of rostral CA2 | layer of hippocampal field | part of@part of | hippocampus stratum lacunosum moleculare@rostral CA2 |
| UBERON:0034834 | UBERON:0014567 | BFO:0000050=UBERON:0005372@BFO:0000050=UBERON:0034778 | BFO:0000050@BFO:0000050 | UBERON:0005372@UBERON:0034778 | stratum radiatum of rostral CA2 | layer of hippocampal field | part of@part of | hippocampus stratum radiatum@rostral CA2 |
| UBERON:0034835 | UBERON:0014567 | BFO:0000050=UBERON:0002313@BFO:0000050=UBERON:0034778 | BFO:0000050@BFO:0000050 | UBERON:0002313@UBERON:0034778 | stratum pyramidale of rostral CA2 | layer of hippocampal field | part of@part of | hippocampus pyramidal layer@rostral CA2 |
| UBERON:0034836 | UBERON:0014567 | BFO:0000050=UBERON:0005371@BFO:0000050=UBERON:0034778 | BFO:0000050@BFO:0000050 | UBERON:0005371@UBERON:0034778 | stratum oriens of rostral CA2 | layer of hippocampal field | part of@part of | hippocampus stratum oriens@rostral CA2 |
| UBERON:0034838 | UBERON:0014567 | BFO:0000050=UBERON:0007640@BFO:0000050=UBERON:0034779 | BFO:0000050@BFO:0000050 | UBERON:0007640@UBERON:0034779 | stratum lacunosum-moleculare of rostral CA3 | layer of hippocampal field | part of@part of | hippocampus stratum lacunosum moleculare@rostral CA3 |
| UBERON:0034839 | UBERON:0014567 | BFO:0000050=UBERON:0005372@BFO:0000050=UBERON:0034779 | BFO:0000050@BFO:0000050 | UBERON:0005372@UBERON:0034779 | stratum radiatum of rostral CA3 | layer of hippocampal field | part of@part of | hippocampus stratum radiatum@rostral CA3 |
| UBERON:0034840 | UBERON:0014567 | BFO:0000050=UBERON:0007637@BFO:0000050=UBERON:0034779 | BFO:0000050@BFO:0000050 | UBERON:0007637@UBERON:0034779 | stratum lucidum of rostral CA3 | layer of hippocampal field | part of@part of | hippocampus stratum lucidum@rostral CA3 |
| UBERON:0034841 | UBERON:0014567 | BFO:0000050=UBERON:0002313@BFO:0000050=UBERON:0034779 | BFO:0000050@BFO:0000050 | UBERON:0002313@UBERON:0034779 | stratum pyramidale of rostral CA3 | layer of hippocampal field | part of@part of | hippocampus pyramidal layer@rostral CA3 |
| UBERON:0034842 | UBERON:0014567 | BFO:0000050=UBERON:0005371@BFO:0000050=UBERON:0034779 | BFO:0000050@BFO:0000050 | UBERON:0005371@UBERON:0034779 | stratum oriens of rostral CA3 | layer of hippocampal field | part of@part of | hippocampus stratum oriens@rostral CA3 |
| UBERON:0034858 | UBERON:0014567 | BFO:0000050=UBERON:0007640@BFO:0000050=UBERON:0034774 | BFO:0000050@BFO:0000050 | UBERON:0007640@UBERON:0034774 | stratum lacunosum-moleculare of uncal CA1 | layer of hippocampal field | part of@part of | hippocampus stratum lacunosum moleculare@uncal CA1 |
| UBERON:0034859 | UBERON:0014567 | BFO:0000050=UBERON:0005372@BFO:0000050=UBERON:0034774 | BFO:0000050@BFO:0000050 | UBERON:0005372@UBERON:0034774 | stratum radiatum of uncal CA1 | layer of hippocampal field | part of@part of | hippocampus stratum radiatum@uncal CA1 |
| UBERON:0034860 | UBERON:0014567 | BFO:0000050=UBERON:0002313@BFO:0000050=UBERON:0034774 | BFO:0000050@BFO:0000050 | UBERON:0002313@UBERON:0034774 | stratum pyramidale of uncal CA1 | layer of hippocampal field | part of@part of | hippocampus pyramidal layer@uncal CA1 |
| UBERON:0034861 | UBERON:0014567 | BFO:0000050=UBERON:0005371@BFO:0000050=UBERON:0034774 | BFO:0000050@BFO:0000050 | UBERON:0005371@UBERON:0034774 | stratum oriens of uncal CA1 | layer of hippocampal field | part of@part of | hippocampus stratum oriens@uncal CA1 |
| UBERON:0034863 | UBERON:0014567 | BFO:0000050=UBERON:0007640@BFO:0000050=UBERON:0034775 | BFO:0000050@BFO:0000050 | UBERON:0007640@UBERON:0034775 | stratum lacunosum-moleculare of uncal CA2 | layer of hippocampal field | part of@part of | hippocampus stratum lacunosum moleculare@uncal CA2 |
| UBERON:0034864 | UBERON:0014567 | BFO:0000050=UBERON:0005372@BFO:0000050=UBERON:0034775 | BFO:0000050@BFO:0000050 | UBERON:0005372@UBERON:0034775 | stratum radiatum of uncal CA2 | layer of hippocampal field | part of@part of | hippocampus stratum radiatum@uncal CA2 |
| UBERON:0034865 | UBERON:0014567 | BFO:0000050=UBERON:0002313@BFO:0000050=UBERON:0034775 | BFO:0000050@BFO:0000050 | UBERON:0002313@UBERON:0034775 | stratum pyramidale of uncal CA2 | layer of hippocampal field | part of@part of | hippocampus pyramidal layer@uncal CA2 |
| UBERON:0034866 | UBERON:0014567 | BFO:0000050=UBERON:0005371@BFO:0000050=UBERON:0034775 | BFO:0000050@BFO:0000050 | UBERON:0005371@UBERON:0034775 | stratum oriens of uncal CA2 | layer of hippocampal field | part of@part of | hippocampus stratum oriens@uncal CA2 |
| UBERON:0034868 | UBERON:0014567 | BFO:0000050=UBERON:0007640@BFO:0000050=UBERON:0034776 | BFO:0000050@BFO:0000050 | UBERON:0007640@UBERON:0034776 | stratum lacunosum-moleculare of uncal CA3 | layer of hippocampal field | part of@part of | hippocampus stratum lacunosum moleculare@uncal CA3 |
| UBERON:0034869 | UBERON:0014567 | BFO:0000050=UBERON:0005372@BFO:0000050=UBERON:0034776 | BFO:0000050@BFO:0000050 | UBERON:0005372@UBERON:0034776 | stratum radiatum of uncal CA3 | layer of hippocampal field | part of@part of | hippocampus stratum radiatum@uncal CA3 |
| UBERON:0034870 | UBERON:0014567 | BFO:0000050=UBERON:0007637@BFO:0000050=UBERON:0034776 | BFO:0000050@BFO:0000050 | UBERON:0007637@UBERON:0034776 | stratum lucidum of uncal CA3 | layer of hippocampal field | part of@part of | hippocampus stratum lucidum@uncal CA3 |
| UBERON:0034871 | UBERON:0014567 | BFO:0000050=UBERON:0002313@BFO:0000050=UBERON:0034776 | BFO:0000050@BFO:0000050 | UBERON:0002313@UBERON:0034776 | stratum pyramidale of uncal CA3 | layer of hippocampal field | part of@part of | hippocampus pyramidal layer@uncal CA3 |
| UBERON:0034872 | UBERON:0014567 | BFO:0000050=UBERON:0005371@BFO:0000050=UBERON:0034776 | BFO:0000050@BFO:0000050 | UBERON:0005371@UBERON:0034776 | stratum oriens of uncal CA3 | layer of hippocampal field | part of@part of | hippocampus stratum oriens@uncal CA3 |
| UBERON:0035606 | UBERON:0034944 | BFO:0000050=UBERON:0001352@BFO:0000050=UBERON:0001867 | BFO:0000050@BFO:0000050 | UBERON:0001352@UBERON:0001867 | cartilage of external acoustic meatus | zone of organ | part of@part of | external acoustic meatus@cartilage of external ear |
| UBERON:0036362 | UBERON:0000060 | BFO:0000050=UBERON:0000159@BFO:0000050=UBERON:0001007 | BFO:0000050@BFO:0000050 | UBERON:0000159@UBERON:0001007 | wall of anal canal | anatomical wall | part of@part of | anal canal@digestive system |
| UBERON:3010200 | UBERON:0001981 | BFO:0000050=UBERON:0001004@BFO:0000050=UBERON:0002199 | BFO:0000050@BFO:0000050 | UBERON:0001004@UBERON:0002199 | vasculature of respiratory integument | blood vessel | part of@part of | respiratory system@integument |
| UBERON:6003007 | UBERON:0000033 | BFO:0000050=NCBITaxon:50557@BFO:0000050=UBERON:0007023 | BFO:0000050@BFO:0000050 | NCBITaxon:50557@UBERON:0007023 | insect adult head | head | part of@part of | Insecta@adult organism |
| UBERON:7500053 | UBERON:0018647 | BFO:0000050=UBERON:0001710@BFO:0000050=UBERON:0007774 | BFO:0000050@BFO:0000050 | UBERON:0001710@UBERON:0007774 | lower fourth secondary premolar tooth | premolar tooth 4 | part of@part of | lower jaw region@secondary dentition |
| UBERON:8410060 | UBERON:0012368 | BFO:0000050=UBERON:0001155@BFO:0000050=UBERON:0004220 | BFO:0000050@BFO:0000050 | UBERON:0001155@UBERON:0004220 | colon smooth muscle circular layer | circular muscle layer of muscular coat | part of@part of | colon@large intestine smooth muscle |
| UBERON:8410061 | UBERON:0012369 | BFO:0000050=UBERON:0001155@BFO:0000050=UBERON:0004220 | BFO:0000050@BFO:0000050 | UBERON:0001155@UBERON:0004220 | colon smooth muscle longitudinal layer | longitudinal muscle layer of muscular coat | part of@part of | colon@large intestine smooth muscle |
Trying to clean up uberon tickets a bit and came back to this, @cmungall wanted you opinion on something we are doing. In mapping the allen brain atlas to uberon, we use a two-part equiv at times, for example:
| ID | A IAO:0000589 | CLASS_TYPE | C part_of some % and (part_of some NCBITaxon:10090) | C % and (part_of some NCBITaxon:10090) | C part_of some % |
|---|---|---|---|---|---|
| http://purl.obolibrary.org/obo/MBA_10726 | folium-tuber vermis (VII), granular layer | equivalent | http://purl.obolibrary.org/obo/UBERON_0002956 | http://purl.obolibrary.org/obo/UBERON_0004081 | |
| http://purl.obolibrary.org/obo/MBA_527 | dorsal auditory area, layer 1 | equivalent | http://purl.obolibrary.org/obo/UBERON_0005390 | http://purl.obolibrary.org/obo/UBERON_0035917 |
Is this problematic? should we change it?
Thanks
@shawntanzk I'm not sure if this fits the anti-pattern. The example that @cmungall gave had to do with a case in which the two part of relations were represented by the precoordinated lower jaw molar term. I.e.:
intersection_of: part_of UBERON:0001710 ! lower jaw region
intersection_of: part_of UBERON:0003655 ! molar tooth
is a lower jaw molar.
Is there already precoordinated term that can be used? Or is it easy to create a precoordinated term?
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