feat: add UBERON brain anatomy matching for all species#1825
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bendichter wants to merge 6 commits intoadd-brain-area-anatomyfrom
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feat: add UBERON brain anatomy matching for all species#1825bendichter wants to merge 6 commits intoadd-brain-area-anatomyfrom
bendichter wants to merge 6 commits intoadd-brain-area-anatomyfrom
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For mice, location tokens are first matched against Allen CCF, then fall back to UBERON. For all other species, UBERON is tried directly. Synonym scope (EXACT, RELATED, NARROW, BROAD) is a settable parameter, defaulting to EXACT only. - Add generate_uberon_structures.py to parse the UBERON OBO file and produce a bundled JSON of ~2,400 nervous-system descendants - Add UBERON lookup/matching functions to brain_areas.py - Update _extract_brain_anatomy in util.py to handle non-mouse species - Add comprehensive tests for UBERON matching and Allen/UBERON fallback Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
bendichter
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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## add-brain-area-anatomy #1825 +/- ##
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+ Coverage 75.34% 75.73% +0.39%
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Files 87 89 +2
Lines 12259 12514 +255
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+ Hits 9237 9478 +241
- Misses 3022 3036 +14
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Instead of passing a flat set of scopes, use a max_synonym_scope parameter (default "EXACT"). Matching tries tiers in precision order: EXACT > NARROW > BROAD > RELATED, up to the specified maximum. Term names are always tried first before any synonym tier. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Thread the scope parameter through so callers can control how permissive UBERON synonym matching is. Defaults to EXACT. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
yarikoptic
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Mar 30, 2026
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most likely my requests could be handled by an agent quite sensibly
| #!/usr/bin/env python3 | ||
| """Regenerate uberon_brain_structures.json from the UBERON OBO file. | ||
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| Run: python -m dandi.data.generate_uberon_structures |
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I would really prefer to avoid breeding scripts which are
- lacking somewhat regular CI testing
- hidden from UI so forgotten etc
I think we should group those all under existing
❯ dandi service-scripts --help
Usage: dandi service-scripts [OPTIONS] COMMAND [ARGS]...
Various utility operations
Options:
--help Show this message and exit.
Commands:
publish-dandiset-version-doi
reextract-metadata Recompute & update the metadata for NWB...
update-dandiset-from-doi Update the metadata for the draft version...and setup some pytest marker for e.g. a weekly run even if only for smoke testing, but likely more for regression testing that it produces the same output as before (in case we carry it here), so we could ensure that code does not get rotten, and that output is deterministic (ordered etc).
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| m = re.match(r'synonym:\s+"(.+?)"\s+(EXACT|RELATED|NARROW|BROAD)', line) | ||
| if m: |
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I tend to instruct my AIs to do walrus for such... I guess we need to adjust DEVELOPMENT.md and/or .lad for that to be auto-picked up
Suggested change
| m = re.match(r'synonym:\s+"(.+?)"\s+(EXACT|RELATED|NARROW|BROAD)', line) | |
| if m: | |
| if (m := re.match(r'synonym:\s+"(.+?)"\s+(EXACT|RELATED|NARROW|BROAD)', line)): |
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| def main() -> None: # pragma: no cover | ||
| url = "http://purl.obolibrary.org/obo/uberon.obo" | ||
| print(f"Downloading {url} ...") |
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especially when moved into service command - use logging to gain logging control/archival etc
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| [{"id":"0000005","name":"chemosensory organ","synonyms":[["chemosensory sensory organ","E"]]},{"id":"0000007","name":"pituitary gland","synonyms":[["glandula pituitaria","E"],["Hp","B"],["hypophysis","R"],["hypophysis cerebri","R"],["pituitary","E"],["pituitary body","E"]]},{"id":"0000010","name":"peripheral nervous system","synonyms":[["pars peripherica","E"],["PNS","B"],["systema nervosum periphericum","E"]]},{"id":"0000012","name":"somatic nervous system","synonyms":[["PNS - somatic","E"],["somatic nervous system, somatic division","E"],["somatic part of peripheral nervous system","E"],["somatic peripheral nervous system","E"]]},{"id":"0000045","name":"ganglion","synonyms":[["ganglia","R"],["neural ganglion","R"]]},{"id":"0000052","name":"fornix of brain","synonyms":[["brain fornix","E"],["cerebral fornix","E"],["forebrain fornix","E"],["fornix","B"],["fornix (column and body of fornix)","R"],["fornix cerebri","R"],["fornix hippocampus","R"],["fornix of neuraxis","E"],["hippocampus fornix","R"],["neuraxis fornix","E"]]},{"id":"0000053","name":"macula lutea","synonyms":[["macula","R"],["macula flava retinae","R"],["macula retinae","R"],["maculae","R"]]},{"id":"0000073","name":"regional part of nervous system","synonyms":[["part of nervous system","E"]]},{"id":"0000120","name":"blood brain barrier","synonyms":[["BBB","R"],["blood-brain barrier","E"]]},{"id":"0000121","name":"perineurium"},{"id":"0000122","name":"neuron projection bundle","synonyms":[["funiculus","E"],["nerve fiber bundle","E"],["neural fiber bundle","E"]]},{"id":"0000123","name":"endoneurium"},{"id":"0000124","name":"epineurium"},{"id":"0000125","name":"neural nucleus","synonyms":[["nervous system nucleus","E"],["neuraxis nucleus","E"],["neuronal nucleus","E"],["nucleus","B"],["nucleus of CNS","E"],["nucleus of neuraxis","R"]]},{"id":"0000126","name":"cranial nerve nucleus","synonyms":[["cranial neural nucleus","E"],["nucleus nervi cranialis","R"],["nucleus of cranial nerve","E"]]},{"id":"0000127","name":"facial nucleus","synonyms":[["facial nerve nucleus","E"],["facial VII motor nucleus","R"],["facial VII nucleus","E"],["nucleus of facial nerve","E"]]},{"id":"0000128","name":"olivary body","synonyms":[["oliva","R"],["olivary nucleus","R"],["olive","R"],["olive body","E"]]},{"id":"0000200","name":"gyrus","synonyms":[["cerebral gyrus","E"],["folia","R"],["folium","R"],["folium of brain","R"],["gyri","R"],["gyri of cerebrum","R"],["gyrus of cerebral hemisphere","R"],["gyrus of cerebrum","R"],["gyrus of neuraxis","E"],["neuraxis gyrus","E"]]},{"id":"0000201","name":"endothelial blood brain barrier"},{"id":"0000202","name":"glial blood brain barrier"},{"id":"0000203","name":"pallium","synonyms":[["area dorsalis telencephali","E"],["dorsal part of telencephalon","E"],["dorsal telencephalic area","E"],["dorsal telencephalon","E"]]},{"id":"0000204","name":"ventral part of telencephalon","synonyms":[["area ventralis telencephali","E"],["subpallium","E"],["subpallium","N"],["ventral telencephalon","E"]]},{"id":"0000315","name":"subarachnoid space","synonyms":[["cavitas subarachnoidea","R"],["cavum subarachnoideale","R"],["spatium leptomeningeum","R"],["spatium subarachnoideum","R"],["subarachnoid cavity","R"],["subarachnoid space of central nervous system","E"],["subarachnoid space of CNS","E"],["subarachnoid space of neuraxis","E"]]},{"id":"0000345","name":"myelin"},{"id":"0000348","name":"ophthalmic nerve","synonyms":[["ciliary nerve","R"],["cranial nerve V, branch V1","E"],["ethmoidal nerve","R"],["first branch of fifth cranial nerve","E"],["first division of fifth cranial nerve","E"],["first division of trigeminal nerve","E"],["nervus ophthalmicus (V1)","E"],["nervus ophthalmicus (Va)","E"],["nervus ophthalmicus [v1]","E"],["nervus ophthalmicus [va]","E"],["ophthalmic division","R"],["ophthalmic division [V1]","E"],["ophthalmic division [Va]","E"],["ophthalmic division of fifth cranial nerve","E"],["ophthalmic division of trigeminal nerve (V1)","E"],["ophthalmic division of trigeminal nerve (Va)","E"],["ophthalmic nerve [V1]","E"],["ophthalmic nerve [Va]","E"],["opthalmic nerve","E"],["profundal nerve","R"],["profundus","R"],["profundus nerve","R"],["ramus opthalmicus profundus (ramus V1)","E"],["rostral branch of trigeminal nerve","E"],["trigeminal nerve ophthalmic division","R"],["trigeminal V nerve ophthalmic division","E"]]},{"id":"0000349","name":"limbic system","synonyms":[["visceral brain","R"]]},{"id":"0000369","name":"corpus striatum","synonyms":[["striate body","R"],["striated body","R"]]},{"id":"0000373","name":"tapetum of corpus callosum","synonyms":[["tapetum","B"],["tapetum corporis callosi","R"]]},{"id":"0000375","name":"mandibular nerve","synonyms":[["inferior maxillary nerve","E"],["mandibular division [V3]","E"],["mandibular division [Vc]","E"],["mandibular division of fifth cranial nerve","E"],["mandibular division of trigeminal nerve [Vc; V3]","E"],["mandibular nerve [V3]","E"],["mandibular nerve [Vc]","E"],["n. mandibularis","R"],["nervus mandibularis","R"],["nervus mandibularis [v3]","E"],["nervus mandibularis [Vc; V3]","E"],["nervus mandibularis [vc]","E"],["ramus mandibularis (ramus V3)","E"],["third division of fifth cranial nerve","E"],["third division of trigeminal nerve","E"],["trigeminal nerve mandibular division","R"],["trigeminal V nerve mandibular division","E"]]},{"id":"0000377","name":"maxillary nerve","synonyms":[["maxillary division [V2]","E"],["maxillary division [Vb]","E"],["maxillary division of fifth cranial nerve","E"],["maxillary division of trigeminal nerve (Vb; V2)","E"],["maxillary nerve [V2]","E"],["maxillary nerve [Vb]","E"],["n. maxillaris","R"],["nervus maxillaris","R"],["nervus maxillaris (Vb; V2)","E"],["nervus maxillaris [v2]","E"],["nervus maxillaris [vb]","E"],["ramus maxillaris (ramus V2)","E"],["second division of fifth cranial nerve","E"],["second division of trigeminal nerve","E"],["trigeminal nerve maxillary division","R"],["trigeminal V nerve maxillary division","E"]]},{"id":"0000391","name":"leptomeninx","synonyms":[["arachnoid mater and pia mater","R"],["arachnoidea mater et pia mater","R"],["leptomeninges","E"],["pia-arachnoid","R"],["pia-arachnoid of neuraxis","R"]]},{"id":"0000395","name":"cochlear ganglion","synonyms":[["cochlear part of vestibulocochlear ganglion","E"],["Corti's ganglion","E"],["ganglion cochlearis","R"],["ganglion of Corti","E"],["ganglion spirale","R"],["ganglion spirale cochleae","R"],["spiral ganglion","E"],["spiral ganglion of cochlea","R"],["vestibulocochlear ganglion cochlear component","R"],["vestibulocochlear VIII ganglion cochlear component","E"]]},{"id":"0000408","name":"vertebral ganglion","synonyms":[["intermediate ganglion","E"]]},{"id":"0000411","name":"visual cortex","synonyms":[["higher-order visual cortex","R"],["visual areas","R"]]},{"id":"0000416","name":"subdural space","synonyms":[["cavum subdurale","R"],["spatium subdurale","R"],["subdural cavity","R"],["subdural cleavage","R"],["subdural cleft","R"]]},{"id":"0000429","name":"enteric plexus","synonyms":[["enteric nerve plexus","E"],["intrinsic nerve plexus","E"],["plexus entericus","E"],["plexus nervosus entericus","E"],["sympathetic enteric nerve plexus","E"]]},{"id":"0000430","name":"ventral intermediate nucleus of thalamus","synonyms":[["intermediate thalamic nuclei","R"],["intermediate thalamic nucleus","R"],["nucleus ventralis intermedius thalami","R"]]},{"id":"0000432","name":"endopeduncular nucleus","synonyms":[["entopeduncular nucleus","R"],["nucleus endopeduncularis","R"],["nucleus entopeduncularis","R"]]},{"id":"0000433","name":"posterior paraventricular nucleus of thalamus","synonyms":[["caecal epithelium","R"],["dorsal paraventricular nucleus of thalamus","E"],["nucleus paraventricularis posterior thalami","R"],["posterior paraventricular nuclei","R"],["posterior paraventricular nucleus of thalamus","R"],["posterior paraventricular nucleus of the thalamus","R"]]},{"id":"0000434","name":"anterior paraventricular nucleus of thalamus","synonyms":[["anterior paraventricular nuclei","R"],["anterior paraventricular nucleus","E"],["anterior paraventricular nucleus of thalamus","R"],["anterior paraventricular nucleus of the thalamus","R"],["anterior periventricular nucleus of the hypothalamus","R"],["nucleus paraventricularis anterior thalami","R"],["periventricular hypothalamic nucleus, anterior part","R"],["ventral paraventricular nucleus of thalamus","E"]]},{"id":"0000435","name":"lateral tuberal nucleus","synonyms":[["lateral tuberal hypothalamic nuclei","E"],["lateral tuberal nuclear complex","E"],["lateral tuberal nuclei","E"],["LTu","B"],["nuclei tuberales laterales","R"],["nucleus tuberis","R"],["nucleus tuberis hypothalami","R"],["nucleus tuberis lateralis","R"]]},{"id":"0000439","name":"arachnoid trabecula","synonyms":[["arachnoid trabeculae","R"],["trabecula arachnoideum","R"]]},{"id":"0000445","name":"habenular trigone","synonyms":[["trigone of habenulae","R"],["trigonum habenulae","R"]]},{"id":"0000446","name":"septum of telencephalon","synonyms":[["area septalis","E"],["massa praecommissuralis","R"],["Se","B"],["septal area","E"],["septal region","R"],["septum","B"],["septum (NN)","E"],["septum pellucidum (BNA,PNA)","R"],["septum telencephali","R"],["telencephalon septum","E"]]},{"id":"0000451","name":"prefrontal cortex","synonyms":[["frontal association cortex","R"],["prefrontal association complex","R"],["prefrontal association cortex","E"]]},{"id":"0000454","name":"cerebral subcortex","synonyms":[["cerebral medulla","E"],["subcortex","R"]]},{"id":"0000908","name":"hippocampal commissure","synonyms":[["commissura hippocampi","E"],["commissure of fornix","R"],["commissure of fornix of forebrain","E"],["commissure of the fornix","R"],["delta fornicis","E"],["dorsal hippocampal commissure","E"],["fornical commissure","E"],["fornix commissure","E"],["hippocampal commissures","R"],["hippocampus commissure","E"]]},{"id":"0000929","name":"pharyngeal branch of vagus nerve","synonyms":[["pharyngeal branch","E"],["pharyngeal branch of inferior vagal ganglion","E"],["pharyngeal branch of vagus","E"],["ramus pharyngealis nervi vagalis","E"],["ramus pharyngeus","E"],["ramus pharyngeus nervi vagi","R"],["tenth cranial nerve pharyngeal branch","E"],["vagal pharyngeal branch","E"],["vagus nerve pharyngeal branch","E"]]},{"id":"0000934","name":"ventral nerve cord","synonyms":[["ventral cord","E"]]},{"id":"0000936","name":"posterior commissure","synonyms":[["caudal commissure","E"],["commissura epithalami","R"],["commissura epithalamica","R"],["commissura posterior","R"],["epithalamic commissure","E"],["posterior commissure (Lieutaud)","R"]]},{"id":"0000941","name":"cranial nerve II","synonyms":[["02 optic nerve","E"],["2n","B"],["CN-II","R"],["cranial II","E"],["nerve II","R"],["nervus opticus","E"],["nervus opticus [II]","E"],["optic","R"],["optic II","E"],["optic II nerve","E"],["optic nerve","B"],["optic nerve [II]","E"],["second cranial nerve","E"]]},{"id":"0000942","name":"frontal nerve (branch of ophthalmic)","synonyms":[["frontal nerve","E"],["nervus frontalis","R"]]},{"id":"0000955","name":"brain","synonyms":[["encephalon","R"],["suprasegmental levels of nervous system","R"],["suprasegmental structures","R"],["synganglion","R"],["the brain","R"]]},{"id":"0000956","name":"cerebral cortex","synonyms":[["brain cortex","R"],["cortex cerebralis","R"],["cortex cerebri","R"],["cortex of cerebral hemisphere","E"],["cortical plate (areas)","R"],["cortical plate (CTXpl)","R"],["pallium of the brain","R"]]},{"id":"0000959","name":"optic chiasma","synonyms":[["chiasma","R"],["chiasma nervorum opticorum","R"],["chiasma opticum","E"],["decussation of optic nerve fibers","E"],["optic chiasm","E"],["optic chiasm (Rufus of Ephesus)","R"]]},{"id":"0000961","name":"thoracic ganglion","synonyms":[["ganglion of thorax","E"],["ganglion thoracicum splanchnicum","E"],["thoracic paravertebral ganglion","E"],["thoracic splanchnic ganglion","E"],["thoracic sympathetic ganglion","E"],["thorax ganglion","E"]]},{"id":"0000962","name":"nerve of cervical vertebra","synonyms":[["cervical nerve","E"],["cervical nerve tree","E"],["cervical spinal nerve","E"],["nervus cervicalis","E"]]},{"id":"0000963","name":"head sensillum"},{"id":"0000966","name":"retina","synonyms":[["inner layer of eyeball","E"],["Netzhaut","R"],["retina of camera-type eye","E"],["retinas","R"],["tunica interna of eyeball","E"]]},{"id":"0000971","name":"ommatidium","synonyms":[["omatidia","R"],["omatidium","E"]]},{"id":"0000988","name":"pons","synonyms":[["pons cerebri","R"],["pons of Varolius","E"],["pons Varolii","E"]]},{"id":"0001016","name":"nervous system","synonyms":[["nerve net","N"],["neurological system","E"],["systema nervosum","R"]]},{"id":"0001017","name":"central nervous system","synonyms":[["cerebrospinal axis","N"],["CNS","E"],["neuraxis","R"],["systema nervosum centrale","E"]]},{"id":"0001018","name":"axon tract","synonyms":[["axonal tract","E"],["nerve tract","N"],["nerve tract","R"],["neuraxis tract","E"],["tract","R"],["tract of neuraxis","E"]]},{"id":"0001019","name":"nerve fasciculus","synonyms":[["fascicle","B"],["fasciculus","E"],["nerve bundle","E"],["nerve fasciculus","E"],["nerve fiber tract","R"],["neural fasciculus","E"]]},{"id":"0001020","name":"nervous system commissure","synonyms":[["commissure","B"],["commissure of neuraxis","E"],["neuraxis commissure","E"],["white matter commissure","N"]]},{"id":"0001021","name":"nerve","synonyms":[["nerves","E"],["neural subtree","R"],["peripheral nerve","E"]]},{"id":"0001027","name":"sensory nerve","synonyms":[["afferent nerve","R"],["nervus sensorius","E"]]},{"id":"0001031","name":"sheath of Schwann","synonyms":[["endoneural membrane","R"],["neurilemma","E"],["neurolemma","E"],["Schwann's membrane","R"],["sheath of Schwann","E"]]},{"id":"0001047","name":"neural glomerulus","synonyms":[["glomerulus","B"]]},{"id":"0001058","name":"mushroom body","synonyms":[["corpora pedunculata","R"],["mushroom bodies","E"]]},{"id":"0001059","name":"pars intercerebralis"},{"id":"0001063","name":"flocculus","synonyms":[["flocculus of cerebellum","E"],["H X","R"],["hemispheric lobule X","R"],["lobule H X of Larsell","R"],["lobule X","R"],["lobule X of hemisphere of cerebellum","R"],["neuraxis flocculus","E"]]},{"id":"0001148","name":"median nerve","synonyms":[["nervus medianus","R"]]},{"id":"0001267","name":"femoral nerve","synonyms":[["anterior crural nerve","E"],["nervus femoralis","R"]]},{"id":"0001322","name":"sciatic nerve","synonyms":[["ischiadic nerve","R"],["ischiatic nerve","R"],["nervus ischiadicus","R"],["nervus sciaticus","R"]]},{"id":"0001323","name":"tibial nerve","synonyms":[["medial popliteal nerve","E"],["n. tibialis","R"]]},{"id":"0001324","name":"common fibular nerve","synonyms":[["common peroneal nerve","E"],["extrernal peroneal nerve","E"],["lateral popliteal nerve","E"],["n. fibularis communis","R"],["n. peroneus communis","R"],["nervus fibularis communis","R"],["nervus peroneus communis","E"]]},{"id":"0001384","name":"primary motor cortex","synonyms":[["excitable area","R"],["gyrus precentralis","R"],["motor area","R"],["motor cortex","E"],["prefrontal gyrus","R"],["primary motor area","R"],["Rolando's area","R"],["somatic motor areas","R"],["somatomotor areas","R"]]},{"id":"0001393","name":"auditory cortex","synonyms":[["A1 (primary auditory cortex)","R"],["anterior transverse temporal area 41","R"],["auditory area","R"],["auditory areas","R"],["auditory cortex","R"],["BA41","R"],["BA42","R"],["Brodmann area 41","R"],["Brodmann area 41 & 42","R"],["Brodmann area 42","R"],["posterior transverse temporal area 42","R"],["primary auditory cortex","R"],["temporal auditory neocortex","R"]]},{"id":"0001492","name":"radial nerve","synonyms":[["nervus radialis","R"]]},{"id":"0001493","name":"axillary nerve","synonyms":[["auxillery nerve","R"],["circumflex humeral nerve","E"],["circumflex nerve","R"],["nervus axillaris","R"]]},{"id":"0001494","name":"ulnar nerve","synonyms":[["nervus ulnaris","R"]]},{"id":"0001579","name":"olfactory nerve","synonyms":[["1n","B"],["CN-I","R"],["cranial nerve I","R"],["fila olfactoria","R"],["first cranial nerve","E"],["nerve I","R"],["nerve of smell","R"],["nervus olfactorius","R"],["nervus olfactorius [i]","E"],["olfactoria fila","R"],["olfactory fila","R"],["olfactory I","E"],["olfactory i nerve","E"],["olfactory nerve [I]","E"]]},{"id":"0001620","name":"central retinal artery","synonyms":[["arteria centralis retinae","R"],["central artery of retina","E"],["central artery of the retina","R"],["retinal artery","E"],["Zinn's artery","E"]]},{"id":"0001629","name":"carotid body","synonyms":[["carotid glomus","E"],["glomus caroticum","E"]]},{"id":"0001641","name":"transverse sinus","synonyms":[["groove for right and left transverse sinuses","R"],["lateral sinus","R"],["sinus transversus","R"],["sinus transversus durae matris","E"],["transverse sinus","R"],["transverse sinus vein","R"]]},{"id":"0001643","name":"oculomotor nerve","synonyms":[["3n","B"],["CN-III","R"],["cranial nerve III","R"],["nerve III","R"],["nervus oculomotorius","E"],["nervus oculomotorius [III]","E"],["occulomotor","R"],["oculomotor III","E"],["oculomotor III nerve","E"],["oculomotor nerve [III]","E"],["oculomotor nerve or its root","R"],["oculomotor nerve tree","E"],["third cranial nerve","E"]]},{"id":"0001644","name":"trochlear nerve","synonyms":[["4n","B"],["CN-IV","R"],["cranial nerve IV","E"],["fourth cranial nerve","E"],["nerve IV","R"],["nervus trochlearis","R"],["nervus trochlearis [IV]","E"],["pathetic nerve","R"],["superior oblique nerve","E"],["trochlear","R"],["trochlear IV nerve","E"],["trochlear nerve [IV]","E"],["trochlear nerve or its root","R"],["trochlear nerve tree","E"],["trochlear nerve/root","R"]]},{"id":"0001645","name":"trigeminal nerve","synonyms":[["5n","B"],["CN-V","R"],["cranial nerve V","R"],["fifth cranial nerve","E"],["nerve V","R"],["nervus trigeminus","E"],["nervus trigeminus","R"],["nervus trigeminus [v]","E"],["trigeminal nerve [V]","E"],["trigeminal nerve tree","E"],["trigeminal V","E"],["trigeminal v nerve","E"],["trigeminus","R"]]},{"id":"0001646","name":"abducens nerve","synonyms":[["6n","B"],["abducens nerve [VI]","E"],["abducens nerve tree","E"],["abducens nerve/root","R"],["abducens VI nerve","E"],["abducent nerve","R"],["abducent nerve [VI]","E"],["abducents VI nerve","R"],["CN-VI","R"],["cranial nerve VI","R"],["lateral rectus nerve","E"],["nerve VI","R"],["nervus abducens","E"],["nervus abducens","R"],["nervus abducens [VI]","E"],["sixth cranial nerve","E"]]},{"id":"0001647","name":"facial nerve","synonyms":[["7n","B"],["branchiomeric cranial nerve","E"],["CN-VII","R"],["cranial nerve VII","R"],["face nerve","E"],["facial nerve 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lateralis","E"]]},{"id":"0002637","name":"ventral anterior nucleus of thalamus","synonyms":[["nucleus lateropolaris","E"],["nucleus ventralis anterior","E"],["nucleus ventralis anterior thalami","E"],["nucleus ventralis anterior thalami","R"],["nucleus ventralis thalami anterior","E"],["VA","B"],["ventral anterior nucleus","E"],["ventral anterior nucleus of thalamus","E"],["ventral anterior nucleus of the thalamus","R"],["ventral anterior thalamic nucleus","E"],["ventroanterior nucleus of the thalamus","E"],["ventroanterior thalamic nucleus","E"]]},{"id":"0002638","name":"medial pulvinar nucleus","synonyms":[["MPul","B"],["nucleus pulvinaris medialis","E"],["nucleus pulvinaris medialis thalami","E"],["nucleus pulvinaris thalami, pars medialis","E"]]},{"id":"0002639","name":"midbrain reticular formation","synonyms":[["formatio reticularis mesencephali","R"],["formatio reticularis tegmentalis","R"],["formatio reticularis tegmenti mesencephali","R"],["MBRF","B"],["reticular formation of 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lemnisci","E"],["decussation of the medial lemniscus","R"],["medial lemniscus decussation","E"],["medullary sensory decussation","E"],["sensory decussation","E"]]},{"id":"0002644","name":"intermediate orbital gyrus"},{"id":"0002645","name":"densocellular part of medial dorsal nucleus","synonyms":[["densocellular part of the medial dorsal nucleus","R"],["MDD","B"],["nucleus medialis dorsalis paralamellaris (Hassler)","E"],["nucleus medialis dorsalis, pars densocellularis","E"]]},{"id":"0002646","name":"dorsal longitudinal fasciculus of medulla","synonyms":[["bundle of Schutz of medulla","E"],["dorsal longitudinal fasciculus of the medulla","R"],["fasciculus longitudinalis dorsalis (myelencephali)","R"],["fasciculus of Schutz of medulla","E"],["medulla bundle of Schutz","E"],["medulla dorsal longitudinal fasciculus","E"],["medulla fasciculus of Schutz","E"],["medulla posterior longitudinal fasciculus","E"],["posterior longitudinal fasciculus of 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lateralis","R"],["ventriculus lateralis, corpus","E"],["ventriculus lateralis, pars centralis","E"]]},{"id":"0002656","name":"periamygdaloid area","synonyms":[["cortical amygdaloid nucleus","R"],["gyrus semilunaris","R"],["para-amygdaloid cortex","R"],["periamygdalar area","R"],["periamygdaloid area","E"],["periamygdaloid cortex","R"],["periamygdaloid region","E"],["periamygdaloid region","R"],["posterior amygdalar nucleus","R"],["posterior nucleus of the amygdala","R"],["regio periamygdalaris","R"],["semilunar gyrus","E"],["semilunar gyrus","R"],["ventral cortical nucleus of amygdala","E"],["ventral cortical nucleus of amygdala","R"]]},{"id":"0002657","name":"posterior parahippocampal gyrus","synonyms":[["gyrus parahippocampalis, pars posterior","R"],["parahippocampal gyrus (amaral)","E"],["parahippocampal gyrus (insausti)","E"],["parahippocampal gyrus, posterior division","R"],["pHp","B"]]},{"id":"0002659","name":"superior medullary velum","synonyms":[["anterior medullary 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cerebri","E"],["ramus anterior sulcus lateralis","R"],["ramus horizontalis fissurae sylvii","R"],["sulcus lateralis, ramus anterior","R"]]},{"id":"0002670","name":"anterior ascending limb of lateral sulcus","synonyms":[["anterior ascending limb of lateral fissure","E"],["anterior ascending limb of the lateral fissure","R"],["anterior ascending ramus of lateral sulcus","E"],["ascending branch of lateral sulcus","E"],["ascending ramus of lateral cerebral sulcus","E"],["ascending ramus of sylvian fissure","E"],["middle ramus of lateral fissure","E"],["ramus anterior ascendens fissurae lateralis","R"],["ramus ascendens sulci cerebri lateralis (Sylvii)","R"],["ramus ascendens sulci lateralis cerebri","E"],["ramus ascendens sulcus lateralis","R"],["ramus verticalis fissurae sylvii","R"],["sulcus lateralis, ramus ascendens","R"],["superior branch of lateral fissure","E"]]},{"id":"0002671","name":"pallidotegmental fasciculus","synonyms":[["fasciculus pallido-tegmentalis","R"],["fibrae 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anterodorsalis of thalamus","R"],["nucleus anterodorsalis thalami","E"],["nucleus anterosuperior","E"],["nucleus thalamicus anterodorsalis","E"]]},{"id":"0002681","name":"anteromedial nucleus of thalamus","synonyms":[["AM","B"],["anteromedial nucleus","E"],["anteromedial nucleus of the thalamus","E"],["anteromedial thalamic nucleus","E"],["nucleus anterior medialis","E"],["nucleus anterior medialis thalami","E"],["nucleus anterior thalami medialis","E"],["nucleus anteromedialis","B"],["nucleus anteromedialis (hassler)","E"],["nucleus anteromedialis thalami","E"],["nucleus thalamicus anteromedialis","E"]]},{"id":"0002682","name":"abducens nucleus","synonyms":[["abducens motor nuclei","E"],["abducens motor nucleus","E"],["abducens nerve nucleus","E"],["abducens nucleus proper","R"],["abducens VI nucleus","E"],["abducent nucleus","E"],["motor nucleus VI","E"],["nucleus abducens","R"],["nucleus nervi abducentis","E"],["nucleus nervi abducentis","R"],["nucleus of abducens nerve","E"],["nucleus of abducens nerve (VI)","E"],["nVI","E"],["sixth cranial nerve nucleus","E"]]},{"id":"0002683","name":"rhinal sulcus","synonyms":[["fissura rhinalis","E"],["fissura rhinalis","R"],["rhinal fissuer (Turner, Rezius)","E"],["rhinal fissure","E"],["rhinal fissure (Turner, Rezius)","R"],["RHS","B"],["sulcus rhinalis","E"],["sulcus rhinalis","R"]]},{"id":"0002684","name":"nucleus raphe obscurus","synonyms":[["nucleus raphC) obscurus","R"],["nucleus raphes obscurus","E"],["nucleus raphes obscurus","R"],["obscurus raphe nucleus","E"],["raphe obscurus nucleus","E"]]},{"id":"0002685","name":"anteroventral nucleus of thalamus","synonyms":[["anterior ventral nucleus of thalamus","E"],["anteroprincipal thalamic nucleus","E"],["anteroventral nucleus","E"],["anteroventral nucleus of thalamus","E"],["anteroventral nucleus of the thalamus","E"],["anteroventral thalamic nucleus","E"],["AV","B"],["nucleus anterior principalis (Hassler)","R"],["nucleus anterior thalami ventralis","E"],["nucleus anterior ventralis","E"],["nucleus anteroinferior","E"],["nucleus anteroventralis","E"],["nucleus anteroventralis thalami","E"],["nucleus thalamicus anteroprincipalis","E"],["nucleus thalamicus anteroventralis","E"],["ventral anterior nucleus of the thalamus","R"],["ventroanterior nucleus","R"]]},{"id":"0002686","name":"angular gyrus","synonyms":[["gyrus angularis","R"],["gyrus parietalis inferior","R"],["middle part of inferior parietal lobule","E"],["prelunate gyrus","R"],["preoccipital gyrus","E"]]},{"id":"0002687","name":"area X of ventral lateral nucleus","synonyms":[["anteromedial part of ventral lateral posterior nucleus (jones)","E"],["area X","E"],["area X of Olszewski","E"],["nucleus lateralis intermedius mediodorsalis situs ventralis medialis","E"],["nucleus ventralis oralis, pars posterior (dewulf)","E"],["nucleus ventro-oralis internus (Hassler)","R"],["nucleus ventrooralis internus (hassler)","E"],["nucleus ventrooralis internus, superior part","E"],["X","B"]]},{"id":"0002688","name":"supramarginal gyrus","synonyms":[["anterior part of inferior parietal lobule","E"],["BA40","R"],["Brodmann area 40","R"],["gyrus supramarginalis","R"],["inferior parietal lobule (krieg)","E"]]},{"id":"0002690","name":"anteroventral periventricular nucleus","synonyms":[["anterior ventral periventricular nucleus of hypothalamus","R"],["anteroventral periventricular nucleus of the hypothalamus","R"],["AVPe","B"],["nucleus periventricularis anteroventralis","R"],["ventral periventricular hypothalamic nucleus","R"]]},{"id":"0002691","name":"ventral tegmental area","synonyms":[["a10a","E"],["area tegmentalis ventralis","R"],["area tegmentalis ventralis (Tsai)","R"],["tegmentum ventrale","R"],["ventral brain stem","R"],["ventral tegmental area (Tsai)","R"],["ventral tegmental area of tsai","E"],["ventral tegmental nucleus (Rioch)","R"],["ventral tegmental nucleus (tsai)","E"],["ventral tegmental nucleus of tsai","E"],["ventromedial mesencephalic tegmentum","R"],["VTA","B"]]},{"id":"0002692","name":"medullary raphe nuclear complex","synonyms":[["nuclei raphe (myelencephali)","R"],["raphe medullae oblongatae","E"],["raphe nuclei of medulla","E"],["raphe nuclei of the medulla","R"],["raphe of medulla oblongata","E"]]},{"id":"0002696","name":"cuneiform nucleus","synonyms":[["area parabigeminalis (Mai)","R"],["CnF","B"],["cuneiform nucleus (Castaldi)","R"],["cunieform nucleus","E"],["nucleus cuneiformis","R"],["parabigeminal area (mai)","E"]]},{"id":"0002697","name":"dorsal supraoptic decussation","synonyms":[["commissura supraoptica dorsalis","E"],["commissura supraoptica dorsalis pars ventralis (Meynert)","R"],["commissure of Meynert","E"],["dorsal supra-optic commissure","E"],["dorsal supraoptic commissure","E"],["dorsal supraoptic commissure (of ganser)","E"],["dorsal supraoptic decussation (of ganser)","E"],["dorsal supraoptic decussation (of Meynert)","E"],["dorsal supraoptic decussation of 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thalami","R"],["nucleus thalamicus mediodorsalis","R"]]},{"id":"0002740","name":"posterior cingulate gyrus","synonyms":[["cGp","B"],["gyrus cinguli posterior","R"],["gyrus limbicus posterior","R"],["PCgG","B"],["posterior cingulate","R"]]},{"id":"0002741","name":"diagonal band of Broca","synonyms":[["band of Broca","R"],["bandaletta diagonalis (Broca)","R"],["bandeletta diagonalis","R"],["broca's diagonal band","E"],["broca's diagonal gyrus","E"],["diagonal band","E"],["diagonal band of Broca","E"],["diagonal band(Broca)","R"],["diagonal gyrus","E"],["fasciculus diagonalis Brocae","R"],["fasciculus olfactorius","R"],["fasciculus olfactorius (hippocampi)","R"],["fasciculus olfactorius cornu Ammonis","R"],["fasciculus septo-amygdalicus","R"],["gyrus diagonalis","R"],["gyrus diagonalis rhinencephli","R"],["olfactory fasciculus","E"],["olfactory radiations of Zuckerkandl","E"],["stria diagonalis","R"],["stria diagonalis (Broca)","R"]]},{"id":"0002742","name":"lamina of septum 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magnocellularis corporis geniculati medialis","R"]]},{"id":"0002760","name":"ventral corticospinal tract","synonyms":[["anterior cerebrospinal fasciculus","R"],["anterior corticospinal tract","E"],["anterior corticospinal tract","R"],["anterior corticospinal tract of the medulla","R"],["anterior pyramidal tract","E"],["anterior tract of turck","E"],["bundle of Turck","E"],["bundle of Turck","R"],["column of Turck","E"],["corticospinal tract, uncrossed","E"],["corticospinal tract, uncrossed","R"],["direct corticospinal tract","R"],["medial corticospinal tract","R"],["tractus corticospinalis anterior","R"],["tractus corticospinalis ventralis","R"],["uncrossed corticospinal tract","R"],["ventral corticospinal tract","R"]]},{"id":"0002761","name":"inferior frontal sulcus","synonyms":[["IFRS","B"],["inferior frontal fissure","E"],["sulcus f2","E"],["sulcus frontalis inferior","R"],["sulcus frontalis secundus","R"]]},{"id":"0002762","name":"internal medullary lamina of 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sulcus","synonyms":[["IROS","B"],["sulcus rostralis inferior","E"]]},{"id":"0002768","name":"vestibulospinal tract","synonyms":[["tractus vestibulospinalis","R"],["vestibulo-spinal tract","E"],["vestibulo-spinal tracts","R"],["vestibulospinal pathway","R"],["vestibulospinal tracts","R"]]},{"id":"0002769","name":"superior temporal gyrus","synonyms":[["gyrus temporalis superior","E"],["gyrus temporalis superior","R"]]},{"id":"0002770","name":"posterior hypothalamic region","synonyms":[["hypothalamus posterior","R"],["mammillary level of hypothalamus","E"],["mammillary region","E"],["PHR","B"],["posterior hypothalamus","E"],["regio hypothalamica posterior","R"]]},{"id":"0002771","name":"middle temporal gyrus","synonyms":[["gyrus temporalis medius","E"],["inferior temporal gyrus (Seltzer)","R"],["intermediate temporal gyrus","E"],["medial temporal gyrus","R"],["middle (medial) temporal gyrus","R"]]},{"id":"0002772","name":"olfactory sulcus","synonyms":[["olfactory groove","E"],["OLFS","B"],["sulcus olfactorius","E"],["sulcus olfactorius lobi frontalis","R"]]},{"id":"0002773","name":"anterior transverse temporal gyrus","synonyms":[["anterior transverse convolution of heschl","E"],["anterior transverse temporal convolution of heschl","E"],["first transverse gyrus of Heschl","E"],["great transverse gyrus of Heschl","E"],["gyrus temporalis transversus anterior","R"],["gyrus temporalis transversus primus","R"]]},{"id":"0002774","name":"posterior transverse temporal gyrus","synonyms":[["gyrus temporalis transversus posterior","R"],["posterior transverse convolution of heschl","E"],["posterior transverse temporal convolution of heschl","E"]]},{"id":"0002776","name":"ventral nuclear group","synonyms":[["dorsal thalamus, ventral group","E"],["nuclei ventrales thalami","E"],["ventral dorsal thalamic nuclear group","R"],["ventral group of dorsal thalamus","E"],["ventral group of the dorsal thalamus","R"],["ventral nuclear group","E"],["ventral nuclear 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superior ganglionis vestibularis","E"],["pars superior vestibularis","R"],["vestibular ganglion superior part","E"]]},{"id":"0002826","name":"inferior part of vestibular ganglion","synonyms":[["pars inferior ganglionis vestibularis","E"],["vestibular ganglion inferior part","E"]]},{"id":"0002828","name":"ventral cochlear nucleus","synonyms":[["accessory cochlear nucleus","R"],["anterior cochlear nucleus","E"],["c1281209","E"],["nucleus acustici accessorici","R"],["nucleus cochlearis anterior","R"],["nucleus cochlearis ventralis","R"],["VCo","B"],["ventral cochlear nuclei","R"],["ventral cochlear nucleus","E"],["ventral coclear nucleus","R"],["ventral division of cochlear nucleus","R"]]},{"id":"0002829","name":"dorsal cochlear nucleus","synonyms":[["DCo","B"],["dorsal cochlear nucleus","E"],["dorsal coclear nucleus","R"],["dorsal division of cochlear nucleus","E"],["nucleus cochlearis dorsalis","R"],["nucleus cochlearis posterior","R"],["posterior cochlear nucleus","E"],["tuberculum 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medial part","R"],["arcuate nucleus-1","E"],["arcuate nucleus-2 of medulla","E"],["arcuate periventricular nucleus of medulla","E"],["infundibular hypothalamic nucleus of medulla","E"],["infundibular nucleus of medulla","E"],["infundibular periventricular nucleus of medulla","E"],["medial arcuate nucleus","E"],["medulla arcuate hypothalamic nucleus","E"],["medulla arcuate nucleus","E"],["medulla arcuate nucleus of hypothalamus","E"],["medulla arcuate nucleus-2","E"],["medulla arcuate periventricular nucleus","E"],["medulla infundibular hypothalamic nucleus","E"],["medulla infundibular nucleus","E"],["medulla infundibular periventricular nucleus","E"],["nuclei arcuati","R"],["nucleus arciformis pyramidalis","E"],["nucleus arcuatus myelencephali","R"],["nucleus arcuatus pyramidalis","R"]]},{"id":"0002866","name":"caudal part of spinal trigeminal nucleus","synonyms":[["caudal nucleus","E"],["caudal nucleus (kandell)","E"],["caudal part of the spinal trigeminal 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commisure","E"]]},{"id":"0002869","name":"diffuse reticular nucleus","synonyms":[["DRt","B"],["Koelliker-Fuse nucleus","E"],["Kolliker-Fuse nucleus","R"],["kolliker-Fuse nucleus","E"],["Kolliker-Fuse subnucleus","R"],["Kolloker-Fuse nucleus","E"],["kvlliker-Fuse subnucleus","R"],["kvlliker-Fuse subnucleus of parabrachial nucleus","R"],["K\u00f6lliker-Fuse nucleus","E"],["nucleus of Kolliker-Fuse","E"],["nucleus reticularis diffusus","R"],["nucleus reticularis diffusus (Koelliker)","R"],["nucleus subparabrachialis","E"],["subparabrachial nucleus","E"]]},{"id":"0002870","name":"dorsal motor nucleus of vagus nerve","synonyms":[["dorsal efferent nucleus of vagus","E"],["dorsal motor nucleus","R"],["dorsal motor nucleus of the vagus","R"],["dorsal motor nucleus of the vagus (vagal nucleus)","E"],["dorsal motor nucleus of the vagus nerve","R"],["dorsal motor nucleus of vagus","R"],["dorsal motor nucleus of vagus nerve","R"],["dorsal motor nucleus of vagus X nerve","E"],["dorsal motor vagal 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juxtasolitarius","E"],["PSol","B"]]},{"id":"0002879","name":"peritrigeminal nucleus","synonyms":[["nucleus peritrigeminalis","R"],["Pe5","B"]]},{"id":"0002880","name":"pontobulbar nucleus","synonyms":[["corpus pontobulbare","R"],["nucleus of circumolivary bundle","E"],["nucleus pontobulbaris","R"],["PnB","B"],["pontobulbar body","E"]]},{"id":"0002881","name":"sublingual nucleus","synonyms":[["inferior central nucleus","R"],["nucleus of roller","E"],["nucleus of roller","R"],["nucleus parvocellularis nervi hypoglossi","R"],["nucleus Roller","R"],["nucleus sublingualis","R"],["Roller's nucleus","E"],["SLg","B"]]},{"id":"0002882","name":"supraspinal nucleus","synonyms":[["nucleus substantiae grisea ventralis","R"],["nucleus substantiae griseae ventralis","R"],["nucleus supraspinalis","R"],["SSp","B"]]},{"id":"0002883","name":"central amygdaloid nucleus","synonyms":[["amygdala central nucleus","R"],["central amygdala","E"],["central amygdala","R"],["central amygdalar 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amygdalae","R"]]},{"id":"0002887","name":"basal amygdaloid nucleus","synonyms":[["basal nucleus of the amygdala","R"],["basolateral amygaloid nucleus","E"],["basolateral amygdalar nucleus","E"],["basolateral amygdaloid nucleus","E"],["basolateral nucleus (de olmos)","E"],["basolateral nucleus of amygdala","R"],["basolateral nucleus of the amygdala","R"],["intermediate principal nucleus","E"],["nucleus amygdalae basalis","R"],["nucleus amygdalae basalis lateralis","E"],["nucleus amygdaloideus basalis","R"],["nucleus amygdaloideus basolateralis","R"],["nucleus basalis amygdalae","R"]]},{"id":"0002888","name":"lateral part of basal amygdaloid nucleus","synonyms":[["lateral basal nucleus of amygdala","E"],["lateral basal nucleus of the amygdala","E"],["lateral division of basal nucleus","E"],["lateral division of the basal nucleus","E"],["lateral part of the basal amygdalar nucleus","R"],["lateral part of the basolateral nucleus","R"],["nucleus amygdalae basalis, pars 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part","E"],["VLO","B"]]},{"id":"0002979","name":"Purkinje cell layer of cerebellar cortex","synonyms":[["cerebellar Purkinje cell layer","E"],["cerebellum Purkinje cell layer","E"],["cerebellum Purkinje layer","E"],["nuclei reticulares (thalami)","R"],["nucleus reticularis","R"],["nucleus reticulatus (thalami)","R"],["nucleus thalamicus reticularis","R"],["Purkinje cell layer","E"],["reticular nucleus thalamus (Arnold)","R"],["reticulatum thalami (Hassler)","R"]]},{"id":"0002981","name":"pulvinar nucleus","synonyms":[["nuclei pulvinares","E"],["nucleus pulvinaris","R"],["nucleus pulvinaris thalami","R"],["posterior nucleus (P)","R"],["Pul","B"],["pulvinar","E"],["pulvinar nuclei","E"],["pulvinar thalami","E"],["pulvinar thalamus","R"]]},{"id":"0002982","name":"inferior pulvinar nucleus","synonyms":[["IPul","B"],["nucleus pulvinaris inferior","E"],["nucleus pulvinaris inferior thalami","E"],["nucleus pulvinaris thalami, pars inferior","E"]]},{"id":"0002983","name":"lateral posterior 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part","E"],["laterodorsal thalamic nucleus","E"],["LD","B"],["nucleus dorsalis lateralis thalami","E"],["nucleus dorsalis superficialis (Hassler)","E"],["nucleus dorsolateralis thalami","E"],["nucleus lateralis dorsalis","E"],["nucleus lateralis dorsalis of thalamus","E"],["nucleus lateralis dorsalis thalami","E"],["nucleus lateralis thalami dorsalis","E"]]},{"id":"0002985","name":"ventral nucleus of medial geniculate body","synonyms":[["medial geniculate complex ventral part","R"],["medial geniculate complex, ventral part","E"],["medial geniculate nucleus ventral part","R"],["medial geniculate nucleus, ventral part","E"],["medial nucleus of medial geniculate complex","E"],["MGV","B"],["nucleus corporis geniculati medialis, pars ventralis","E"],["nucleus geniculatus medialis fasciculosis (Hassler)","E"],["nucleus geniculatus medialis fasciculosus (Hassler)","E"],["nucleus geniculatus medialis pars ventralis","E"],["nucleus ventralis corporis geniculati medialis","E"],["ventral 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of the thalamus","R"],["paratenial thalamic nucleus","E"],["PT","B"]]},{"id":"0002995","name":"substantia nigra pars lateralis","synonyms":[["internal capsule (Burdach)","R"],["lateral part of substantia nigra","E"],["pars lateralis","E"],["pars lateralis substantiae nigrae","E"],["substantia nigra lateral part","R"],["substantia nigra, lateral division","R"],["substantia nigra, lateral part","E"],["substantia nigra, pars lateralis","R"]]},{"id":"0002996","name":"nucleus of optic tract","synonyms":[["large-celled nucleus of optic tract","E"],["lentiform nucleus of pretectal area","E"],["nucleus magnocellularis tractus optici","R"],["nucleus of the optic tract","E"],["nucleus tractus optici","R"],["optic tract nucleus","E"]]},{"id":"0002997","name":"nucleus of medial eminence","synonyms":[["medial eminence nucleus","E"],["nucleus eminentiae teretis","E"],["nucleus of eminentia teres","E"]]},{"id":"0002998","name":"inferior frontal gyrus","synonyms":[["gyrus F3","R"],["gyrus frontalis 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cerebral hemisphere of third ventricle","E"],["epithelium of choroid plexus of third ventricle","E"],["third ventricle chorioid plexus of cerebral hemisphere epithelial tissue","E"],["third ventricle chorioid plexus of cerebral hemisphere epithelium","E"],["third ventricle choroid plexus epithelial tissue","E"],["third ventricle epithelial tissue of chorioid plexus of cerebral hemisphere","E"],["third ventricle epithelial tissue of choroid plexus","E"],["third ventricle epithelium of chorioid plexus of cerebral hemisphere","E"],["third ventricle epithelium of choroid plexus","E"]]},{"id":"0004276","name":"fourth ventricle choroid plexus epithelium","synonyms":[["chorioid plexus of cerebral hemisphere epithelial tissue of fourth ventricle","E"],["chorioid plexus of cerebral hemisphere epithelium of fourth ventricle","E"],["choroid plexus epithelial tissue of fourth ventricle","E"],["choroid plexus epithelium of fourth ventricle","E"],["epithelial tissue of chorioid plexus of cerebral hemisphere of fourth ventricle","E"],["epithelial tissue of choroid plexus of fourth ventricle","E"],["epithelium of chorioid plexus of cerebral hemisphere of fourth ventricle","E"],["epithelium of choroid plexus of fourth ventricle","E"],["fourth ventricle chorioid plexus of cerebral hemisphere epithelial tissue","E"],["fourth ventricle chorioid plexus of cerebral hemisphere epithelium","E"],["fourth ventricle choroid plexus epithelial tissue","E"],["fourth ventricle epithelial tissue of chorioid plexus of cerebral hemisphere","E"],["fourth ventricle epithelial tissue of choroid plexus","E"],["fourth ventricle epithelium of chorioid plexus of cerebral hemisphere","E"],["fourth ventricle epithelium of choroid plexus","E"]]},{"id":"0004293","name":"parasympathetic nerve","synonyms":[["nerve of parasympathetic nervous system","E"]]},{"id":"0004295","name":"sympathetic nerve trunk","synonyms":[["nerve trunk of sympathetic nervous system","E"],["nerve trunk of sympathetic part of autonomic division of nervous system","E"],["sympathetic nervous system nerve trunk","E"]]},{"id":"0004545","name":"external capsule of telencephalon","synonyms":[["brain external capsule","B"],["capsula externa","R"],["corpus callosum external capsule","R"],["external capsule","B"]]},{"id":"0004642","name":"third ventricle ependyma","synonyms":[["3rd ventricle ependyma","E"],["ependyma of third ventricle","E"]]},{"id":"0004643","name":"lateral ventricle ependyma","synonyms":[["ependyma of lateral ventricle","E"]]},{"id":"0004644","name":"fourth ventricle ependyma","synonyms":[["4th ventricle ependyma","R"],["ependyma of fourth ventricle","E"]]},{"id":"0004668","name":"fourth ventricle aperture","synonyms":[["aperture of 4th ventricle","E"],["aperture of fourth ventricle","E"]]},{"id":"0004670","name":"ependyma","synonyms":[["ependyma of neuraxis","E"],["ependymal epithelium","E"],["lamina epithelialis","R"]]},{"id":"0004672","name":"posterior horn lateral ventricle","synonyms":[["cornu occipitale (ventriculi lateralis)","E"],["cornu occipitale ventriculi lateralis","E"],["cornu posterius (ventriculi lateralis)","E"],["cornu posterius ventriculi lateralis","E"],["occipital horn","E"],["occipital horn of lateral ventricle","E"],["posterior horn lateral ventricle","E"],["posterior horn of lateral ventricle","E"],["posterior horn of the lateral ventricle","E"],["ventriculus lateralis, cornu occipitale","E"],["ventriculus lateralis, cornu posterius","E"]]},{"id":"0004673","name":"trigeminal nerve root","synonyms":[["descending trigeminal root","R"],["radix descendens nervi trigemini","E"],["root of trigeminal nerve","E"],["root of trigeminal V nerve","E"],["trigeminal nerve root","E"],["trigeminal neural root","E"]]},{"id":"0004674","name":"facial nerve root","synonyms":[["central part of facial nerve","E"],["facial nerve fibers","E"],["facial nerve or its root","R"],["facial nerve root","E"],["facial nerve/root","R"],["facial neural root","E"],["fibrae nervi facialis","E"],["root of facial nerve","E"]]},{"id":"0004675","name":"hypoglossal nerve root","synonyms":[["central part of hypoglossal nerve","E"],["central part of hypoglossal nerve","R"],["fibrae nervi hypoglossi","E"],["hypoglossal nerve fiber bundle","E"],["hypoglossal nerve fibers","E"],["hypoglossal nerve fibers","R"],["hypoglossal nerve root","E"],["hypoglossal nerve tract","E"],["hypoglossal nerve/ root","R"],["root of hypoglossal nerve","E"],["root of hypoglossal nerve","R"]]},{"id":"0004676","name":"spinal cord lateral horn","synonyms":[["columna grisea intermedia medullare spinalis","E"],["cornu laterale medullae spinalis","R"],["intermediate gray column of spinal cord","E"],["intermediate grey column of spinal cord","R"],["lateral gray column of spinal cord","E"],["lateral gray horn","E"],["lateral gray matter of spinal cord","E"],["lateral horn of spinal cord","E"],["spinal cord intermediate horn","E"],["spinal cord lateral horn","E"]]},{"id":"0004678","name":"apex of spinal cord dorsal horn","synonyms":[["apex columnae posterioris","E"],["apex cornu posterioris medullae spinalis","E"],["apex of dorsal gray column","E"],["apex of dorsal gray column of spinal cor | |||
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I believe in compression for storage etc... here I think it might be handy for humans and better diff's in the future -- even now for review to get better idea on what are we storing there -- please store indented etc.
pyproject.toml
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| [tool.codespell] | ||
| skip = "_version.py,due.py,versioneer.py,*.vcr.yaml,venv,venvs,pyproject.toml,allen_ccf_structures.json" | ||
| skip = "_version.py,due.py,versioneer.py,*.vcr.yaml,venv,venvs,pyproject.toml,allen_ccf_structures.json,uberon_brain_structures.json" |
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eventually we would need get back to that allen_ccf_structures.json to unify with what to be done here. but also I think we can just
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| skip = "_version.py,due.py,versioneer.py,*.vcr.yaml,venv,venvs,pyproject.toml,allen_ccf_structures.json,uberon_brain_structures.json" | |
| skip = "_version.py,due.py,versioneer.py,*.vcr.yaml,venv,venvs,pyproject.toml,*_structures.json" |
- Move UBERON generator to service-scripts CLI subcommand - Use logging instead of print in generator - Use walrus operators in generator and brain_areas.py - Pretty-print UBERON JSON (indent=1) for better diffs - Use glob patterns for codespell/pre-commit excludes - Exclude *_structures.json from large-file check Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Addressed all review feedback in e40872c:
Not yet addressed: weekly CI smoke test for the generator — happy to add a pytest marker for that if you'd like it in this PR. |
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develop the test itself here, and mark with a new (to be added) |
Adds a regression test that re-downloads the UBERON OBO file and verifies the generated output matches the committed JSON. Marked with data_regeneration and skipif_no_network for scheduled CI runs. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Added in 69a328e:
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Summary
frozenset[str]), defaulting to EXACT onlyNew files
dandi/data/generate_uberon_structures.py— downloads and parsesuberon.obo, extracts nervous system descendantsdandi/data/uberon_brain_structures.json— bundled lookup data (2,408 structures, 9,717 synonyms)Modified files
dandi/metadata/brain_areas.py— UBERON loading, lookup, and matching functions;locations_to_mouse_anatomy()with Allen→UBERON fallbackdandi/metadata/util.py—_extract_brain_anatomy()now handles all speciesdandi/tests/test_brain_areas.py— tests for UBERON matching, synonym scope control, and Allen/UBERON fallback.pre-commit-config.yaml,pyproject.toml— codespell exclusions for new JSONTest plan
🤖 Generated with Claude Code