From ed4ebe2137294ca8ba52ba6738da7280df3f7e48 Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Sun, 29 Mar 2026 11:37:03 -0400 Subject: [PATCH 1/5] feat: add UBERON brain anatomy matching for all species 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) --- .pre-commit-config.yaml | 2 +- dandi/data/generate_uberon_structures.py | 133 +++++++++++++++++ dandi/data/uberon_brain_structures.json | 1 + dandi/metadata/brain_areas.py | 173 +++++++++++++++++++++++ dandi/metadata/util.py | 17 ++- dandi/tests/test_brain_areas.py | 102 +++++++++++++ pyproject.toml | 2 +- 7 files changed, 423 insertions(+), 7 deletions(-) create mode 100644 dandi/data/generate_uberon_structures.py create mode 100644 dandi/data/uberon_brain_structures.json diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 13133dcd3..6a44e29d5 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -22,7 +22,7 @@ repos: rev: v2.4.1 hooks: - id: codespell - exclude: ^(dandi/_version\.py|dandi/due\.py|versioneer\.py|pyproject\.toml|dandi/data/allen_ccf_structures\.json)$ + exclude: ^(dandi/_version\.py|dandi/due\.py|versioneer\.py|pyproject\.toml|dandi/data/allen_ccf_structures\.json|dandi/data/uberon_brain_structures\.json)$ additional_dependencies: - tomli; python_version<'3.11' - repo: https://github.com/PyCQA/flake8 diff --git a/dandi/data/generate_uberon_structures.py b/dandi/data/generate_uberon_structures.py new file mode 100644 index 000000000..f4158c5eb --- /dev/null +++ b/dandi/data/generate_uberon_structures.py @@ -0,0 +1,133 @@ +#!/usr/bin/env python3 +"""Regenerate uberon_brain_structures.json from the UBERON OBO file. + +Run: python -m dandi.data.generate_uberon_structures + +Downloads the UBERON OBO file, parses it without any library dependency, +extracts brain/nervous system descendants, and writes a compact JSON file. +""" + +from __future__ import annotations + +from collections import defaultdict +import json +from pathlib import Path +import re + +import requests + +# Root terms whose descendants (via is_a and part_of) we collect. +_ROOT_IDS = frozenset({"UBERON:0001016", "UBERON:0000955"}) # nervous system, brain + + +def _parse_obo_terms(text: str) -> list[dict]: # pragma: no cover + """Parse [Term] stanzas from raw OBO text.""" + terms: list[dict] = [] + in_term = False + current: dict = {} + + for line in text.splitlines(): + line = line.strip() + if line == "[Term]": + if current.get("id"): + terms.append(current) + current = {"id": "", "name": "", "synonyms": [], "parents": []} + in_term = True + continue + if line.startswith("[") and line.endswith("]"): + # Another stanza type (e.g. [Typedef]) + if current.get("id"): + terms.append(current) + current = {} + in_term = False + continue + if not in_term: + continue + if not line or line.startswith("!"): + continue + + if line == "is_obsolete: true": + current["id"] = "" # mark for skipping + continue + if line.startswith("id: "): + current["id"] = line[4:] + elif line.startswith("name: "): + current["name"] = line[6:] + elif line.startswith("is_a: "): + parent_id = line[6:].split("!")[0].strip() + if parent_id.startswith("UBERON:"): + current["parents"].append(parent_id) + elif line.startswith("relationship: part_of "): + parent_id = line[len("relationship: part_of ") :].split("!")[0].strip() + if parent_id.startswith("UBERON:"): + current["parents"].append(parent_id) + elif line.startswith("synonym: "): + m = re.match(r'synonym:\s+"(.+?)"\s+(EXACT|RELATED|NARROW|BROAD)', line) + if m: + current["synonyms"].append({"text": m.group(1), "scope": m.group(2)}) + + if current.get("id"): + terms.append(current) + return terms + + +def _collect_descendants( + terms: list[dict], root_ids: frozenset[str] +) -> set[str]: # pragma: no cover + """BFS from root_ids through children (reverse of is_a/part_of) edges.""" + children: dict[str, list[str]] = defaultdict(list) + for t in terms: + for parent in t["parents"]: + children[parent].append(t["id"]) + + visited: set[str] = set() + queue = list(root_ids) + while queue: + node = queue.pop() + if node in visited: + continue + visited.add(node) + queue.extend(children.get(node, [])) + return visited + + +def main() -> None: # pragma: no cover + url = "http://purl.obolibrary.org/obo/uberon.obo" + print(f"Downloading {url} ...") + resp = requests.get(url, timeout=120) + resp.raise_for_status() + print(f"Downloaded {len(resp.text)} bytes, parsing ...") + + all_terms = _parse_obo_terms(resp.text) + print(f"Parsed {len(all_terms)} terms") + + # Filter to UBERON terms only (skip cross-ontology references) + uberon_terms = [t for t in all_terms if t["id"].startswith("UBERON:")] + print(f"UBERON terms: {len(uberon_terms)}") + + descendant_ids = _collect_descendants(uberon_terms, _ROOT_IDS) + print(f"Nervous system descendants (including roots): {len(descendant_ids)}") + + structures: list[dict] = [] + for t in uberon_terms: + if t["id"] not in descendant_ids: + continue + numeric_id = t["id"].replace("UBERON:", "") + entry: dict = {"id": numeric_id, "name": t["name"]} + if t["synonyms"]: + # Compact format: [text, scope_letter] to keep file under 500KB + entry["synonyms"] = [ + [syn["text"], syn["scope"][0]] for syn in t["synonyms"] + ] + structures.append(entry) + + structures.sort(key=lambda s: s["id"]) + out_path = Path(__file__).with_name("uberon_brain_structures.json") + with open(out_path, "w") as f: + json.dump(structures, f, separators=(",", ":")) + f.write("\n") + print(f"Wrote {len(structures)} structures to {out_path}") + + +if __name__ == "__main__": # pragma: no cover + main() diff --git a/dandi/data/uberon_brain_structures.json b/dandi/data/uberon_brain_structures.json new file mode 100644 index 000000000..61f62727f --- /dev/null +++ b/dandi/data/uberon_brain_structures.json @@ -0,0 +1 @@ +[{"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 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geniculati medialis","E"],["capsule of the medial geniculate body","R"],["medial geniculate body capsule","E"]]},{"id":"0002628","name":"tail of caudate nucleus","synonyms":[["cauda (caudatus)","R"],["cauda nuclei caudati","R"],["caudate nuclear tail","E"],["tail of the caudate nucleus","R"]]},{"id":"0002630","name":"body of caudate nucleus","synonyms":[["body of the caudate nucleus","R"],["caudate body","R"],["caudate nuclear body","E"],["corpus (caudatus)","E"],["corpus nuclei caudati","R"]]},{"id":"0002631","name":"cerebral crus","synonyms":[["base of cerebral peduncle","R"],["basis cerebri (Oertel)","R"],["basis pedunculi (Oertel)","R"],["basis pedunculi cerebri (Willis)","R"],["CCR","B"],["cerebral peduncle (clinical definition)","E"],["cerebral peduncle, basal part","R"],["crura cerebri","E"],["crus cerebri","E"],["crus cerebri","R"],["crus of the cerebral peduncle","R"],["pars neo-encephalica pedunculi","R"],["pedunculus cerebri, pars basalis","R"],["pes pedunculi","R"],["pes pedunculi of midbrain","R"]]},{"id":"0002632","name":"medial part of medial mammillary nucleus","synonyms":[["medial mamillary nucleus","R"],["medial mammillary nucleus (carpenter)","E"],["medial mammillary nucleus median part","R"],["medial mammillary nucleus, medial part","E"],["medial mammillary nucleus, median part","E"],["medial part of the medial mammillary nucleus","R"],["medial subdivision of medial mammillary nucleus","E"],["MML","B"],["nucleus corporis mamillaris medialis, pars medialis","R"],["nucleus medialis corpus mamillaris (Shantha)","R"]]},{"id":"0002633","name":"motor nucleus of trigeminal nerve","synonyms":[["motor nucleus","R"],["motor nucleus of cranial nerve v","E"],["motor nucleus of the trigeminal","R"],["motor nucleus of the trigeminal nerve","R"],["motor nucleus of trigeminal","R"],["motor nucleus of trigeminal nerve","E"],["motor nucleus V","E"],["motor trigeminal nucleus","E"],["nucleus motorius nervi trigeminalis","R"],["nucleus motorius nervi trigemini","E"],["nucleus motorius nervi trigemini","R"],["nucleus motorius trigeminalis","R"],["nV","E"],["trigeminal motor nuclei","E"],["trigeminal motor nucleus","E"],["trigeminal V motor nucleus","E"]]},{"id":"0002634","name":"anterior nucleus of hypothalamus","synonyms":[["AH","B"],["anterior hypothalamic area","R"],["anterior hypothalamic area anterior part","R"],["anterior hypothalamic area, anterior part","R"],["anterior hypothalamic nucleus","E"],["anterior nucleus of the hypothalamus","R"],["area hypothalamica rostralis","E"],["fundamental gray substance","E"],["nucleus anterior hypothalami","R"],["nucleus hypothalamicus anterior","R"],["parvocellular nucleus of hypothalamus","E"]]},{"id":"0002636","name":"lateral pulvinar nucleus","synonyms":[["lateral pulvinar nucleus of thalamus","E"],["LPul","B"],["nucleus pulvinaris lateralis","E"],["nucleus pulvinaris lateralis (Hassler)","E"],["nucleus pulvinaris lateralis thalami","E"],["nucleus pulvinaris thalami, pars 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 midbrain","E"],["substantia reticularis mesencephali","R"],["tegmental reticular formation","E"]]},{"id":"0002640","name":"cuneocerebellar tract","synonyms":[["cuneocerebellar fibers","E"],["tractus cuneocerebelli","R"]]},{"id":"0002641","name":"oral pulvinar nucleus","synonyms":[["anterior pulvinar nucleus","E"],["nucleus pulvinaris anterior","E"],["nucleus pulvinaris oralis","E"],["nucleus pulvinaris oralis thalami","E"],["OPul","B"],["oral nuclear group of pulvinar","E"],["oral part of pulvinar","E"],["oral portion of pulvinar","E"]]},{"id":"0002642","name":"cuneate fasciculus of medulla","synonyms":[["fasciculus cuneatus (myelencephali)","E"],["nucleus pulvinaris oromedialis (Hassler)","R"]]},{"id":"0002643","name":"decussation of medial lemniscus","synonyms":[["decussatio lemnisci medialis","R"],["decussatio lemniscorum","R"],["decussatio lemniscorum medialium","R"],["decussatio sensoria","R"],["decussation of lemnisci","E"],["decussation of lemniscus","E"],["decussation of medial 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 medulla","E"]]},{"id":"0002647","name":"magnocellular part of medial dorsal nucleus","synonyms":[["dorsomedial thalamic nucleus, magnocellular part","E"],["magnocellular mediodorsal nucleus","E"],["magnocellular nucleus of medial dorsal nucleus of thalamus","E"],["magnocellular part of dorsomedial nucleus","E"],["magnocellular part of mediodorsal nucleus","E"],["magnocellular part of the medial dorsal nucleus","R"],["MDM","B"],["MDmc","E"],["mediodorsal nucleus of the thalamus, medial part","E"],["nucleus medialis dorsalis, pars magnocellularis","E"],["nucleus medialis fibrosus","E"],["nucleus medialis fibrosus (hassler)","E"],["pars magnocellularis nuclei mediodorsalis thalami","E"]]},{"id":"0002648","name":"anterior median eminence","synonyms":[["AME","B"],["eminentia mediana anterior","R"]]},{"id":"0002650","name":"paralaminar part of medial dorsal nucleus","synonyms":[["dorsomedial thalamic nucleus, paralaminar part","E"],["MDPL","B"],["mediodorsal thalamic nucleus paralaminar 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ventricle","E"],["ventriculus lateralis, cornu anterius","E"]]},{"id":"0002652","name":"posterior median eminence","synonyms":[["eminentia mediana posterior","R"],["PME","B"]]},{"id":"0002653","name":"gracile fasciculus of medulla","synonyms":[["column of Goll","E"],["fasciculus dorsolateralis gracilis (Golli)","R"],["fasciculus gracilis (myelencephali)","R"],["fasciculus of goll","E"],["Goll's tract","E"],["gracile fascicle (Gall)","R"],["gracile fascicle (Goll)","R"],["gracile fascicle of medulla","E"],["gracile fasciculus of the medulla","R"],["medulla segment of fasciculus gracilis","E"],["medulla segment of gracile fasciculus","E"],["tract of Gall","R"]]},{"id":"0002654","name":"parvocellular part of medial dorsal nucleus","synonyms":[["dorsomedial thalamic nucleus, parvicellular part","E"],["lateral mediodorsal nucleus","E"],["lateral nucleus of medial dorsal nucleus of thalamus","E"],["MDPC","B"],["mediodorsal thalamic nucleus, pars fasciculosa","E"],["nucleus medialis dorsalis 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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 velum","E"],["rostral medullary velum","R"],["velum medullare anterius","R"],["velum medullare craniale","R"],["velum medullare rostralis","R"],["velum medullare superior","R"],["velum medullare superius","R"]]},{"id":"0002660","name":"medial longitudinal fasciculus of midbrain","synonyms":[["fasciculus longitudinalis medialis (mesencephali)","R"],["medial longitudinal fasciculus of the midbrain","R"],["midbrain medial longitudinal fasciculus","E"],["MLFMB","B"]]},{"id":"0002661","name":"superior frontal gyrus","synonyms":[["gyrus F1","R"],["gyrus frontalis primus","R"],["gyrus frontalis superior","R"],["marginal gyrus","E"],["superior frontal convolution","E"]]},{"id":"0002662","name":"medial pes lemniscus","synonyms":[["MPL","B"],["pes lemniscus medialis","R"],["superficial pes lemniscus","E"]]},{"id":"0002663","name":"septal nuclear complex","synonyms":[["nuclei septales","R"],["parolfactory nuclei","E"],["septal nuclei","E"],["septal nucleus","E"]]},{"id":"0002664","name":"lateral 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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 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metathalami","E"]]},{"id":"0002705","name":"midline nuclear group","synonyms":[["median nuclei of thalamus","E"],["midline group of the dorsal thalamus","R"],["midline nuclear group","E"],["midline nuclear group of thalamus","E"],["midline nuclei of thalamus","E"],["midline thalamic group","E"],["midline thalamic nuclear group","R"],["midline thalamic nuclei","R"],["nuclei mediani (thalami)","E"],["nuclei mediani thalami","E"],["nuclei mediani thalami","R"],["nucleus mediani thalami","R"],["periventricular nuclei of thalamus","E"]]},{"id":"0002706","name":"posterior nucleus of hypothalamus","synonyms":[["area hypothalamica posterior","E"],["area posterior hypothalami","R"],["nucleus hypothalamicus posterior","R"],["nucleus posterior hypothalami","R"],["PH","B"],["posterior hypothalamic area","E"],["posterior hypothalamic nucleus","E"],["posterior nucleus","R"],["posterior nucleus of the hypothalamus","R"]]},{"id":"0002707","name":"corticospinal tract","synonyms":[["corticospinal 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thalamus","R"],["intralaminar nuclear complex","E"],["intralaminar nuclear group","E"],["intralaminar nuclear group of thalamus","E"],["intralaminar nuclei of thalamus","E"],["intralaminar nuclei of the dorsal thalamus","R"],["intralaminar thalamic nuclear group","R"],["intralaminar thalamic nuclei","E"],["nonspecific thalamic system","E"],["nuclei intralaminares (thalami)","E"],["nuclei intralaminares thalami","E"]]},{"id":"0002734","name":"superior temporal sulcus","synonyms":[["parallel sulcus","E"],["STS","B"],["sulcus t1","E"],["sulcus temporalis primus","R"],["sulcus temporalis superior","R"],["superior temporal fissure","E"]]},{"id":"0002735","name":"transverse pontine fibers","synonyms":[["fibrae pontis superficiales","R"],["fibrae pontis transversae","E"],["fibrae transversae superficiales pontis","R"],["superficial transverse fibers of pons","E"],["transverse fibers of pons","E"],["transverse fibers of the pons","R"],["transverse pontine fibers","E"],["transverse pontine fibres","E"],["transverse pontine tract","E"]]},{"id":"0002736","name":"lateral nuclear group of thalamus","synonyms":[["lateral group of nuclei","E"],["lateral group of the dorsal thalamus","E"],["lateral nuclear group","E"],["lateral nuclear group of dorsal thalamus","E"],["lateral nuclear group of thalamus","E"],["lateral nucleus of thalamus","E"],["lateral thalamic group","E"],["lateral thalamic nuclear group","R"],["lateral thalamic nuclear region","R"],["lateral thalamic nuclei","E"],["lateral thalamic nucleus","E"],["LNG","B"],["nuclei laterales thalami","E"],["nucleus lateralis thalami","E"]]},{"id":"0002738","name":"isthmus of cingulate gyrus","synonyms":[["cingulate gyrus isthmus","E"],["isthmus cinguli","R"],["isthmus gyri cingulatus","R"],["isthmus gyri cinguli","R"],["isthmus of cingulate cortex","R"],["isthmus of fornicate gyrus","E"],["isthmus of gyrus fornicatus","R"],["isthmus of limbic lobe","E"],["isthmus of the cingulate gyrus","R"],["isthmus-2","R"]]},{"id":"0002739","name":"medial dorsal nucleus of thalamus","synonyms":[["dorsal medial nucleus of thalamus","E"],["dorsal thalamus medial division","R"],["dorsomedial nuclear group","B"],["dorsomedial nucleus","B"],["dorsomedial nucleus of thalamus","E"],["medial dorsal nucleus","B"],["medial dorsal nucleus of thalamus","E"],["medial dorsal thalamic nucleus","E"],["medial group of the dorsal thalamus","R"],["medial nuclear group","B"],["medial nuclear group of thalamus","E"],["medial thalamic nuclear group","R"],["medial thalamic nuclei","B"],["medial thalamic nucleus","B"],["mediodorsal nucleus","B"],["mediodorsal nucleus of thalamus","E"],["mediodorsal nucleus of the thalamus","R"],["mediodorsal thalamic nucleus","E"],["nuclei mediales (thalami)","R"],["nucleus dorsomedialis thalami","E"],["nucleus medialis dorsalis","B"],["nucleus medialis dorsalis (Hassler)","R"],["nucleus medialis dorsalis thalami","R"],["nucleus mediodorsalis 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 pellucidum","synonyms":[["lamina of the septum pellucidum","R"],["lamina septi pellucidi","R"],["laminae septi pellucidi","E"],["septum pellucidum lamina","E"]]},{"id":"0002743","name":"basal forebrain","synonyms":[["basal forebrain area","R"],["pars basalis telencephali","R"]]},{"id":"0002746","name":"intermediate periventricular nucleus","synonyms":[["hPe","E"],["intermediate periventricular hypothalamic nucleus","R"],["intermediate periventricular nucleus of hypothalamus","E"],["intermediate periventricular nucleus of the hypothalamus","R"],["IPe","B"],["nucleus periventricularis hypothalami","R"],["periventricular hypothalamic nucleus, intermediate part","R"],["periventricular nucleus at the tuberal level","E"]]},{"id":"0002747","name":"neodentate part of dentate nucleus","synonyms":[["neodentate portion of dentate nucleus","E"],["neodentate portion of the dentate nucleus","R"],["pars neodentata","R"]]},{"id":"0002749","name":"regional part of cerebellar cortex","synonyms":[["cerebellar cortical segment","E"],["segment of cerebellar cortex","E"]]},{"id":"0002750","name":"medial longitudinal fasciculus of medulla","synonyms":[["fasciculus longitudinalis medialis (myelencephali)","R"],["medial longitudinal fasciculus of medulla oblongata","E"],["medial longitudinal fasciculus of the medulla","R"],["medulla medial longitudinal fasciculus","E"]]},{"id":"0002751","name":"inferior temporal gyrus","synonyms":[["gyrus temporalis inferior","E"],["gyrus temporalis inferior","R"],["inferotemporal cortex","R"],["IT cortex","R"],["lateral occipitotemporal gyrus (heimer-83)","E"]]},{"id":"0002752","name":"olivocerebellar tract","synonyms":[["fibrae olivocerebellares","R"],["olivocerebellar fibers","R"],["t. olivocerebellaris","R"],["tractus olivocerebellaris","R"]]},{"id":"0002753","name":"posterior spinocerebellar tract","synonyms":[["dorsal spinocerebellar tract","E"],["dorsal spinocerebellar tract of the medulla","R"],["flechsig's tract","E"]]},{"id":"0002754","name":"predorsal bundle","synonyms":[["fasciculus praedorsalis (Tschermak)","R"],["fasciculus predorsalis","R"],["predorsal bundle of Edinger","E"],["predorsal fasciculus","E"],["tectospinal fibers","E"]]},{"id":"0002755","name":"pyramidal decussation","synonyms":[["corticospinal decussation","E"],["decussatio motoria","R"],["decussatio pyramidum","E"],["decussatio pyramidum medullae oblongatae","E"],["decussation of corticospinal tract","E"],["decussation of pyramidal tract fibers","E"],["decussation of pyramids","E"],["decussation of pyramids of medulla","E"],["decussation of the pyramidal tract","E"],["motor decussation","E"],["motor decussation of medulla","E"],["pyramidal decussation","R"],["pyramidal decussation (pourfour du petit)","E"],["pyramidal tract decussation","E"]]},{"id":"0002756","name":"anterior cingulate gyrus","synonyms":[["anterior cingulate","R"],["cGa","B"],["cingulate gyrus, anterior division","B"],["cortex cingularis 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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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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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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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recurrens"},{"id":"3010757","name":"ramus superficial ophthalmic"},{"id":"3010759","name":"ramus buccal"},{"id":"3010764","name":"laryngeus ventralis"},{"id":"3010765","name":"ramus mandibularis externus"},{"id":"3010778","name":"jugal ramule"},{"id":"3010794","name":"oral ramule"},{"id":"3010795","name":"preopercular ramule"},{"id":"3010796","name":"ramus supraotic"},{"id":"3010798","name":"ramulus suprabranchialis anterior"},{"id":"3010799","name":"ramulus suprabranchialis posterior"},{"id":"3010801","name":"ramus lateral"},{"id":"3010804","name":"ramus ventral"},{"id":"4450000","name":"medial prefrontal cortex","synonyms":[["mPFC","E"]]},{"id":"6001060","name":"insect embryonic brain"},{"id":"6001911","name":"insect embryonic/larval nervous system","synonyms":[["larval nervous system","E"]]},{"id":"6001919","name":"insect embryonic/larval central nervous system","synonyms":[["larval central nervous system","E"]]},{"id":"6001920","name":"insect embryonic/larval brain","synonyms":[["larval brain","N"],["larval supraesophageal ganglion","N"]]},{"id":"6001925","name":"insect embryonic/larval protocerebrum","synonyms":[["larval protocerebrum","R"]]},{"id":"6003559","name":"insect adult nervous system"},{"id":"6003623","name":"insect adult central nervous system"},{"id":"6003624","name":"insect adult brain"},{"id":"6003626","name":"insect supraesophageal ganglion","synonyms":[["SPG","R"]]},{"id":"6003627","name":"insect protocerebrum","synonyms":[["protocerebral neuromere","E"]]},{"id":"6003632","name":"insect adult central complex","synonyms":[["adult central body complex","E"],["central body","R"],["central body complex","R"],["CX","E"]]},{"id":"6005096","name":"insect stomatogastric nervous system","synonyms":[["stomodaeal nervous system","R"],["stomodeal nervous system","R"]]},{"id":"6005177","name":"insect chaeta","synonyms":[["sensillum chaeticum","E"]]},{"id":"6005805","name":"insect Bolwig organ","synonyms":[["Bolwig's 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neuropil","R"]]},{"id":"6041000","name":"insect synaptic neuropil block","synonyms":[["level 1 neuropil","E"]]},{"id":"6110636","name":"insect adult cerebral ganglion","synonyms":[["brain","R"],["cerebrum","R"],["CRG","E"],["SPG","R"],["supraesophageal ganglion","R"]]},{"id":"8000004","name":"central retina"},{"id":"8000005","name":"Henle's fiber layer","synonyms":[["Henle fiber layer","E"],["HFL","E"],["nerve fiber layer of Henle","E"]]},{"id":"8410006","name":"submucous nerve plexus of anorectum","synonyms":[["anorectum submucous nerve plexus","E"]]},{"id":"8410007","name":"myenteric nerve plexus of anorectum","synonyms":[["anorectum myenteric nerve plexus","E"]]},{"id":"8410011","name":"myenteric nerve plexus of appendix","synonyms":[["myenteric nerve plexus of appendix vermiformis","E"],["myenteric nerve plexus of vermiform appendix","E"]]},{"id":"8410012","name":"submucous nerve plexus of appendix","synonyms":[["submucous nerve plexus of appendix vermiformis","E"],["submucous nerve plexus of vermiform appendix","E"]]},{"id":"8410049","name":"serosal nerve fiber of appendix","synonyms":[["nerve fiber of serosa of appendix","E"],["nerve fibre of serosa of appendix","E"],["serosal nerve fiber of appendix vermiformis","E"],["serosal nerve fiber of vermiform appendix","E"],["serosal nerve fibre of appendix","E"],["serosal nerve fibre of appendix vermiformis","E"],["serosal nerve fibre of vermiform appendix","E"]]},{"id":"8410058","name":"myenteric nerve plexus of colon"},{"id":"8410059","name":"submucous nerve plexus of colon"},{"id":"8410062","name":"parasympathetic cholinergic nerve"},{"id":"8410063","name":"myenteric nerve plexus of small intestine"},{"id":"8410064","name":"submucous nerve plexus of small intestine"},{"id":"8440000","name":"cortical layer II/III","synonyms":[["cerebral cortex layer 2/3","E"],["neocortex layer 2/3","E"]]},{"id":"8440001","name":"cortical layer IV/V","synonyms":[["cerebral cortex layer 4/5","E"],["neocortex layer 4/5","E"]]},{"id":"8440002","name":"cortical layer V/VI","synonyms":[["cerebral cortex layer 5/6","E"],["neocortex layer 5/6","E"]]},{"id":"8440003","name":"cortical layer VIb","synonyms":[["cerebral cortex layer 6b","E"],["neocortex layer 6b","E"]]},{"id":"8440004","name":"laminar subdivision of the cortex"},{"id":"8440005","name":"rostral periventricular region of the third ventricle","synonyms":[["RP3V","E"]]},{"id":"8440007","name":"periventricular hypothalamic nucleus, anterior part","synonyms":[["PVa","E"]]},{"id":"8440008","name":"periventricular hypothalamic nucleus, intermediate part","synonyms":[["PVi","E"]]},{"id":"8440010","name":"Brodmann (1909) area 17","synonyms":[["area 17 of Brodmann","R"],["area 17 of Brodmann-1909","E"],["area striata","R"],["B09-17","B"],["b09-17","E"],["BA17","E"],["BA17","R"],["Brodmann area 17","E"],["Brodmann area 17","R"],["Brodmann area 17, striate","E"],["calcarine cortex","R"],["human primary visual cortex","R"],["nerve X","R"],["occipital visual neocortex","R"],["primary visual area","R"],["primate striate cortex","E"],["striate area","R"],["V1","R"],["visual area one","R"],["visual area V1","R"],["visual association area","R"],["visual association cortex","R"]]},{"id":"8440011","name":"cortical visual area"},{"id":"8440012","name":"cerebral nuclei","synonyms":[["CNU","E"]]},{"id":"8440013","name":"fasciola cinerea","synonyms":[["FC","E"]]},{"id":"8440014","name":"ventrolateral preoptic nucleus","synonyms":[["intermediate nucleus of the preoptic area (IPA)","E"],["VLPO","E"]]},{"id":"8440015","name":"noradrenergic cell groups"},{"id":"8440016","name":"noradrenergic cell group A1"},{"id":"8440017","name":"noradrenergiccell group A2"},{"id":"8440018","name":"noradrenergic cell group A4"},{"id":"8440019","name":"noradrenergic cell group A5"},{"id":"8440021","name":"noradrenergic cell group A7"},{"id":"8440022","name":"noradrenergic cell group A6sc"},{"id":"8440023","name":"noradrenergic cell group Acg"},{"id":"8440024","name":"visceral area","synonyms":[["VISC","E"]]},{"id":"8440025","name":"parapyramidal nucleus","synonyms":[["PPY","E"]]},{"id":"8440026","name":"parapyramidal nucleus, deep part","synonyms":[["PPYd","E"]]},{"id":"8440027","name":"parapyramidal nucleus, superficial part","synonyms":[["PPYs","E"]]},{"id":"8440028","name":"Perihypoglossal nuclei","synonyms":[["nuclei perihypoglossales","E"],["perihypoglossal complex","E"],["perihypoglossal nuclear complex","E"],["PHY","E"],["satellite nuclei","E"]]},{"id":"8440029","name":"rubroreticular tract"},{"id":"8440030","name":"striatum-like amygdalar nuclei","synonyms":[["sAMY","E"]]},{"id":"8440031","name":"medial corticohypothalmic tract","synonyms":[["mct","E"]]},{"id":"8440032","name":"prelimbic area","synonyms":[["PL","E"],["prelimbic cortex","E"],["PrL","E"]]},{"id":"8440033","name":"infralimbic area","synonyms":[["IL (brain)","E"],["ILA","E"],["infralimbic cortex","E"]]},{"id":"8440034","name":"bulbocerebellar tract","synonyms":[["bct","E"]]},{"id":"8440035","name":"sublaterodorsal nucleus","synonyms":[["SLD","E"],["sublaterodorsal tegmental nucleus","E"]]},{"id":"8440036","name":"supratrigeminal nucleus","synonyms":[["SUT","E"],["Vsup","E"]]},{"id":"8440037","name":"accessory facial motor nucleus","synonyms":[["ACVII","E"]]},{"id":"8440038","name":"efferent vestibular nucleus","synonyms":[["EV","E"]]},{"id":"8440039","name":"piriform-amygdalar area","synonyms":[["PAA (brain)","E"]]},{"id":"8440040","name":"dorsal peduncular area","synonyms":[["DP","E"]]},{"id":"8440041","name":"tuberal nucleus (sensu Rodentia)","synonyms":[["lateral tuberal nucleus (sensu Rodentia)","B"],["lateral tuberal nucleus (sensu Rodentia)","E"]]},{"id":"8440042","name":"nucleus lateralis tuberis system (sensu Teleostei)","synonyms":[["NLT system (sensu Teleostei)","E"]]},{"id":"8440043","name":"superior paraolivary nucleus","synonyms":[["SPON","E"]]},{"id":"8440044","name":"upper layers of the cortex"},{"id":"8440045","name":"second visual cortical area (sensu Mustela putorius furo)","synonyms":[["area 18 (sensu Mustela putorius furo)","E"]]},{"id":"8440046","name":"third visual cortical area (sensu Mustela putorius furo)","synonyms":[["area 19 (sensu Mustela putorius furo)","E"]]},{"id":"8440047","name":"fourth visual cortical area (sensu Mustela putorius furo)","synonyms":[["area 21 (sensu Mustela putorius furo)","E"]]},{"id":"8440048","name":"temporal visual area a (sensu Mustela putorius furo)","synonyms":[["area 20a (sensu Mustela putorius furo)","E"]]},{"id":"8440049","name":"temporal visual area b (sensu Mustela putorius furo)","synonyms":[["area 20b (sensu Mustela putorius furo)","E"]]},{"id":"8440050","name":"posterior parietal rostral cortical area (sensu Mustela putorius furo)","synonyms":[["posterior parietal cortex, rostral part (sensu Mustela putorius furo)","E"],["PPr (sensu Mustela putorius furo)","E"]]},{"id":"8440051","name":"lower layers of the cortex"},{"id":"8440052","name":"posterior parietal caudal cortical area (sensu Mustela putorius furo)","synonyms":[["posterior parietal cortex, caudal part (sensu Mustela putorius furo)","E"],["PPc (sensu Mustela putorius furo)","E"]]},{"id":"8440054","name":"anteromedial lateral suprasylvian visual area (sensu Mustela putorius furo)","synonyms":[["AMLS (sensu Mustela putorius furo)","E"]]},{"id":"8440055","name":"anterolateral lateral suprasylvian visual area (sensu Mustela putorius furo)","synonyms":[["ALLS (sensu Mustela putorius furo)","E"]]},{"id":"8440056","name":"posteromedial lateral suprasylvian visual area (sensu Mustela putorius furo)","synonyms":[["PMLS (sensu Mustela putorius furo)","E"],["PPS (sensu Mustela putorius furo)","E"],["PSS (sensu Mustela putorius furo)","E"],["SSY (sensu Mustela putorius furo)","E"],["Ssy (sensu Mustela putorius furo)","E"],["suprasylvian sulcal visual area (sensu Mustela putorius furo)","E"]]},{"id":"8440059","name":"posterolateral lateral suprasylvian visual area (sensu Mustela putorius furo)","synonyms":[["PLLS (sensu Mustela putorius furo)","E"]]},{"id":"8440060","name":"dorsal lateral suprasylvian visual cortical area (sensu Mustela putorius furo)","synonyms":[["DLS (sensu Mustela putorius furo)","E"]]},{"id":"8440061","name":"ventral lateral suprasylvian visual area (sensu Mustela putorius furo)","synonyms":[["VLS (sensu Mustela putorius furo)","E"]]},{"id":"8440062","name":"posterior suprasylvian visual cortical area (sensu Mustela putorius furo)","synonyms":[["PS (sensu Mustela putorius furo)","E"]]},{"id":"8440072","name":"lateral tegmental nucleus","synonyms":[["LTN","E"]]},{"id":"8440073","name":"magnocellular reticular nucleus","synonyms":[["MARN","E"]]},{"id":"8440074","name":"interstitial nucleus of the vestibular nerve","synonyms":[["INV","E"],["ISVe","E"]]},{"id":"8440075","name":"gustatory cortex","synonyms":[["gustatory area","E"]]},{"id":"8440076","name":"somatomotor area"},{"id":"8480001","name":"capillary of brain"},{"id":"8600066","name":"basivertebral vein"},{"id":"8600076","name":"suboccipital venous plexus"},{"id":"8600090","name":"hypophyseal vein"},{"id":"8600103","name":"anterior internal vertebral venous plexus"},{"id":"8600104","name":"intervertebral vein"},{"id":"8600118","name":"myenteric ganglion","synonyms":[["myenteric plexus ganglion","E"]]},{"id":"8600119","name":"myenteric ganglion of small intestine"},{"id":"8600120","name":"atrial intrinsic cardiac ganglion","synonyms":[["atrial ganglionated plexus","R"]]},{"id":"8600121","name":"lumbar ganglion","synonyms":[["lumbar paravertebral ganglion","E"],["lumbar sympathetic ganglion","E"]]},{"id":"8600122","name":"sacral ganglion","synonyms":[["sacral sympathetic ganglion","E"]]},{"id":"8600123","name":"lower airway ganglion","synonyms":[["lower airway parasympathetic ganglion","E"]]},{"id":"8900000","name":"sensory corpuscle","synonyms":[["COEC","R"],["cutaneous end-organ complex","E"]]}] diff --git a/dandi/metadata/brain_areas.py b/dandi/metadata/brain_areas.py index 4174166b8..21e87de37 100644 --- a/dandi/metadata/brain_areas.py +++ b/dandi/metadata/brain_areas.py @@ -14,6 +14,7 @@ lgr = get_logger() MBAO_URI_TEMPLATE = "http://purl.obolibrary.org/obo/MBA_{}" +UBERON_URI_TEMPLATE = "http://purl.obolibrary.org/obo/UBERON_{}" # Values that should be treated as missing / uninformative _TRIVIAL_VALUES = frozenset( @@ -253,3 +254,175 @@ def locations_to_ccf_mouse_anatomy(locations: list[str]) -> list[models.Anatomy] seen_ids.add(id_str) results.append(anatomy) return results + + +# --------------------------------------------------------------------------- +# UBERON matching +# --------------------------------------------------------------------------- + + +@lru_cache(maxsize=1) +def _load_uberon_structures() -> list[dict[str, Any]]: + """Load the bundled UBERON brain structures JSON.""" + data_path = ( + Path(__file__).resolve().parent.parent / "data" / "uberon_brain_structures.json" + ) + with open(data_path) as f: + structures: list[dict[str, Any]] = json.load(f) + return structures + + +@lru_cache(maxsize=4) +def _build_uberon_lookup_dicts( + synonym_scopes: frozenset[str] = frozenset({"EXACT"}), +) -> tuple[dict[str, dict], dict[str, dict]]: + """Build lookup dictionaries for UBERON structures. + + Parameters + ---------- + synonym_scopes : frozenset[str] + Which synonym scopes to include (e.g. ``{"EXACT"}``, + ``{"EXACT", "RELATED"}``). + + Returns + ------- + tuple of 2 dicts + (name_exact, name_lower) mapping term names and synonym texts to + structure dicts. + """ + structures = _load_uberon_structures() + name_exact: dict[str, dict] = {} + name_lower: dict[str, dict] = {} + for s in structures: + name = s["name"] + if name not in name_exact: + name_exact[name] = s + name_low = name.lower() + if name_low not in name_lower: + name_lower[name_low] = s + # Synonyms stored as [text, scope_letter] compact format + _scope_map = {"E": "EXACT", "R": "RELATED", "N": "NARROW", "B": "BROAD"} + for syn in s.get("synonyms", []): + scope = _scope_map.get(syn[1], syn[1]) + if scope not in synonym_scopes: + continue + text = syn[0] + if text not in name_exact: + name_exact[text] = s + text_low = text.lower() + if text_low not in name_lower: + name_lower[text_low] = s + return name_exact, name_lower + + +def match_location_to_uberon( + token: str, + synonym_scopes: frozenset[str] = frozenset({"EXACT"}), +) -> models.Anatomy | None: + """Match a single location token against UBERON brain structures. + + Tries exact name/synonym, then case-insensitive name/synonym. + + Parameters + ---------- + token : str + Location string to match. + synonym_scopes : frozenset[str] + Synonym scopes to include in matching. + + Returns + ------- + models.Anatomy or None + """ + name_exact, name_lower = _build_uberon_lookup_dicts(synonym_scopes) + token_stripped = token.strip() + if not token_stripped: + return None + + # 1. Exact name/synonym match + s = name_exact.get(token_stripped) + if s is not None: + return _uberon_structure_to_anatomy(s) + + # 2. Case-insensitive name/synonym match + s = name_lower.get(token_stripped.lower()) + if s is not None: + return _uberon_structure_to_anatomy(s) + + return None + + +def _uberon_structure_to_anatomy(s: dict[str, Any]) -> models.Anatomy: + """Convert a UBERON structure dict to a ``dandischema`` Anatomy model.""" + return models.Anatomy( + identifier=UBERON_URI_TEMPLATE.format(s["id"]), + name=s["name"], + ) + + +def locations_to_uberon_anatomy( + locations: list[str], + synonym_scopes: frozenset[str] = frozenset({"EXACT"}), +) -> list[models.Anatomy]: + """Convert raw NWB location strings to deduplicated UBERON Anatomy list. + + Parameters + ---------- + locations : list[str] + Raw location strings from NWB file. + synonym_scopes : frozenset[str] + Synonym scopes to include in matching. + + Returns + ------- + list[models.Anatomy] + Matched and deduplicated anatomy entries. + """ + seen_ids: set[str] = set() + results: list[models.Anatomy] = [] + for loc in locations: + tokens = _parse_location_string(loc) + for token in tokens: + anatomy = match_location_to_uberon(token, synonym_scopes) + if anatomy is not None: + id_str = str(anatomy.identifier) + if id_str not in seen_ids: + seen_ids.add(id_str) + results.append(anatomy) + return results + + +def locations_to_mouse_anatomy( + locations: list[str], + synonym_scopes: frozenset[str] = frozenset({"EXACT"}), +) -> list[models.Anatomy]: + """Convert raw NWB location strings for mouse. + + Tries Allen CCF first for each token, falls back to UBERON. + + Parameters + ---------- + locations : list[str] + Raw location strings from NWB file. + synonym_scopes : frozenset[str] + Synonym scopes for UBERON fallback matching. + + Returns + ------- + list[models.Anatomy] + Matched and deduplicated anatomy entries. + """ + seen_ids: set[str] = set() + results: list[models.Anatomy] = [] + for loc in locations: + tokens = _parse_location_string(loc) + for token in tokens: + anatomy = match_location_to_allen(token) + if anatomy is None: + anatomy = match_location_to_uberon(token, synonym_scopes) + if anatomy is not None: + id_str = str(anatomy.identifier) + if id_str not in seen_ids: + seen_ids.add(id_str) + results.append(anatomy) + return results diff --git a/dandi/metadata/util.py b/dandi/metadata/util.py index 38b067093..56d03bcb8 100644 --- a/dandi/metadata/util.py +++ b/dandi/metadata/util.py @@ -13,7 +13,7 @@ import tenacity from yarl import URL -from .brain_areas import locations_to_ccf_mouse_anatomy +from .brain_areas import locations_to_mouse_anatomy, locations_to_uberon_anatomy from .. import __version__ from ..utils import ensure_datetime @@ -576,7 +576,7 @@ def extract_wasDerivedFrom(metadata: dict) -> list[models.BioSample] | None: if deepest is None: deepest = sample - # Compute anatomy from brain locations (mouse only) + # Compute anatomy from brain locations anatomy = _extract_brain_anatomy(metadata) if anatomy: if deepest is not None: @@ -601,15 +601,22 @@ def extract_wasDerivedFrom(metadata: dict) -> list[models.BioSample] | None: def _extract_brain_anatomy(metadata: dict) -> list[models.Anatomy]: - """Extract brain anatomy from metadata, if the species is mouse.""" + """Extract brain anatomy from metadata. + + For mice, tries Allen CCF first then falls back to UBERON. + For other species, tries UBERON directly. + """ if not (locations := metadata.get("brain_locations")): return [] species = extract_species(metadata) - if species is None or str(species.identifier) != _MOUSE_URI: + if species is None: return [] - return locations_to_ccf_mouse_anatomy(locations) + if str(species.identifier) == _MOUSE_URI: + return locations_to_mouse_anatomy(locations) + else: + return locations_to_uberon_anatomy(locations) extract_wasAttributedTo = extract_model_list( diff --git a/dandi/tests/test_brain_areas.py b/dandi/tests/test_brain_areas.py index f6c2ae66c..7f1929ae9 100644 --- a/dandi/tests/test_brain_areas.py +++ b/dandi/tests/test_brain_areas.py @@ -5,7 +5,10 @@ from ..metadata.brain_areas import ( _parse_location_string, locations_to_ccf_mouse_anatomy, + locations_to_mouse_anatomy, + locations_to_uberon_anatomy, match_location_to_allen, + match_location_to_uberon, ) @@ -128,3 +131,102 @@ def test_mixed_matched_unmatched(self) -> None: def test_comma_separated_input(self) -> None: result = locations_to_ccf_mouse_anatomy(["VISp,CA1"]) assert len(result) == 2 + + +@pytest.mark.ai_generated +class TestMatchLocationToUberon: + @pytest.mark.parametrize( + "token, expected_name", + [ + ("brain", "brain"), + ("hippocampal formation", "hippocampal formation"), + ("primary visual cortex", "primary visual cortex"), + ("cerebral cortex", "cerebral cortex"), + ], + ) + def test_matches(self, token: str, expected_name: str) -> None: + result = match_location_to_uberon(token) + assert result is not None + assert "UBERON_" in str(result.identifier) + assert result.name == expected_name + + def test_case_insensitive(self) -> None: + result = match_location_to_uberon("Hippocampal Formation") + assert result is not None + assert result.name == "hippocampal formation" + + def test_exact_synonym(self) -> None: + # "brain fornix" is an EXACT synonym for "fornix of brain" + result = match_location_to_uberon("brain fornix") + assert result is not None + assert result.name == "fornix of brain" + + def test_related_synonym_excluded_by_default(self) -> None: + # "encephalon" is a RELATED synonym for "brain" + result = match_location_to_uberon("encephalon") + assert result is None + + def test_related_synonym_included_when_requested(self) -> None: + result = match_location_to_uberon( + "encephalon", synonym_scopes=frozenset({"EXACT", "RELATED"}) + ) + assert result is not None + assert result.name == "brain" + + @pytest.mark.parametrize("token", ["nonexistent_area_xyz", ""]) + def test_no_match(self, token: str) -> None: + assert match_location_to_uberon(token) is None + + def test_ca1_synonym(self) -> None: + # CA1 is an exact synonym for "CA1 field of hippocampus" + result = match_location_to_uberon("CA1") + assert result is not None + assert "CA1" in result.name + + +@pytest.mark.ai_generated +class TestLocationsToUberonAnatomy: + def test_basic(self) -> None: + result = locations_to_uberon_anatomy(["hippocampal formation"]) + assert len(result) == 1 + assert result[0].name == "hippocampal formation" + + def test_deduplication(self) -> None: + result = locations_to_uberon_anatomy( + ["hippocampal formation", "Hippocampal Formation"] + ) + assert len(result) == 1 + + def test_empty(self) -> None: + assert locations_to_uberon_anatomy([]) == [] + + def test_unmatched(self) -> None: + assert locations_to_uberon_anatomy(["nonexistent_xyz"]) == [] + + +@pytest.mark.ai_generated +class TestLocationsToMouseAnatomy: + def test_allen_preferred(self) -> None: + """Allen CCF match should be used over UBERON for mouse.""" + result = locations_to_mouse_anatomy(["VISp"]) + assert len(result) == 1 + assert "MBA_" in str(result[0].identifier) + + def test_uberon_fallback(self) -> None: + """Tokens not in Allen CCF should fall back to UBERON.""" + # "visual cortex" is in UBERON but not Allen CCF + result = locations_to_mouse_anatomy(["visual cortex"]) + assert len(result) == 1 + assert "UBERON_" in str(result[0].identifier) + + def test_mixed_allen_and_uberon(self) -> None: + """Allen-matched and UBERON-matched tokens should coexist.""" + result = locations_to_mouse_anatomy(["VISp", "visual cortex"]) + assert len(result) == 2 + identifiers = {str(r.identifier) for r in result} + assert any("MBA_" in i for i in identifiers) + assert any("UBERON_" in i for i in identifiers) + + def test_deduplication(self) -> None: + result = locations_to_mouse_anatomy(["VISp", "VISp"]) + assert len(result) == 1 diff --git a/pyproject.toml b/pyproject.toml index e62405bfa..8feab9796 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -161,7 +161,7 @@ tag_prefix = "" parentdir_prefix = "" [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" # Don't warn about "[l]ist" in the abbrev_prompt() docstring: # TE is present in the BIDS schema ignore-regex = "(\\[\\w\\]\\w+|TE|ignore \"bu\" strings)" From 8e8262aeb0b56fca74ea7e15b53291a14b5269a2 Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Sun, 29 Mar 2026 11:39:22 -0400 Subject: [PATCH 2/5] fix: resolve mypy error for optional name field in test Co-Authored-By: Claude Opus 4.6 (1M context) --- dandi/tests/test_brain_areas.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dandi/tests/test_brain_areas.py b/dandi/tests/test_brain_areas.py index 7f1929ae9..a01083f19 100644 --- a/dandi/tests/test_brain_areas.py +++ b/dandi/tests/test_brain_areas.py @@ -181,7 +181,7 @@ def test_ca1_synonym(self) -> None: # CA1 is an exact synonym for "CA1 field of hippocampus" result = match_location_to_uberon("CA1") assert result is not None - assert "CA1" in result.name + assert result.name is not None and "CA1" in result.name @pytest.mark.ai_generated From a2a51ba2399e38822c69aee664ee1d590f5439cd Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Sun, 29 Mar 2026 12:44:26 -0400 Subject: [PATCH 3/5] refactor: tiered synonym scope matching for UBERON 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) --- dandi/metadata/brain_areas.py | 119 ++++++++++++++++++++------------ dandi/tests/test_brain_areas.py | 9 ++- 2 files changed, 81 insertions(+), 47 deletions(-) diff --git a/dandi/metadata/brain_areas.py b/dandi/metadata/brain_areas.py index 21e87de37..6530ee586 100644 --- a/dandi/metadata/brain_areas.py +++ b/dandi/metadata/brain_areas.py @@ -272,82 +272,111 @@ def _load_uberon_structures() -> list[dict[str, Any]]: return structures +# Synonym scopes ordered from most to least precise. +_SCOPE_ORDER = ("EXACT", "NARROW", "BROAD", "RELATED") +_SCOPE_LETTER = {"E": "EXACT", "N": "NARROW", "B": "BROAD", "R": "RELATED"} + + +def _scopes_up_to(max_scope: str) -> tuple[str, ...]: + """Return scope tiers from EXACT up to and including *max_scope*.""" + idx = _SCOPE_ORDER.index(max_scope) + return _SCOPE_ORDER[: idx + 1] + + @lru_cache(maxsize=4) def _build_uberon_lookup_dicts( - synonym_scopes: frozenset[str] = frozenset({"EXACT"}), + scope: str, ) -> tuple[dict[str, dict], dict[str, dict]]: - """Build lookup dictionaries for UBERON structures. + """Build lookup dictionaries for a single UBERON synonym scope. + + Term names are always included (they are not scope-gated). + Synonyms are filtered to only those matching *scope*. Parameters ---------- - synonym_scopes : frozenset[str] - Which synonym scopes to include (e.g. ``{"EXACT"}``, - ``{"EXACT", "RELATED"}``). + scope : str + A single scope to include (``"EXACT"``, ``"NARROW"``, etc.). + Pass ``"_NAME"`` to build a name-only dict (no synonyms). Returns ------- tuple of 2 dicts - (name_exact, name_lower) mapping term names and synonym texts to - structure dicts. + (name_exact, name_lower) mapping texts to structure dicts. """ structures = _load_uberon_structures() name_exact: dict[str, dict] = {} name_lower: dict[str, dict] = {} for s in structures: - name = s["name"] - if name not in name_exact: - name_exact[name] = s - name_low = name.lower() - if name_low not in name_lower: - name_lower[name_low] = s - # Synonyms stored as [text, scope_letter] compact format - _scope_map = {"E": "EXACT", "R": "RELATED", "N": "NARROW", "B": "BROAD"} - for syn in s.get("synonyms", []): - scope = _scope_map.get(syn[1], syn[1]) - if scope not in synonym_scopes: - continue - text = syn[0] - if text not in name_exact: - name_exact[text] = s - text_low = text.lower() - if text_low not in name_lower: - name_lower[text_low] = s + if scope == "_NAME": + # Name-only tier (always tried first) + name = s["name"] + if name not in name_exact: + name_exact[name] = s + name_low = name.lower() + if name_low not in name_lower: + name_lower[name_low] = s + else: + # Synonym tier for the given scope + for syn in s.get("synonyms", []): + syn_scope = _SCOPE_LETTER.get(syn[1], syn[1]) + if syn_scope != scope: + continue + text = syn[0] + if text not in name_exact: + name_exact[text] = s + text_low = text.lower() + if text_low not in name_lower: + name_lower[text_low] = s return name_exact, name_lower +def _lookup_in_dicts( + token: str, name_exact: dict[str, dict], name_lower: dict[str, dict] +) -> dict | None: + """Try exact then case-insensitive lookup, return structure or None.""" + s = name_exact.get(token) + if s is not None: + return s + return name_lower.get(token.lower()) + + def match_location_to_uberon( token: str, - synonym_scopes: frozenset[str] = frozenset({"EXACT"}), + max_synonym_scope: str = "EXACT", ) -> models.Anatomy | None: """Match a single location token against UBERON brain structures. - Tries exact name/synonym, then case-insensitive name/synonym. + Matching is tiered: term names are tried first, then synonyms in + precision order (EXACT > NARROW > BROAD > RELATED) up to and + including *max_synonym_scope*. Parameters ---------- token : str Location string to match. - synonym_scopes : frozenset[str] - Synonym scopes to include in matching. + max_synonym_scope : str + Most permissive synonym scope to try. ``"EXACT"`` (default) + only uses exact synonyms. ``"BROAD"`` tries EXACT, then + NARROW, then BROAD. Returns ------- models.Anatomy or None """ - name_exact, name_lower = _build_uberon_lookup_dicts(synonym_scopes) token_stripped = token.strip() if not token_stripped: return None - # 1. Exact name/synonym match - s = name_exact.get(token_stripped) + # Always try term names first + s = _lookup_in_dicts(token_stripped, *_build_uberon_lookup_dicts("_NAME")) if s is not None: return _uberon_structure_to_anatomy(s) - # 2. Case-insensitive name/synonym match - s = name_lower.get(token_stripped.lower()) - if s is not None: - return _uberon_structure_to_anatomy(s) + # Try synonym tiers in precision order + for scope in _scopes_up_to(max_synonym_scope): + s = _lookup_in_dicts(token_stripped, *_build_uberon_lookup_dicts(scope)) + if s is not None: + return _uberon_structure_to_anatomy(s) return None @@ -362,7 +391,7 @@ def _uberon_structure_to_anatomy(s: dict[str, Any]) -> models.Anatomy: def locations_to_uberon_anatomy( locations: list[str], - synonym_scopes: frozenset[str] = frozenset({"EXACT"}), + max_synonym_scope: str = "EXACT", ) -> list[models.Anatomy]: """Convert raw NWB location strings to deduplicated UBERON Anatomy list. @@ -370,8 +399,9 @@ def locations_to_uberon_anatomy( ---------- locations : list[str] Raw location strings from NWB file. - synonym_scopes : frozenset[str] - Synonym scopes to include in matching. + max_synonym_scope : str + Most permissive synonym scope to try (see + :func:`match_location_to_uberon`). Returns ------- @@ -383,7 +413,7 @@ def locations_to_uberon_anatomy( for loc in locations: tokens = _parse_location_string(loc) for token in tokens: - anatomy = match_location_to_uberon(token, synonym_scopes) + anatomy = match_location_to_uberon(token, max_synonym_scope) if anatomy is not None: id_str = str(anatomy.identifier) if id_str not in seen_ids: @@ -394,7 +424,7 @@ def locations_to_uberon_anatomy( def locations_to_mouse_anatomy( locations: list[str], - synonym_scopes: frozenset[str] = frozenset({"EXACT"}), + max_synonym_scope: str = "EXACT", ) -> list[models.Anatomy]: """Convert raw NWB location strings for mouse. @@ -404,8 +434,9 @@ def locations_to_mouse_anatomy( ---------- locations : list[str] Raw location strings from NWB file. - synonym_scopes : frozenset[str] - Synonym scopes for UBERON fallback matching. + max_synonym_scope : str + Most permissive synonym scope for UBERON fallback (see + :func:`match_location_to_uberon`). Returns ------- @@ -419,7 +450,7 @@ def locations_to_mouse_anatomy( for token in tokens: anatomy = match_location_to_allen(token) if anatomy is None: - anatomy = match_location_to_uberon(token, synonym_scopes) + anatomy = match_location_to_uberon(token, max_synonym_scope) if anatomy is not None: id_str = str(anatomy.identifier) if id_str not in seen_ids: diff --git a/dandi/tests/test_brain_areas.py b/dandi/tests/test_brain_areas.py index a01083f19..973e6f20f 100644 --- a/dandi/tests/test_brain_areas.py +++ b/dandi/tests/test_brain_areas.py @@ -166,10 +166,13 @@ def test_related_synonym_excluded_by_default(self) -> None: result = match_location_to_uberon("encephalon") assert result is None + def test_related_synonym_excluded_at_broad(self) -> None: + # BROAD doesn't include RELATED + result = match_location_to_uberon("encephalon", max_synonym_scope="BROAD") + assert result is None + def test_related_synonym_included_when_requested(self) -> None: - result = match_location_to_uberon( - "encephalon", synonym_scopes=frozenset({"EXACT", "RELATED"}) - ) + result = match_location_to_uberon("encephalon", max_synonym_scope="RELATED") assert result is not None assert result.name == "brain" From 2dc05ecc7729fdf42ae9248f21657947a022a01e Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Sun, 29 Mar 2026 12:44:58 -0400 Subject: [PATCH 4/5] feat: add max_synonym_scope parameter to _extract_brain_anatomy 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) --- dandi/metadata/util.py | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/dandi/metadata/util.py b/dandi/metadata/util.py index 56d03bcb8..272296513 100644 --- a/dandi/metadata/util.py +++ b/dandi/metadata/util.py @@ -600,11 +600,21 @@ def extract_wasDerivedFrom(metadata: dict) -> list[models.BioSample] | None: _MOUSE_URI = NCBITAXON_URI_TEMPLATE.format("10090") -def _extract_brain_anatomy(metadata: dict) -> list[models.Anatomy]: +def _extract_brain_anatomy( + metadata: dict, max_synonym_scope: str = "EXACT" +) -> list[models.Anatomy]: """Extract brain anatomy from metadata. For mice, tries Allen CCF first then falls back to UBERON. For other species, tries UBERON directly. + + Parameters + ---------- + metadata : dict + NWB metadata dictionary. + max_synonym_scope : str + Most permissive UBERON synonym scope to try. Tiers are tried + in precision order: EXACT > NARROW > BROAD > RELATED. """ if not (locations := metadata.get("brain_locations")): return [] @@ -614,9 +624,9 @@ def _extract_brain_anatomy(metadata: dict) -> list[models.Anatomy]: return [] if str(species.identifier) == _MOUSE_URI: - return locations_to_mouse_anatomy(locations) + return locations_to_mouse_anatomy(locations, max_synonym_scope) else: - return locations_to_uberon_anatomy(locations) + return locations_to_uberon_anatomy(locations, max_synonym_scope) extract_wasAttributedTo = extract_model_list( From e40872cf09cf180977a89f48e2c47f1962501f1e Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Mon, 30 Mar 2026 11:33:59 -0400 Subject: [PATCH 5/5] refactor: address PR review feedback - 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) --- .pre-commit-config.yaml | 3 +- dandi/cli/cmd_service_scripts.py | 14 + dandi/data/generate_uberon_structures.py | 51 +- dandi/data/uberon_brain_structures.json | 52483 ++++++++++++++++++++- dandi/metadata/brain_areas.py | 10 +- pyproject.toml | 2 +- 6 files changed, 52531 insertions(+), 32 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6a44e29d5..1f3ed5c30 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -8,6 +8,7 @@ repos: - id: end-of-file-fixer - id: check-yaml - id: check-added-large-files + exclude: ^dandi/data/.*_structures\.json$ - repo: https://github.com/psf/black rev: 22.3.0 hooks: @@ -22,7 +23,7 @@ repos: rev: v2.4.1 hooks: - id: codespell - exclude: ^(dandi/_version\.py|dandi/due\.py|versioneer\.py|pyproject\.toml|dandi/data/allen_ccf_structures\.json|dandi/data/uberon_brain_structures\.json)$ + exclude: ^(dandi/_version\.py|dandi/due\.py|versioneer\.py|pyproject\.toml|dandi/data/.*_structures\.json)$ additional_dependencies: - tomli; python_version<'3.11' - repo: https://github.com/PyCQA/flake8 diff --git a/dandi/cli/cmd_service_scripts.py b/dandi/cli/cmd_service_scripts.py index 8e55645c0..853f244b8 100644 --- a/dandi/cli/cmd_service_scripts.py +++ b/dandi/cli/cmd_service_scripts.py @@ -42,6 +42,20 @@ def service_scripts() -> None: pass +@service_scripts.command() +@map_to_click_exceptions +def generate_uberon_structures() -> None: + """Regenerate uberon_brain_structures.json from the UBERON OBO file. + + Downloads the UBERON ontology, extracts brain/nervous-system + descendants (~2,400 terms), and writes the bundled JSON used for + anatomy matching. + """ + from ..data.generate_uberon_structures import generate + + generate() + + @service_scripts.command() @click.option("--diff", is_flag=True, help="Show diffs of old & new metadata") @click.option( diff --git a/dandi/data/generate_uberon_structures.py b/dandi/data/generate_uberon_structures.py index f4158c5eb..668a9d968 100644 --- a/dandi/data/generate_uberon_structures.py +++ b/dandi/data/generate_uberon_structures.py @@ -1,26 +1,32 @@ -#!/usr/bin/env python3 """Regenerate uberon_brain_structures.json from the UBERON OBO file. -Run: python -m dandi.data.generate_uberon_structures - Downloads the UBERON OBO file, parses it without any library dependency, -extracts brain/nervous system descendants, and writes a compact JSON file. +extracts brain/nervous system descendants, and writes the bundled JSON. + +Can be run via:: + + dandi service-scripts generate-uberon-structures """ from __future__ import annotations from collections import defaultdict import json +import logging from pathlib import Path import re import requests +lgr = logging.getLogger(__name__) + # Root terms whose descendants (via is_a and part_of) we collect. _ROOT_IDS = frozenset({"UBERON:0001016", "UBERON:0000955"}) # nervous system, brain +_OUTPUT_PATH = Path(__file__).with_name("uberon_brain_structures.json") -def _parse_obo_terms(text: str) -> list[dict]: # pragma: no cover + +def _parse_obo_terms(text: str) -> list[dict]: """Parse [Term] stanzas from raw OBO text.""" terms: list[dict] = [] in_term = False @@ -62,8 +68,9 @@ def _parse_obo_terms(text: str) -> list[dict]: # pragma: no cover if parent_id.startswith("UBERON:"): current["parents"].append(parent_id) elif line.startswith("synonym: "): - 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 + ): current["synonyms"].append({"text": m.group(1), "scope": m.group(2)}) if current.get("id"): @@ -71,9 +78,7 @@ def _parse_obo_terms(text: str) -> list[dict]: # pragma: no cover return terms -def _collect_descendants( - terms: list[dict], root_ids: frozenset[str] -) -> set[str]: # pragma: no cover +def _collect_descendants(terms: list[dict], root_ids: frozenset[str]) -> set[str]: """BFS from root_ids through children (reverse of is_a/part_of) edges.""" children: dict[str, list[str]] = defaultdict(list) for t in terms: @@ -91,22 +96,23 @@ def _collect_descendants( return visited -def main() -> None: # pragma: no cover +def generate(output: Path = _OUTPUT_PATH) -> None: + """Download UBERON OBO and write brain/nervous-system structures JSON.""" url = "http://purl.obolibrary.org/obo/uberon.obo" - print(f"Downloading {url} ...") + lgr.info("Downloading %s ...", url) resp = requests.get(url, timeout=120) resp.raise_for_status() - print(f"Downloaded {len(resp.text)} bytes, parsing ...") + lgr.info("Downloaded %d bytes, parsing ...", len(resp.text)) all_terms = _parse_obo_terms(resp.text) - print(f"Parsed {len(all_terms)} terms") + lgr.info("Parsed %d terms", len(all_terms)) # Filter to UBERON terms only (skip cross-ontology references) uberon_terms = [t for t in all_terms if t["id"].startswith("UBERON:")] - print(f"UBERON terms: {len(uberon_terms)}") + lgr.info("UBERON terms: %d", len(uberon_terms)) descendant_ids = _collect_descendants(uberon_terms, _ROOT_IDS) - print(f"Nervous system descendants (including roots): {len(descendant_ids)}") + lgr.info("Nervous system descendants (including roots): %d", len(descendant_ids)) structures: list[dict] = [] for t in uberon_terms: @@ -115,19 +121,14 @@ def main() -> None: # pragma: no cover numeric_id = t["id"].replace("UBERON:", "") entry: dict = {"id": numeric_id, "name": t["name"]} if t["synonyms"]: - # Compact format: [text, scope_letter] to keep file under 500KB + # Compact format: [text, scope_letter] entry["synonyms"] = [ [syn["text"], syn["scope"][0]] for syn in t["synonyms"] ] structures.append(entry) structures.sort(key=lambda s: s["id"]) - out_path = Path(__file__).with_name("uberon_brain_structures.json") - with open(out_path, "w") as f: - json.dump(structures, f, separators=(",", ":")) + with open(output, "w") as f: + json.dump(structures, f, indent=1) f.write("\n") - print(f"Wrote {len(structures)} structures to {out_path}") - - -if __name__ == "__main__": # pragma: no cover - main() + lgr.info("Wrote %d structures to %s", len(structures), output) diff --git a/dandi/data/uberon_brain_structures.json b/dandi/data/uberon_brain_structures.json index 61f62727f..5f83cbef0 100644 --- a/dandi/data/uberon_brain_structures.json +++ b/dandi/data/uberon_brain_structures.json @@ -1 +1,52482 @@ -[{"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 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Rolando","R"]]},{"id":"0002622","name":"preoptic periventricular nucleus","synonyms":[["dorsal periventricular hypothalamic nucleus","R"],["nucleus periventricularis hypothalami, pars dorsalis","R"],["nucleus periventricularis praeopticus","R"],["nucleus periventricularis preopticus","R"],["nucleus preopticus periventricularis","E"],["periventricular hypothalamic nucleus, preoptic part","R"],["periventricular nucleus, anterior portion","R"],["periventricular preoptic nucleus","E"],["POP","B"],["preoptic periventricular hypothalamic nucleus","E"]]},{"id":"0002623","name":"cerebral peduncle","synonyms":[["cerebal peduncle","R"],["cerebral peduncle","E"],["cerebral peduncle (archaic)","R"],["CP","B"],["peduncle of midbrain","E"],["pedunculi cerebri","R"],["pedunculus cerebralis","R"],["pedunculus cerebri","E"],["pedunculus cerebri","R"],["tegmentum","R"]]},{"id":"0002624","name":"orbital part of inferior frontal gyrus","synonyms":[["brodmann's area 36","R"],["gyrus frontalis inferior, 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nucleus","R"]]},{"id":"0002630","name":"body of caudate nucleus","synonyms":[["body of the caudate nucleus","R"],["caudate body","R"],["caudate nuclear body","E"],["corpus (caudatus)","E"],["corpus nuclei caudati","R"]]},{"id":"0002631","name":"cerebral crus","synonyms":[["base of cerebral peduncle","R"],["basis cerebri (Oertel)","R"],["basis pedunculi (Oertel)","R"],["basis pedunculi cerebri (Willis)","R"],["CCR","B"],["cerebral peduncle (clinical definition)","E"],["cerebral peduncle, basal part","R"],["crura cerebri","E"],["crus cerebri","E"],["crus cerebri","R"],["crus of the cerebral peduncle","R"],["pars neo-encephalica pedunculi","R"],["pedunculus cerebri, pars basalis","R"],["pes pedunculi","R"],["pes pedunculi of midbrain","R"]]},{"id":"0002632","name":"medial part of medial mammillary nucleus","synonyms":[["medial mamillary nucleus","R"],["medial mammillary nucleus (carpenter)","E"],["medial mammillary nucleus median part","R"],["medial mammillary nucleus, medial part","E"],["medial mammillary nucleus, median part","E"],["medial part of the medial mammillary nucleus","R"],["medial subdivision of medial mammillary nucleus","E"],["MML","B"],["nucleus corporis mamillaris medialis, pars medialis","R"],["nucleus medialis corpus mamillaris (Shantha)","R"]]},{"id":"0002633","name":"motor nucleus of trigeminal nerve","synonyms":[["motor nucleus","R"],["motor nucleus of cranial nerve v","E"],["motor nucleus of the trigeminal","R"],["motor nucleus of the trigeminal nerve","R"],["motor nucleus of trigeminal","R"],["motor nucleus of trigeminal nerve","E"],["motor nucleus V","E"],["motor trigeminal nucleus","E"],["nucleus motorius nervi trigeminalis","R"],["nucleus motorius nervi trigemini","E"],["nucleus motorius nervi trigemini","R"],["nucleus motorius trigeminalis","R"],["nV","E"],["trigeminal motor nuclei","E"],["trigeminal motor nucleus","E"],["trigeminal V motor nucleus","E"]]},{"id":"0002634","name":"anterior nucleus of hypothalamus","synonyms":[["AH","B"],["anterior hypothalamic area","R"],["anterior hypothalamic area anterior part","R"],["anterior hypothalamic area, anterior part","R"],["anterior hypothalamic nucleus","E"],["anterior nucleus of the hypothalamus","R"],["area hypothalamica rostralis","E"],["fundamental gray substance","E"],["nucleus anterior hypothalami","R"],["nucleus hypothalamicus anterior","R"],["parvocellular nucleus of hypothalamus","E"]]},{"id":"0002636","name":"lateral pulvinar nucleus","synonyms":[["lateral pulvinar nucleus of thalamus","E"],["LPul","B"],["nucleus pulvinaris lateralis","E"],["nucleus pulvinaris lateralis (Hassler)","E"],["nucleus pulvinaris lateralis thalami","E"],["nucleus pulvinaris thalami, pars 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 midbrain","E"],["substantia reticularis mesencephali","R"],["tegmental reticular formation","E"]]},{"id":"0002640","name":"cuneocerebellar tract","synonyms":[["cuneocerebellar fibers","E"],["tractus cuneocerebelli","R"]]},{"id":"0002641","name":"oral pulvinar 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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 medulla","E"]]},{"id":"0002647","name":"magnocellular part of medial dorsal nucleus","synonyms":[["dorsomedial thalamic nucleus, magnocellular part","E"],["magnocellular mediodorsal nucleus","E"],["magnocellular nucleus of medial dorsal nucleus of thalamus","E"],["magnocellular part of dorsomedial 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part","R"],["paralaminar part of dorsomedial nucleus","E"],["paralaminar part of medial dorsal nucleus of thalamus","E"],["paralaminar part of the medial dorsal nucleus","R"],["pars paralaminaris nuclei mediodorsalis thalami","E"],["pars paralaminaris of medial dorsal nucleus of thalamus","E"],["ventral mediodorsal nucleus","E"]]},{"id":"0002651","name":"anterior horn of lateral ventricle","synonyms":[["anterior horn of lateral ventricle","E"],["cornu anterius","R"],["cornu anterius (ventriculi lateralis)","E"],["cornu anterius ventriculi lateralis","E"],["cornu frontale (ventriculi lateralis)","E"],["cornu frontale ventriculi lateralis","E"],["frontal horn of lateral ventricle","E"],["ventriculus lateralis, cornu anterius","E"]]},{"id":"0002652","name":"posterior median eminence","synonyms":[["eminentia mediana posterior","R"],["PME","B"]]},{"id":"0002653","name":"gracile fasciculus of medulla","synonyms":[["column of Goll","E"],["fasciculus dorsolateralis gracilis (Golli)","R"],["fasciculus gracilis (myelencephali)","R"],["fasciculus of goll","E"],["Goll's tract","E"],["gracile fascicle (Gall)","R"],["gracile fascicle (Goll)","R"],["gracile fascicle of medulla","E"],["gracile fasciculus of the medulla","R"],["medulla segment of fasciculus gracilis","E"],["medulla segment of gracile fasciculus","E"],["tract of Gall","R"]]},{"id":"0002654","name":"parvocellular part of medial dorsal nucleus","synonyms":[["dorsomedial thalamic nucleus, parvicellular part","E"],["lateral mediodorsal nucleus","E"],["lateral nucleus of medial dorsal nucleus of thalamus","E"],["MDPC","B"],["mediodorsal thalamic nucleus, pars fasciculosa","E"],["nucleus medialis dorsalis fasciculosis (hassler)","E"],["nucleus medialis dorsalis nucleus fasciculosis (hassler)","E"],["nucleus medialis dorsalis nucleus fasciculosus (Hassler)","R"],["nucleus medialis dorsalis, pars parvicellularis","E"],["nucleus medialis dorsalis, pars parvocellularis","R"],["pars parvocellularis lateralis nuclei mediodorsalis thalami","E"],["pars principalis nuclei ventralis anterior thalami","E"],["parvicellular part of dorsomedial nucleus","E"],["parvicellular part of medial dorsal nucleus","E"],["parvicellular part of the medial dorsal nucleus","R"],["parvocellular nucleus of medial dorsal nucleus of thalamus","E"],["principal division of ventral anterior nucleus of thalamus","E"]]},{"id":"0002655","name":"body of lateral ventricle","synonyms":[["central part of lateral ventricle","E"],["corpus ventriculi lateralis","E"],["lateral ventricular body","E"],["pars centralis (ventriculi lateralis)","E"],["pars centralis ventriculi lateralis","E"],["pars centralis ventriculi 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 velum","E"],["rostral medullary velum","R"],["velum medullare anterius","R"],["velum medullare craniale","R"],["velum medullare rostralis","R"],["velum medullare superior","R"],["velum medullare superius","R"]]},{"id":"0002660","name":"medial longitudinal fasciculus of midbrain","synonyms":[["fasciculus longitudinalis medialis (mesencephali)","R"],["medial longitudinal fasciculus of the midbrain","R"],["midbrain medial longitudinal fasciculus","E"],["MLFMB","B"]]},{"id":"0002661","name":"superior frontal gyrus","synonyms":[["gyrus F1","R"],["gyrus frontalis primus","R"],["gyrus frontalis superior","R"],["marginal gyrus","E"],["superior frontal convolution","E"]]},{"id":"0002662","name":"medial pes lemniscus","synonyms":[["MPL","B"],["pes lemniscus medialis","R"],["superficial pes lemniscus","E"]]},{"id":"0002663","name":"septal nuclear complex","synonyms":[["nuclei septales","R"],["parolfactory nuclei","E"],["septal nuclei","E"],["septal nucleus","E"]]},{"id":"0002664","name":"lateral part of medial mammillary nucleus","synonyms":[["intercalated mammillary nucleus","E"],["intermediate mammillary nucleus","E"],["lateral mammillary nucleus (gagel)","E"],["lateral part of the medial mammillary nucleus","R"],["lateral subdivision of medial mammillary nucleus","E"],["medial mammillary nucleus lateral part","R"],["medial mammillary nucleus, lateral part","E"],["MML","B"],["nucleus corporis mamillaris medialis, pars lateralis","R"],["nucleus intercalatus corporis mammillaris","R"],["nucleus intermedius corpus mamillaris","R"]]},{"id":"0002666","name":"mesencephalic tract of trigeminal nerve","synonyms":[["me5","B"],["mesencephalic root of v","E"],["mesencephalic tract of the trigeminal nerve","R"],["mesencephalic trigeminal tract","E"],["midbrain tract of the trigeminal nerve","R"],["tractus mesencephalicus nervi trigeminalis","R"],["tractus mesencephalicus nervi trigemini","R"],["tractus mesencephalicus trigeminalis","R"]]},{"id":"0002667","name":"lateral septal nucleus","synonyms":[["lateral parolfactory nucleus","E"],["lateral septal nucleus (cajal)","E"],["lateral septum","E"],["lateral septum nucleus","E"],["nucleus lateralis septi","R"],["nucleus septalis lateralis","R"],["nucleus septi lateralis","R"]]},{"id":"0002668","name":"oculomotor nerve 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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 pallidoolivares","R"],["pallidotegmental fascicle","R"],["pallidotegmental tract","E"],["PTF","B"]]},{"id":"0002672","name":"anterior subcentral sulcus","synonyms":[["anterior subcentral sulcus","R"],["sulcus subcentralis anterior","R"]]},{"id":"0002673","name":"vestibular nuclear complex","synonyms":[["nuclei vestibulares","R"],["nuclei vestibulares in medulla oblongata","E"],["vestibular nuclei","E"],["vestibular nuclei in medulla oblongata","E"],["vestibular nucleus","R"]]},{"id":"0002675","name":"diagonal sulcus","synonyms":[["sulcus diagonalis","R"]]},{"id":"0002679","name":"anterodorsal nucleus of thalamus","synonyms":[["AD","B"],["anterior dorsal thalamic nucleus","E"],["anterodorsal nucleus","E"],["anterodorsal nucleus of the thalamus","E"],["anterodorsal thalamic nucleus","E"],["nucleus anterior dorsalis","E"],["nucleus anterior dorsalis thalami","E"],["nucleus anterior thalami dorsalis","E"],["nucleus anterodorsalis","E"],["nucleus anterodorsalis (hassler)","E"],["nucleus 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 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part","E"],["medial geniculate nucleus medial part","R"],["medial geniculate nucleus, medial part","E"],["medial magnocellular nucleus of medial geniculate body","E"],["medial nucleus of medial geniculate body","E"],["MMG","B"],["nucleus corporis geniculati medialis, pars magnocelluaris","E"],["nucleus corporis geniculati medialis, pars magnocellularis","R"],["nucleus geniculatus medialis magnocelluaris (hassler)","E"],["nucleus geniculatus medialis magnocellularis (Hassler)","R"],["nucleus geniculatus medialis, pars magnocelluaris","E"],["nucleus geniculatus medialis, pars magnocellularis","R"],["nucleus medialis 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 thalamus","synonyms":[["envelope (involucrum medial) (Hassler)","E"],["internal medullary lamina","E"],["internal medullary lamina of thalamus","E"],["internal medullary lamina of the thalamus","R"],["lamina medullaris interna","E"],["lamina medullaris interna thalami","E"],["lamina medullaris medialis","B"],["lamina medullaris medialis thalami","E"],["lamina medullaris thalami interna","E"]]},{"id":"0002764","name":"inferior precentral sulcus","synonyms":[["inferior part of precentral fissure","E"],["sulcus praecentralis inferior","E"],["sulcus precentralis inferior","E"]]},{"id":"0002766","name":"fusiform gyrus","synonyms":[["gyrus fusiformis","R"],["gyrus occipito-temporalis lateralis","R"],["gyrus occipitotemporalis lateralis","E"],["lateral occipito-temporal gyrus","R"],["lateral occipitotemporal gyrus","E"],["medial occipitotemporal gyrus-1 (heimer)","E"],["occipito-temporal gyrus","R"],["occipitotemporal gyrus","E"],["t4","R"]]},{"id":"0002767","name":"inferior rostral 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 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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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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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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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+ { + "id": "8440011", + "name": "cortical visual area" + }, + { + "id": "8440012", + "name": "cerebral nuclei", + "synonyms": [ + [ + "CNU", + "E" + ] + ] + }, + { + "id": "8440013", + "name": "fasciola cinerea", + "synonyms": [ + [ + "FC", + "E" + ] + ] + }, + { + "id": "8440014", + "name": "ventrolateral preoptic nucleus", + "synonyms": [ + [ + "intermediate nucleus of the preoptic area (IPA)", + "E" + ], + [ + "VLPO", + "E" + ] + ] + }, + { + "id": "8440015", + "name": "noradrenergic cell groups" + }, + { + "id": "8440016", + "name": "noradrenergic cell group A1" + }, + { + "id": "8440017", + "name": "noradrenergiccell group A2" + }, + { + "id": "8440018", + "name": "noradrenergic cell group A4" + }, + { + "id": "8440019", + "name": "noradrenergic cell group A5" + }, + { + "id": "8440021", + "name": "noradrenergic cell group A7" + }, + { + "id": "8440022", + "name": "noradrenergic cell group A6sc" + }, + { + "id": "8440023", + "name": "noradrenergic cell group Acg" + }, + { + "id": "8440024", + "name": "visceral area", + "synonyms": [ + [ + "VISC", + "E" + ] + ] + }, + { + "id": "8440025", + "name": "parapyramidal nucleus", + "synonyms": [ + [ + "PPY", + "E" + ] + ] + }, + { + "id": "8440026", + "name": "parapyramidal nucleus, deep part", + "synonyms": [ + [ + "PPYd", + "E" + ] + ] + }, + { + "id": "8440027", + "name": "parapyramidal nucleus, superficial part", + "synonyms": [ + [ + "PPYs", + "E" + ] + ] + }, + { + "id": "8440028", + "name": "Perihypoglossal nuclei", + "synonyms": [ + [ + "nuclei perihypoglossales", + "E" + ], + [ + "perihypoglossal complex", + "E" + ], + [ + "perihypoglossal nuclear complex", + "E" + ], + [ + "PHY", + "E" + ], + [ + "satellite nuclei", + "E" + ] + ] + }, + { + "id": "8440029", + "name": "rubroreticular tract" + }, + { + "id": "8440030", + "name": "striatum-like amygdalar nuclei", + "synonyms": [ + [ + "sAMY", + "E" + ] + ] + }, + { + "id": "8440031", + "name": "medial corticohypothalmic tract", + "synonyms": [ + [ + "mct", + "E" + ] + ] + }, + { + "id": "8440032", + "name": "prelimbic area", + "synonyms": [ + [ + "PL", + "E" + ], + [ + "prelimbic cortex", + "E" + ], + [ + "PrL", + "E" + ] + ] + }, + { + "id": "8440033", + "name": "infralimbic area", + "synonyms": [ + [ + "IL (brain)", + "E" + ], + [ + "ILA", + "E" + ], + [ + "infralimbic cortex", + "E" + ] + ] + }, + { + "id": "8440034", + "name": "bulbocerebellar tract", + "synonyms": [ + [ + "bct", + "E" + ] + ] + }, + { + "id": "8440035", + "name": "sublaterodorsal nucleus", + "synonyms": [ + [ + "SLD", + "E" + ], + [ + "sublaterodorsal tegmental nucleus", + "E" + ] + ] + }, + { + "id": "8440036", + "name": "supratrigeminal nucleus", + "synonyms": [ + [ + "SUT", + "E" + ], + [ + "Vsup", + "E" + ] + ] + }, + { + "id": "8440037", + "name": "accessory facial motor nucleus", + "synonyms": [ + [ + "ACVII", + "E" + ] + ] + }, + { + "id": "8440038", + "name": "efferent vestibular nucleus", + "synonyms": [ + [ + "EV", + "E" + ] + ] + }, + { + "id": "8440039", + "name": "piriform-amygdalar area", + "synonyms": [ + [ + "PAA (brain)", + "E" + ] + ] + }, + { + "id": "8440040", + "name": "dorsal peduncular area", + "synonyms": [ + [ + "DP", + "E" + ] + ] + }, + { + "id": "8440041", + "name": "tuberal nucleus (sensu Rodentia)", + "synonyms": [ + [ + "lateral tuberal nucleus (sensu Rodentia)", + "B" + ], + [ + "lateral tuberal nucleus (sensu Rodentia)", + "E" + ] + ] + }, + { + "id": "8440042", + "name": "nucleus lateralis tuberis system (sensu Teleostei)", + "synonyms": [ + [ + "NLT system (sensu Teleostei)", + "E" + ] + ] + }, + { + "id": "8440043", + "name": "superior paraolivary nucleus", + "synonyms": [ + [ + "SPON", + "E" + ] + ] + }, + { + "id": "8440044", + "name": "upper layers of the cortex" + }, + { + "id": "8440045", + "name": "second visual cortical area (sensu Mustela putorius furo)", + "synonyms": [ + [ + "area 18 (sensu Mustela putorius furo)", + "E" + ] + ] + }, + { + "id": "8440046", + "name": "third visual cortical area (sensu Mustela putorius furo)", + "synonyms": [ + [ + "area 19 (sensu Mustela putorius furo)", + "E" + ] + ] + }, + { + "id": "8440047", + "name": "fourth visual cortical area (sensu Mustela putorius furo)", + "synonyms": [ + [ + "area 21 (sensu Mustela putorius furo)", + "E" + ] + ] + }, + { + "id": "8440048", + "name": "temporal visual area a (sensu Mustela putorius furo)", + "synonyms": [ + [ + "area 20a (sensu Mustela putorius furo)", + "E" + ] + ] + }, + { + "id": "8440049", + "name": "temporal visual area b (sensu Mustela putorius furo)", + "synonyms": [ + [ + "area 20b (sensu Mustela putorius furo)", + "E" + ] + ] + }, + { + "id": "8440050", + "name": "posterior parietal rostral cortical area (sensu Mustela putorius furo)", + "synonyms": [ + [ + "posterior parietal cortex, rostral part (sensu Mustela putorius furo)", + "E" + ], + [ + "PPr (sensu Mustela putorius furo)", + "E" + ] + ] + }, + { + "id": "8440051", + "name": "lower layers of the cortex" + }, + { + "id": "8440052", + "name": "posterior parietal caudal cortical area (sensu Mustela putorius furo)", + "synonyms": [ + [ + "posterior parietal cortex, caudal part (sensu Mustela putorius furo)", + "E" + ], + [ + "PPc (sensu Mustela putorius furo)", + "E" + ] + ] + }, + { + "id": "8440054", + "name": "anteromedial lateral suprasylvian visual area (sensu Mustela putorius furo)", + "synonyms": [ + [ + "AMLS (sensu Mustela putorius furo)", + "E" + ] + ] + }, + { + "id": "8440055", + "name": "anterolateral lateral suprasylvian visual area (sensu Mustela putorius furo)", + "synonyms": [ + [ + "ALLS (sensu Mustela putorius furo)", + "E" + ] + ] + }, + { + "id": "8440056", + "name": "posteromedial lateral suprasylvian visual area (sensu Mustela putorius furo)", + "synonyms": [ + [ + "PMLS (sensu Mustela putorius furo)", + "E" + ], + [ + "PPS (sensu Mustela putorius furo)", + "E" + ], + [ + "PSS (sensu Mustela putorius furo)", + "E" + ], + [ + "SSY (sensu Mustela putorius furo)", + "E" + ], + [ + "Ssy (sensu Mustela putorius furo)", + "E" + ], + [ + "suprasylvian sulcal visual area (sensu Mustela putorius furo)", + "E" + ] + ] + }, + { + "id": "8440059", + "name": "posterolateral lateral suprasylvian visual area (sensu Mustela putorius furo)", + "synonyms": [ + [ + "PLLS (sensu Mustela putorius furo)", + "E" + ] + ] + }, + { + "id": "8440060", + "name": "dorsal lateral suprasylvian visual cortical area (sensu Mustela putorius furo)", + "synonyms": [ + [ + "DLS (sensu Mustela putorius furo)", + "E" + ] + ] + }, + { + "id": "8440061", + "name": "ventral lateral suprasylvian visual area (sensu Mustela putorius furo)", + "synonyms": [ + [ + "VLS (sensu Mustela putorius furo)", + "E" + ] + ] + }, + { + "id": "8440062", + "name": "posterior suprasylvian visual cortical area (sensu Mustela putorius furo)", + "synonyms": [ + [ + "PS (sensu Mustela putorius furo)", + "E" + ] + ] + }, + { + "id": "8440072", + "name": "lateral tegmental nucleus", + "synonyms": [ + [ + "LTN", + "E" + ] + ] + }, + { + "id": "8440073", + "name": "magnocellular reticular nucleus", + "synonyms": [ + [ + "MARN", + "E" + ] + ] + }, + { + "id": "8440074", + "name": "interstitial nucleus of the vestibular nerve", + "synonyms": [ + [ + "INV", + "E" + ], + [ + "ISVe", + "E" + ] + ] + }, + { + "id": "8440075", + "name": "gustatory cortex", + "synonyms": [ + [ + "gustatory area", + "E" + ] + ] + }, + { + "id": "8440076", + "name": "somatomotor area" + }, + { + "id": "8480001", + "name": "capillary of brain" + }, + { + "id": "8600066", + "name": "basivertebral vein" + }, + { + "id": "8600076", + "name": "suboccipital venous plexus" + }, + { + "id": "8600090", + "name": "hypophyseal vein" + }, + { + "id": "8600103", + "name": "anterior internal vertebral venous plexus" + }, + { + "id": "8600104", + "name": "intervertebral vein" + }, + { + "id": "8600118", + "name": "myenteric ganglion", + "synonyms": [ + [ + "myenteric plexus ganglion", + "E" + ] + ] + }, + { + "id": "8600119", + "name": "myenteric ganglion of small intestine" + }, + { + "id": "8600120", + "name": "atrial intrinsic cardiac ganglion", + "synonyms": [ + [ + "atrial ganglionated plexus", + "R" + ] + ] + }, + { + "id": "8600121", + "name": "lumbar ganglion", + "synonyms": [ + [ + "lumbar paravertebral ganglion", + "E" + ], + [ + "lumbar sympathetic ganglion", + "E" + ] + ] + }, + { + "id": "8600122", + "name": "sacral ganglion", + "synonyms": [ + [ + "sacral sympathetic ganglion", + "E" + ] + ] + }, + { + "id": "8600123", + "name": "lower airway ganglion", + "synonyms": [ + [ + "lower airway parasympathetic ganglion", + "E" + ] + ] + }, + { + "id": "8900000", + "name": "sensory corpuscle", + "synonyms": [ + [ + "COEC", + "R" + ], + [ + "cutaneous end-organ complex", + "E" + ] + ] + } +] diff --git a/dandi/metadata/brain_areas.py b/dandi/metadata/brain_areas.py index 6530ee586..5733a1277 100644 --- a/dandi/metadata/brain_areas.py +++ b/dandi/metadata/brain_areas.py @@ -368,14 +368,16 @@ def match_location_to_uberon( return None # Always try term names first - s = _lookup_in_dicts(token_stripped, *_build_uberon_lookup_dicts("_NAME")) - if s is not None: + if ( + s := _lookup_in_dicts(token_stripped, *_build_uberon_lookup_dicts("_NAME")) + ) is not None: return _uberon_structure_to_anatomy(s) # Try synonym tiers in precision order for scope in _scopes_up_to(max_synonym_scope): - s = _lookup_in_dicts(token_stripped, *_build_uberon_lookup_dicts(scope)) - if s is not None: + if ( + s := _lookup_in_dicts(token_stripped, *_build_uberon_lookup_dicts(scope)) + ) is not None: return _uberon_structure_to_anatomy(s) return None diff --git a/pyproject.toml b/pyproject.toml index 8feab9796..a8d8a5e12 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -161,7 +161,7 @@ tag_prefix = "" parentdir_prefix = "" [tool.codespell] -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" # Don't warn about "[l]ist" in the abbrev_prompt() docstring: # TE is present in the BIDS schema ignore-regex = "(\\[\\w\\]\\w+|TE|ignore \"bu\" strings)"