diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 13133dcd3..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)$ + 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 new file mode 100644 index 000000000..668a9d968 --- /dev/null +++ b/dandi/data/generate_uberon_structures.py @@ -0,0 +1,134 @@ +"""Regenerate uberon_brain_structures.json from the UBERON OBO file. + +Downloads the UBERON OBO file, parses it without any library dependency, +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]: + """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: "): + 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"): + terms.append(current) + return terms + + +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: + 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 generate(output: Path = _OUTPUT_PATH) -> None: + """Download UBERON OBO and write brain/nervous-system structures JSON.""" + url = "http://purl.obolibrary.org/obo/uberon.obo" + lgr.info("Downloading %s ...", url) + resp = requests.get(url, timeout=120) + resp.raise_for_status() + lgr.info("Downloaded %d bytes, parsing ...", len(resp.text)) + + all_terms = _parse_obo_terms(resp.text) + 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:")] + lgr.info("UBERON terms: %d", len(uberon_terms)) + + descendant_ids = _collect_descendants(uberon_terms, _ROOT_IDS) + lgr.info("Nervous system descendants (including roots): %d", 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] + entry["synonyms"] = [ + [syn["text"], syn["scope"][0]] for syn in t["synonyms"] + ] + structures.append(entry) + + structures.sort(key=lambda s: s["id"]) + with open(output, "w") as f: + json.dump(structures, f, indent=1) + f.write("\n") + 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 new file mode 100644 index 000000000..5f83cbef0 --- /dev/null +++ b/dandi/data/uberon_brain_structures.json @@ -0,0 +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 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"2005020", + "name": "central artery", + "synonyms": [ + [ + "CtA", + "E" + ] + ] + }, + { + "id": "2005021", + "name": "cerebellar central artery", + "synonyms": [ + [ + "CCtA", + "E" + ] + ] + }, + { + "id": "2005031", + "name": "dorsal longitudinal vein", + "synonyms": [ + [ + "DLV", + "E" + ] + ] + }, + { + "id": "2005052", + "name": "anterior mesencephalic central artery", + "synonyms": [ + [ + "AMCtA", + "E" + ], + [ + "rostral mesencephalic central artery", + "E" + ] + ] + }, + { + "id": "2005078", + "name": "middle mesencephalic central artery", + "synonyms": [ + [ + "MMCtA", + "E" + ] + ] + }, + { + "id": "2005079", + "name": "posterior mesencephalic central artery", + "synonyms": [ + [ + "caudal mesencephalic central artery", + "E" + ], + [ + "PMCtA", + "E" + ] + ] + }, + { + "id": "2005144", + "name": "ampullary nerve" + }, + { + "id": "2005219", + "name": "choroid plexus vascular circuit", + "synonyms": [ + [ + "choroid vascular circuit", + "R" + ], + [ + "CVC", + "E" + ] + 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"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..5733a1277 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 +254,208 @@ 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 + + +# 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( + scope: str, +) -> tuple[dict[str, dict], dict[str, dict]]: + """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 + ---------- + 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 texts to structure dicts. + """ + structures = _load_uberon_structures() + name_exact: dict[str, dict] = {} + name_lower: dict[str, dict] = {} + for s in structures: + 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, + max_synonym_scope: str = "EXACT", +) -> models.Anatomy | None: + """Match a single location token against UBERON brain structures. + + 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. + 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 + """ + token_stripped = token.strip() + if not token_stripped: + return None + + # Always try term names first + 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): + if ( + s := _lookup_in_dicts(token_stripped, *_build_uberon_lookup_dicts(scope)) + ) 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], + max_synonym_scope: str = "EXACT", +) -> list[models.Anatomy]: + """Convert raw NWB location strings to deduplicated UBERON Anatomy list. + + Parameters + ---------- + locations : list[str] + Raw location strings from NWB file. + max_synonym_scope : str + Most permissive synonym scope to try (see + :func:`match_location_to_uberon`). + + 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, max_synonym_scope) + 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], + max_synonym_scope: str = "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. + max_synonym_scope : str + Most permissive synonym scope for UBERON fallback (see + :func:`match_location_to_uberon`). + + 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, max_synonym_scope) + 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..272296513 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: @@ -600,16 +600,33 @@ 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]: - """Extract brain anatomy from metadata, if the species is mouse.""" +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 [] 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, max_synonym_scope) + else: + return locations_to_uberon_anatomy(locations, max_synonym_scope) extract_wasAttributedTo = extract_model_list( diff --git a/dandi/tests/test_brain_areas.py b/dandi/tests/test_brain_areas.py index f6c2ae66c..973e6f20f 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 +131,105 @@ 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_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", max_synonym_scope="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 result.name is not None and "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..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" +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)"