add hra brain terms

bulk_ntr_workflow/outputs/definitions/input/uberon_0001876.json

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+{
+  "group_name": "uberon_0001876",
+  "parent_id": "UBERON:0001876",
+  "parent_label": "",
+  "term_counts": {
+    "leaf": 1,
+    "group": 0
+  },
+  "note": "parent_label is best-effort; subagent should resolve via OLS4. For term_type='group' terms: use obo-grep on uberon-edit.obo to find similar UBERON groupings, identify the genus + part_of pattern, and fill genus + location. If pattern doesn't fit, route to manual_curation.",
+  "terms": [
+    {
+      "ntr_id": "http://purl.obolibrary.org/obo/UBERON_9920005",
+      "label": "extended amygdala",
+      "term_type": "leaf",
+      "system": "default",
+      "is_a": "INFER:UBERON:0001876",
+      "part_of": "INFER:UBERON:0001876",
+      "def_xref": "https://purl.org/ccf/ASCTB-TEMP_extended-amygdala"
+    }
+  ]
+}

bulk_ntr_workflow/outputs/definitions/input/uberon_0002021.json

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+{
+  "group_name": "uberon_0002021",
+  "parent_id": "UBERON:0002021",
+  "parent_label": "",
+  "term_counts": {
+    "leaf": 3,
+    "group": 0
+  },
+  "note": "parent_label is best-effort; subagent should resolve via OLS4. For term_type='group' terms: use obo-grep on uberon-edit.obo to find similar UBERON groupings, identify the genus + part_of pattern, and fill genus + location. If pattern doesn't fit, route to manual_curation.",
+  "terms": [
+    {
+      "ntr_id": "http://purl.obolibrary.org/obo/UBERON_9920015",
+      "label": "occipitoparietal transition region",
+      "term_type": "leaf",
+      "system": "default",
+      "is_a": "INFER:UBERON:0002021",
+      "part_of": "INFER:UBERON:0002021",
+      "def_xref": "https://purl.org/ccf/ASCTB-TEMP_occipitoparietal-transition-region"
+    },
+    {
+      "ntr_id": "http://purl.obolibrary.org/obo/UBERON_9920016",
+      "label": "occipitotemporal (fusiform) gyrus, occipital part",
+      "term_type": "leaf",
+      "system": "default",
+      "is_a": "INFER:UBERON:0002021",
+      "part_of": "INFER:UBERON:0002021",
+      "def_xref": "https://purl.org/ccf/ASCTB-TEMP_occipitotemporal-fusiform-gyrus-occipital-part"
+    },
+    {
+      "ntr_id": "http://purl.obolibrary.org/obo/UBERON_9920017",
+      "label": "occipitotemporal transition region",
+      "term_type": "leaf",
+      "system": "default",
+      "is_a": "INFER:UBERON:0002021",
+      "part_of": "INFER:UBERON:0002021",
+      "def_xref": "https://purl.org/ccf/ASCTB-TEMP_occipitotemporal-transition-region"
+    }
+  ]
+}

bulk_ntr_workflow/outputs/definitions/input/uberon_0002285.json

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+{
+  "group_name": "uberon_0002285",
+  "parent_id": "UBERON:0002285",
+  "parent_label": "",
+  "term_counts": {
+    "leaf": 1,
+    "group": 0
+  },
+  "note": "parent_label is best-effort; subagent should resolve via OLS4. For term_type='group' terms: use obo-grep on uberon-edit.obo to find similar UBERON groupings, identify the genus + part_of pattern, and fill genus + location. If pattern doesn't fit, route to manual_curation.",
+  "terms": [
+    {
+      "ntr_id": "http://purl.obolibrary.org/obo/UBERON_9920002",
+      "label": "atrium of lateral ventricle",
+      "term_type": "leaf",
+      "system": "default",
+      "is_a": "INFER:UBERON:0002285",
+      "part_of": "INFER:UBERON:0002285",
+      "def_xref": "https://purl.org/ccf/ASCTB-TEMP_atrium-of-lateral-ventricle"
+    }
+  ]
+}

bulk_ntr_workflow/outputs/definitions/input/uberon_0002421.json

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+{
+  "group_name": "uberon_0002421",
+  "parent_id": "UBERON:0002421",
+  "parent_label": "",
+  "term_counts": {
+    "leaf": 2,
+    "group": 0
+  },
+  "note": "parent_label is best-effort; subagent should resolve via OLS4. For term_type='group' terms: use obo-grep on uberon-edit.obo to find similar UBERON groupings, identify the genus + part_of pattern, and fill genus + location. If pattern doesn't fit, route to manual_curation.",
+  "terms": [
+    {
+      "ntr_id": "http://purl.obolibrary.org/obo/UBERON_9920003",
+      "label": "body of hippocampus",
+      "term_type": "leaf",
+      "system": "default",
+      "is_a": "INFER:UBERON:0002421",
+      "part_of": "INFER:UBERON:0002421",
+      "def_xref": "https://purl.org/ccf/ASCTB-TEMP_body-of-hippocampus"
+    },
+    {
+      "ntr_id": "http://purl.obolibrary.org/obo/UBERON_9920007",
+      "label": "head of hippocampus",
+      "term_type": "leaf",
+      "system": "default",
+      "is_a": "INFER:UBERON:0002421",
+      "part_of": "INFER:UBERON:0002421",
+      "def_xref": "https://purl.org/ccf/ASCTB-TEMP_head-of-hippocampus"
+    }
+  ]
+}

bulk_ntr_workflow/outputs/definitions/input/uberon_0002743.json

@@ -0,0 +1,21 @@
+{
+  "group_name": "uberon_0002743",
+  "parent_id": "UBERON:0002743",
+  "parent_label": "",
+  "term_counts": {
+    "leaf": 1,
+    "group": 0
+  },
+  "note": "parent_label is best-effort; subagent should resolve via OLS4. For term_type='group' terms: use obo-grep on uberon-edit.obo to find similar UBERON groupings, identify the genus + part_of pattern, and fill genus + location. If pattern doesn't fit, route to manual_curation.",
+  "terms": [
+    {
+      "ntr_id": "http://purl.obolibrary.org/obo/UBERON_9920018",
+      "label": "septal nuclei",
+      "term_type": "leaf",
+      "system": "default",
+      "is_a": "INFER:UBERON:0002743",
+      "part_of": "INFER:UBERON:0002743",
+      "def_xref": "https://purl.org/ccf/ASCTB-TEMP_septal-nuclei"
+    }
+  ]
+}

bulk_ntr_workflow/outputs/definitions/input/uberon_0002761.json

@@ -0,0 +1,48 @@
+{
+  "group_name": "uberon_0002761",
+  "parent_id": "UBERON:0002761",
+  "parent_label": "",
+  "term_counts": {
+    "leaf": 4,
+    "group": 0
+  },
+  "note": "parent_label is best-effort; subagent should resolve via OLS4. For term_type='group' terms: use obo-grep on uberon-edit.obo to find similar UBERON groupings, identify the genus + part_of pattern, and fill genus + location. If pattern doesn't fit, route to manual_curation.",
+  "terms": [
+    {
+      "ntr_id": "http://purl.obolibrary.org/obo/UBERON_9920010",
+      "label": "ifs1",
+      "term_type": "leaf",
+      "system": "default",
+      "is_a": "INFER:UBERON:0002761",
+      "part_of": "INFER:UBERON:0002761",
+      "def_xref": "https://purl.org/ccf/ASCTB-TEMP_ifs1"
+    },
+    {
+      "ntr_id": "http://purl.obolibrary.org/obo/UBERON_9920011",
+      "label": "ifs2",
+      "term_type": "leaf",
+      "system": "default",
+      "is_a": "INFER:UBERON:0002761",
+      "part_of": "INFER:UBERON:0002761",
+      "def_xref": "https://purl.org/ccf/ASCTB-TEMP_ifs2"
+    },
+    {
+      "ntr_id": "http://purl.obolibrary.org/obo/UBERON_9920012",
+      "label": "ifs3",
+      "term_type": "leaf",
+      "system": "default",
+      "is_a": "INFER:UBERON:0002761",
+      "part_of": "INFER:UBERON:0002761",
+      "def_xref": "https://purl.org/ccf/ASCTB-TEMP_ifs3"
+    },
+    {
+      "ntr_id": "http://purl.obolibrary.org/obo/UBERON_9920013",
+      "label": "ifs4",
+      "term_type": "leaf",
+      "system": "default",
+      "is_a": "INFER:UBERON:0002761",
+      "part_of": "INFER:UBERON:0002761",
+      "def_xref": "https://purl.org/ccf/ASCTB-TEMP_ifs4"
+    }
+  ]
+}

bulk_ntr_workflow/outputs/definitions/input/uberon_0002967.json

@@ -0,0 +1,21 @@
+{
+  "group_name": "uberon_0002967",
+  "parent_id": "UBERON:0002967",
+  "parent_label": "",
+  "term_counts": {
+    "leaf": 1,
+    "group": 0
+  },
+  "note": "parent_label is best-effort; subagent should resolve via OLS4. For term_type='group' terms: use obo-grep on uberon-edit.obo to find similar UBERON groupings, identify the genus + part_of pattern, and fill genus + location. If pattern doesn't fit, route to manual_curation.",
+  "terms": [
+    {
+      "ntr_id": "http://purl.obolibrary.org/obo/UBERON_9920004",
+      "label": "cingulate gyrus, retrospleninal part",
+      "term_type": "leaf",
+      "system": "default",
+      "is_a": "INFER:UBERON:0002967",
+      "part_of": "INFER:UBERON:0002967",
+      "def_xref": "https://purl.org/ccf/ASCTB-TEMP_cingulate-gyrus-retrospleninal-part"
+    }
+  ]
+}

bulk_ntr_workflow/outputs/definitions/input/uberon_0016525.json

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+{
+  "group_name": "uberon_0016525",
+  "parent_id": "UBERON:0016525",
+  "parent_label": "",
+  "term_counts": {
+    "leaf": 2,
+    "group": 0
+  },
+  "note": "parent_label is best-effort; subagent should resolve via OLS4. For term_type='group' terms: use obo-grep on uberon-edit.obo to find similar UBERON groupings, identify the genus + part_of pattern, and fill genus + location. If pattern doesn't fit, route to manual_curation.",
+  "terms": [
+    {
+      "ntr_id": "http://purl.obolibrary.org/obo/UBERON_9920006",
+      "label": "frontomarginal gyrus",
+      "term_type": "leaf",
+      "system": "default",
+      "is_a": "INFER:UBERON:0016525",
+      "part_of": "INFER:UBERON:0016525",
+      "def_xref": "https://purl.org/ccf/ASCTB-TEMP_frontomarginal-gyrus"
+    },
+    {
+      "ntr_id": "http://purl.obolibrary.org/obo/UBERON_9920014",
+      "label": "inferior frontal junction",
+      "term_type": "leaf",
+      "system": "default",
+      "is_a": "INFER:UBERON:0016525",
+      "part_of": "INFER:UBERON:0016525",
+      "def_xref": "https://purl.org/ccf/ASCTB-TEMP_inferior-frontal-junction"
+    }
+  ]
+}

bulk_ntr_workflow/outputs/definitions/input/uberon_0019264.json

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+{
+  "group_name": "uberon_0019264",
+  "parent_id": "UBERON:0019264",
+  "parent_label": "",
+  "term_counts": {
+    "leaf": 2,
+    "group": 0
+  },
+  "note": "parent_label is best-effort; subagent should resolve via OLS4. For term_type='group' terms: use obo-grep on uberon-edit.obo to find similar UBERON groupings, identify the genus + part_of pattern, and fill genus + location. If pattern doesn't fit, route to manual_curation.",
+  "terms": [
+    {
+      "ntr_id": "http://purl.obolibrary.org/obo/UBERON_9920001",
+      "label": "amygdaloid complex",
+      "term_type": "leaf",
+      "system": "default",
+      "is_a": "INFER:UBERON:0019264",
+      "part_of": "INFER:UBERON:0019264",
+      "def_xref": "https://doi.org/10.1101/2022.10.12.511898|https://purl.org/ccf/ASCTB-TEMP_amygdaloid-complex"
+    },
+    {
+      "ntr_id": "http://purl.obolibrary.org/obo/UBERON_9920019",
+      "label": "thalamus",
+      "term_type": "leaf",
+      "system": "default",
+      "is_a": "INFER:UBERON:0019264",
+      "part_of": "INFER:UBERON:0019264",
+      "def_xref": "https://doi.org/10.1101/2022.10.12.511898|https://purl.org/ccf/ASCTB-TEMP_thalamus"
+    }
+  ]
+}

bulk_ntr_workflow/outputs/definitions/input/unresolvable_inferior_frontal_junction.json

@@ -0,0 +1,30 @@
+{
+  "group_name": "unresolvable_inferior_frontal_junction",
+  "parent_id": "UNRESOLVABLE:inferior frontal junction",
+  "parent_label": "",
+  "term_counts": {
+    "leaf": 2,
+    "group": 0
+  },
+  "note": "parent_label is best-effort; subagent should resolve via OLS4. For term_type='group' terms: use obo-grep on uberon-edit.obo to find similar UBERON groupings, identify the genus + part_of pattern, and fill genus + location. If pattern doesn't fit, route to manual_curation.",
+  "terms": [
+    {
+      "ntr_id": "http://purl.obolibrary.org/obo/UBERON_9920008",
+      "label": "ifj1",
+      "term_type": "leaf",
+      "system": "default",
+      "is_a": "UNRESOLVABLE:inferior frontal junction",
+      "part_of": "UNRESOLVABLE:inferior frontal junction",
+      "def_xref": "https://purl.org/ccf/ASCTB-TEMP_ifj1"
+    },
+    {
+      "ntr_id": "http://purl.obolibrary.org/obo/UBERON_9920009",
+      "label": "ifj2",
+      "term_type": "leaf",
+      "system": "default",
+      "is_a": "UNRESOLVABLE:inferior frontal junction",
+      "part_of": "UNRESOLVABLE:inferior frontal junction",
+      "def_xref": "https://purl.org/ccf/ASCTB-TEMP_ifj2"
+    }
+  ]
+}

bulk_ntr_workflow/outputs/definitions/uberon_0001876.json

@@ -0,0 +1,31 @@
+{
+  "definitions": {
+    "extended amygdala": "A regional part of brain involved in reward cognition, defined by its distinctive connectivity and neurochemical staining patterns, comprising the central medial amygdala, sublenticular substantia innominata, and bed nucleus of the stria terminalis."
+  },
+  "wikipedia_images": {},
+  "xrefs": {
+    "extended amygdala": "Wikipedia:Extended_amygdala"
+  },
+  "def_xrefs_to_add": {},
+  "leaf_template_rows": {
+    "extended amygdala": {
+      "is_a": "UBERON:0002616",
+      "part_of": "UBERON:0001893"
+    }
+  },
+  "resolved_relationships": {},
+  "resolved_parents": {},
+  "group_template_rows": {},
+  "confirmed_matches": [],
+  "possible_matches": [],
+  "out_of_scope": [],
+  "name_corrections": [],
+  "manual_curation": [],
+  "unresolvable": [
+    {
+      "label": "extended amygdala",
+      "reason": "No PMID references found in Wikipedia article. The concept of extended amygdala was defined by neuroanatomists Alheid and Heimer in the late 1980s-1990s, but specific PMIDs require additional literature search.",
+      "suggestion": "Search PubMed for: 'extended amygdala Alheid Heimer' or 'extended amygdala neuroanatomy review' to find authoritative anatomical descriptions."
+    }
+  ]
+}

bulk_ntr_workflow/outputs/definitions/uberon_0002021.json

@@ -0,0 +1,54 @@
+{
+  "definitions": {
+    "occipitoparietal transition region": "A regional part of the cerebral hemisphere located at the anatomical boundary between the occipital lobe and the parietal lobe, representing cortical areas that transition between these two lobar divisions.",
+    "occipitotemporal transition region": "A regional part of the cerebral hemisphere located at the anatomical boundary between the occipital lobe and the temporal lobe, representing cortical areas that transition between these two lobar divisions."
+  },
+  "wikipedia_images": {},
+  "xrefs": {
+    "occipitotemporal (fusiform) gyrus, occipital part": "FMA:71033"
+  },
+  "def_xrefs_to_add": {},
+  "leaf_template_rows": {
+    "occipitoparietal transition region": {
+      "is_a": "UBERON:0002616",
+      "part_of": "UBERON:0001869"
+    },
+    "occipitotemporal transition region": {
+      "is_a": "UBERON:0002616",
+      "part_of": "UBERON:0001869"
+    }
+  },
+  "resolved_relationships": {
+    "occipitoparietal transition region": "part_of",
+    "occipitotemporal transition region": "part_of"
+  },
+  "resolved_parents": {
+    "occipitoparietal transition region": "UBERON:0001869",
+    "occipitotemporal transition region": "UBERON:0001869"
+  },
+  "confirmed_matches": [
+    {
+      "label": "occipitotemporal (fusiform) gyrus, occipital part",
+      "uberon_id": "UBERON:0022364",
+      "confidence": "high",
+      "uberon_definition": "The fusiform gyrus is part of the temporal lobe. It is also known as the (discontinuous) occipitotemporal gyrus. The occipital fusiform gyrus is the occipital part of this structure.",
+      "wikipedia_summary": "The fusiform gyrus, also known as the occipitotemporal gyrus, is part of the temporal and occipital lobes of the brain. It is involved in visual processing, particularly in face and word recognition.",
+      "note": "Exact synonym match in UBERON:0022364. FMA:71033 cross-reference already present in UBERON term."
+    }
+  ],
+  "possible_matches": [],
+  "out_of_scope": [],
+  "name_corrections": [],
+  "unresolvable": [
+    {
+      "label": "occipitoparietal transition region",
+      "reason": "No PMID reference found for this specific 'transition region' terminology. This appears to be atlas-specific nomenclature from ASCTB-TEMP.",
+      "suggestion": "Curator should verify if this term represents a recognized anatomical region or if it's specific to the Human Reference Atlas. General references about parieto-occipital boundary regions could be used: PMID:25316338 (cortical parcellation), PMID:28981612 (brain atlases)."
+    },
+    {
+      "label": "occipitotemporal transition region",
+      "reason": "No PMID reference found for this specific 'transition region' terminology. This appears to be atlas-specific nomenclature from ASCTB-TEMP.",
+      "suggestion": "Curator should verify if this term represents a recognized anatomical region or if it's specific to the Human Reference Atlas. The occipitotemporal cortex is well-documented but 'transition region' as a specific anatomical entity may need curator review. Potential reference: PMID:19457377 (occipitotemporal cortex development)."
+    }
+  ]
+}