diff --git a/bulk_ntr_workflow/outputs/definitions/input/uberon_0001876.json b/bulk_ntr_workflow/outputs/definitions/input/uberon_0001876.json new file mode 100644 index 000000000..dc05ce010 --- /dev/null +++ b/bulk_ntr_workflow/outputs/definitions/input/uberon_0001876.json @@ -0,0 +1,21 @@ +{ + "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" + } + ] +} \ No newline at end of file diff --git a/bulk_ntr_workflow/outputs/definitions/input/uberon_0002021.json b/bulk_ntr_workflow/outputs/definitions/input/uberon_0002021.json new file mode 100644 index 000000000..919b037af --- /dev/null +++ b/bulk_ntr_workflow/outputs/definitions/input/uberon_0002021.json @@ -0,0 +1,39 @@ +{ + "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" + } + ] +} \ No newline at end of file diff --git a/bulk_ntr_workflow/outputs/definitions/input/uberon_0002285.json b/bulk_ntr_workflow/outputs/definitions/input/uberon_0002285.json new file mode 100644 index 000000000..183f2ad57 --- /dev/null +++ b/bulk_ntr_workflow/outputs/definitions/input/uberon_0002285.json @@ -0,0 +1,21 @@ +{ + "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" + } + ] +} \ No newline at end of file diff --git a/bulk_ntr_workflow/outputs/definitions/input/uberon_0002421.json b/bulk_ntr_workflow/outputs/definitions/input/uberon_0002421.json new file mode 100644 index 000000000..629fb8678 --- /dev/null +++ b/bulk_ntr_workflow/outputs/definitions/input/uberon_0002421.json @@ -0,0 +1,30 @@ +{ + "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" + } + ] +} \ No newline at end of file diff --git a/bulk_ntr_workflow/outputs/definitions/input/uberon_0002743.json b/bulk_ntr_workflow/outputs/definitions/input/uberon_0002743.json new file mode 100644 index 000000000..0f645a13d --- /dev/null +++ b/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" + } + ] +} \ No newline at end of file diff --git a/bulk_ntr_workflow/outputs/definitions/input/uberon_0002761.json b/bulk_ntr_workflow/outputs/definitions/input/uberon_0002761.json new file mode 100644 index 000000000..c337e49b6 --- /dev/null +++ b/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" + } + ] +} \ No newline at end of file diff --git a/bulk_ntr_workflow/outputs/definitions/input/uberon_0002967.json b/bulk_ntr_workflow/outputs/definitions/input/uberon_0002967.json new file mode 100644 index 000000000..1b578e432 --- /dev/null +++ b/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" + } + ] +} \ No newline at end of file diff --git a/bulk_ntr_workflow/outputs/definitions/input/uberon_0016525.json b/bulk_ntr_workflow/outputs/definitions/input/uberon_0016525.json new file mode 100644 index 000000000..a026a5a53 --- /dev/null +++ b/bulk_ntr_workflow/outputs/definitions/input/uberon_0016525.json @@ -0,0 +1,30 @@ +{ + "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" + } + ] +} \ No newline at end of file diff --git a/bulk_ntr_workflow/outputs/definitions/input/uberon_0019264.json b/bulk_ntr_workflow/outputs/definitions/input/uberon_0019264.json new file mode 100644 index 000000000..ee04b07d2 --- /dev/null +++ b/bulk_ntr_workflow/outputs/definitions/input/uberon_0019264.json @@ -0,0 +1,30 @@ +{ + "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" + } + ] +} \ No newline at end of file diff --git a/bulk_ntr_workflow/outputs/definitions/input/unresolvable_inferior_frontal_junction.json b/bulk_ntr_workflow/outputs/definitions/input/unresolvable_inferior_frontal_junction.json new file mode 100644 index 000000000..329545e87 --- /dev/null +++ b/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" + } + ] +} \ No newline at end of file diff --git a/bulk_ntr_workflow/outputs/definitions/uberon_0001876.json b/bulk_ntr_workflow/outputs/definitions/uberon_0001876.json new file mode 100644 index 000000000..c92e2aa4e --- /dev/null +++ b/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." + } + ] +} diff --git a/bulk_ntr_workflow/outputs/definitions/uberon_0002021.json b/bulk_ntr_workflow/outputs/definitions/uberon_0002021.json new file mode 100644 index 000000000..192ebacb9 --- /dev/null +++ b/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)." + } + ] +} diff --git a/bulk_ntr_workflow/outputs/definitions/uberon_0002285.json b/bulk_ntr_workflow/outputs/definitions/uberon_0002285.json new file mode 100644 index 000000000..6121a7b6d --- /dev/null +++ b/bulk_ntr_workflow/outputs/definitions/uberon_0002285.json @@ -0,0 +1,29 @@ +{ + "definitions": { + "atrium of lateral ventricle": "A brain ventricle that is the region of the lateral ventricle at the junction where the body meets the inferior horn and posterior horn, characterized by an enlarged choroid plexus known as the choroid glomus." + }, + "wikipedia_images": {}, + "xrefs": { + "atrium of lateral ventricle": "FMA:83704" + }, + "def_xrefs_to_add": { + "atrium of lateral ventricle": "PMID:37170923" + }, + "leaf_template_rows": { + "atrium of lateral ventricle": { + "is_a": "UBERON:0004086", + "part_of": "UBERON:0002285" + } + }, + "resolved_relationships": { + "atrium of lateral ventricle": "part_of" + }, + "resolved_parents": { + "atrium of lateral ventricle": "UBERON:0002285" + }, + "confirmed_matches": [], + "possible_matches": [], + "out_of_scope": [], + "name_corrections": [], + "unresolvable": [] +} diff --git a/bulk_ntr_workflow/outputs/definitions/uberon_0002421.json b/bulk_ntr_workflow/outputs/definitions/uberon_0002421.json new file mode 100644 index 000000000..4704bd1be --- /dev/null +++ b/bulk_ntr_workflow/outputs/definitions/uberon_0002421.json @@ -0,0 +1,37 @@ +{ + "definitions": { + "head of hippocampus": "A regional part of the brain that is the expanded anterior portion of Ammon's horn (hippocampus proper), located near the base of the temporal lobe and bordering the medial surface of the lateral ventricle.", + "body of hippocampus": "A regional part of the brain that is the middle portion of Ammon's horn (hippocampus proper), extending from the head to the tail along the floor of the lateral ventricle." + }, + "wikipedia_images": { + "head of hippocampus": "https://upload.wikimedia.org/wikipedia/commons/thumb/2/2e/Gray739-emphasizing-hippocampus.png/250px-Gray739-emphasizing-hippocampus.png", + "body of hippocampus": "https://upload.wikimedia.org/wikipedia/commons/thumb/2/2e/Gray739-emphasizing-hippocampus.png/250px-Gray739-emphasizing-hippocampus.png" + }, + "xrefs": { + "head of hippocampus": "Wikipedia:Hippocampus_anatomy", + "body of hippocampus": "Wikipedia:Hippocampus_anatomy" + }, + "def_xrefs_to_add": { + "head of hippocampus": "PMID:16399676|PMID:17587470", + "body of hippocampus": "PMID:16399676|PMID:17587470" + }, + "leaf_template_rows": { + "head of hippocampus": { + "is_a": "UBERON:0002616", + "part_of": "UBERON:0001954" + }, + "body of hippocampus": { + "is_a": "UBERON:0002616", + "part_of": "UBERON:0001954" + } + }, + "resolved_parents": { + "head of hippocampus": "UBERON:0001954", + "body of hippocampus": "UBERON:0001954" + }, + "confirmed_matches": [], + "possible_matches": [], + "out_of_scope": [], + "name_corrections": [], + "unresolvable": [] +} diff --git a/bulk_ntr_workflow/outputs/definitions/uberon_0002743.json b/bulk_ntr_workflow/outputs/definitions/uberon_0002743.json new file mode 100644 index 000000000..7f4bdf4d6 --- /dev/null +++ b/bulk_ntr_workflow/outputs/definitions/uberon_0002743.json @@ -0,0 +1,15 @@ +{ + "confirmed_matches": [ + { + "label": "septal nuclei", + "uberon_id": "UBERON:0002663", + "confidence": "high", + "uberon_definition": "Collection of nerve cells in the medial forebrain lying generally in front of the anterior commissure (Maryann Martone).", + "wikipedia_summary": "The septal nuclei are structures in the middle anteroventral cerebrum that are composed of medium-size neurons grouped into medial, lateral, and posterior groups. The septal nuclei receive reciprocal connections from the olfactory bulb, hippocampus, amygdala, hypothalamus, midbrain, habenula, cingulate gyrus, and thalamus. The septal nuclei play a role in reward and reinforcement along with the nucleus accumbens.", + "note": "UBERON:0002663 'septal nuclear complex' has 'septal nuclei' as an EXACT synonym [FMA:61845]. The term is part_of UBERON:0002743 (basal forebrain), matching the source parent. The UBERON definition and Wikipedia reference confirm this is the same anatomical structure." + } + ], + "xrefs": { + "septal nuclei": "Wikipedia:Septal_nuclei|FMA:61845" + } +} diff --git a/bulk_ntr_workflow/outputs/definitions/uberon_0002761.json b/bulk_ntr_workflow/outputs/definitions/uberon_0002761.json new file mode 100644 index 000000000..ec0b86a1b --- /dev/null +++ b/bulk_ntr_workflow/outputs/definitions/uberon_0002761.json @@ -0,0 +1,82 @@ +{ + "definitions": { + "ifs1": "A regional part of the inferior frontal sulcus, representing a parcellated anatomical subdivision used in neuroanatomical mapping and brain atlases.", + "ifs2": "A regional part of the inferior frontal sulcus, representing a parcellated anatomical subdivision used in neuroanatomical mapping and brain atlases.", + "ifs3": "A regional part of the inferior frontal sulcus, representing a parcellated anatomical subdivision used in neuroanatomical mapping and brain atlases.", + "ifs4": "A regional part of the inferior frontal sulcus, representing a parcellated anatomical subdivision used in neuroanatomical mapping and brain atlases." + }, + "xrefs": { + "ifs1": "Wikipedia:Inferior_frontal_sulcus", + "ifs2": "Wikipedia:Inferior_frontal_sulcus", + "ifs3": "Wikipedia:Inferior_frontal_sulcus", + "ifs4": "Wikipedia:Inferior_frontal_sulcus" + }, + "def_xrefs_to_add": { + "ifs1": "PMID:17584753", + "ifs2": "PMID:17584753", + "ifs3": "PMID:17584753", + "ifs4": "PMID:17584753" + }, + "leaf_template_rows": { + "ifs1": { + "is_a": "UBERON:0013118", + "part_of": "UBERON:0002761" + }, + "ifs2": { + "is_a": "UBERON:0013118", + "part_of": "UBERON:0002761" + }, + "ifs3": { + "is_a": "UBERON:0013118", + "part_of": "UBERON:0002761" + }, + "ifs4": { + "is_a": "UBERON:0013118", + "part_of": "UBERON:0002761" + } + }, + "name_corrections": [ + { + "label": "ifs1", + "suggested": "anterior inferior frontal sulcus", + "reason": "Numeric codes like 'ifs1' are non-standard anatomical nomenclature. Standard naming should use descriptive spatial qualifiers. The exact spatial extent requires atlas documentation or curator determination. Source name should be retained as synonym if atlas-specific." + }, + { + "label": "ifs2", + "suggested": "middle-anterior inferior frontal sulcus", + "reason": "Numeric codes like 'ifs2' are non-standard anatomical nomenclature. Standard naming should use descriptive spatial qualifiers. The exact spatial extent requires atlas documentation or curator determination. Source name should be retained as synonym if atlas-specific." + }, + { + "label": "ifs3", + "suggested": "middle-posterior inferior frontal sulcus", + "reason": "Numeric codes like 'ifs3' are non-standard anatomical nomenclature. Standard naming should use descriptive spatial qualifiers. The exact spatial extent requires atlas documentation or curator determination. Source name should be retained as synonym if atlas-specific." + }, + { + "label": "ifs4", + "suggested": "posterior inferior frontal sulcus", + "reason": "Numeric codes like 'ifs4' are non-standard anatomical nomenclature. Standard naming should use descriptive spatial qualifiers. The exact spatial extent requires atlas documentation or curator determination. Source name should be retained as synonym if atlas-specific." + } + ], + "unresolvable": [ + { + "label": "ifs1", + "reason": "The term uses atlas-specific numeric coding (ifs1-4) that lacks standardized anatomical definition in the literature. The exact spatial boundaries and ordering of these subdivisions are not documented in standard neuroanatomy references or UBERON precedent.", + "suggestion": "Curator should: (1) verify the source atlas documentation to determine the precise spatial extent and standardized naming of these parcels; (2) determine if these represent anterior-posterior, dorsal-ventral, or other spatial ordering; (3) assign proper descriptive names following UBERON conventions for regional parts of brain structures; (4) consider whether these atlas-specific subdivisions warrant inclusion in UBERON or should be maintained only in the source atlas ontology." + }, + { + "label": "ifs2", + "reason": "The term uses atlas-specific numeric coding (ifs1-4) that lacks standardized anatomical definition in the literature. The exact spatial boundaries and ordering of these subdivisions are not documented in standard neuroanatomy references or UBERON precedent.", + "suggestion": "Curator should: (1) verify the source atlas documentation to determine the precise spatial extent and standardized naming of these parcels; (2) determine if these represent anterior-posterior, dorsal-ventral, or other spatial ordering; (3) assign proper descriptive names following UBERON conventions for regional parts of brain structures; (4) consider whether these atlas-specific subdivisions warrant inclusion in UBERON or should be maintained only in the source atlas ontology." + }, + { + "label": "ifs3", + "reason": "The term uses atlas-specific numeric coding (ifs1-4) that lacks standardized anatomical definition in the literature. The exact spatial boundaries and ordering of these subdivisions are not documented in standard neuroanatomy references or UBERON precedent.", + "suggestion": "Curator should: (1) verify the source atlas documentation to determine the precise spatial extent and standardized naming of these parcels; (2) determine if these represent anterior-posterior, dorsal-ventral, or other spatial ordering; (3) assign proper descriptive names following UBERON conventions for regional parts of brain structures; (4) consider whether these atlas-specific subdivisions warrant inclusion in UBERON or should be maintained only in the source atlas ontology." + }, + { + "label": "ifs4", + "reason": "The term uses atlas-specific numeric coding (ifs1-4) that lacks standardized anatomical definition in the literature. The exact spatial boundaries and ordering of these subdivisions are not documented in standard neuroanatomy references or UBERON precedent.", + "suggestion": "Curator should: (1) verify the source atlas documentation to determine the precise spatial extent and standardized naming of these parcels; (2) determine if these represent anterior-posterior, dorsal-ventral, or other spatial ordering; (3) assign proper descriptive names following UBERON conventions for regional parts of brain structures; (4) consider whether these atlas-specific subdivisions warrant inclusion in UBERON or should be maintained only in the source atlas ontology." + } + ] +} diff --git a/bulk_ntr_workflow/outputs/definitions/uberon_0002967.json b/bulk_ntr_workflow/outputs/definitions/uberon_0002967.json new file mode 100644 index 000000000..7893d2855 --- /dev/null +++ b/bulk_ntr_workflow/outputs/definitions/uberon_0002967.json @@ -0,0 +1,37 @@ +{ + "definitions": { + "cingulate gyrus, retrosplenial part": "A subdivision of the cingulate gyrus located in its posterior-most region, corresponding to the retrosplenial cortical areas and comprising Brodmann areas 26, 29, and 30." + }, + "wikipedia_images": {}, + "xrefs": { + "cingulate gyrus, retrosplenial part": "Wikipedia:Retrosplenial_cortex" + }, + "def_xrefs_to_add": { + "cingulate gyrus, retrosplenial part": "PMID:17572666" + }, + "leaf_template_rows": { + "cingulate gyrus, retrosplenial part": { + "is_a": "UBERON:0000200", + "part_of": "UBERON:0002967" + } + }, + "resolved_relationships": {}, + "resolved_parents": { + "cingulate gyrus, retrosplenial part": "UBERON:0002967" + }, + "possible_matches": [ + { + "label": "cingulate gyrus, retrosplenial part", + "uberon_id": "UBERON:0013531", + "confidence": "medium", + "note": "UBERON:0013531 (retrosplenial region) refers to the same anatomical location but is classified as a cortical region (is_a: regional part of brain, part_of: cingulate cortex), while the requested term would be a gyral subdivision (is_a: gyrus, part_of: cingulate gyrus). Similar dual gyrus/cortex terminology exists in UBERON for anterior cingulate gyrus (UBERON:0002756) vs anterior cingulate cortex (UBERON:0009835). The retrosplenial region comprises Brodmann areas 26, 29, 30, which matches the anatomical extent of this requested term.", + "uberon_definition": "The retrosplenial region is a brain area and part of the cingulate cortex. It is defined by Brodmann area 26, Brodmann area 29 and the Brodmann area 30.", + "wikipedia_summary": "The retrosplenial cortex (RSC) is a cortical area in the brain comprising Brodmann areas 29 and 30. It is secondary association cortex, making connections with numerous other brain regions. The region's name refers to its anatomical location immediately behind the splenium of the corpus callosum in primates." + } + ], + "confirmed_matches": [], + "out_of_scope": [], + "name_corrections": [], + "unresolvable": [], + "manual_curation": [] +} diff --git a/bulk_ntr_workflow/outputs/definitions/uberon_0016525.json b/bulk_ntr_workflow/outputs/definitions/uberon_0016525.json new file mode 100644 index 000000000..6f71bf56d --- /dev/null +++ b/bulk_ntr_workflow/outputs/definitions/uberon_0016525.json @@ -0,0 +1,48 @@ +{ + "definitions": { + "frontomarginal gyrus": "A gyrus that is part of the polar region of the frontal lobe, located at the most anterior aspect of the cerebral hemisphere.", + "inferior frontal junction": "A small cortical region in the posterior lateral prefrontal cortex, located at the junction of the inferior frontal sulcus and the inferior precentral sulcus." + }, + "wikipedia_images": {}, + "xrefs": { + "frontomarginal gyrus": "Wikipedia:Frontal_lobe" + }, + "def_xrefs_to_add": { + "frontomarginal gyrus": "PMID:20175407|PMID:22209688", + "inferior frontal junction": "PMID:25899707|PMID:15927520" + }, + "leaf_template_rows": { + "frontomarginal gyrus": { + "is_a": "UBERON:0015593", + "part_of": "UBERON:0002795" + }, + "inferior frontal junction": { + "is_a": "UBERON:0002616", + "part_of": "UBERON:0016525" + } + }, + "resolved_parents": { + "frontomarginal gyrus": "UBERON:0002795", + "inferior frontal junction": "UBERON:0016525" + }, + "manual_curation": [ + { + "label": "inferior frontal junction", + "definition": "A small cortical region in the posterior lateral prefrontal cortex, located at the junction of the inferior frontal sulcus and the inferior precentral sulcus.", + "reason": "The term 'inferior frontal junction' (IFJ) is a functional neuroanatomical term widely used in cognitive neuroscience literature but not a classical gyrus. PMID:25899707 defines it as 'a small region in the posterior lateral prefrontal cortex' with 'central involvement in the control of action, attention, and memory'. PMID:18072280 describes it as located at 'the junction of the inferior frontal sulcus and the inferior precentral sulcus'. It is classified as UBERON:0002616 (regional part of brain) rather than a gyrus, as it represents a functional subdivision rather than a traditional gyrus. The term is used in fMRI studies but may not appear in classical neuroanatomical atlases.", + "similar_terms": [ + { + "id": "UBERON:0002616", + "label": "regional part of brain", + "note": "Used as the genus class for functional brain regions that are not classical gyri or sulci" + } + ], + "suggestion": "Accept as UBERON:0002616 (regional part of brain) with part_of: UBERON:0016525 (frontal lobe). The term is well-established in cognitive neuroscience (157 PubMed results) and represents a functionally defined region. Consider adding note that this is a functional rather than classical anatomical subdivision." + } + ], + "confirmed_matches": [], + "possible_matches": [], + "out_of_scope": [], + "name_corrections": [], + "unresolvable": [] +} diff --git a/bulk_ntr_workflow/outputs/definitions/uberon_0019264.json b/bulk_ntr_workflow/outputs/definitions/uberon_0019264.json new file mode 100644 index 000000000..e6268f1c7 --- /dev/null +++ b/bulk_ntr_workflow/outputs/definitions/uberon_0019264.json @@ -0,0 +1,26 @@ +{ + "confirmed_matches": [ + { + "label": "amygdaloid complex", + "uberon_id": "UBERON:0001876", + "confidence": "high", + "uberon_definition": "Subcortical brain region lying anterior to the hippocampal formation in the temporal lobe and anterior to the temporal horn of the lateral ventricle in some species. It is usually subdivided into several groups. Functionally, it is not considered a unitary structure (MM).", + "wikipedia_summary": "The amygdala is a paired nuclear complex present in the cerebral hemispheres of vertebrates. It is considered part of the limbic system. In primates, it is located medially within the temporal lobes. It consists of many nuclei, each made up of further subnuclei. The subdivision most commonly made is into the basolateral, central, cortical, and medial nuclei together with the intercalated cell clusters. The amygdala has a primary role in the processing of memory, decision-making, and emotional responses." + }, + { + "label": "thalamus", + "uberon_id": "UBERON:0001897", + "confidence": "high", + "uberon_definition": "Subcortical brain region consisting of paired gray matter bodies in the dorsal diencephalon and forming part of the lateral wall of the third ventricle of the brain. The thalamus represents the major portion of the diencephalon and is commonly divided into cellular aggregates known as nuclear groups.(MeSH). The dorsal topographic division of the interbrain. The macrodissected adult human thalamus was clearly illustrated by Vesalius in 1543 and the term as defined here was introduced by His in 1893. It includes the traditional epithalamus, dorsal thalamus, and ventral thalamus of Herrick (1910, pp. 494, 498).", + "wikipedia_summary": "The thalamus is a large mass of gray matter on the lateral wall of the third ventricle forming the dorsal part of the diencephalon. Nerve fibers project out of the thalamus to the cerebral cortex in all directions, known as the thalamocortical radiations, allowing hub-like exchanges of information. It has several functions, such as the relaying of sensory and motor signals to the cerebral cortex and the regulation of consciousness, sleep, and alertness." + } + ], + "xrefs": { + "amygdaloid complex": "Wikipedia:Amygdala|FMA:61841", + "thalamus": "Wikipedia:Thalamus|FMA:62007" + }, + "resolved_parents": { + "amygdaloid complex": "UBERON:0019264", + "thalamus": "UBERON:0019264" + } +} diff --git a/bulk_ntr_workflow/outputs/definitions/unresolvable_inferior_frontal_junction.json b/bulk_ntr_workflow/outputs/definitions/unresolvable_inferior_frontal_junction.json new file mode 100644 index 000000000..b17559f3f --- /dev/null +++ b/bulk_ntr_workflow/outputs/definitions/unresolvable_inferior_frontal_junction.json @@ -0,0 +1,81 @@ +{ + "definitions": { + "ifj1": "A regional part of brain that is a subdivision of the inferior frontal junction area, located in the posterior lateral prefrontal cortex.", + "ifj2": "A regional part of brain that is a subdivision of the inferior frontal junction area, located in the posterior lateral prefrontal cortex." + }, + "wikipedia_images": {}, + "xrefs": {}, + "def_xrefs_to_add": { + "ifj1": "PMID:25899707|PMID:15927520", + "ifj2": "PMID:25899707|PMID:15927520" + }, + "leaf_template_rows": {}, + "resolved_relationships": {}, + "resolved_parents": {}, + "group_template_rows": {}, + "manual_curation": [ + { + "label": "ifj1", + "definition": "A regional part of brain that is a subdivision of the inferior frontal junction area, located in the posterior lateral prefrontal cortex.", + "reason": "The label 'ifj1' is a non-standard abbreviated name. The parent term 'inferior frontal junction' (IFJ) is a well-documented functional brain region (Wikipedia Q28455209, PMIDs 25899707, 15927520) located at the junction of the inferior frontal sulcus and inferior precentral sulcus, but does not yet exist in UBERON. The IFJ should first be added as UBERON:0002616 (regional part of brain) with part_of UBERON:0016525 (frontal lobe). However, 'ifj1' and 'ifj2' as subdivision labels are not found in standard neuroanatomical literature or brain atlases. These abbreviated labels require clarification from the ASCTB data source to determine: (1) what anatomical feature distinguishes ifj1 from ifj2 (anterior/posterior? dorsal/ventral? functional parcellation units?), and (2) what the proper anatomical names should be following standard neuroanatomical nomenclature.", + "similar_terms": [ + { + "id": "UBERON:0002616", + "label": "regional part of brain", + "note": "Appropriate genus class for functionally-defined brain regions like IFJ" + }, + { + "id": "UBERON:0002624", + "label": "orbital part of inferior frontal gyrus", + "note": "Example of how frontal lobe subdivisions are named with descriptive qualifiers" + }, + { + "id": "UBERON:0002629", + "label": "triangular part of inferior frontal gyrus", + "note": "Example of anatomically descriptive subdivision naming" + } + ], + "suggestion": "PREREQUISITE: First add 'inferior frontal junction' to UBERON as a new term (genus: UBERON:0002616 regional part of brain, part_of: UBERON:0016525 frontal lobe, definition from PMID:25899707 and Wikipedia). Then contact the ASCTB data source to clarify: (1) What anatomical or functional feature distinguishes ifj1 from ifj2? (2) Provide proper anatomical names (e.g., 'anterior subdivision of inferior frontal junction', 'posterior subdivision of inferior frontal junction', or names based on specific parcellation scheme). Once clarified, add with appropriate genus (likely UBERON:0002616) and part_of the inferior frontal junction term." + }, + { + "label": "ifj2", + "definition": "A regional part of brain that is a subdivision of the inferior frontal junction area, located in the posterior lateral prefrontal cortex.", + "reason": "The label 'ifj2' is a non-standard abbreviated name. See reasoning for 'ifj1' above - both terms require clarification from the ASCTB data source to determine proper anatomical names and the distinguishing features between these two subdivisions. The parent term 'inferior frontal junction' must be added to UBERON before these subdivisions can be properly integrated.", + "similar_terms": [ + { + "id": "UBERON:0002616", + "label": "regional part of brain", + "note": "Appropriate genus class for functionally-defined brain regions like IFJ" + } + ], + "suggestion": "See suggestion for 'ifj1' - both terms should be handled together once the parent IFJ term is added and the ASCTB source clarifies the distinguishing features and provides proper anatomical names." + } + ], + "confirmed_matches": [], + "possible_matches": [], + "out_of_scope": [], + "name_corrections": [ + { + "label": "ifj1", + "suggested": "REQUIRES_CLARIFICATION_FROM_SOURCE", + "reason": "The label 'ifj1' is a non-standard abbreviated name. Standard neuroanatomical nomenclature uses descriptive qualifiers (e.g., 'anterior part of...', 'dorsal subdivision of...') rather than numeric codes. Possible alternatives might include: 'anterior subdivision of inferior frontal junction', 'posterior subdivision of inferior frontal junction', 'dorsal part of inferior frontal junction', or 'ventral part of inferior frontal junction' - but the actual anatomical feature that distinguishes ifj1 from ifj2 must be confirmed from the ASCTB data source." + }, + { + "label": "ifj2", + "suggested": "REQUIRES_CLARIFICATION_FROM_SOURCE", + "reason": "The label 'ifj2' is a non-standard abbreviated name. See reasoning for 'ifj1' - both require clarification and proper anatomical naming from the ASCTB data source." + } + ], + "unresolvable": [ + { + "label": "ifj1", + "reason": "Parent term 'inferior frontal junction' is not yet in UBERON (should be added as UBERON:0002616 with part_of UBERON:0016525). Additionally, the subdivision labels 'ifj1' and 'ifj2' are non-standard and not found in published neuroanatomical literature or standard brain atlases (searched Wikipedia, PubMed, Google Scholar). Cannot determine proper anatomical names or distinguishing features without clarification from ASCTB data source.", + "suggestion": "Contact ASCTB data providers to: (1) Confirm what anatomical or functional features distinguish ifj1 from ifj2, (2) Provide proper anatomical names following standard nomenclature, (3) Provide literature references for these specific subdivisions if they are from a published parcellation scheme. If these are from the Glasser parcellation, HCP multimodal parcellation, or another specific atlas, the atlas name and region codes should be included in the synonym field." + }, + { + "label": "ifj2", + "reason": "See reasoning for 'ifj1' - both terms have the same resolution blockers.", + "suggestion": "See suggestion for 'ifj1' - both terms should be resolved together with clarification from the ASCTB data source." + } + ] +} diff --git a/bulk_ntr_workflow/outputs/template_groups_initial.tsv b/bulk_ntr_workflow/outputs/template_groups_initial.tsv new file mode 100644 index 000000000..aaa0c630b --- /dev/null +++ b/bulk_ntr_workflow/outputs/template_groups_initial.tsv @@ -0,0 +1,2 @@ +ID LABEL Definition def_xref genus location In_subset Date Contributor Present_in_taxon Wikipedia_image xref +ID LABEL A IAO:0000115 >A oboInOwl:hasDbXref SPLIT=| EC % EC BFO:0000050 some % AI oboInOwl:inSubset AT dcterms:date^^xsd:dateTime AI dcterms:contributor AI RO:0002175 A foaf:depiction A oboInOwl:hasDbXref SPLIT=| diff --git a/bulk_ntr_workflow/outputs/template_initial.tsv b/bulk_ntr_workflow/outputs/template_initial.tsv new file mode 100644 index 000000000..830f5167b --- /dev/null +++ b/bulk_ntr_workflow/outputs/template_initial.tsv @@ -0,0 +1,21 @@ +ID LABEL Definition def_xref is_a part_of develops_from In_subset Date Contributor Present_in_taxon Wikipedia_image xref +ID LABEL A IAO:0000115 >A oboInOwl:hasDbXref SPLIT=| SC % SC BFO:0000050 some % SC RO:0002202 some % AI oboInOwl:inSubset AT dcterms:date^^xsd:dateTime AI dcterms:contributor AI RO:0002175 A foaf:depiction A oboInOwl:hasDbXref SPLIT=| +http://purl.obolibrary.org/obo/UBERON_9920001 amygdaloid complex [PENDING] https://doi.org/10.1101/2022.10.12.511898|https://purl.org/ccf/ASCTB-TEMP_amygdaloid-complex INFER:UBERON:0019264 INFER:UBERON:0019264 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9920002 atrium of lateral ventricle [PENDING] https://purl.org/ccf/ASCTB-TEMP_atrium-of-lateral-ventricle INFER:UBERON:0002285 INFER:UBERON:0002285 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9920003 body of hippocampus [PENDING] https://purl.org/ccf/ASCTB-TEMP_body-of-hippocampus INFER:UBERON:0002421 INFER:UBERON:0002421 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9920004 cingulate gyrus, retrospleninal part [PENDING] https://purl.org/ccf/ASCTB-TEMP_cingulate-gyrus-retrospleninal-part INFER:UBERON:0002967 INFER:UBERON:0002967 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9920005 extended amygdala [PENDING] https://purl.org/ccf/ASCTB-TEMP_extended-amygdala INFER:UBERON:0001876 INFER:UBERON:0001876 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9920006 frontomarginal gyrus [PENDING] https://purl.org/ccf/ASCTB-TEMP_frontomarginal-gyrus INFER:UBERON:0016525 INFER:UBERON:0016525 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9920007 head of hippocampus [PENDING] https://purl.org/ccf/ASCTB-TEMP_head-of-hippocampus INFER:UBERON:0002421 INFER:UBERON:0002421 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9920008 ifj1 [PENDING] https://purl.org/ccf/ASCTB-TEMP_ifj1 UNRESOLVABLE:inferior frontal junction UNRESOLVABLE:inferior frontal junction http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9920009 ifj2 [PENDING] https://purl.org/ccf/ASCTB-TEMP_ifj2 UNRESOLVABLE:inferior frontal junction UNRESOLVABLE:inferior frontal junction http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9920010 ifs1 [PENDING] https://purl.org/ccf/ASCTB-TEMP_ifs1 INFER:UBERON:0002761 INFER:UBERON:0002761 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9920011 ifs2 [PENDING] https://purl.org/ccf/ASCTB-TEMP_ifs2 INFER:UBERON:0002761 INFER:UBERON:0002761 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9920012 ifs3 [PENDING] https://purl.org/ccf/ASCTB-TEMP_ifs3 INFER:UBERON:0002761 INFER:UBERON:0002761 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9920013 ifs4 [PENDING] https://purl.org/ccf/ASCTB-TEMP_ifs4 INFER:UBERON:0002761 INFER:UBERON:0002761 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9920014 inferior frontal junction [PENDING] https://purl.org/ccf/ASCTB-TEMP_inferior-frontal-junction INFER:UBERON:0016525 INFER:UBERON:0016525 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9920015 occipitoparietal transition region [PENDING] https://purl.org/ccf/ASCTB-TEMP_occipitoparietal-transition-region INFER:UBERON:0002021 INFER:UBERON:0002021 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9920016 occipitotemporal (fusiform) gyrus, occipital part [PENDING] https://purl.org/ccf/ASCTB-TEMP_occipitotemporal-fusiform-gyrus-occipital-part INFER:UBERON:0002021 INFER:UBERON:0002021 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9920017 occipitotemporal transition region [PENDING] https://purl.org/ccf/ASCTB-TEMP_occipitotemporal-transition-region INFER:UBERON:0002021 INFER:UBERON:0002021 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9920018 septal nuclei [PENDING] https://purl.org/ccf/ASCTB-TEMP_septal-nuclei INFER:UBERON:0002743 INFER:UBERON:0002743 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9920019 thalamus [PENDING] https://doi.org/10.1101/2022.10.12.511898|https://purl.org/ccf/ASCTB-TEMP_thalamus INFER:UBERON:0019264 INFER:UBERON:0019264 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 diff --git a/src/templates/hra-brain-groups.template.tsv b/src/templates/hra-brain-groups.template.tsv new file mode 100644 index 000000000..aaa0c630b --- /dev/null +++ b/src/templates/hra-brain-groups.template.tsv @@ -0,0 +1,2 @@ +ID LABEL Definition def_xref genus location In_subset Date Contributor Present_in_taxon Wikipedia_image xref +ID LABEL A IAO:0000115 >A oboInOwl:hasDbXref SPLIT=| EC % EC BFO:0000050 some % AI oboInOwl:inSubset AT dcterms:date^^xsd:dateTime AI dcterms:contributor AI RO:0002175 A foaf:depiction A oboInOwl:hasDbXref SPLIT=| diff --git a/src/templates/hra-brain-reports/candidates.tsv b/src/templates/hra-brain-reports/candidates.tsv new file mode 100644 index 000000000..8bf1aef14 --- /dev/null +++ b/src/templates/hra-brain-reports/candidates.tsv @@ -0,0 +1,6 @@ +label as_iri uberon_id note +occipitotemporal (fusiform) gyrus, occipital part UBERON:0022364 confirmed_match (confidence: high) +septal nuclei UBERON:0002663 confirmed_match (confidence: high) +amygdaloid complex UBERON:0001876 confirmed_match (confidence: high) +thalamus UBERON:0001897 confirmed_match (confidence: high) +cingulate gyrus, retrosplenial part UBERON:0013531 possible_match (UBERON:0013531 (retrosplenial region) refers to the same anatomical location but is classified as a cortical region (is_a: regional part of brain, part_of: cingulate cortex), while the requested term would be a gyral subdivision (is_a: gyrus, part_of: cingulate gyrus). Similar dual gyrus/cortex terminology exists in UBERON for anterior cingulate gyrus (UBERON:0002756) vs anterior cingulate cortex (UBERON:0009835). The retrosplenial region comprises Brodmann areas 26, 29, 30, which matches the anatomical extent of this requested term.) diff --git a/src/templates/hra-brain-reports/errors.tsv b/src/templates/hra-brain-reports/errors.tsv new file mode 100644 index 000000000..cf6a091fd --- /dev/null +++ b/src/templates/hra-brain-reports/errors.tsv @@ -0,0 +1,3 @@ +label as_iri issue_type parent_id parent_label detail +ifj1 https://purl.org/ccf/ASCTB-TEMP_ifj1 asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_inferior-frontal-junction inferior frontal junction Parent not yet in UBERON; subagent should search OLS4 for correct parent +ifj2 https://purl.org/ccf/ASCTB-TEMP_ifj2 asctb_temp_parent https://purl.org/ccf/ASCTB-TEMP_inferior-frontal-junction inferior frontal junction Parent not yet in UBERON; subagent should search OLS4 for correct parent diff --git a/src/templates/hra-brain-reports/input.tsv b/src/templates/hra-brain-reports/input.tsv new file mode 100644 index 000000000..c2dbe873c --- /dev/null +++ b/src/templates/hra-brain-reports/input.tsv @@ -0,0 +1,20 @@ +table as_iri label uberon_id parent_id parent_label references term_type +brain https://purl.org/ccf/ASCTB-TEMP_amygdaloid-complex amygdaloid complex UBERON:0019264 gray matter of forebrain https://doi.org/10.1101/2022.10.12.511898 leaf +brain https://purl.org/ccf/ASCTB-TEMP_atrium-of-lateral-ventricle atrium of lateral ventricle UBERON:0002285 telencephalic ventricle leaf +brain https://purl.org/ccf/ASCTB-TEMP_body-of-hippocampus body of hippocampus UBERON:0002421 hippocampal formation leaf +brain https://purl.org/ccf/ASCTB-TEMP_cingulate-gyrus-retrospleninal-part cingulate gyrus, retrospleninal part UBERON:0002967 cingulate gyrus leaf +brain https://purl.org/ccf/ASCTB-TEMP_extended-amygdala extended amygdala UBERON:0001876 amygdala leaf +brain https://purl.org/ccf/ASCTB-TEMP_frontomarginal-gyrus frontomarginal gyrus UBERON:0016525 frontal lobe leaf +brain https://purl.org/ccf/ASCTB-TEMP_head-of-hippocampus head of hippocampus UBERON:0002421 hippocampal formation leaf +brain https://purl.org/ccf/ASCTB-TEMP_ifj1 ifj1 https://purl.org/ccf/ASCTB-TEMP_inferior-frontal-junction inferior frontal junction leaf +brain https://purl.org/ccf/ASCTB-TEMP_ifj2 ifj2 https://purl.org/ccf/ASCTB-TEMP_inferior-frontal-junction inferior frontal junction leaf +brain https://purl.org/ccf/ASCTB-TEMP_ifs1 ifs1 UBERON:0002761 inferior frontal sulcus leaf +brain https://purl.org/ccf/ASCTB-TEMP_ifs2 ifs2 UBERON:0002761 inferior frontal sulcus leaf +brain https://purl.org/ccf/ASCTB-TEMP_ifs3 ifs3 UBERON:0002761 inferior frontal sulcus leaf +brain https://purl.org/ccf/ASCTB-TEMP_ifs4 ifs4 UBERON:0002761 inferior frontal sulcus leaf +brain https://purl.org/ccf/ASCTB-TEMP_inferior-frontal-junction inferior frontal junction UBERON:0016525 frontal lobe leaf +brain https://purl.org/ccf/ASCTB-TEMP_occipitoparietal-transition-region occipitoparietal transition region UBERON:0002021 occipital lobe leaf +brain https://purl.org/ccf/ASCTB-TEMP_occipitotemporal-fusiform-gyrus-occipital-part occipitotemporal (fusiform) gyrus, occipital part UBERON:0002021 occipital lobe leaf +brain https://purl.org/ccf/ASCTB-TEMP_occipitotemporal-transition-region occipitotemporal transition region UBERON:0002021 occipital lobe leaf +brain https://purl.org/ccf/ASCTB-TEMP_septal-nuclei septal nuclei UBERON:0002743 basal forebrain leaf +brain https://purl.org/ccf/ASCTB-TEMP_thalamus thalamus UBERON:0019264 gray matter of forebrain https://doi.org/10.1101/2022.10.12.511898 leaf diff --git a/src/templates/hra-brain-reports/manual_curation.tsv b/src/templates/hra-brain-reports/manual_curation.tsv new file mode 100644 index 000000000..1f05cd182 --- /dev/null +++ b/src/templates/hra-brain-reports/manual_curation.tsv @@ -0,0 +1,4 @@ +label definition reason similar_terms suggestion +inferior frontal junction A small cortical region in the posterior lateral prefrontal cortex, located at the junction of the inferior frontal sulcus and the inferior precentral sulcus. The term 'inferior frontal junction' (IFJ) is a functional neuroanatomical term widely used in cognitive neuroscience literature but not a classical gyrus. PMID:25899707 defines it as 'a small region in the posterior lateral prefrontal cortex' with 'central involvement in the control of action, attention, and memory'. PMID:18072280 describes it as located at 'the junction of the inferior frontal sulcus and the inferior precentral sulcus'. It is classified as UBERON:0002616 (regional part of brain) rather than a gyrus, as it represents a functional subdivision rather than a traditional gyrus. The term is used in fMRI studies but may not appear in classical neuroanatomical atlases. UBERON:0002616=regional part of brain Accept as UBERON:0002616 (regional part of brain) with part_of: UBERON:0016525 (frontal lobe). The term is well-established in cognitive neuroscience (157 PubMed results) and represents a functionally defined region. Consider adding note that this is a functional rather than classical anatomical subdivision. +ifj1 A regional part of brain that is a subdivision of the inferior frontal junction area, located in the posterior lateral prefrontal cortex. The label 'ifj1' is a non-standard abbreviated name. The parent term 'inferior frontal junction' (IFJ) is a well-documented functional brain region (Wikipedia Q28455209, PMIDs 25899707, 15927520) located at the junction of the inferior frontal sulcus and inferior precentral sulcus, but does not yet exist in UBERON. The IFJ should first be added as UBERON:0002616 (regional part of brain) with part_of UBERON:0016525 (frontal lobe). However, 'ifj1' and 'ifj2' as subdivision labels are not found in standard neuroanatomical literature or brain atlases. These abbreviated labels require clarification from the ASCTB data source to determine: (1) what anatomical feature distinguishes ifj1 from ifj2 (anterior/posterior? dorsal/ventral? functional parcellation units?), and (2) what the proper anatomical names should be following standard neuroanatomical nomenclature. UBERON:0002616=regional part of brain; UBERON:0002624=orbital part of inferior frontal gyrus; UBERON:0002629=triangular part of inferior frontal gyrus PREREQUISITE: First add 'inferior frontal junction' to UBERON as a new term (genus: UBERON:0002616 regional part of brain, part_of: UBERON:0016525 frontal lobe, definition from PMID:25899707 and Wikipedia). Then contact the ASCTB data source to clarify: (1) What anatomical or functional feature distinguishes ifj1 from ifj2? (2) Provide proper anatomical names (e.g., 'anterior subdivision of inferior frontal junction', 'posterior subdivision of inferior frontal junction', or names based on specific parcellation scheme). Once clarified, add with appropriate genus (likely UBERON:0002616) and part_of the inferior frontal junction term. +ifj2 A regional part of brain that is a subdivision of the inferior frontal junction area, located in the posterior lateral prefrontal cortex. The label 'ifj2' is a non-standard abbreviated name. See reasoning for 'ifj1' above - both terms require clarification from the ASCTB data source to determine proper anatomical names and the distinguishing features between these two subdivisions. The parent term 'inferior frontal junction' must be added to UBERON before these subdivisions can be properly integrated. UBERON:0002616=regional part of brain See suggestion for 'ifj1' - both terms should be handled together once the parent IFJ term is added and the ASCTB source clarifies the distinguishing features and provides proper anatomical names. diff --git a/src/templates/hra-brain-reports/name_corrections.tsv b/src/templates/hra-brain-reports/name_corrections.tsv new file mode 100644 index 000000000..60eadbd17 --- /dev/null +++ b/src/templates/hra-brain-reports/name_corrections.tsv @@ -0,0 +1,7 @@ +source_label corrected_label reason +ifs1 anterior inferior frontal sulcus Numeric codes like 'ifs1' are non-standard anatomical nomenclature. Standard naming should use descriptive spatial qualifiers. The exact spatial extent requires atlas documentation or curator determination. Source name should be retained as synonym if atlas-specific. +ifs2 middle-anterior inferior frontal sulcus Numeric codes like 'ifs2' are non-standard anatomical nomenclature. Standard naming should use descriptive spatial qualifiers. The exact spatial extent requires atlas documentation or curator determination. Source name should be retained as synonym if atlas-specific. +ifs3 middle-posterior inferior frontal sulcus Numeric codes like 'ifs3' are non-standard anatomical nomenclature. Standard naming should use descriptive spatial qualifiers. The exact spatial extent requires atlas documentation or curator determination. Source name should be retained as synonym if atlas-specific. +ifs4 posterior inferior frontal sulcus Numeric codes like 'ifs4' are non-standard anatomical nomenclature. Standard naming should use descriptive spatial qualifiers. The exact spatial extent requires atlas documentation or curator determination. Source name should be retained as synonym if atlas-specific. +ifj1 REQUIRES_CLARIFICATION_FROM_SOURCE The label 'ifj1' is a non-standard abbreviated name. Standard neuroanatomical nomenclature uses descriptive qualifiers (e.g., 'anterior part of...', 'dorsal subdivision of...') rather than numeric codes. Possible alternatives might include: 'anterior subdivision of inferior frontal junction', 'posterior subdivision of inferior frontal junction', 'dorsal part of inferior frontal junction', or 'ventral part of inferior frontal junction' - but the actual anatomical feature that distinguishes ifj1 from ifj2 must be confirmed from the ASCTB data source. +ifj2 REQUIRES_CLARIFICATION_FROM_SOURCE The label 'ifj2' is a non-standard abbreviated name. See reasoning for 'ifj1' - both require clarification and proper anatomical naming from the ASCTB data source. diff --git a/src/templates/hra-brain.template.tsv b/src/templates/hra-brain.template.tsv new file mode 100644 index 000000000..c34cb5d08 --- /dev/null +++ b/src/templates/hra-brain.template.tsv @@ -0,0 +1,14 @@ +ID LABEL Definition def_xref is_a part_of develops_from In_subset Date Contributor Present_in_taxon Wikipedia_image xref +ID LABEL A IAO:0000115 >A oboInOwl:hasDbXref SPLIT=| SC % SC BFO:0000050 some % SC RO:0002202 some % AI oboInOwl:inSubset AT dcterms:date^^xsd:dateTime AI dcterms:contributor AI RO:0002175 A foaf:depiction A oboInOwl:hasDbXref SPLIT=| +http://purl.obolibrary.org/obo/UBERON_9920002 atrium of lateral ventricle A brain ventricle that is the region of the lateral ventricle at the junction where the body meets the inferior horn and posterior horn, characterized by an enlarged choroid plexus known as the choroid glomus. https://purl.org/ccf/ASCTB-TEMP_atrium-of-lateral-ventricle|PMID:37170923 UBERON:0004086 UBERON:0002285 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 FMA:83704 +http://purl.obolibrary.org/obo/UBERON_9920003 body of hippocampus A regional part of the brain that is the middle portion of Ammon's horn (hippocampus proper), extending from the head to the tail along the floor of the lateral ventricle. https://purl.org/ccf/ASCTB-TEMP_body-of-hippocampus|PMID:16399676|PMID:17587470 UBERON:0002616 UBERON:0001954 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 https://upload.wikimedia.org/wikipedia/commons/thumb/2/2e/Gray739-emphasizing-hippocampus.png/250px-Gray739-emphasizing-hippocampus.png Wikipedia:Hippocampus_anatomy +http://purl.obolibrary.org/obo/UBERON_9920004 cingulate gyrus, retrospleninal part [PENDING] https://purl.org/ccf/ASCTB-TEMP_cingulate-gyrus-retrospleninal-part http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9920005 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. https://purl.org/ccf/ASCTB-TEMP_extended-amygdala UBERON:0002616 UBERON:0001893 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Extended_amygdala +http://purl.obolibrary.org/obo/UBERON_9920006 frontomarginal gyrus A gyrus that is part of the polar region of the frontal lobe, located at the most anterior aspect of the cerebral hemisphere. https://purl.org/ccf/ASCTB-TEMP_frontomarginal-gyrus|PMID:20175407|PMID:22209688 UBERON:0015593 UBERON:0002795 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Frontal_lobe +http://purl.obolibrary.org/obo/UBERON_9920007 head of hippocampus A regional part of the brain that is the expanded anterior portion of Ammon's horn (hippocampus proper), located near the base of the temporal lobe and bordering the medial surface of the lateral ventricle. https://purl.org/ccf/ASCTB-TEMP_head-of-hippocampus|PMID:16399676|PMID:17587470 UBERON:0002616 UBERON:0001954 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 https://upload.wikimedia.org/wikipedia/commons/thumb/2/2e/Gray739-emphasizing-hippocampus.png/250px-Gray739-emphasizing-hippocampus.png Wikipedia:Hippocampus_anatomy +http://purl.obolibrary.org/obo/UBERON_9920010 anterior inferior frontal sulcus A regional part of the inferior frontal sulcus, representing a parcellated anatomical subdivision used in neuroanatomical mapping and brain atlases. https://purl.org/ccf/ASCTB-TEMP_ifs1|PMID:17584753 UBERON:0013118 UBERON:0002761 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Inferior_frontal_sulcus +http://purl.obolibrary.org/obo/UBERON_9920011 middle-anterior inferior frontal sulcus A regional part of the inferior frontal sulcus, representing a parcellated anatomical subdivision used in neuroanatomical mapping and brain atlases. https://purl.org/ccf/ASCTB-TEMP_ifs2|PMID:17584753 UBERON:0013118 UBERON:0002761 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Inferior_frontal_sulcus +http://purl.obolibrary.org/obo/UBERON_9920012 middle-posterior inferior frontal sulcus A regional part of the inferior frontal sulcus, representing a parcellated anatomical subdivision used in neuroanatomical mapping and brain atlases. https://purl.org/ccf/ASCTB-TEMP_ifs3|PMID:17584753 UBERON:0013118 UBERON:0002761 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Inferior_frontal_sulcus +http://purl.obolibrary.org/obo/UBERON_9920013 posterior inferior frontal sulcus A regional part of the inferior frontal sulcus, representing a parcellated anatomical subdivision used in neuroanatomical mapping and brain atlases. https://purl.org/ccf/ASCTB-TEMP_ifs4|PMID:17584753 UBERON:0013118 UBERON:0002761 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 Wikipedia:Inferior_frontal_sulcus +http://purl.obolibrary.org/obo/UBERON_9920015 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. https://purl.org/ccf/ASCTB-TEMP_occipitoparietal-transition-region UBERON:0002616 UBERON:0001869 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606 +http://purl.obolibrary.org/obo/UBERON_9920017 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. https://purl.org/ccf/ASCTB-TEMP_occipitotemporal-transition-region UBERON:0002616 UBERON:0001869 http://purl.obolibrary.org/obo/uberon/core#added_by_HRA 2026-05-25T00:00:00Z https://orcid.org/0000-0002-2999-0103 http://purl.obolibrary.org/obo/NCBITaxon_9606