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add hra brain terms #3712

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5d3e1ca
add hra brain terms
zhengj2007 May 25, 2026
877206a
Move report artifacts out of src/templates to bulk_ntr_workflow/outputs/
dosumis Jul 6, 2026
2ab42a8
Merge branch 'master' into add-hra-brain-ntr
zhengj2007 Jul 22, 2026
1416520
Remove brain NTR generated outputs and template artifacts
zhengj2007 Jul 22, 2026
36b589d
Update hra-brain template IDs and def_xrefs
zhengj2007 Jul 22, 2026
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6 changes: 6 additions & 0 deletions bulk_ntr_workflow/outputs/hra-brain-reports/candidates.tsv
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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.)
3 changes: 3 additions & 0 deletions bulk_ntr_workflow/outputs/hra-brain-reports/errors.tsv
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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
20 changes: 20 additions & 0 deletions bulk_ntr_workflow/outputs/hra-brain-reports/input.tsv
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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
4 changes: 4 additions & 0 deletions bulk_ntr_workflow/outputs/hra-brain-reports/manual_curation.tsv
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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.
2 changes: 2 additions & 0 deletions bulk_ntr_workflow/outputs/template_groups_initial.tsv
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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=|
13 changes: 13 additions & 0 deletions src/templates/hra-brain.template.tsv
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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_8930234 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_8930235 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_8930236 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|PMID:12724159 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_8930237 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_8930238 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_8930239 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_8930240 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_8930241 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_8930242 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_8930243 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|PMID:39976051 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_8930244 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|PMID:39976051 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
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