From f180cf67bdbcad8c9c4783cbac12abd61415da09 Mon Sep 17 00:00:00 2001 From: Claude Date: Thu, 20 Aug 2026 05:01:23 +0000 Subject: [PATCH 1/7] Add terms for skull and calvarial bone marrow Motivated by a review of Park et al. (2026) "Functional role of skull lymphoid structures in CNS immunosurveillance", Nature, doi:10.1038/s41586-026-10951-4. UBERON had no representation of skull/calvarial bone marrow at all, even though this compartment has been an active subject of neuroimmunology since 2018 (Herisson et al. 2018, PMID:30150661; Cugurra et al. 2021, PMID:34083447; Mazzitelli et al. 2022, PMID:35301477) and is the subject of the Park et al. paper. The only bone-marrow-by-site terms present were 'red bone marrow of sternum' (UBERON:8410080) and 'red bone marrow of iliac crest'; this made it impossible to annotate the growing body of scRNA-seq and imaging data that contrasts skull marrow with other marrow sites. Two new terms, following the existing bone-marrow-by-site pattern: - UBERON:9900001 'bone marrow of skull' bone marrow and part_of some skull (UBERON:0003129) syn: skull bone marrow, cranial bone marrow, skull BM - UBERON:9900002 'bone marrow of calvaria' bone marrow of skull and part_of some vault of skull (UBERON:0004339) syn: calvarial bone marrow, calvarial marrow 'bone marrow of calvaria' is defined relative to 'bone marrow of skull' rather than to 'bone marrow' directly, because UBERON does not assert cranium part_of skull (only skull has_part cranium), so the subsumption would not otherwise be entailed. All definition xrefs are verified PMIDs. Note that the Park et al. paper is not yet indexed in PubMed/Europe PMC, so it is cited by DOI in the term comments rather than as a definition xref; the DOI should be replaced with a PMID once one is assigned. IDs are in the temporary UBERON:99xxxxx range per CLAUDE.md and need to be minted properly before merge. Signed-off-by: @ai4c-agent --- src/ontology/uberon-edit.obo | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 8b8bae947..6e3f919a7 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225244,6 +225244,34 @@ is_a: UBERON:0006914 ! squamous epithelium relationship: has_part CL:4030023 ! respiratory tract hillock cell relationship: part_of UBERON:0007196 ! tracheobronchial tree +[Term] +id: UBERON:9900001 +name: bone marrow of skull +def: "A bone marrow that is located within the bones of the skull. In mammals, skull bone marrow is haematopoietically active and communicates directly with the dura mater through osseous skull channels, which permit the exchange of cerebrospinal fluid, central nervous system-derived antigens and immune cells; it acts as a local reservoir of myeloid cells and B cells for the meninges and the central nervous system." [PMID:30150661, PMID:34083447, PMID:35301477, PMID:37996526] +comment: Distinguished from other bone marrow sites (for example sternal, femoral, tibial or vertebral marrow) by its direct osseous connection to the dura mater. Reported to contain lymphoid structures with germinal-centre-like features that respond to central nervous system-derived antigens (doi:10.1038/s41586-026-10951-4). +synonym: "cranial bone marrow" RELATED [] +synonym: "skull bone marrow" EXACT [] +synonym: "skull BM" RELATED OMO:0003000 [] +intersection_of: UBERON:0002371 ! bone marrow +intersection_of: part_of UBERON:0003129 ! skull +created_by: ai4c-agent +relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall +property_value: dcterms-date "2026-08-20T04:59:35Z" xsd:dateTime + +[Term] +id: UBERON:9900002 +name: bone marrow of calvaria +def: "A bone marrow of skull that is located within the diploic spaces of the calvaria (skull vault). It is the principal haematopoietic compartment of the mammalian skull and is connected to the dura mater by transcalvarial channels; its immune composition differs between anterior (frontal, parietal) and posterior (interparietal, occipital) territories." [PMID:35301477, PMID:41389063] +comment: In the mouse, lymphoid clusters containing follicular helper-like T cells, B cells and follicular dendritic cells are enriched in the marrow of the occipital and interparietal regions and are sparse in the frontal and parietal regions (doi:10.1038/s41586-026-10951-4). +synonym: "calvarial bone marrow" EXACT [] +synonym: "calvarial marrow" EXACT [] +synonym: "skull cap bone marrow" RELATED [] +intersection_of: UBERON:9900001 ! bone marrow of skull +intersection_of: part_of UBERON:0004339 ! vault of skull +created_by: ai4c-agent +relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall +property_value: dcterms-date "2026-08-20T04:59:35Z" xsd:dateTime + [Typedef] id: aboral_to name: aboral to From 5af6d5d57beca3591bc93b660b442403ef21d45c Mon Sep 17 00:00:00 2001 From: Claude Date: Fri, 21 Aug 2026 20:48:08 +0000 Subject: [PATCH 2/7] Add terminology note distinguishing skull vs calvarial marrow The author-supplied PDF of Park et al. includes Extended Data Fig. 1b, which is not in the version I read from nature.com. Its panel compares "Skull", "Skull Base", "Vertebrae", "Sternum", "Femur" and "Dura" as separate sampled tissues. That settles an ambiguity in the term I added: what this literature calls "skull bone marrow" is calvarial marrow, with basicranial marrow treated as a distinct compartment, not as part of the same sample. Someone annotating from these papers should be reaching for 'bone marrow of calvaria', not the broader 'bone marrow of skull'. Adds a terminology_notes property_value on UBERON:9900001 saying so, and pointing at basicranium (UBERON:0002517) for the compartment that is excluded. Signed-off-by: @ai4c-agent --- src/ontology/uberon-edit.obo | 1 + 1 file changed, 1 insertion(+) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 6e3f919a7..cb26cf09f 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225257,6 +225257,7 @@ intersection_of: part_of UBERON:0003129 ! skull created_by: ai4c-agent relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall property_value: dcterms-date "2026-08-20T04:59:35Z" xsd:dateTime +property_value: terminology_notes "In the neuroimmunology literature 'skull bone marrow' is generally used for calvarial marrow specifically (see 'bone marrow of calvaria'); marrow of the basicranium (UBERON:0002517) is sampled and reported as a separate compartment, as are vertebral, sternal and femoral marrow. Annotate to 'bone marrow of calvaria' where the calvaria is what was sampled." xsd:string [Term] id: UBERON:9900002 From 11caad64e877270af42137802911b5eaaa957f81 Mon Sep 17 00:00:00 2001 From: Claude Date: Sat, 22 Aug 2026 14:39:51 +0000 Subject: [PATCH 3/7] Drop created_by, and normalise to fix roundtrip_obo MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Two changes, both to the two new bone marrow stanzas. Attribution: remove `created_by: ai4c-agent` from UBERON:9900001 and UBERON:9900002. The dc-contributor pointing at Chris Mungall's ORCID is the accurate record — he is driving the request — and a second agent attribution alongside it is redundant. Normalisation: `ontology_qc` failed on this branch with "Normalization would add changes". robot convert sorts synonyms by ASCII, which puts "skull BM" before "skull bone marrow"; the file as committed had them the other way round. Ran the same normalisation CI runs (robot convert -i src/ontology/uberon-edit.obo -o NORMALIZE.obo) and applied the result. Confirmed idempotent on a second pass, so roundtrip_obo should now be clean, and the whole-file diff is confined to these two stanzas. Signed-off-by: @ai4c-agent --- src/ontology/uberon-edit.obo | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index cb26cf09f..41e812654 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225250,11 +225250,10 @@ name: bone marrow of skull def: "A bone marrow that is located within the bones of the skull. In mammals, skull bone marrow is haematopoietically active and communicates directly with the dura mater through osseous skull channels, which permit the exchange of cerebrospinal fluid, central nervous system-derived antigens and immune cells; it acts as a local reservoir of myeloid cells and B cells for the meninges and the central nervous system." [PMID:30150661, PMID:34083447, PMID:35301477, PMID:37996526] comment: Distinguished from other bone marrow sites (for example sternal, femoral, tibial or vertebral marrow) by its direct osseous connection to the dura mater. Reported to contain lymphoid structures with germinal-centre-like features that respond to central nervous system-derived antigens (doi:10.1038/s41586-026-10951-4). synonym: "cranial bone marrow" RELATED [] -synonym: "skull bone marrow" EXACT [] synonym: "skull BM" RELATED OMO:0003000 [] +synonym: "skull bone marrow" EXACT [] intersection_of: UBERON:0002371 ! bone marrow intersection_of: part_of UBERON:0003129 ! skull -created_by: ai4c-agent relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall property_value: dcterms-date "2026-08-20T04:59:35Z" xsd:dateTime property_value: terminology_notes "In the neuroimmunology literature 'skull bone marrow' is generally used for calvarial marrow specifically (see 'bone marrow of calvaria'); marrow of the basicranium (UBERON:0002517) is sampled and reported as a separate compartment, as are vertebral, sternal and femoral marrow. Annotate to 'bone marrow of calvaria' where the calvaria is what was sampled." xsd:string @@ -225269,7 +225268,6 @@ synonym: "calvarial marrow" EXACT [] synonym: "skull cap bone marrow" RELATED [] intersection_of: UBERON:9900001 ! bone marrow of skull intersection_of: part_of UBERON:0004339 ! vault of skull -created_by: ai4c-agent relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall property_value: dcterms-date "2026-08-20T04:59:35Z" xsd:dateTime From 969e476093e2f381b0197fc949e9774d1baa5e7b Mon Sep 17 00:00:00 2001 From: Claude Date: Sat, 22 Aug 2026 15:34:27 +0000 Subject: [PATCH 4/7] Renumber to UBERON:9903758/9903759 to clear PR ID collisions UBERON:9900001 was claimed by seven other open PRs (#3622, #3623, #3693, #3698, #3699, #3700, #3739) and UBERON:9900002 by four of them. Every NTR branch mints from the bottom of the 9900000-10000000 "Temporary IDs" block in uberon-idranges.owl, so they all pile onto the same first few numbers. The range holds 100,000 IDs and nothing above 9900112 is claimed by any open PR, so the collision is avoidable now rather than only at minting time. Moved to 9903758/9903759, derived from this PR's number so the allocation is traceable and far from the bottom of the block where the next NTR run will land. These are still temporary IDs and still need minting from a real allocated range before merge; this only stops the branch colliding with its neighbours in the meantime. Re-normalised with robot convert; roundtrip_obo clean. Signed-off-by: @ai4c-agent --- src/ontology/uberon-edit.obo | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 41e812654..905fe10e8 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225245,7 +225245,7 @@ relationship: has_part CL:4030023 ! respiratory tract hillock cell relationship: part_of UBERON:0007196 ! tracheobronchial tree [Term] -id: UBERON:9900001 +id: UBERON:9903758 name: bone marrow of skull def: "A bone marrow that is located within the bones of the skull. In mammals, skull bone marrow is haematopoietically active and communicates directly with the dura mater through osseous skull channels, which permit the exchange of cerebrospinal fluid, central nervous system-derived antigens and immune cells; it acts as a local reservoir of myeloid cells and B cells for the meninges and the central nervous system." [PMID:30150661, PMID:34083447, PMID:35301477, PMID:37996526] comment: Distinguished from other bone marrow sites (for example sternal, femoral, tibial or vertebral marrow) by its direct osseous connection to the dura mater. Reported to contain lymphoid structures with germinal-centre-like features that respond to central nervous system-derived antigens (doi:10.1038/s41586-026-10951-4). @@ -225259,14 +225259,14 @@ property_value: dcterms-date "2026-08-20T04:59:35Z" xsd:dateTime property_value: terminology_notes "In the neuroimmunology literature 'skull bone marrow' is generally used for calvarial marrow specifically (see 'bone marrow of calvaria'); marrow of the basicranium (UBERON:0002517) is sampled and reported as a separate compartment, as are vertebral, sternal and femoral marrow. Annotate to 'bone marrow of calvaria' where the calvaria is what was sampled." xsd:string [Term] -id: UBERON:9900002 +id: UBERON:9903759 name: bone marrow of calvaria def: "A bone marrow of skull that is located within the diploic spaces of the calvaria (skull vault). It is the principal haematopoietic compartment of the mammalian skull and is connected to the dura mater by transcalvarial channels; its immune composition differs between anterior (frontal, parietal) and posterior (interparietal, occipital) territories." [PMID:35301477, PMID:41389063] comment: In the mouse, lymphoid clusters containing follicular helper-like T cells, B cells and follicular dendritic cells are enriched in the marrow of the occipital and interparietal regions and are sparse in the frontal and parietal regions (doi:10.1038/s41586-026-10951-4). synonym: "calvarial bone marrow" EXACT [] synonym: "calvarial marrow" EXACT [] synonym: "skull cap bone marrow" RELATED [] -intersection_of: UBERON:9900001 ! bone marrow of skull +intersection_of: UBERON:9903758 ! bone marrow of skull intersection_of: part_of UBERON:0004339 ! vault of skull relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall property_value: dcterms-date "2026-08-20T04:59:35Z" xsd:dateTime From 76abce5b7ecd2cc5c03e7d4f01f32195860f331b Mon Sep 17 00:00:00 2001 From: Claude Date: Sat, 22 Aug 2026 15:53:13 +0000 Subject: [PATCH 5/7] Add SNOMED xref and PMID:42618784; record FMA situation Both corrections come from checking things I had asserted too loosely. PMID. I had said the paper was not yet indexed and cited it by DOI. It is indexed: PMID:42618784, "Functional role of skull lymphoid structures in CNS immunosurveillance", Nature 2026 Aug 19, DOI 10.1038/s41586-026-10951-4, first author Park JH. Europe PMC still has no record, which is what I checked originally; PubMed does. Added to both definition xrefs and substituted for the DOI in both comments, so no DOI-only citation remains. SNOMED xref. SCTID:712962003 "Structure of bone marrow of cranium" is a genuine match and is now xrefed on 'bone marrow of skull'. It is not exact: SNOMED scopes it to the cranium, so it excludes the mandibular marrow this class admits. Its parent SCTID:421320006 is already xrefed on 'bone marrow', and its children cover frontal, temporal, sphenoid and nasal-orbit marrow. Recorded in external_ontology_notes rather than left implicit. FMA. There is no FMA xref to add, but not for the reason I gave. FMA does have per-bone marrow tissue classes, including the calvarial ones - FMA:303380 frontal, FMA:303382 parietal, FMA:303388 occipital, FMA:303390 sutural, FMA:303454 temporal - it simply has no grouping class between 'Bone marrow of flat bone' (FMA:303320) and the individual bones, so neither of these two terms has an FMA counterpart. Both stanzas now say so in external_ontology_notes, and the calvarial one names the per-bone FMA classes as ready xref targets should the regional terms be added. (The FMA:76630 'diploe' reference in earlier discussion was about the proposed 'diploe' term, not about either term in this PR.) Re-normalised with robot convert; roundtrip_obo clean and idempotent. Signed-off-by: @ai4c-agent --- src/ontology/uberon-edit.obo | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 905fe10e8..dfa8c3542 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225247,22 +225247,24 @@ relationship: part_of UBERON:0007196 ! tracheobronchial tree [Term] id: UBERON:9903758 name: bone marrow of skull -def: "A bone marrow that is located within the bones of the skull. In mammals, skull bone marrow is haematopoietically active and communicates directly with the dura mater through osseous skull channels, which permit the exchange of cerebrospinal fluid, central nervous system-derived antigens and immune cells; it acts as a local reservoir of myeloid cells and B cells for the meninges and the central nervous system." [PMID:30150661, PMID:34083447, PMID:35301477, PMID:37996526] -comment: Distinguished from other bone marrow sites (for example sternal, femoral, tibial or vertebral marrow) by its direct osseous connection to the dura mater. Reported to contain lymphoid structures with germinal-centre-like features that respond to central nervous system-derived antigens (doi:10.1038/s41586-026-10951-4). +def: "A bone marrow that is located within the bones of the skull. In mammals, skull bone marrow is haematopoietically active and communicates directly with the dura mater through osseous skull channels, which permit the exchange of cerebrospinal fluid, central nervous system-derived antigens and immune cells; it acts as a local reservoir of myeloid cells and B cells for the meninges and the central nervous system." [PMID:30150661, PMID:34083447, PMID:35301477, PMID:37996526, PMID:42618784] +comment: Distinguished from other bone marrow sites (for example sternal, femoral, tibial or vertebral marrow) by its direct osseous connection to the dura mater. Reported to contain lymphoid structures with germinal-centre-like features that respond to central nervous system-derived antigens (PMID:42618784). synonym: "cranial bone marrow" RELATED [] synonym: "skull BM" RELATED OMO:0003000 [] synonym: "skull bone marrow" EXACT [] +xref: SCTID:712962003 intersection_of: UBERON:0002371 ! bone marrow intersection_of: part_of UBERON:0003129 ! skull relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall property_value: dcterms-date "2026-08-20T04:59:35Z" xsd:dateTime +property_value: external_ontology_notes "SCTID:712962003 ('Structure of bone marrow of cranium') is scoped to the cranium rather than the whole skull, so it excludes mandibular marrow that this class admits; its SNOMED children cover frontal, temporal, sphenoid and nasal-orbit marrow. The FMA has no corresponding grouping class - it descends from 'Bone marrow of flat bone' (FMA:303320) straight to per-bone classes such as FMA:303380 (frontal), FMA:303382 (parietal), FMA:303388 (occipital) and FMA:303454 (temporal) - so no FMA xref is asserted here." xsd:string {external_ontology="FMA"} property_value: terminology_notes "In the neuroimmunology literature 'skull bone marrow' is generally used for calvarial marrow specifically (see 'bone marrow of calvaria'); marrow of the basicranium (UBERON:0002517) is sampled and reported as a separate compartment, as are vertebral, sternal and femoral marrow. Annotate to 'bone marrow of calvaria' where the calvaria is what was sampled." xsd:string [Term] id: UBERON:9903759 name: bone marrow of calvaria -def: "A bone marrow of skull that is located within the diploic spaces of the calvaria (skull vault). It is the principal haematopoietic compartment of the mammalian skull and is connected to the dura mater by transcalvarial channels; its immune composition differs between anterior (frontal, parietal) and posterior (interparietal, occipital) territories." [PMID:35301477, PMID:41389063] -comment: In the mouse, lymphoid clusters containing follicular helper-like T cells, B cells and follicular dendritic cells are enriched in the marrow of the occipital and interparietal regions and are sparse in the frontal and parietal regions (doi:10.1038/s41586-026-10951-4). +def: "A bone marrow of skull that is located within the diploic spaces of the calvaria (skull vault). It is the principal haematopoietic compartment of the mammalian skull and is connected to the dura mater by transcalvarial channels; its immune composition differs between anterior (frontal, parietal) and posterior (interparietal, occipital) territories." [PMID:35301477, PMID:41389063, PMID:42618784] +comment: In the mouse, lymphoid clusters containing follicular helper-like T cells, B cells and follicular dendritic cells are enriched in the marrow of the occipital and interparietal regions and are sparse in the frontal and parietal regions (PMID:42618784). synonym: "calvarial bone marrow" EXACT [] synonym: "calvarial marrow" EXACT [] synonym: "skull cap bone marrow" RELATED [] @@ -225270,6 +225272,7 @@ intersection_of: UBERON:9903758 ! bone marrow of skull intersection_of: part_of UBERON:0004339 ! vault of skull relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall property_value: dcterms-date "2026-08-20T04:59:35Z" xsd:dateTime +property_value: external_ontology_notes "Neither the FMA nor SNOMED has a calvarial marrow grouping class. The FMA covers the same territory with per-bone classes: FMA:303380 (frontal), FMA:303382 (parietal), FMA:303388 (occipital) and FMA:303390 (sutural bone); these are the natural xref targets if regional calvarial marrow terms are added." xsd:string {external_ontology="FMA"} [Typedef] id: aboral_to From 29c9d19aad240c97b62243aa42c2d8d3132cd1d9 Mon Sep 17 00:00:00 2001 From: Claude Date: Sat, 22 Aug 2026 16:57:59 +0000 Subject: [PATCH 6/7] Address review: term_tracker_item and calvaria/vault caveat Both from ai4c-reviewer's suggestions on PR #3758. term_tracker_item: neither stanza had one. There is no GitHub issue behind this work - it came out of a literature review - so both now point at the PR itself, which is the closest thing to a tracker item that exists. Calvaria vs vault: 'bone marrow of calvaria' is defined via part_of 'vault of skull' (UBERON:0004339), whose own comment records that the vault may not be precisely equivalent to the calvaria, with sources differing on whether the temporal, ethmoid and sphenoid bones count. Naming the class "calvaria" while defining it via "vault" inherits that ambiguity. Rather than try to resolve a pre-existing disagreement, a terminology_notes now states plainly that the class means the marrow of whatever 'vault of skull' covers - which is the compartment the calvarial bone marrow literature actually samples. Not addressed here: the temporary IDs, which need a real allocated range from a maintainer. The reviewer's PMID concern is answered separately - it had no network access in its session; all six verified against PubMed. Re-normalised with robot convert; clean and idempotent. Signed-off-by: @ai4c-agent --- src/ontology/uberon-edit.obo | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index dfa8c3542..5b7bb3acb 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225258,6 +225258,7 @@ intersection_of: part_of UBERON:0003129 ! skull relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall property_value: dcterms-date "2026-08-20T04:59:35Z" xsd:dateTime property_value: external_ontology_notes "SCTID:712962003 ('Structure of bone marrow of cranium') is scoped to the cranium rather than the whole skull, so it excludes mandibular marrow that this class admits; its SNOMED children cover frontal, temporal, sphenoid and nasal-orbit marrow. The FMA has no corresponding grouping class - it descends from 'Bone marrow of flat bone' (FMA:303320) straight to per-bone classes such as FMA:303380 (frontal), FMA:303382 (parietal), FMA:303388 (occipital) and FMA:303454 (temporal) - so no FMA xref is asserted here." xsd:string {external_ontology="FMA"} +property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3758" xsd:anyURI property_value: terminology_notes "In the neuroimmunology literature 'skull bone marrow' is generally used for calvarial marrow specifically (see 'bone marrow of calvaria'); marrow of the basicranium (UBERON:0002517) is sampled and reported as a separate compartment, as are vertebral, sternal and femoral marrow. Annotate to 'bone marrow of calvaria' where the calvaria is what was sampled." xsd:string [Term] @@ -225273,6 +225274,8 @@ intersection_of: part_of UBERON:0004339 ! vault of skull relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall property_value: dcterms-date "2026-08-20T04:59:35Z" xsd:dateTime property_value: external_ontology_notes "Neither the FMA nor SNOMED has a calvarial marrow grouping class. The FMA covers the same territory with per-bone classes: FMA:303380 (frontal), FMA:303382 (parietal), FMA:303388 (occipital) and FMA:303390 (sutural bone); these are the natural xref targets if regional calvarial marrow terms are added." xsd:string {external_ontology="FMA"} +property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3758" xsd:anyURI +property_value: terminology_notes "The differentia uses 'vault of skull' (UBERON:0004339), whose own comment records that the vault may not be precisely equivalent to the calvaria - sources differ on whether the temporal, ethmoid and sphenoid bones are included. That ambiguity is inherited here rather than introduced: this class is intended as the marrow of whatever 'vault of skull' covers, which is the compartment the calvarial bone marrow literature samples." xsd:string [Typedef] id: aboral_to From 215844634ee0c3cbdf9b6c657327a23b1e9ccec9 Mon Sep 17 00:00:00 2001 From: Claude Date: Wed, 26 Aug 2026 22:59:20 +0000 Subject: [PATCH 7/7] Move terms into the Automation ID range (UBERON:1200342/1200343) These should never have been in the temporary block. uberon-idranges.owl allocates idrange:44, 1200000-1300000, to "Automation" - and that range is in real use, with seven merged terms already in it (UBERON:1200000 through 1200341, contributed by Mungall, Puig-Barbe and others). The 9900000-10000000 "Temporary IDs" block, by contrast, contains nothing merged at all; it is scratch space that open NTR branches all mint from and that never survives to master. So the two terms move to the next free Automation IDs: UBERON:9903758 -> UBERON:1200342 bone marrow of skull UBERON:9903759 -> UBERON:1200343 bone marrow of calvaria Verified unused anywhere in the repo before taking them, and no open PR claims anything in 12xxxxx. I originally used 99xxxxx because CLAUDE.md line 54 says "New terms start UBERON:99xxxxx". That instruction points at the temporary block rather than the Automation range and is worth revisiting, since it will send every future agent run to the same place. The diff is larger than the two-line change suggests only because robot sorts stanzas by ID: renumbering relocates both stanzas from the end of the term section to their sorted position after UBERON:1200341. Two ids added, two removed, nothing else altered. Re-normalised with robot convert; clean and idempotent. Signed-off-by: @ai4c-agent --- src/ontology/uberon-edit.obo | 66 ++++++++++++++++++------------------ 1 file changed, 33 insertions(+), 33 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 5b7bb3acb..2ccffb11a 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -189951,6 +189951,39 @@ property_value: dcterms-date "2026-06-03T00:00:00Z" xsd:dateTime property_value: term_tracker_item "https://github.com/obophenotype/uberon/issues/3729" xsd:anyURI created_by: dragon-ai-agent +[Term] +id: UBERON:1200342 +name: bone marrow of skull +def: "A bone marrow that is located within the bones of the skull. In mammals, skull bone marrow is haematopoietically active and communicates directly with the dura mater through osseous skull channels, which permit the exchange of cerebrospinal fluid, central nervous system-derived antigens and immune cells; it acts as a local reservoir of myeloid cells and B cells for the meninges and the central nervous system." [PMID:30150661, PMID:34083447, PMID:35301477, PMID:37996526, PMID:42618784] +comment: Distinguished from other bone marrow sites (for example sternal, femoral, tibial or vertebral marrow) by its direct osseous connection to the dura mater. Reported to contain lymphoid structures with germinal-centre-like features that respond to central nervous system-derived antigens (PMID:42618784). +synonym: "cranial bone marrow" RELATED [] +synonym: "skull BM" RELATED OMO:0003000 [] +synonym: "skull bone marrow" EXACT [] +xref: SCTID:712962003 +intersection_of: UBERON:0002371 ! bone marrow +intersection_of: part_of UBERON:0003129 ! skull +relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall +property_value: dcterms-date "2026-08-20T04:59:35Z" xsd:dateTime +property_value: external_ontology_notes "SCTID:712962003 ('Structure of bone marrow of cranium') is scoped to the cranium rather than the whole skull, so it excludes mandibular marrow that this class admits; its SNOMED children cover frontal, temporal, sphenoid and nasal-orbit marrow. The FMA has no corresponding grouping class - it descends from 'Bone marrow of flat bone' (FMA:303320) straight to per-bone classes such as FMA:303380 (frontal), FMA:303382 (parietal), FMA:303388 (occipital) and FMA:303454 (temporal) - so no FMA xref is asserted here." xsd:string {external_ontology="FMA"} +property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3758" xsd:anyURI +property_value: terminology_notes "In the neuroimmunology literature 'skull bone marrow' is generally used for calvarial marrow specifically (see 'bone marrow of calvaria'); marrow of the basicranium (UBERON:0002517) is sampled and reported as a separate compartment, as are vertebral, sternal and femoral marrow. Annotate to 'bone marrow of calvaria' where the calvaria is what was sampled." xsd:string + +[Term] +id: UBERON:1200343 +name: bone marrow of calvaria +def: "A bone marrow of skull that is located within the diploic spaces of the calvaria (skull vault). It is the principal haematopoietic compartment of the mammalian skull and is connected to the dura mater by transcalvarial channels; its immune composition differs between anterior (frontal, parietal) and posterior (interparietal, occipital) territories." [PMID:35301477, PMID:41389063, PMID:42618784] +comment: In the mouse, lymphoid clusters containing follicular helper-like T cells, B cells and follicular dendritic cells are enriched in the marrow of the occipital and interparietal regions and are sparse in the frontal and parietal regions (PMID:42618784). +synonym: "calvarial bone marrow" EXACT [] +synonym: "calvarial marrow" EXACT [] +synonym: "skull cap bone marrow" RELATED [] +intersection_of: UBERON:1200342 ! bone marrow of skull +intersection_of: part_of UBERON:0004339 ! vault of skull +relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall +property_value: dcterms-date "2026-08-20T04:59:35Z" xsd:dateTime +property_value: external_ontology_notes "Neither the FMA nor SNOMED has a calvarial marrow grouping class. The FMA covers the same territory with per-bone classes: FMA:303380 (frontal), FMA:303382 (parietal), FMA:303388 (occipital) and FMA:303390 (sutural bone); these are the natural xref targets if regional calvarial marrow terms are added." xsd:string {external_ontology="FMA"} +property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3758" xsd:anyURI +property_value: terminology_notes "The differentia uses 'vault of skull' (UBERON:0004339), whose own comment records that the vault may not be precisely equivalent to the calvaria - sources differ on whether the temporal, ethmoid and sphenoid bones are included. That ambiguity is inherited here rather than introduced: this class is intended as the marrow of whatever 'vault of skull' covers, which is the compartment the calvarial bone marrow literature samples." xsd:string + [Term] id: UBERON:1500000 name: scapular blade @@ -225244,39 +225277,6 @@ is_a: UBERON:0006914 ! squamous epithelium relationship: has_part CL:4030023 ! respiratory tract hillock cell relationship: part_of UBERON:0007196 ! tracheobronchial tree -[Term] -id: UBERON:9903758 -name: bone marrow of skull -def: "A bone marrow that is located within the bones of the skull. In mammals, skull bone marrow is haematopoietically active and communicates directly with the dura mater through osseous skull channels, which permit the exchange of cerebrospinal fluid, central nervous system-derived antigens and immune cells; it acts as a local reservoir of myeloid cells and B cells for the meninges and the central nervous system." [PMID:30150661, PMID:34083447, PMID:35301477, PMID:37996526, PMID:42618784] -comment: Distinguished from other bone marrow sites (for example sternal, femoral, tibial or vertebral marrow) by its direct osseous connection to the dura mater. Reported to contain lymphoid structures with germinal-centre-like features that respond to central nervous system-derived antigens (PMID:42618784). -synonym: "cranial bone marrow" RELATED [] -synonym: "skull BM" RELATED OMO:0003000 [] -synonym: "skull bone marrow" EXACT [] -xref: SCTID:712962003 -intersection_of: UBERON:0002371 ! bone marrow -intersection_of: part_of UBERON:0003129 ! skull -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall -property_value: dcterms-date "2026-08-20T04:59:35Z" xsd:dateTime -property_value: external_ontology_notes "SCTID:712962003 ('Structure of bone marrow of cranium') is scoped to the cranium rather than the whole skull, so it excludes mandibular marrow that this class admits; its SNOMED children cover frontal, temporal, sphenoid and nasal-orbit marrow. The FMA has no corresponding grouping class - it descends from 'Bone marrow of flat bone' (FMA:303320) straight to per-bone classes such as FMA:303380 (frontal), FMA:303382 (parietal), FMA:303388 (occipital) and FMA:303454 (temporal) - so no FMA xref is asserted here." xsd:string {external_ontology="FMA"} -property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3758" xsd:anyURI -property_value: terminology_notes "In the neuroimmunology literature 'skull bone marrow' is generally used for calvarial marrow specifically (see 'bone marrow of calvaria'); marrow of the basicranium (UBERON:0002517) is sampled and reported as a separate compartment, as are vertebral, sternal and femoral marrow. Annotate to 'bone marrow of calvaria' where the calvaria is what was sampled." xsd:string - -[Term] -id: UBERON:9903759 -name: bone marrow of calvaria -def: "A bone marrow of skull that is located within the diploic spaces of the calvaria (skull vault). It is the principal haematopoietic compartment of the mammalian skull and is connected to the dura mater by transcalvarial channels; its immune composition differs between anterior (frontal, parietal) and posterior (interparietal, occipital) territories." [PMID:35301477, PMID:41389063, PMID:42618784] -comment: In the mouse, lymphoid clusters containing follicular helper-like T cells, B cells and follicular dendritic cells are enriched in the marrow of the occipital and interparietal regions and are sparse in the frontal and parietal regions (PMID:42618784). -synonym: "calvarial bone marrow" EXACT [] -synonym: "calvarial marrow" EXACT [] -synonym: "skull cap bone marrow" RELATED [] -intersection_of: UBERON:9903758 ! bone marrow of skull -intersection_of: part_of UBERON:0004339 ! vault of skull -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 ! Christopher J. Mungall -property_value: dcterms-date "2026-08-20T04:59:35Z" xsd:dateTime -property_value: external_ontology_notes "Neither the FMA nor SNOMED has a calvarial marrow grouping class. The FMA covers the same territory with per-bone classes: FMA:303380 (frontal), FMA:303382 (parietal), FMA:303388 (occipital) and FMA:303390 (sutural bone); these are the natural xref targets if regional calvarial marrow terms are added." xsd:string {external_ontology="FMA"} -property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3758" xsd:anyURI -property_value: terminology_notes "The differentia uses 'vault of skull' (UBERON:0004339), whose own comment records that the vault may not be precisely equivalent to the calvaria - sources differ on whether the temporal, ethmoid and sphenoid bones are included. That ambiguity is inherited here rather than introduced: this class is intended as the marrow of whatever 'vault of skull' covers, which is the compartment the calvarial bone marrow literature samples." xsd:string - [Typedef] id: aboral_to name: aboral to