obophenotype/uberon: 2025-12-05 Release

<details> <summary>Mappings removed: 6</summary>

| Subject | Predicate | Object | ----|----|----| | vestibular nerve (UBERON:0003723) | oio:hasDbXref | DHBA:12869 | | cerebellum interpositus nucleus (UBERON:0004073) | oio:hasDbXref | DHBA:12399 | | olfactory tract (UBERON:0002265) | oio:hasDbXref | DHBA:12074 | | subiculum (UBERON:0002191) | oio:hasDbXref | DHBA:10301 | | pontine raphe nucleus (UBERON:0002047) | oio:hasDbXref | DHBA:12471 | | fourth ventricle (UBERON:0002422) | oio:hasDbXref | DHBA:10669 |

</details>

<details> <summary>Nodes added to subset: 11</summary>

| Term | Subset | ----|----| | olfactory cortex (UBERON:0002894) | human_reference_atlas | | sixth lumbar dorsal root ganglion (UBERON:1200001) | defined_by_ordinal_series | | ventral striatum (UBERON:0005403) | human_reference_atlas | | internodal tract (UBERON:0009966) | human_reference_atlas | | basal ganglion (UBERON:0002420) | human_reference_atlas | | dorsal striatum (UBERON:0005382) | human_reference_atlas | | cardiac muscle tissue of interatrial septum (UBERON:0004491) | human_reference_atlas | | coronary sinus valve (UBERON:0004150) | human_reference_atlas | | striatum (UBERON:0002435) | human_reference_atlas | | diencephalon (UBERON:0001894) | human_reference_atlas | | olfactory tubercle (UBERON:0001883) | human_reference_atlas |

</details>

<details> <summary>Nodes renamed: 2</summary>

| ID | Old Label | New Label | ----|----|----| | UBERON:0009548 | hepatic sinusoid of left of lobe of liver | hepatic sinusoid of left lobe of liver | | UBERON:0009549 | hepatic sinusoid of right of lobe of liver | hepatic sinusoid of right lobe of liver |

</details>

<details> <summary>Text definitions changed: 2</summary>

| Term | Old Text Definition | New Text Definition | ----|----|----| | tracheal mucosa (UBERON:0000379) | A mucosa that is part of a respiratory airway. | A mucosa that is part of a trachea. | | carotid body (UBERON:0001629) | A small epithelioid structure consisting of a small cluster of chemoreceptive and supporting cells located near the bifurcation of the common carotid artery that serves as a chemoreceptive organ that senses the pH, carbon dioxide, and oxygen concentrations in the blood and plays a crucial role in their homeostatic control. | A bilateral sensory organ in the peripheral nervous system located in the adventitia of the bifurcation of the common carotid artery. The carotid body is a chemoreceptive organ that senses the pH, carbon dioxide, and oxygen concentrations in the blood and plays a crucial role in their homeostatic control. |

</details>

<details> <summary>Relationships removed: 7</summary>

| Subject| Predicate| Object| ----|----|----| | nasal cavity mucosa (UBERON:0001826) | subClassOf (rdfs:subClassOf) | tracheal mucosa (UBERON:0000379) | | carotid body (UBERON:0001629) | BFO:0000050 | common carotid artery plus branches (UBERON:0001530) | | mucosa of bronchiole (UBERON:0005039) | subClassOf (rdfs:subClassOf) | tracheal mucosa (UBERON:0000379) | | mucosa of larynx (UBERON:0001824) | subClassOf (rdfs:subClassOf) | tracheal mucosa (UBERON:0000379) | | mucosa of nasopharynx (UBERON:0005022) | subClassOf (rdfs:subClassOf) | tracheal mucosa (UBERON:0000379) | | tracheal mucosa (UBERON:0000379) | BFO:0000050 | respiratory airway (UBERON:0001005) | | bronchial mucosa (UBERON:0000410) | subClassOf (rdfs:subClassOf) | tracheal mucosa (UBERON:0000379) |

</details>

<details> <summary>Relationships added: 20</summary>

| Subject | Predicate | Object| ----|----|----| | tracheal mucosa (UBERON:0000379) | BFO:0000050 | trachea (UBERON:0003126) | | mucosa of bronchiole (UBERON:0005039) | subClassOf (rdfs:subClassOf) | respiratory system mucosa (UBERON:0004785) | | sixth lumbar dorsal root ganglion (UBERON:1200001) | subClassOf (rdfs:subClassOf) | lumbar dorsal root ganglion (UBERON:0002836) | | carotid body (UBERON:0001629) | BFO:0000050 | peripheral nervous system (UBERON:0000010) | | carotid artery intima-media region (UBERON:1200002) | subClassOf (rdfs:subClassOf) | multi-tissue structure (UBERON:0000481) | | mucosa of larynx (UBERON:0001824) | subClassOf (rdfs:subClassOf) | respiratory system mucosa (UBERON:0004785) | | bivalve adductor muscle (UBERON:7770010) | RO:0002162 | NCBITaxon:6544 | | occlusal surface of tooth (UBERON:8600149) | subClassOf (rdfs:subClassOf) | tooth surface structure (UBERON:8600148) | | bronchial mucosa (UBERON:0000410) | subClassOf (rdfs:subClassOf) | respiratory system mucosa (UBERON:0004785) | | bivalve adductor muscle (UBERON:7770010) | subClassOf (rdfs:subClassOf) | somatic muscle, invertebrate (UBERON:0014895) | | kidney interpolar region (UBERON:7770009) | BFO:0000050 | kidney (UBERON:0002113) | | nasal cavity mucosa (UBERON:0001826) | subClassOf (rdfs:subClassOf) | respiratory system mucosa (UBERON:0004785) | | carotid artery intima-media region (UBERON:1200002) | BFO:0000051 | tunica intima (UBERON:0002523) | | uterine fundus (UBERON:1200003) | BFO:0000050 | uterus (UBERON:0000995) | | uterine fundus (UBERON:1200003) | subClassOf (rdfs:subClassOf) | organ part (UBERON:0000064) | | carotid artery intima-media region (UBERON:1200002) | BFO:0000050 | carotid artery segment (UBERON:0005396) | | carotid artery intima-media region (UBERON:1200002) | BFO:0000051 | tunica media (UBERON:0002522) | | ileocecal fold (UBERON:1200000) | subClassOf (rdfs:subClassOf) | fold of peritoneum (UBERON:0034696) | | uterine fundus (UBERON:1200003) | subClassOf (rdfs:subClassOf) | reproductive structure (UBERON:0005156) | | kidney interpolar region (UBERON:7770009) | subClassOf (rdfs:subClassOf) | organ part (UBERON:0000064) |

</details>

<details> <summary>Classes added: 7</summary>

| Term | ----| | sixth lumbar dorsal root ganglion (UBERON:1200001) | | uterine fundus (UBERON:1200003) | | kidney interpolar region (UBERON:7770009) | | occlusal surface of tooth (UBERON:8600149) | | bivalve adductor muscle (UBERON:7770010) | | ileocecal fold (UBERON:1200000) | | carotid artery intima-media region (UBERON:1200002) |

</details>

<details> <summary>Text definitions added: 7</summary>

| Term | New Text Definition | ----|----| | kidney interpolar region (UBERON:7770009) | The middle portion of the kidney situated between the upper pole and the lower pole, representing approximately the middle third of the kidney along its longitudinal axis. | | uterine fundus (UBERON:1200003) | The superior, dome-shaped portion of the uterus. | | bivalve adductor muscle (UBERON:7770010) | The main muscular system in bivalve mollusks, responsible for closing the valves of the shell when contracting; bivalve mollusks generally have either one or two adductor muscles. | | carotid artery intima-media region (UBERON:1200002) | A region of the carotid artery wall composed of the tunica intima and tunica media. | | sixth lumbar dorsal root ganglion (UBERON:1200001) | The group of nerve cell bodies located on the dorsal spinal roots within the vertebral column at the level of the sixth lumbar vertebra. | | occlusal surface of tooth (UBERON:8600149) | A tooth surface structure that forms the chewing edge of premolar or molar tooth. It functions to chew or grind food during biting. | | ileocecal fold (UBERON:1200000) | A fold of peritoneum between the ileum and cecum. The upper border of the ileocecal fold is fixed to the ileum opposite its mesenteric attachment, and the lower border passes over the ileocecal junction to join the mesentery of the appendix (and sometimes the appendix itself as well). Behind the ileocecal fold is the inferior ileocecal fossa. |

</details>

<details> <summary>Synonyms added: 12</summary>

| Term | New Synonym | Predicate | ----|----|----| | kidney interpolar region (UBERON:7770009) | central pole of kidney | oio:hasExactSynonym | | occlusal surface of tooth (UBERON:8600149) | masticatory surface | oio:hasRelatedSynonym | | kidney interpolar region (UBERON:7770009) | interpolar region of kidney | oio:hasExactSynonym | | sixth lumbar dorsal root ganglion (UBERON:1200001) | sixth lumbar spinal ganglion | oio:hasExactSynonym | | occlusal surface of tooth (UBERON:8600149) | occlusal surface | oio:hasExactSynonym | | uterine fundus (UBERON:1200003) | fundus of uterus | oio:hasExactSynonym | | ileocecal fold (UBERON:1200000) | ileocaecal fold | oio:hasExactSynonym | | carotid artery intima-media region (UBERON:1200002) | carotid intima-media | oio:hasExactSynonym | | uterine fundus (UBERON:1200003) | fundus uteri | oio:hasExactSynonym | | sixth lumbar dorsal root ganglion (UBERON:1200001) | L6 dorsal root ganglion | oio:hasExactSynonym | | bivalve adductor muscle (UBERON:7770010) | catch muscle | oio:hasRelatedSynonym | | occlusal surface of tooth (UBERON:8600149) | chewing surface | oio:hasRelatedSynonym |

</details>

<details> <summary>Mappings added: 1</summary>

| Subject | Predicate | Object | ----|----|----| | ileocecal fold (UBERON:1200000) | oio:hasDbXref | FMA:16532 |

</details>

What's Changed

• Update how to deploy release by @aleixpuigb in https://github.com/obophenotype/uberon/pull/3599
• Remove inputs from copilot-setup-steps.yml by @aleixpuigb in https://github.com/obophenotype/uberon/pull/3600
• Add occlusal surface of tooth (UBERON:8600149) by @dragon-ai-agent in https://github.com/obophenotype/uberon/pull/3603
• Fixing AI permissions by @cmungall in https://github.com/obophenotype/uberon/pull/3606
• Add kidney interpolar region term (UBERON:7770009) by @dragon-ai-agent in https://github.com/obophenotype/uberon/pull/3607
• Add UBERON:7770010 bivalve adductor muscle by @dragon-ai-agent in https://github.com/obophenotype/uberon/pull/3608
• Fix carotid body classification (Fixes #3591) by @cmungall in https://github.com/obophenotype/uberon/pull/3595
• Fix the automatic ID allocation workflow. by @gouttegd in https://github.com/obophenotype/uberon/pull/3612
• Add new term: ileocecal fold (UBERON:9900001) by @dragon-ai-agent in https://github.com/obophenotype/uberon/pull/3609
• Test: Move a tag out of place. by @gouttegd in https://github.com/obophenotype/uberon/pull/3614
• Fix typos in labels for UBERON:0009548 and UBERON:0009549 by @dragon-ai-agent in https://github.com/obophenotype/uberon/pull/3616
• Fix tracheal mucosa logical definition to prevent incorrect inference by @dragon-ai-agent in https://github.com/obophenotype/uberon/pull/3619
• Add sixth lumbar dorsal root ganglion (UBERON:9900001) by @dragon-ai-agent in https://github.com/obophenotype/uberon/pull/3620
• Remove DHBA:12869 xref from vestibular nerve by @dragon-ai-agent in https://github.com/obophenotype/uberon/pull/3626
• Remove incorrect DHBA xrefs from 5 UBERON terms by @dragon-ai-agent in https://github.com/obophenotype/uberon/pull/3628
• Update CLAUDE.md by @dosumis in https://github.com/obophenotype/uberon/pull/3547
• Update occlusal surface of tooth term (UBERON:8600149) by @dragon-ai-agent in https://github.com/obophenotype/uberon/pull/3633
• Add term: carotid artery intima-media region (UBERON:9900000) by @dragon-ai-agent in https://github.com/obophenotype/uberon/pull/3630
• Refresh imports in preparation of Uberon release 2025-12-01 by @aleixpuigb in https://github.com/obophenotype/uberon/pull/3635
• [NTR] Add uterine fundus (UBERON:9900001) by @dragon-ai-agent in https://github.com/obophenotype/uberon/pull/3638
• Uberon release v2025-12-04 by @aleixpuigb in https://github.com/obophenotype/uberon/pull/3639

Full Changelog: https://github.com/obophenotype/uberon/compare/v2025-08-15...v2025-12-04