obophenotype/uberon: v2024-11-25 Release

<details> <summary>Classes added: 5</summary>

| Term | ----| | embryonic craniocervical region (UBERON:8450003) | | follicle associated epithelium (UBERON:8700001) | | antimesosalpinx (UBERON:8600117) | | stratum spinosum of esophageal epithelium (UBERON:8700002) | | aorta-gonad-mesonephros (UBERON:8700000) |

</details>

<details> <summary>Relationships removed: 28</summary>

| Subject| Predicate| Object| ----|----|----| | pharyngeal arch (UBERON:0002539) | BFO:0000050 | embryonic head (UBERON:0008816) | | efferent filamental artery (UBERON:2005018) | subClassOf (rdfs:subClassOf) | head blood vessel (UBERON:0003496) | | efferent lamellar arteriole (UBERON:2005019) | subClassOf (rdfs:subClassOf) | head blood vessel (UBERON:0003496) | | ascending vasa recta (UBERON:0009091) | subClassOf (rdfs:subClassOf) | mesoderm-derived structure (UBERON:0004120) | | 1st arch mesenchyme from head mesenchyme (UBERON:0010341) | subClassOf (rdfs:subClassOf) | head mesenchyme from mesoderm (UBERON:0006904) | | outer medulla ascending vasa recta (UBERON:0009093) | subClassOf (rdfs:subClassOf) | mesoderm-derived structure (UBERON:0004120) | | afferent filamental artery (UBERON:2005012) | subClassOf (rdfs:subClassOf) | head blood vessel (UBERON:0003496) | | concurrent branch afferent branchial artery (UBERON:2005013) | subClassOf (rdfs:subClassOf) | head blood vessel (UBERON:0003496) | | outer medulla descending vasa recta (UBERON:0009090) | subClassOf (rdfs:subClassOf) | mesoderm-derived structure (UBERON:0004120) | | descending vasa recta (UBERON:0009202) | subClassOf (rdfs:subClassOf) | mesoderm-derived structure (UBERON:0004120) | | afferent lamellar arteriole (UBERON:2005015) | subClassOf (rdfs:subClassOf) | head blood vessel (UBERON:0003496) | | 6th arch mesenchyme from head mesenchyme (UBERON:0010347) | subClassOf (rdfs:subClassOf) | head mesenchyme from mesoderm (UBERON:0006904) | | 3rd arch mesenchyme from head mesenchyme (UBERON:0010344) | subClassOf (rdfs:subClassOf) | head mesenchyme from mesoderm (UBERON:0006904) | | outer renal medulla vasa recta (UBERON:0004775) | subClassOf (rdfs:subClassOf) | renal venous blood vessel (UBERON:0014401) | | inner medulla descending vasa recta (UBERON:0009089) | subClassOf (rdfs:subClassOf) | mesoderm-derived structure (UBERON:0004120) | | inner renal medulla vasa recta (UBERON:0004776) | subClassOf (rdfs:subClassOf) | vein of abdomen (UBERON:0013126) | | inner medulla ascending vasa recta (UBERON:0009092) | subClassOf (rdfs:subClassOf) | mesoderm-derived structure (UBERON:0004120) | | pharyngeal arch artery (UBERON:0004363) | subClassOf (rdfs:subClassOf) | head blood vessel (UBERON:0003496) | | outer renal medulla vasa recta (UBERON:0004775) | subClassOf (rdfs:subClassOf) | vein of abdomen (UBERON:0013126) | | 2nd arch mesenchyme from head mesenchyme (UBERON:0010343) | subClassOf (rdfs:subClassOf) | head mesenchyme from mesoderm (UBERON:0006904) | | hyaloid vessel (UBERON:0005492) | BFO:0000050 | embryo (UBERON:0000922) | | vasa recta (UBERON:0004726) | subClassOf (rdfs:subClassOf) | renal vein (UBERON:0001140) | | recurrent branch afferent branchial artery (UBERON:2005014) | subClassOf (rdfs:subClassOf) | head blood vessel (UBERON:0003496) | | afferent portion of pharyngeal arch artery (UBERON:2000716) | subClassOf (rdfs:subClassOf) | head blood vessel (UBERON:0003496) | | efferent portion of pharyngeal arch artery (UBERON:2000202) | subClassOf (rdfs:subClassOf) | head blood vessel (UBERON:0003496) | | inner renal medulla vasa recta (UBERON:0004776) | subClassOf (rdfs:subClassOf) | renal venous blood vessel (UBERON:0014401) | | 4th arch mesenchyme from head mesenchyme (UBERON:0010345) | subClassOf (rdfs:subClassOf) | head mesenchyme from mesoderm (UBERON:0006904) | | pharyngeal arch mesenchymal region (UBERON:0009494) | subClassOf (rdfs:subClassOf) | head mesenchyme (UBERON:0005253) |

</details>

<details> <summary>Nodes renamed: 6</summary>

| ID | Old Label | New Label | ----|----|----| | UBERON:0009089 | inner medulla vasa recta descending limb | inner medulla descending vasa recta | | UBERON:0009092 | inner medulla vasa recta ascending limb | inner medulla ascending vasa recta | | UBERON:0009202 | vasa recta descending limb | descending vasa recta | | UBERON:0009091 | vasa recta ascending limb | ascending vasa recta | | UBERON:0009090 | outer medulla vasa recta descending limb | outer medulla descending vasa recta | | UBERON:0009093 | outer medulla vasa recta ascending limb | outer medulla ascending vasa recta |

</details>

<details> <summary>Nodes added to subset: 60</summary>

| Term | Subset | ----|----| | basivertebral vein (UBERON:8600066) | human_reference_atlas | | dorsal lingual artery (UBERON:8600098) | human_reference_atlas | | thyrocervical trunk (UBERON:8600062) | human_reference_atlas | | tonsil (UBERON:0002372) | human_reference_atlas | | intervertebral vein (UBERON:8600104) | human_reference_atlas | | deep lingual artery (UBERON:8600097) | human_reference_atlas | | external nasal vein (UBERON:8600087) | human_reference_atlas | | dorsal lingual vein (UBERON:8600070) | human_reference_atlas | | radial vein (UBERON:8600092) | human_reference_atlas | | hepatic portal venule (UBERON:8600085) | human_reference_atlas | | ulnar vein (UBERON:8600093) | human_reference_atlas | | artery of pterygoid canal (UBERON:8600100) | human_reference_atlas | | anterior internal vertebral venous plexus (UBERON:8600103) | human_reference_atlas | | mucosa of descending colon (UBERON:0004992) | human_reference_atlas | | pulmonary arteriole (UBERON:8600077) | human_reference_atlas | | dural artery (UBERON:8600079) | human_reference_atlas | | descending palatine artery (UBERON:8600101) | human_reference_atlas | | transverse cervical vein (UBERON:8600075) | human_reference_atlas | | mucosa of transverse colon (UBERON:0004991) | human_reference_atlas | | mucosa of rectum (UBERON:0003346) | human_reference_atlas | | mucosa of ascending colon (UBERON:0004990) | human_reference_atlas | | submental artery (UBERON:8600096) | human_reference_atlas | | uterine vein (UBERON:8600058) | human_reference_atlas | | supreme intercostal vein (UBERON:8600054) | human_reference_atlas | | lymphoid system (UBERON:0002465) | human_reference_atlas | | supratrochlear vein (UBERON:8600088) | human_reference_atlas | | intra-acinar venule (UBERON:8600061) | human_reference_atlas | | middle hemorrhoidal vein (UBERON:8600057) | human_reference_atlas | | sublingual vein (UBERON:8600071) | human_reference_atlas | | transverse nasal root vein (UBERON:8600089) | human_reference_atlas | | intra-acinar arteriole (UBERON:8600094) | human_reference_atlas | | posterolateral artery (UBERON:8600064) | human_reference_atlas | | bronchial venule (UBERON:8600067) | human_reference_atlas | | suboccipital venous plexus (UBERON:8600076) | human_reference_atlas | | septal perforating artery (UBERON:8600063) | human_reference_atlas | | lumbar vein (UBERON:8600105) | human_reference_atlas | | pericardial artery (UBERON:8600080) | human_reference_atlas | | thoracoacromial vein (UBERON:8600074) | human_reference_atlas | | ascending pharyngeal artery (UBERON:8600078) | human_reference_atlas | | circumflex humeral vein (UBERON:8600073) | human_reference_atlas | | lymphatic part of lymphoid system (UBERON:0006558) | human_reference_atlas | | deep lingual vein (UBERON:8600069) | human_reference_atlas | | percardiacophrenic artery (UBERON:8600081) | human_reference_atlas | | mucosa of sigmoid colon (UBERON:0004993) | human_reference_atlas | | esophageal vein (UBERON:8600053) | human_reference_atlas | | ascending palatine artery (UBERON:8600095) | human_reference_atlas | | superficial iliac circumflex vein (UBERON:8600082) | human_reference_atlas | | left anterior descending artery (UBERON:8600102) | human_reference_atlas | | deep cervical vein (UBERON:8600059) | human_reference_atlas | | subsegmental pulmonary vein (UBERON:8600052) | human_reference_atlas | | mental vein (UBERON:8600068) | human_reference_atlas | | prostatic venule (UBERON:8600084) | human_reference_atlas | | subsegmental pulmonary artery (UBERON:8600060) | human_reference_atlas | | lateral sacral vein (UBERON:8600056) | human_reference_atlas | | incisor artery (UBERON:8600086) | human_reference_atlas | | lateral femoral circumflex vein (UBERON:8600065) | human_reference_atlas | | hypophyseal vein (UBERON:8600090) | human_reference_atlas | | accessory meningeal artery (UBERON:8600099) | human_reference_atlas | | glandular venous plexus (UBERON:8600072) | human_reference_atlas | | inferior anastomotic vein (UBERON:8600091) | human_reference_atlas |

</details>

<details> <summary>Mappings added: 2</summary>

| Subject | Predicate | Object | ----|----|----| | coelom (UBERON:0011997) | oio:hasDbXref | ZFA:0001438 | | craniocervical region (UBERON:0007811) | oio:hasDbXref | ZFA:0001114 |

</details>

<details> <summary>Synonyms removed: 8</summary>

| Term | Removed Synonym | ----|----| | vasa recta (UBERON:0004726) | renal medullary capillary | | vasa recta (UBERON:0004726) | arteriolae rectae renis | | vasa recta (UBERON:0004726) | set of straight arterioles of kidney | | fallopian tube (UBERON:0003889) | mammalian oviduct | | oviduct (UBERON:0000993) | uterine tube | | vasa recta (UBERON:0004726) | straight arterioles of kidney | | vasa recta (UBERON:0004726) | arteria recta | | vasa recta (UBERON:0004726) | arteriae rectae |

</details>

<details> <summary>Synonyms added: 14</summary>

| Term | New Synonym | Predicate | ----|----|----| | follicle associated epithelium (UBERON:8700001) | FAE | oio:hasExactSynonym | | oviduct (UBERON:0000993) | uterine tube | oio:hasNarrowSynonym | | vasa recta (UBERON:0004726) | renal medullary capillary | oio:hasNarrowSynonym | | mesosalpinx (UBERON:0012331) | mesentery of uterine tube | oio:hasExactSynonym | | mesosalpinx (UBERON:0012331) | serous layer of fallopian tube | oio:hasExactSynonym | | antimesosalpinx (UBERON:8600117) | posterior free edge of mesosalpinx | oio:hasExactSynonym | | mesosalpinx (UBERON:0012331) | fallopian tube mesosalpinx | oio:hasExactSynonym | | fallopian tube (UBERON:0003889) | mammalian oviduct | oio:hasBroadSynonym | | vasa recta (UBERON:0004726) | arteriolae rectae renis | oio:hasNarrowSynonym | | mesosalpinx (UBERON:0012331) | mesentery of fallopian tube | oio:hasExactSynonym | | vasa recta (UBERON:0004726) | straight arterioles of kidney | oio:hasNarrowSynonym | | vasa recta (UBERON:0004726) | set of straight arterioles of kidney | oio:hasNarrowSynonym | | antimesosalpinx (UBERON:8600117) | posterior free border of mesosalpinx | oio:hasExactSynonym | | antimesosalpinx (UBERON:8600117) | anti-mesosalpinx | oio:hasExactSynonym |

</details>

<details> <summary>Mappings removed: 4</summary>

| Subject | Predicate | Object | ----|----|----| | central gray substance of midbrain (UBERON:0003040) | oio:hasDbXref | ZFA:0000518 | | head (UBERON:0000033) | oio:hasDbXref | ZFA:0001114 | | dorsal raphe nucleus (UBERON:0002043) | oio:hasDbXref | ZFA:0000366 | | coelemic cavity lumen (UBERON:0002323) | oio:hasDbXref | ZFA:0001438 |

</details>

<details> <summary>Text definitions changed: 3</summary>

| Term | Old Text Definition | New Text Definition | ----|----|----| | mesosalpinx (UBERON:0012331) | The mesosalpinx is part of the lining of the abdominal cavity in higher vertebrates, specifically the portion of the broad ligament that stretches from the uterine tube to the level of the ovary. | A serous layer that is part of the peritoneal lining of the abdominal cavity in higher vertebrates, specifically the portion of the broad ligament that stretches from the uterine (fallopian) tube to the ovary. It is made up of epithelial cells of mesothelium and a mesh of serous membrane lining. | | Peyer's patch epithelium (UBERON:0004693) | The specialized epithelium of the Peyer's patch. | The specialized epithelial layer covering the entire Peyer's patch, including both the follicular and interfollicular areas and forming part of the gut-associated lymphoid tissue. | | vasa recta (UBERON:0004726) | In the blood supply of the kidney, the vasa recta renis (or straight arteries of kidney, or straight arterioles of kidney) form a series of straight capillaries in the medulla. They lie parallel to the loop of Henle. These vessels branch off the efferent arterioles of juxtamedullary nephrons (those nephrons closest to the medulla), enter the medulla, and surround the loop of Henle. | A group of microvessels that are part of the kidney. A vasa recta has a hairpin-like shape, entering the renal medulla as the straight arterioles and surrounds the loop of Henle, forming a capillary network. Finally it leaves the renal medulla to ascend to the cortex as the straight venules. The primary function of the vasa recta is to facilitate countercurrent exchange, which is essential for the kidney's ability to concentrate urine |

</details>

<details> <summary>Relationships added: 13</summary>

| Subject | Predicate | Object| ----|----|----| | stratum spinosum of esophageal epithelium (UBERON:8700002) | subClassOf (rdfs:subClassOf) | non-keratinized stratified squamous epithelium (UBERON:0010304) | | embryonic craniocervical region (UBERON:8450003) | BFO:0000050 | embryo (UBERON:0000922) | | antimesosalpinx (UBERON:8600117) | subClassOf (rdfs:subClassOf) | mesentery (UBERON:0002095) | | aorta-gonad-mesonephros (UBERON:8700000) | subClassOf (rdfs:subClassOf) | embryonic structure (UBERON:0002050) | | pharyngeal arch (UBERON:0002539) | BFO:0000050 | embryonic craniocervical region (UBERON:8450003) | | lung (UBERON:0002048) | BFO:0000051 | bronchus (UBERON:0002185) | | vasa recta (UBERON:0004726) | subClassOf (rdfs:subClassOf) | kidney vasculature (UBERON:0006544) | | stratum spinosum of esophageal epithelium (UBERON:8700002) | subClassOf (rdfs:subClassOf) | esophagus squamous epithelium (UBERON:0006920) | | mesosalpinx (UBERON:0012331) | RO:0002221 | fallopian tube (UBERON:0003889) | | pharyngeal arch mesenchymal region (UBERON:0009494) | subClassOf (rdfs:subClassOf) | embryonic tissue (UBERON:0005291) | | antimesosalpinx (UBERON:8600117) | BFO:0000050 | mesosalpinx (UBERON:0012331) | | embryonic craniocervical region (UBERON:8450003) | subClassOf (rdfs:subClassOf) | craniocervical region (UBERON:0007811) | | follicle associated epithelium (UBERON:8700001) | subClassOf (rdfs:subClassOf) | Peyer's patch epithelium (UBERON:0004693) |

</details>

<details> <summary>Text definitions added: 5</summary>

| Term | New Text Definition | ----|----| | aorta-gonad-mesonephros (UBERON:8700000) | A transient organ in the developing embryo composed of the dorsal aorta, developing gonads, and embryonic kidney. This structure is located in the embryonic mesoderm and serves as the primary site for the generation of definitive hematopoietic stem cells. | | antimesosalpinx (UBERON:8600117) | A posterior free border of a mesosalpinx. | | embryonic craniocervical region (UBERON:8450003) | A craniocervical region that is part of an embryo. | | follicle associated epithelium (UBERON:8700001) | A specialized epithelial layer overlying the luminal surface of lymphoid follicles in gut-associated lymphoid tissue. It is found in Peyer's patches of the small intestine and appendix in humans and in the intestine and caecal patches in mice. This layer contains specialised M cells and has fewer goblet cells compared to surrounding tissue. This layer plays a crucial role in mucosal immune surveillance. | | stratum spinosum of esophageal epithelium (UBERON:8700002) | The second deepest layer of the stratified squamous epithelium lining the esophagus, positioned directly above the stratum basale. It consists of multiple layers of keratinocytes connected by strong intercellular junctions called desmosomes, giving the cells a characteristic "spiny" appearance. This layer provides structural support, contributes to the epithelial barrier function, and serves as a transitional zone for keratinocytes migrating towards the luminal surface, playing a crucial role in maintaining the integrity and protective properties of the esophageal lining. |

</details>

<details> <summary>Nodes removed from subset: 3</summary>

| Term | Subset | ----|----| | arterial system (UBERON:0004572) | human_reference_atlas | | venous system (UBERON:0004582) | human_reference_atlas | | circulatory system (UBERON:0001009) | human_reference_atlas |

</details>

What's Changed

• Fixes #2914 revise vasa recta by @aleixpuigb in https://github.com/obophenotype/uberon/pull/3349
• Do not "add OBO shorthands" to the RO mirror. by @gouttegd in https://github.com/obophenotype/uberon/pull/3359
• Overhaul taxon subsets by @gouttegd in https://github.com/obophenotype/uberon/pull/3363
• Filter out dangling gene IRIs in imports by @gouttegd in https://github.com/obophenotype/uberon/pull/3379
• Remove redundant injections about RO terms. by @gouttegd in https://github.com/obophenotype/uberon/pull/3380
• Fix some ZFA mapping errors by @gouttegd in https://github.com/obophenotype/uberon/pull/3361
• Fix incompatibility with ZFA's "head". by @gouttegd in https://github.com/obophenotype/uberon/pull/3360
• Refresh external resources in preparation of Uberon release October 2024 by @aleixpuigb in https://github.com/obophenotype/uberon/pull/3398
• Refresh imports after obo PR slim update by @aleixpuigb in https://github.com/obophenotype/uberon/pull/3400
• Update foreign SSSOM sets from the ontology. by @gouttegd in https://github.com/obophenotype/uberon/pull/3415
• Generate the release diff with the OAK output by @aleixpuigb in https://github.com/obophenotype/uberon/pull/3377
• Peyer's patch epithelium name update by @JABelfiore in https://github.com/obophenotype/uberon/pull/3387
• Fixes #3411 to revise 'mesosalpinx' textual/logical definition, synonyms and oviduct synonyms by @aleixpuigb in https://github.com/obophenotype/uberon/pull/3417
• Remove Anita from CODEOWNERS by @matentzn in https://github.com/obophenotype/uberon/pull/3418
• Fixes #3410 has_part bronchus to lung by @aleixpuigb in https://github.com/obophenotype/uberon/pull/3419
• stratum spinosum of esophageal epithelium by @JABelfiore in https://github.com/obophenotype/uberon/pull/3422
• Add GitHub action that assigns reviewers when equivalent class axioms are updated by @matentzn in https://github.com/obophenotype/uberon/pull/3425
• new term aorta-gonad-mesonephros by @JABelfiore in https://github.com/obophenotype/uberon/pull/3397
• Add ID range for the NDI Cloud project. by @gouttegd in https://github.com/obophenotype/uberon/pull/3429
• Addresses part of #3414 NTR antimesosalpinx by @aleixpuigb in https://github.com/obophenotype/uberon/pull/3420
• Refresh external resources in preparation of Uberon release by @aleixpuigb in https://github.com/obophenotype/uberon/pull/3433
• Do not run the diff GA workflow on closed PRs. by @gouttegd in https://github.com/obophenotype/uberon/pull/3437
• Uberon release v2024-11-25 by @aleixpuigb in https://github.com/obophenotype/uberon/pull/3435

Full Changelog: https://github.com/obophenotype/uberon/compare/v2024-09-03...v2024-11-25