2022-06-30 Release

What's Changed

• Changes to makefile for release by @shawntanzk in #2543
• Fixes #2528 iliac vein smooth muscle tissue by @paulacalipho in #2541
• Update Uberon release workflow by @shawntanzk in #2546
• Add missing subsets to odk config file by @anitacaron in #2550
• Fixes #2392 vasculature terms by @paulacalipho in #2549
• Remove bogus alt_ids. by @gouttegd in #2553
• Fix parent of some nerves by @anitacaron in #2518
• Update BSPO import by @anitacaron in #2554
• Clean staged subset files by @anitacaron in #2557
• Release 2022-06-30 by @anitacaron in #2558

New Contributors

• @paulacalipho made their first contribution in #2541

Full Changelog: v2022-06-20...v2022-06-30

2022-06-20 Release

What's Changed

• Fixes #2407 NTR sublumbar lymph node by @bvarner-ebi in #2500
• Clean up Bgee curator xrefs by @cthoyt in #2513
• First additions of terms for aba by @shawntanzk in #2484
• Added tuberal nucleus for rodents and fish by @shawntanzk in #2441
• Change braininfo.rprc.washington.edu to neuronames by @shawntanzk in #2520
• Associated with 2493 and 2514 by @bvarner-ebi in #2521
• swap left and right in unreasoned diff by @shawntanzk in #2522
• Major fixes to visual areas in the brain by @shawntanzk in #2450
• Update cl_import.owl by @shawntanzk in #2535
• Fix template based components by @matentzn in #2527
• Added superior paraolivary nucleus by @shawntanzk in #2525
• Adding Paula's ID range by @bvarner-ebi in #2538
• Overwriting mba/dmba bridge to custom component by @shawntanzk in #2529
• 2022-06-20 release by @shawntanzk in #2542

Full Changelog: v2022-05-27...v2022-06-20

2022-05-27 Release

What's Changed

• Update vasculature_class template by @anitacaron in #2475
• Add human_reference_atlas subset by @anitacaron in #2346
• Add taxon constraint check back by @matentzn in #2487
• Remove old alt ID by @shawntanzk in #2486
• Adding some additional checks to CI by @matentzn in #2488
• Auto refresh fbbt mappings by @gouttegd in #2492
• Addresses #2493 Update 'genital system' by @bvarner-ebi in #2494
• tubercle of calcaneus synonyms by @megbalk in #2481
• adding coracoid process of calcaneus by @megbalk in #2483
• Polysemy: temporal pole. Delete offending synonym from UBERON:0006479 by @vasvir in #2470
• Addresses #2493 Update 'genital system' [updates] by @bvarner-ebi in #2496
• Reformat the ID ranges file to proper Manchester syntax. by @gouttegd in #2501
• adding life-stages-minimal subset by @cmungall in #2425
• Update vasculature template by @anitacaron in #2503
• Release 27 May 2022 by @matentzn in #2502

Full Changelog: v2022-05-17...v2022-05-27

2022-05-17 release

What's Changed

• Uberon adding additional QC checks by @matentzn in #2435
• Clean up xrefs by @cthoyt in #2433
• Add Bgee anatomical homology to Menu by @matentzn in #2410
• Add new MESH xrefs by @bgyori in #2432
• Undoing EMAPA obsoletion by @matentzn in #2442
• 2198-taxon-reporting-pipeline by @ubyndr in #2408
• --left and --right argument adjustment by @ubyndr in #2444
• Add Ellen's ORCID to 4 lymph node terms by @paolaroncaglia in #2446
• Fix typo in def of UBERON:0001271 'pelvic girdle region' by @paolaroncaglia in #2447
• Add red bone marrow of iliac crest / sternum by @paolaroncaglia in #2448
• 2436 add automated diff to uberon by @ubyndr in #2443
• Map ZFA_0005829 to canal of Schlemm by @shawntanzk in #2414
• Edit 'external anal sphincter' and 'descending thin limb' by @paolaroncaglia in #2451
• Add taxon-specific GCIs for existential relations. by @balhoff in #2390
• Edit UBERON:0000382 'apocrine sweat gland' by @paolaroncaglia in #2454
• Add UBERON:8410081 'blood microvessel' and related edits by @paolaroncaglia in #2456
• updating def for astragalus head by @megbalk in #2460
• depreciating FOVT terms by @megbalk in #2457
• Edit equivalence axiom of 'capillary' by @paolaroncaglia in #2461
• Delete all external axioms on base file by @anitacaron in #2377
• Fix main branch (uberon-edit) by @matentzn in #2469
• preorbital edits by @megbalk in #2416
• bridges: Change relation to life cycle terms to BFO:0000066. by @gouttegd in #2466
• Fix sparql query to update bridge files by @anitacaron in #2471
• Update bridges by @matentzn in #2473
• Add Mammalia Taxon GCI for jugular vein to be partof neck by @shawntanzk in #2415
• Replace MeSH tree numbers with unique IDs by @rays22 in #2472
• sort vasculature table by @anitacaron in #2476
• Polysemy: gasserian ganglion. Obsolete offending UBERON:3011045 by @vasvir in #2465
• Uberon release 17 May 2022 by @matentzn in #2474

New Contributors

• @cthoyt made their first contribution in #2433
• @ubyndr made their first contribution in #2408
• @vasvir made their first contribution in #2465

Full Changelog: v2022-04-18...v2022-05-17

2022-04-18 release

What's Changed

• Mass clean 2022 by @matentzn in #2387
• Fixes #1801 NTR placental blood by @bvarner-ebi in #2379
• Update NBO import by @anitacaron in #2409
• Updating pro import by @shawntanzk in #2413
• Fix egg chamber by @gouttegd in #2426
• Replace MeSH tree numbers with IDs by @bgyori in #2431
• release 2022-04-18 by @matentzn in #2430

New Contributors

• @bgyori made their first contribution in #2431

Full Changelog: v2022-04-05...v2022-04-18

Uberon 2022-04-05

What's Changed

• Fix typos in defs of UBERON:0015222 and UBERON:0034767 by @paolaroncaglia in #2317
• Add syns + dbxref to 'Brodmann (1909) area 38' by @paolaroncaglia in #2319
• Add subcapsular sinus ceiling + floor by @paolaroncaglia in #2321
• Add plural synonyms to trabecula terms by @paolaroncaglia in #2322
• Edit some former children of 'anatomical junction' by @paolaroncaglia in #2323
• Disambiguate label of UBERON:4200169 'process 2' by @paolaroncaglia in #2324
• Add taxon constraints to some terms by @paolaroncaglia in #2325
• Add lymph node paracortical sinus and cord by @paolaroncaglia in #2326
• Add glomus coccygeum by @paolaroncaglia in #2327
• Update FBbt mappings by @gouttegd in #2298
• Remove restriction to latin-9 character set. by @gouttegd in #2316
• updated to ODK 1.3.0 by @shawntanzk in #2329
• Fixes #2335 major and minor kidney calyces miss-classified as renal v… by @bvarner-ebi in #2336
• Fix axioms on uncinate fasciculus and added disjoint for brainstem by @shawntanzk in #2343
• Obsolete children of insect anlage in statu nascendi. by @gouttegd in #2347
• Automatically ping PRs after one month of inactivity. by @gouttegd in #2351
• Add a new inSubset ROBOT template by @rays22 in #2196
• Do not ping unreviewed draft PRs. by @gouttegd in #2355
• Update bridge files by @anitacaron in #2359
• Fovt depreciate by @megbalk in #2334
• fix nerve plexus issues by @shawntanzk in #2314
• Issue 1698 by @wdahdul in #2002
• Add UBERON:8410077 airway submucosal gland by @paolaroncaglia in #2360
• Relaxed axiomatisaion of surface structure by @dosumis in #1781
• Fix label and synonyms for UBERON:8410070 by @paolaroncaglia in #2361
• Add UBERON:8410078 right lymphatic duct by @paolaroncaglia in #2362
• Issue 1623 by @megbalk in #2007
• Rename and re-classify 'panarthropod tagma` by @gouttegd in #2134
• adding upper tooth tsv by @megbalk in #2302
• new terms for #2035 by @cmungall in #2044
• Subarachnoid space should not be part of brain fixes #2006 by @cmungall in #2008
• Updating bridges 26 March 2022 by @matentzn in #2365
• Add obsolete report with replaced_by information by @anitacaron in #2372
• Add ID range for Joshua Fortriede by @JoshuaFortriede in #2380
• Release 2022 03 31 (easier review) by @matentzn in #2376

New Contributors

• @JoshuaFortriede made their first contribution in #2380

Full Changelog: v2022-02-21...2022-04-05

2022-02-21 Release

What's Changed

• Extend SPARQL to delete dot-definition by @anitacaron in #2200
• Remove spatial disjointness AP on PNS/CNS. by @gouttegd in #2202
• WIP: uberon pattern work by @cmungall in #2146
• Add synonym type properties for #1665 by @paolaroncaglia in #2226
• Add 3 TCs for #2194 by @paolaroncaglia in #2227
• Added part_of cerebral cortex to laminar subdivision of the cortex by @shawntanzk in #2217
• small intestine capillary #2150 by @paolaroncaglia in #2228
• Fix broken image links in uberon-edit.obo by @rays22 in #2234
• adding antorbital notch by @megbalk in #2221
• Fix typos for #2080 by @paolaroncaglia in #2236
• Add comment for #2111 by @paolaroncaglia in #2237
• Move 'zona limitans intrathalamica' under 'anatomical junction'. by @balhoff in #2219
• Added lymphoid nodule by @paolaroncaglia in #2243
• Added synonyms for Lymph_node_trabeculae #1749 by @paolaroncaglia in #2244
• made nerve plexus a subtype of anatomical junction, obophenotype/cell-ontology#1306 by @cmungall in #2181
• Fix string on euarch by @shawntanzk in #2248
• Edit for #1754 by @paolaroncaglia in #2251
• Pr import to use slim by @shawntanzk in #2252
• Changed all UBERON:2X terms with anatomical lines to anatomical junction by @shawntanzk in #2246
• adding synonym by @megbalk in #2245
• adding nasal bones by @megbalk in #2220
• Add synonym to UBERON:0003886 future coelemic cavity lumen by @paolaroncaglia in #2255
• Added UBERON:8410070 'levatores costarum' for #1904 by @paolaroncaglia in #2256
• Fix annotation for #1904 by @paolaroncaglia in #2257
• updated DEL (UBERON:2000711) label by @sabrinatoro in #2254
• Changed property_value taxon stuff to relationship by @shawntanzk in #2260
• Obsolete 'cestode' (UBERON:0018387). by @gouttegd in #2258
• Unify all attribution to ORCID using dct:contributor by @anitacaron in #2206
• Added RP3V by @shawntanzk in #2250
• Add sparql check for taxon range by @anitacaron in #2241
• Fix space mistake by @shawntanzk in #2265
• Change Makefile to remove uberon terms from pato and nbo imports by @shawntanzk in #2269
• adding rostrum by @megbalk in #2262
• moved bone-related terms under "surface structure" to "surface of bone" by @megbalk in #2247
• Fixed never_in_taxon in rostrum by @shawntanzk in #2271
• adding zygomatic arch sides by @megbalk in #2223
• Add test to check obo serialisation by @anitacaron in #2264
• new terms and edits related to pudendal structures, see https://pubmed.ncbi.nlm.nih.gov/33259666/ by @cmungall in #2170
• Fix typo in UBERON:0001272 by @paolaroncaglia in #2278
• Add UBERON:8410073 medullary region of kidney by @paolaroncaglia in #2279
• Reinstate obsolete terms by @anitacaron in #2277
• Edit UBERON:0001284 renal column by @paolaroncaglia in #2280
• Add comments to 'medullary region of kidney' and 'renal medulla' by @paolaroncaglia in #2282
• Add vasculature template by @anitacaron in #2209
• Added xrefs to defs by @shawntanzk in #2285
• Create upper_tooth_pattern.yaml by @megbalk in #2231
• insect dorsal vessel definitions by @cmungall in #2272
• Request to add new editor to uberon-idranges.owl by @bvarner-ebi in #2297
• Closes #2230 'glomerular visceral epithelium' should be part of (or merged with) glomerular visceral layer by @bvarner-ebi in #2299
• removed reflexive develops from by @shawntanzk in #2295
• Change equivalent-classes-allowed from none to asserted-only to generate materialized.owl by @anitacaron in #2306
• clean up makefile by @matentzn in #2307
• Increase severity of QC test by @matentzn in #2309
• Change external pudendal vein tributary_of to connected_to by @shawntanzk in #2304
• Changed parvicellular to parvocellular by @shawntanzk in #2311
• Remove Harderian gland taxon restriction by @rays22 in #2312
• Change vertebrate_skeletal_anatomy_curators from created_by to oboInOwl:source by @anitacaron in #2239
• Add contributor value check by @anitacaron in #2273

New Contributors

• @sabrinatoro made their first contribution in #2254
• @bvarner-ebi made their first contribution in #2297

Full Changelog: v2021-11-28...v2022-02-21

2021-11-28 release

• All release artefacts are now correctly versioned, without imports
• Ontology subsets (human, xenopus, metazoan and mouse view, as well as -basic subsets) are now published as "simple" files, i.e. without imported terms.
• The core release artefact has been retired, as it is not anymore needed (it was needed in the past when Uberon was co-curated by Phenoscape).

2021-11-12 Release

Summary of changes:

The most important change in this release is the addition of of a large number of "taxon-constraints", which enable us to filter terms from Uberon to generate taxon-specific subsets.

• 684 taxon constraints added, 26 removed
• Long bone has been reclassified
• Cross-references to Snomed, Wikipedia and DOIs now use URI syntax

New terms:

ID	Label
UBERON:7500062	tibial tuberosity
UBERON:7500083	greater palatine foramen
UBERON:7500084	lesser palatine foramen
UBERON:8410062	parasympathetic cholinergic nerve
UBERON:8420000	hair of scalp
UBERON:8440000	cortical layer II/III
UBERON:8440001	cortical layer IV/V
UBERON:8440002	cortical layer V/VI
UBERON:8440003	cortical layer VIb
UBERON:8440004	laminar subdivision of the cortex

2021-10-01 Release

This is a patch release as a faulty ID made it into the release published yesterday (#2077). Some other Changes were merged in the meantime, as follows:

Changed introduced

Peyer's patch epithelium http://purl.obolibrary.org/obo/UBERON_0004693

Added

• Peyer's patch epithelium has_exact_synonym "Peyer's patch epithelium"^^string
  • database_cross_reference "MA:0000731"^^string

Removed

• Peyer's patch epithelium has_exact_synonym "peyer's patch epithelium"^^string
  • database_cross_reference "MA:0000731"^^string

Peyer's patch follicle http://purl.obolibrary.org/obo/UBERON_0010386

Added

• Peyer's patch follicle has_exact_synonym "Peyer's patch follicle"^^string
  • database_cross_reference "MA:0000732"^^string

Removed

• Peyer's patch follicle has_exact_synonym "peyer's patch follicle"^^string
  • database_cross_reference "MA:0000732"^^string

articular surface for the tibia on the talus http://purl.obolibrary.org/obo/UBERON_7500081

Added

• articular surface for the tibia on the talus id "UBERON:7500081"^^string

• articular surface for the tibia on the talus label "articular surface for the tibia on the talus"^^string

• articular surface for the tibia on the talus definition "Contact surface between the tibia and the talus located on the talus."^^string

  • database_cross_reference "https://en.wikipedia.org/wiki/Talus_bone"^^[string](http://www.w3.org/2001/XMLSchema#string)

• articular surface for the tibia on the talus term_editor 0000-0003-2699-3066

• articular surface for the tibia on the talus date "2021-07-27T17:04:35Z"^^dateTime

• articular surface for the tibia on the talus has_obo_namespace "uberon"^^string

• Class: articular surface for the tibia on the talus

• articular surface for the tibia on the talus SubClassOf articular surface

• articular surface for the tibia on the talus SubClassOf part_of some talus

• articular surface for the tibia on the talus SubClassOf surface of bone

cementocyte lacuna http://purl.obolibrary.org/obo/UBERON_8000008

Added

• cementocyte lacuna label "cementocyte lacuna"^^string

• cementocyte lacuna id "UBERON:8000008"^^string

• cementocyte lacuna created_by "http://orcid.org/0000-0001-5208-3432"^^[string](http://www.w3.org/2001/XMLSchema#string)

• cementocyte lacuna has_obo_namespace "uberon"^^string

• cementocyte lacuna definition "The small cavity within the cellular cementum that is occupied by a cementocyte cell body."^^string

  • database_cross_reference "MP:0030555"^^string

  • database_cross_reference "PMID:27029548"^^string

• Class: cementocyte lacuna

• cementocyte lacuna SubClassOf part_of some cementum

• cementocyte lacuna SubClassOf anatomical cavity

copepodite stage 1 http://purl.obolibrary.org/obo/UBERON_8200002

Added

• copepodite stage 1 label "copepodite stage 1"^^string

• copepodite stage 1 has_obo_namespace "uberon"^^string

• copepodite stage 1 creator 0000-0002-2908-3327

• copepodite stage 1 definition "A development stage of copepods which immediately follows the nauplius stage. It is characterized by the presence of 2 swimming legs."^^string

  • database_cross_reference "http://orcid.org/0000-0002-2908-3327"^^[string](http://www.w3.org/2001/XMLSchema#string)

• copepodite stage 1 date "2021-07-26T14:57:48Z"^^dateTime

• copepodite stage 1 id "UBERON:8200002"^^string

• Class: copepodite stage 1

• copepodite stage 1 SubClassOf preceded_by some nauplius stage

• copepodite stage 1 SubClassOf life cycle stage

• copepodite stage 1 SubClassOf part_of some copepodite stage

copepodite stage 2 http://purl.obolibrary.org/obo/UBERON_8200003

Added

• copepodite stage 2 date "2021-07-26T15:07:18Z"^^dateTime

• copepodite stage 2 label "copepodite stage 2"^^string

• copepodite stage 2 creator 0000-0002-2908-3327

• copepodite stage 2 definition "A development stage of copepods which immediately follows copepodite stage 1. It is characterized by the presence of 3 swimming legs."^^string

  • database_cross_reference "http://orcid.org/0000-0002-2908-3327"^^[string](http://www.w3.org/2001/XMLSchema#string)

• copepodite stage 2 id "UBERON:8200003"^^string

• copepodite stage 2 [has_obo_name...