v2023-10-27 Release

What's Changed

• Fixes #2417 make neck general by @aleixpuigb in #3060
• 2972 Obsolete terms for insect anlagen. by @gouttegd in #3059
• Addresses #3068 NTR placental structures by @aleixpuigb in #3069
• Import ORCIDIO by @anitacaron in #3071
• Fixes #2970 pulmonary acinus edits by @aleixpuigb in #2971
• Add definition to definitive endoderm by @shawntanzk in #3075
• Fix 3D images links not available in uberon.owl by @anitacaron in #3089
• Update ODK image to v1.4.3 in QC by @anitacaron in #3087
• Add explanatory comment after #3087 by @gouttegd in #3090
• Change foaf:depicted_by to foaf:depiction by @anitacaron in #3091
• Serialisation protégé 5.6.3 by @aleixpuigb in #3085
• Fixes #3081 Unsats caused by an issue involving tail by @aleixpuigb in #3094
• Add xrefs curated in Biomappings by @cthoyt in #2950
• Addresses #3086 NTR pulmonary interlobular septum by @aleixpuigb in #3095
• Make base for GO import by @anitacaron in #3097
• Fix composite unsats by @gouttegd in #3099
• Import OMO terms by @anitacaron in #3092
• Normalize uberon-edit.obo by @anitacaron in #3100
• Replace type definition for abbreviation synonyms by @cthoyt in #3082
• Replace type definition for plural form synonyms by @cthoyt in #3083
• 2023-10-27 Release by @anitacaron in #3103

Full Changelog: v2023-09-05...v2023-10-27

v2023-09-05 Release

What's Changed

• Add secretory coil of eccrine sweat gland and def to duct of eccrine sweat gland by @paulacalipho in #2916
• Add parents to orphaned terms by @shawntanzk in #2988
• Update page by @bvarner-ebi in #3000
• Update c_revise_textual_def.md by @nicolevasilevsky in #3006
• Update b_adding_synonym.md by @nicolevasilevsky in #3007
• Update uberon-idranges.owl by @aleixpuigb in #3012
• Add broad synonyms pararenal lymph node, para-renal lymph node and perirenal lymph node to renal lymph node by @paulacalipho in #3011
• Do not (try to) rebuild the merged developmental stage ontologies. by @gouttegd in #3010
• Add hra_depiction_3d_images component by @anitacaron in #3015
• Update uberon-editor-sop.md by @bvarner-ebi in #3023
• Addresses #3020 Edit nociceptor --> 'nociceptor nerve ending' by @bvarner-ebi in #3021
• Update editing_guidelines.md re: MeSH cross-references by @bvarner-ebi in #3026
• Undo using dev in QC and change "see also" in synonym annotation to xref by @matentzn in #3029
• Update guidance on adding URL dbxrefs (uberon-editor-sop.md) by @bvarner-ebi in #3030
• Addresses #3035 Edit 'pulmonary neuroendocrine body' by @bvarner-ebi in #3036
• Add lower limb skin to hindlimb skin by @paulacalipho in #3034
• Fixes #3019 Removes logical definition of 'endocrine system' by @aleixpuigb in #3039
• Cleaning up makefile by @gouttegd in #3028
• Add skin terms by @paulacalipho in #3044
• NTR: saphenous vein smooth muscle tissue by @paulacalipho in #3048
• 3049 Classify 'endocrine system' as a 'non-connected functional system'. by @gouttegd in #3050
• Add related synonym pretibial to front hindlimb zeugopod by @paulacalipho in #3041
• Closes #3043 NTR neuroendocrine system by @aleixpuigb in #3045
• Add CODEOWNERS file to Uberon by @matentzn in #3038
• 3051 Fix 'insect pharynx' bogus ID and add ID format check by @gouttegd in #3052
• Changing contains to be location_of. See oborel/obo-relations#739 by @cmungall in #2998
• Update imports for release by @anitacaron in #3053
• 20230905 Release by @anitacaron in #3054

Full Changelog: v2023-07-25...v2023-09-05

v2023-07-25

What's Changed

• Update auto-pr-ontobot.yml by @hrshdhgd in #2959
• Addresses #2957 revision of distal pulmonary hierarchy by @aleixpuigb in #2958
• Addresses #2960 adds has_part CT-AS by @aleixpuigb in #2962
• Addresses #2363 Add guidance on abbreviations & #1997 Add guidance on dbxref formats by @bvarner-ebi in #2966
• Update uberon-editor-sop.md to align with CL documentation regarding database cross-references by @bvarner-ebi in #2969
• Restrict current 'parallel fiber' to teleost; [NTR] new non-teleost term 'parallel fiber, bifurcated'; [NTR] grouping class 'parallel fiber' #2961 by @bvarner-ebi in #2965
• Fix preprocessing step. by @gouttegd in #2968
• Addresses #2952 terminal bronchiole part of secondary pulmonary lobule by @aleixpuigb in #2953
• Addresses #2976 Revise 'dentate gyrus granule cell layer' by @bvarner-ebi in #2977
• Fix invalid IRI to RO relation in preprocessing step. by @gouttegd in #2979
• Addresses #2981 NTR 'bronchopulmonary segment' by @aleixpuigb in #2982
• Fixes #2884 harmonise spine segments by @aleixpuigb in #2983
• Refresh imports by @aleixpuigb in #2984
• add bone marrow microvessel by @paulacalipho in #2946
• update PR#2946 by @paulacalipho in #2985
• Release 2023-07-25 by @bvarner-ebi in #2986

Full Changelog: v2023-06-28...v2023-07-25

v2023-06-28 Release

What's Changed

• Added euryon, supraorbital foramen, supraorbitale and entorbitale by @helenamachado in #2890
• Add femoral head cartilage by @paulacalipho in #2905
• Closes #2904 include 'has part' to AS by @aleixpuigb in #2906
• Fixes #2912 add dorsal iris by @paulacalipho in #2913
• Revise definition of Brodmann (1909) area 44 by @nicolevasilevsky in #2924
• Added taxon GCI to between organogenesis and neurula stage. by @cmungall in #2829
• Add labial gland by @paulacalipho in #2929
• Add logical axioms to UBERON:0039850 by @shawntanzk in #2925
• Assert UBERON:7500102 parent as Uberon Anatomical Entity by @shawntanzk in #2935
• Fixes #2937 kidney arcuate artery image by @aleixpuigb in #2939
• Fixes #2926 to add connecting branch of Object Property by @aleixpuigb in #2943
• Add part of to 'preorbital bone region' structures by @shawntanzk in #2942
• NTR: interscapular region by @paulacalipho in #2941
• Add common-anatomy.owl artifact in release pipeline by @anitacaron in #2947
• Update links on Allen bridge by @anitacaron in #2938
• 2023-06-28 Release by @anitacaron in #2948

Full Changelog: v2023-05-23...v2023-06-28

v2023-05-23 Release

What's Changed

• Fixes #2864 alveolus of lung part of alveolar sac by @aleixpuigb in #2865
• Fix classification of 'cardiac muscle tissue'. by @gouttegd in #2877
• Add IAO:0000233 to the list of allowed annotation properties. by @gouttegd in #2879
• #2872-add new terms thoracolumbar junction, skin of thoracolumbar junction and skin of umbilical area by @paulacalipho in #2873
• 2867 Fix histoblast-related terms by @gouttegd in #2878
• Closes #2874 NTR submucosal gland structures by @aleixpuigb in #2876
• Fixes #2406-NTR-subiliac-lymph-node by @paulacalipho in #2786
• Fixes #2886 by @paulacalipho in #2888
• Adding temporal line by @helenamachado in #2881
• Revert to new serialisation format. by @gouttegd in #2893
• Ileocecal, subcarinal, right supraclavicular, left supraclavicular, Virchow's, and perigastric lymph nodes by @paulacalipho in #2892
• Addresses #2885 NTR liver right lobe sections by @aleixpuigb in #2894
• Revise def and logical axiom to cranial temporal crest by @nicolevasilevsky in #2883
• NTR: paraspinal and pericardial regions by @paulacalipho in #2896
• Remove reference to 'primary neuron' by @gouttegd in #2870
• Refresh imports by @aleixpuigb in #2900
• Release 2023-05-23 by @anitacaron in #2901

New Contributors

• @helenamachado made their first contribution in #2881

Full Changelog: v2023-04-19...v2023-05-23

v2023-04-19 Release

What's Changed

• Generic pharnx changes, part 1. See #2728. by @cmungall in #2847
• Remove trailing slashes from 17 ORCID urls by @cthoyt in #2846
• Fix an ORCID reference with double domain by @cthoyt in #2845
• Replace myself as PR creator by GitHub-actions when ontobot creates a PR by @hrshdhgd in #2848
• Fix download docs by @shawntanzk in #2851
• Fixes #2842 logical definition trachea gland by @aleixpuigb in #2843
• Change insect mouthpart to be a multicellular anatomical structure by @shawntanzk in #2858
• Remove two stray description properties by @matentzn in #2861
• Fixes 2857 text ref midgut loop by @aleixpuigb in #2859
• Fix hierarchy under anatomical cluster (part 1) by @gouttegd in #2862
• Addresses #2838 NTR subsegmental bronchus by @aleixpuigb in #2839
• Replace local properties conduit for and synapsed by to RO by @anitacaron in #2825
• Update imports by @anitacaron in #2866
• 2023-04-19 Release by @anitacaron in #2868

Full Changelog: v2023-03-15...v2023-04-19

v2023-03-15 Release

What's Changed

• Fix some invalid relations by @gouttegd in #2820
• Fixes #2773 text def for lens of camera-type eye by @aleixpuigb in #2823
• 2813 NTR visceral muscle and subclasses by @aleixpuigb in #2814
• Update ODK 14 by @matentzn in #2821
• Update imports, components and fbbt mappings by @anitacaron in #2824
• Uberon Editor SOP by @shawntanzk in #2720
• Remove local logical axioms from simultaneous with by @anitacaron in #2830
• Remove calf synonyms from UBERON:0003823. Create 3 new terms: calf, skin of calf and front hindlimb zeugopod by @paulacalipho in #2826
• Revert orcid-contributor-violation https check by @anitacaron in #2505
• Adding temporal crest by @megbalk in #2778
• Adding abbreviations by @megbalk in #2758
• Update imports by @anitacaron in #2840
• Release 2023-03-15 by @anitacaron in #2841

Full Changelog: v2023-02-14...v2023-03-15

v2023-02-14 Release

What's Changed

• Change files to upload in release by @anitacaron in #2764
• Use domain-appropriate relation for phrenic nerve. by @gouttegd in #2769
• Remove RO logical axioms by @anitacaron in #2771
• Fixes #2394-NTR-developmental_terms by @paulacalipho in #2725
• Created general_subset, to replace CARO ontology by @balhoff in #2614
• Issue 2692: missing human teeth when comparing FMA to UBERON by @wdduncan in #2713
• Adding id ranges for @helenamachado by @megbalk in #2766
• Long-bone-cartilage-element by @paulacalipho in #2780
• Mappings: Allow the use of semapv:crossSpeciesExactMatch. by @gouttegd in #2783
• Add ID Range by @aleixpuigb in #2785
• Add ontobot-change-agent workfow by @hrshdhgd in #2784
• Addresses #2788 to update text definition of perineurium by @aleixpuigb in #2789
• Update the stale-issues workflow. by @gouttegd in #2792
• Addresses #2791 relationship update by @aleixpuigb in #2793
• Fixes #2404 mucosa of rumen by @paulacalipho in #2797
• Adding otion by @megbalk in #2779
• Add new term retroauricular region by @paulacalipho in #2799
• Removing related synonym squama temporalis by @megbalk in #2808
• Otooccipital exact synonym by @megbalk in #2806
• Addresses #2795 to create new terms related to lobular bronchiole by @aleixpuigb in #2803
• 2023-02-14 Release by @anitacaron in #2810

New Contributors

• @wdduncan made their first contribution in #2713
• @aleixpuigb made their first contribution in #2785
• @hrshdhgd made their first contribution in #2784

Full Changelog: v2023-01-09...v2023-02-14

2023-01-09 Release

Major change

UBERON has moved to the base module approach the same way as in CL.

What's Changed

• Fixes #2397-NTR-menstrual blood by @paulacalipho in #2740
• Add upper and lower layers of the cortex by @shawntanzk in #2733
• Addresses #2714 NTR 'moderator band' by @bvarner-ebi in #2741
• Fixes #2398-NTR-larynx posterior commissure by @paulacalipho in #2731
• Fixes #2402-NTR-pelvic wall by @paulacalipho in #2746
• Create term ectorbitale by @megbalk in #2753
• Create zygion by @megbalk in #2754
• Create paroccipital process by @megbalk in #2755
• Adding back ectoribtale and pelvic wall by @megbalk in #2756
• Create parent tooth terms by @megbalk in #2760
• Make gogoeditdiff manual by @shawntanzk in #2745
• Updated MBA bridge to fix some issues by @shawntanzk in #2762
• Fixes #2396-NTR-cervical transformation zone epithelium by @paulacalipho in #2726
• UBERON base approach by @anitacaron in #2204
• 2023-01-09 Release by @anitacaron in #2763

Full Changelog: v2022-12-13...v2023-01-09

2022-12-13 Release

What's Changed

• Updating MBA bridge by @shawntanzk in #2669
• Fixes #2358-skin-tissues by @paulacalipho in #2637
• Update mba bridge by @shawntanzk in #2673
• Fixes #2393-NTR-stroma-of-the-human-mammary-gland by @paulacalipho in #2671
• Add interstitial nucleus of the vestibular nerve by @shawntanzk in #2594
• Remove incorrect relation in taste bud by @shawntanzk in #2676
• Opisthocranion by @megbalk in #2652
• Polysemy: prelimbic area Obsolete offending UBERON:8440032 by @vasvir in #2642
• Polysemy: PHY. Demote synonymity to RELATED in UBERON:8440028 by @vasvir in #2643
• Polysemy: NV. Demote synonymity to RELATED in UBERON:2005093 by @vasvir in #2641
• Create tooth patterns by @megbalk in #2467
• Adding hormion by @megbalk in #2576
• Fixes #2395-NTR-subserosa of uterine tube by @paulacalipho in #2680
• Update logical axioms for otic glangion by @anitacaron in #2678
• Remove external_ontology_notes from Edinger-Westphal nucleus by @shawntanzk in #2662
• Redoing #2662 by @shawntanzk in #2687
• Disjointing immaterial/material anatomical entity by @shawntanzk in #2690
• Fix MBA bridge miscuration by @shawntanzk in #2701
• Add def to extends_fibers_into by @shawntanzk in #2685
• Fix neural glomerulus by @gouttegd in #2694
• Make interventricular sulcus exact synonym of interventricular groove by @shawntanzk in #2704
• Extend SPARQL query to tag children of 'life cycle stage' by @anitacaron in #2679
• Remove OpenCyc xrefs by @anitacaron in #2705
• Fix typo. by @balhoff in #2709
• Typo fix, one word change for clarity by @nlharris in #2708
• Fix various classification issues by @gouttegd in #2693
• Check for both Label and Synonym polysemy across Terms by @vasvir in #2681
• Fixes #2400-NTR-fish-terms by @paulacalipho in #2702
• Add gogoeditdiff trigger by @shawntanzk in #2715
• Fixes #2401-arthropod-terms by @paulacalipho in #2721
• Make surface groove immaterial by @shawntanzk in #2691
• Fix classification for disconnected entities by @gouttegd in #2695
• Addresses #2729 change cardial to cardiac by @bvarner-ebi in #2730
• Update MBA bridges by @shawntanzk in #2732
• #gogoeditdiff trigger on new comment by @shawntanzk in #2736
• Inject property chain in develops from by @anitacaron in #2735
• 2022-12-13 Release by @anitacaron in #2742

Full Changelog: v2022-09-30...v2022-12-13