Difference in `uberon-simple.owl` from actual approach and base approach

[anitacaron]

This is related to #2495.

This is a sample of the differences.

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-09-23/uberon-simple.owl
• Loaded from: file:/Users/anitac/Documents/GitHub/uberon-simple.owl (current approach)

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-09-22/uberon-simple.owl
• Loaded from: file:/Users/anitac/Documents/GitHub/uberon-simple-branch.owl (base approach)

Ontology imports

Ontology annotations

Removed

• versionInfo "2022-09-23"^^string

Added

• versionInfo "2022-09-22"^^string

1st arch mandibular ectoderm http://purl.obolibrary.org/obo/UBERON_0013155

Removed

• 1st arch mandibular ectoderm SubClassOf ecto-epithelium

1st arch maxillary ectoderm http://purl.obolibrary.org/obo/UBERON_0012313

Removed

• 1st arch maxillary ectoderm SubClassOf ecto-epithelium

2nd arch mesenchyme from neural crest http://purl.obolibrary.org/obo/UBERON_0010254

Removed

• 2nd arch mesenchyme from neural crest SubClassOf mesenchyme from rhombencephalic neural crest

Added

• 2nd arch mesenchyme from neural crest SubClassOf mesenchyme derived from head neural crest

Ammon's horn http://purl.obolibrary.org/obo/UBERON_0001954

Removed

• Ammon's horn SubClassOf structure with developmental contribution from neural crest

Brodmann area http://purl.obolibrary.org/obo/UBERON_0013529

Removed

• Brodmann area SubClassOf structure with developmental contribution from neural crest

Bruch's membrane http://purl.obolibrary.org/obo/UBERON_0003957

Removed

• Bruch's membrane SubClassOf neural crest-derived structure

Descemet's membrane http://purl.obolibrary.org/obo/UBERON_0004367

Removed

• Descemet's membrane SubClassOf neural crest-derived structure

Eimer's organ http://purl.obolibrary.org/obo/UBERON_0011255

Removed

• Eimer's organ SubClassOf ectoderm-derived structure

Guérin's valve http://purl.obolibrary.org/obo/UBERON_0012295

Removed

• Guérin's valve SubClassOf mesoderm-derived structure

Hadjikhani et al. (1998) visuotopic partition scheme region http://purl.obolibrary.org/obo/UBERON_0026765

Removed

• Hadjikhani et al. (1998) visuotopic partition scheme region SubClassOf structure with developmental contribution from neural crest

Haller's layer http://purl.obolibrary.org/obo/UBERON_0036168

Removed

• Haller's layer SubClassOf neural crest-derived structure

Harderian gland http://purl.obolibrary.org/obo/UBERON_0004187

Removed

• Harderian gland SubClassOf ectoderm-derived structure

Harderian gland duct http://purl.obolibrary.org/obo/UBERON_0015151

Removed

• Harderian gland duct SubClassOf ectoderm-derived structure

Hassall's corpuscle http://purl.obolibrary.org/obo/UBERON_0003987

Removed

• Hassall's corpuscle SubClassOf mixed endoderm/mesoderm-derived structure

Hensen stripe http://purl.obolibrary.org/obo/UBERON_0035806

Removed

• Hensen stripe SubClassOf structure with developmental contribution from neural crest

• Hensen stripe SubClassOf ectoderm-derived structure

Kimura membrane http://purl.obolibrary.org/obo/UBERON_0035941

Removed

• Kimura membrane SubClassOf ectoderm-derived structure

• Kimura membrane SubClassOf structure with developmental contribution from neural crest

Nobelian rod http://purl.obolibrary.org/obo/UBERON_3010240

Removed

• Nobelian rod SubClassOf mesoderm-derived structure

Ongur, Price, and Ferry (2003) prefrontal cortical partition scheme region http://purl.obolibrary.org/obo/UBERON_0026777

Removed

• Ongur, Price, and Ferry (2003) prefrontal cortical partition scheme region SubClassOf structure with developmental contribution from neural crest

P1 area of pallium (Myxiniformes) http://purl.obolibrary.org/obo/UBERON_0014751

Removed

• P1 area of pallium (Myxiniformes) SubClassOf structure with developmental contribution from neural crest

P2 area of pallium (Myxiniformes) http://purl.obolibrary.org/obo/UBERON_0014752

Removed

• P2 area of pallium (Myxiniformes) SubClassOf structure with developmental contribution from neural crest

P3 area of pallium (Myxiniformes) http://purl.obolibrary.org/obo/UBERON_0014753

Removed

• P3 area of pallium (Myxiniformes) SubClassOf structure with developmental contribution from neural crest

P4 area of pallium (Myxiniformes) http://purl.obolibrary.org/obo/UBERON_0014754

Removed

• P4 area of pallium (Myxiniformes) SubClassOf structure with developmental contribution from neural crest

P5 area of pallium (Myxiniformes) http://purl.obolibrary.org/obo/UBERON_0014755

Removed

• P5 area of pallium (Myxiniformes) SubClassOf structure with developmental contribution from neural crest

Press, Brewer, Dougherty, Wade and Wandell (2001) visuotopic area V7 http://purl.obolibrary.org/obo/UBERON_0026776

Removed

• Press, Brewer, Dougherty, Wade and Wandell (2001) visuotopic area V7 SubClassOf structure with developmental contribution from neural crest

Purkinje cell layer corpus cerebelli http://purl.obolibrary.org/obo/UBERON_2002240

Removed

• Purkinje cell layer corpus cerebelli SubClassOf structure with developmental contribution from neural crest

• Purkinje cell layer corpus cerebelli SubClassOf ectoderm-derived structure

Purkinje cell layer valvula cerebelli http://purl.obolibrary.org/obo/UBERON_2002241

Removed

• Purkinje cell layer valvula cerebelli SubClassOf structure with developmental contribution from neural crest

• Purkinje cell layer valvula cerebelli SubClassOf ectoderm-derived structure

Reichert's cartilage http://purl.obolibrary.org/obo/UBERON_0004368

Removed

• Reichert's cartilage SubClassOf endoderm-derived structure

Reichert's cartilage pre-cartilage condensation http://purl.obolibrary.org/obo/UBERON_0010354

Removed

• Reichert's cartilage pre-cartilage condensation SubClassOf mesenchyme from rhombencephalic neural crest

Added

• Reichert's cartilage pre-cartilage condensation SubClassOf mesenchyme derived from neural crest

• Reichert's cartilage pre-cartilage condensation SubClassOf mesenchyme derived from head neural crest

Reissner's fiber http://purl.obolibrary.org/obo/UBERON_0011357

Removed

• Reissner's fiber SubClassOf ectoderm-derived structure

Sattler's layer http://purl.obolibrary.org/obo/UBERON_0036167

Removed

• Sattler's layer SubClassOf neural crest-derived structure

Schweigger-Seidel sheath http://purl.obolibrary.org/obo/UBERON_0010174

Removed

• Schweigger-Seidel sheath SubClassOf mesoderm-derived structure

Sommer's sector http://purl.obolibrary.org/obo/UBERON_0023932

Removed

• Sommer's sector SubClassOf structure with developmental contribution from neural crest

Tootell and Hadjikhani (2001) LOC/LOP complex http://purl.obolibrary.org/obo/UBERON_0026775

Removed

• Tootell and Hadjikhani (2001) LOC/LOP complex SubClassOf structure with developmental contribution from neural crest

Verson's gland http://purl.obolibrary.org/obo/UBERON_0011147

Removed

• Verson's gland SubClassOf ectoderm-derived structure

Westoll line http://purl.obolibrary.org/obo/UBERON_4300197

Removed

• Westoll line SubClassOf neural crest-derived structure

accessory foramen http://purl.obolibrary.org/obo/UBERON_4200150

Removed

• accessory foramen SubClassOf mesoderm-derived structure

accessory olfactory bulb http://purl.obolibrary.org/obo/UBERON_0004069

Removed

• accessory olfactory bulb SubClassOf structure with developmental contribution from neural crest

acetabular notch http://purl.obolibrary.org/obo/UBERON_0014446

Removed

• acetabular notch SubClassOf mesoderm-derived structure

acetabular part of hip bone http://purl.obolibrary.org/obo/UBERON_0001269

Removed

• acetabular part of hip bone SubClassOf mesoderm-derived structure

acetabular rim http://purl.obolibrary.org/obo/UBERON_0006802

Removed

• acetabular rim SubClassOf mesoderm-derived structure

acinus of lacrimal gland http://purl.obolibrary.org/obo/UBERON_0011857

Removed

• acinus of lacrimal gland SubClassOf structure with developmental contribution from neural crest

• acinus of lacrimal gland SubClassOf ectoderm-derived structure

acinus of lactiferous gland http://purl.obolibrary.org/obo/UBERON_0011856

Removed

• acinus of lactiferous gland SubClassOf ectoderm-derived structure

acinus of olfactory gland http://purl.obolibrary.org/obo/UBERON_0015785

Removed

• acinus of olfactory gland SubClassOf endoderm-derived structure

• acinus of olfactory gland SubClassOf ectoderm-derived structure

acinus of parotid gland http://purl.obolibrary.org/obo/UBERON_0011847

Removed

• acinus of parotid gland SubClassOf structure with developmental contribution from neural crest

acinus of sebaceous gland http://purl.obolibrary.org/obo/UBERON_0011846

Removed

• acinus of sebaceous gland SubClassOf ectoderm-derived structure

acropodial skeleton http://purl.obolibrary.org/obo/UBERON_0010543

Removed

• acropodial skeleton SubClassOf mesoderm-derived structure

actinotrichium http://purl.obolibrary.org/obo/UBERON_2000089

Removed

• actinotrichium SubClassOf ectoderm-derived structure

adductor blade http://purl.obolibrary.org/obo/UBERON_4200028

Removed

• adductor blade SubClassOf mesoderm-derived structure

adductor crest http://purl.obolibrary.org/obo/UBERON_4200029

Removed

• adductor crest SubClassOf mesoderm-derived structure

adjacent_to http://purl.obolibrary.org/obo/RO_0002220

Removed

• adjacent_to definition "x adjacent_to y iff: x and y share a boundary"

• adjacent_to label "adjacent_to"

adrenal cortex http://purl.obolibrary.org/obo/UBERON_0001235

Removed

• adrenal cortex SubClassOf neural crest-derived structure

adrenal gland http://purl.obolibrary.org/obo/UBERON_0002369

Added

• adrenal gland SubClassOf structure with developmental contribution from neural crest

adrenal gland capsule http://purl.obolibrary.org/obo/UBERON_0002052

Removed

• adrenal gland capsule SubClassOf neural crest-derived structure

• adrenal gland capsule SubClassOf mesoderm-derived structure

adrenal gland cortex zone http://purl.obolibrary.org/obo/UBERON_0009753

Removed

• adrenal gland cortex zone SubClassOf mesoderm-derived structure

• adrenal gland cortex zone SubClassOf neural crest-derived structure

adrenal medulla http://purl.obolibrary.org/obo/UBERON_0001236

Removed

• adrenal medulla SubClassOf mesoderm-derived structure

adrenal tissue http://purl.obolibrary.org/obo/UBERON_0018303

Removed

• adrenal tissue SubClassOf neural crest-derived structure

• adrenal tissue SubClassOf mesoderm-derived structure

adrenal/interrenal gland http://purl.obolibrary.org/obo/UBERON_0006858

Removed

• adrenal/interrenal gland SubClassOf neural crest-derived structure

adventitia of epididymis http://purl.obolibrary.org/obo/UBERON_0006645

Removed

• adventitia of epididymis SubClassOf mesoderm-derived structure

adventitia of seminal vesicle http://purl.obolibrary.org/obo/UBERON_0006648

Removed

• adventitia of seminal vesicle SubClassOf mesoderm-derived structure

adventitia of ureter http://purl.obolibrary.org/obo/UBERON_0001252

Removed

• adventitia of ureter SubClassOf mesoderm-derived structure

afferent lamellar arteriole http://purl.obolibrary.org/obo/UBERON_2005015

Removed

• afferent lamellar arteriole SubClassOf structure with developmental contribution from neural crest

• afferent lamellar arteriole SubClassOf mixed endoderm/mesoderm-derived structure

afterfeather http://purl.obolibrary.org/obo/UBERON_0008290

Removed

• afterfeather SubClassOf ectoderm-derived structure

agger limitans anterior of ilium http://purl.obolibrary.org/obo/UBERON_3000866

Removed

• agger limitans anterior of ilium SubClassOf mesoderm-derived structure

agger limitans anterior of ischium http://purl.obolibrary.org/obo/UBERON_3000867

Removed

• agger limitans anterior of ischium SubClassOf mesoderm-derived structure

agranular insular cortex http://purl.obolibrary.org/obo/UBERON_0034893

Removed

• agranular insular cortex SubClassOf structure with developmental contribution from neural crest

airway submucosal gland http://purl.obolibrary.org/obo/UBERON_8410077

Removed

• airway submucosal gland SubClassOf endoderm-derived structure

ala of nose http://purl.obolibrary.org/obo/UBERON_0006906

Removed

• ala of nose SubClassOf ectoderm-derived structure

alar plate midbrain http://purl.obolibrary.org/obo/UBERON_2001357

Removed

• alar plate midbrain SubClassOf ectoderm-derived structure

alary cartilage http://purl.obolibrary.org/obo/UBERON_3000002

Removed

• alary cartilage SubClassOf neural crest-derived structure

alary process of premaxilla http://purl.obolibrary.org/obo/UBERON_3000003

Removed

• alary process of premaxilla SubClassOf neural crest-derived structure

alisphenoid bone http://purl.obolibrary.org/obo/UBERON_0006721

Added

• alisphenoid bone SubClassOf structure with developmental contribution from neural crest

alisphenoid endochondral element http://purl.obolibrary.org/obo/UBERON_0015058

Removed

• alisphenoid endochondral element SubClassOf structure with developmental contribution from neural crest

allocortex http://purl.obolibrary.org/obo/UBERON_0014734

Removed

• allocortex SubClassOf structure with developmental contribution from neural crest

alveolar artery http://purl.obolibrary.org/obo/UBERON_0009654

Removed

• alveolar artery SubClassOf structure with developmental contribution from neural crest

alveolar atrium http://purl.obolibrary.org/obo/UBERON_0002172

Removed

• alveolar atrium SubClassOf endoderm-derived structure

alveolar canal http://purl.obolibrary.org/obo/UBERON_0006669

Removed

• alveolar canal SubClassOf structure with developmental contribution from neural crest

alveolar pore http://purl.obolibrary.org/obo/UBERON_0008873

Removed

• alveolar pore SubClassOf endoderm-derived structure

alveolar ridge http://purl.obolibrary.org/obo/UBERON_0004103

Removed

• alveolar ridge SubClassOf neural crest-derived structure

Added

• alveolar ridge SubClassOf structure with developmental contribution from neural crest

alveolar system http://purl.obolibrary.org/obo/UBERON_0006524

Removed

• alveolar system SubClassOf endoderm-derived structure

alveolar wall http://purl.obolibrary.org/obo/UBERON_0004894

Removed

• alveolar wall SubClassOf endoderm-derived structure

alveolus of lung http://purl.obolibrary.org/obo/UBERON_0002299

Removed

• alveolus of lung SubClassOf endoderm-derived structure

ambient gyrus http://purl.obolibrary.org/obo/UBERON_0036164

Removed

• ambient gyrus SubClassOf structure with developmental contribution from neural crest

ambiguous_for_taxon http://purl.obolibrary.org/obo/RO_0002173

Added

• ambiguous_for_taxon see also Taxon-constraints

• ambiguous_for_taxon label "ambiguous for taxon"@en

• ambiguous_for_taxon definition "S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]"

amnion http://purl.obolibrary.org/obo/UBERON_0000305

Removed

• amnion SubClassOf mesoderm-derived structure

amniotic ectoderm http://purl.obolibrary.org/obo/UBERON_0003254

Removed

• amniotic ectoderm SubClassOf meso-epithelium

Added

• amniotic ectoderm SubClassOf develops from some epiblast (generic)

  • source "ISBN:9780878932504"

  • source "EHDAA2-via-amnioblasts"

ampulla of uterine tube http://purl.obolibrary.org/obo/UBERON_0012648

Removed

• ampulla of uterine tube SubClassOf mesoderm-derived structure

ampullary organ http://purl.obolibrary.org/obo/UBERON_0008917

Removed

• ampullary organ SubClassOf ectoderm-derived structure

amygdalohippocampal area, magnocellular division http://purl.obolibrary.org/obo/UBERON_0035027

Removed

• amygdalohippocampal area, magnocellular division SubClassOf structure with developmental contribution from neural crest

amygdalohippocampal area, parvocellular division http://purl.obolibrary.org/obo/UBERON_0035028

Removed

• amygdalohippocampal area, parvocellular division SubClassOf structure with developmental contribution from neural crest

amygdalohippocampal transition area http://purl.obolibrary.org/obo/UBERON_0035026

Removed

• amygdalohippocampal transition area SubClassOf structure with developmental contribution from neural crest

amygdalopiriform transition area http://purl.obolibrary.org/obo/UBERON_0034989

Removed

• amygdalopiriform transition area SubClassOf structure with developmental contribution from neural crest

anal canal http://purl.obolibrary.org/obo/UBERON_0000159

Removed

• anal canal SubClassOf ectoderm-derived structure

anal column http://purl.obolibrary.org/obo/UBERON_0009882

Removed

• anal column SubClassOf ectoderm-derived structure

angulosplenial coronoid process http://purl.obolibrary.org/obo/UBERON_3000012

Removed

• angulosplenial coronoid process SubClassOf neural crest-derived structure

anterior cartilage of palatine http://purl.obolibrary.org/obo/UBERON_2001690

Removed

• anterior cartilage of palatine SubClassOf neural crest-derived structure

anterior cerebral artery http://purl.obolibrary.org/obo/UBERON_0001624

Removed

• anterior cerebral artery SubClassOf structure with developmental contribution from neural crest

anterior choroidal artery http://purl.obolibrary.org/obo/UBERON_0014696

Removed

• anterior choroidal artery SubClassOf structure with developmental contribution from neural crest

anterior cingulate cortex http://purl.obolibrary.org/obo/UBERON_0009835

Removed

• anterior cingulate cortex SubClassOf structure with developmental contribution from neural crest

anterior corona radiata http://purl.obolibrary.org/obo/UBERON_0022425

Removed

• anterior corona radiata SubClassOf structure with developmental contribution from neural crest

anterior dentation of pectoral fin spine http://purl.obolibrary.org/obo/UBERON_2002001

Removed

• anterior dentation of pectoral fin spine SubClassOf structure with developmental contribution from neural crest

• anterior dentation of pectoral fin spine SubClassOf mesoderm-derived structure

• anterior dentation of pectoral fin spine SubClassOf ectoderm-derived structure

anterior distal condyle of femur http://purl.obolibrary.org/obo/UBERON_4100114

Removed

• anterior distal condyle of femur SubClassOf mesoderm-derived structure

anterior distal serration of pectoral fin spine http://purl.obolibrary.org/obo/UBERON_2002002

Removed

• anterior distal serration of pectoral fin spine SubClassOf ectoderm-derived structure

• anterior distal serration of pectoral fin spine SubClassOf mesoderm-derived structure

• anterior distal serration of pectoral fin spine SubClassOf structure with developmental contribution from neural crest

anterior division of bed nuclei of stria terminalis http://purl.obolibrary.org/obo/UBERON_0011173

Removed

• anterior division of bed nuclei of stria terminalis SubClassOf structure with developmental contribution from neural crest

anterior dorsomedial process of autopalatine http://purl.obolibrary.org/obo/UBERON_2001578

Removed

• anterior dorsomedial process of autopalatine SubClassOf neural crest-derived structure

anterior humeral ridge http://purl.obolibrary.org/obo/UBERON_4200197

Removed

• anterior humeral ridge SubClassOf mesoderm-derived structure

anterior lamina recurvata http://purl.obolibrary.org/obo/UBERON_3000832

Removed

• anterior lamina recurvata SubClassOf structure with developmental contribution from neural crest

• anterior lamina recurvata SubClassOf ectoderm-derived structure

anterior lateral mesoderm http://purl.obolibrary.org/obo/UBERON_2005039

Removed

• anterior lateral mesoderm SubClassOf mesoderm-derived structure

anterior lateral plate mesoderm http://purl.obolibrary.org/obo/UBERON_0009881

Removed

• anterior lateral plate mesoderm SubClassOf mesoderm-derived structure

anterior limb of ceratobranchial 5 bone http://purl.obolibrary.org/obo/UBERON_2002017

Removed

• anterior limb of ceratobranchial 5 bone SubClassOf structure with developmental contribution from neural crest

anterior limb of ceratobranchial 5 cartilage http://purl.obolibrary.org/obo/UBERON_2002018

Removed

• anterior limb of ceratobranchial 5 cartilage SubClassOf structure with developmental contribution from neural crest

anterior limiting lamina of cornea http://purl.obolibrary.org/obo/UBERON_0004370

Removed

• anterior limiting lamina of cornea SubClassOf neural crest-derived structure

anterior maxillary process http://purl.obolibrary.org/obo/UBERON_3000015

Removed

• anterior maxillary process SubClassOf neural crest-derived structure

anterior meningeal artery http://purl.obolibrary.org/obo/UBERON_0010251

Removed

• anterior meningeal artery SubClassOf structure with developmental contribution from neural crest

anterior nasal spine of maxilla http://purl.obolibrary.org/obo/UBERON_0035139

Removed

• anterior nasal spine of maxilla SubClassOf neural crest-derived structure

anterior nasal wall http://purl.obolibrary.org/obo/UBERON_3000016

Removed

• anterior nasal wall SubClassOf neural crest-derived structure

anterior neural keel http://purl.obolibrary.org/obo/UBERON_2007024

Removed

• anterior neural keel SubClassOf ectoderm-derived structure

anterior neural rod http://purl.obolibrary.org/obo/UBERON_2007031

Removed

• anterior neural rod SubClassOf ectoderm-derived structure

anterior parahippocampal gyrus http://purl.obolibrary.org/obo/UBERON_0022383

Removed

• anterior parahippocampal gyrus SubClassOf structure with developmental contribution from neural crest

anterior part of tympanic bone http://purl.obolibrary.org/obo/UBERON_0013173

Removed

• anterior part of tympanic bone SubClassOf structure with developmental contribution from neural crest

anterior perforated substance http://purl.obolibrary.org/obo/UBERON_0018141

Removed

• anterior perforated substance SubClassOf structure with developmental contribution from neural crest

anterior prenasal cartilage http://purl.obolibrary.org/obo/UBERON_3010827

Removed

• anterior prenasal cartilage SubClassOf neural crest-derived structure

anterior presumptive neural plate http://purl.obolibrary.org/obo/UBERON_2007014

Removed

• anterior presumptive neural plate SubClassOf ectoderm-derived structure

anterior process of hyoid apparatus http://purl.obolibrary.org/obo/UBERON_3000670

Removed

• anterior process of hyoid apparatus SubClassOf structure with developmental contribution from neural crest

anterior process of malleus http://purl.obolibrary.org/obo/UBERON_0018160

Removed

• anterior process of malleus SubClassOf neural crest-derived structure

anterior process of pars palatina of maxilla http://purl.obolibrary.org/obo/UBERON_3000017

Removed

• anterior process of pars palatina of maxilla SubClassOf neural crest-derived structure

anterior process of the palatoquadrate http://purl.obolibrary.org/obo/UBERON_3010560

Removed

• anterior process of the palatoquadrate SubClassOf structure with developmental contribution from neural crest

anterior process of vomer http://purl.obolibrary.org/obo/UBERON_3000649

Removed

• anterior process of vomer SubClassOf neural crest-derived structure

anterior quadratocranial commissure http://purl.obolibrary.org/obo/UBERON_3010061

Removed

• anterior quadratocranial commissure SubClassOf neural crest-derived structure

anterior radial http://purl.obolibrary.org/obo/UBERON_3000951

Removed

• anterior radial SubClassOf structure with developmental contribution from neural crest

anterior ramus of cleithrum http://purl.obolibrary.org/obo/UBERON_3000792

Removed

• anterior ramus of cleithrum SubClassOf ectoderm-derived structure

• anterior ramus of cleithrum SubClassOf structure with developmental contribution from neural crest

anterior ramus of pterygoid http://purl.obolibrary.org/obo/UBERON_3000018

Removed

• anterior ramus of pterygoid SubClassOf neural crest-derived structure

anterior root of zygomatic arch http://purl.obolibrary.org/obo/UBERON_0018265

Removed

• anterior root of zygomatic arch SubClassOf neural crest-derived structure

anterior segment of eyeball http://purl.obolibrary.org/obo/UBERON_0001801

Removed

• anterior segment of eyeball SubClassOf ectoderm-derived structure

anterior segment of paracentral lobule http://purl.obolibrary.org/obo/UBERON_0035932

Removed

• anterior segment of paracentral lobule SubClassOf structure with developmental contribution from neural crest

anterior stroma of cornea http://purl.obolibrary.org/obo/UBERON_0003952

Removed

• anterior stroma of cornea SubClassOf neural crest-derived structure

anterior subdivision of masseter http://purl.obolibrary.org/obo/UBERON_0011314

Removed

• anterior subdivision of masseter SubClassOf structure with developmental contribution from neural crest

• anterior subdivision of masseter SubClassOf mesoderm-derived structure

anterior temporal fusiform gyrus http://purl.obolibrary.org/obo/UBERON_0022396

Removed

• anterior temporal fusiform gyrus SubClassOf structure with developmental contribution from neural crest

anterior uvea http://purl.obolibrary.org/obo/UBERON_0011892

Removed

• anterior uvea SubClassOf ectoderm-derived structure

anterior_to http://purl.obolibrary.org/obo/BSPO_0000096

Removed

• anterior_to label "anterior_to"

• anterior_to definition "x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer"

  • database_cross_reference 0000-0002-6601-2165

• anterior_to created_by "cjm"

• anterior_to creation_date "2009-07-31T02:15:46Z"

anteriorly connected to http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to

Removed

• anteriorly connected to definition "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y."
  • database_cross_reference Connectivity-Design-Pattern

anterolateral lateral suprasylvian visual area (sensu Mustela putorius furo) http://purl.obolibrary.org/obo/UBERON_8440055

Removed

• anterolateral lateral suprasylvian visual area (sensu Mustela putorius furo) SubClassOf structure with developmental contribution from neural crest

anterolateral process of frontoparietal http://purl.obolibrary.org/obo/UBERON_3000020

Removed

• anterolateral process of frontoparietal SubClassOf structure with developmental contribution from neural crest

• anterolateral process of frontoparietal SubClassOf ectoderm-derived structure

anterolateral process of hyoid plate http://purl.obolibrary.org/obo/UBERON_3000671

Removed

• anterolateral process of hyoid plate SubClassOf structure with developmental contribution from neural crest

anterolateral visual area http://purl.obolibrary.org/obo/UBERON_0035894

Removed

• anterolateral visual area SubClassOf structure with developmental contribution from neural crest

anterolateral visual area, layer 5 http://purl.obolibrary.org/obo/UBERON_0035908

Removed

• anterolateral visual area, layer 5 SubClassOf structure with developmental contribution from neural crest

anteromedial lateral suprasylvian visual area (sensu Mustela putorius furo) http://purl.obolibrary.org/obo/UBERON_8440054

Removed

• anteromedial lateral suprasylvian visual area (sensu Mustela putorius furo) SubClassOf structure with developmental contribution from neural crest

anteromedial visual area http://purl.obolibrary.org/obo/UBERON_0035893

Removed

• anteromedial visual area SubClassOf structure with developmental contribution from neural crest

anteromedial visual area, layer 5 http://purl.obolibrary.org/obo/UBERON_0035913

Removed

• anteromedial visual area, layer 5 SubClassOf structure with developmental contribution from neural crest

anteroventral process of cleithrum http://purl.obolibrary.org/obo/UBERON_4200226

Removed

• anteroventral process of cleithrum SubClassOf ectoderm-derived structure

• anteroventral process of cleithrum SubClassOf structure with developmental contribution from neural crest

antitrochanter http://purl.obolibrary.org/obo/UBERON_4200030

Removed

• antitrochanter SubClassOf mesoderm-derived structure

antorbital process http://purl.obolibrary.org/obo/UBERON_3000022

Removed

• antorbital process SubClassOf neural crest-derived structure

antotic pillar http://purl.obolibrary.org/obo/UBERON_0035957

Removed

• antotic pillar SubClassOf mesoderm-derived structure

• antotic pillar SubClassOf neural crest-derived structure

aorta collagen fibril http://purl.obolibrary.org/obo/UBERON_0011861

Removed

• aorta collagen fibril SubClassOf mesoderm-derived structure

aortic body http://purl.obolibrary.org/obo/UBERON_0034971

Removed

• aortic body SubClassOf mesoderm-derived structure

aortic valve anulus http://purl.obolibrary.org/obo/UBERON_0005991

Removed

• aortic valve anulus SubClassOf neural crest-derived structure

aortico-pulmonary spiral septum http://purl.obolibrary.org/obo/UBERON_0006207

Removed

• aortico-pulmonary spiral septum SubClassOf neural crest-derived structure

apex of arytenoid http://purl.obolibrary.org/obo/UBERON_0006494

Removed

• apex of arytenoid SubClassOf structure with developmental contribution from neural crest

apex of cochlea http://purl.obolibrary.org/obo/UBERON_0002819

Removed

• apex of cochlea SubClassOf structure with developmental contribution from neural crest

• apex of cochlea SubClassOf ectoderm-derived structure

apical region of heart ventricle http://purl.obolibrary.org/obo/UBERON_0035837

Removed

• apical region of heart ventricle SubClassOf mesoderm-derived structure

apophysis distalis of tibiale fibulare http://purl.obolibrary.org/obo/UBERON_3000917

Removed

• apophysis distalis of tibiale fibulare SubClassOf mesoderm-derived structure

apophysis distalis of tibiofibula http://purl.obolibrary.org/obo/UBERON_3000904

Removed

• apophysis distalis of tibiofibula SubClassOf mesoderm-derived structure

apophysis proximalis http://purl.obolibrary.org/obo/UBERON_3000916

Removed

• apophysis proximalis SubClassOf mesoderm-derived structure

aqueous drainage system http://purl.obolibrary.org/obo/UBERON_0003956

Removed

• aqueous drainage system SubClassOf ectoderm-derived structure

aqueous vein http://purl.obolibrary.org/obo/UBERON_0004030

Removed

• aqueous vein SubClassOf ectoderm-derived structure

arachnoid barrier layer http://purl.obolibrary.org/obo/UBERON_0000437

Removed

• arachnoid barrier layer SubClassOf neural crest-derived structure

• arachnoid barrier layer SubClassOf mesoderm-derived structure

arachnoid trabecula http://purl.obolibrary.org/obo/UBERON_0000439

Removed

• arachnoid trabecula SubClassOf neural crest-derived structure

arachnoid villus http://purl.obolibrary.org/obo/UBERON_0013153

Removed

• arachnoid villus SubClassOf neural crest-derived structure

arcopallium http://purl.obolibrary.org/obo/UBERON_0007350

Removed

• arcopallium SubClassOf structure with developmental contribution from neural crest

area postrema http://purl.obolibrary.org/obo/UBERON_0002162

Removed

• area postrema SubClassOf structure with developmental contribution from neural crest

areola http://purl.obolibrary.org/obo/UBERON_0002032

Removed

• areola SubClassOf ectoderm-derived structure

areolar tubercle http://purl.obolibrary.org/obo/UBERON_0011828

Removed

• areolar tubercle SubClassOf ectoderm-derived structure

arrector pili muscle of vibrissa http://purl.obolibrary.org/obo/UBERON_0011940

Removed

• arrector pili muscle of vibrissa SubClassOf structure with developmental contribution from neural crest

• arrector pili muscle of vibrissa SubClassOf ectoderm-derived structure

artery of lower lip http://purl.obolibrary.org/obo/UBERON_0003471

Removed

• artery of lower lip SubClassOf structure with developmental contribution from neural crest

artery of upper lip http://purl.obolibrary.org/obo/UBERON_0003470

Removed

• artery of upper lip SubClassOf structure with developmental contribution from neural crest

arthropod optic lobe http://purl.obolibrary.org/obo/UBERON_0006795

Removed

• arthropod optic lobe SubClassOf ectoderm-derived structure

articular process http://purl.obolibrary.org/obo/UBERON_3000948

Removed

• articular process SubClassOf endoderm-derived structure

• articular process SubClassOf structure with developmental contribution from neural crest

articular process of palatoquadrate http://purl.obolibrary.org/obo/UBERON_3010528

Removed

• articular process of palatoquadrate SubClassOf neural crest-derived structure

aryepiglottic fold http://purl.obolibrary.org/obo/UBERON_0014385

Removed

• aryepiglottic fold SubClassOf endoderm-derived structure

arytenoid swellings http://purl.obolibrary.org/obo/UBERON_0010215

Removed

• arytenoid swellings SubClassOf endoderm-derived structure

ascending limb of ceratobranchial 5 bone http://purl.obolibrary.org/obo/UBERON_2002013

Removed

• ascending limb of ceratobranchial 5 bone SubClassOf structure with developmental contribution from neural crest

ascending limb of ceratobranchial 5 cartilage http://purl.obolibrary.org/obo/UBERON_2002014

Removed

• ascending limb of ceratobranchial 5 cartilage SubClassOf structure with developmental contribution from neural crest

ascending process of clavicle http://purl.obolibrary.org/obo/UBERON_4200176

Removed

• ascending process of clavicle SubClassOf structure with developmental contribution from neural crest

ascending process of palatoquadrate http://purl.obolibrary.org/obo/UBERON_3000031

Removed

• ascending process of palatoquadrate SubClassOf neural crest-derived structure

ascending process of the astragalus http://purl.obolibrary.org/obo/UBERON_4200025

Removed

• ascending process of the astragalus SubClassOf mesoderm-derived structure

ascending process of the parasphenoid http://purl.obolibrary.org/obo/UBERON_2002021

Removed

• ascending process of the parasphenoid SubClassOf ectoderm-derived structure

• ascending process of the parasphenoid SubClassOf structure with developmental contribution from neural crest

associated mesenchyme of midgut http://purl.obolibrary.org/obo/UBERON_0009478

Removed

• associated mesenchyme of midgut SubClassOf mesoderm-derived structure

astragalus head http://purl.obolibrary.org/obo/UBERON_4200181

Removed

• astragalus head SubClassOf mesoderm-derived structure

astragalus-calcaneum unit http://purl.obolibrary.org/obo/UBERON_4200021

Removed

• astragalus-calcaneum unit SubClassOf mesoderm-derived structure

atrial foramen intermedium http://purl.obolibrary.org/obo/UBERON_0015225

Removed

• atrial foramen intermedium SubClassOf mesoderm-derived structure

atrioventricular region http://purl.obolibrary.org/obo/UBERON_0011820

Removed

• atrioventricular region SubClassOf mesoderm-derived structure

atrium auricular region http://purl.obolibrary.org/obo/UBERON_0006618

Removed

• atrium auricular region SubClassOf mesoderm-derived structure

atrium myocardial trabecula http://purl.obolibrary.org/obo/UBERON_0005988

Removed

• atrium myocardial trabecula SubClassOf mesoderm-derived structure

attached to http://purl.obolibrary.org/obo/RO_0002371

Removed

• attached to see also FMA_85990

• attached to label "attaches_to"

• attached to SubPropertyOf: connects

Added

• attached to shorthand "attached_to"

[shawntanzk]

Looks like a lot of these are developmental, which suggests a change in developmental axioms or something

check uberon-simple for two things:

1. look at develops_from axioms -> are they different?
2. semantics of developmental relationships (eg transitive?) -> are the OP the same between both?

[anitacaron]

Yes, they're different.

In the current uberon-simple, develops_from has two properties chains not present in the uberon-simple base

I'll investigate where this is coming from.

[shawntanzk]

@anitacaron I think its from here: https://github.com/obophenotype/uberon/blob/master/src/ontology/components/develops-from-chains.owl

[anitacaron]

Yes, but both approaches should have this component merged. And there's only one of them there.

[anitacaron]

Completing the answer above. This component is only used in the materialized.owl target but is unmerged after reasoning.

Actually, the two axioms are coming from NBO import.

Should these property chains be included in the RO?

[shawntanzk]

Should these property chains be included in the RO?

I feel like this has been discussed before, though it might be just bad gut feeling lol. I've a feeling that those properties aren't actually accurate -> I can't think of any atm but I'd imagine that being part of something does not require the same developmental origins as migration happens. That being said, from the changes in simple file, it looks like it might actually be doing some work. I think we need input from @dosumis & @cmungall here :)

[anitacaron]

I found this discussion https://github.com/oborel/obo-relations/issues/279

[dosumis]

There was definitely a discussion of those two property chains somewhere relatively recently - I think coming rom @balhoff . I think they may have been deleted from RO (although I'd support keeping one of them). Anyway, if they are coming from NBO, they need to be removed from there. Can give you access (although no idea why we are importing from it to Uberon).

[shawntanzk]

tracked it down :) https://github.com/obophenotype/uberon/pull/1808 further to this: https://github.com/obophenotype/uberon/issues/2381 I think in that case, the base approach removal of developmental axiom from not having them from NBO works well then :)

[cmungall]

I thought I objected to removal of these chains but it seems not

I think we need a way of inferring that all or a majority of the cells in a structure can trace lineage back to something like ectoderm or NC. That will require some priority chains unless we over assert.

I had always thought the “structure with contribution from NC” to be useless but here it is doing work as a canary class; it would be good to have diffs of the inferred relation graph to see impact on paths where we have no probe classes

On Fri, Oct 7, 2022 at 3:55 AM Shawn Tan @.***> wrote:

tracked it down :) #1808 https://github.com/obophenotype/uberon/pull/1808 further to this: #2381 https://github.com/obophenotype/uberon/issues/2381 I think in that case, the base approach removal of developmental axiom from not having NBO works well then :)

— Reply to this email directly, view it on GitHub https://github.com/obophenotype/uberon/issues/2664#issuecomment-1271439403, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOOAPEWTNU53PP7APHDWB76TXANCNFSM6AAAAAAQUCLEGA . You are receiving this because you were mentioned.Message ID: @.***>

[shawntanzk]

@balhoff - should grab you into this conversation, its back to the property chains in develops_from. @cmungall - not 100% sure what "probe classes" is?

[cmungall]

I have plans to formally define all of these pattern terms i use like query/probe/sentinel class, stay tuned

I may have gotten this one from @dosumis. The idea is you add a grouping class that just acts to collect the results of a query in one place, like "all structures with a contribution from the neural crest", the reasoner will place these such that they are easy to see in protege and diffs, but their utility to the user is more questionable. Their overall utility will decrease as we use relationgraph more, including in diffs. Right now we don't have a good way of seeing how even minor changes may impact entailed relation diffs - without query classes - which is a bit worrying.

[shawntanzk]

Action item:

Add back the property chain for now and create a ticket to remove it when we figure it out Inject in to get classification, and remove it again in the process -> does not bleed into other ontologies that import uberon @balhoff & @cmungall & @dosumis - if there are issues, perhaps we can solve it in another ticket, we need to push through base approach @anitacaron will open another ticket to remove the injection when things are fully decided

[anitacaron]

I added, provisionally, the two properties chains to develops_from in the base branch, and this is the new diff.

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-11-28/uberon-simple.owl
• Loaded from: file:/Users/anitac/Documents/uberon-simple.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-11-28/uberon-simple.owl
• Loaded from: file:/Users/anitac/Documents/uberon-simple-branch.owl

Ontology imports

Ontology annotations

Eimer's organ http://purl.obolibrary.org/obo/UBERON_0011255

Added

• Eimer's organ SubClassOf structure with developmental contribution from neural crest

acellular bone tissue http://purl.obolibrary.org/obo/UBERON_4000122

Added

• acellular bone tissue SubClassOf structure with developmental contribution from neural crest

adenohypophysis http://purl.obolibrary.org/obo/UBERON_0002196

Added

• adenohypophysis SubClassOf structure with developmental contribution from neural crest

bone condensation http://purl.obolibrary.org/obo/UBERON_0015062

Added

• bone condensation SubClassOf structure with developmental contribution from neural crest

cellular bone tissue http://purl.obolibrary.org/obo/UBERON_4000118

Added

• cellular bone tissue SubClassOf structure with developmental contribution from neural crest

dorsal fin http://purl.obolibrary.org/obo/UBERON_0003097

Added

• dorsal fin SubClassOf structure with developmental contribution from neural crest

dorsal fin radial bone http://purl.obolibrary.org/obo/UBERON_2001672

Added

• dorsal fin radial bone SubClassOf structure with developmental contribution from neural crest

inner cambium layer of periosteum http://purl.obolibrary.org/obo/UBERON_0000312

Added

• inner cambium layer of periosteum SubClassOf structure with developmental contribution from neural crest

mole http://purl.obolibrary.org/obo/UBERON_1000010

Added

• mole SubClassOf structure with developmental contribution from neural crest

nasal tentacle http://purl.obolibrary.org/obo/UBERON_0013206

Added

• nasal tentacle SubClassOf structure with developmental contribution from neural crest

parenchyma of thyroid gland http://purl.obolibrary.org/obo/UBERON_0001747

Added

• parenchyma of thyroid gland SubClassOf structure with developmental contribution from neural crest

pituitary gland http://purl.obolibrary.org/obo/UBERON_0000007

Added

• pituitary gland SubClassOf structure with developmental contribution from neural crest

podocyte slit diaphragm http://purl.obolibrary.org/obo/UBERON_0004032

Removed

• podocyte slit diaphragm SubClassOf anatomical structure

Added

• podocyte slit diaphragm SubClassOf mesoderm-derived structure

podocyte slit junction http://purl.obolibrary.org/obo/UBERON_0004033

Removed

• podocyte slit junction SubClassOf anatomical structure

Added

• podocyte slit junction SubClassOf mesoderm-derived structure

stratum basale of epidermis http://purl.obolibrary.org/obo/UBERON_0002025

Added

• stratum basale of epidermis SubClassOf structure with developmental contribution from neural crest

subendocardium layer http://purl.obolibrary.org/obo/UBERON_0005984

Added

• subendocardium layer SubClassOf structure with developmental contribution from neural crest

trabecula carnea http://purl.obolibrary.org/obo/UBERON_0002511

Added

• trabecula carnea SubClassOf structure with developmental contribution from neural crest

trunk neural crest http://purl.obolibrary.org/obo/UBERON_0003083

Added

• trunk neural crest SubClassOf structure with developmental contribution from neural crest

vasculature of muscle organ http://purl.obolibrary.org/obo/UBERON_0004521

Removed

• vasculature of muscle organ SubClassOf vasculature of musculoskeletal system

[rays22]

I added, provisionally, the two properties chains to develops_from in the base branch, and this is the new diff.

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-11-28/uberon-simple.owl
• Loaded from: file:/Users/anitac/Documents/uberon-simple.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-11-28/uberon-simple.owl
• Loaded from: file:/Users/anitac/Documents/uberon-simple-branch.owl

The changes proposed in the branch look fine to me.

[anitacaron]

Thank you to everyone who helped change the UBERON base approach! I have added the property chain as a provisional solution.