2016-05-11 release

This release features new mammalian neuroanatomical regions aligned with BrainInfo and Allen Brain Atlases
2016-05-11 release image

Ontology Diff Report

  • Additional neuro terms from Allen atlases and NN added
  • BTO alignment.
  • Fixing PNS syns. removing incorrect neuronames xref. Fixes 1214
  • generalizing def and label of optic canal, fixes 1213. Adding related structures from Hyman. Fixing typo pillar/pilar, see https://github.com/obophenotype/mammalian-phenotype-ontology/issues/2165
  • Not classifying echioderm ampulla as tooth-like, as it appears non skeletal https://github.com/BgeeDB/anatomical-similarity-annotations/issues/18
  • fixed def of collagen/cuticulin cuticle
  • obsoleting protein-based cuticle
  • NT: epididymal lumen. Fixes 1209
  • linking tickets to terms
  • Relaxed syn scope of cerebrum for telencephalon to RELATED.
  • Also clarified source of synonyms, added comments.
  • Added an immediately obsoleted concept for Cerebrum denoting the ambiguous concept, with CONSIDER links to alternate more precisely defined concepts. Fixes 1208
  • consistent nomenclature for postcranial, fixes 1205
  • Syns for start of neonate stage, 1204 - also placing process boundary in the upper_level category
  • Added start of neonate stage. Fixes 1204

Original Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2016-04-19/uberon.owl

New Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2016-05-11/uberon.owl

Report for classes

Class objects lost from source: 0

Class objects new in target: 38

New Class : Aaq dopaminergic cell group

New Class : telencephalic dopaminergic cell group

New Class : nucleus of the brachium of the inferior colliculus

New Class : A8 dopaminergic cell group

New Class : A14 dopaminergic cell group

New Class : A15 dopaminergic cell group

New Class : A9 dopaminergic cell group

New Class : A17 dopaminergic cell group

New Class : A10 dopaminergic cell group

New Class : A11 dopaminergic cell group

New Class : A13 dopaminergic cell group

New Class : A16 dopaminergic cell group

New Class : A12 dopaminergic cell group

New Class : dopaminergic cell groups

New Class : velum feeding organ

New Class : obsolete proboscis

New Class : supravaginal part of cervix

New Class : epithelial lining fluid

New Class : promontory of tympanic cavity

New Class : wall of blood vessel

New Class : scleral lamina cribrosa

New Class : alveolar mucosa

New Class : bulboid corpuscle

New Class : encapsulated tactile receptor

New Class : calcar avis of the lateral ventricle

New Class : postsubiculum

New Class : interanterodorsal nucleus of the thalamus

New Class : nucleus incertus

New Class : anteroventral preoptic nucleus

New Class : intergeniculate leaflet of the lateral geniculate complex

New Class : accessory abducens nucleus

New Class : bed nucleus of the accessory olfactory tract

New Class : start of neonate stage

New Class : obsolete cerebrum

New Class : epididymal lumen

New Class : antotic pillar

New Class : preoptic pillar

New Class : orbital pillar

Changed Class objects: 128

Changes for: sulcus of brain

Changes for: immune system

Changes for: autopod region

Changes for: arachnoid villus

Changes for: endostylar duct

Changes for: elephant trunk

Changes for: notochord

Changes for: molar tooth

Changes for: mucosa of vagina

Changes for: axon tract

Changes for: aorta tunica intima

Changes for: juxtaglomerular apparatus

Changes for: mesenchyme derived from neural crest

Changes for: embryoid body

Changes for: muscle layer of ileum

Changes for: incisor tooth

Changes for: atrioventricular node

Changes for: inguinal canal

Changes for: Pacinian corpuscle

Changes for: nerve root

Changes for: nephron tubule epithelium

Changes for: ventral horn of spinal cord

Changes for: neuromere

Changes for: dermal skeletal element

Changes for: blood vessel layer

Changes for: mole

Changes for: alular digit

Changes for: crustacean post-larval stage

Changes for: ophthalmic artery

Changes for: respiratory velum

Changes for: feather barbicel

Changes for: bone element

Changes for: osteon

Changes for: hyperpallium apicale

Changes for: pallium

Changes for: peripheral nervous system

Changes for: umbilical artery

Changes for: layer of hippocampal field

Changes for: accessory lacrimal gland

Changes for: intramembranous bone

Changes for: innominate bone

Changes for: neuropil

Changes for: emboliform nucleus

Changes for: cerebellum globose nucleus

Changes for: branchial basket

Changes for: lateral mammillary nucleus

Changes for: medial mammillary nucleus

Changes for: endothelium

Changes for: ampulla of uterine tube

Changes for: crypt of Lieberkuhn

Changes for: jaw depressor muscle

Changes for: Herbst’s corpuscle

Changes for: anal tooth

Changes for: postcranial axial skeletal system

Changes for: Meissner’s corpuscle

Changes for: Ruffini nerve ending

Changes for: sensory ganglion

Changes for: cerebral hemisphere

Changes for: telencephalon

Changes for: peripheral region of retina

Changes for: nasal bone

Changes for: artery wall

Changes for: basibranchial element

Changes for: taste bud

Changes for: tongue

Changes for: oropharynx

Changes for: soft palate

Changes for: palatine uvula

Changes for: tube foot ampulla

Changes for: plastron

Changes for: vaned feather

Changes for: feather rachis

Changes for: feather vane

Changes for: optic radiation

Changes for: stomodeum

Changes for: germ layer

Changes for: adductor mandibulae

Changes for: bulb of aorta

Changes for: endometrial cavity

Changes for: seminal vesicle fluid

Changes for: unencapsulated tactile receptor

Changes for: clavicle bone primordium

Changes for: vertebral element

Changes for: metoptic pillar

Changes for: calcar

Changes for: posterior paracentral gyrus

Changes for: anterior paracentral gyrus

Changes for: feather barbule

Changes for: feather barb

Changes for: life cycle temporal boundary

Changes for: renal medulla collecting duct

Changes for: albumen

Changes for: hoof

Changes for: dermal bone

Changes for: descending thin limb

Changes for: neural tube derived brain

Changes for: prostate gland dorsolateral lobe

Changes for: enamel knot

Changes for: bronchus smooth muscle

Changes for: scapula

Changes for: foramen cecum of frontal bone

Changes for: optic fissure

Changes for: corpus cavernosum

Changes for: atrium auricular region

Changes for: spongiotrophoblast layer

Changes for: obsolete protein-based cuticle

Changes for: foramen cecum of tongue

Changes for: olfactory bulb glomerular layer

  • Deleted
    • - olfactory bulb glomerular layer definition The glomerular layer is the most superficial layer, consisting of mitral cell dendritic arborizations (glomeruli), olfactory nerve fibers, and periglomerular cells. Periglomerular cells contact multiple mitral cell dendrites within the glomeruli and provide lateral inhibition of neighboring glomeruli while allowing excitation of a specific mitral cell dendritic tree. Each mitral cell is contacted by at least 1000 olfactory nerve fibers[BTO]. Portion of tissue which is located in between the primary olfactory fiber layer and the external cellular layer of the olfactory bulb[ZFA]. { database cross reference=BTO:0001317 }
  • Added
    • + olfactory bulb glomerular layer definition The glomerular layer is the most superficial layer, consisting of mitral cell dendritic arborizations (glomeruli), olfactory nerve fibers, and periglomerular cells. Periglomerular cells contact multiple mitral cell dendrites within the glomeruli and provide lateral inhibition of neighboring glomeruli while allowing excitation of a specific mitral cell dendritic tree. Each mitral cell is contacted by at least 1000 olfactory nerve fibers[BTO]. Portion of tissue which is located in between the primary olfactory fiber layer and the external cellular layer of the olfactory bulb[ZFA]. { database cross reference=https://github.com/obophenotype/uberon/issues/260 , database cross reference=BTO:0001317 }

Changes for: membrane bone

Changes for: brain commissure

Changes for: occipital region

Changes for: zona reticularis of adrenal gland

Changes for: umbilical vein

Changes for: aorta wall

Changes for: pharyngeal epithelium

Changes for: postcranial axial skeleton

Changes for: dopaminergic system

Changes for: epididymis epithelium

Changes for: tunica adventitia of blood vessel

Changes for: optic foramen

Changes for: adventitia

Changes for: dermatocranium

Changes for: vertebral centrum element

Changes for: vestibular epithelium

Changes for: buccal gland

Changes for: sclerotome

  • Deleted
    • - sclerotome definition Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. { database cross reference=http://en.wikipedia.org/wiki/Sclerotome , database cross reference=XB:curator }
  • Added

Changes for: collagen and cuticulin-based cuticle

Changes for: pharyngeal arch 2

Report for properties

ObjectProperty objects lost from source: 0

ObjectProperty objects new in target: 0

Changed ObjectProperty objects: 0

May 11, 2016 |

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