2016-06-12 release

This release sees the introduction of 5 Allen Brain atlases into Composite-Metazoa
2016-06-12 release image

This release features improved alignment with neuroanatomical resources.

For the first time, the uberon Composite Metazoan ontology incorporates the entirety of the Allen Atlases. Where an Atlas term can be assigned to a species-neutral equivalent in Uberon, the class will have an Uberon ID, with Allen IDs as xrefs. In the remaining cases, the Allen region will be placed at the appropriate level in the ontology.

See the following screenshot (Uberon grey, Allen-specific regions are color coded) CA fields

See 1222

Important notice on OWL edition

Please note this is the first version built using the OWLAPI v4. This means that various classes that were merged in previous version of Uberon here seem to appear for the first time as ‘new’ classes. See owlapi ticket 317

Ontology Diff Report

  • neuroanatomy
    • Include allen atlases in composite metazoan. Fixes 1222
    • Multiple CA layer improvements in textual defs and logical defs. Override NIFSTD definition which was wrong, fixes 1224
    • Fixed incorrect NIF-provided xref for CA stratum stratum lacunosum. Fixes 1223
    • fixed anterior lobe xref for PBA. Stopped using alt_id for some OPs
    • cerebellum lobule fixes
  • cardiovascular system
    • Fixed syn for superior endocardial cushion == dorsal. 1226
    • NTs for dorsal and ventral endocardial cushions. Fixes 1226
    • Adding TC for His-Purkinje system, and removing incorrect xrefs to ZFA. Fixes https://github.com/geneontology/go-ontology/issues/12451
    • AV syns
  • substances
    • refactored vomiting, to be a subclass of a more generic regurgitated substance.
    • Placed cud under regurgiated substance.
    • NTR: honey, placed under regurgiated substance.
    • Added various species-specific subclasses for anal sac gland secretion
    • NTR: castoreum
  • head
    • conjunctiva fixes.
    • Resolving some confusion between ectodermal and ectodermal cranial placodes. See https://github.com/geneontology/go-ontology/issues/12223#issuecomment-215692347 And also taxon notes in 135
  • upper ontology and technical issues
    • fixing axioms for material-immaterial disjointness violation
    • changing has_part with cardinality to has_component to avoid non-simple property cardinality DL error. Fixes 1225
    • undeclaring APs to force export as property_value in obo
    • sexually-homologous-to should not be an AP, Fixes 1221
    • Addition of more PATO Qs.
    • Taxon constraints for sharks
    • Builting using OWLAPI v4 and new alt_id behavior, see owlapi ticket 317
  • other
    • merged transitional epithelium into urothelium. Fixes 92
    • Obsoleting intergluteal cleft as the definition was inconsistent with the label. Added two new classes, one for the intergluteal cleft, the other for the sulcus. Fixes 1216

Original Ontology

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

New Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2016-06-12/uberon.owl

Report for classes

Class objects lost from source: 0

Class objects new in target: 330

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New Class : quadrangular lobule

New Class : cerebellum vermis lobule VIIAt

New Class : inferior endocardial cushion

New Class : superior endocardial cushion

New Class : paravermic lobule X

New Class : cerebellum vermis lobule VIIAf

New Class : intergluteal cleft

New Class : gluteal sulcus

New Class : castoreum

New Class : honey

New Class : regurgitated substance

New Class : regurgitated pellet

New Class : castor sac

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Changed Class objects: 5890

Changes for: sternothyroid muscle

Changes for: clavicle bone

Changes for: primary visual cortex

Changes for: cephalic vein

Changes for: sternohyoid muscle

Changes for: ventral tegmental nucleus

Changes for: omohyoid muscle

Changes for: myenteric nerve plexus

Changes for: heterogeneous tissue

Changes for: external jugular vein

Changes for: pars intermedia of adenohypophysis

Changes for: cartilage of main bronchus

Changes for: diaphragm

Changes for: pituitary stalk

Changes for: anterior jugular vein

Changes for: striatum

Changes for: pectoralis minor

Changes for: palatine gland

Changes for: caudate lobe of liver

Changes for: fungiform papilla

Changes for: lobe of thyroid gland

Changes for: fibularis quartus

Changes for: latissimus dorsi muscle

Changes for: lobe of liver

Changes for: patella

Changes for: thyrohyoid muscle

Changes for: intercostal muscle

Changes for: serratus dorsalis inferior muscle

Changes for: sternocleidomastoid

Changes for: subscapularis muscle

Changes for: viper venom

Changes for: hydrophid venom

Changes for: transitional epithelium of prostatic urethra

Changes for: ischiopubic ramus

Changes for: venom gland musculature

Changes for: haemal node

Changes for: scalenus posterior

Changes for: serratus ventralis

Changes for: internal thoracic artery

Changes for: serratus dorsalis superior muscle

Changes for: decidua

Changes for: endometrial gland

Changes for: longus colli muscle

Changes for: scalenus medius

Changes for: ethmoid sinus

Changes for: superior mesenteric vein

Changes for: esophagus mucosa

Changes for: common iliac vein

Changes for: dense regular elastic tissue

Changes for: epithelium of duct of salivary gland

Changes for: mixed stratified cuboidal and columnar epithelium

Changes for: elapid venom

Changes for: skeletal muscle tissue

Changes for: lymphoid system

Changes for: mesothelium

Changes for: foliate papilla

Changes for: vertebral column

Changes for: anterior abdominal wall muscle

Changes for: vertebral foramen

Changes for: erector spinae muscle group

Changes for: parathyroid gland

Changes for: muscle of posterior compartment of hindlimb stylopod

Changes for: cardiac muscle tissue

Changes for: nerve trunk

Changes for: mediastinum

Changes for: mouth mucosa

Changes for: anterior cranial fossa

Changes for: middle cranial fossa

Changes for: pericardium

Changes for: pericardial fluid

Changes for: internal intercostal muscle

Changes for: transversus thoracis

Changes for: pericardial sac

Changes for: splenium of the corpus callosum

Changes for: sagittal sinus

Changes for: visceral pleura

Changes for: pleural cavity

Changes for: cartilage tissue

Changes for: anterior superior frontal sulcus

Changes for: lumbar vertebra

Changes for: abdominal segment of trunk

Changes for: renal venous blood vessel

Changes for: autonomic nervous system

Changes for: clitoris

Changes for: vertebra

Changes for: cervical vertebra

Changes for: visceral serous pericardium

Changes for: chest muscle

Changes for: limb bone

Changes for: hippocampal formation

Changes for: fourth ventricle

Changes for: oral epithelium

Changes for: basal ganglion

Changes for: cricoarytenoid ligament

Changes for: cricotracheal ligament

Changes for: dorsal bursa

Changes for: phonic lip

Changes for: electrosensory lateral line lobe

Changes for: superior mesenteric artery

Changes for: renal artery

Changes for: superior recess of lesser sac

Changes for: testicular artery

Changes for: right lateral ventricle

Changes for: left lateral ventricle

Changes for: cricopharyngeal ligament

Changes for: vestibular ligament

Changes for: thyroepiglottic ligament

Changes for: inferior pancreaticoduodenal artery

Changes for: common iliac artery

Changes for: mucosa of stomach

Changes for: ovarian cortex

Changes for: entotympanic bone

Changes for: parakeratinized epithelium of gingiva

Changes for: cocoon

Changes for: superior phrenic artery

Changes for: penicillar arteriole

Changes for: cardiac ganglion

Changes for: coronary ligament of liver

Changes for: induseum griseum

Changes for: ansoparamedian fissure of cerebellum

Changes for: vein of lip

Changes for: autopod region

Changes for: medial globus pallidus

Changes for: orbitosphenoid

Changes for: median nerve

Changes for: dorsal lateral geniculate nucleus

Changes for: stylopod

Changes for: hepatic vein

Changes for: cerebellar peduncular complex

Changes for: testicular vein

Changes for: respiratory segment of nasal mucosa

Changes for: visceral abdominal adipose tissue

Changes for: gustatory epithelium of tongue

Changes for: eyelid submuscular connective tissue

Changes for: tongue taste bud

Changes for: vein of abdomen

Changes for: subcutaneous abdominal adipose tissue

Changes for: bone tissue

Changes for: bulb of vestibule

Changes for: tail of pancreas

Changes for: bulb of penis

Changes for: ascending colon

Changes for: transverse colon

Changes for: helix

Changes for: inferior occipital sulcus

Changes for: descending colon

Changes for: sigmoid colon

Changes for: cystic duct

Changes for: caecum

Changes for: vermiform appendix

Changes for: prostate duct

Changes for: inferior calcarine sulcus

Changes for: colon

Changes for: ectocalcarine sulcus

Changes for: interventricular foramen of heart

Changes for: future brain vesicle

Changes for: 1st arch mandibular endoderm

Changes for: 1st arch mandibular ectoderm

Changes for: 1st arch maxillary endoderm

Changes for: arachnoid villus

Changes for: 1st arch maxillary-mandibular cleft

Changes for: frontal suture

Changes for: lambdoid suture

Changes for: body of stomach

Changes for: sagittal suture

Changes for: uterine artery

Changes for: wall of stomach

Changes for: cochlear labyrinth

Changes for: lesser curvature of stomach

Changes for: greater curvature of stomach

Changes for: pyloric antrum

Changes for: stapes base

Changes for: capillary bed

Changes for: primary fissure of cerebellum

Changes for: accessory saphenous vein

Changes for: vein of genicular venous plexus

Changes for: gastrocnemius vein

Changes for: postcentral fissure of cerebellum

Changes for: soleal vein

Changes for: precentral fissure of cerebellum

Changes for: hindbrain vesicle

Changes for: early midbrain vesicle

Changes for: early mesencephalic vesicle

Changes for: cotylephore

Changes for: venous system of brain

Changes for: mesentery of small intestine

Changes for: portal lobule

Changes for: hepatic acinus

Changes for: ovipositor

Changes for: peritoneal cavity

Changes for: common bile duct

Changes for: common hepatic duct

Changes for: thoracic segment bone

Changes for: abdominal segment bone

Changes for: hindlimb zeugopod

Changes for: forelimb stylopod

Changes for: metapodium bone

Changes for: prostate bud

Changes for: iris epithelium

Changes for: abdominal lymph node

Changes for: celiac lymph node

Changes for: mesenteric lymph node

Changes for: abdominal segment muscle

Changes for: greater trochanter

Changes for: lesser trochanter

Changes for: spiral modiolar artery

Changes for: thoracic segment muscle

Changes for: zygomatic arch

Changes for: esophagus muscle

Changes for: metacarpal bone of digit 3

Changes for: white matter

Changes for: metacarpal bone of digit 2

Changes for: white matter of cerebellum

Changes for: metacarpal bone of digit 5

Changes for: metacarpal bone of digit 4

Changes for: obsolete nodulus of cerebellum

Changes for: respiratory system arterial blood vessel

Changes for: pedal digit 3 phalanx

Changes for: hippocampus pyramidal layer

Changes for: metacarpal bone of digit 1

Changes for: kidney arterial blood vessel

Changes for: midbrain tectum

Changes for: pedal digit 2 phalanx

Changes for: hippocampus fimbria

Changes for: pedal digit 1 phalanx

Changes for: lamina propria of urethra

Changes for: hip muscle

Changes for: notochord

Changes for: somite

Changes for: metatarsal bone of digit 5

Changes for: coelemic cavity lumen

Changes for: metatarsal bone of digit 4

Changes for: mesopodium bone

Changes for: muscle of back

Changes for: epithelium of urethra

Changes for: metatarsal bone of digit 1

Changes for: mucosa of ureter

Changes for: glomerular mesangium

Changes for: metatarsal bone of digit 3

Changes for: extraglomerular mesangium

Changes for: metatarsal bone of digit 2

Changes for: fascia lata

Changes for: lamina propria of bronchus

Changes for: pulmonary trunk

Changes for: macula densa

Changes for: lower jaw molar

Changes for: corpus callosum

Changes for: upper jaw molar

Changes for: mucosa of pyloric antrum

Changes for: limb muscle

Changes for: vas deferens

Changes for: hindlimb muscle

Changes for: forelimb muscle

Changes for: central nervous system

Changes for: epicardium

Changes for: axon tract

Changes for: myocardium

Changes for: adipose tissue

Changes for: patellar ligament

Changes for: neurectoderm

Changes for: nervous system

Changes for: thoracic vertebra

Changes for: cuspid

Changes for: neural crest

Changes for: head of radius

Changes for: forelimb long bone

Changes for: limb long bone

Changes for: hindlimb long bone

Changes for: descending trunk of arch of aorta

Changes for: lingual cusp of tooth

Changes for: preductal region of aortic arch

Changes for: postductal region of aortic arch

Changes for: juxtaductal region of aortic arch

Changes for: aorta tunica media

Changes for: trachea elastic tissue

Changes for: aorta tunica intima

Changes for: cardiovascular system elastic tissue

Changes for: bronchus elastic tissue

Changes for: lung elastic tissue

Changes for: upper vermilion

Changes for: lower vermilion

Changes for: frenulum of upper lip

Changes for: frenulum of lower lip

Changes for: lamina lucida

Changes for: submucosa of urinary bladder

Changes for: respiratory system elastic tissue

Changes for: paravermic lobule VIII

Changes for: paravermic lobule VII

Changes for: manual digit 5

Changes for: manual digit 4

Changes for: lower premolar tooth

Changes for: upper premolar tooth

Changes for: manual digit 1 phalanx

Changes for: manual digit 3

Changes for: manual digit 2

Changes for: paravermic lobule VI

Changes for: paravermic lobule V

Changes for: paravermic lobule IX

Changes for: paravermic lobule IV

Changes for: nucleus of brain

Changes for: manual digit 5 phalanx

Changes for: manual digit 2 phalanx

Changes for: pedal digit 5

Changes for: paravermic lobule III

Changes for: manual digit 4 phalanx

Changes for: paravermic lobule II

Changes for: manual digit 3 phalanx

Changes for: metapterygium cartilage

Changes for: pedal digit 2

Changes for: pedal digit 1

Changes for: pedal digit 4

Changes for: juxtaglomerular apparatus

Changes for: pedal digit 3

Changes for: flexor digitorum brevis muscle

Changes for: mesenchyme derived from neural crest

Changes for: aryepiglottic fold

Changes for: pharyngotympanic tube

Changes for: flocculus

Changes for: bile duct

Changes for: hematopoietic system

Changes for: skin of back

Changes for: lesser omentum

Changes for: head of pancreas

Changes for: ventral pancreatic duct

Changes for: parotid main excretory duct

Changes for: vomer

Changes for: maxilla

Changes for: manus

Changes for: fibroelastic membrane of larynx

Changes for: future telencephalon

Changes for: extrastriate cortex

Changes for: hypothenar muscle

Changes for: thenar muscle

Changes for: intrinsic muscle of manus

Changes for: embryoid body

Changes for: adductor hallucis muscle

Changes for: intrinsic muscle of pes

Changes for: pericardial cavity

Changes for: external carotid artery

Changes for: bony vertebral centrum

Changes for: snake venom

Changes for: myocardium of ventricle

Changes for: endocardium of ventricle

Changes for: pleural fluid

Changes for: proximal mesopodial bone

Changes for: sinusoidal space

Changes for: respiratory muscle

Changes for: lateral process of malleus

Changes for: interscapular fat pad

Changes for: vertebral bone 2

Changes for: sacral vertebra

Changes for: caudal vertebra

Changes for: synovial fluid

Changes for: calcareous tooth

Changes for: axillary lymph node

Changes for: fibrous pericardium

Changes for: pectoral fin proximal radial bone 1

Changes for: pectoral fin proximal radial bone 3

Changes for: pectoral fin proximal radial bone 2

Changes for: masticatory muscle

Changes for: conducting system of heart

Changes for: pectoral fin proximal radial bone 4

Changes for: perineum

Changes for: tooth socket

Changes for: serous pericardium

Changes for: sella turcica

Changes for: peritoneum

Changes for: sinoatrial node

Changes for: nerve

Changes for: atrioventricular node

Changes for: atrioventricular bundle

Changes for: cranial suture

Changes for: purkinje fiber

Changes for: abdominal cavity

Changes for: fused sacrum

Changes for: meninx

Changes for: acromioclavicular joint

Changes for: pterotic-posttemporal-supracleithrum

Changes for: dento-alveolar joint

Changes for: bulbo-urethral gland

Changes for: subtalar joint

Changes for: strand of hair

Changes for: adrenal gland

Changes for: pubic symphysis

Changes for: dura mater

Changes for: tympanic membrane

Changes for: thymus

Changes for: bone marrow

Changes for: yolk sac

Changes for: tonsil

Changes for: muscle of neck

Changes for: hindgut

Changes for: muscle of abdomen

Changes for: primordium

Changes for: perineal muscle

Changes for: neural tube

Changes for: chordate pharynx

Changes for: palatine tonsil

Changes for: esophagus

Changes for: metacarpal bone

Changes for: saliva-secreting gland

Changes for: cricoid cartilage

Changes for: cranial muscle

Changes for: trapezius muscle

Changes for: pectoralis major

Changes for: rectus abdominis muscle

Changes for: rectum

Changes for: supraspinatus muscle

Changes for: corpus allatum

Changes for: manual digit

Changes for: pars intercerebralis

Changes for: arthropod neurohemal organ

Changes for: Malpighian tubule

Changes for: muscle tissue

Changes for: forelimb zeugopod

Changes for: corpus cardiacum

Changes for: pes

Changes for: superior calcarine sulcus

Changes for: laryngeal vocal fold

Changes for: Meckel’s diverticulum

Changes for: sinus of Valsalva

Changes for: inguinal canal

Changes for: calcaneal tendon

Changes for: intrahepatic bile duct

Changes for: circle of Willis

Changes for: temporomandibular joint

Changes for: recurrent laryngeal nerve

Changes for: Pacinian corpuscle

Changes for: splanchnic nerve

Changes for: individual digit of digitopodial skeleton

Changes for: respiratory system lymphatic vessel endothelium

Changes for: respiratory system capillary

Changes for: kidney capillary

Changes for: lateral nucleus of trapezoid body

Changes for: retroambiguus nucleus

Changes for: gastrointestinal system mesentery

Changes for: fibrous joint

Changes for: manubrium of sternum

Changes for: left lung alveolar duct

Changes for: mammillary body

Changes for: right lung alveolar duct

Changes for: xiphoid process

Changes for: sternebra

Changes for: parietal organ

Changes for: paratrigeminal nucleus

Changes for: vasculature of eye

Changes for: actinopterygian frontal bone

Changes for: musculoskeletal system

Changes for: actinopterygian parietal bone

Changes for: left lung alveolus

Changes for: right lung alveolus

Changes for: symphysis

Changes for: tympanic ring

Changes for: subfornical organ

Changes for: brain pia mater

Changes for: cartilaginous joint

Changes for: left lung respiratory bronchiole

Changes for: somatopleure

Changes for: distal convoluted tubule macula densa

Changes for: visceral endoderm

Changes for: urogenital fold

Changes for: right lung terminal bronchiole

Changes for: somatic layer of lateral plate mesoderm

Changes for: superficial cervical lymph node

Changes for: right lung respiratory bronchiole

Changes for: splanchnopleure

Changes for: posterior superior frontal sulcus

Changes for: nerve root

Changes for: left lung terminal bronchiole

Changes for: splanchnic layer of lateral plate mesoderm

Changes for: spiral organ of cochlea

Changes for: hindbrain arachnoid mater

Changes for: rib

Changes for: diencephalon arachnoid mater

Changes for: interparietal bone

Changes for: dorsal part of optic cup

Changes for: ventral part of optic cup

Changes for: nucleus of phrenic nerve

Changes for: renal fascia

Changes for: skin scent gland

Changes for: chordamesoderm

Changes for: endolymphatic sac

Changes for: spinal cord pia mater

Changes for: hindbrain pia mater

Changes for: costal arch

Changes for: midbrain arachnoid mater

Changes for: basilar membrane of cochlea

Changes for: forebrain arachnoid mater

Changes for: midbrain pia mater

Changes for: forebrain pia mater

Changes for: fontanelle

Changes for: diencephalon pia mater

Changes for: perichondrium

Changes for: telencephalon pia mater

Changes for: nephron tubule epithelium

Changes for: urethra skeletal muscle tissue

Changes for: pulmonary alveolus epithelium

Changes for: paramedian medullary reticular complex

Changes for: dorsal paramedian reticular nucleus

Changes for: esophagus skeletal muscle

Changes for: retina blood vessel

Changes for: respiratory system venous endothelium

Changes for: kidney blood vessel

Changes for: respiratory system arterial endothelium

Changes for: iris blood vessel

Changes for: genu of corpus callosum

Changes for: hyaloid artery

Changes for: perilymphatic space

Changes for: lamina of spiral limbus

Changes for: spiral sulcus

Changes for: stria vascularis of cochlear duct

Changes for: otolith

Changes for: midbrain cerebral aqueduct

Changes for: telencephalic ventricle

Changes for: third ventricle

Changes for: piriform cortex layer 2

Changes for: endopiriform nucleus

Changes for: piriform cortex layer 3

Changes for: medial accessory olive

Changes for: dorsal cap of Kooy

Changes for: costovertebral joint

Changes for: costochondral joint

Changes for: scala media

Changes for: choroid plexus of fourth ventricle

Changes for: central canal of spinal cord

Changes for: dorsal mesentery

Changes for: brainstem

Changes for: alveolus of lung

Changes for: piriform cortex layer 1

Changes for: future nervous system

Changes for: entire extraembryonic component

Changes for: primordial hindbrain channel

Changes for: transitional anatomical structure

Changes for: future internal carotid artery

Changes for: intertarsal-type crurotarsal joint

Changes for: shoulder joint

Changes for: spinal cord arachnoid mater

Changes for: right lung accessory lobe

Changes for: proximal phalanx of manus

Changes for: tubercle of rib

Changes for: hindbrain dura mater

Changes for: head of rib

Changes for: midbrain dura mater

Changes for: body of rib

Changes for: forebrain dura mater

Changes for: diencephalon dura mater

Changes for: tectorial membrane of cochlea

Changes for: telencephalon dura mater

Changes for: median artery

Changes for: digit 6 digitopodial skeleton

Changes for: digit 7 digitopodial skeleton

Changes for: digit 8 digitopodial skeleton

Changes for: spinal cord

Changes for: cerebellar hemisphere

Changes for: dorsal thoracic nucleus

Changes for: uterine horn

Changes for: transverse pericardial sinus

Changes for: nucleus pulposus

Changes for: premaxilla

Changes for: iliocostalis muscle

Changes for: dorsal horn of spinal cord

Changes for: ventral horn of spinal cord

Changes for: dorsal funiculus of spinal cord

Changes for: splenius

Changes for: thyroglossal duct

Changes for: vomeronasal organ

Changes for: dermis connective tissue

Changes for: intrahepatic branch of portal vein

Changes for: ventral root of spinal cord

Changes for: dorsal root of spinal cord

Changes for: celiac ganglion

Changes for: laterodorsal tegmental nucleus

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