2015-02-02 release

This maintenance release includes multiple new brain region terms based on finer-grained distinctions from neuro atlases, as well as various improvements to other areas such as the digit skeleton
2015-02-02 release image

Ontology Diff Report

  • neuro
    • More alignment with Allen.
    • Fixing cortex vs lobe distinctions. Issue: #412
    • new subdivisions of CA fields from dhba
    • NTs for neuro regions. Issue #630
  • Relations
    • use location_of between material and material. Issue #636
  • Misc
    • pituitary and renal fixes
    • digit skeleton
    • forestomach
    • vestigial embryonic structures
    • bug fix: removed logical axioms accidentally associated with obs classes

Original Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2015-01-01/uberon.owl

New Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2015-02-02/uberon.owl

Report for classes

Class objects lost from source: 0

Class objects new in target: 89

New Class : posterior thalamic radiation

New Class : retrolenticular part of internal capsule

New Class : inferior longitudinal fasciculus

New Class : radiation of thalamus

New Class : anterior thalamic radiation

New Class : coracoclavicular ligament

New Class : glabella skin

New Class : glabella region

New Class : buccal vestibule

New Class : morphological feature

New Class : lymphomyeloid tissue

New Class : areolar sweat gland

New Class : remnant of cardiac valve

New Class : hindbrain commissure

New Class : occipitofrontal fasciculus

New Class : inferior occipitofrontal fasciculus

New Class : secondary auditory cortex

New Class : primary auditory cortex

New Class : visual association cortex

New Class : caudal CA1

New Class : caudal CA2

New Class : caudal CA3

New Class : rostral CA3

New Class : rostral CA2

New Class : rostral CA1

New Class : uncal CA3

New Class : uncal CA1

New Class : uncal CA2

New Class : margin of eyelid

New Class : uncus of parahippocampal gyrus

New Class : bulbourethral gland epithelium

New Class : ventral commissural nucleus of spinal cord

New Class : stratum radiatum of caudal CA1

New Class : stratum lacunosum-moleculare of caudal CA1

New Class : palatine process of premaxilla

New Class : medial nucleus of stria terminalis

New Class : ansa peduncularis

New Class : agranular insular cortex

New Class : lateral nucleus of stria terminalis

New Class : insular cortex

New Class : granular insular cortex

New Class : alveolar ridge of premaxilla

New Class : viscerocranial mucosa

New Class : juxtaglomerular arteriole

New Class : primary motor cortex layer 1

New Class : posterior parietal cortex

New Class : stratum lucidum of uncal CA3

New Class : respiratory air

New Class : bodily gas

New Class : stratum oriens of uncal CA3

New Class : stratum pyramidale of uncal CA3

New Class : angioblastic cord

New Class : prechordal mesoderm

New Class : future pituitary gland

New Class : future neurohypophysis

New Class : stratum oriens of uncal CA1

New Class : stratum pyramidale of uncal CA1

New Class : stratum lacunosum-moleculare of uncal CA2

New Class : stratum lacunosum-moleculare of uncal CA3

New Class : stratum radiatum of uncal CA3

New Class : stratum radiatum of uncal CA2

New Class : stratum pyramidale of uncal CA2

New Class : stratum oriens of uncal CA2

New Class : stratum radiatum of uncal CA1

New Class : stratum lacunosum-moleculare of uncal CA1

New Class : stratum oriens of rostral CA3

New Class : stratum lucidum of rostral CA3

New Class : stratum pyramidale of rostral CA3

New Class : stratum radiatum of rostral CA3

New Class : stratum oriens of rostral CA1

New Class : stratum radiatum of rostral CA2

New Class : stratum lacunosum-moleculare of rostral CA2

New Class : stratum oriens of rostral CA2

New Class : stratum pyramidale of rostral CA2

New Class : stratum lacunosum-moleculare of rostral CA3

New Class : stratum pyramidale of rostral CA1

New Class : stratum radiatum of rostral CA1

New Class : stratum lacunosum-moleculare of rostral CA1

New Class : stratum lucidum of caudal CA3

New Class : stratum oriens of caudal CA3

New Class : stratum pyramidale of caudal CA3

New Class : stratum pyramidale of caudal CA1

New Class : stratum oriens of caudal CA1

New Class : stratum radiatum of caudal CA2

New Class : stratum pyramidale of caudal CA2

New Class : stratum lacunosum-moleculare of caudal CA2

New Class : stratum lacunosum-moleculare of caudal CA3

New Class : stratum radiatum of caudal CA3

New Class : stratum oriens of caudal CA2

Changed Class objects: 574

Changes for: obsolete superficial feature part of hypophysis

Changes for: obsolete regional part of cingulate gyrus

Changes for: obsolete regional part of outer ear

Changes for: obsolete regional part of basilar membrane

Changes for: digit 3 digitopodial skeleton

Changes for: digit 4 digitopodial skeleton

Changes for: digit 5 digitopodial skeleton

Changes for: digit 2 digitopodial skeleton

Changes for: digit 1 digitopodial skeleton

Changes for: obsolete predominantly gray regional part of pontine reticular formation

Changes for: obsolete predominantly gray regional part of dentate nucleus

Changes for: obsolete regional part of hippocampal formation

Changes for: obsolete regional part of substantia nigra

Changes for: obsolete regional part of anterior commissure

Changes for: ramus posterior profundus of V3

Changes for: obsolete superficial feature part of temporal lobe

Changes for: obsolete regional part of solitary nucleus

Changes for: ramus nasalis medialis

Changes for: obsolete regional part of septum

Changes for: velar skeleton

Changes for: parietal serous membrane

Changes for: visceral serous membrane

Changes for: jaw region

Changes for: obsolete predominantly gray part of basal amygdaloid nucleus

Changes for: zeugopodial skeleton

Changes for: paired limb/fin skeleton

Changes for: stylopodial skeleton

Changes for: obsolete regional part of caudate nucleus

Changes for: obsolete predominantly gray regional part of dentate gyrus

Changes for: obsolete predominantly gray regional part of substantia nigra

Changes for: obsolete superficial feature part of posterior hypothalamic region

Changes for: obsolete predominantly gray regional part of Preoptic area

Changes for: obsolete pars nervosa

Changes for: obsolete regional part of inferior frontal gyrus

Changes for: articular process of palatoquadrate

Changes for: digestive system element

Changes for: puboischiofemoralis internus muscle

Changes for: obsolete regional part of hypophysis

Changes for: obsolete regional part of cerebral white matter

Changes for: surface of eyeball

Changes for: obsolete regional part of neuraxis cavity

Changes for: obsolete predominantly white regional part of globus pallidus

Changes for: obsolete regional part of globus pallidus

Changes for: obsolete predominantly gray regional part of neostriatum

Changes for: white matter radiation

Changes for: subcallosal fasciculus

Changes for: obsolete predominantly gray regional part of medial dorsal nucleus

Changes for: obsolete regional part of lateral ventricle

Changes for: obsolete predominantly gray regional part of median eminence

Changes for: obsolete regional part of cochlea

Changes for: mentomeckelian

Changes for: nucleus of spinal cord

Changes for: dorsal commissural nucleus of spinal cord

Changes for: obsolete regional part of cingulate cortex

Changes for: obsolete regional part of inferior parietal cortex

Changes for: obsolete regional part of neurohypophysis

Changes for: primary remex feather

  • Deleted
    • - primary remex feather comment these are the longest and narrowest of the remiges (particularly those attached to the phalanges), and they can be individually rotated. These feathers are especially important for flapping flight, as they are the principal source of thrust, moving the bird forward through the air. Most thrust is generated on the downstroke of flapping flight. However, on the upstroke (when the bird often draws its wing in close to its body), the primaries are separated and rotated, reducing air resistance while still helping to provide some thrust
  • Added
    • + primary remex feather function notes these are the longest and narrowest of the remiges (particularly those attached to the phalanges), and they can be individually rotated. These feathers are especially important for flapping flight, as they are the principal source of thrust, moving the bird forward through the air. Most thrust is generated on the downstroke of flapping flight. However, on the upstroke (when the bird often draws its wing in close to its body), the primaries are separated and rotated, reducing air resistance while still helping to provide some thrust

Changes for: obsolete superficial feature part of frontal lobe

Changes for: pedal digit 4 plus metapodial segment

Changes for: obsolete predominantly gray regional part of superior olivary complex

Changes for: processus triangularis of palatoquadrate cartilage

Changes for: suboccular arch

Changes for: obsolete predominantly white regional part of superior olivary complex

Changes for: obsolete predominantly gray part of corticomedial nuclear complex

Changes for: obsolete regional part of superior olive

Changes for: obsolete regional part of ventral cochlear nucleus

Changes for: obsolete regional part of Parahippocampal gyrus

Changes for: obsolete regional part of transverse frontopolar gyri complex

Changes for: ramus posterior of CN VIII

Changes for: ramus anterior of CN VIII

Changes for: obsolete regional part of orbital gyri complex

Changes for: obsolete cytoarchitectural part of cerebral cortex

Changes for: obsolete predominantly white regional part of anterior hypothalamic region

Changes for: ramus hyomandibularis

Changes for: pars convoluta of oviduct

Changes for: obsolete regional part of basolateral nuclear complex

Changes for: ramus recurrens

Changes for: palatoquadrate arch

Changes for: vertebra pre-cartilage condensation

Changes for: vertebra cartilage element

Changes for: obsolete regional part of pons

Changes for: obsolete regional part of anterior hypothalamic region

Changes for: obsolete predominantly gray regional part of hippocampal formation

Changes for: obsolete predominantly gray regional part of globus pallidus

Changes for: webbing of bone in vertebral column

Changes for: obsolete regional part of basal nuclear complex

Changes for: posterior fascicle of palatopharyngeus

Changes for: epithelium of small intestine

Changes for: presubiculum

Changes for: terminal bronchiole epithelium

Changes for: neocortex

Changes for: dorsal hyoid arch skeleton

Changes for: ventral hyoid arch skeleton

Changes for: palatal taste bud

Changes for: amygdalohippocampal area

Changes for: axillary sweat gland

Changes for: obsolete regional part of corticomedial nuclear complex

Changes for: acropodium region

Changes for: fin skeleton

Changes for: isla magna of Calleja

Changes for: appendicular skeletal system

Changes for: dentate gyrus of hippocampal formation

Changes for: frontal cortex

Changes for: parietal lobe

Changes for: temporal lobe

Changes for: amygdala

Changes for: obsolete cytoarchitectural part of the cerebellum

Changes for: nasal cartilage

Changes for: obsolete predominantly Gray regional part of inferior parietal cortex

Changes for: obsolete regional part of neostriatum

Changes for: suprarostral cartilage

Changes for: hemopoietic tissue

Changes for: articular process

Changes for: suprarostral ala

Changes for: skeleton of pectoral complex

Changes for: skeleton of pelvic complex

Changes for: obsolete regional part of hindbrain

Changes for: obsolete gross anatomical part of cerebral cortex

Changes for: palatine raphe

Changes for: surface of mandible

Changes for: lymphoid tissue

Changes for: capsule of parathyroid gland

Changes for: substantia propria of cornea

Changes for: lower jaw region

Changes for: secondary palate

Changes for: obsolete regional part of fornix

Changes for: upper jaw region

Changes for: jaw skeleton

Changes for: obsolete predominantly gray regional part of cingulate gyrus

Changes for: neurocranium

Changes for: obsolete regional part of Preoptic area

Changes for: obsolete regional part of middle ear

Changes for: soft palate

Changes for: palatine uvula

Changes for: orbit of skull

Changes for: obsolete regional part of septal nuclear complex

Changes for: obsolete predominantly gray regional part of superior olive

Changes for: obsolete superficial feature part of telencephalon

Changes for: obsolete cytoarchitectural part of frontal lobe

Changes for: obsolete cytoarchitectural part of occipital lobe

Changes for: vestibular nuclear complex

  • Deleted
    • - vestibular nuclear complex editor note In TA they are grouped in both the pons and medulla; WP+MA says the SVN is in the pons, and GO includes VNC development under pons development, but this is not supported by ABA. Todo - check with NIF.
  • Added
    • + vestibular nuclear complex editor note In TA they are grouped in both the pons and medulla; DHBA has ‘vestibular nuclei of pons’, with LVN and SVN underneath; WP+MA says the SVN is in the pons, and GO includes VNC development under pons development, but this is not supported by ABA. Todo - check with NIF.

Changes for: anterior median eminence

Changes for: anterior nucleus of hypothalamus

Changes for: supracallosal gyrus

Changes for: periamygdaloid area

Changes for: posterior median eminence

Changes for: inferior olivary commissure

Changes for: extrastriate cortex

Changes for: depressor labii inferioris

Changes for: obsolete pars dentalis of maxilla

Changes for: obsolete pars dentalis of premaxilla

Changes for: skeleton of digitopodium

Changes for: upper beak

Changes for: spiral valve of intestine

Changes for: skin apocrine gland

Changes for: otic process

Changes for: otic ligament

Changes for: obsolete palatine process of pars palatina of premaxilla

Changes for: palatoquadrate articular process

Changes for: lateral sulcus

Changes for: claustral amygdaloid area

Changes for: sesamoid bone of the peroneus longus muscle

Changes for: digitopodium region

Changes for: set of upper jaw teeth

Changes for: prepollex skeleton

Changes for: prehallux

Changes for: anterior hypothalamic region

Changes for: digit

Changes for: paired fin

Changes for: glabella region of bone

Changes for: rib skeletal system

Changes for: hindlimb skeleton

Changes for: forelimb skeleton

Changes for: skeleton of pes

Changes for: skeleton of manus

Changes for: muscle of arm

  • Deleted
    • - muscle of arm comment See notes on UBERON:0001460 for possible terminological confusion over term ‘arm’. MA uses this consistent with uberon (forelimb muscle is subdivided into shoulder, arm and hand)
  • Added
    • + muscle of arm terminology notes See notes on UBERON:0001460 for possible terminological confusion over term ‘arm’. MA uses this consistent with uberon (forelimb muscle is subdivided into shoulder, arm and hand)

Changes for: obsolete pars palatina of maxilla

Changes for: obsolete pars palatina of premaxilla

Changes for: prepyriform area

Changes for: cardiac mesenchyme

Changes for: forestomach-glandular stomach junction

Changes for: post-anal tail muscle

Changes for: palatoquadrate cartilage

Changes for: cranial salt gland

Changes for: rectal salt gland

  • Deleted
    • - rectal salt gland comment does not include FMA:15724 Rectal gland // epithelial tissue gland - concentrates & secretes excess Na & Cl in sharks. large shark liver produces copious amounts of urea, making the shark hyperosmotic to seawater, & thus a shark acts like a fresh water fish, constantly gaining water. Excess salts are concentrated by the rectal gland and secreted
  • Added
    • + rectal salt gland function notes shark liver produces copious amounts of urea, making the shark hyperosmotic to seawater, & thus a shark acts like a fresh water fish, constantly gaining water. Excess salts are concentrated by the rectal gland and secreted

Changes for: palatal muscle

Changes for: acromioclavicular joint

Changes for: manual major digit (Aves)

Changes for: alular digit

Changes for: manual minor digit (Aves)

Changes for: central amygdaloid nucleus

Changes for: accessory basal amygdaloid nucleus

Changes for: lateral part of basal amygdaloid nucleus

Changes for: medial part of basal amygdaloid nucleus

Changes for: anterior amygdaloid area

Changes for: auditory cortex

Changes for: primary motor cortex

Changes for: white matter of cerebral lobe

Changes for: cortex of cerebral lobe

Changes for: parietal cortex

Changes for: processus pterygoideus of maxilla

Changes for: temporal cortex

Changes for: occipital cortex

Changes for: limbic cortex

Changes for: pterygoid process of palatoquadrate

Changes for: quadrate process of palatoquadrate

Changes for: pseudobasal process

Changes for: symphysis maxillaris

Changes for: distal convoluted tubule macula densa

Changes for: metapodium region

Changes for: mesopodial skeleton

Changes for: tarsal skeleton

Changes for: carpal skeleton

Changes for: anterior parolfactory sulcus

Changes for: anterior quadratocranial commissure

Changes for: bladder organ

Changes for: quadratoethmoid process

Changes for: arachnoid villus

Changes for: interdental plate

Changes for: basal regeneration epithelium of regenerating fin/limb

Changes for: parakeratinized epithelium

Changes for: premotor cortex

Changes for: quadratus lumborum

Changes for: gravid uterus

Changes for: sulcus of brain

Changes for: prominentia apicalis ventralis

Changes for: prominentia apicalis dorsalis

Changes for: esophageal process

Changes for: lateral process of cricoid cartilage

Changes for: bronchial process

Changes for: anterior thoracic air sac

Changes for: mesenchyme of hard palate

Changes for: bony part of hard palate

Changes for: mesenchyme of soft palate

Changes for: cingulum of upper canine tooth

Changes for: vomeronasal nerve

Changes for: accessory cuneate nucleus

Changes for: thoracic dorsal root ganglion

Changes for: cervical dorsal root ganglion

Changes for: sacral dorsal root ganglion

Changes for: lumbar dorsal root ganglion

Changes for: second cervical dorsal root ganglion

Changes for: seventh cervical dorsal root ganglion

Changes for: fourth cervical dorsal root ganglion

Changes for: fifth cervical dorsal root ganglion

Changes for: third cervical dorsal root ganglion

Changes for: acropodial skeleton

Changes for: metacarpus skeleton

Changes for: metatarsus skeleton

Changes for: metapodial skeleton

Changes for: telencephalic ventricle

Changes for: alveolar gland

Changes for: vertebral column

Changes for: obsolete regional part of basal part of pons

Changes for: paleocortex

Changes for: obsolete regional part of autonomic nervous system

Changes for: cardia of stomach

  • Deleted
    • - cardia of stomach comment Boundary notes: There were previously conflicting statements in the academic anatomy community[10][11][12] over whether the cardia is part of the stomach, part of the esophagus or a distinct entity. Modern surgical and medical textbooks have agreed that “The gastric cardia is now clearly considered to be part of the stomach”[13][14]. Classical anatomy textbooks, and some other resources[15], describe the cardia as the first of 4 regions of the stomach. This makes sense histologically because the mucosa of the cardia is the same as that of the stomach[WP]
  • Added
    • + cardia of stomach editor note There were previously conflicting statements in the academic anatomy community[10][11][12] over whether the cardia is part of the stomach, part of the esophagus or a distinct entity. Modern surgical and medical textbooks have agreed that ‘The gastric cardia is now clearly considered to be part of the stomach’[13][14]. Classical anatomy textbooks, and some other resources[15], describe the cardia as the first of 4 regions of the stomach. This makes sense histologically because the mucosa of the cardia is the same as that of the stomach[WP]

Changes for: nerve root

Changes for: manual minor digit (Aves) digitopodial skeleton

Changes for: manual major digit (Aves) digitopodial skeleton

Changes for: alular digit digitopodial skeleton

Changes for: palatine aponeurosis

Changes for: surface of cartilage

Changes for: obsolete anterior catecholaminergic tract

Changes for: geschmacksstreifen

Changes for: oropharyngeal choana

Changes for: flat bone

  • Deleted
    • - flat bone definition Flat bones are those bones which are found where the principal requirement is either extensive protection or the provision of broad surfaces for muscular attachment, the bones are expanded into broad, flat plates, as in the cranium, the ilium, sternum, rib cage, the sacrum and the scapula. These bones are composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow. In an adult, most red blood cells are formed in flat bones. In the cranial bones, the layers of compact tissue are familiarly known as the tables of the skull; the outer one is thick and tough; the inner is thin, dense, and brittle, and hence is termed the vitreous table. The intervening cancellous tissue is called the diploC+, and this, in certain regions of the skull, becomes absorbed so as to leave spaces filled with air (air-sinuses) between the two tables. The flat bones are: the occipital, parietal, frontal, nasal, lacrimal, vomer, scapula, os coxC&, sternum, and ribs. { database cross reference=http://en.wikipedia.org/wiki/Flat_bone }
  • Added
    • + flat bone comment Examples: cranium, the ilium, sternum, rib cage, the sacrum and the scapula; the occipital, parietal, frontal, nasal, lacrimal, vomer, scapula, os coxC&, sternum, and ribs
    • + flat bone definition A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow. { database cross reference=http://en.wikipedia.org/wiki/Flat_bone }
    • + flat bone function notes Flat bones are those bones which are found where the principal requirement is either extensive protection or the provision of broad surfaces for muscular attachment
    • + flat bone taxon notes In an adult mammal, most red blood cells are formed in flat bones

Changes for: respiratory airway

Changes for: obsolete regional part of dorsal cochlear nucleus

Changes for: plantar skin crease

Changes for: palmar skin crease

Changes for: skin crease

Changes for: obsolete regional part of adenohypophysis

Changes for: chin

Changes for: limb

Changes for: pedal digit 7 digitopodial skeleton

Changes for: pedal digit 8 digitopodial skeleton

Changes for: obsolete regional part of pontine tegmentum

Changes for: dento-alveolar joint

Changes for: obsolete regional part of inner ear

Changes for: ocular surface region

Changes for: meckelian bone

Changes for: meckelian foramen

Changes for: obsolete superficial feature part of cerebral cortex

Changes for: calcareous tooth

Changes for: caudal vertebra

Changes for: sacral vertebra

Changes for: velar vocal fold

Changes for: thalamic eminence

Changes for: down feather

Changes for: medial cartilage of palatine

Changes for: obsolete regional part of superior olivary complex

Changes for: obsolete regional part of pontine reticular formation

Changes for: basal process of palatoquadrate

Changes for: Peyer’s patch follicle

Changes for: ascending process of palatoquadrate

Changes for: forehead

Changes for: anterior process of pars palatina of maxilla

Changes for: subiculum

Changes for: adenohypophysis

Changes for: median eminence of neurohypophysis

Changes for: neurohypophysis

Changes for: obsolete regional part of dentate gyrus

Changes for: obsolete predominantly white regional part of hippocampal formation

Changes for: conjunctival fornix

Changes for: obsolete germ layer / neural crest derived structure

Changes for: pyramidal layer of CA2

Changes for: pyramidal layer of CA1

Changes for: obsolete regional part of nucleus accumbens

Changes for: obsolete cytoarchitectural part of dorsal tegmental nucleus

Changes for: vertebra

Changes for: lumbar vertebra

Changes for: fourth ventricle

Changes for: pyramidal layer of CA3

Changes for: pituitary stalk

Changes for: primary visual cortex

Changes for: obsolete predominantly white regional part of anterior commissure

Changes for: obsolete predominantly gray regional part of inferior frontal gyrus

Changes for: infundibular stem

Changes for: obsolete regional part of hippocampus proper

Changes for: obsolete regional part of dentate nucleus

Changes for: obsolete predominantly gray regional part of basal part of pons

Changes for: obsolete regional part of enteric nervous system

Changes for: crista dentalis of maxilla

Changes for: crista dentalis of premaxilla

Changes for: swim bladder gas gland

Changes for: thymus corticomedullary boundary

Changes for: merocrine gland

Changes for: obsolete predominantly gray regional part of orbital gyri complex

Changes for: posterior stroma of cornea

Changes for: anterior stroma of cornea

Changes for: retrosplenial region

Changes for: bulbo-urethral gland

  • Deleted
    • - bulbo-urethral gland external definition any of the small paired racemose (compound tubulo-alveolar) glands below the apex of the prostate in males, located posterolateral to the membranous portion of the urethra at the base of the penis, between the two layers of the fascia of the urogenital diaphragm, in the deep perineal pouch, and enclosed by transverse fibers of the sphincter urethrae membranaceae muscle; they secrete a clear fluid known as pre-ejaculate (Cowper’s fluid), and are homologous to the greater vestibular (Bartholin’s) glands in the female[MP]. { ontology=MP , source=MP:0001169 }

Changes for: obsolete hindbrain commissure

Changes for: juxtaglomerular apparatus

Changes for: infraglenoid buttress

Changes for: macula densa

Changes for: thoracic vertebra

Changes for: dorsal gray commissure of spinal cord

Changes for: white matter

Changes for: mesenchyme of submandibular gland primordium

Changes for: right atrium venous valve

Changes for: infrarostral cartilage

Changes for: inner lining mucosa of the abomasum

Changes for: moustache

Changes for: median symphysis

Changes for: arcopallium

  • Deleted
    • - arcopallium comment The arcopallium refers to regions of the avian brain which partially overlap regions homologous to the amygdala of mammals. These regions have formerly been referred to as archistriatum, and before this epistriatum or amygdaloid complex, and a recent change of nomenclature has divided the region into the arcopallium and posterior pallial amygdala. The new nomenclature, adopted in 2004, reflects a modern understanding that the avian brain is broadly similar to the mammalian brain, containing large regions homologous to the mammalian neocortex, claustrum, and pallial amygdala. The outdated nomenclature it replaced perceived the avian brain as consisting almost entirely of enlarged basal ganglia, to which more complex outer layers had been added during a progress toward mammalian intelligence. [Wikipedia:Arcopallium]
  • Added
    • + arcopallium taxon notes The arcopallium refers to regions of the avian brain which partially overlap regions homologous to the amygdala of mammals. These regions have formerly been referred to as archistriatum, and before this epistriatum or amygdaloid complex, and a recent change of nomenclature has divided the region into the arcopallium and posterior pallial amygdala. The new nomenclature, adopted in 2004, reflects a modern understanding that the avian brain is broadly similar to the mammalian brain, containing large regions homologous to the mammalian neocortex, claustrum, and pallial amygdala. The outdated nomenclature it replaced perceived the avian brain as consisting almost entirely of enlarged basal ganglia, to which more complex outer layers had been added during a progress toward mammalian intelligence. [Wikipedia:Arcopallium]

Changes for: surface of tongue

Changes for: cervical mammary gland

Changes for: obsolete medial forebrain bundle diencephalon

Changes for: infundibular recess of 3rd ventricle

Changes for: lens pit

Changes for: obsolete pretecto-mamillary tract

Changes for: metanephric macula densa

Changes for: vestibular nucleus

Changes for: pectoral appendage skeleton

Changes for: pelvic appendage skeleton

Changes for: corticomedial nuclear complex

Changes for: basolateral amygdaloid nuclear complex

Changes for: obsolete commissure infima of Haller

Changes for: obsolete Drosophila lymph gland

Changes for: obsolete lateral forebrain bundle diencephalon

Changes for: mucosa of palate

Changes for: brain ventricle

Changes for: alveolar ridge

Changes for: mitral valve leaflet

Changes for: Harderian gland

Changes for: obsolete commissure of the caudal tuberculum

Changes for: obsolete decussation of medial funicular nucleus

Changes for: pedal digit bone

Changes for: manual digit bone

Changes for: mentalis muscle

Changes for: cardiac mesoderm

Changes for: obsolete horizontal commissure

Changes for: tongue intermolar eminence

Changes for: obsolete lateral longitudinal fasciculus

Changes for: adrenal gland capsule

Changes for: insula

Changes for: occipital lobe

Changes for: anterior cartilage of palatine

Changes for: posterior cartilage of palatine

Changes for: pterygoquadrate cartilage

Changes for: palatine cartilage

Changes for: hindlimb zeugopod muscle

Changes for: skeleton of lower jaw

Changes for: skeleton of upper jaw

Changes for: tooth of upper jaw

Changes for: hard palate

Changes for: fin

Changes for: epithelium of upper jaw

Changes for: epithelium of lower jaw

Changes for: taenia tectum of brain

Changes for: optic eminence

Changes for: gyrus

Changes for: pharyngeal arch artery

Changes for: obsolete dorsoventral diencephalic tract

Changes for: induseum griseum

Changes for: skeleton of limb

Changes for: lung epithelium

  • Added
    • + lung epithelium taxon notes A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[doi:10.1242/dev.115469]

Changes for: respiratory tube

Changes for: digit 6 plus metapodial segment

Changes for: digit 7 plus metapodial segment

Changes for: digit 8 plus metapodial segment

Changes for: sixth cervical dorsal root ganglion

Changes for: murine forestomach

Changes for: digit 6 digitopodial skeleton

Changes for: digit 8 digitopodial skeleton

Changes for: digit 7 digitopodial skeleton

Changes for: digit 1 plus metapodial segment

Changes for: digit 2 plus metapodial segment

Changes for: epithelium of hard palate

Changes for: epithelium of soft palate

Changes for: transverse palatine fold

Changes for: ganglion of central nervous system

Changes for: digit 3 plus metapodial segment

Changes for: digit 5 plus metapodial segment

Changes for: digit 4 plus metapodial segment

Changes for: mesenchyme of upper jaw

Changes for: gastric gland

Changes for: lateral recess of fourth ventricle

Changes for: musculature of leg

  • Deleted
    • - musculature of leg comment see notes on UBERON:0000978 for possible confusion over the term ‘leg’. This class represents the class-union of upper leg musculature and lower leg musculature (and thus may not mean precisely the same thing as the EHDAA2 class)
  • Added
    • + musculature of leg terminology notes see notes on UBERON:0000978 for possible confusion over the term ‘leg’. This class represents the class-union of upper leg musculature and lower leg musculature (and thus may not mean precisely the same thing as the EHDAA2 class)

Changes for: alveolar ridge of mandible

Changes for: anatomical projection

Changes for: alveolar process of maxilla

Changes for: cingulate cortex

Changes for: prechordal plate

Changes for: dorsal fin

Changes for: esophagus muscularis mucosa

Changes for: compound organ

  • Deleted
    • - compound organ comment Curator notes: this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under ‘organ’ rather than subdividing into compound and simple organs
  • Added
    • + compound organ curator notes this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under ‘organ’ rather than subdividing into compound and simple organs

Changes for: reproductive organ

Changes for: arthropod tibia

  • Deleted
    • - arthropod tibia comment that the ancestral leg need not have been so complex, and that other events, such as the successive loss of function of a Hox-gene could result in parallel gains of leg segments.

Changes for: apocrine gland

Changes for: parasubiculum

Changes for: spinal cord gray commissure

Changes for: follicular fluid

  • Deleted
    • - follicular fluid comment The follicular fluid contains sex steroids, glycoprotein hormones, plasma proteins, mucopolysaccharides, and enzymes and is rich in hyaluronic acid.
  • Added
    • + follicular fluid structure notes The follicular fluid contains sex steroids, glycoprotein hormones, plasma proteins, mucopolysaccharides, and enzymes and is rich in hyaluronic acid.

Changes for: follicular antrum

Changes for: ganglion

  • Deleted
    • - ganglion comment Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com).

Changes for: forelimb wing

Changes for: wing

Changes for: pituitary gland

Changes for: corpuscles of Stannius

Changes for: ureteral valve

Changes for: primary somatosensory cortex

Changes for: extraembryonic endoderm

Changes for: mesonephros

  • Deleted
    • - mesonephros comment By contrast to the pronephros, the histological features of the mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP] comment: Taxon notes: The mesonephros persists and form the permanent kidneys in fishes and amphibians, but in reptiles, birds, and mammals, it atrophies and for the most part disappears rapidly as the permanent kidney (metanephros) begins to develop during the sixth or seventh week. By the beginning of the fifth month only the ducts and a few of the tubules of the mesonephros remain[WP]
    • - mesonephros taxon notes In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the mesonephros will form the mature kidney[GO]
  • Added
    • + mesonephros function notes By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified]
    • + mesonephros taxon notes In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney

Changes for: vessel

Changes for: lateral recess of third vetricle

Changes for: obsolete regional part of peripheral nervous system

Changes for: individual digit of digitopodial skeleton

Changes for: obsolete regional part of cerebral ventricular cavity

Changes for: obsolete regional part of median eminence

Changes for: obsolete predominantly gray regional part of transverse frontopolar gyri complex

Changes for: pedal digit digitopodial skeleton

Changes for: manual digit 1 digitopodial skeleton

Changes for: manual digit 5 digitopodial skeleton

Changes for: manual digit 4 digitopodial skeleton

Changes for: manual digit 3 digitopodial skeleton

Changes for: manual digit 2 digitopodial skeleton

Changes for: pedal digit 4 digitopodial skeleton

Changes for: pedal digit 3 digitopodial skeleton

Changes for: pedal digit 2 digitopodial skeleton

Changes for: pedal digit 1 digitopodial skeleton

Changes for: pedal digit 5 digitopodial skeleton

Changes for: obsolete predominantly gray regional part of Parahippocampal gyrus

Changes for: manual digit 7 plus metapodial segment

Changes for: manual digit 6 plus metapodial segment

Changes for: pedal digit 6 plus metapodial segment

Changes for: manual digit 8 plus metapodial segment

Changes for: ansiform lobule crus I

Changes for: ansiform lobule crus II

Changes for: obsolete regional part of cerebral peduncle

Changes for: obsolete regional part of spiral organ of Corti

Changes for: obsolete superficial feature part of midbrain tectum

Changes for: obsolete regional part of central nervous system

Changes for: stomach glandular epithelium

Changes for: glandular columnar epithelium

Changes for: palatine process of maxilla

Changes for: post-hyoid pharyngeal arch skeleton

Changes for: stomach glandular region mucosa

Changes for: glandular cuboidal epithelium

Changes for: hyoid arch skeleton

Changes for: autopodial extension

Changes for: prepollex

Changes for: obsolete regional part of medial mammillary nucleus

Changes for: obsolete superficial feature part of intermediate hypothalamic region

Changes for: rostral ventrolateral medulla

Changes for: bone of craniocervical region

Changes for: obsolete tuber

Changes for: reticuloendothelial system

Changes for: renal medulla

  • Deleted
    • - renal medulla comment The renal medulla is split up into a number of sections, known as the renal pyramids. Blood enters into the kidney via the renal artery, which then splits up to form the arcuate arterioles. The arcuate arterioles each in turn branch into interlobular arterioles, which finally reach the glomeruli. At the glomerulus the blood reaches a highly disfavourable pressure gradient and a large exchange surface area, which forces the serum portion of the blood out of the vessel into the renal tubules. Flow continues through the renal tubules, including the proximal tubule, the Loop of Henle, and finally leaves the kidney by means of the collecting duct, leading to the renal ureter. The renal medulla contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. The renal medulla is hypertonic to the filtrate in the nephron and aids in the reabsorption of water
  • Added
    • + renal medulla structure notes The renal medulla is split up into a number of sections, known as the renal pyramids. Blood enters into the kidney via the renal artery, which then splits up to form the arcuate arterioles. The arcuate arterioles each in turn branch into interlobular arterioles, which finally reach the glomeruli. At the glomerulus the blood reaches a highly disfavourable pressure gradient and a large exchange surface area, which forces the serum portion of the blood out of the vessel into the renal tubules. Flow continues through the renal tubules, including the proximal tubule, the Loop of Henle, and finally leaves the kidney by means of the collecting duct, leading to the renal ureter. The renal medulla contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. The renal medulla is hypertonic to the filtrate in the nephron and aids in the reabsorption of water

Changes for: proximal sesamoid bone of pes

Changes for: proximal sesamoid bone of manus

Changes for: obsolete myelin membrane

  • Deleted
    • - obsolete myelin membrane comment BTO has def The multilamellar myelin membrane is a specisalised lipid-rich domain of the glial cell plasma membrane. FMA has primary term name Myelinated plasma membrane of Schwann cell
  • Added

Changes for: pedal digit 6 digitopodial skeleton

Changes for: manual digit 6 digitopodial skeleton

Changes for: manual digit 8 digitopodial skeleton

Changes for: manual digit 7 digitopodial skeleton

Changes for: obsolete superficial feature part of diencephalon

Changes for: obsolete regional part of oculomotor nuclear complex

Changes for: obsolete regional part of red nucleus

Changes for: obsolete regional part of habenula

Changes for: secondary palatal shelf mesenchyme

Changes for: upper jaw incisor epithelium

Changes for: lower jaw incisor epithelium

Changes for: solid compound organ

  • Deleted
    • - solid compound organ comment Curator notes: this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future. Note also that we place the FMA class ‘solid organ’ here, and the FMA includes many glands plus the liver as solid organs, which some may find confusing
  • Added
    • + solid compound organ curator notes this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future. Note also that we place the FMA class ‘solid organ’ here, and the FMA includes many glands plus the liver as solid organs, which some may find confusing

Changes for: pelvic girdle skeleton

Changes for: pectoral girdle skeleton

Changes for: appendage girdle region

Changes for: cavitated compound organ

  • Deleted
    • - cavitated compound organ comment Curator notes: this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future
  • Added
    • + cavitated compound organ curator notes this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future

Changes for: simple organ

  • Deleted
    • - simple organ comment Curator notes: this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future
  • Added
    • + simple organ curator notes this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future

Changes for: compound organ component

  • Deleted
    • - compound organ component comment Curator notes: this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future
  • Added
    • + compound organ component curator notes this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future

Changes for: obsolete regional part of thalamus

Changes for: secondary palatal shelf epithelium

Changes for: lower jaw molar epithelium

Changes for: upper jaw molar epithelium

Changes for: primary palate epithelium

Changes for: obsolete superficial feature part of medulla oblongata

Changes for: secondary palatal shelf

Changes for: hindlimb zeugopod skeleton

Changes for: pectoral fin skeleton

Changes for: pelvic fin skeleton

Changes for: paired fin skeleton

Changes for: girdle skeleton

Changes for: alular digit plus metapodial segment

Changes for: manual minor digit (Aves) plus metapodial segment

Changes for: manual major digit (Aves) plus metapodial segment

Changes for: forelimb zeugopod skeleton

Changes for: incisive canal

Changes for: obsolete supraoptic commissure

Changes for: atrium auricular region

Changes for: obsolete ventral rhombencephalic commissure brain stem

Changes for: obsolete bulbo-spinal tract

Changes for: obsolete ansulate commissure

Changes for: obsolete decussation of the medial octavolateralis nucleus

Changes for: right atrium auricular region

Changes for: left atrium auricular region

Changes for: obsolete predominantly gray part of Intralaminar nuclear group

Changes for: digit plus metapodial segment

Changes for: obsolete regional part of cerebellar peduncular complex

Changes for: tricuspid valve leaflet

Changes for: valve of inferior vena cava

Changes for: pedal digit 7 plus metapodial segment

Changes for: pedal digit 8 plus metapodial segment

Changes for: transformed vein

Changes for: transformed artery

Changes for: remnant of embryonic structure

Changes for: obsolete regional part of Anterior cingulate cortex

Changes for: obsolete predominantly gray regional part of neurohypophysis

Changes for: optic fissure

Changes for: ansiform lobule

Changes for: obsolete cytoarchitectural part of dorsal cochlear nucleus

Changes for: manual digit digitopodial skeleton

Changes for: swim bladder

Changes for: body of sternum

Changes for: nasal skeleton

Changes for: mesonephric macula densa

Changes for: stomach non-glandular region

Changes for: stomach glandular region

Changes for: myelencephalon

Changes for: manual digit 8

Changes for: manual digit 7

Changes for: manual digit 6

Changes for: glandular epithelium

Changes for: obsolete striosomal part of tail of caudate nucleus

Changes for: obsolete matrix part of body of caudate nucleus

Changes for: cardial valve

Changes for: corneo-scleral junction

Changes for: obsolete cytoarchitectural part of retina

Changes for: autopodial skeleton

Changes for: embryo

  • Deleted
    • - embryo comment Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
  • Added

Changes for: thoracic segment of trunk

Changes for: obsolete regional part of basal amygdaloid nucleus

Changes for: obsolete predominantly gray part of basolateral nuclear complex

Changes for: obsolete predominantly gray regional part of amygdala

Report for properties

ObjectProperty objects lost from source: 0

ObjectProperty objects new in target: 2

New ObjectProperty : boundary of

New ObjectProperty : skeleton of

Changed ObjectProperty objects: 1

Changes for: has skeleton

February 2, 2015 |

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