2015-04-23 release

Minor release mostly focusing on the skeletal system and craniofacial improvements
2015-04-23 release image

Ontology Diff Report

  • neuro
    • NTs: sacci vasculosi {tract,nucleus}
    • associating medial dorsal thalamic nucleus in EMAPA with MBA:636 Issue https://github.com/obophenotype/mouse-anatomy-ontology/issues/10
    • NTs: lateral and central parts of ediodorsal nucleus of the thalamus
  • Skeletal, oral and craniofacial
    • implementing endochondral design pattern for basihyal. Issue 688
    • NT: anterior nasal spine of maxilla. Fixes 679
    • NT: longitudinal arch. Fixes 678
    • fixed musculature typo. Issue 686
    • NTs for palatine sutures
    • NT: for generic incisor diastema. 687
    • NTs for specific diastemas. Fixes 671
    • narwhal tusk metadata
  • Other
    • NT for axochord, UBERON:0035147. Fixes 574
    • syns and xref for epicanthal fold. Fixes 676
    • NT: contents of DT. Fixes https://github.com/EnvironmentOntology/envo/issues/110
    • more explicit primary name for inter-nipple line. Issue 671
    • EMAPA xrefs updated

Original Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2015-04-12/uberon.owl

New Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2015-04-23/uberon.owl

Report for classes

Class objects lost from source: 0

Class objects new in target: 42

New Class : profundus foramen

New Class : axochord

New Class : tractus sacci vasculosi

New Class : gingival epithelial attachment

New Class : presumptive axochord

New Class : preputial space of female

New Class : preputial space of male

New Class : nucleus sacci vasculosi

New Class : preputial space

New Class : dorsolateral prefrontal cortex layer 6

New Class : dorsolateral prefrontal cortex layer 5

New Class : dorsolateral prefrontal cortex layer 4

New Class : dorsolateral prefrontal cortex layer 3

New Class : dorsolateral prefrontal cortex layer 2

New Class : dorsolateral prefrontal cortex layer 1

New Class : internal cerebral vein

New Class : dorsal cerebral vein

New Class : superior cerebral vein

New Class : interincisive suture

New Class : palatomaxillary suture

New Class : fauces

New Class : transverse palatine suture

New Class : suture of hard palate

New Class : palatoethmoidal suture

New Class : pes cartilage element

New Class : manus cartilage element

New Class : auditory ossicle endochondral element

New Class : auditory ossicle cartilage element

New Class : auditory ossicle pre-cartilage element

New Class : longitudinal arch of pes

New Class : anterior nasal spine of maxilla

New Class : plantar nerve

New Class : mediodorsal nucleus of the thalamus, central part

New Class : mediodorsal nucleus of the thalamus, lateral part

New Class : diastema between central incisors

New Class : diastema between upper central incisors

New Class : lateral plantar nerve

New Class : medial plantar nerve

New Class : intrinsic muscle

New Class : material entity in digestive tract

New Class : diastema between lower central incisors

New Class : diastema between incisors

Changed Class objects: 299

Changes for: supra-orbital ridge

Changes for: cloacal bursa

Changes for: lenticular process of incus bone

Changes for: pre-dentine

Changes for: basihyal bone

Changes for: basihyal element

Changes for: basihyal cartilage

Changes for: supragenual nucleus of pontine tegmentum

Changes for: uterine lumen

Changes for: epicanthal fold

Changes for: line connecting laterally paired nipples

Changes for: medial subnucleus of solitary tract

Changes for: feather follicle placode

Changes for: non-neurogenic ectodermal placode

Changes for: retractor lateralis posterior muscle

Changes for: retractor lateralis anterior muscle

Changes for: postminimus

Changes for: endothelium of capillary

Changes for: endothelium of venule

Changes for: endothelium of vein

Changes for: endothelium of arteriole

Changes for: terminal bronchiole epithelium

Changes for: flexor cruris lateralis muscle

Changes for: serratus dorsalis muscle

Changes for: flexor cruris lateralis pars accessoria muscle

Changes for: retractor lateralis muscle

Changes for: internal anal region

Changes for: body of mandible

Changes for: saccus vasculosus

Changes for: pharyngeal bar

Changes for: external anal region

Changes for: blood vessel internal elastic membrane

Changes for: nail

  • Deleted
    • - nail editor note TODO - check claw vs nail. A primate’s nail consists of the unguis alone; the subunguis has disappeared.
  • Added
    • + nail comment The nails of humans and the claws are moth are highly similar. Both species have a proximal nail fold, cuticle, nail matrix, nail bed, nail plate, and hyponychium. Distinguishing features are the shape of the nail and the presence of an extended hyponychium in the mouse [PMC3579226]
    • + nail curator notes Use this class for both the nails of primates and the homologous claws of mammals such as mouse.
    • + nail has exact synonym nail/claw { database cross reference=UBERON:cjm }
    • + nail taxon notes A primate’s nail consists of the unguis alone; the subunguis has disappeared

Changes for: submandibular gland

Changes for: triceps surae

Changes for: auditory ossicle bone

Changes for: ventral wall of dorsal aorta

Changes for: magnocellular part of medial dorsal nucleus

Changes for: bronchial vein

Changes for: venous plexus

Changes for: thymic vein

Changes for: intrinsic muscle of pes

Changes for: hypothenar muscle

Changes for: thenar muscle

Changes for: intrinsic muscle of manus

Changes for: future telencephalon

Changes for: vertebral vein

Changes for: femur cartilage element

Changes for: prostate bud

Changes for: future dorsal motor nucleus of vagus

Changes for: lingual artery

Changes for: stapes cartilage element

Changes for: malleus cartilage element

Changes for: future common hepatic duct

Changes for: future myelencephalon

Changes for: future hindbrain meninx

Changes for: future metencephalon

Changes for: future falx cerebri

Changes for: medial dorsal nucleus of thalamus

Changes for: bolus of food

Changes for: ingested food

Changes for: diastema

Changes for: intergluteal cleft

Changes for: post-anal tail bud

Changes for: tunica intima

Changes for: tunica media

Changes for: median palatine suture

Changes for: skeleton of manus

Changes for: metaphysis

Changes for: left common cardinal vein

Changes for: cardiac mesenchyme

Changes for: blood vessel elastic tissue

Changes for: blood vessel layer

Changes for: smegma

Changes for: tooth root

  • Added
    • + tooth root definition The part of a tooth that is implanted in the gum; the root is normally located below the neck of the tooth, covered by cementum rather than enamel, and attached by the periodontal ligament to the alveolar bone { database cross reference=MP:0011165 }

Changes for: interosseous muscle of manus

Changes for: dorsal interosseous of manus

Changes for: coracoid bone

Changes for: male urethral meatus

Changes for: urethral meatus

Changes for: anal region

Changes for: rectus femoris

Changes for: spongiose part of urethra

Changes for: intertarsal sesamoid

Changes for: tibia endochondral element

Changes for: tibiotarsus endochondral element

Changes for: fibula endochondral element

Changes for: incus endochondral element

Changes for: stapes endochondral element

Changes for: malleus endochondral element

Changes for: hindlimb endochondral element

Changes for: femur endochondral element

Changes for: lower rhombic lip

Changes for: prostate epithelial cord

Changes for: proximal carpal cartilage

Changes for: proximal carpal bone pre-cartilage condensation

Changes for: distal carpal cartilage element

Changes for: distal carpal bone 5 pre-cartilage condensation

Changes for: distal carpal bone 5 cartilage

Changes for: distal carpal bone 4 pre-cartilage condensation

Changes for: distal carpal bone 4 cartilage

Changes for: distal carpal bone 3 pre-cartilage condensation

Changes for: distal carpal bone 1 pre-cartilage condensation

Changes for: distal carpal bone 1 cartilage

Changes for: distal carpal bone 2 cartilage

Changes for: proximal tarsal cartilage

Changes for: proximal tarsal bone pre-cartilage condensation

Changes for: distal carpal bone 2 pre-cartilage condensation

Changes for: distal carpal bone 3 cartilage

Changes for: capillary bed

Changes for: glomerular capsule

Changes for: renal corpuscle

Changes for: distal tarsal bone 3 cartilage

Changes for: distal tarsal bone 2 pre-cartilage condensation

Changes for: distal tarsal bone 2 cartilage

Changes for: distal tarsal bone 1 pre-cartilage condensation

Changes for: distal tarsal bone 1 cartilage

Changes for: distal tarsal bone pre-cartilage condensation

Changes for: distal tarsal cartilage

Changes for: distal tarsal bone 5 pre-cartilage condensation

Changes for: distal tarsal bone 5 cartilage

Changes for: distal tarsal bone 4 cartilage

Changes for: distal tarsal bone 4 pre-cartilage condensation

Changes for: distal tarsal bone 3 pre-cartilage condensation

Changes for: primitive superior sagittal sinus

Changes for: neurogenic placode

Changes for: patella pre-cartilage condensation

Changes for: pelvic appendage bud mesenchyme

Changes for: pectoral appendage bud mesenchyme

Changes for: tarsus pre-cartilage condensation

Changes for: primitive nephron

Changes for: choroid plexus of third ventricle

Changes for: pedal digit phalanx pre-cartilage condensation

Changes for: manual digit phalanx pre-cartilage condensation

Changes for: septohypothalamic nucleus

Changes for: sigmoid colon

Changes for: terminal bronchiole

Changes for: rostral gyrus

Changes for: respiratory system

Changes for: artery smooth muscle tissue

Changes for: neural tube

Changes for: incurrent foramen of ectepicondylar foramen

Changes for: skin of back

Changes for: styliform cartilage

Changes for: hippocampal formation

Changes for: pyramidal layer of CA3

Changes for: lens fiber

Changes for: otic ganglion

Changes for: pterygopalatine ganglion

Changes for: styloid process of temporal bone

Changes for: cranial muscle

Changes for: Brodmann (1909) area 32

Changes for: extracleithrum

Changes for: myocardium

Changes for: nail of pedal digit

Changes for: raphe of scrotum

  • Deleted
    • - raphe of scrotum comment Development notes: The scrotal raphe is formed when the embryonic, urethral groove closes (week 12 in humans)
  • Added

Changes for: extraembryonic coelom

Changes for: parvocellular layer of dorsal nucleus of lateral geniculate body

Changes for: magnocellular layer of dorsal nucleus of lateral geniculate body

Changes for: incus cartilage element

Changes for: egg yolk

Changes for: obsolete dorsal cerebral vein

Changes for: future diencephalon

Changes for: rhombic lip

Changes for: carpus pre-cartilage condensation

Changes for: incus pre-cartilage condensation

Changes for: humerus pre-cartilage condensation

Changes for: renal medulla collecting duct

Changes for: femur pre-cartilage condensation

Changes for: malleus pre-cartilage condensation

Changes for: radius-ulna pre-cartilage condensation

Changes for: tooth enamel organ

Changes for: stapes pre-cartilage condensation

Changes for: metanephric cortical collecting duct

Changes for: tunica media of artery

Changes for: presumptive paraxial mesoderm

Changes for: presumptive atrioventricular canal

Changes for: presumptive midbrain hindbrain boundary

Changes for: tunica media of vein

Changes for: tunica intima of vein

Changes for: tunica adventitia of vein

Changes for: tunica adventitia of artery

Changes for: embryonic cement gland

Changes for: tooth placode

Changes for: metanephric ureteric bud

Changes for: ureter ureteric bud

Changes for: hindbrain-spinal cord boundary

Changes for: forebrain-midbrain boundary

Changes for: tailgut

Changes for: podocyte slit junction

Changes for: podocyte slit diaphragm

Changes for: ganglionic eminence

  • Deleted
  • Added
    • + ganglionic eminence comment Development notes: contributes significantly in building up the GABAergic cortical cell population[WP]
    • + ganglionic eminence definition The transient proliferative population of neurons that expands exponentially during late prenatal development; it is a continuous germinal zone distinct from the ventricular zone that surrounds the brain ventricles[MP]. { database cross reference=MP:0004274 }

Changes for: alveolar ridge

Changes for: interosseous muscle of pes

Changes for: dorsal pes interosseous muscle

Changes for: arteriole smooth muscle

Changes for: lymphatic vessel smooth muscle

Changes for: skin of body

Changes for: outer medullary collecting duct

Changes for: cortical collecting duct

Changes for: inner medullary collecting duct

Changes for: renal vesicle

Changes for: presumptive gut

Changes for: narwhal tusk

  • Added
    • + narwhal tusk comment Typically the left incisor with the right vestigial, but some males have two tusks

Changes for: distal early tubule

Changes for: submandibular ganglion

Changes for: striated muscle tissue

Changes for: root of molar tooth

Changes for: Descemet’s membrane

Changes for: cauda epididymis

Changes for: pharyngeal arch artery

Changes for: corpus epididymis

Changes for: caput epididymis

Changes for: podocyte foot process

Changes for: interphalangeal joint of manus

Changes for: interphalangeal joint of pes

Changes for: lobe of lung

Changes for: transverse foramen

Changes for: cloaca

Changes for: orifice

Changes for: gingival groove

Changes for: future nervous system

Changes for: future central nervous system

Changes for: pelvic appendage bud ectoderm

Changes for: pectoral appendage bud ectoderm

Changes for: epaxial musculature

Changes for: hypaxial musculature

Changes for: mesoderm blood island

Changes for: future meninx

Changes for: anterior lateral line system

Changes for: presumptive mesencephalic artery

Changes for: hypochord

Changes for: ear vesicle

Changes for: olfactory placode

Changes for: epibranchial placode

Changes for: eye primordium

Changes for: neural plate

Changes for: developing epithelial placode

Changes for: submocosal esophageal gland

Changes for: scrotum skin

Changes for: blood vessel external elastic membrane

Changes for: forelimb bone

Changes for: ansiform lobule crus I

Changes for: urinary bladder muscularis mucosa

Changes for: manus bone

Changes for: ejaculatory duct epithelium

Changes for: jejunal mucosa

Changes for: lens nucleus

Changes for: tunica intima of artery

Changes for: visual cortex

Changes for: tunica adventitia of blood vessel

Changes for: major vestibular gland

Changes for: presumptive enteric nervous system

Changes for: manual digit phalanx cartilage element

Changes for: pedal digit metatarsal pre-cartilage condensation

Changes for: pedal digit phalanx cartilage element

Changes for: manual digit metacarpus cartilage element

Changes for: manual digit metacarpus pre-cartilage condensation

Changes for: pedal digit metatarsal cartilage element

Changes for: vitelline vein

Changes for: female urethral meatus

Changes for: presumptive hypochord

Changes for: presumptive structure

Changes for: presumptive blood

Changes for: palmar interosseous muscle of manus

Changes for: plantar interosseous muscle of pes

Changes for: interosseous muscle of autopod

Changes for: presumptive neural retina

Changes for: presumptive retinal pigmented epithelium

Changes for: raphe of perineum

  • Deleted
    • - raphe of perineum comment Development notes: It is the result of a fetal developmental phenomenon whereby the scrotum (the developmental equivalent of the labia in females) and penis close toward the midline and fuse. The resulting ridge of tissue is evident as the perineal raphe
  • Added
    • + raphe of perineum development notes It is the result of a fetal developmental phenomenon whereby the scrotum (the developmental equivalent of the labia in females) and penis close toward the midline and fuse. The resulting ridge of tissue is evident as the perineal raphe

Changes for: paraflocculus

Changes for: cortical layer VI

Changes for: tibiotarsus pre-cartilage condensation

Changes for: tarsometatarsus cartilage element

Changes for: tibiotarsus cartilage element

Changes for: tarsometatarsus pre-cartilage condensation

Changes for: interrenal primordium

Changes for: chorion-containing eggshell

Changes for: transverse tarsal joint

Changes for: fibula pre-cartilage condensation

Changes for: fibula cartilage element

Changes for: tibia pre-cartilage condensation

Changes for: hindlimb pre-cartilage condensation

Changes for: hindlimb cartilage element

Changes for: forelimb bone pre-cartilage condensation

Changes for: forelimb cartilage element

Changes for: tibia cartilage element

Changes for: calcaneum cartilage element

Changes for: radius pre-cartilage condensation

Changes for: ulna pre-cartilage condensation

Changes for: cardial valve

Changes for: ventral nerve cord

  • Deleted
    • - ventral nerve cord comment The ventral nerve cords make up the nervous system of some phyla of the invertebrates, particularly within the nematodes, annelids and the arthropods. It usually consists of cerebral ganglia anteriorly with the nerve cords running down the ventral (‘belly’, as opposed to back) plane of the organism. This characteristic is important in qualifying the difference compared to the chordates, which have a dorsal nerve cord. Ventral nerve cords from anterior to posterior (the thoracic and abdominal tagma in the arthropods) are made up of segmented ganglia that are connected by a tract of nerve fibers passing from one side to the other of the nerve cord called commissures. The complete system bears some likeness to a rope ladder. In some animals the bilateral ganglia are fused into a single large ganglion per segment. This characteristic is found mostly in the insects.
  • Added
    • + ventral nerve cord external definition A cluster of neurons that extends posteriorly from the embryonic and larval brain and is surrounded by a connective tissue sheath. { source=FBbt:00001102 }
    • + ventral nerve cord taxon notes The ventral nerve cords make up the nervous system of some phyla of the invertebrates, particularly within the nematodes, annelids and the arthropods. It usually consists of cerebral ganglia anteriorly with the nerve cords running down the ventral (‘belly’, as opposed to back) plane of the organism. This characteristic is important in qualifying the difference compared to the chordates, which have a dorsal nerve cord. Ventral nerve cords from anterior to posterior (the thoracic and abdominal tagma in the arthropods) are made up of segmented ganglia that are connected by a tract of nerve fibers passing from one side to the other of the nerve cord called commissures. The complete system bears some likeness to a rope ladder. In some animals the bilateral ganglia are fused into a single large ganglion per segment. This characteristic is found mostly in the insects.

Changes for: stomodeum

Changes for: calcaneum pre-cartilage condensation

Changes for: cerebral cortex

  • Added
    • + cerebral cortex curator notes We follow NIFSTD in defining cerebral cortex and including both neocortex and hippocampal formation (DG+hippocampus).

Changes for: pterygoid muscle

  • Deleted
    • - pterygoid muscle comment Taxon notes: We use this class to group the medial and lateral pterygoids of mammals as well as the pterygoideus of amphibians and reptiles. Note that FEED includes a distinct class for the reptilian pterygoideus. In future, this branch of the ontology may be refined to include a more complete classification of jaw adductors across gnathostomes. See for example http://dx.doi.org/10.1134/S1062359010090050
  • Added
    • + pterygoid muscle taxon notes We use this class to group the medial and lateral pterygoids of mammals as well as the pterygoideus of amphibians and reptiles. Note that FEED includes a distinct class for the reptilian pterygoideus. In future, this branch of the ontology may be refined to include a more complete classification of jaw adductors across gnathostomes. See for example http://dx.doi.org/10.1134/S1062359010090050

Changes for: lateral pterygoid muscle

Changes for: chyme

Changes for: chyle

Report for properties

ObjectProperty objects lost from source: 0

ObjectProperty objects new in target: 0

Changed ObjectProperty objects: 0

April 23, 2015 |

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