2015-03-15 release

Cephalopods and comb jellies and sponges, oh my!
2015-03-15 release image

This release see the incorporation of 3 invertebrate ontologies into the Uberon composite-metazoan edition. The 3 ontologies are:

Classes from these ontologies appear as children of generalized uberon classes such ‘nervous system’ in composite-metazoa. For more details, see the composite ontologies docs

Classes from these ontologies can therefore be used in making homology assertions - for example between the gastroderm of eumetazoa and the choanocyte chamber of sponges.

This release also incorporates a number of improvements from the Uberon community, see diffs below for details.

Ontology Diff Report

  • Composite Metazoa
    • Added PORO: Fixes 658
    • Added CTENO
    • Added CEPH
  • Invertebrate and cyclostomes
    • relabeled gut epithelium and added gastrodermis as a synonym. BGEE:ANN. Issue 578
    • Fixed def of blastopore. BGEE:ANN. Fixes 660
    • changed label for oral/aboral sides. Fixes 661
    • Referencing BSPO in definition of spatial subdivisions
    • NT: Pharyngeal bar
    • NT: Mucocartilage tissue (as found in lampreys)
    • NT: future piston
  • Upper
    • NTs: cell cluster, multi organ part structures. From CARO
    • organ component layer review: reclassified many layered structures and ensured most has their composition defined
    • removed some axioms from bone tissue and added them to mineralized child. Issue 27
    • CARO: replacing clusters with multi organ part structures
    • NT: external soft tissue zone
  • Neuro
    • Reviewing pan-vertebrate brain structures
    • Brain taxon constraints. michaelerice. Issue 659
    • alignment with MP: def and syns for infundibular stem
    • Some fixes to neurilemma to address 646 - No longer grouping insect structure here (functional grouping would be at a higher level)
  • Glands and integumentary system
    • alignment with MP: mucuous glands. https://sourceforge.net/p/obo/mammalian-phenotype-requests/2036/
    • NT: Weber gland. parts of ciliary body. https://sourceforge.net/p/obo/mammalian-phenotype-requests/2035/
    • def-of-suprabasal
  • Circulatory and duct systems
    • Taxon constraint on retina vasculature (and hence all blood vessels) for Aves. Fixes 657
    • various edits, incl elastic layers and blood vessel layers
    • fixed confusion between arcuate veins
    • Multiple improvements to representation of biliary system. Related to issue 653
    • NT: biliary tree epithelium. Fixes 653
    • Improved definitions of biliary structures using MP and sources provided by @cindyJax
  • Other
    • TCs for peyers patch [michael e rice]. Issue 647
    • Fixing mouse-derived incorrect placement of bronchus BM, omitting from checks until https://sourceforge.net/p/obo/mouse-anatomy-requests/94/
    • Fixed Bruch’s membrane
    • Fixed sp. errors. Fixes 585
    • Fixed def typo. Fixes 520
  • Stages and development
    • NT: juvenile stage. Fixes 645
    • NT: infant stage. Fixes 644
    • Taxon constraints for nursing stage. Issue 576
    • pituitary now immediate transform of future pituitary. Issue 438

Original Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2015-02-14/uberon.owl

New Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2015-03-15/uberon.owl

Report for classes

Class objects lost from source: 1

Class objects new in target: 21

New Class : pars plicata of ciliary body

New Class : Weber’s gland

New Class : pharyngeal bar

New Class : pars plana of ciliary body

New Class : perforant path

New Class : auricular feather

New Class : layer of smooth muscle tissue

New Class : epithelium of biliary system

New Class : future piston

New Class : mucocartilage tissue

New Class : external soft tissue zone

New Class : arcuate artery of foot

New Class : dorsal surface of penis

New Class : multi organ part structure

New Class : cell cluster

New Class : infant stage

New Class : anatomical collection

New Class : anatomical row

New Class : disconnected anatomical group

New Class : aligned anatomical group

New Class : juvenile stage

Changed Class objects: 727

Changes for: mycetome

Changes for: cephalodorsosubpharyngeus

Changes for: buttock

Changes for: cerebral cortex neuropil

Changes for: aproctal bone of priapium

Changes for: velar skeleton

Changes for: dilatator laryngis

Changes for: zeugopodial skeleton

Changes for: paired limb/fin skeleton

Changes for: stylopodial skeleton

Changes for: dorsal fin distal radial element

Changes for: paired fin radial skeleton

Changes for: temporal cortex cingulum

Changes for: cingulate cortex cingulum

Changes for: pleural plate of carapace

Changes for: hypoplastron

Changes for: xiphiplastron

Changes for: pontocerebellar tract

Changes for: enameloid

Changes for: orbital part of frontal bone

Changes for: epiplastron

Changes for: hippocampus cortex cingulum

Changes for: corticopontine fibers

Changes for: corticobulbar tract

Changes for: cerebral nerve fasciculus

Changes for: entorhinal cortex layer 4

Changes for: dorsal cochlear nucleus pyramidal cell layer

Changes for: entorhinal cortex layer 3

Changes for: entorhinal cortex layer 5

Changes for: entorhinal cortex layer 6

Changes for: superior colliculus stratum zonale

Changes for: primary motor cortex layer 6

Changes for: primary motor cortex layer 5

Changes for: olfactory cortex layer 2

Changes for: olfactory cortex layer 1

Changes for: piriform cortex layer 2a

Changes for: piriform cortex layer 2b

Changes for: dentate gyrus granule cell layer outer blade

Changes for: dentate gyrus granule cell layer inner blade

Changes for: dentate gyrus molecular layer inner

Changes for: dentate gyrus molecular layer middle

Changes for: entorhinal cortex layer 1

Changes for: entorhinal cortex layer 2

Changes for: short ciliary nerve

Changes for: nervous system cell part layer

  • Added
    • + nervous system cell part layer editor note this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer

Changes for: collection of feathers

Changes for: acinus of parotid gland

Changes for: anterior uvea

Changes for: palatoquadrate arch

Changes for: left pelvic girdle region

Changes for: right pelvic girdle region

Changes for: angular bone

Changes for: articular cartilage element

Changes for: mammary lobe

Changes for: hindbrain commissure

Changes for: margin of eyelid

Changes for: ventricular musculature

Changes for: hindbrain marginal layer

Changes for: cranial neuron projection bundle

Changes for: upper urinary tract

Changes for: facial skeleton

Changes for: pretectal region

  • Deleted
    • - pretectal region comment AO notes: part of diencephalon in ZFA - modify to adjacent here, supported by pub. Note there is some inconsistency in resources between the region vs nuclei - sometimes they are treated equivalent, sometimes separate (e.g. MP)
  • Added
    • + pretectal region external ontology notes part of diencephalon in ZFA - modify to adjacent here, supported by pub. Note there is some inconsistency in resources between the region vs nuclei - sometimes they are treated equivalent, sometimes separate (e.g. MP) { external ontology=ZFA }

Changes for: bile

Changes for: periarterial lymphatic sheath

Changes for: post-cranial axial skeletal system

Changes for: type 1 adrenal tissue

Changes for: skeletal musculature

Changes for: central nervous system cell part cluster

Changes for: pulmonary part of lymphatic system

Changes for: pulmonary lymphatic vessel

Changes for: renin-angiotensin system

Changes for: accessory articulation

Changes for: subserosa

Changes for: sensory ganglion

Changes for: circular muscle layer of muscular coat

Changes for: longitudinal muscle layer of muscular coat

Changes for: holocrine gland

Changes for: ethmoid region

Changes for: dentate gyrus of hippocampal formation

Changes for: mastoid process of temporal bone

Changes for: cartilaginous external acoustic tube

Changes for: lobule of pinna

Changes for: internal ear

Changes for: cochlea

Changes for: white matter of telencephalon

Changes for: parotid gland

Changes for: bony labyrinth

Changes for: superior laryngeal nerve

Changes for: cranial nerve

Changes for: layer of retina

Changes for: pigmented layer of retina

Changes for: gray matter of telencephalon

Changes for: inner limiting layer of retina

Changes for: nerve fiber layer of retina

Changes for: proximal convoluted tubule brush border

Changes for: intestinal brush border layer

Changes for: short microvillus layer

Changes for: striated border microvillus layer

Changes for: layer of microvilli

Changes for: taenia coli

Changes for: midbody melanophore spot

Changes for: prehallux skeleton

Changes for: palatine process of premaxilla

  • Deleted
    • - palatine process of premaxilla comment Taxon notes: A posterior extension of the premaxilla that lies along the palatine and fuses to some extent with it. In the Passeres it may be fused, unfused, free or a lateral flange. Evolved multiple times in Passerines [http://www.biodiversitylibrary.org/part/29066]
  • Added
    • + palatine process of premaxilla taxon notes A posterior extension of the premaxilla that lies along the palatine and fuses to some extent with it. In the Passeres it may be fused, unfused, free or a lateral flange. Evolved multiple times in Passerines [http://www.biodiversitylibrary.org/part/29066]

Changes for: caudal melanophore spot

Changes for: cloacal villus

Changes for: tunica fibrosa of eyeball

Changes for: row of scales

Changes for: Merkel nerve ending

Changes for: nerve ending

Changes for: dentine

Changes for: lacrimal apparatus

Changes for: enamel

Changes for: middle ear

Changes for: arytenoid cartilage

Changes for: ciliary body

Changes for: ciliary epithelium

Changes for: iris stroma

Changes for: iris

Changes for: uvea

Changes for: jaw skeleton

Changes for: pudendal nerve

Changes for: blood vessel internal elastic membrane

Changes for: nail

Changes for: neurocranium

Changes for: larynx

Changes for: soft palate

Changes for: palatine uvula

Changes for: oropharynx

Changes for: nasopharynx

Changes for: primary motor cortex layer 1

Changes for: temporal bone

Changes for: lacrimal bone

Changes for: nasal bone

Changes for: palatine bone

Changes for: jugal bone

Changes for: sensory root of facial nerve

Changes for: external ear

Changes for: orbit of skull

Changes for: articulation

Changes for: organ component layer

Changes for: postnatal subventricular zone

Changes for: biliary bud

Changes for: hepatopancreatic ampulla

Changes for: dorsolateral fasciculus of medulla

Changes for: dorsal longitudinal fasciculus of medulla

Changes for: cuneate fasciculus of medulla

Changes for: decussation of medial lemniscus

Changes for: cuneocerebellar tract

Changes for: cerebral crus

Changes for: periamygdaloid area

Changes for: gracile fasciculus of medulla

Changes for: kidney arcuate artery

Changes for: popliteal vein

Changes for: granular cell layer of dorsal cochlear nucleus

Changes for: pineal complex

Changes for: septal olfactory organ

Changes for: olfactory nerve

Changes for: cheek

Changes for: temporalis muscle

Changes for: extrastriate cortex

Changes for: aryepiglottic fold

Changes for: vestibular nerve

Changes for: collection of basal ganglia

Changes for: skeleton of digitopodium

Changes for: coccygeal nerve

Changes for: ciliary muscle

Changes for: muscle of iris

Changes for: nephron tubule basement membrane

Changes for: bronchus basement membrane

Changes for: central tegmental tract

Changes for: carotid body

Changes for: echolocation organ

Changes for: future common hepatic duct

Changes for: vestibulocochlear nerve

Changes for: abducens nerve

Changes for: oculomotor nerve

Changes for: chromaffin system

Changes for: rubrospinal tract

Changes for: spinal trigeminal tract of medulla

Changes for: solitary tract

Changes for: spino-olivary tract

Changes for: future hindbrain meninges

Changes for: vestibulocochlear nerve root

Changes for: longitudinal pontine fibers

Changes for: transverse pontine fibers

Changes for: lamina of septum pellucidum

Changes for: eponychium

Changes for: diagonal band of Broca

Changes for: medial lemniscus of medulla

Changes for: ventral amygdalofugal projection

Changes for: hilum of dentate nucleus

Changes for: set of lower jaw teeth

Changes for: tooth row

Changes for: bile duct epithelium

Changes for: extrahepatic bile duct epithelium

Changes for: telencephalic nucleus

Changes for: hindbrain nucleus

Changes for: intrahepatic bile duct epithelium

Changes for: esophagus skeletal muscle

Changes for: hepatic duct smooth muscle

Changes for: set of upper jaw teeth

Changes for: prepollex skeleton

Changes for: lateral corticospinal tract

Changes for: heart vasculature

Changes for: nursing stage

Changes for: basal part of pons

Changes for: temporal operculum

Changes for: intermediate hypothalamic region

Changes for: vestibulocerebellar tract

Changes for: anterior hypothalamic region

Changes for: ventral trigeminal tract

Changes for: gland

Changes for: limb segment

Changes for: dorsal side of post-anal tail

Changes for: ventral side of post-anal tail

Changes for: elastic tissue

Changes for: tunica intima

Changes for: basicranium

Changes for: thoracic skeleton

Changes for: subdivision of head

Changes for: Pacinian corpuscle

Changes for: recurrent laryngeal nerve

Changes for: neural tissue

Changes for: aggregate regional part of brain

Changes for: laryngeal vocal fold

Changes for: cell cluster organ

Changes for: intrahepatic bile duct

Changes for: extrahepatic bile duct

Changes for: vaginal venous plexus

Changes for: orbital operculum

Changes for: spermaceti organ

Changes for: paraganglion

Changes for: aorta tunica intima

Changes for: blood vessel elastic tissue

Changes for: border between sublaminar layers

Changes for: blood vessel layer

Changes for: mouth floor

Changes for: dentition

Changes for: pars superior ear

Changes for: articular system

Changes for: pars inferior ear

Changes for: skeletal tissue

Changes for: regional part of brain

Changes for: cartilaginous neurocranium

Changes for: tuber cinereum

Changes for: skeletal element

Changes for: metanephric juxtaglomerular apparatus

Changes for: dentary

Changes for: fused sacrum

Changes for: precentral operculum

Changes for: incisor region of dentition

Changes for: conceptus

Changes for: septum pellucidum

Changes for: cochlear nerve

Changes for: digestive syncytial vacuole

Changes for: cervical gland

Changes for: urinary bladder vasculature

Changes for: inner optic circle

Changes for: coccyx

Changes for: femoral vein

Changes for: cumulus oophorus

Changes for: placentome of cotyledonary placenta

Changes for: scrotum

Changes for: urethral gland

Changes for: brain gray matter

Changes for: prostate epithelial cord

Changes for: glandular acinus

Changes for: mesopodial skeleton

Changes for: pole of cerebral hemisphere

Changes for: interlobar vein

Changes for: ciliary stroma

Changes for: interlobar artery

Changes for: parietal operculum

Changes for: dentate gyrus polymorphic layer

Changes for: terminal nerve

Changes for: tectopontine tract

Changes for: tectospinal tract

Changes for: frontal operculum

Changes for: spinothalamic tract of medulla

Changes for: dorsal hypothalamic area

Changes for: medial lemniscus of pons

Changes for: anterior spinocerebellar tract

Changes for: central tegmental tract of pons

Changes for: decussation of trochlear nerve

Changes for: root of abducens nerve

Changes for: posterior hypothalamic region

Changes for: olivocochlear bundle

Changes for: vestibulospinal tract

Changes for: predorsal bundle

Changes for: olivocerebellar tract

Changes for: medial longitudinal fasciculus of medulla

Changes for: pyramidal decussation

Changes for: myometrium

Changes for: core of melon organ

Changes for: ampullary nerve

Changes for: bile canaliculus

  • Deleted
    • - bile canaliculus definition Fine tubular canals running between liver cells, throughout the parenchyma, usually occurring singly between each adjacent pair of cells, and forming a three-dimensional network of polyhedral meshes, with a single cell in each mesh[BTO]. A thin tube that collects bile secreted by hepatocytes. The bile canaliculi merge and form bile ductules, which eventually become common hepatic duct. Hepatocytes are polyhedral in shape, therefore having no set shape or design. They have surfaces facing the sinusoids, (called sinusoidal faces) and surfaces which contact other hepatocytes, (called lateral faces). Bile canaliculi are formed by grooves on some of the lateral faces of these hepatocytes. Microvilli are present in the canaliculi but are sparse. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Bile_canaliculus , database cross reference=BTO:0002841 }
    • - bile canaliculus editor note This class was created automatically from a combination of ontologies
  • Added
    • + bile canaliculus definition An intercellular channel that takes up bile from hepatocytes, transporting it to the bile ducts. { database cross reference=MP:0008991 }
    • + bile canaliculus function notes conducts the flow of bile countercurrent to the direction of portal blood flow and connects with the canal of Hering[doi:10.1002/cphy.c120027]
    • + bile canaliculus structure notes The bile canaliculi merge and form bile ductules, which eventually become common hepatic duct. Hepatocytes are polyhedral in shape, therefore having no set shape or design. They have surfaces facing the sinusoids, (called sinusoidal faces) and surfaces which contact other hepatocytes, (called lateral faces). Bile canaliculi are formed by grooves on some of the lateral faces of these hepatocytes. Microvilli are present in the canaliculi but are sparse. [WP]

Changes for: ovarian medulla

  • Deleted
    • - ovarian medulla definition The medulla of ovary (or Zona vasculosa of Waldeyer) is a highly vascular stroma in the center of the ovary. It forms from embryonic mesenchyme and contains blood vessels, lymphatic vessels, and nerves. This stroma forms the tissue of the hilum by which the ovarian ligament is attached, and through which the blood vessels enter: it does not contain any ovarian follicles. { database cross reference=http://en.wikipedia.org/wiki/Medulla_of_ovary }
  • Added
    • + ovarian medulla definition highly vascular stroma found in the center of the ovary that forms from embryonic mesenchyme and contains blood vessels, lymphatic vessels, and nerves; this stroma forms the tissue of the hilum by which the ovarian ligament is attached, and through which the blood vessels enter; it does not contain any ovarian follicles. { database cross reference=MGI:anna }

Changes for: ovarian cortex

  • Deleted
  • Added
    • + ovarian cortex SubClassOf part of some ovary stroma
    • + ovarian cortex definition the layer of the ovarian stroma lying immediately beneath the tunica albuginea, composed of connective tissue cells and fibers, among which are scattered primary and secondary (antral) follicles in various stages of development; the cortex varies in thickness according to the age of the individual, becoming thinner with advancing years; included in the follicles are the cumulus oophorus, membrana granulosa (and the granulosa cells inside it), corona radiata, zona pellucida, and primary oocyte; the zona pellucida, theca of follicle, antrum and liquor folliculi are also contained in the follicle; also in the cortex is the corpus luteum derived from the follicles. { database cross reference=MGI:anna }

Changes for: portal triad

Changes for: pubis

Changes for: ischium

Changes for: ilium

Changes for: neurovascular bundle

Changes for: innominate bone

Changes for: pelvic girdle region

Changes for: extrahepatic duct

Changes for: dorsal trigeminal tract

Changes for: spinothalamic tract of pons

Changes for: dorsal longitudinal fasciculus of pons

Changes for: medial longitudinal fasciculus of pons

Changes for: baleen feeding system

Changes for: auditory hillocks, pharyngeal arch 2 derived

Changes for: auditory hillocks, pharyngeal arch 1 derived

Changes for: branch of Y-shaped fibrocartilage skeleton of ventral pouch

Changes for: interlobular bile duct

Changes for: lunge feeding vibrissa

Changes for: subepicardial layer of epicardium

Changes for: intestinal villus

  • Deleted
    • - intestinal villus editor note in mammals, villi are (largely?) absent from the large intestine, so we treat this as equivalent to small intestinal villus. small/large subdivision may not make sense for all speciesi for which this is present (see ZFA). Note that VHOG quotes ISBN:978-0030223693 as suggesting there are some villi in the large intestine
  • Added

Changes for: connective tissue of prostate gland

Changes for: sensory root of trigeminal nerve

Changes for: renal lobule

Changes for: superior branch of oculomotor nerve

Changes for: inferior branch of oculomotor nerve

Changes for: gland of ocular region

Changes for: bony part of hard palate

Changes for: vomeronasal nerve

Changes for: right atrium endocardium

Changes for: branchial basket

Changes for: apex of cochlea

Changes for: spinal trigeminal tract of pons

Changes for: acropodial skeleton

Changes for: metapodial skeleton

Changes for: reticular formation

Changes for: hyponychium

Changes for: primitive nephron

Changes for: olfactory pathway

Changes for: choroid plexus of fourth ventricle

Changes for: biliary system

Changes for: ventrum

Changes for: entire embryonic mesenchyme

Changes for: clavicle bone

Changes for: nuchal plate series

Changes for: dorsal horn of spinal cord

Changes for: ventral horn of spinal cord

Changes for: dorsal funiculus of spinal cord

Changes for: olfactory tract

Changes for: vertebral column

Changes for: pupillary membrane

Changes for: dorsum

Changes for: laterodorsal tegmental nucleus

Changes for: glossopharyngeal nerve root

Changes for: dorsal ventricular ridge of pallium

Changes for: compound cell cluster organ

Changes for: vasculature of eye

Changes for: subfornical organ

Changes for: biliary tree

Changes for: portal lobule

Changes for: fontanelle

Changes for: cell group

Changes for: caudal-fin organ

Changes for: branchiostegal ray series

Changes for: epibranchial series

Changes for: ceratobranchial series

Changes for: commissure of telencephalon

Changes for: ventral funiculus of spinal cord

Changes for: ciliary processes

Changes for: gray matter of hindbrain

Changes for: endocardium

Changes for: white matter of hindbrain

Changes for: musculature

Changes for: central nervous system

Changes for: gall bladder

Changes for: thymus lobule

Changes for: chordate pharynx

Changes for: nail plate

Changes for: neural tube

Changes for: liver

  • Deleted
    • - liver comment Function notes: secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
  • Added
    • + liver function notes secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].

Changes for: pair of nares

Changes for: mushroom body

Changes for: hypopharynx

Changes for: neuromuscular junction

Changes for: sheath of Schwann

Changes for: endocardium of ventricle

Changes for: epidermis suprabasal layer

Changes for: meckelian bone

Changes for: ventral pancreatic duct

Changes for: pedicle of vertebra

Changes for: velar vocal fold

Changes for: genu of facial nerve

Changes for: cerebellopontine angle

Changes for: feather vane

Changes for: aboral subdivision of organism

Changes for: oral subdivision of organism

Changes for: lymphocyte domain

Changes for: enteric nerve

Changes for: Peyer’s patch T cell area

Changes for: dorsal nerve of clitoris

Changes for: dorsal nerve of penis

Changes for: orbitosphenoid

Changes for: cerebellar peduncular complex

Changes for: epicranium

Changes for: helix

Changes for: glottis

Changes for: trabecular bone tissue

Changes for: bone tissue

Changes for: pulmonary lobule

Changes for: gustatory gland

  • Added
    • + gustatory gland function notes posterior deep lingual glands produce lingual lipase, which hydrolyzes triacylglycerols in the acidic gastric lumen, the first step in the digestion of dietary fat (Hamosh & Scow, 1973; Hamosh & Burns, 1977). In view of their close proximity to the lingual lymphatic tissues, the glands were also thought to be involved in antimicrobial action and local immune response (Nair & Schroeder, 1983)[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667924/]
    • + gustatory gland has exact synonym posterior deep lingual gland { database cross reference=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667924 }
    • + gustatory gland structure notes a group of tubulo-acinar serous glands located beneath the circumvallate and foliate papillae of the tongue and their ducts open into the trough at the base of the papillae. The saliva from posterior deep lingual glands is known to modulate the microenvironment at taste reception sites, and affect chemoreception (Gurkan & Bradley, 1988) and it is an important source of growth factors for taste receptor cells (Morris-Wiman et al. 2000)[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667924/]

Changes for: pyramidal layer of CA2

Changes for: white matter lamina of cerebellum

Changes for: white matter lamina of cerebral hemisphere

Changes for: superficial cervical fascia

Changes for: synarcual region of vertebral column

Changes for: layer of hippocampal field

Changes for: integumental system

Changes for: hepatobiliary system

Changes for: pituitary stalk

Changes for: lateral hypothalamic area

Changes for: palatine gland

Changes for: endometrial gland

Changes for: lymphoid system

Changes for: lamina of omasum

Changes for: iris epithelium

Changes for: zygomatic arch

Changes for: layer of sclera

Changes for: axilla

Changes for: placental labyrinth vasculature

Changes for: ventral surface of penis

Changes for: operculum of brain

Changes for: hyoid apparatus

Changes for: midbrain basal plate

Changes for: Hassall’s corpuscle

Changes for: row of feathers

Changes for: merocrine gland

Changes for: aqueous drainage system

Changes for: Bruch’s membrane

Changes for: caudal principal ray set

Changes for: photoreceptor inner segment layer

Changes for: photoreceptor outer segment layer

Changes for: digestive tract epithelium

Changes for: laryngeal apparatus

Changes for: subdivision of tube

Changes for: meninx

Changes for: pia mater

Changes for: atrioventricular canal endocardium

Changes for: dura mater

Changes for: hyolaryngeal complex

Changes for: epithelial tube

Changes for: maxilla

Changes for: bile duct

Changes for: astragalus-calcaneum unit

Changes for: layer of neocortex

Changes for: layer of hippocampus

Changes for: layer of dentate gyrus

Changes for: myocardium

Changes for: hippocampus fimbria

Changes for: white matter of cerebellum

Changes for: costal plate of carapace

Changes for: hyoplastron

Changes for: hypothenar eminence

Changes for: thenar eminence

Changes for: withers

Changes for: aortic system

Changes for: nutrient foramen artery

Changes for: bulb of aorta

Changes for: sinotubular junction

Changes for: nutrient foramen vein

Changes for: region of neural crest

Changes for: rumen papilla

Changes for: collection of hairs

Changes for: neural tube lumen

Changes for: pancreatic lobule

Changes for: infraorbital series

Changes for: stria vascularis vasculature

Changes for: pharyngeal vasculature

Changes for: auditory hillocks

Changes for: segmental spinal nerve

Changes for: gall bladder primordium

Changes for: midline column

Changes for: scapula cartilage element

Changes for: scapula pre-cartilage condensation

Changes for: hepatic duct

Changes for: late embryonic stage

Changes for: osseus cochlea

Changes for: hilum of inferior olivary complex

Changes for: olfactory bulb layer

Changes for: nuclear complex of neuraxis

Changes for: tunica intima of vein

Changes for: superior colliculus superficial gray layer

Changes for: accessory nerve fiber bundle

Changes for: posterior column of fornix

Changes for: vagal nerve fiber bundle

Changes for: aqueous vein

Changes for: mucosa of gallbladder

Changes for: canal of Schlemm

Changes for: Weberian ossicle set

Changes for: periorbital region

Changes for: neural tube marginal layer

Changes for: biliary ductule

Changes for: subungual region

Changes for: anatomical conduit

Changes for: myocardial layer

Changes for: myocardium trabecular layer

Changes for: myocardial compact layer

Changes for: stroma of bone marrow

Changes for: external acoustic meatus osseus part

Changes for: renal glomerulus vasculature

Changes for: mammary gland cord

Changes for: prostate glandular acinus

  • Deleted
    • - prostate glandular acinus comment Concurrent with branching morphogenesis, the solid cords of epithelium formed by budding arborize and differentiate postnatally into glandular acin. The basic prostate architecture is established by puberty and acquires secretory function thereafter[PMID:18977204]
  • Added
    • + prostate glandular acinus development notes Concurrent with branching morphogenesis, the solid cords of epithelium formed by budding arborize and differentiate postnatally into glandular acin. The basic prostate architecture is established by puberty and acquires secretory function thereafter[PMID:18977204]
    • + prostate glandular acinus editor note the muscle layer is implicitly treated as outside the acinus

Changes for: medulla reticulospinal tract

Changes for: pons reticulospinal tract

Changes for: cerebellar layer

Changes for: branchiomeric muscle

Changes for: iris smooth muscle

Changes for: muscular coat of vas deferens

Changes for: postcranial axial skeleton

Changes for: skin of body

Changes for: stratum lucidum of epidermis

Changes for: levator veli palatini

Changes for: tensor veli palatini

Changes for: external ear margin

Changes for: labial commissure

Changes for: nose anterior margin

Changes for: nose vertex

Changes for: tip of snout

Changes for: tip of external ear

Changes for: root of nail

Changes for: medial column

Changes for: anterior lingual gland

Changes for: nucleus lateralis valvulae

Changes for: ocular refractive media

Changes for: stratum granulosum of epidermis

Changes for: adrenal gland capsule

  • Deleted
    • - adrenal gland capsule definition the thick capsule of dense irregular connective tissue that surrounds each adrenal gland and contains scattered elastic fibers; the capsule contains a rich plexus of blood vessels (mainly small arteries) and numerous nerve fibers; some blood vessels and nerves enter the substance of the gland in the trabeculae that extend inward from the capsule and then leave the trabeculae to enter the cortex. { database cross reference=MGI:anna }
  • Added
    • + adrenal gland capsule definition the thick capsule of dense irregular connective tissue that surrounds each adrenal gland and contains scattered elastic fibers; the capsule contains a rich plexus of blood vessels (mainly small arteries) and numerous nerve fibers; some blood vessels and nerves enter the substance of the gland in the trabeculae that extend inward from the capsule and then leave the trabeculae to enter the cortex. { database cross reference=MP:0013565 }

Changes for: areola

Changes for: substantia nigra

Changes for: cerebellum

Changes for: stratum basale of epidermis

Changes for: skeleton

Changes for: stratum corneum of epidermis

Changes for: gray matter

Changes for: enteric nervous system

Changes for: enamel knot

Changes for: thoracic rib cage

Changes for: pyloric gastric gland

Changes for: stomach smooth muscle inner oblique layer

Changes for: stomach muscularis externa

Changes for: cardiac gastric gland

Changes for: vesical venous plexus

Changes for: skeleton of lower jaw

Changes for: skeleton of upper jaw

Changes for: hard palate

Changes for: splanchnocranium

Changes for: vault of skull

Changes for: ventral part of telencephalon

Changes for: lung vasculature

Changes for: blastopore

Changes for: sexually immature stage

Changes for: membranous layer

Changes for: pair of lungs

Changes for: embryonic head

Changes for: ovarian fossa

Changes for: neural complex of Weberian apparatus

Changes for: pharyngeal slit

Changes for: pharyngeal arch system

Changes for: liver bud

Changes for: intervening zone

Changes for: epaxial musclulature

Changes for: hypaxial musclulature

Changes for: breast

Changes for: musculature of larynx

Changes for: tongue musculature

Changes for: tendon sheath

Changes for: set of muscles of vertebral column

Changes for: hippocampus stratum lacunosum moleculare

Changes for: trigeminal nuclear complex

Changes for: hippocampus stratum lucidum

Changes for: accessory olfactory bulb glomerular layer

Changes for: hippocampus alveus

Changes for: layer of synovial tissue

Changes for: atlanto-occipital joint

Changes for: muscle tissue of prostate

Changes for: obsolete left side of organism

Changes for: obsolete right side of organism

Changes for: subdivision of vertebral column

Changes for: internal arcuate fiber bundle

Changes for: dorsal external arcuate fiber bundle

Changes for: uncinate fasciculus

Changes for: periderm

  • Deleted
    • - periderm comment Taxon notes: In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo’s physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP]
  • Added
    • + periderm taxon notes In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo’s physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP]

Changes for: ventricular zone

Changes for: pre-Botzinger complex

Changes for: ciliary marginal zone

Changes for: neural plate

Changes for: otic region

Changes for: sphenoid region

Changes for: olfactory region

Changes for: suspensorium

Changes for: Weberian apparatus

Changes for: vasculature of brain

Changes for: obsolete arthropod hypopharynx

Changes for: skull

Changes for: body of fornix

Changes for: dentate gyrus molecular layer

Changes for: spinal cord lateral horn

Changes for: facial nerve root

Changes for: hypoglossal nerve root

Changes for: trigeminal nerve root

Changes for: ganglion

Changes for: parasympathetic nervous system

Changes for: zone of skin

Changes for: vermilion

Changes for: upper vermilion

Changes for: lower vermilion

Changes for: tube

Changes for: pituitary gland

Changes for: islet of Langerhans

Changes for: blood vessel external elastic membrane

Changes for: hilar portion of hepatic duct

Changes for: pharyngeal arch 7 skeleton

Changes for: pharyngeal arch 3 skeleton

Changes for: pharyngeal arch 6 skeleton

Changes for: pharyngeal arch 4 skeleton

Changes for: pharyngeal arch 5 skeleton

Changes for: melon organ

Changes for: membrane organ

Changes for: dorsal scute series

Changes for: abdominal scute series

Changes for: ampullary organ

  • Added
    • + ampullary organ has broad synonym ampullary receptor
    • + ampullary organ has exact synonym ampullary electroreceptor
    • + ampullary organ taxon notes The presence of these organs varies greatly among anamniotes, but an out-group analysis of their distribution in adult anamniotes suggests that they were present in primitive vertebrates and retained in living lampreys, cartilaginous fishes, lobe-finned fishes and basal ray-finned fishes (bichirs, sturgeons and paddlefishes). Ampullary organs do not occur in gars and bowfins, two of the three groups of neopterygian fishes, nor are they found in most teleost fishes, but they do appear to have re-evolved at least twice (and more likely three or more times) in five groups of teleosts (Northcutt, 1997).[http://icb.oxfordjournals.org/content/42/4/743]

Changes for: substratum of layer of retina

Changes for: fornix of brain

Changes for: organ part

Changes for: lateral line nerve

Changes for: anatomical structure

Changes for: organ

Changes for: individual digit of digitopodial skeleton

Changes for: subendocardium layer

Changes for: heart layer

Changes for: eye trabecular meshwork

Changes for: axial skeleton plus cranial skeleton

Changes for: inferior nasal concha

Changes for: occipital region

Changes for: post-hyoid pharyngeal arch skeleton

Changes for: hyoid arch skeleton

Changes for: mineralized skeletal tissue

Changes for: musculature of body

Changes for: epiglottis

Changes for: red bone marrow

Changes for: reticuloendothelial system

Changes for: preputial gland

Changes for: throat

Changes for: limbic system

Changes for: yellow bone marrow

Changes for: septum of telencephalon

Changes for: tunica intima of artery

Changes for: mucous gland

Changes for: scalp

Changes for: sympathetic trunk

Changes for: tunica adventitia of blood vessel

Changes for: mineralized bone tissue

Changes for: cellular bone tissue

Changes for: acellular bone tissue

  • Deleted
    • - acellular bone tissue provenance notes This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon

Changes for: connecting stalk vasculature

Changes for: fascia of Camper

Changes for: pelvic girdle skeleton

Changes for: major vestibular gland

Changes for: anatomical system

Changes for: anatomical group

Changes for: anatomical cluster

Changes for: hyaloid vascular plexus

Changes for: intrahepatic part of hepatic duct

Changes for: extrahepatic part of hepatic duct

Changes for: cerebellum vasculature

Changes for: mammillary axonal complex

Changes for: meningeal cluster

Changes for: valvula cerebelli

Changes for: visceromotor column

Changes for: lymphatic part of lymphoid system

Changes for: non-lymphatic part of lymphoid system

Changes for: statolith

Changes for: quadrate bone

Changes for: right lung alveolar system

Changes for: left lung alveolar system

Changes for: alveolar system

Changes for: ansa cervicalis

Changes for: cerebral hemisphere gray matter

Changes for: hippocampus molecular layer

  • Deleted
  • Added
    • + hippocampus molecular layer definition A cytoarchitectural region of the hippocampus consisting of a composite of the two outermost layers of the hippocampus, the Stratum lacunosum-moleculare and the Stratum radiatum (Carpenter-83). In CA3, there is an additional layer lying above the pyramidal cell layer, the stratum lucidum, which is also included here. { database cross reference=NIFSTD:birnlex_1211 }

Changes for: gill raker row

Changes for: hippocampus stratum oriens

  • Deleted
  • Added
    • + hippocampus stratum oriens definition Layer that is part of the CA fields of the hippocampus consisting of a narrow relatively cell free layer located deep to the pyramidal cell layer extending through areas CA1, CA2 and CA3. (adapted from Paxinos The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995) { database cross reference=NIFSTD:birnlex_4113 }

Changes for: epibranchial arborescent organ

Changes for: spermatic cord

Changes for: photoreceptor array

Changes for: olfactory glomerulus

Changes for: caudate-putamen

Changes for: vasculature of liver

Changes for: nasal skeleton

Changes for: mammary bud

Changes for: mesonephric juxtaglomerular apparatus

Changes for: mammary duct terminal end bud

Changes for: mammary placode

Changes for: cerebellar glomerulus

Changes for: pilosebaceous unit

Changes for: mammary gland luminal epithelium

Changes for: prostate luminal epithelium

Changes for: endometrium luminal epithelium

Changes for: ureter subluminal urothelium

Changes for: ureter luminal urothelium

Changes for: piston cartilage

Changes for: inter limb-segment region

Changes for: deep layer of superior colliculus

Changes for: superficial layer of superior colliculus

Changes for: intermediate layer of superior colliculus

Changes for: deep white layer of superior colliculus

Changes for: arthropod optic lobe

Changes for: cephalopod optic lobe

Changes for: cranial nerve II

Changes for: deep gray layer of superior colliculus

Changes for: cornea

  • Deleted
    • - cornea taxon notes Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman’s membrane in mammals
  • Added

Changes for: middle gray layer of superior colliculus

Changes for: middle white layer of superior colliculus

Changes for: white matter of superior colliculus

Changes for: gray matter layer of superior colliculus

Changes for: layer of superior colliculus

Changes for: zonal layer of superior colliculus

Changes for: superficial white layer of superior colliculus

Changes for: cerebral cortex

Changes for: alisphenoid bone

Changes for: autopodial skeleton

Changes for: anal fin distal radial element

Changes for: organismal segment

Report for properties

ObjectProperty objects lost from source: 6

ObjectProperty objects new in target: 2

New ObjectProperty : aboral_to

New ObjectProperty : oral_to

Changed ObjectProperty objects: 1

Changes for: contains process

March 15, 2015 |

Comments Section

Feel free to comment on the post but keep it clean and on topic.

comments powered by Disqus

logo Uberon is an integrated cross-species ontology covering anatomical structures in animals. See the about page for more info.

github.com/obophenotype/uberon
 

Google+