2014-05-03 release

Digits
2014-05-03 release image

Ontology Diff Report

  • limb/fin: digits issue #420
    • Addition of new classes to represent the extended concept of digit.
    • We include two pairs of classes:
      1. the ‘digitopodial skeleton’ ie proximo-distal series of phalanges plus a metapodial
      1. 1+soft tissue
    • Note the 2nd concept typically does not correspond to a distinct subdivision of the
    • whole hand or foot (e.g. in humans this is continuous in the metapodial region)
  • NTs for dorsal and ventral optic cup. #419
  • NT: skin scent gland. NT: interdigital gland

Original Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-04-30/uberon.owl

New Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-05-03/uberon.owl

Report for classes

Class objects lost from source: 0

Class objects new in target: 58

New Class : digit 3 digitopodial skeleton

New Class : digit 4 digitopodial skeleton

New Class : digit 5 digitopodial skeleton

New Class : digit 2 digitopodial skeleton

New Class : digit 1 digitopodial skeleton

New Class : manual digit 5 plus metapodial segment

New Class : manual digit 4 plus metapodial segment

New Class : manual digit 3 plus metapodial segment

New Class : manual digit 2 plus metapodial segment

New Class : pedal digit 5 plus metapodial segment

New Class : pedal digit 4 plus metapodial segment

New Class : pedal digit 1 plus metapodial segment

New Class : pedal digit 3 plus metapodial segment

New Class : pedal digit 2 plus metapodial segment

New Class : pedal digit plus metapodial segment

New Class : manual digit 1 plus metapodial segment

New Class : manual minor digit (Aves) digitopodial skeleton

New Class : manual major digit (Aves) digitopodial skeleton

New Class : alular digit digitopodial skeleton

New Class : pedal digit 7 digitopodial skeleton

New Class : pedal digit 8 digitopodial skeleton

New Class : ventral part of optic cup

New Class : interdigital gland

New Class : dorsal part of optic cup

New Class : skin scent gland

New Class : digit 1 plus metapodial segment

New Class : digit 2 plus metapodial segment

New Class : digit 3 plus metapodial segment

New Class : digit 5 plus metapodial segment

New Class : digit 4 plus metapodial segment

New Class : digit digitopodial skeleton

New Class : pedal digit digitopodial skeleton

New Class : manual digit 1 digitopodial skeleton

New Class : manual digit 5 digitopodial skeleton

New Class : manual digit 4 digitopodial skeleton

New Class : manual digit 3 digitopodial skeleton

New Class : manual digit 2 digitopodial skeleton

New Class : pedal digit 4 digitopodial skeleton

New Class : pedal digit 3 digitopodial skeleton

New Class : pedal digit 2 digitopodial skeleton

New Class : pedal digit 1 digitopodial skeleton

New Class : pedal digit 5 digitopodial skeleton

New Class : manual digit 7 plus metapodial segment

New Class : manual digit 6 plus metapodial segment

New Class : pedal digit 6 plus metapodial segment

New Class : manual digit 8 plus metapodial segment

New Class : pedal digit 6 digitopodial skeleton

New Class : manual digit 6 digitopodial skeleton

New Class : manual digit 8 digitopodial skeleton

New Class : manual digit 7 digitopodial skeleton

New Class : alular digit plus metapodial segment

New Class : manual minor digit (Aves) plus metapodial segment

New Class : manual major digit (Aves) plus metapodial segment

New Class : digit plus metapodial segment

New Class : pedal digit 7 plus metapodial segment

New Class : pedal digit 8 plus metapodial segment

New Class : manual digit plus metapodial segment

New Class : manual digit digitopodial skeleton

Changed Class objects: 159

Changes for: jaw depressor muscle

Changes for: substantia nigra pars reticulata

Changes for: thyroid follicle epithelium

Changes for: tunica fibrosa of eyeball

Changes for: infundibular organ

Changes for: uvea

Changes for: stapes bone

  • Deleted
    • - stapes bone definition The stapes or stirrup is the stirrup-shaped small bone or ossicle in the middle ear which is attached to the incus laterally and to the fenestra ovalis, the ‘oval window’ medially. The oval window is adjacent to the vestibule of the inner ear. The stapes is the smallest and lightest bone in the human body. The stapes transmits the sound vibrations from the incus to the membrane of the inner ear inside the fenestra ovalis. The stapes is also stabilized by the stapedius muscle, which is innervated by the facial nerve. In non-mammalian vertebrates, the bone homologous to the stapes is usually called the columella; however, in reptiles, either term may be used[WP,unvetted]. { database cross reference=http://dx.doi.org//10.1111/j.1469-7580.2005.00441.x , database cross reference=http://en.wikipedia.org/wiki/Stapes }
  • Added
    • + stapes bone definition The stapes or stirrup is the stirrup-shaped small bone or ossicle in the middle ear which is attached to the incus laterally and to the fenestra ovalis, the ‘oval window’ medially. The oval window is adjacent to the vestibule of the inner ear. The stapes is the smallest and lightest bone in the human body. The stapes transmits the sound vibrations from the incus to the membrane of the inner ear inside the fenestra ovalis. The stapes is also stabilized by the stapedius muscle, which is innervated by the facial nerve. In non-mammalian vertebrates, the bone homologous to the stapes is usually called the columella; however, in reptiles, either term may be used[WP,unvetted]. { database cross reference=http://dx.doi.org/10.1111/j.1469-7580.2005.00441.x , database cross reference=http://en.wikipedia.org/wiki/Stapes }

Changes for: nasal fin

  • Deleted
    • - nasal fin definition The nasal fin is an epithelial seam that develops by fusion between the epithelial linings of the medial and lateral nasal swellings. Shortly after its formation the nasal fin regresses and is replaced by mesenchyme, with exception of its most posterior portion which remains as the bucconasal membrane. { database cross reference=DOI:10.1002/aja.1001500308 }
  • Added

Changes for: pedal digit 8

Changes for: pedal digit 7

Changes for: prehallux

Changes for: digit

Changes for: distal phalanx of digit 2

Changes for: distal phalanx of digit 3

Changes for: distal phalanx of digit 4

Changes for: distal phalanx of digit 5

Changes for: middle phalanx of digit 2

Changes for: middle phalanx of digit 3

Changes for: phalanx of pes

Changes for: distal phalanx of digit 1

Changes for: phalanx of manus

Changes for: middle phalanx of digit 5

Changes for: middle phalanx of digit 4

Changes for: pedal digit

Changes for: manual digit 1

Changes for: manual digit 4

Changes for: manual digit 5

Changes for: manual digit 3

Changes for: manual digit 2

Changes for: manual digit 1 phalanx

Changes for: pedal digit 5

Changes for: manual digit 2 phalanx

Changes for: manual digit 3 phalanx

Changes for: manual digit 4 phalanx

Changes for: manual digit 5 phalanx

Changes for: pedal digit 2

Changes for: pedal digit 1

Changes for: pedal digit 4

Changes for: pedal digit 3

Changes for: neurohypophyseal duct

Changes for: coronal organ

Changes for: cupular organ

  • Deleted
    • - cupular organ definition Epithelial sense organ containing the cupula housing a gelatinous material elongated from the basement of the organ toward the atrial cavity. The basement of the cupular organ consists of two cell types: sensory cells and support cell { database cross reference=DOI:10.2108/zsj.27.842 }
  • Added

Changes for: pedal digit 3 phalanx

Changes for: pedal digit 1 phalanx

Changes for: pedal digit 2 phalanx

Changes for: neuromere

  • Deleted
    • - neuromere definition A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres). { database cross reference=DOI:10.1016/j.tins.2013.06.004 }
  • Added

Changes for: pectoral appendage

Changes for: manual major digit (Aves)

Changes for: alular digit

Changes for: manual minor digit (Aves)

Changes for: pelvic appendage

Changes for: pedal digit 4 phalanx endochondral element

Changes for: pedal digit 5 phalanx endochondral element

Changes for: pedal digit 2 phalanx endochondral element

Changes for: pedal digit 3 phalanx endochondral element

Changes for: pedal digit phalanx endochondral element

Changes for: pedal digit 1 phalanx endochondral element

Changes for: manual digit phalanx endochondral element

Changes for: manual digit 1 phalanx endochondral element

Changes for: manual digit 2 phalanx endochondral element

Changes for: manual digit 3 phalanx endochondral element

Changes for: manual digit 4 phalanx endochondral element

Changes for: manual digit 5 phalanx endochondral element

Changes for: entotympanic bone

Changes for: red pulp of spleen

Changes for: pyloric sphincter

Changes for: proximal phalanx of manus

Changes for: levator cloacae

Changes for: transverse cloacal muscle

Changes for: atrioventricular valve

Changes for: medulla of thymus

Changes for: cortex of thymus

Changes for: anterolateral ligament of knee

Changes for: velar vocal fold

Changes for: ventral pallium

Changes for: bone marrow cavity

Changes for: papillary muscle of heart

Changes for: amnioserosa

Changes for: skin gland

Changes for: proximal phalanx of digit 5

Changes for: proximal phalanx of digit 3

Changes for: proximal phalanx of digit 4

Changes for: proximal phalanx of digit 2

Changes for: proximal phalanx of digit 1

Changes for: scleral mesenchyme

Changes for: manual digit

Changes for: exocrine gland

Changes for: somite

Changes for: distal segment of digit

  • Deleted
    • - distal segment of digit definition A segment of a digit containing the distal phalanx, and overlapping the distal interphalangeal joint[CJM]. The digit tip is derived from multiple and distinct embryonic origins, and includes the distal bone with associated marrow cavity and haematopoietic cells, ventral (flexor) and dorsal (extensor) tendons, sweat glands with myoepithelial and luminal secreting cells and associated neurons for innervation, dermis with resident melanocytes and dendritic cells, mesenchyme with resident fibroblasts, skin epidermis with hair follicles, a nail organ composed of six specific parts (the root, nail bed, nail plate, eponychium (cuticle), perionychium and hyponychium). { database cross reference=http://dx.doi.org//10.1038/nature10346 }
  • Added
    • + distal segment of digit definition A segment of a digit containing the distal phalanx, and overlapping the distal interphalangeal joint[CJM]. The digit tip is derived from multiple and distinct embryonic origins, and includes the distal bone with associated marrow cavity and haematopoietic cells, ventral (flexor) and dorsal (extensor) tendons, sweat glands with myoepithelial and luminal secreting cells and associated neurons for innervation, dermis with resident melanocytes and dendritic cells, mesenchyme with resident fibroblasts, skin epidermis with hair follicles, a nail organ composed of six specific parts (the root, nail bed, nail plate, eponychium (cuticle), perionychium and hyponychium). { database cross reference=http://dx.doi.org/10.1038/nature10346 }

Changes for: distal segment of manual digit

Changes for: distal segment of pedal digit

Changes for: middle phalanx of manus

Changes for: distal phalanx of manus

Changes for: pedal digit 4 phalanx

Changes for: pedal digit 5 phalanx

Changes for: proximal phalanx of pes

Changes for: distal phalanx of pes

Changes for: middle phalanx of pes

Changes for: embryonic intraretinal space

Changes for: stapes pre-cartilage condensation

Changes for: head kidney

Changes for: pedal digit bone

Changes for: manual digit bone

Changes for: cardiac ventricle

Changes for: phalanx

Changes for: proximal phalanx of manual digit 3

Changes for: proximal phalanx of manual digit 2

Changes for: middle phalanx of pedal digit 2

Changes for: middle phalanx of pedal digit 3

Changes for: middle phalanx of pedal digit 4

Changes for: middle phalanx of pedal digit 5

Changes for: middle phalanx of manual digit 2

Changes for: middle phalanx of manual digit 3

Changes for: middle phalanx of manual digit 4

Changes for: middle phalanx of manual digit 5

Changes for: distal phalanx of pedal digit 5

Changes for: distal phalanx of pedal digit 4

Changes for: distal phalanx of pedal digit 3

Changes for: distal phalanx of pedal digit 1

Changes for: distal phalanx of pedal digit 2

Changes for: distal phalanx of manual digit 4

Changes for: distal phalanx of manual digit 5

Changes for: distal phalanx of manual digit 2

Changes for: distal phalanx of manual digit 3

Changes for: proximal phalanx of pedal digit 3

Changes for: proximal phalanx of pedal digit 2

Changes for: proximal phalanx of pedal digit 1

Changes for: proximal phalanx of manual digit 5

Changes for: proximal phalanx of manual digit 1

Changes for: distal phalanx of manual digit 1

Changes for: proximal phalanx of pedal digit 5

Changes for: proximal phalanx of pedal digit 4

Changes for: proximal phalanx of manual digit 4

Changes for: Reichert’s membrane

  • Deleted
    • - Reichert’s membrane definition An nonvascular extraembryonic basement membrane that forms on the inner surface of the trophectoderm during placenta morphogenesis and is secreted by the distal parietal endoderm; required for the maternofetal exchange of nutrients and is important for the postgastrulation development[MP]. a thick multilayered basement membrane between the parietal endoderm cells and the trophoblast cells { database cross reference=DOI:10.1007/BF00184752 , database cross reference=MP:0003954 }
  • Added

Changes for: Reichert’s cartilage

Changes for: blood brain barrier

Changes for: pecten oculi

Changes for: digit 1

Changes for: digit 2

Changes for: digit 5

Changes for: digit 3

Changes for: digit 4

Changes for: pinhole eye

Changes for: cardiac neural crest

Changes for: limb outgrowth

Changes for: prepollex

Changes for: organism subdivision

Changes for: central tendon of diaphragm

  • Deleted
    • - central tendon of diaphragm homology notes In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm’s apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001399 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1016/j.resp.2006.06.003 }
  • Added

Changes for: pectoral appendage apical ectodermal ridge

  • Deleted
    • - pectoral appendage apical ectodermal ridge homology notes Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (…) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001064 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1111/j.1440-169X.2007.00942.x }
  • Added
    • + pectoral appendage apical ectodermal ridge homology notes Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (…) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001064 , ontology=VHOG , source=http://bgee.unil.ch/ , source=http://dx.doi.org/10.1111/j.1440-169X.2007.00942.x }

Changes for: pelvic appendage apical ectodermal ridge

  • Deleted
    • - pelvic appendage apical ectodermal ridge homology notes Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (…) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001066 , ontology=VHOG , source=http://bgee.unil.ch/ , source=DOI:10.1111/j.1440-169X.2007.00942.x }
  • Added
    • + pelvic appendage apical ectodermal ridge homology notes Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (…) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0001066 , ontology=VHOG , source=http://bgee.unil.ch/ , source=http://dx.doi.org/10.1111/j.1440-169X.2007.00942.x }

Changes for: optic fissure

Changes for: interrenal gland

Changes for: pedal digit 6

Changes for: manual digit 8

Changes for: manual digit 7

Changes for: manual digit 6

Changes for: anterior commissure

Changes for: median lingual swelling

Changes for: kidney interstitium

Report for properties

ObjectProperty objects lost from source: 0

ObjectProperty objects new in target: 0

Changed ObjectProperty objects: 0

May 3, 2014 |

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