2014-06-21 release

Various improvements to facial muscles and supporting skeletal structures from FEED project, plus assorted minor changes
2014-06-21 release image
  • Musculoskeletal
    • NTs: skin of lower lip, upper lip
    • NT: angle of oral opening
    • Adding a “human preferred” tag to zygomatic as syn for jugal. Issue #490
    • Started work on improving zygomatic muscles, using FEED. Issue #492, #491
    • Fixed incorrect WP def for iliopsoas, added part_of. Fixes #478 [Bgee:ann]
    • added has_parts for digit-plus-metapodial-segment-X classes. Fixes issue #484
    • NTs for ligaments of middle ear
  • Renal
    • relaxed taxon constraint for loop of henle (todo: investigate non-amniotes)
    • adding provenance links to GO kidney paper
  • Other
    • Started obsoleting cell parts, in prep for #489
    • aligned cervical sinus def with MP
    • part_of digestive system for baleen feeding system. Addresses #479 [Bgee:ann]

Ontology Diff Report

Original Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-06-15/uberon.owl

New Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-06-21/uberon.owl

Report for classes

Class objects lost from source: 1

Class objects new in target: 13

New Class : annular ligament of stapes

New Class : posterior incudal ligament

New Class : ligament of middle ear

New Class : lateral malleal ligament

New Class : malleal ligament

New Class : skin of upper lip

New Class : skin of lower lip

New Class : pars tensa of tympanic membrane

New Class : pars flaccida of tympanic membrane

New Class : anterior malleal ligament

New Class : superior malleal ligament

New Class : anterior process of malleus

New Class : angle of oral opening

Changed Class objects: 80

Changes for: manual digit 5 plus metapodial segment

Changes for: manual digit 4 plus metapodial segment

Changes for: manual digit 3 plus metapodial segment

Changes for: manual digit 2 plus metapodial segment

Changes for: pedal digit 5 plus metapodial segment

Changes for: pedal digit 4 plus metapodial segment

Changes for: pedal digit 1 plus metapodial segment

Changes for: pedal digit 3 plus metapodial segment

Changes for: pedal digit 2 plus metapodial segment

Changes for: pedal digit plus metapodial segment

Changes for: manual digit 1 plus metapodial segment

Changes for: olfactory epithelium

Changes for: iliopsoas

Changes for: temporal lobe

Changes for: lymphoid tissue

Changes for: nasal septum

Changes for: jugal bone

Changes for: periamygdaloid area

Changes for: septal organ of Masera

Changes for: stapedius muscle

Changes for: depressor labii inferioris

Changes for: stomach non-glandular epithelium

Changes for: tensor tympani

Changes for: entorhinal area

  • Added
    • + entorhinal area comment Taxon notes: In primates it is found on the medial surface of the temporal lobe, partially bounded ventrolaterally by the collateral sulcus in the human and by the rhinal sulcus in the macaque. It is subdivided on the basis of internal structure into eight parts in the human ( Insausti-2004 ),and seven parts in the macaque ( Paxinos-2009a ). In the rat and mouse it is divided into a lateral part of the entorhinal area and a medial part of the entorhinal area; the latter is further divided into dorsal and ventral zones to produce three subdivisions in the rodent ( Swanson-2004 )

Changes for: renal tubule

Changes for: pronephric glomerulus

Changes for: digestive syncytial vacuole

Changes for: parahippocampal gyrus

Changes for: outer medulla of kidney

Changes for: loop of Henle

Changes for: baleen feeding system

Changes for: Y-shaped fibrocartilage skeleton of ventral pouch

Changes for: neurogenic placode

  • Deleted
  • Added
    • + neurogenic placode taxon notes While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000) { source=NCBIBook:NBK53171 }

Changes for: geniculate placode

Changes for: petrosal placode

Changes for: nodosal placode

Changes for: Grueneberg ganglion

Changes for: zygomaticus muscle

Changes for: renal system

Changes for: obsolete cell body

Changes for: zygomatic arch

  • Deleted
    • - zygomatic arch definition The zygomatic arch or cheek bone is formed by the zygomatic process of temporal bone (a bone extending forward from the side of the skull, over the opening of the ear) and the temporal process of the zygomatic bone (the side of the cheekbone), the two being united by an oblique suture; the tendon of the Temporalis passes medial to the arch to gain insertion into the coronoid process of the mandible. The term zygomatic derives from the Latin zyosislymore meaning malar bone or cheekbone. The zygomatic arch is occasionally referred to as the zygoma, but this term usually refers to the zygomatic bone or occasionally the zygomatic process. The zygomatic process of the temporal arises by two roots: an anterior, directed inward in front of the mandibular fossa, where it expands to form the articular tubercle. a posterior, which runs backward above the external acoustic meatus and is continuous with the supramastoid crest. The upper border of the arch gives attachment to the temporal fascia; the lower border and medial surface give origin to the Masseter. The zygomatic arch is significant in evolutionary biology, as it is part of the structures derived from the ancestral single temporal fenestra of the synapsid ancestor of mammals. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Zygomatic_arch }
  • Added
    • + zygomatic arch comment Terminology notes: The zygomatic arch is occasionally referred to as the zygoma, but this term usually refers to the zygomatic bone or occasionally the zygomatic process. Structure notes: The zygomatic process of the temporal arises by two roots: an anterior, directed inward in front of the mandibular fossa, where it expands to form the articular tubercle. a posterior, which runs backward above the external acoustic meatus and is continuous with the supramastoid crest. The upper border of the arch gives attachment to the temporal fascia; the lower border and medial surface give origin to the Masseter. Taxon notes: The zygomatic arch is significant in evolutionary biology, as it is part of the structures derived from the ancestral single temporal fenestra of the synapsid ancestor of mammals.
    • + zygomatic arch definition The zygomatic arch or cheek bone is formed by the zygomatic process of temporal bone (a bone extending forward from the side of the skull, over the opening of the ear) and the temporal process of the zygomatic bone (the side of the cheekbone), the two being united by an oblique suture; the tendon of the Temporalis passes medial to the arch to gain insertion into the coronoid process of the mandible. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Zygomatic_arch }

Changes for: rumen

  • Deleted
    • - rumen definition The first stomach of ruminants. It lies on the left side of the body, occupying the whole of the left side of the abdomen and even stretching across the median plane of the body to the right side. It is capacious, divided into an upper and a lower sac, each of which has a blind sac at its posterior extremity. The rumen is lined by mucous membrane containing no digestive glands, but mucus-secreting glands are present in large numbers. Coarse, partially chewed food is stored and churned in the rumen until the animal finds circumstances convenient for rumination. When this occurs, little balls of food are regurgitated through the esophagus into the mouth, and are subjected to a second more thorough mastication, swallowed, and passed on into other parts of the compound stomach. (From Black’s Veterinary Dictionary, 17th ed). { database cross reference=http://en.wikipedia.org/wiki/Rumen , database cross reference=MESH:A13.869.804 }
    • - rumen structure notes There is no muscularis mucosae in the rumen
  • Added
    • + rumen comment Function notes: Coarse, partially chewed food is stored and churned in the rumen until the animal finds circumstances convenient for rumination. When this occurs, little balls of food are regurgitated through the esophagus into the mouth, and are subjected to a second more thorough mastication, swallowed, and passed on into other parts of the compound stomach. (From Black’s Veterinary Dictionary, 17th ed)
    • + rumen definition The first compartment of the ruminant stomach. It lies on the left side of the body, occupying the whole of the left side of the abdomen and even stretching across the median plane of the body to the right side. It is capacious, divided into an upper and a lower sac, each of which has a blind sac at its posterior extremity. { database cross reference=http://en.wikipedia.org/wiki/Rumen , database cross reference=MESH:A13.869.804 }
    • + rumen structure notes There is no muscularis mucosae in the rumen. The rumen is lined by mucous membrane containing no digestive glands, but mucus-secreting glands are present in large numbers

Changes for: cervical sinus of His

Changes for: mesonephric capsule

Changes for: muscle of auditory ossicle

Changes for: zygomaticus minor muscle

Changes for: zygomaticus major muscle

Changes for: mentalis

  • Deleted
    • - mentalis definition The Mentalis is a paired central muscle of the lower lip, situated at the tip of the chin. It raises and pushes up the lower lip, causing wrinkling of the chin, as in doubt or displeasure. It is ometimes referred to as the ‘pouting muscle. ‘ Its fibers arise from the incisive fossa of the mandible, then course vertically downward to insert in the skin of the chin. A movement disorder of the mentalis muscle is Geniospasm which is a benign but socially excluding genetic disorder. { database cross reference=http://en.wikipedia.org/wiki/Mentalis }
  • Added
    • + mentalis database cross reference MFMO:0000122
    • + mentalis definition A muscle of facial expression, innervated by the facial nerve, attached to the skin of the lower lip and inferior to the lower lip (in humans this region is called the chin or mental region), the orbicularis oris muscle, and the mandible in the symphyseal region. See Diogo et al., 2009; Burrows et al., 2011) { database cross reference=MFMO:0000122 }

Changes for: primitive gut

Changes for: digit 6 plus metapodial segment

Changes for: digit 7 plus metapodial segment

Changes for: digit 8 plus metapodial segment

Changes for: oral opening

Changes for: vomit

Changes for: digit 1 plus metapodial segment

Changes for: digit 2 plus metapodial segment

Changes for: digit 3 plus metapodial segment

Changes for: digit 5 plus metapodial segment

Changes for: digit 4 plus metapodial segment

Changes for: kidney field

Changes for: otic placode

  • Deleted
  • Added
    • + otic placode definition A cranial placode which, once specified, invaginates to form an otic cup, which eventually separates from the surface ectoderm to form the otic vesicle or otocyst, a rounded structure without appar- ent polarity. As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII[NBK] { database cross reference=http://en.wikipedia.org/wiki/Otic_placode , database cross reference=NCBIBook:NBK53175 }
    • + otic placode development notes With the exception of the pigment cells of the stria vascularis and the secretory epithelium of the cochlea, which are of neural crest origin, all compo- nents of the inner ear derive from the otic placode. In most species the thickening of the ectoderm into a placode occurs in a region adjacent to rhombomere 5 (reviewed in Ohyama et al., 2007), while in amphibians the otic placode is centered onto rhombomere 4 (Ruiz i Altaba and Jessell, 1991). { source=NCBIBook:NBK53175 }

Changes for: epibranchial placode

  • Deleted
    • - epibranchial placode development notes Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively { source=http://www.ncbi.nlm.nih.gov/books/NBK53175 }
  • Added
    • + epibranchial placode development notes Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively { source=NCBIBook:NBK53175 }

Changes for: lens placode

  • Deleted
    • - lens placode development notes Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006) { source=http://www.ncbi.nlm.nih.gov/books/NBK53175 }
  • Added
    • + lens placode development notes Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006) { source=NCBIBook:NBK53175 }

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: stomach glandular epithelium

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: digit plus metapodial segment

Changes for: platysma

Changes for: pedal digit 7 plus metapodial segment

Changes for: pedal digit 8 plus metapodial segment

Changes for: manual digit plus metapodial segment

Changes for: renal cortex interstitium

  • Deleted
  • Added
    • + renal cortex interstitium comment Structure notes: In the renal cortex, interstitial fibroblasts produce erythropoietin and are distinguished from other interstitial cells by their prominent F-actin cytoskeleton, abundance of rough endoplasmic reticulum, and by ecto-5′-nucleotidase expression in their plasma membrane. The resident dendritic cells belong to the mononuclear phagocyte system and fulfil a sentinel function. They are characterized by their expression of MHC class II and CD11c.[PMID:18575881]
    • + renal cortex interstitium definition A compartment of the renal cortex situated between basement membranes of epithelia and vessels that contains two contiguous cellular networks in mutual contact, one formed by interstitial fibroblasts, the other by dendritic cells. { database cross reference=http://www.ncbi.nlm.nih.gov/pubmed/18575881 }

Changes for: spiral ligament

Changes for: manubrium of malleus

  • Added
    • + manubrium of malleus comment Taxon notes: Conical in shape, with the cone extending inwards (e.g. mammals) or outwards (e.g. in birds)[http://audilab.bmed.mcgill.ca/AudiLab/teach/me_saf/me_saf.html]

Changes for: kidney interstitium

Report for properties

ObjectProperty objects lost from source: 0

ObjectProperty objects new in target: 0

Changed ObjectProperty objects: 0

June 21, 2014 |

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