2014-07-31 release

Multiple improvements to muscles courtesy of FEED project
2014-07-31 release image

This release incorporates new terms and improvements to feeding muscles courtesy of Robert Druzisnky and the FEED group. For more details see:

http://www.feedexp.org/wiki/

  • FEED
    • anterior digastric, from FEED. Fixes issue #538
    • changed scope of syns for lateral ptyeryoid to exact, vetted by FEED:rd. Issue #539
    • aligned masseter with FEED. Fixes issue #540
    • logical def of mentalis. Fixes issue #483
    • made attachment to parotid species-specific. Issue #488
    • NT: symphyseal region. Issue #483
    • aligned risorius. Issue #488
    • aligned zygomaticus major. Fixes issue #491
    • aligned zygomaticus major. Fixes issue #492
    • tagged Crico-arytenoid muscle as candidate for deletion. Issue #530
  • BGee:
    • fixed multi-cell-component axiom. Issue #541
    • added: pharyngula part_of organogenesis. Bgee:FB Fixes issue #533
    • tadpode stage “wholly aquatic larval stage in the life cycle of an amphibian” is_a amphibian larval stage. Bgee:FB Fixes issue #534
    • spelling: multi-cellular=>multicellular. Fixes issue #474
    • made life stage a proper part of life cycle. Added starts and ends with. Fixues issue #532
  • Other
    • various def changes. NTs: Feather types by body location
    • Removed ref to obs taxon. Issue #531
    • further cardiac conduction system enhancesents - provenance of syns and relationships
    • Fixed isa->part_of for conducting system of heart. Issue #527
    • nucleus accumbens dupe syn fixed
    • fixed def of sense organ
    • merged substance of tooth into odontoid tissue

Ontology Diff Report

Original Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-07-15/uberon.owl

New Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-07-31/uberon.owl

Report for classes

Class objects lost from source: 3

Class objects new in target: 10

New Class : forelimb feather

New Class : wing feather

New Class : tail feather

New Class : breast feather

New Class : dorsal feather

New Class : symphyseal region

New Class : breast feather tract

New Class : nucleus of the bulbocavernosus

New Class : lumen of intestine

New Class : trigeminal nerve muscle

Changed Class objects: 140

Changes for: levator mandibulae externus

Changes for: levator mandibulae articularis

Changes for: levator mandibulae lateralis

Changes for: longissimus atlantis muscle

Changes for: levator palatoquadrati

Changes for: adductor mandibulae

Changes for: spiracularis muscle

Changes for: preorbitalis muscle

Changes for: feather follicle

  • Deleted
    • - feather follicle comment The follicle consists of a series of tissue layers (from peripheral to central), including the dermis of the follicle, the epidermis of the follicle (outer epidermal layer), the follicle cavity or lumen (the space between epidermal layers), the follicle (epidermal) collar (or inner epidermal layer), and the dermal pulp (tissue at the center of the follicle). The proliferation of feather keratinocytes and most of the growth of the feather occurs in the follicle, or epidermal, collar (From: Prum 1999).
  • Added
    • + feather follicle structure notes The follicle consists of a series of tissue layers (from peripheral to central), including the dermis of the follicle, the epidermis of the follicle (outer epidermal layer), the follicle cavity or lumen (the space between epidermal layers), the follicle (epidermal) collar (or inner epidermal layer), and the dermal pulp (tissue at the center of the follicle). The proliferation of feather keratinocytes and most of the growth of the feather occurs in the follicle, or epidermal, collar (From: Prum 1999).

Changes for: remex feather

Changes for: rectrix feather

Changes for: tertial remex feather

  • Deleted
    • - tertial remex feather comment tertials are connected to the humerus in some species. These elongated “true” tertials act as a protective cover for all or part of the folded primaries and secondaries, and do not qualify as flight feathers as such.[11] However, many authorities use the term tertials to refer to the shorter, more symmetrical innermost secondaries of passerines (which perform the same function as true tertials) in an effort to distinguish them from the other secondaries.
  • Added
    • + tertial remex feather comment tertials are connected to the humerus in some species. These elongated “true” tertials act as a protective cover for all or part of the folded primaries and secondaries, and do not qualify as flight feathers as such. However, many authorities use the term tertials to refer to the shorter, more symmetrical innermost secondaries of passerines (which perform the same function as true tertials) in an effort to distinguish them from the other secondaries.

Changes for: inner epidermal layer of feather follicle

Changes for: pterygoideus

Changes for: levator quadrati

Changes for: epimysium

Changes for: left pelvic girdle region

Changes for: right pelvic girdle region

Changes for: obturator internus

  • Deleted
    • - obturator internus comment Definition generalized to accommodate AAO class - “Originates on the entire lateral surface of the pelvic rim. Dorsal fibers insert distally to the dorso-medial surface of the caput femoris and ventral fibers extend around the acetabulum to insert on the tendon of the caput femoris.” [AAO:0010052]
  • Added
    • + obturator internus external ontology notes Definition generalized to accommodate AAO class - ‘Originates on the entire lateral surface of the pelvic rim. Dorsal fibers insert distally to the dorso-medial surface of the caput femoris and ventral fibers extend around the acetabulum to insert on the tendon of the caput femoris.’ [AAO:0010052] { external ontology=AAO }

Changes for: retractor lateralis posterior muscle

Changes for: retractor lateralis anterior muscle

Changes for: adductor muscle

Changes for: retractor lateralis muscle

Changes for: circular muscle layer of muscular coat

Changes for: longitudinal muscle layer of muscular coat

Changes for: nucleus accumbens

Changes for: Eimer’s organ

  • Deleted
    • - Eimer’s organ definition sensory organs in which the epidermis is modified to form bulbous papillae. present in many moles, and are particularly common in the star-nosed mole, which bears 30,000 of them on its unique tentacled snout. The organs are formed from a stack of epidermal cells, which is innervated by nerve processes from myelinated fibers in the dermis, which form terminal swellings just below the outer keratinized layer of epidermis. They contain a Merkel cell-neurite complex in the epidermis and a lamellated corpuscle in the dermal connective tissue. { database cross reference=http://en.wikipedia.org/wiki/Eimer’s_organ }
  • Added
    • + Eimer’s organ definition A sensory organ in which the epidermis is modified to form bulbous papillae. The organs are formed from a stack of epidermal cells, which is innervated by nerve processes from myelinated fibers in the dermis, which form terminal swellings just below the outer keratinized layer of epidermis. They contain a Merkel cell-neurite complex in the epidermis and a lamellated corpuscle in the dermal connective tissue. { database cross reference=http://en.wikipedia.org/wiki/Eimer’s_organ }
    • + Eimer’s organ taxon notes present in many moles, and are particularly common in the star-nosed mole, which bears 30,000 of them on its unique tentacled snout

Changes for: deep fascia

Changes for: visceral fascia

Changes for: cloacal lumen

  • Deleted
    • - cloacal lumen comment the ZFA class belongs here as it is an anatomical space. See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/102/
  • Added

Changes for: dentine

Changes for: cementum

Changes for: enamel

Changes for: mylohyoid muscle

Changes for: masseter muscle

Changes for: obsolete frontal-parietal joint

Changes for: ventral patch of Leydig’s organ

Changes for: tensor tympani

Changes for: dorsal patch of Leydig’s organ

Changes for: trigeminal nerve

Changes for: actinopterygian frontal bone

Changes for: postcentral gyrus

  • Deleted
    • - postcentral gyrus definition The lateral postcentral gyrus is a prominent structure in the parietal lobe of the human brain and an important landmark. It was initially defined from surface stimulation studies of Penfield, and parallel surface potential studies of Bard, Woolsey, and Marshall. Although initially defined to be roughly the same as Brodmann areas 3, 1 and 2, more recent work by Kaas has suggested that for homogeny with other sensory fields only area 3 should be referred to as ‘primary somatosensory cortex’, as it received the bulk of the thalamocortical projection from the sensory input fields. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Postcentral_gyrus }
  • Added

Changes for: basicranium

Changes for: gastrula

Changes for: neuromere

  • Deleted
    • - neuromere comment We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted
  • Added
    • + neuromere editor note We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted

Changes for: masticatory muscle

Changes for: pharyngula stage

Changes for: lobe of cerebral hemisphere

Changes for: obturator externus

  • Deleted
    • - obturator externus comment Definition generalized to accommodate AAO class - “Originates on the ventro-lateral pelvic rim and inserts on the ventral aspect of the femur, medial to the insertion of the pectineus.” [AAO:0010043]
  • Added

Changes for: nematode larva

Changes for: tadpole stage

Changes for: Hatschek’s left diverticulum

Changes for: Hatschek’s right diverticulum

Changes for: internal anal sphincter

Changes for: internodal tract

Changes for: post-embryonic organism

Changes for: nasal tentacle

Changes for: electroreceptor organ

Changes for: megalopa stage

Changes for: down feather

Changes for: cerebral cortex marginal layer

Changes for: odontoid tissue

Changes for: structure with developmental contribution from neural crest

Changes for: neural crest-derived structure

Changes for: row of feathers

Changes for: somatic sensory system

Changes for: eyeball of camera-type eye

Changes for: ventral pancreatic bud

Changes for: sinoatrial node

Changes for: atrioventricular node

Changes for: atrioventricular bundle

Changes for: purkinje fiber

Changes for: white matter

Changes for: coat of hair

Changes for: conducting tissue of heart

Changes for: polar trophectoderm

  • Deleted
    • - polar trophectoderm comment unlike mural trophectoderm cells which stop proliferating and become large polyploid cells (the primary trophoblastic giant cells) by endoreduplication, polar trophectoderm cells remain diploid, continue to proliferate and give rise to both the ectoplacental cone and the extraembryonic ectoderm[MP]
  • Added
    • + polar trophectoderm development notes unlike mural trophectoderm cells which stop proliferating and become large polyploid cells (the primary trophoblastic giant cells) by endoreduplication, polar trophectoderm cells remain diploid, continue to proliferate and give rise to both the ectoplacental cone and the extraembryonic ectoderm[MP]

Changes for: neural tube marginal layer

Changes for: endoderm-derived structure

Changes for: mesoderm-derived structure

Changes for: ectoderm-derived structure

Changes for: hermaphroditic organism

Changes for: His-Purkinje system

Changes for: zygomaticus minor muscle

Changes for: zygomaticus major muscle

Changes for: risorius muscle

Changes for: mentalis muscle

Changes for: vocalis muscle

Changes for: tensor veli palatini

Changes for: superior longitudinal muscle of tongue

Changes for: sexually immature organism

Changes for: adult organism

Changes for: lagenar capsule

Changes for: ciliary ganglion

Changes for: zona reticularis of adrenal gland

  • Deleted
    • - zona reticularis of adrenal gland definition The zona reticularis is the innermost layer of the adrenal cortex, lying deep to the zona fasciculata and superficial to the adrenal medulla. The cells are arranged cords that project in different directions giving a net-like appearance (L. reticulum - net). Cells in the zona reticularis produce precursor androgens including dehydroepiandrosterone (DHEA) and androstenedione from cholesterol. DHEA is further converted to DHEA-sulfate via a sulfotransferase, SULT2A1. These precursors are not further converted in the adrenal cortex as the cells lack 3β-hydroxysteroid dehydrogenase. Instead, they are released into the blood stream and taken up in the testis and ovaries to produce testosterone and the estrogens respectively. In some animals like rodents, the reticularis layer does contain 3β-hydroxysteroid dehydrogenase, which along with other enzymes present results in the production of corticosteroids like the fasciculata. In rodents too, the lack of 17alpha-hydroxylase results in the synthesis of corticosterone instead of cortisol as in the human. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Zona_reticularis }
  • Added
    • + zona reticularis of adrenal gland definition The zona reticularis is the innermost layer of the adrenal cortex, lying deep to the zona fasciculata and superficial to the adrenal medulla. The cells are arranged cords that project in different directions giving a net-like appearance (L. reticulum - net). Cells in the zona reticularis produce precursor androgens including dehydroepiandrosterone (DHEA) and androstenedione from cholesterol. DHEA is further converted to DHEA-sulfate via a sulfotransferase, SULT2A1. These precursors are not further converted in the adrenal cortex as the cells lack 3beta-hydroxysteroid dehydrogenase. Instead, they are released into the blood stream and taken up in the testis and ovaries to produce testosterone and the estrogens respectively. In some animals like rodents, the reticularis layer does contain 3beta-hydroxysteroid dehydrogenase, which along with other enzymes present results in the production of corticosteroids like the fasciculata. In rodents too, the lack of 17alpha-hydroxylase results in the synthesis of corticosterone instead of cortisol as in the human. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Zona_reticularis }

Changes for: stomach smooth muscle outer longitudinal layer

Changes for: stomach smooth muscle inner oblique layer

Changes for: stomach muscularis externa

Changes for: stomach smooth muscle circular layer

Changes for: ligament of pinna

Changes for: pharyngeal arch 1

Changes for: pharyngeal gill

  • Deleted
    • - pharyngeal gill comment Gills are made of filaments which help increase surface area for oxygen exchange. In bony fish, the gills are covered by a bony cover called an operculum. When a fish breathes, it opens its mouth at regular times and draws in a mouthful of water. It then draws the sides of its throat together, forcing the water through the gill openings. The water passes over the gills on the outside. Valves inside the mouth keep the water from escaping through the mouth again. The operculum can be very important in adjusting the pressure of water inside of the pharynx to allow proper ventilation of the gills. Lampreys and sharks lack an operculum, they have multiple gill openings. Also, they must use different methods to force water over the gills. In sharks and rays, this ventilation of the gills is achieved either by the use of spiracles or ram ventilation (ventilation by constantly swimming). Although some animals use this method it is much better for animals to use a spiracle because they are less susceptible to injury
  • Added
    • + pharyngeal gill function notes Gills are made of filaments which help increase surface area for oxygen exchange
    • + pharyngeal gill taxon notes In bony fish, the gills are covered by a bony cover called an operculum. When a fish breathes, it opens its mouth at regular times and draws in a mouthful of water. It then draws the sides of its throat together, forcing the water through the gill openings. The water passes over the gills on the outside. Valves inside the mouth keep the water from escaping through the mouth again. The operculum can be very important in adjusting the pressure of water inside of the pharynx to allow proper ventilation of the gills. Lampreys and sharks lack an operculum, they have multiple gill openings. Also, they must use different methods to force water over the gills. In sharks and rays, this ventilation of the gills is achieved either by the use of spiracles or ram ventilation (ventilation by constantly swimming). Although some animals use this method it is much better for animals to use a spiracle because they are less susceptible to injury

Changes for: life cycle stage

Changes for: life cycle

Changes for: neural nucleus

  • Deleted
    • - neural nucleus comment Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in “subcortical” because I don’t think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in “relatively compact” and “distiguishable by histology” because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don’t tend to consider nuclei because they don’t occupy an easily defined territory. But all is open to debate.
  • Added
    • + neural nucleus external ontology notes Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in ‘subcortical’ because I don’t think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in ‘relatively compact’ and ‘distiguishable by histology’ because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don’t tend to consider nuclei because they don’t occupy an easily defined territory. But all is open to debate.

Changes for: embryonic cloaca

Changes for: body cavity or lining

Changes for: mandible condylar process

Changes for: follicular fluid

Changes for: rostral margin of orbit

Changes for: endocrine pancreas

Changes for: feather

  • Deleted
    • - feather definition one of the epidermal growths that form the distinctive outer covering, or plumage, on birds. Feathers are formed in tiny follicles in the epidermis, or outer skin layer, that produce keratin proteins. The β-keratins in feathers, beaks and claws — and the claws, scales and shells of reptiles — are composed of protein strands hydrogen-bonded into β-pleated sheets, which are then further twisted and crosslinked by disulfide bridges into structures even tougher than the α-keratins of mammalian hair, horns and hoof. The exact signals that induce the growth of feathers on the skin are not known but it has been found that the transcription factor cDermo-1 induces the growth of feathers on skin and scales on the leg. { database cross reference=http://en.wikipedia.org/wiki/Feather }
    • - feather structure notes The β-keratins in feathers, beaks and claws — and the claws, scales and shells of reptiles — are composed of protein strands hydrogen-bonded into β-pleated sheets, which are then further twisted and crosslinked by disulfide bridges into structures even tougher than the α-keratins of mammalian hair, horns and hoof.
  • Added
    • + feather definition one of the epidermal growths that form the distinctive outer covering, or plumage, on birds. Feathers are formed in tiny follicles in the epidermis, or outer skin layer, that produce keratin proteins. The beta-keratins in feathers, beaks and claws — and the claws, scales and shells of reptiles — are composed of protein strands hydrogen-bonded into beta-pleated sheets, which are then further twisted and crosslinked by disulfide bridges into structures even tougher than the α-keratins of mammalian hair, horns and hoof. The exact signals that induce the growth of feathers on the skin are not known but it has been found that the transcription factor cDermo-1 induces the growth of feathers on skin and scales on the leg. { database cross reference=http://en.wikipedia.org/wiki/Feather }
    • + feather structure notes The beta-keratins in feathers, beaks and claws — and the claws, scales and shells of reptiles — are composed of protein strands hydrogen-bonded into beta-pleated sheets, which are then further twisted and crosslinked by disulfide bridges into structures even tougher than the α-keratins of mammalian hair, horns and hoof.

Changes for: sense organ

Changes for: abdominal ganglion of visceral hump

Changes for: somatosensory cortex

Changes for: secondary somatosensory cortex

Changes for: primary somatosensory cortex

Changes for: pleural ganglion

Changes for: parietal ganglion

Changes for: extraembryonic endoderm

Changes for: mixed ectoderm/mesoderm/endoderm-derived structure

Changes for: mixed endoderm/mesoderm-derived structure

  • Deleted
    • - mixed endoderm/mesoderm-derived structure comment Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple
  • Added

Changes for: hypoblast (generic)

Changes for: mesonephros

  • Deleted
    • - mesonephros definition In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the mesonephros will form the mature kidney[GO]. One of three excretory organs that develop in vertebrates. It serves as the main excretory organ of aquatic vertebrates and as a temporary kidney in higher vertebrates. composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo. { database cross reference=http://en.wikipedia.org/wiki/Mesonephros , database cross reference=GO:0001823 }
  • Added
    • + mesonephros definition The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo. { database cross reference=http://en.wikipedia.org/wiki/Mesonephros , database cross reference=GO:0001823 }
    • + mesonephros taxon notes In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the mesonephros will form the mature kidney[GO]

Changes for: Bachmann’s bundle

Changes for: corpus striatum

  • Deleted
    • - corpus striatum comment The term has been used in a few different ways: * It is a pair of nuclear masses which form the basal ganglia, along with the subthalamic nucleus and the substantia nigra. * It may also refer to both the basal ganglia and internal capsule collectively.[2] * According to the 1917 version of Gray’s Anatomy, it is the combination of the lentiform nucleus (also known as the lenticular nucleus) and the caudate nucleus * According to BrainInfo it is a part of the basal ganglia comprising the globus pallidus and striatum
  • Added
    • + corpus striatum comment * According to the 1917 version of Gray’s Anatomy, it is the combination of the lentiform nucleus (also known as the lenticular nucleus) and the caudate nucleus * According to BrainInfo it is a part of the basal ganglia comprising the globus pallidus and striatum
    • + corpus striatum terminology notes The term has been used in a few different ways: * It is a pair of nuclear masses which form the basal ganglia, along with the subthalamic nucleus and the substantia nigra. * It may also refer to both the basal ganglia and internal capsule collectively.[2]

Changes for: multicellular organism

Changes for: left external ear

Changes for: right external ear

Changes for: left vitelline vein

Changes for: right umbilical vein

Changes for: right vitelline vein

Changes for: left umbilical vein

Changes for: anterior digastric muscle

Changes for: crico-arytenoid muscle

Changes for: obsolete orbit

Changes for: anterior commissure

Changes for: lateral pterygoid muscle

Changes for: abdomen

Changes for: thoracic segment of trunk

Changes for: kidney interstitium

Report for properties

ObjectProperty objects lost from source: 0

ObjectProperty objects new in target: 2

New ObjectProperty : ends with

New ObjectProperty : starts with

Changed ObjectProperty objects: 1

Changes for: starts

July 31, 2014 |

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