2014-05-27 release

odds and ends
2014-05-27 release image

Ontology Diff Report

  • Fixes to reproductive system and renal system, aligned with GO and MP
  • various NTs to support logical definitions
  • definition overhaul
  • multiple changes. Improved definitions from WP, made more concise. Myotome overhaul
  • translated comments to specific APs
  • Added roman numeral digit labels as preferred terms for comparative anatomists. Fixes #458

Original Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-05-24/uberon.owl

New Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-05-27/uberon.owl

Report for classes

Class objects lost from source: 0

Class objects new in target: 28

New Class : internal surface of frontal bone

New Class : internal surface of cranial base

New Class : paired venous dural sinus

New Class : marginal venous sinus

New Class : primitive marginal sinus

New Class : sinus of von Szily

New Class : unpaired venous dural sinus

New Class : prevertebral muscle of neck

New Class : ventral body wall

New Class : internal mammary vein

New Class : external thoracic vein

New Class : meningeal branch of spinal nerve

New Class : communicating branch of spinal nerve

New Class : dorsal body wall

New Class : developing mesenchymal structure

New Class : salivary gland primordium

New Class : ventral surface of penis

New Class : intermaxillary gland (sensu Osteolepiformes)

New Class : intermaxillary salivary gland

New Class : buccal gland

New Class : bony part of cervical vertebral arch

New Class : bony part of vertebral arch of first sacral vertebra

New Class : abdominal viscera

New Class : hypothenar eminence

New Class : thenar eminence

New Class : lower primary incisor tooth

New Class : withers

New Class : raphe of scrotum

Changed Class objects: 1101

Changes for: digit 3 digitopodial skeleton

Changes for: digit 4 digitopodial skeleton

Changes for: digit 5 digitopodial skeleton

Changes for: digit 2 digitopodial skeleton

Changes for: digit 1 digitopodial skeleton

Changes for: lophophore

Changes for: zeugopodial skeleton

Changes for: hyomandibular bone

  • Deleted
    • - hyomandibular bone comment In most teleosts, there is a symplectic, and the hyomandibula articulates with it anteroventrally.
  • Added

Changes for: neural plate of carapace

Changes for: surangular bone

  • Deleted
    • - surangular bone comment In some lepospondyls, and in frogs and salamanders, the surangular is absent. However, it becomes increasingly significant in the anthracosaur lineage. In turtles, it is one of the two principle bones of the lower jaw. In lepidosaurs, it is less important because of the development of a separate coronoid bone. In advanced lizards and pythonomorphs, it may fuse with the articular and perhaps other bones and loses its separate identity. In syanapsids, a secondary jaw joint develops between the surangular and the squamosal, which becomes the unique mammalian jaw articulation. However, the surangular fuses with the dentary and becomes the unitary mammalian “mandible” without a separate identity
  • Added
    • + surangular bone taxon notes In some lepospondyls, and in frogs and salamanders, the surangular is absent. However, it becomes increasingly significant in the anthracosaur lineage. In turtles, it is one of the two principle bones of the lower jaw. In lepidosaurs, it is less important because of the development of a separate coronoid bone. In advanced lizards and pythonomorphs, it may fuse with the articular and perhaps other bones and loses its separate identity. In syanapsids, a secondary jaw joint develops between the surangular and the squamosal, which becomes the unique mammalian jaw articulation. However, the surangular fuses with the dentary and becomes the unitary mammalian ‘mandible’ without a separate identity

Changes for: dorsal head of rib

  • Deleted
    • - dorsal head of rib comment . Terminology notes: sometimes called the tuberculum, but not to be confused with the tubercle, which is between body and neck
  • Added

Changes for: secondary remex feather

  • Deleted
    • - secondary remex feather comment In some species, the ligaments that bind these remiges to the bone connect to small, rounded projections, known as quill knobs, on the ulna; in other species, no such knobs exist. Secondary feathers remain close together in flight (they cannot be individually separated like the primaries can) and help to provide lift by creating the airfoil shape of the bird’s wing. Secondaries tend to be shorter and broader than primaries, with blunter ends
  • Added
    • + secondary remex feather taxon notes In some species, the ligaments that bind these remiges to the bone connect to small, rounded projections, known as quill knobs, on the ulna; in other species, no such knobs exist. Secondary feathers remain close together in flight (they cannot be individually separated like the primaries can) and help to provide lift by creating the airfoil shape of the bird’s wing. Secondaries tend to be shorter and broader than primaries, with blunter ends

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: manual digit 1 plus metapodial segment

Changes for: musculus rectus abdominis profundus

Changes for: follicle placode

Changes for: acinus of parotid gland

Changes for: collagen fibril

Changes for: anterior uvea

Changes for: flexor hallucis brevis muscle

  • Deleted
    • - flexor hallucis brevis muscle definition The Flexor hallucis brevis arises, by a pointed tendinous process, from the medial part of the under surface of the cuboid bone, from the contiguous portion of the third cuneiform, and from the prolongation of the tendon of the Tibialis posterior which is attached to that bone. It divides in front into two portions, which are inserted into the medial and lateral sides of the base of the first phalanx of the great toe, a sesamoid bone being present in each tendon at its insertion. The medial portion is blended with the Abductor hallucis previous to its insertion; the lateral portion with the Adductor hallucis; the tendon of the Flexor hallucis longus lies in a groove between them; the lateral portion is sometimes described as the first Interosseous plantaris. { database cross reference=http://en.wikipedia.org/wiki/Flexor_hallucis_brevis_muscle }
  • Added

Changes for: lobule of lactiferous gland

  • Deleted
    • - lobule of lactiferous gland comment TODO - ensure correct terminology for lobes/lobules. FMA uses lobule for core term, but also has ‘set of mammary gland lobes’. ISBN10:0123813611 states no separate lobes in mouse
  • Added
    • + lobule of lactiferous gland editor note TODO - ensure correct terminology for lobes/lobules. FMA uses lobule for core term, but also has ‘set of mammary gland lobes’. ISBN10:0123813611 states no separate lobes in mouse

Changes for: paracentral nucleus

Changes for: gingival epithelium

  • Deleted
    • - gingival epithelium comment In humans: 15% orthokeratinized, 75% parakeratinized, 10% non-keratinized; diurnal; decreased keratinization with age. Note that in FMA this is classified as keratinized squamous - this perhaps refers to the epithelium of the attached or free gingiva
  • Added
    • + gingival epithelium taxon notes In humans: 15% orthokeratinized, 75% parakeratinized, 10% non-keratinized; diurnal; decreased keratinization with age. Note that in FMA this is classified as keratinized squamous - this perhaps refers to the epithelium of the attached or free gingiva

Changes for: epithelium of esophagus

  • Deleted
    • - epithelium of esophagus comment todo check epithelium types: in FMA: Nonkeratinizing stratified squamous epithelium; mouse has basal and squamous subtypes; in ZFA it is columnar
  • Added
    • + epithelium of esophagus editor note TODO check epithelium types: in FMA: Nonkeratinizing stratified squamous epithelium; mouse has basal and squamous subtypes; in ZFA it is columnar

Changes for: substance of tooth

  • Deleted
    • - substance of tooth comment note the asserted dual parentage. This is deliberate, pending better definitions of the distinction between substance and tissue

Changes for: fibrocartilage

  • Deleted
    • - fibrocartilage comment The white fibrocartilages admit of arrangement into four groups—interarticular, connecting, circumferential, and stratiform – WP. TODO: add mineralized
  • Added
    • + fibrocartilage comment The white fibrocartilages admit of arrangement into four groups—interarticular, connecting, circumferential, and stratiform – WP. EDITOR NOTE: TODO add mineralized

Changes for: humeroradial joint

  • Deleted
    • - humeroradial joint definition The humeroradial joint, the joint between the head of the radius and the capitulum of the humerus, is a hinge joint. The bony surfaces would of themselves constitute an enarthrosis and allow movement in all directions, were it not for the annular ligament, by which the head of the radius is bound to the radial notch of the ulna, and which prevents any separation of the two bones laterally. It is to the same ligament that the head of the radius owes its security from dislocation, which would otherwise tend to occur, from the shallowness of the cup-like surface on the head of the radius. In fact, but for this ligament, the tendon of the Biceps brachii would be liable to pull the head of the radius out of the joint. The head of the radius is not in complete contact with the capitulum of the humerus in all positions of the joint. The capitulum occupies only the anterior and inferior surfaces of the lower end of the humerus, so that in complete extension a part of the radial head can be plainly felt projecting at the back of the articulation. In full flexion the movement of the radial head is hampered by the compression of the surrounding soft parts, so that the freest rotatory movement of the radius on the humerus (pronation and supination) takes place in semiflexion, in which position the two articular surfaces are in most intimate contact. Flexion and extension of the elbow-joint are limited by the tension of the structures on the front and back of the joint; the limitation of flexion is also aided by the soft structures of the arm and forearm coming into contact. { database cross reference=http://en.wikipedia.org/wiki/Humeroradial_joint }
  • Added

Changes for: blood vessel

  • Deleted
    • - blood vessel comment Taxon notes: annelids have blood vessels, but this class is not applicable to annelids.
  • Added

Changes for: intermetatarsal joint

  • Deleted
    • - intermetatarsal joint comment In humans: The base of the first metatarsal is not connected with that of the second by any ligaments; in this respect the great toe resembles the thumb[WP]
  • Added
    • + intermetatarsal joint taxon notes In humans: The base of the first metatarsal is not connected with that of the second by any ligaments; in this respect the great toe resembles the thumb[WP]

Changes for: root of vagus nerve

Changes for: urachus mesenchyme

Changes for: inferior central nucleus

  • Deleted
  • Added
    • + inferior central nucleus editor note TODO - compare with UBERON:0002881 ! sublingual nucleus; also to dorsal raphe nucleus. Check if the same as ZFA ‘inferior raphe nucleus’. See comments on https://sourceforge.net/tracker/?func=detail&atid=440764&aid=3248146&group_id=36855

Changes for: somatic nerve plexus

Changes for: conjunctiva

Changes for: nerve plexus

Changes for: pedal acropodium region

Changes for: acropodium region

Changes for: manual acropodium region

Changes for: retrocerebral complex

Changes for: choroid plexus

  • Deleted
    • - choroid plexus comment TODO - check relationship to ventricle. Check subclass - ZFA says vasculature. Note that FMA:61934 (choroid plexus of cerebral hemisphere) has exact synonym ‘choroid plexus’ but it is not clear that this belongs here, as the fourth ventricle is not in the cerebral hemisphere
  • Added
    • + choroid plexus editor note TODO - check relationship to ventricle. Check subclass - ZFA says vasculature. Note that FMA:61934 (choroid plexus of cerebral hemisphere) has exact synonym ‘choroid plexus’ but it is not clear that this belongs here, as the fourth ventricle is not in the cerebral hemisphere

Changes for: lacrimal duct

Changes for: nail of pedal digit 4

Changes for: nail of pedal digit 5

Changes for: semicircular duct

Changes for: cochlear duct of membranous labyrinth

Changes for: nail of pedal digit 3

Changes for: semicircular canal

Changes for: minor salivary gland

  • Deleted
    • - minor salivary gland SubClassOf part of some exocrine system
    • - minor salivary gland definition the smaller, largely mucus-secreting, exocrine glands of the oral cavity, consisting of the labial, buccal, molar, lingual, and palatine glands[MP]. There are over 600 minor salivary glands located throughout the oral cavity within the lamina propria of the oral mucosa. They are 1-2mm in diameter and unlike the other glands, they are not encapsulated by connective tissue only surrounded by it. The gland is usually a number of acini connected in a tiny lobule. A minor salivary gland may have a common excretory duct with another gland, or may have its own excretory duct. Their secretion is mainly mucous in nature (except for Von Ebner’s glands) and have many functions such as coating the oral cavity with saliva. Problems with dentures are usually associated with minor salivary glands[WP]. { database cross reference=Minor Salivary Glands , database cross reference=MP:0003791 }
  • Added
    • + minor salivary gland comment There are over 600 minor salivary glands located throughout the oral cavity within the lamina propria of the oral mucosa. They are 1-2mm in diameter and unlike the other glands, they are not encapsulated by connective tissue only surrounded by it. The gland is usually a number of acini connected in a tiny lobule. A minor salivary gland may have a common excretory duct with another gland, or may have its own excretory duct. Their secretion is mainly mucous in nature (except for Von Ebner’s glands) and have many functions such as coating the oral cavity with saliva[WP].
    • + minor salivary gland definition One of the smaller, largely mucus-secreting, exocrine glands of the oral cavity, consisting of the labial, buccal, molar, lingual, and palatine glands[MP]. { database cross reference=Minor Salivary Glands , database cross reference=MP:0003791 }

Changes for: parotid gland

Changes for: saliva

  • Deleted
    • - saliva comment This class was created automatically from a combination of ontologies
    • - saliva definition In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin[GO]. { database cross reference=http://en.wikipedia.org/wiki/Saliva , database cross reference=GO:0046541 }
  • Added
    • + saliva comment Taxon notes: We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin[GO]
    • + saliva definition A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. { database cross reference=http://en.wikipedia.org/wiki/Saliva , database cross reference=GO:0046541 }

Changes for: sublingual duct

  • Deleted
    • - sublingual duct definition The excretory ducts of the sublingual gland are from eight to twenty in number. Of the smaller sublingual ducts (ducts of Rivinus), some join the submandibular duct; others open separately into the mouth, on the elevated crest of mucous membrane (plica sublingualis), caused by the projection of the gland, on either side of the frenulum linguae. One or more join to form the major sublingual duct (larger sublingual duct, duct of Bartholin), which opens into the submandibular duct. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Sublingual_duct }
  • Added

Changes for: duct of salivary gland

Changes for: carpometacarpal joint of digit 1

Changes for: sweat gland

Changes for: nasal cavity mucosa

Changes for: nail of manual digit 4

Changes for: nail of manual digit 5

Changes for: major salivary gland

Changes for: nail of pedal digit 1

Changes for: nail of pedal digit 2

Changes for: nail of manual digit 1

Changes for: nail of manual digit 2

Changes for: nail of manual digit 3

Changes for: hyoepiglottic muscle

Changes for: pigmented layer of retina

Changes for: vitreous chamber of eyeball

Changes for: vitreous body

Changes for: inner limiting layer of retina

Changes for: lacrimal apparatus

Changes for: distal part of styloid process of temporal bone

Changes for: sclera

Changes for: corneal epithelium

Changes for: ciliary body

Changes for: muscle of trunk

Changes for: lacrimal canaliculus

Changes for: substantia propria of cornea

Changes for: ciliary epithelium

Changes for: iris stroma

Changes for: iris

Changes for: uvea

  • Deleted
    • - uvea comment TODO - check child terms, isa vs partof. See also MA:0001284
  • Added
    • + uvea editor note TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus

Changes for: oculomotor nuclear complex

  • Deleted
    • - oculomotor nuclear complex definition The fibers of the oculomotor nerve arise from a nucleus in the midbrain, which lies in the gray substance of the floor of the cerebral aqueduct and extends in front of the aqueduct for a short distance into the floor of the third ventricle. From this nucleus the fibers pass forward through the tegmentum, the red nucleus, and the medial part of the substantia nigra, forming a series of curves with a lateral convexity, and emerge from the oculomotor sulcus on the medial side of the cerebral peduncle. The nucleus of the oculomotor nerve does not consist of a continuous column of cells, but is broken up into a number of smaller nuclei, which are arranged in two groups, anterior and posterior. Those of the posterior group are six in number, five of which are symmetrical on the two sides of the middle line, while the sixth is centrally placed and is common to the nerves of both sides. The anterior group consists of two nuclei, an antero-medial and an antero-lateral . The nucleus of the oculomotor nerve, considered from a physiological standpoint, can be subdivided into several smaller groups of cells, each group controlling a particular muscle. A nearby nucleus, the Edinger-Westphal nucleus, is responsible for the autonomic functions of the oculomotor nerve, including pupillary constriction and lens accommodation. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Nucleus_of_oculomotor_nerve }
  • Added
    • + oculomotor nuclear complex definition Nuclear complex containing subnuclei that give rise to the axons of the occulomotor nerve, both motor and parasympathetic fibers, situated at the midline at the level of the superior colliculus in the midbrain tegmentum (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 533-534). { database cross reference=Neurolex:birnlex_1240 }

Changes for: jaw skeleton

  • Deleted
    • - jaw skeleton comment TODO: move ZFA:0001227 (it is the entire jaw skeleton). Editor notes: in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates. Development notes: There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983).
  • Added
    • + jaw skeleton development notes There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983).
    • + jaw skeleton editor note TODO - move ZFA:0001227 (it is the entire jaw skeleton). Editor notes: in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates

Changes for: nail

  • Deleted
    • - nail comment TODO: check claw vs nail. A primate’s nail consists of the unguis alone; the subunguis has disappeared.
  • Added
    • + nail editor note TODO - check claw vs nail. A primate’s nail consists of the unguis alone; the subunguis has disappeared.

Changes for: neurocranium

  • Deleted
    • - neurocranium comment AO notes: It seems MA uses ‘neurocranium’ as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, …
  • Added

Changes for: nasopharynx

  • Deleted
    • - nasopharynx comment In humans: in front it communicates through the choanae with the nasal cavities. On its lateral wall is the pharyngeal ostium of the auditory tube, somewhat triangular in shape, and bounded behind by a firm prominence, the torus tubarius or cushion, caused by the medial end of the cartilage of the tube which elevates the mucous membrane
  • Added
    • + nasopharynx taxon notes In humans - in front it communicates through the choanae with the nasal cavities. On its lateral wall is the pharyngeal ostium of the auditory tube, somewhat triangular in shape, and bounded behind by a firm prominence, the torus tubarius or cushion, caused by the medial end of the cartilage of the tube which elevates the mucous membrane

Changes for: tongue

Changes for: central retinal vein

Changes for: lacrimal bone

  • Deleted
    • - lacrimal bone comment In early lobe-finned fishes and ancestral tetrapods, the lacrimal bone is a relatively large and robust bone, running from the orbit to the nostrils. It forms part of the side of the face, between the nasal bones and the maxilla. In primitive forms, it is often accompanied by a much smaller septomaxilla bone, lying immediately behind the nasal opening, but this is lost in most modern species. The lacrimal bone is often smaller in living vertebrates, and is no longer always directly associated with the nasal opening, although it retains its connection with the orbit. The bone is entirely absent in living amphibians, as well as some reptilian species[WP, ISBN 0-03-910284-X]
  • Added
    • + lacrimal bone taxon notes In early lobe-finned fishes and ancestral tetrapods, the lacrimal bone is a relatively large and robust bone, running from the orbit to the nostrils. It forms part of the side of the face, between the nasal bones and the maxilla. In primitive forms, it is often accompanied by a much smaller septomaxilla bone, lying immediately behind the nasal opening, but this is lost in most modern species. The lacrimal bone is often smaller in living vertebrates, and is no longer always directly associated with the nasal opening, although it retains its connection with the orbit. The bone is entirely absent in living amphibians, as well as some reptilian species[WP, ISBN 0-03-910284-X]

Changes for: exoccipital bone

  • Deleted
    • - exoccipital bone comment TODO - check FMA - currently we place this as both of a zone of bone organ and an (endochondral) bone. Removed endochondral bone classification for now, violates disjointness axiom
  • Added
    • + exoccipital bone editor note TODO - check FMA - currently we place this as both of a zone of bone organ and an (endochondral) bone. Removed endochondral bone classification for now, violates disjointness axiom

Changes for: basioccipital bone

Changes for: lower digestive tract

  • Deleted
    • - lower digestive tract comment WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L
  • Added

Changes for: upper digestive tract

  • Deleted
    • - upper digestive tract comment WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L. In Galen, entire GI tract excludes esophagus
  • Added

Changes for: subdivision of digestive tract

Changes for: cuneate fasciculus of medulla

Changes for: motor nucleus of trigeminal nerve

Changes for: oculomotor nerve fibers

Changes for: digestive tract

Changes for: orbicularis oculi muscle

  • Deleted
    • - orbicularis oculi definition A circumorbital muscle in the face that closes the eyelid[HP]. It arises from the nasal part of the frontal bone, from the frontal process of the maxilla in front of the lacrimal groove, and from the anterior surface and borders of a short fibrous band, the medial palpebral ligament. From this origin, the fibers are directed lateralward, forming a broad and thin layer, which occupies the eyelids or palpebræ, surrounds the circumference of the orbit, and spreads over the temple, and downward on the cheek. The palpebral portion of the muscle is thin and pale; it arises from the bifurcation of the medial palpebral ligament, forms a series of concentric curves, and is inserted into the lateral palpebral raphé. The orbital portion is thicker and of a reddish color; its fibers form a complete ellipse without interruption at the lateral palpebral commissure; the upper fibers of this portion blend with the Frontalis and Corrugator. The lacrimal part (Tensor tarsi) is a small, thin muscle, about 6 mm. in breadth and 12 mm. in length, situated behind the medial palpebral ligament and lacrimal sac. It arises from the posterior crest and adjacent part of the orbital surface of the lacrimal bone, and passing behind the lacrimal sac, divides into two slips, upper and lower, which are inserted into the superior and inferior tarsi medial to the puncta lacrimalia; occasionally it is very indistinct. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Orbicularis_oculi_muscle }
    • - orbicularis oculi has exact synonym orbicularis oculi muscle { database cross reference=http://en.wikipedia.org/wiki/Orbicularis_oculi_muscle }
    • - orbicularis oculi label orbicularis oculi
  • Added
    • + orbicularis oculi muscle comment It arises from the nasal part of the frontal bone, from the frontal process of the maxilla in front of the lacrimal groove, and from the anterior surface and borders of a short fibrous band, the medial palpebral ligament. From this origin, the fibers are directed lateralward, forming a broad and thin layer, which occupies the eyelids or palpebræ, surrounds the circumference of the orbit, and spreads over the temple, and downward on the cheek. The palpebral portion of the muscle is thin and pale; it arises from the bifurcation of the medial palpebral ligament, forms a series of concentric curves, and is inserted into the lateral palpebral raphé. The orbital portion is thicker and of a reddish color; its fibers form a complete ellipse without interruption at the lateral palpebral commissure; the upper fibers of this portion blend with the Frontalis and Corrugator. The lacrimal part (Tensor tarsi) is a small, thin muscle, about 6 mm. in breadth and 12 mm. in length, situated behind the medial palpebral ligament and lacrimal sac. It arises from the posterior crest and adjacent part of the orbital surface of the lacrimal bone, and passing behind the lacrimal sac, divides into two slips, upper and lower, which are inserted into the superior and inferior tarsi medial to the puncta lacrimalia; occasionally it is very indistinct. [WP,unvetted]. [Wikipedia:Orbicularis_oculi_muscle]
    • + orbicularis oculi muscle definition A circumorbital muscle in the face that closes the eyelid[HP]. { database cross reference=http://en.wikipedia.org/wiki/Orbicularis_oculi_muscle }
    • + orbicularis oculi muscle has exact synonym orbicularis oculi { database cross reference=http://en.wikipedia.org/wiki/Orbicularis_oculi_muscle }
    • + orbicularis oculi muscle label orbicularis oculi muscle

Changes for: longus capitis muscle

Changes for: constrictor muscle of pharynx

Changes for: embryoid body

  • Deleted
    • - embryoid body comment In future this class may be ceded to another ontology if it falls outside the scope of in-vivo, non-pathological biology
  • Added
    • + embryoid body editor note in future this class may be ceded to another ontology if it falls outside the scope of in-vivo, non-pathological biology

Changes for: subclavian vein

Changes for: anterior vena cava

Changes for: kidney collecting duct epithelium

  • Deleted
    • - kidney collecting duct epithelium comment In mouse, the mature and differentiated CD epithelium comprises two unique cells types with principal cells responsible for vasopressin-regulated water reabsorption, and intercalated cells regulating acid-base homeostasis; injury to the epithelium is believed to cause epithelial cells to acquire mesenchymal characteristics via epithelial-mesenchymal transition (EMT), a process through which tubular epithelial cells may transform into interstitial fibroblasts and promote renal fibrosis
  • Added
    • + kidney collecting duct epithelium taxon notes In mouse, the mature and differentiated CD epithelium comprises two unique cells types with principal cells responsible for vasopressin-regulated water reabsorption, and intercalated cells regulating acid-base homeostasis; injury to the epithelium is believed to cause epithelial cells to acquire mesenchymal characteristics via epithelial-mesenchymal transition (EMT), a process through which tubular epithelial cells may transform into interstitial fibroblasts and promote renal fibrosis

Changes for: internal thoracic vein

Changes for: femur cartilage element

Changes for: future inferior salivatory nucleus

Changes for: forelimb stylopod

  • Deleted
    • - forelimb stylopod comment WP states: anatomical usage, the term arm refers specifically to the segment between the shoulder and the elbow, while the segment between the elbow and wrist is the forearm. However, in common, literary, and historical usage, arm refers to the entire upper limb from shoulder to wrist. FMA uses the term Arm for this class, so we place it here. // comment: todo - check fore propodium in AAO // Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here
  • Added
    • + forelimb stylopod comment WP states: anatomical usage, the term arm refers specifically to the segment between the shoulder and the elbow, while the segment between the elbow and wrist is the forearm. However, in common, literary, and historical usage, arm refers to the entire upper limb from shoulder to wrist. FMA uses the term Arm for this class, so we place it here. // comment: editor note: TODO - check fore propodium in AAO // Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here

Changes for: basal nucleus of telencephalon

Changes for: spiracle

  • Deleted
    • - spiracle comment Taxon notes: In elasmobranchs (sharks and rays), a spiracle is found behind each eye, and is often used to pump water through the gills while the animal is at rest (Fouts, 2003). A spiracle is also found in primitive bony fishes as the chirrups.
  • Added
    • + spiracle taxon notes In elasmobranchs (sharks and rays), a spiracle is found behind each eye, and is often used to pump water through the gills while the animal is at rest (Fouts, 2003). A spiracle is also found in primitive bony fishes as the chirrups.

Changes for: ciliary muscle

Changes for: muscle of iris

Changes for: sphincter pupillae

Changes for: oral gland

Changes for: dilatator pupillae

Changes for: spermatic artery

Changes for: bone of pelvis

  • Deleted
    • - bone of pelvis comment In MA, this is the superclass of the 3 innominate elements (pelvic girdle bones) and caudal and sacral vertebrae. This class is included to ensure consistency across anatomical ontologies
  • Added

Changes for: food storage organ

  • Deleted
    • - food storage organ comment This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates
  • Added
    • + food storage organ curator notes This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates

Changes for: tympanic plate

  • Deleted
    • - tympanic plate comment Consider merging with tympanic ring. See discussion page on wikipedia page for ectotympanic. todo: distinguish ecto- and ento- tympanics
  • Added
    • + tympanic plate comment Consider merging with tympanic ring. See discussion page on wikipedia page for ectotympanic. editor note: TODO distinguish ecto- and ento- tympanics

Changes for: central retinal artery

Changes for: right lung accessory lobe

  • Deleted
    • - right lung accessory lobe comment In mouse this is sometimes divided into intermediate and diaphragmatic lobes[ISBN10:0123813611] // In humans, the right lung typically has 3 lobes (superior, middle, inferior). The lobar fissures are often incomplete, making a connection between two apposed lobes. Conversely, more than the expected number of lobes may be produced by new fissures e.g. the azygous lobe of the lung. The additional lobes are termed ‘accessory lobes’ – http://www.gpnotebook.co.uk/simplepage.cfm?ID=1120927803
  • Added
    • + right lung accessory lobe comment In humans, the right lung typically has 3 lobes (superior, middle, inferior). The lobar fissures are often incomplete, making a connection between two apposed lobes. Conversely, more than the expected number of lobes may be produced by new fissures e.g. the azygous lobe of the lung. The additional lobes are termed ‘accessory lobes’ – http://www.gpnotebook.co.uk/simplepage.cfm?ID=1120927803
    • + right lung accessory lobe taxon notes In mouse this is sometimes divided into intermediate and diaphragmatic lobes[ISBN10:0123813611]

Changes for: vein

  • Deleted
    • - vein comment TODO - check with MA - vein vs venous blood vessel
  • Added

Changes for: transverse sinus

  • Deleted
    • - transverse sinus SubClassOf venous sinus
    • - transverse sinus comment todo - check su
    • - transverse sinus definition The transverse sinuses (left and right lateral sinuses), within a human head, are two areas beneath the brain, which allow blood veins to span the area, from the back of the head towards the nose. They drain from the straight sinus and superior sagittal sinus (along the top and back of the brain) to the sigmoid sinuses (at the center of the head), at the internal jugular vein. See diagram (at right): labeled under the brain as ‘’ . The transverse sinuses are of large size and begin at the internal occipital protuberance; one, generally the right, being the direct continuation of the superior sagittal sinus, the other of the straight sinus. Each transverse sinus passes lateralward and forward, describing a slight curve with its convexity upward, to the base of the petrous portion of the temporal bone, and lies, in this part of its course, in the attached margin of the tentorium cerebelli; it then leaves the tentorium and curves downward and medialward to reach the jugular foramen, where it ends in the internal jugular vein. In its course it rests upon the squama of the occipital, the mastoid angle of the parietal, the mastoid part of the temporal, and, just before its termination, the jugular process of the occipital; the portion which occupies the groove on the mastoid part of the temporal is sometimes termed the sigmoid sinus. The transverse sinuses are frequently of unequal size, with the one formed by the superior sagittal sinus being the larger; they increase in size as they proceed, from back to center. On transverse section, the horizontal portion exhibits a prismatic form, the curved portion has a semicylindrical form. They receive the blood from the superior petrosal sinuses at the base of the petrous portion of the temporal bone; they communicate with the veins of the pericranium by means of the mastoid and condyloid emissary veins; and they receive some of the inferior cerebral and inferior cerebellar veins, and some veins from the diploë. The petrosquamous sinus, when present, runs backward along the junction of the squama and petrous portion of the temporal, and opens into the transverse sinus. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Transverse_sinuses }
  • Added

Changes for: superior sagittal sinus

Changes for: presumptive midbrain

Changes for: midbrain hindbrain boundary neural plate

Changes for: layer of tympanic membrane

Changes for: right pulmonary artery

Changes for: left pulmonary artery

Changes for: right lung associated mesenchyme

Changes for: left lung associated mesenchyme

Changes for: entorhinal area

  • Deleted
    • - entorhinal area comment todo - check area vs complex. ABA:ENT this is part of the hippocampal formation via retrohippocampal region
  • Added
    • + entorhinal area editor note TODO - check area vs complex. ABA:ENT this is part of the hippocampal formation via retrohippocampal region

Changes for: splanchnopleure

Changes for: marginal zone of embryo

Changes for: perinatal stage

  • Deleted
    • - perinatal stage comment In birds, the paranatal stage starts when the beak penetrates into the air pocket (air cell) between the inner and outer shell membranes
  • Added
    • + perinatal stage taxon notes In birds, the paranatal stage starts when the beak penetrates into the air pocket (air cell) between the inner and outer shell membranes

Changes for: buccal salivary gland

Changes for: basal forebrain

  • Deleted
    • - basal forebrain definition The basal forebrain is a collection of structures located ventrally to the striatum. It is considered to be the major cholinergic output of the CNS. It includes a group of structures that lie near the bottom of the front of the brain, including the nucleus basalis, diagonal band of Broca, and medial septal nuclei. These structures are important in the production of acetylcholine, which is then distributed widely throughout the brain. Acetylcholine affects the ability of brain cells to transmit information to one another, and also encourages plasticity, or learning. Thus, damage to the basal forebrain can reduce the amount of acetylcholine in the brain and impair learning. This may be one reason why basal forebrain damage can result in memory impairments such as amnesia and confabulation. One common cause of basal forebrain damage is aneurysm of the anterior communicating artery. Research, conducted by investigators from Children’s Hospital Boston and the University of Helsinki, ties together previous observations about sleep and finds that nitric oxide production in the basal forebrain is both necessary and sufficient to produce sleep. This structure is defined, in part, as the place where adenosine acts on A1 receptors of cholinergic neurons. This results in hyperpolarization of cholinergic neurons, which inhibits the release of acetylcholine. Acetylcholine is known to promote wakefulness in the basal forebrain. Inhibition of acetylcholine release in the basal forebrain by adenosine causes slow wave sleep. The basal forebrain and adjacent areas are a focus for sleep research. Stimulating the basal forebrain gives rise to EEG sychrony and sleep. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Basal_forebrain }
  • Added
    • + basal forebrain definition A region of the brain consisting of ventral and rostral subcortical regions of the telencephalon, including among others, the basal ganglia, septal nuclei, amygdala, ventral pallidum, substantia innominata, and basal nucleus of Meynert. { database cross reference=Neurolex:birnlex_1560 }

Changes for: fibulare

  • Deleted
    • - fibulare comment In salamanders this element is aproximatelly rounded, whereas in anurans it is an elongate, cylindrical bone with the proximal and distal heads fused to the heads of the tibiale[AAO]
  • Added
    • + fibulare taxon notes In salamanders this element is aproximatelly rounded, whereas in anurans it is an elongate, cylindrical bone with the proximal and distal heads fused to the heads of the tibiale[AAO]

Changes for: bile duct epithelium

Changes for: dental lamina

Changes for: pedal digit 8

Changes for: lateral-intermediate intercuneiform joint

Changes for: prepollex skeleton

  • Deleted
    • - prepollex skeleton comment A prepollex does not contain phalanges nor does it articulate with a metacarpal. It articulates with elements of the carpal (wrist) skeleton[AAO:DB]. TODO: add articulation relations
  • Added
    • + prepollex skeleton comment A prepollex does not contain phalanges nor does it articulate with a metacarpal. It articulates with elements of the carpal (wrist) skeleton[AAO:DB]. EDITOR NOTE: TODO add articulation relations

Changes for: medial-intermediate intercuneiform joint

Changes for: pedal digit 7

Changes for: metathalamus

Changes for: salivary gland epithelium

Changes for: oviduct epithelium

  • Deleted
    • - oviduct epithelium comment in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label
  • Added

Changes for: larva

  • Deleted
    • - larva comment This class was created automatically from a combination of ontologies. TODO: discriminate between stages and organisms
  • Added
    • + larva comment This class was created automatically from a combination of ontologies. EDITOR NOTE: TODO discriminate between stages and organisms

Changes for: germ ring

  • Deleted
    • - germ ring comment todo - check timing of appearance and disappearance - check relationship with primitive streak. he blastopore lips in amphibians appear to have the equivalent function of the germ ring in zebrafish (ES)
  • Added
    • + germ ring editor note TODO - check timing of appearance and disappearance - check relationship with primitive streak. he blastopore lips in amphibians appear to have the equivalent function of the germ ring in zebrafish (ES)

Changes for: pharyngeal arch

  • Deleted
    • - pharyngeal arch comment Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering
  • Added
    • + pharyngeal arch terminology notes Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering

Changes for: ureteral orifice

Changes for: epiblast (generic)

  • Deleted
    • - epiblast (generic) comment MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class
  • Added
    • + epiblast (generic) editor note MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class

Changes for: limb segment

  • Deleted
    • - limb segment comment note FMA has both limb segment and free limb segment, the former includes the girdles. Note that MA uses the term more generally and includes A,S,Z,S+Z(arm/leg), whereas FMA is just A,S,Z
  • Added

Changes for: navicular bone of pes

Changes for: forelimb skeleton

Changes for: chest

  • Deleted
    • - chest comment editor note - FMA:24216 present in FMA1, but gone in subsequent versions
  • Added
    • + chest comment editor note: FMA:24216 present in FMA1, but gone in subsequent versions

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: tarsal bone

  • Deleted
    • - tarsal bone comment In primitive tetrapods, such as Trematops, the tarsus consists of three rows of bones. There are three proximal tarsals, the tibiale, intermedium, and fibulare, named for their points of articulation with the bones of the lower limb. These are followed by a second row of four bones, referred to as the centralia (singular: centrale), and then a row of five distal tarsals, each articulating with a single metatarsal. In the great majority of tetrapods, including all of those alive today, this simple pattern is modified by the loss and fusion of various of the bones.[3] In reptiles and mammals, there are normally just two proximal tarsals, the calcaneus (equivalent to the amphibian fibulare) and the talus (probably derived from a fusion of multiple bones). In mammals, including humans, the talus forms a hinge joint with the tibia, a feature especially well developed in the artiodactyls. The calcaneus is also modified, forming a heel for the attachment of the Achilles tendon. Neither of these adaptations is found in reptiles, which have a relatively simple structure to both bones.[3] The fifth distal tarsal disappears relatively early in evolution, with the remainder becoming the cuneiform and cuboid bones. Reptiles usually retain two centralia, while mammals typically have only one (the navicular).[3] In birds, the tarsus has disappeared, with the proximal tarsals having fused with the tibia, the centralia having disappeared, and the distal bones having fused with the metatarsals to form a single tarsometatarsus bone, effectively giving the leg a third segment[Wikipedia:Tarsus_(skeleton)]
  • Added
    • + tarsal bone taxon notes In primitive tetrapods, such as Trematops, the tarsus consists of three rows of bones. There are three proximal tarsals, the tibiale, intermedium, and fibulare, named for their points of articulation with the bones of the lower limb. These are followed by a second row of four bones, referred to as the centralia (singular: centrale), and then a row of five distal tarsals, each articulating with a single metatarsal. In the great majority of tetrapods, including all of those alive today, this simple pattern is modified by the loss and fusion of various of the bones.[3] In reptiles and mammals, there are normally just two proximal tarsals, the calcaneus (equivalent to the amphibian fibulare) and the talus (probably derived from a fusion of multiple bones). In mammals, including humans, the talus forms a hinge joint with the tibia, a feature especially well developed in the artiodactyls. The calcaneus is also modified, forming a heel for the attachment of the Achilles tendon. Neither of these adaptations is found in reptiles, which have a relatively simple structure to both bones.[3] The fifth distal tarsal disappears relatively early in evolution, with the remainder becoming the cuneiform and cuboid bones. Reptiles usually retain two centralia, while mammals typically have only one (the navicular).[3] In birds, the tarsus has disappeared, with the proximal tarsals having fused with the tibia, the centralia having disappeared, and the distal bones having fused with the metatarsals to form a single tarsometatarsus bone, effectively giving the leg a third segment[Wikipedia:Tarsus_(skeleton)]

Changes for: distal phalanx of digit 1

Changes for: pectoral girdle region

  • Deleted
    • - pectoral girdle region comment Usage Notes: this class describes the organism subdivision, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831).
  • Added

Changes for: scaphoid

  • Deleted
    • - scaphoid comment todo - check AAO placement; in rodents this is fused with the lunate to make the scapholunate
  • Added
    • + scaphoid editor note TODO - check AAO placement; in rodents this is fused with the lunate to make the scapholunate

Changes for: neural tissue

Changes for: articular capsule

Changes for: manus joint

Changes for: pes joint

Changes for: circle of Willis

  • Deleted
    • - circle of Willis comment In zebrafish, the circle of vessels comprised of the basal communicating artery (BCA) and posterior communicating segments (PCS) superficially resemble but are not homologous to the human circle of Willis[http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html]. Editor note:
  • Added
    • + circle of Willis taxon notes In zebrafish, the circle of vessels comprised of the basal communicating artery (BCA) and posterior communicating segments (PCS) superficially resemble but are not homologous to the human circle of Willis[http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html]

Changes for: middle phalanx of digit 5

Changes for: middle phalanx of digit 4

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: extensor carpi ulnaris muscle

Changes for: post-anal tail muscle

Changes for: dentition

Changes for: metacarpal bone of digit 5

Changes for: metacarpal bone of digit 4

Changes for: metacarpal bone of digit 3

Changes for: metacarpal bone of digit 2

Changes for: metacarpal bone of digit 1

Changes for: pedal digit 3 phalanx

Changes for: pedal digit 1 phalanx

Changes for: posterior nasal aperture

  • Deleted
    • - posterior nasal aperture comment Fish don’t have choanae, instead they have two pairs of external nostrils[WP] In addition to tetrapods, the lungfish has internal nostrils too. TODO: check part_of vs adjacent_to nasal cavity. In tetrapods the exhalant nostril (choana) empties into the buccal cavity.
  • Added

Changes for: pedal digit 2 phalanx

Changes for: metatarsal bone of digit 4

Changes for: metatarsal bone of digit 5

Changes for: respiratory system mucosa

Changes for: metatarsal bone of digit 1

Changes for: metatarsal bone of digit 2

Changes for: metatarsal bone of digit 3

Changes for: obsolete node of ranvier

Changes for: regional part of cerebral cortex

Changes for: skeletal element

Changes for: cranial bone

Changes for: vertebral centrum element

  • Deleted
    • - vertebral centrum element comment The vertebral centrum may be cartilaginous, develop as cartilage but be replaced by bone or mineralized, or form directly through intramembranous ossification.
  • Added
    • + vertebral centrum element taxon notes The vertebral centrum may be cartilaginous, develop as cartilage but be replaced by bone or mineralized, or form directly through intramembranous ossification.

Changes for: coracoid bone

  • Deleted
    • - coracoid bone comment Terminology notes: see discussion in Kardong - suggests using procoracoid (anterior coracoid) for the element in birds, reptiles, amphibians and fish, and reserving coracoid for the new synapsid/therian structure.
  • Added
    • + coracoid bone terminology notes see discussion in Kardong - suggests using procoracoid (anterior coracoid) for the element in birds, reptiles, amphibians and fish, and reserving coracoid for the new synapsid/therian structure.

Changes for: pubic symphysis

  • Deleted
    • - pubic symphysis comment In birds, the pubic symphysis is present only in the ostrich, and the two hip bones are usually widely separated, making it easier to lay large eggs - Romer, Alfred Sherwood; Parsons, Thomas S. (1977). The Vertebrate Body. Philadelphia, PA: Holt-Saunders International. pp. 188–192. ISBN 0-03-910284-X.
  • Added
    • + pubic symphysis taxon notes In birds, the pubic symphysis is present only in the ostrich, and the two hip bones are usually widely separated, making it easier to lay large eggs - Romer, Alfred Sherwood; Parsons, Thomas S. (1977). The Vertebrate Body. Philadelphia, PA: Holt-Saunders International. pp. 188–192. ISBN 0-03-910284-X.

Changes for: articular/anguloarticular

Changes for: fasciolar gyrus

  • Deleted
    • - fasciolar gyrus comment TODO - existing definitions, synonyms and relationships in existing AOs seem contradictory; to be resolved. We take the dentate gyrus relationship from BTO, and it is also implied by the FMA synonym. However, FMA says archiortex (embryonic archicortex corresponds to the cortex of the dentate gyrus and hippocampus) and NIF says limbic lobe (which is more general than hippocampus). ABA xref made on basis of BTO related synonym
  • Added
    • + fasciolar gyrus editor note TODO - existing definitions, synonyms and relationships in existing AOs seem contradictory; to be resolved. We take the dentate gyrus relationship from BTO, and it is also implied by the FMA synonym. However, FMA says archiortex (embryonic archicortex corresponds to the cortex of the dentate gyrus and hippocampus) and NIF says limbic lobe (which is more general than hippocampus). ABA xref made on basis of BTO related synonym

Changes for: equine hindlimb splint bone

Changes for: equine forelimb splint bone

Changes for: equine splint bone

  • Deleted
    • - equine splint bone comment In future this class may be replaced by a more taxon-neutral class grouping metapodial bones 2 or 4
  • Added

Changes for: vasa recta

  • Deleted
    • - vasa recta comment TODO - is this a vein or set of veins? in MA it is a venous blood vessel
  • Added

Changes for: inferior phrenic artery

  • Deleted
    • - inferior phrenic artery SubClassOf supplies some diaphragm
    • - inferior phrenic artery definition The inferior phrenic arteries are two small vessels, which supply the diaphragm but present much variety in their origin. They may arise separately from the front of the aorta, immediately above the celiac artery, or by a common trunk, which may spring either from the aorta or from the celiac artery. Sometimes one is derived from the aorta, and the other from one of the renal arteries; they rarely arise as separate vessels from the aorta. They diverge from one another across the crura of the diaphragm, and then run obliquely upward and lateralward upon its under surface. The left phrenic passes behind the esophagus, and runs forward on the left side of the esophageal hiatus. The right phrenic passes behind the inferior vena cava, and along the right side of the foramen which transmits that vein. Near the back part of the central tendon each vessel divides into a medial and a lateral branch. The medial branch curves forward, and anastomoses with its fellow of the opposite side, and with the musculophrenic and pericardiacophrenic arteries. The lateral branch passes toward the side of the thorax, and anastomoses with the lower intercostal arteries, and with the musculophrenic. The lateral branch of the right phrenic gives off a few vessels to the inferior vena cava; and the left one, some branches to the esophagus. Each vessel gives off superior suprarenal branches to the suprarenal gland of its own side. The spleen and the liver also receive a few twigs from the left and right vessels respectively. { database cross reference=http://en.wikipedia.org/wiki/Inferior_phrenic_arteries }

Changes for: bulbus cordis

Changes for: pelvic appendage

  • Deleted

Changes for: dorsal thalamus

Changes for: fenestra

  • Deleted
    • - fenestra comment TODO check fenestra vs fossa. fenestra = hole, fossa = depression with bottom?
  • Added
    • + fenestra editor note TODO check fenestra vs fossa. fenestra = hole, fossa = depression with bottom?

Changes for: secondary olfactory cortex

Changes for: flexor hallucis longus

  • Deleted
    • - flexor hallucis longus definition The Flexor hallucis longus muscle (FHL) is a muscle of the leg. It is one of the deep muscles of the posterior compartment of the leg. The other deep muscles of the leg are flexor digitorum longus and tibialis posterior. FHL is the largest and most powerful of these deep muscles. The Flexor hallucis longus is situated on the fibular side of the leg. It arises from the inferior two-thirds of the posterior surface of the body of the fibula, with the exception of 2.5 cm. at its lowest part; from the lower part of the interosseous membrane; from an intermuscular septum between it and the Peronæi, laterally, and from the fascia covering the Tibialis posterior, medially. The fibers pass obliquely downward and backward, and end in a tendon which occupies nearly the whole length of the posterior surface of the muscle. This tendon lies in a groove which crosses the posterior surface of the lower end of the tibia, the posterior surface of the talus, and the under surface of the sustentaculum tali of the calcaneus; in the sole of the foot it runs forward between the two heads of the Flexor hallucis brevis, and is inserted into the base of the last phalanx of the great toe. The grooves on the talus and calcaneus, which contain the tendon of the muscle, are converted by tendinous fibers into distinct canals, lined by a mucous sheath. As the tendon passes forward in the sole of the foot, it is situated above, and crosses from the lateral to the medial side of the tendon of the Flexor digitorum longus, to which it is connected by a fibrous slip. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Flexor_hallucis_longus_muscle }
  • Added

Changes for: sural artery

Changes for: axillary artery

Changes for: primary motor cortex

  • Deleted
    • - primary motor cortex comment TODO: in MA this is asserted to be part_of BOTH frontal and parietal cortex. in ABA these are disjoint. FMA makes no commitment beyond cerebral cortex. Wikipedia says frontal lobe. Check if species difference or difference in definition. Removed relationship: part_of UBERON:0001872 { source=MA-modified }
  • Added
    • + primary motor cortex editor note TODO - in MA this is asserted to be part_of BOTH frontal and parietal cortex. in ABA these are disjoint. FMA makes no commitment beyond cerebral cortex. Wikipedia says frontal lobe. Check if species difference or difference in definition. Removed relationship: part_of UBERON:0001872 {source=’MA-modified’} ! parietal lobe

Changes for: cornual diverticulum

Changes for: coccyx

  • Deleted
    • - coccyx comment In MA the subclass hierarchy is cocc V is_a caud V is_a tail bone. Taxon notes: In humans: The coccyx, commonly referred to as the tailbone, is the final segment of the human vertebral column. Comprising three to five separate or fused vertebrae (the coccygeal vertebrae) below the sacrum, it is attached to the sacrum by a fibrocartilaginous joint, the sacrococcygeal symphysis, which permits limited movement between the sacrum and the coccyx. The term coccyx comes originally from the Greek language and means ‘cuckoo’, referring to the curved shape of a cuckoo’s beak when viewed from the side. [WP,unvetted].
  • Added
    • + coccyx comment .
    • + coccyx external ontology notes In MA the subclass hierarchy is cocc V is_a caud V is_a tail bone. Taxon notes: In humans: The coccyx, commonly referred to as the tailbone, is the final segment of the human vertebral column. Comprising three to five separate or fused vertebrae (the coccygeal vertebrae) below the sacrum, it is attached to the sacrum by a fibrocartilaginous joint, the sacrococcygeal symphysis, which permits limited movement between the sacrum and the coccyx. The term coccyx comes originally from the Greek language and means ‘cuckoo’, referring to the curved shape of a cuckoo’s beak when viewed from the side. [WP,unvetted] { external ontology=MA }

Changes for: epithelium of vagina

  • Deleted
    • - epithelium of vagina comment FMA: nonkeratinizing stratified squamous epithelium; BTO: Vaginal epithelium is stratified squamous epithelium having a thickness of 15-200 microns; MA has single subclass (squamous)
  • Added
    • + epithelium of vagina comment AO notes: FMA: nonkeratinizing stratified squamous epithelium; BTO: Vaginal epithelium is stratified squamous epithelium having a thickness of 15-200 microns; MA has single subclass (squamous)

Changes for: epididymis

  • Deleted
    • - epididymis comment . Kardong has epididymis in elasmobranch.Structures notes: Typically divided into three main regions. In reptiles, there is an additional canal between the testis and the head of the epididymis, which receives the various efferent ducts. This is, however, absent in all birds and mammals. The epididymis is covered by a two layered pseudostratified epithelium. The epithelium is separated by a basement membrane from the connective tissue wall which has smooth muscle cells.
  • Added
    • + epididymis comment Structures notes: Typically divided into three main regions. In reptiles, there is an additional canal between the testis and the head of the epididymis, which receives the various efferent ducts. This is, however, absent in all birds and mammals. The epididymis is covered by a two layered pseudostratified epithelium. The epithelium is separated by a basement membrane from the connective tissue wall which has smooth muscle cells.
    • + epididymis editor note Kardong has epididymis in elasmobranch

Changes for: male urethra

Changes for: female urethra

Changes for: prostate gland anterior lobe

Changes for: pedal digit 1 metatarsal endochondral element

Changes for: pedal digit 4 phalanx endochondral element

Changes for: pedal digit 5 phalanx endochondral element

Changes for: pedal digit 2 metatarsal endochondral element

Changes for: pedal digit 3 metatarsal endochondral element

Changes for: pedal digit 2 phalanx endochondral element

Changes for: pedal digit 3 phalanx endochondral element

Changes for: pedal digit 1 phalanx endochondral element

Changes for: hindlimb skin

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: forelimb skin

Changes for: manual digit 3 metacarpus endochondral element

Changes for: manual digit 4 metacarpus endochondral element

Changes for: manual digit 5 metacarpus endochondral element

Changes for: pedal digit 5 metatarsal endochondral element

Changes for: manual digit 1 metacarpus endochondral element

Changes for: manual digit 2 metacarpus endochondral element

Changes for: pedal digit 4 metatarsal endochondral element

Changes for: tarsal skeleton

  • Deleted
    • - tarsal skeleton comment . AO notes: we assume MA:tarsus belongs here, as there is a distinct class MA:ankle, with the tarsal bone being part of the former. XAO:tarsus is part of the hindlimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent.
  • Added
    • + tarsal skeleton external ontology notes we assume MA:tarsus belongs here, as there is a distinct class MA:ankle, with the tarsal bone being part of the former. XAO:tarsus is part of the hindlimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent. { external ontology=MA }

Changes for: retina blood vessel

Changes for: facial mesenchyme

Changes for: interlobar vein

Changes for: ciliary stroma

Changes for: interlobar artery

Changes for: medullary ray

  • Deleted
    • - medullary ray comment Terminology notes: Their name is potentially misleading – the “medullary” refers to their destination, not their location. They are located only in the renal cortex, and not in the renal medulla. AO notes: FMA says parenchyma, MP says cortex
  • Added
    • + medullary ray comment AO notes: FMA says parenchyma, MP says cortex
    • + medullary ray terminology notes Their name is potentially misleading – the ‘medullary’ refers to their destination, not their location. They are located only in the renal cortex, and not in the renal medulla

Changes for: iris blood vessel

Changes for: trigeminal nucleus

  • Deleted
    • - trigeminal nucleus comment note massive inconsistencies between GO, MA, wikipedia. Part of pons in MA, but this leads to inconsistencies with ABA. See https://sourceforge.net/tracker/?func=detail&aid=3291162&group_id=76834&atid=1205376
  • Added

Changes for: future brain vesicle

  • Deleted
    • - future brain vesicle comment todo - resolve space vs structure inconsistency; consider adding all secondary vesicles (e.g. diencephalic; my/metencephalic. See http://www.dartmouth.edu/~rswenson/NeuroSci/chapter_4.html). Note that some sources may treat the term vesicle as the progenitor of the whole brain region; for example ‘The retina develops directly from the neural tube as an outpouching from the diencephalic vesicle’
  • Added
    • + future brain vesicle editor note TODO - resolve space vs structure inconsistency; consider adding all secondary vesicles (e.g. diencephalic; my/metencephalic. See http://www.dartmouth.edu/~rswenson/NeuroSci/chapter_4.html). Note that some sources may treat the term vesicle as the progenitor of the whole brain region; for example ‘The retina develops directly from the neural tube as an outpouching from the diencephalic vesicle’

Changes for: vein of abdomen

  • Deleted
    • - vein of abdomen comment This class groups all veins that are in the abdomen. The term ‘abdominal vein’ may have specific meanings in different contexts. The lateral abdominal veins are present in fishes but usually merged or absent in tetrapods; in amphibians, the L&R abdominal veins merge into the ventral abdominal vein. TODO: mirror representation of abdominal aorta
  • Added
    • + vein of abdomen comment This class groups all veins that are in the abdomen. The term ‘abdominal vein’ may have specific meanings in different contexts. The lateral abdominal veins are present in fishes but usually merged or absent in tetrapods; in amphibians, the L&R abdominal veins merge into the ventral abdominal vein. EDITOR NOTE: TODO mirror representation of abdominal aorta

Changes for: superior phrenic artery

Changes for: serosa of uterus

Changes for: proximal straight tubule

Changes for: thick ascending limb of loop of Henle

Changes for: Bowman’s space

Changes for: loop of Henle

  • Deleted
    • - loop of Henle comment Taxon Notes: the definitions of some kidney parts refer to Henle’s loop, even in species where this may not be present. Requires review.
  • Added
    • + loop of Henle taxon notes the definitions of some kidney parts refer to Henle’s loop, even in species where this may not be present. Requires review.

Changes for: epithelium of stomach

Changes for: innominate bone

  • Deleted
    • - innominate bone comment Editor notes: currently this class is restricted to exclude the teleost bone as the definition mentions ilium, ischium and pubis. In future we may add a grouping class for girdle bones that supports the appendage
  • Added
    • + innominate bone editor note currently this class is restricted to exclude the teleost bone as the definition mentions ilium, ischium and pubis. In future we may add a grouping class for girdle bones that supports the appendage

Changes for: pelvic girdle region

  • Deleted
    • - pelvic girdle region comment Usage Notes: this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list
  • Added
    • + pelvic girdle region curator notes this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list

Changes for: bony pelvis

Changes for: acetabular part of hip bone

Changes for: motor root of trigeminal nerve

Changes for: serosa of urinary bladder

Changes for: serosa of intestine

Changes for: falciform ligament

Changes for: right adrenal gland

Changes for: left adrenal gland

Changes for: renal straight tubule

Changes for: Peyer’s patch

Changes for: serosa of large intestine

Changes for: serosa of stomach

Changes for: root of optic nerve

Changes for: mesenchyme of sublingual gland

Changes for: mesenchyme of vomeronasal organ

Changes for: mesenchyme of hard palate

Changes for: mesenchyme of umbilical cord

Changes for: primitive superior sagittal sinus

Changes for: excretory gland

Changes for: iris nerve

Changes for: nerve of trunk region

Changes for: main olfactory bulb

Changes for: mesenchyme of mandible

Changes for: mesenchyme of parotid

Changes for: palate bone

Changes for: mesenchyme of tongue

Changes for: mesenchyme of nasal septum

Changes for: mesenchyme of submandibular gland

Changes for: mesenchyme of soft palate

Changes for: fovea capitis of femur

Changes for: vomeronasal nerve

Changes for: hyaloid artery

  • Deleted
    • - hyaloid artery SubClassOf head blood vessel
    • - hyaloid artery SubClassOf structure with developmental contribution from neural crest
    • - hyaloid artery comment ZFA def is: Artery that is internal to the eye; this is more general than the human-centric definition here..
    • - hyaloid artery definition The hyaloid artery is a branch of the ophthalmic artery, which is itself a branch of the internal carotid artery. It is contained within the optic stalk of the eye and extends from the optic disc through the vitreous humor to the lens. Usually fully regressed before birth, its purpose is to supply nutrient to the developing lens in the growing fetus. During the tenth week of development in humans (time varies depending on species), the lens grows independent of a blood supply and the hyaloid artery usually regresses. Its proximal portion remains as the central artery of the retina. Regression of the hyaloid artery leaves a clear central zone through the vitreous called the hyaloid canal or Cloquet’s canal. Occasionally the artery may not fully regress, resulting in the condition persistent hyaloid artery. More commonly, small remnants of the artery may remain. Free remnants can sometimes be seen as ‘floaters’. An anterior remnant of the hyaloid artery can be seen in some people as Mittendorf’s dot, a small pinpoint-like scar on the posterior surface of the lens. A posterior remnant may be seen where the artery left the optic disc, and is known as Bergmeister’s papilla. { database cross reference=http://en.wikipedia.org/wiki/Hyaloid_artery }
  • Added
    • + hyaloid artery SubClassOf hyaloid vessel
    • + hyaloid artery SubClassOf supplies some lens of camera-type eye
    • + hyaloid artery comment Taxon notes: In humans, Usually fully regressed before birth, its purpose is to supply nutrient to the developing lens in the growing fetus. During the tenth week of development the lens grows independent of a blood supply and the hyaloid artery usually regresses. Its proximal portion remains as the central artery of the retina. Regression of the hyaloid artery leaves a clear central zone through the vitreous called the hyaloid canal or Cloquet’s canal. Occasionally the artery may not fully regress, resulting in the condition persistent hyaloid artery. More commonly, small remnants of the artery may remain. Free remnants can sometimes be seen as ‘floaters’. An anterior remnant of the hyaloid artery can be seen in some people as Mittendorf’s dot, a small pinpoint-like scar on the posterior surface of the lens. A posterior remnant may be seen where the artery left the optic disc, and is known as Bergmeister’s papilla
    • + hyaloid artery definition An artery that is part of the optic stalk of the eye and extends from the optic disc through the vitreous humor to the lens. { database cross reference=http://en.wikipedia.org/wiki/Hyaloid_artery }

Changes for: reticular formation

  • Deleted
    • - reticular formation comment note that this class denotes the generic structure, and not a specific one such as medullary or pontine reticular formation.
  • Added
    • + reticular formation comment Usage notes: this class denotes the generic structure, and not a specific one such as medullary or pontine reticular formation.

Changes for: pedal digit 1 metatarsal pre-cartilage condensation

Changes for: pedal digit 2 metatarsal pre-cartilage condensation

Changes for: pedal digit 3 metatarsal pre-cartilage condensation

Changes for: sphenoid bone pre-cartilage condensation

Changes for: basioccipital pre-cartilage condensation

Changes for: optic recess of third ventricle

Changes for: scala media

Changes for: manual digit 5 metacarpus pre-cartilage condensation

Changes for: manual digit 1 metacarpus pre-cartilage condensation

Changes for: manual digit 2 metacarpus pre-cartilage condensation

Changes for: manual digit 3 metacarpus pre-cartilage condensation

Changes for: manual digit 4 metacarpus pre-cartilage condensation

Changes for: pedal digit 1 mesenchyme

Changes for: pedal digit 5 metatarsal cartilage element

Changes for: manual digit 1 mesenchyme

Changes for: pedal digit 4 metatarsal cartilage element

Changes for: supraorbital gland

  • Deleted
    • - supraorbital gland definition The supraorbital gland is a type of lateral nasal gland found in some species of marine birds, particularly penguins, which removes sodium chloride from the bloodstream. The gland’s function is similar to that of the kidneys, though it is much more efficient at removing salt, allowing Penguins to survive without access to fresh water. Contrary to popular belief, the gland does not directly convert saltwater to freshwater. The term supraorbital refers to the area just above the eye socket (which is known as the orbit of the eye. ) Living in saltwater environments would naturally pose a large problem for penguins because the ingestion of saltwater would be detrimental to a penguin’s health. Although penguins do not directly drink water, it is taken in when they engulf prey. As a result, saltwater enters their system and must be effectively excreted. The supraorbital gland has thus enabled the penguins’ survival in such environments due to its water-filtering capability. The gland is located just above the eyes and surrounds a capillary in the head. This capillary constantly strains out the salt in the saltwater that a penguin takes in. Since the byproduct of the gland has roughly five times as much salt as would normally be found in the animal’s fluids, the supraorbital gland is highly efficient. The penguin excretes the salt byproduct as a brine through its bill. Often, the fluid drips out, and this gives the appearance of a runny nose. However, the fluid may also be sneezed out. In the absence of saltwater, caused by captivity, the supraorbital gland will lie dormant as it has no other purpose. Having a dormant supraorbital gland does not negatively affect the health of a penguin. { database cross reference=http://en.wikipedia.org/wiki/Supraorbital_gland }
  • Added
    • + supraorbital gland comment Function notes: The gland’s function is similar to that of the kidneys, though it is much more efficient at removing salt, allowing Penguins to survive without access to fresh water. Contrary to popular belief, the gland does not directly convert saltwater to freshwater. The term supraorbital refers to the area just above the eye socket (which is known as the orbit of the eye. ) Living in saltwater environments would naturally pose a large problem for penguins because the ingestion of saltwater would be detrimental to a penguin’s health. Although penguins do not directly drink water, it is taken in when they engulf prey. As a result, saltwater enters their system and must be effectively excreted. The supraorbital gland has thus enabled the penguins’ survival in such environments due to its water-filtering capability. The gland is located just above the eyes and surrounds a capillary in the head. This capillary constantly strains out the salt in the saltwater that a penguin takes in. Since the byproduct of the gland has roughly five times as much salt as would normally be found in the animal’s fluids, the supraorbital gland is highly efficient. The penguin excretes the salt byproduct as a brine through its bill. Often, the fluid drips out, and this gives the appearance of a runny nose. However, the fluid may also be sneezed out. In the absence of saltwater, caused by captivity, the supraorbital gland will lie dormant as it has no other purpose. Having a dormant supraorbital gland does not negatively affect the health of a penguin
    • + supraorbital gland definition A lateral nasal gland that removes sodium chloride from the bloodstream. { database cross reference=http://en.wikipedia.org/wiki/Supraorbital_gland }

Changes for: pedal digit 2 metatarsal cartilage element

Changes for: pedal digit 3 metatarsal cartilage element

Changes for: pedal digit 1 metatarsal cartilage element

Changes for: pedal digit 5 metatarsal pre-cartilage condensation

Changes for: pedal digit 4 metatarsal pre-cartilage condensation

Changes for: foramen of Panizza

  • Deleted
    • - foramen of Panizza definition The Foramen of Panizza is a hole with that connects the left and right aorta as they leave the heart of all animals of the order Crocodilia. Crocodilians have a completely separated ventricle with deoxygenated blood from the body, or systemic circulation, in the right ventricle and oxygenated blood from the lungs, or pulmonary circulation, in the left ventricle, as in birds and mammals. Two vessels, the left aorta and the pulmonary artery, exit the right ventricle. Blood from the right ventricle goes to the lungs through the pulmonary artery, as in mammals and birds. However, when a unique active valve leading to the pulmonary artery contracts, pressure in the right ventricle can increase and blood can leave the right ventricle, enter the left aortic arch, and therefore bypass the pulmonary circulation. The foramen of panizza connects the left and right aorta. Deoxygenated blood from the right ventricle, sitting in the left aorta, can flow into the right aorta through the foramen of panizza. When the heart is relaxed, some oxygenated blood from the left ventricle, sitting in the right aorta, can flow into the left aorta across the foramen of panizza. However, some species of Crocodilians have regulatory sphincters that prevent unwanted flow of blood through the foramen of panizza during non-diving. { database cross reference=http://en.wikipedia.org/wiki/Foramen_of_Panizza }
  • Added
    • + foramen of Panizza comment Crocodilians have a completely separated ventricle with deoxygenated blood from the body, or systemic circulation, in the right ventricle and oxygenated blood from the lungs, or pulmonary circulation, in the left ventricle, as in birds and mammals. Two vessels, the left aorta and the pulmonary artery, exit the right ventricle. Blood from the right ventricle goes to the lungs through the pulmonary artery, as in mammals and birds. However, when a unique active valve leading to the pulmonary artery contracts, pressure in the right ventricle can increase and blood can leave the right ventricle, enter the left aortic arch, and therefore bypass the pulmonary circulation. The foramen of panizza connects the left and right aorta. Deoxygenated blood from the right ventricle, sitting in the left aorta, can flow into the right aorta through the foramen of panizza. When the heart is relaxed, some oxygenated blood from the left ventricle, sitting in the right aorta, can flow into the left aorta across the foramen of panizza. However, some species of Crocodilians have regulatory sphincters that prevent unwanted flow of blood through the foramen of panizza during non-diving
    • + foramen of Panizza definition A hole with that connects the left and right aorta in animals of the order Crocodilia. { database cross reference=http://en.wikipedia.org/wiki/Foramen_of_Panizza }

Changes for: entire embryonic mesenchyme

Changes for: pedal digit 1 phalanx pre-cartilage condensation

Changes for: pedal digit 2 phalanx pre-cartilage condensation

Changes for: pedal digit 3 phalanx pre-cartilage condensation

Changes for: pedal digit 4 phalanx pre-cartilage condensation

Changes for: pedal digit 5 phalanx pre-cartilage condensation

Changes for: uterine horn

  • Deleted

Changes for: manual digit 5 phalanx pre-cartilage condensation

Changes for: manual digit 4 phalanx pre-cartilage condensation

Changes for: manual digit 3 phalanx pre-cartilage condensation

Changes for: manual digit 2 phalanx pre-cartilage condensation

Changes for: spinal cord

Changes for: manual digit 1 metacarpus cartilage element

Changes for: manual digit 2 metacarpus cartilage element

Changes for: manual digit 5 metacarpus cartilage element

Changes for: manual digit 1 phalanx pre-cartilage condensation

Changes for: lobe of thyroid gland

  • Deleted
    • - lobe of thyroid gland SubClassOf organ part
    • - lobe of thyroid gland comment This class was created automatically from a combination of ontologies
    • - lobe of thyroid gland definition The lobes of the thyroid gland are conical in shape, the apex of each being directed upward and lateralward as far as the junction of the middle with the lower third of the thyroid cartilage; the base looks downward, and is on a level with the fifth or sixth tracheal ring. Each lobe is about 5 cm. long; its greatest width is about 3 cm. , and its thickness about 2 cm. The lateral or superficial surface is convex, and covered by the skin, the superficial and deep fasciæ, the Sternocleidomastoideus, the superior belly of the Omohyoideus, the Sternohyoideus and Sternothyreoideus, and beneath the last muscle by the pretracheal layer of the deep fascia, which forms a capsule for the gland. The deep or medial surface is moulded over the underlying structures, viz. , the thyroid and cricoid cartilages, the trachea, the Constrictor pharyngis inferior and posterior part of the Cricothyreoideus, the esophagus (particularly on the left side of the neck), the superior and inferior thyroid arteries, and the recurrent nerves. The anterior border is thin, and inclines obliquely from above downward toward the middle line of the neck, while the posterior border is thick and overlaps the common carotid artery, and, as a rule, the parathyroids. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Lobes_of_thyroid_gland }
  • Added
    • + lobe of thyroid gland EquivalentTo anatomical lobe and part of some thyroid gland
    • + lobe of thyroid gland SubClassOf anatomical lobe
    • + lobe of thyroid gland comment The lobes of the thyroid gland are conical in shape, the apex of each being directed upward and lateralward as far as the junction of the middle with the lower third of the thyroid cartilage; the base looks downward, and is on a level with the fifth or sixth tracheal ring. Each lobe is about 5 cm. long; its greatest width is about 3 cm. , and its thickness about 2 cm. The lateral or superficial surface is convex, and covered by the skin, the superficial and deep fasciæ, the Sternocleidomastoideus, the superior belly of the Omohyoideus, the Sternohyoideus and Sternothyreoideus, and beneath the last muscle by the pretracheal layer of the deep fascia, which forms a capsule for the gland. The deep or medial surface is moulded over the underlying structures, viz. , the thyroid and cricoid cartilages, the trachea, the Constrictor pharyngis inferior and posterior part of the Cricothyreoideus, the esophagus (particularly on the left side of the neck), the superior and inferior thyroid arteries, and the recurrent nerves. The anterior border is thin, and inclines obliquely from above downward toward the middle line of the neck, while the posterior border is thick and overlaps the common carotid artery, and, as a rule, the parathyroids
    • + lobe of thyroid gland definition A lobe of tissue that is part of a thyroid gland. { database cross reference=UBERON:cjm }

Changes for: manual digit 3 metacarpus cartilage element

Changes for: manual digit 4 metacarpus cartilage element

Changes for: splenius

Changes for: thyroglossal duct

Changes for: vomeronasal organ

  • Deleted
    • - vomeronasal organ definition The vomeronasal organ (VNO), or Jacobson’s organ, is an auxiliary olfactory sense organ that is found in many animals. It was discovered by Ludwig Jacobson in 1813. During embryological development, it forms from the nasal (olfactory) placode, at the anterior edge of the neural plate. It is a chemoreceptor organ which is completely separated from the nasal cavity the majority of the time, being enclosed in a separate bony or cartilaginous capsule which opens into the base of the nasal cavity. It is a tubular crescent shape and split into two pairs, separated by the nasal septum. It is the first processing stage of the accessory olfactory system, after which chemical stimuli go to the accessory olfactory bulb, then to targets in the amygdala and hypothalamus. The vomeronasal organ is mainly used to detect pheromones, chemical messengers that carry information between individuals of the same species, hence is sometimes referred to as the ‘sixth sense. ‘ The VNO has two separate types of neuronal receptors, V1R and V2R, which are seven-transmembrane receptors that are coupled to G proteins. The receptors are distinct from each other and form the large family of receptors in the main olfactory system. Evidence shows that the VNO responds to nonvolatile cues which stimulate the receptor neurons. Information is then transferred to the accessory olfactory bulb as well as other centres of the brain such as the anterior part of the hypothalamus. Its presence in many animals has been widely studied and the importance of the vomeronasal system to the role of reproduction and social behavior (through influence on anterior hypothalamus) has been shown in many studies. Its presence and functionality in humans is widely controversial, though most studies agree the organ regresses during fetal development. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Vomeronasal_organ }
    • - vomeronasal organ has exact synonym organon vomeronasale
    • - vomeronasal organ has exact synonym organum vomeronasale { database cross reference=BTO:0002608 }
    • - vomeronasal organ has related synonym organum vomeronasale { database cross reference=http://en.wikipedia.org/wiki/Vomeronasal_organ , has synonym type=latin term }
  • Added

Changes for: pupillary membrane

Changes for: skeletal muscle tissue

  • Deleted
    • - skeletal muscle tissue comment TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle.
  • Added
    • + skeletal muscle tissue editor note TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle.

Changes for: dorsal root of spinal cord

Changes for: ventral root of spinal cord

Changes for: testicular vein

Changes for: vasculature of eye

Changes for: colon

  • Deleted
    • - colon comment TODO: abstract this such that it legitimately covers all vertebrates
  • Added
    • + colon editor note TODO - abstract this such that it legitimately covers all vertebrates

Changes for: synovial joint

Changes for: interparietal bone

  • Deleted
    • - interparietal bone comment . Editor notes: consider splitting classes for inter-parietal and post-parietal. postparietals paired in reptiles, fused in mammals.
  • Added
    • + interparietal bone editor note consider splitting classes for inter-parietal and post-parietal. postparietals paired in reptiles, fused in mammals.

Changes for: common hepatic duct

  • Deleted
    • - common hepatic duct comment TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same. Common is part of extra-hepatic part
  • Added
    • + common hepatic duct editor note TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same. Common is part of extra-hepatic part

Changes for: left testicular artery

Changes for: right testicular artery

Changes for: testicular artery

  • Deleted
    • - testicular artery SubClassOf artery
    • - testicular artery definition The testicular artery (the male gonadal artery, also called the internal spermatic arteries in older texts) is a branch of the abdominal aorta that supplies blood to the testis. It is a paired artery, with one for each of the testes. It is the male equivalent of the ovarian artery. Because the testis is found in a different location than that of its female equivalent, it has a different course than the ovarian artery. They are two slender vessels of considerable length, and arise from the front of the aorta a little below the renal arteries. Each passes obliquely downward and lateralward behind the peritoneum, resting on the Psoas major, the right spermatic lying in front of the inferior vena cava and behind the middle colic and ileocolic arteries and the terminal part of the ileum, the left behind the left colic and sigmoid arteries and the iliac colon. Each crosses obliquely over the ureter and the lower part of the external iliac artery to reach the abdominal inguinal ring, through which it passes, and accompanies the other constituents of the spermatic cord along the inguinal canal to the scrotum, where it becomes tortuous, and divides into several branches. Two or three of these accompany the ductus deferens, and supply the epididymis, anastomosing with the artery of the ductus deferens; others pierce the back part of the tunica albuginea, and supply the substance of the testis. The internal spermatic artery supplies one or two small branches to the ureter, and in the inguinal canal gives one or two twigs to the Cremaster. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Testicular_artery }
  • Added

Changes for: embryonic urethral groove

Changes for: bronchus

  • Deleted
    • - bronchus comment In humans, the main bronchus is histologically identical to trachea; 2ary and 3ary bronchi are not; epithelium becomes simple columnar, goblet cell number decreases, elastic fibers in lamina propria increases, distribution more uniform. Muscular layer between mucosa and submucosa appears. cartilage rings become discontinuous plates connected by fibrous connective tissue
  • Added
    • + bronchus taxon notes In humans, the main bronchus is histologically identical to trachea; 2ary and 3ary bronchi are not; epithelium becomes simple columnar, goblet cell number decreases, elastic fibers in lamina propria increases, distribution more uniform. Muscular layer between mucosa and submucosa appears. cartilage rings become discontinuous plates connected by fibrous connective tissue

Changes for: main bronchus

Changes for: lateral reticular nucleus

Changes for: ciliary processes

Changes for: chitin-based cuticle

Changes for: vas deferens

  • Deleted
    • - vas deferens comment Taxon notes (from WP): Most vertebrates have some form of duct to transfer the sperm from the testes to the urethra. In cartilaginous fish and amphibians, sperm is carried through the archinephric duct, which also partially helps to transport urine from the kidneys. In teleosts, there is a distinct sperm duct, separate from the ureters, and often called the vas deferens, although probably not truly homologous with that in humans. In cartilaginous fishes, the part of the archinephric duct closest to the testis is coiled up to form an epididymis. Below this are a number of small glands secreting components of the seminal fluid. The final portion of the duct also receives ducts from the kidneys in most species. In amniotes, however, the archinephric duct has become a true vas deferens, and is used only for conducting sperm, never urine. As in cartilaginous fish, the upper part of the duct forms the epididymis. In many species, the vas deferens ends in a small sac for storing sperm. The only vertebrates to lack any structure resembling a vas deferens are the primitive jawless fishes, which release sperm directly into the body cavity, and then into the surrounding water through a simple opening in the body wall.
  • Added
    • + vas deferens taxon notes Most vertebrates have some form of duct to transfer the sperm from the testes to the urethra. In cartilaginous fish and amphibians, sperm is carried through the archinephric duct, which also partially helps to transport urine from the kidneys. In teleosts, there is a distinct sperm duct, separate from the ureters, and often called the vas deferens, although probably not truly homologous with that in humans. In cartilaginous fishes, the part of the archinephric duct closest to the testis is coiled up to form an epididymis. Below this are a number of small glands secreting components of the seminal fluid. The final portion of the duct also receives ducts from the kidneys in most species. In amniotes, however, the archinephric duct has become a true vas deferens, and is used only for conducting sperm, never urine. As in cartilaginous fish, the upper part of the duct forms the epididymis. In many species, the vas deferens ends in a small sac for storing sperm. The only vertebrates to lack any structure resembling a vas deferens are the primitive jawless fishes, which release sperm directly into the body cavity, and then into the surrounding water through a simple opening in the body wall.[WP]

Changes for: respiratory airway

  • Deleted
    • - respiratory airway comment This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends
  • Added
    • + respiratory airway curator notes This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends

Changes for: cuticle

  • Deleted
    • - cuticle comment TODO - check cuticle vs exoskeleton. Note that GO has a very generic definition of cuticle. See also arthropod-anatomy ontology. Note in ncit Cuticle is a plant part
  • Added
    • + cuticle editor note TODO - check cuticle vs exoskeleton. Note that GO has a very generic definition of cuticle. See also arthropod-anatomy ontology. Note in ncit Cuticle is a plant part

Changes for: renal system

  • Deleted
    • - renal system comment In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here
  • Added
    • + renal system editor note In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here

Changes for: circulatory system

Changes for: locus ceruleus

Changes for: adipose tissue

  • Deleted
    • - adipose tissue comment Taxon notes: n humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen.
  • Added
    • + adipose tissue taxon notes In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen.

Changes for: nerve fasciculus

  • Deleted
    • - nerve fasciculus comment TODO - invert specific? note FBbt class not disjoint from tract. Consider merging with ‘neuron projection bundle’
  • Added
    • + nerve fasciculus editor note TODO - invert specific? note FBbt class not disjoint from tract. Consider merging with ‘neuron projection bundle’

Changes for: jejunum

  • Deleted
    • - jejunum comment TODO consider ZFA:0001323 mid intestine, see also small intestine
  • Added

Changes for: ileum

  • Deleted
    • - ileum comment TODO consider ZFA:0000706 posterior intestine, see also colon
  • Added
    • + ileum editor note TODO consider ZFA:0000706 posterior intestine, see also colon

Changes for: gallbladder

Changes for: distal epiphysis of distal phalanx of manual digit 3

Changes for: distal epiphysis of distal phalanx of manual digit 2

Changes for: distal epiphysis of distal phalanx of manual digit 1

Changes for: distal epiphysis of distal phalanx of manual digit 5

Changes for: distal epiphysis of distal phalanx of manual digit 4

Changes for: saliva-secreting gland

  • Deleted
    • - salivary gland SubClassOf gland of foregut
    • - salivary gland SubClassOf part of some foregut
    • - salivary gland comment currently we define saliva and salivary glands very generally in functional terms but it may be more appropriate to split this class. From WP: In most vertebrates, saliva does not contain any enzymes, consisting of mucus and water only, and its primary function is to moisten food while eating. As a result, true salivary glands are rarely found in fish or aquatic tetrapods, although there are often individual mucus-secreting cells. Amphibians have a single salivary gland, the intermaxillary gland, located in the forward part of the palate. Reptiles and birds normally have only very small glands on the lips, palate, and base of the mouth, although there are some birds with large glands, which produce a sticky saliva that helps in nest-building. The distinct parotid, submandibular, and sublingual glands are only developed in mammals.[3] The salivary glands of some species, however, are modified to produce enzymes; salivary amylase is found in many, but by no means all, bird and mammal species (including humans, as noted above). Furthermore, the venom glands of poisonous snakes, Gila monsters, and some shrews, are modified salivary glands
    • - salivary gland definition saliva-secreting exocrine glands of the oral cavity[GO]. The salivary glands in mammals are exocrine glands, glands with ducts, that produce saliva. They also secrete amylase, an enzyme that breaks down starch into maltose. In other organisms such as insects, salivary glands are often used to produce biologically important proteins like silk or glues, and fly salivary glands contain polytene chromosomes that have been useful in genetic research[WP]. { database cross reference=http://en.wikipedia.org/wiki/Salivary_gland , database cross reference=GO:0007431 }
    • - salivary gland label salivary gland
  • Added
    • + saliva-secreting gland SubClassOf part of some exocrine system
    • + saliva-secreting gland comment Taxon notes: The salivary glands in mammals are exocrine glands, glands with ducts, that produce saliva. They also secrete amylase, an enzyme that breaks down starch into maltose. In other organisms such as insects, salivary glands are often used to produce biologically important proteins like silk or glues, and fly salivary glands contain polytene chromosomes that have been useful in genetic research. The salivary glands of some species are modified to produce enzymes; salivary amylase is found in many, but by no means all, bird and mammal species (including humans, as noted above). Furthermore, the venom glands of poisonous snakes, Gila monsters, and some shrews, are modified salivary glands
    • + saliva-secreting gland curator notes currently we define saliva and salivary glands very generally in functional terms but it may be more appropriate to split this class. From WP: In most vertebrates, saliva does not contain any enzymes, consisting of mucus and water only, and its primary function is to moisten food while eating. As a result, true salivary glands are rarely found in fish or aquatic tetrapods, although there are often individual mucus-secreting cells. Amphibians have a single salivary gland, the intermaxillary gland, located in the forward part of the palate. Reptiles and birds normally have only very small glands on the lips, palate, and base of the mouth, although there are some birds with large glands, which produce a sticky saliva that helps in nest-building. The distinct parotid, submandibular, and sublingual glands are only developed in mammals.[3]
    • + saliva-secreting gland definition saliva-secreting exocrine glands of the oral cavity[GO] { database cross reference=http://en.wikipedia.org/wiki/Salivary_gland , database cross reference=GO:0007431 }
    • + saliva-secreting gland has exact synonym salivary gland { database cross reference=MA:0000346 }
    • + saliva-secreting gland label saliva-secreting gland

Changes for: neural tube

  • Deleted
    • - neural tube comment The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium[GO:0021915]
  • Added
    • + neural tube development notes The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium[GO:0021915]

Changes for: distal epiphysis of distal phalanx of pedal digit 2

Changes for: distal epiphysis of distal phalanx of pedal digit 1

Changes for: distal epiphysis of distal phalanx of pedal digit 4

Changes for: distal epiphysis of distal phalanx of pedal digit 3

Changes for: distal epiphysis of distal phalanx of pedal digit 5

Changes for: spleen

Changes for: trunk

Changes for: neuromuscular junction

Changes for: sensory nerve

  • Deleted

Changes for: cell body

Changes for: pedal digit 7 digitopodial skeleton

Changes for: pedal digit 8 digitopodial skeleton

Changes for: strand of hair

  • Deleted
    • - strand of hair comment this class defines an individual hair. todo - consider fur / coat of fur, which has_part hair. TODO: for now we treat vibrissa/whisker as a syonym, but these have different follicles. We could introduce subclasses (see also: Pangolin scales)
  • Added

Changes for: chordotonal organ

Changes for: dento-alveolar joint

Changes for: gustatory system

Changes for: neurilemma

  • Deleted
    • - neurilemma comment FMA def is ‘Neural tissue which consists of Schwann cells’ which does not fit, but we still use ‘neural tissue’ here. WP def specifically states Schwann cells, which would restrict it to PNS
  • Added
    • + neurilemma external ontology notes FMA def is ‘Neural tissue which consists of Schwann cells’ which does not fit, but we still use ‘neural tissue’ here. WP def specifically states Schwann cells, which would restrict it to PNS { external ontology=FMA }

Changes for: choroidal gland

Changes for: stratum argenteum of choroid

Changes for: blood vessel layer of choroid

Changes for: myocardium of ventricle

Changes for: epicardium of ventricle

Changes for: skin of trunk

  • Deleted
    • - skin of trunk comment todo - distinguish between entire skin of region and arbitrary zone of skin on region
  • Added

Changes for: skin of head

  • Deleted
    • - skin of head comment todo - distinguish between entire skin of region and arbitrary zone of skin on region
  • Added

Changes for: pleural fluid

  • Deleted

Changes for: sweat

Changes for: urine

Changes for: cortical marginal zone

Changes for: vertebral bone 1

Changes for: synovial fluid

Changes for: vertebral bone 2

Changes for: skin of back

  • Deleted
    • - skin of back comment todo - distinguish between entire skin of region and arbitrary zone of skin on region
  • Added

Changes for: parotid duct

  • Deleted
    • - parotid duct comment This class was created automatically from a combination of ontologies
    • - parotid duct definition The parotid duct, also known as Stensen’s duct, is the route that saliva takes from the parotid gland into the mouth. It passes through the buccal fat, buccopharyngeal fascia, and buccinator muscle then opens into the vestibule of the mouth opposite the upper second molar tooth. The buccinator acts as a valve that prevents inflation of the duct during blowing. Running along with the duct superiorly is the transverse facial artery and upper buccal nerve; running along with the duct inferiorly is the lower buccal nerve. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Parotid_duct }
  • Added
    • + parotid duct comment It passes through the buccal fat, buccopharyngeal fascia, and buccinator muscle then opens into the vestibule of the mouth opposite the upper second molar tooth. The buccinator acts as a valve that prevents inflation of the duct during blowing. Running along with the duct superiorly is the transverse facial artery and upper buccal nerve; running along with the duct inferiorly is the lower buccal nerve[Wikipedia:Parotid_duct]
    • + parotid duct definition The duct portion of the parotid gland. { database cross reference=UBERON:cjm }

Changes for: intervertebral disk

  • Deleted
    • - intervertebral disk comment Taxon/Terminology notes: strictly speaking the term intervertebral disk [applies to intervertebral cartilage] whose gel-like core is nucleus puloposus, by this definition only in mammals
  • Added

Changes for: ileocecal junction

Changes for: posterior vena cava

Changes for: prezygapophysis

Changes for: pennate muscle

Changes for: plastron

Changes for: carapace

Changes for: cerebral cortex marginal layer

Changes for: spine appendage

Changes for: T cell domain

Changes for: B cell domain

Changes for: lymphocyte domain

Changes for: spleen marginal sinus

  • Deleted
    • - spleen marginal sinus comment Note that there is no consensus in the literature about which compartments constitute the white pulp or the ramifications of the microvasculature. In addition, notable differences exist between humans and rodents. In this ontology, the marginal sinus (which may not exist in human) has been included as part of the white pulp. The perifollicular zone, which is present in human and not rodents, may be the functional equivalent of the marginal sinus in rodents.[MP:0002363]
  • Added
    • + spleen marginal sinus editor note Note that there is no consensus in the literature about which compartments constitute the white pulp or the ramifications of the microvasculature. In addition, notable differences exist between humans and rodents. In this ontology, the marginal sinus (which may not exist in human) has been included as part of the white pulp. The perifollicular zone, which is present in human and not rodents, may be the functional equivalent of the marginal sinus in rodents.[MP:0002363]

Changes for: bone of hip region

  • Deleted
    • - bone of hip region comment in MA, this includes the femur. i.e. pelvic girdle bone or femur; note that this makes the ilium etc in MA hindlimb bones. in MA this is a hindlimb bone
  • Added

Changes for: scute

Changes for: neurohypophysis

Changes for: otic capsule pre-cartilage condensation

Changes for: cerebellar peduncular complex

  • Deleted
    • - cerebellar peduncular complex comment todo - this requires work for making consistent with ABA, which strictly separates cerebellum from brainstem. in MA, cerebellar peduncle is part of both brainstem and cerebellar white matter.
  • Added
    • + cerebellar peduncular complex editor note TODO - this requires work for making consistent with ABA, which strictly separates cerebellum from brainstem. in MA, cerebellar peduncle is part of both brainstem and cerebellar white matter.

Changes for: epicranium

Changes for: eyelid mesenchyme

Changes for: conjunctival vein

Changes for: epithelial scleral papilla layer

  • Deleted
    • - epithelial scleral papilla layer comment Taxon notes: Scleral papillae (which induce scleral ossicles in birds) have not been reported in teleosts, but evidence for their presence may not have been sought
  • Added

Changes for: palpebral bone

  • Deleted
    • - palpebral bone comment Editor notes http://www.ncbi.nlm.nih.gov/pubmed/16496288 says ‘invests’ the eyelid, is this consistent across taxa?
  • Added

Changes for: gustatory gland

Changes for: cecal tonsil

  • Deleted
    • - cecal tonsil comment In avians the polycryptic cecal tissue is similar to the mammalian palatine tonsil
  • Added

Changes for: cranial skeletal system

  • Deleted
    • - cranial skeletal system comment Usage notes: that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called ‘skull’ belongs here, as it includes the whole splanchnocranium. Editor notes: we use ‘cranial skeletal system’, so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints)
  • Added
    • + cranial skeletal system curator notes that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called ‘skull’ belongs here, as it includes the whole splanchnocranium
    • + cranial skeletal system editor note we use ‘cranial skeletal system’, so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints)

Changes for: pyramidal layer of CA1

Changes for: pleural cavity

Changes for: cervical vertebra

  • Deleted
    • - cervical vertebra comment In some species, some parts of the skull may be composed of vertebra-like elements, e.g. the occipital bone in humans is composed of four vertebra-like segments. In many vertebrate species, cervical vertebrae are variable in number; however, almost all mammals have seven (including those with very short necks relative to body size, such as elephants or whales, and those with very long necks, such as giraffes). The few exceptions include the manatee and the sloths, of which the two-toed sloth has six cervical vertebrae and the three-toed sloth has up to nine cervical vertebrae. In many species, though not in mammals, the cervical vertebrae bear ribs. In many other groups, such as lizards and saurischian dinosaurs, the cervical ribs are large; in birds they are small and completely fused to the vertebrae. The transverse processes of mammals are homologous to the cervical ribs of other amniotes. Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. n humans, cervical vertebrae are the smallest of the true vertebrae, and can be readily distinguished from those of the thoracic or lumbar regions by the presence of a foramen (hole) in each transverse process, through which passes the vertebral artery.
  • Added
    • + cervical vertebra taxon notes In some species, some parts of the skull may be composed of vertebra-like elements, e.g. the occipital bone in humans is composed of four vertebra-like segments. In many vertebrate species, cervical vertebrae are variable in number; however, almost all mammals have seven (including those with very short necks relative to body size, such as elephants or whales, and those with very long necks, such as giraffes). The few exceptions include the manatee and the sloths, of which the two-toed sloth has six cervical vertebrae and the three-toed sloth has up to nine cervical vertebrae. In many species, though not in mammals, the cervical vertebrae bear ribs. In many other groups, such as lizards and saurischian dinosaurs, the cervical ribs are large; in birds they are small and completely fused to the vertebrae. The transverse processes of mammals are homologous to the cervical ribs of other amniotes. Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. n humans, cervical vertebrae are the smallest of the true vertebrae, and can be readily distinguished from those of the thoracic or lumbar regions by the presence of a foramen (hole) in each transverse process, through which passes the vertebral artery.

Changes for: autonomic nervous system

Changes for: hippocampal formation

  • Deleted
    • - hippocampal formation comment . BTO:0000601 is placed here since it includes the DG. GO also includes dentate gyrus development as part of hippocampus development, so we assume when GO says “hippocampus” it means “hippocampal formation”. In ABA HPF = (.. subiculum) + HIP, HIP = DG + AH.
  • Added
    • + hippocampal formation comment BTO:0000601 is placed here since it includes the DG. GO also includes dentate gyrus development as part of hippocampus development, so we assume when GO says “hippocampus” it means “hippocampal formation”. In ABA HPF = (.. subiculum) + HIP, HIP = DG + AH.

Changes for: limb bone

  • Deleted
    • - limb bone comment Note that the formal definition is very inclusive, and includes sesamoids
  • Added
    • + limb bone comment Usage Notes: the formal definition is very inclusive, and includes sesamoids

Changes for: distal interphalangeal joint of pedal digit 3

Changes for: distal interphalangeal joint of manual digit 3

Changes for: proximal phalanx of digit 5

Changes for: distal interphalangeal joint of digit 3

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: lens fiber

  • Deleted
    • - lens fiber comment TODO - check plural vs singular. in FMA lens fiber is a cell - FMA:70950 Lens cell. Other ontologies don’t appear to commit one way or another.
  • Added
    • + lens fiber editor note TODO - check plural vs singular. in FMA lens fiber is a cell - FMA:70950 Lens cell. Other ontologies don’t appear to commit one way or another.

Changes for: choroidal blood vessel

Changes for: ulnare

  • Deleted
    • - ulnare comment note this bone is termed the triquetral bone in some mammalian taxa, notably humans
  • Added

Changes for: uterine gland

Changes for: decidua

Changes for: internal thoracic artery

Changes for: lymphoid system

  • Deleted
    • - lymphoid system comment We follow FMA and MA in distinguishing between lymphatic system and lymphoid system, with lymhoid tissue part of the non-lymphatic component, although these terms are often used interchangeably. We assume the ZFA term lymphatic tissue actually corresponds to the broader class (e.g. ZFA lymph node in the ZFA lymphatic system). See tracker for more comments.
  • Added
    • + lymphoid system external ontology notes We follow FMA and MA in distinguishing between lymphatic system and lymphoid system, with lymhoid tissue part of the non-lymphatic component, although these terms are often used interchangeably. We assume the ZFA term lymphatic tissue actually corresponds to the broader class (e.g. ZFA lymph node in the ZFA lymphatic system). See tracker for more comments. { external ontology=FMA }

Changes for: iris epithelium

Changes for: layer of sclera

Changes for: associated mesenchyme of midgut

Changes for: hyoid bone greater horn

  • Deleted
    • - hyoid bone greater horn comment In humans, the greater cornua are the larger, more lateral projections from the left and right borders of the body of hyoid bone. They are in contrast to the lesser cornua, which also occur in pairs but are comparatively smaller and conical in shape. The greater cornua are derived from the third pharyngeal arches. [http://www.biology-online.org/dictionary/Greater_cornua]
  • Added
    • + hyoid bone greater horn taxon notes In humans, the greater cornua are the larger, more lateral projections from the left and right borders of the body of hyoid bone. They are in contrast to the lesser cornua, which also occur in pairs but are comparatively smaller and conical in shape. The greater cornua are derived from the third pharyngeal arches. [http://www.biology-online.org/dictionary/Greater_cornua]

Changes for: musculus retractor bulbi

  • Deleted
    • - musculus retractor bulbi comment In most other mammals it also innervates the musculus retractor bulbi, which can retract the eye for protection[wiki/Abducens_nerve]
  • Added

Changes for: conus arteriosus

Changes for: brain ventricle/choroid plexus

Changes for: anterior buccal gland

Changes for: blood-air barrier

Changes for: choroid tapetum lucidum

Changes for: zygomatic gland

Changes for: placenta labyrinth

Changes for: molar gland

Changes for: bone marrow

  • Deleted
    • - bone marrow comment TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs
  • Added
    • + bone marrow editor note TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs

Changes for: somatic sensory system

Changes for: aqueous drainage system

Changes for: Bruch’s membrane

Changes for: ocular fundus

Changes for: peritoneum

Changes for: mesenchyme pectoral fin

Changes for: mesenchyme pelvic fin

Changes for: pectoral flipper tubercle

  • Deleted
    • - pectoral flipper tubercle comment In a humpback the number of tubercles ranges from 9 to 11, with the first at the joint between the radius and metacarpal of digit II (with digit I absent)
  • Added
    • + pectoral flipper tubercle taxon notes In a humpback the number of tubercles ranges from 9 to 11, with the first at the joint between the radius and metacarpal of digit II (with digit I absent)

Changes for: prostate gland

Changes for: epaxial myotome region

Changes for: retinal neural layer

  • Deleted
    • - retinal neural layer comment editor note - we follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers; the neural layers are further divided into 9 layers. Note that in MA this class is a leaf node.

Changes for: nictitating membrane

Changes for: fused metacarpal bones 3 and 4

Changes for: fused metatarsal bones 3 and 4

Changes for: nasolacrimal duct

Changes for: distal interphalangeal joint of digit 5

Changes for: distal interphalangeal joint of digit 4

Changes for: myocardium of atrium

Changes for: layer of hippocampus

Changes for: choroid plexus of lateral ventricle

Changes for: nasal mucus

Changes for: distal interphalangeal joint of manual digit 4

Changes for: distal interphalangeal joint of manural digit 5

Changes for: distal interphalangeal joint of pedal digit 2

Changes for: distal interphalangeal joint of pedal digit 4

Changes for: distal interphalangeal joint of pedal digit 5

Changes for: distal interphalangeal joint of digit 2

Changes for: distal interphalangeal joint of manual digit 2

Changes for: macula densa

Changes for: abdomen musculature

Changes for: epicardium

  • Deleted
    • - epicardium comment TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium – When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer.
  • Added
    • + epicardium editor note TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium – When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer.

Changes for: myocardium

  • Deleted
    • - myocardium comment TODO - check ‘Myocardum proper’ in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a ‘cardiac muscle’ (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium
  • Added
    • + myocardium editor note TODO - check ‘Myocardum proper’ in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a ‘cardiac muscle’ (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium

Changes for: midbrain tectum

Changes for: somite

Changes for: mesenchyme of submandibular gland primordium

Changes for: mesenchyme of sublingual gland primordium

Changes for: associated mesenchyme of main bronchus

Changes for: associated mesenchyme of hindgut

Changes for: associated mesenchyme of middle ear

Changes for: associated mesenchyme of trachea

Changes for: myelencephalon basal plate

Changes for: ventral midline

Changes for: carotid duct

Changes for: pastern region of limb

Changes for: pastern bone

Changes for: long pastern bone

Changes for: hypaxial myotome region

Changes for: short pastern bone

Changes for: distal segment of manual digit

Changes for: intraembryonic coelom

  • Deleted
    • - intraembryonic coelom editor note consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. Todo: check ZFA, which appears to be a structure present in adults
  • Added
    • + intraembryonic coelom editor note consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults

Changes for: CA4 field of hippocampus

Changes for: CA3 field of hippocampus

Changes for: CA2 field of hippocampus

Changes for: CA1 field of hippocampus

Changes for: fallopian tube

Changes for: hippocampal field

Changes for: hindlimb mesenchyme

Changes for: pedal digit 4 phalanx

Changes for: pedal digit 5 phalanx

Changes for: horny papilla of tongue

Changes for: short bone

Changes for: mesenchyme of interdigital region between pedal digits 4 and 5

Changes for: mesenchyme of interdigital region between pedal digits 3 and 4

Changes for: mesenchyme of interdigital region between digits 4 and 5

Changes for: mesenchyme of interdigital region between digits 3 and 4

Changes for: mesenchyme of interdigital region between digits 2 and 3

Changes for: mesenchyme of interdigital region between digits 1 and 2

Changes for: forelimb mesenchyme

Changes for: gonad mesenchyme

Changes for: lower eyelid mesenchyme

Changes for: upper eyelid mesenchyme

Changes for: neural tube lumen

Changes for: dental epithelium

  • Deleted
    • - dental epithelium comment . Editor notes: todo - full developmental relationships
    • - dental epithelium editor note see comments for dentail organ. Development notes: In the developing molar dentition of the mouse, tooth inductive po- tential resides in the dental epithelium until embryonic day (E)12.5 (3). Thereafter, tooth inductive potential shifts to neural crest-derived dental mesenchyme, which acquires the ability to direct tooth formation in nonodontogenic tissues (3, 4)[PMID:10954731]
  • Added
    • + dental epithelium comment Development notes: In the developing molar dentition of the mouse, tooth inductive po- tential resides in the dental epithelium until embryonic day (E)12.5 (3). Thereafter, tooth inductive potential shifts to neural crest-derived dental mesenchyme, which acquires the ability to direct tooth formation in nonodontogenic tissues (3, 4)[PMID:10954731]
    • + dental epithelium editor note see comments for dental organ.
    • + dental epithelium editor note todo - full developmental relationships

Changes for: mesenchyme of interdigital region between manual digits 1 and 2

Changes for: interdigital region mesenchyme

Changes for: mesenchyme of interdigital region between manual digits 3 and 4

Changes for: mesenchyme of interdigital region between manual digits 2 and 3

Changes for: mesenchyme of interdigital region between manual digits 4 and 5

Changes for: primary molar tooth

Changes for: mesenchyme of interdigital region between pedal digits 1 and 2

Changes for: mesenchyme of interdigital region between pedal digits 2 and 3

Changes for: pancreatic duct

  • Deleted
    • - pancreatic duct comment Usage notes: this class groups together accessory (dorsal) and main (ventral) pancreatic ducts. AO notes: in EHDAA2, the dorsal and ventral ducts are classified as epithelial sacs - review after overhaul of duct/epithelia terms
  • Added

Changes for: pancreatic lobe

Changes for: rectus capitis posterior minor

Changes for: rectus capitis posterior major

Changes for: lateral saphenous vein

Changes for: rectus capitis anterior

Changes for: cartilage of pharyngotympanic tube

  • Deleted
    • - cartilage of pharyngotympanic tube definition The cartilage of pharyngotympanic tube, about 24 mm. in length, is formed of a triangular plate of elastic fibrocartilage, the apex of which is attached to the margin of the medial end of the osseous portion of the tube, while its base lies directly under the mucous membrane of the nasal part of the pharynx, where it forms an elevation, the torus tubarius or cushion, behind the pharyngeal orifice of the tube. The upper edge of the cartilage is curled upon itself, being bent laterally so as to present on transverse section the appearance of a hook; a groove or furrow is thus produced, which is open below and laterally, and this part of the canal is completed by fibrous membrane. The cartilage lies in a groove between the petrous part of the temporal and the great wing of the sphenoid; this groove ends opposite the middle of the medial pterygoid plate. The cartilaginous and bony portions of the tube are not in the same plane, the former inclining downward a little more than the latter. The diameter of the tube is not uniform throughout, being greatest at the pharyngeal orifice, least at the junction of the bony and cartilaginous portions, and again increased toward the tympanic cavity; the narrowest part of the tube is termed the isthmus. The position and relations of the pharyngeal orifice are described with the nasal part of the pharynx. The mucous membrane of the tube is continuous in front with that of the nasal part of the pharynx, and behind with that of the tympanic cavity; it is covered with ciliated epithelium and is thin in the osseous portion, while in the cartilaginous portion it contains many mucous glands and near the pharyngeal orifice a considerable amount of adenoid tissue, which has been named by Gerlach the tube tonsil. The tube is opened during deglutition by the Salpingopharyngeus and Dilatator tubC&. The latter arises from the hook of the cartilage and from the membranous part of the tube, and blends below with the Tensor veli palatini. { database cross reference=http://en.wikipedia.org/wiki/Cartilage_of_pharyngotympanic_tube }
  • Added

Changes for: medial saphenous vein

Changes for: reticulorumen

  • Deleted
    • - reticulorumen definition first chamber in the alimentary canal of ruminant animals. It is composed of the rumen and reticulum. The reticulum differs from the rumen with regard to the texture of its lining. The rumen wall is covered in small finger like projections called papillae, which are flattened, approximately 0.5 cm in length and 0.3 cm wide in cattle. The reticulum is lined with ridges that form a hexagonal honeycomb pattern. The ridges are approximately 0.1 - 0.2 mm wide and are raised 0.5 cm above the reticulum wall. The hexagons in the reticulum are approximately 2-5 cm wide in cattle. Despite the differences in the texture of the lining of the two parts of the reticulorumen, it represents one functional space. Microbial fermentation degrades ingested carbohydrates in the reticulorumen to the volatile fatty acids acetate, propionate and butyrate, and proteins to short peptides, amino acids and ammonia. This fermentation is anaerobic and allows the microbes in the reticulorumen to derive the energy and amino nitrogen in order that they can reproduce. Ruminants absorb the volatile fatty acids across the reticulorumen wall and use them for energy, while the microbes eventually flow out of the rumen into the remainder of the alimentary canal, where they are eventually digested and absorbed. The reticulum, at approximately 5-20 litres, is considerably smaller in capacity than the rumen, which is approximately 100-200 litres in cattle. The oesophageal groove, which links the oesophagus and the omasum is located in the reticulum[WP]. { database cross reference=http://en.wikipedia.org/wiki/Reticulorumen }
  • Added

Changes for: stratum compactum

  • Deleted
    • - stratum compactum comment connective tissue in the skin is usually diffuse and irregular, although in some species collagen bundles are arranged in a distinct ordered layer in the dermis
  • Added
    • + stratum compactum comment Histology notes: connective tissue in the skin is usually diffuse and irregular, although in some species collagen bundles are arranged in a distinct ordered layer in the dermis

Changes for: exoccipital pre-cartilage condensation

Changes for: body-wall mesenchyme

Changes for: segmental spinal nerve

Changes for: future forebrain

  • Deleted
    • - future forebrain comment TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate)
  • Added

Changes for: iliac pre-cartilage condensation

Changes for: incus pre-cartilage condensation

Changes for: humerus pre-cartilage condensation

Changes for: femur pre-cartilage condensation

Changes for: malleus pre-cartilage condensation

Changes for: Meckel’s cartilage pre-cartilage condensation

Changes for: notochordal plate

Changes for: ischial pre-cartilage condensation

Changes for: rib pre-cartilage condensation

Changes for: pubic pre-cartilage condensation

Changes for: radius-ulna pre-cartilage condensation

Changes for: scapula pre-cartilage condensation

Changes for: hepatic duct

  • Deleted
    • - hepatic duct comment TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same
  • Added
    • + hepatic duct editor note TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same

Changes for: stapes pre-cartilage condensation

Changes for: submandibular gland primordium

Changes for: ascending limb of loop of Henle

Changes for: sublingual gland primordium

Changes for: metanephric cap

Changes for: late distal convoluted tubule

Changes for: metanephric proximal straight tubule

Changes for: osseus cochlea

Changes for: olfactory bulb layer

Changes for: cerebellum hemisphere lobule

Changes for: crista of ampulla of anterior semicircular duct of membranous laybrinth

Changes for: crista of ampulla of lateral semicircular duct of membranous laybrinth

Changes for: crista of ampulla of posterior semicircular duct of membranous laybrinth

Changes for: common penile artery

Changes for: presumptive hindbrain

Changes for: nuclear complex of neuraxis

Changes for: odontoid process of cervical vertebra 2

  • Deleted
    • - odontoid process of cervical vertebra 2 comment TODO check AAO:0000721 odontoid_process – Anterior process located between the atlantal cotyles that projects into the foramen magnum of the skull and bears facets that articulate with the lateral walls of the foramen
  • Added
    • + odontoid process of cervical vertebra 2 editor note TODO check AAO:0000721 odontoid_process – Anterior process located between the atlantal cotyles that projects into the foramen magnum of the skull and bears facets that articulate with the lateral walls of the foramen

Changes for: beak

Changes for: short descending thin limb

Changes for: sweat gland placode

Changes for: sebaceous gland placode

Changes for: anterior definitive endoderm

Changes for: semicircular canal ampulla

  • Deleted
    • - semicircular canal ampulla comment TODO check duct vs canal. Also check FMA - has many subtypes of semicircular canal such as ‘ampulla of anterior semicircular canal’
  • Added

Changes for: pronephric sinus

Changes for: aqueous vein

Changes for: podocyte slit junction

Changes for: podocyte slit diaphragm

Changes for: median dorsal digital artery for digit 1

Changes for: canal of Schlemm

Changes for: lateral dorsal digital artery for digit 5

Changes for: dermatome

Changes for: vena cava

Changes for: ocular region

  • Deleted
    • - ocular region comment TODO: consider the following: eyeball (eye proper) part_of eye (= eyeball+eyelid etc) part_of ocular region (= eye + adnexa such as eyebrow); note the FMA class is more narrow though, and is more like eye + muscles + vasculature // in HP covers eyelid, eyebrow.
  • Added

Changes for: cerebellum vermis lobule

Changes for: cerebellum vermis lobule I

Changes for: spinal cord alar plate

Changes for: primitive pit

Changes for: mesonephric sinus

Changes for: trabecular layer of ventricle

Changes for: optic vesicle

Changes for: head kidney

  • Deleted
    • - head kidney comment in GO, head kidney isa pronephros. Modified the ZFA relationships - the HK is derived from the anterior part of the pronephros and persists until adulthood
  • Added

Changes for: inferior petrosal sinus

Changes for: inferior sagittal sinus

Changes for: superior epigastric vein

Changes for: muscle of pelvic diaphragm

  • Deleted
    • - muscle of pelvic diaphragm definition The pelvic floor or pelvic diaphragm is composed of muscle fibers of the levator ani, the coccygeus, and associated connective tissue which span the area underneath the pelvis. The pelvic diaphragm is a muscular partition formed by the levatores ani and coccygei, with which may be included the parietal pelvic fascia on their upper and lower aspects. The pelvic floor separates the pelvic cavity above from the perineal region below. The right and left levator ani lie almost horizontally in the floor of the pelvis, separated by a narrow gap that transmits the urethra, vagina, and anal canal. The levator ani is usually considered in three parts: pubococcygeus, puborectalis, and iliococcygeus. The pubococcygeus, the main part of the levator, runs backward from the body of the pubis toward the coccyx and may be damaged during parturition. Some fibers are inserted into the prostate, urethra, and vagina. The right and left puborectalis unite behind the anorectal junction to form a muscular sling . Some regard them as a part of the sphincter ani externus. The iliococcygeus, the most posterior part of the levator ani, is often poorly developed. The coccygeus, situated behind the levator ani and frequently tendinous as much as muscular, extends from the ischial spine to the lateral margin of the sacrum and coccyx. The pelvic cavity of the true pelvis has the pelvic floor as its inferior border (and the pelvic brim as its superior border. ) The perineum has the pelvic floor as its superior border. Some sources do not consider ‘pelvic floor’ and ‘pelvic diaphragm’ to be identical, with the ‘diaphragm’ consisting of only the levator ani and coccygeus, while the ‘floor’ also includes the perineal membrane and deep perineal pouch. However, other sources include the fascia as part of the diaphragm. In practice, the two terms are often used interchangeably. Inferiorly, the pelvic floor extends into the anal triangle. { database cross reference=http://en.wikipedia.org/wiki/Pelvic_floor }
  • Added

Changes for: superior nasal meatus

Changes for: vesicular gland

Changes for: chordo neural hinge

  • Deleted
    • - chordo neural hinge comment In mouse and chick, the derivative of the NSB (with a minor contribution from the CLE), the `chordo-neural-hinge’(CNH) (Cambray and Wilson, 2007; Catala et al., 1995; Charrier et al., 1999), contains progenitors for the ventral neural tube, somites and notochord (Cambray and Wilson, 2002; McGrew et al., 2008). The CNH is continuous with the most recently formed neural tube and notochord (Fig. 2C-D′). By contrast, the tissue immediately caudal to the CNH exclusively produces somites in mouse and chick (McGrew et al., 2008).
  • Added
    • + chordo neural hinge taxon notes In mouse and chick, the derivative of the NSB (with a minor contribution from the CLE), the `chordo-neural-hinge’(CNH) (Cambray and Wilson, 2007; Catala et al., 1995; Charrier et al., 1999), contains progenitors for the ventral neural tube, somites and notochord (Cambray and Wilson, 2002; McGrew et al., 2008). The CNH is continuous with the most recently formed neural tube and notochord (Fig. 2C-D′). By contrast, the tissue immediately caudal to the CNH exclusively produces somites in mouse and chick (McGrew et al., 2008).

Changes for: glomerular epithelium

Changes for: prostate gland stroma

Changes for: mammary gland cord

Changes for: S-shaped body

Changes for: trigeminal sensory nucleus

Changes for: somitomeric trunk muscle

Changes for: cardiogenic plate

Changes for: proximal tubule

Changes for: intermediate tubule

Changes for: coronary sinus valve

Changes for: iris smooth muscle

Changes for: vas deferens smooth muscle

Changes for: cardiac septum

  • Deleted
    • - cardiac septum comment Note in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this. Taxon notes: “Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations”
  • Added

Changes for: viscus

  • Deleted
    • - viscus definition An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. // An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper. { database cross reference=http://en.wikipedia.org/wiki/Viscus , database cross reference=BTO:0001491 }
  • Added
    • + viscus definition An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. { database cross reference=http://en.wikipedia.org/wiki/Viscus , database cross reference=BTO:0001491 }

Changes for: hair shaft

Changes for: primitive gut

  • Deleted
    • - primitive gut comment The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis[NBK10107]
  • Added
    • + primitive gut development notes The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis[NBK10107]

Changes for: prevertebral muscle

Changes for: splenius cervicis

Changes for: top of head

Changes for: nasal capsule

  • Deleted
    • - nasal capsule comment . Avian def: The nasal capsule is dorsoventrally divided into two parts: the upper part, the ectethmoid, serves olfaction and is composed of the lamina cribosa, the crista galli apophysis and the conchae. The lower part, the mesethmoid, is a thick cartilage bar extending from the corpus sphenoidalis to the rostral extremity of the nose (Fig. 1A-B). In the avian embryo, the mesethmoid constitutes the cartilage primordium of the upper beak
    • - nasal capsule taxon notes In most mammals, the nasal capsule remains unossified, except in mammals where the ethmoid portion ossifies to form the turbinates[Kardong]. In avians, the mesethmoid supports upper beak formation, whereas the ectethmoid comprises elements of the olfactory system, including the lamina cribosa, the crista galli apophysis and the conchae. Editor’s note - consider splitting this class. Developing cartilage in mammals? Connective tissue sheath in TAO. Structure that has both respiratory and olfactory functions and lies anterior to the braincase, in the foremost section of the cranium[AAO]. Cartilaginous envelope containing the nasal organ[FishBase] Multi-tissue structure composed of connective tissue that surrounds, the internal portions of the olfactory epithelium[ZFA]
  • Added
    • + nasal capsule comment Editor’s note: consider splitting this class. Developing cartilage in mammals? Connective tissue sheath in TAO. Structure that has both respiratory and olfactory functions and lies anterior to the braincase, in the foremost section of the cranium[AAO]. Cartilaginous envelope containing the nasal organ[FishBase] Multi-tissue structure composed of connective tissue that surrounds, the internal portions of the olfactory epithelium[ZFA]
    • + nasal capsule taxon notes In Aves: The nasal capsule is dorsoventrally divided into two parts: the upper part, the ectethmoid, serves olfaction and is composed of the lamina cribosa, the crista galli apophysis and the conchae. The lower part, the mesethmoid, is a thick cartilage bar extending from the corpus sphenoidalis to the rostral extremity of the nose (Fig. 1A-B). In the avian embryo, the mesethmoid constitutes the cartilage primordium of the upper beak.
    • + nasal capsule taxon notes In avians, the mesethmoid supports upper beak formation, whereas the ectethmoid comprises elements of the olfactory system, including the lamina cribosa, the crista galli apophysis and the conchae.
    • + nasal capsule taxon notes In most mammals, the nasal capsule remains unossified, except in mammals where the ethmoid portion ossifies to form the turbinates[Kardong]

Changes for: distal early tubule

  • Deleted
    • - distal early tubule comment in XAO this is pronephric; in ZFA it is an adult structure. we treat it here as generic. consider placing XAO under proneprhic subclass. check relationship with EDCT.
  • Added

Changes for: cerebellum ventricular layer

Changes for: sinus venosus

  • Deleted
    • - sinus venosus comment In zebrafish, “the sinus venosus also acts as a pacemaker and is the first to contract”[ZFA:0000154]
    • - sinus venosus definition The sinus venosus is a large quadrangular cavity which precedes the atrium on the venous side of the chordate heart. In humans, it exists distinctly only in the embryonic heart, where it is found between the two venae cavae. In the adult, it is incorporated into the wall of the right atrium to form a smooth part called the sinus venarum, also known as the venarum sinus, which is separated from the rest of the atrium by a ridge of fibres called the crista terminalis. The sinus venosus also forms the SA node and the coronary sinus. In the embryo, the thin walls of the sinus venosus are connected below with the right ventricle, and medially with the left atrium, but are free in the rest of their extent. It receives blood from the vitelline vein, umbilical vein and common cardinal vein. It originally starts as a paired structure but shifts towards associating only with the right atrium as the embryonic heart develops. The left portion shrinks in size and eventually forms the coronary sinus and oblique vein of the left atrium, whereas the right part becomes incorporated into the right atrium to form the sinus venarum. { database cross reference=http://en.wikipedia.org/wiki/Sinus_venosus }
  • Added
    • + sinus venosus comment Taxon notes: In humans, it exists distinctly only in the embryonic heart, where it is found between the two venae cavae. In the adult, it is incorporated into the wall of the right atrium to form a smooth part called the sinus venarum, also known as the venarum sinus, which is separated from the rest of the atrium by a ridge of fibres called the crista terminalis. The sinus venosus also forms the SA node and the coronary sinus. In the embryo, the thin walls of the sinus venosus are connected below with the right ventricle, and medially with the left atrium, but are free in the rest of their extent. It receives blood from the vitelline vein, umbilical vein and common cardinal vein. It originally starts as a paired structure but shifts towards associating only with the right atrium as the embryonic heart develops. The left portion shrinks in size and eventually forms the coronary sinus and oblique vein of the left atrium, whereas the right part becomes incorporated into the right atrium to form the sinus venarmu
    • + sinus venosus definition The sinus venosus is a large cardiac chamber which precedes the atrium on the venous side of the chordate heart. { database cross reference=http://en.wikipedia.org/wiki/Sinus_venosus }
    • + sinus venosus taxon notes In zebrafish, the sinus venosus also acts as a pacemaker and is the first to contract[ZFA:0000154]

Changes for: embryonic structure

Changes for: dorsal raphe nucleus

Changes for: lung

  • Deleted
    • - lung comment respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi // Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]
    • - lung definition Respiration organ present in all air-breathing animals whose principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere[WP]. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax[GO]. { database cross reference=http://en.wikipedia.org/wiki/Lung , database cross reference=BTO:0000763 }
  • Added
    • + lung comment Taxon notes: respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi // Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]
    • + lung definition Respiration organ that develops as an oupocketing of the esophagus. { database cross reference=UBERON:cjm }

Changes for: dermomyotome

Changes for: substantia nigra

  • Deleted
    • - substantia nigra comment TODO: In BTO and NIF, part of basal ganglion which is part of telencephalon - but this is inconsistent with being part of midbrain, if these are spatially disjoint, as in ABA
  • Added
    • + substantia nigra editor note TODO - In BTO and NIF, part of basal ganglion which is part of telencephalon - but this is inconsistent with being part of midbrain, if these are spatially disjoint, as in ABA

Changes for: hindbrain

  • Deleted
    • - hindbrain comment in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps
  • Added

Changes for: stratum corneum of epidermis

Changes for: accessory XI nerve

  • Added
    • + accessory XI nerve comment AO notes: FMA has distinct cranian and spinal parts - WP says ‘Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] However, because the cranial component rapidly joins the vagus nerve, becoming an integral part of said nerve, modern descriptions often consider the cranial component to be part of the vagus nerve and not part of the accessory nerve proper.[2] For this reason, in contemporary discussions of the accessory nerve, the common practice is to dismiss the cranial part altogether, referring to the accessory nerve specifically as the spinal accessory nerve.’
    • + accessory XI nerve database cross reference FMA:80284

Changes for: peripheral nerve

Changes for: rectus capitis lateralis muscle

Changes for: endoderm of foregut

Changes for: yolk sac endoderm

Changes for: endoderm of midgut

Changes for: epithelium of utricle

Changes for: epithelium of saccule

Changes for: endoderm of hindgut

Changes for: chorionic mesenchyme

Changes for: mesoderm of yolk sac

Changes for: hard palate

Changes for: neural lobe of neurohypophysis

Changes for: chorion syncytiotrophoblast

Changes for: supinator muscle

  • Deleted
    • - supinator muscle comment TODO: The term “supinator” can also refer more generally to a muscle that causes supination of a part of the body. In older texts, the term “supinator longus” was used to refer to the brachioradialis, and “supinator brevis” was used to the muscle now known as the supinator.
  • Added
    • + supinator muscle editor note TODO - The term ‘supinator’ can also refer more generally to a muscle that causes supination of a part of the body. In older texts, the term ‘supinator longus’ was used to refer to the brachioradialis, and ‘supinator brevis’ was used to the muscle now known as the supinator.

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: metatarsophalangeal joint of pedal 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: paramedian reticular nucleus

Changes for: ascitic fluid

Changes for: vascular system

Changes for: pharyngeal gill

  • Deleted
    • - pharyngeal gill definition Gills of vertebrates are developed in the walls of the pharynx along a series of gill slits opening to the exterior. In fish, the gills are located on both sides of the pharynx. 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. { database cross reference=Vertebrate gills }
  • Added
    • + 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
    • + pharyngeal gill definition A gill that develops in the walls of the pharynx along a series of gill slits opening to the exterior. In fish, the gills are located on both sides of the pharynx. { database cross reference=Vertebrate gills }

Changes for: apical ectodermal ridge

  • Deleted
    • - apical ectodermal ridge comment . Function notes: maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop
  • Added
    • + apical ectodermal ridge comment Function notes: maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop

Changes for: podocyte foot process

Changes for: interphalangeal joint of pedal digit 3

Changes for: interphalangeal joint of pedal digit 2

Changes for: interphalangeal joint of pedal digit 1

Changes for: interphalangeal joint of manual digit 1

Changes for: interphalangeal joint of manual digit 2

Changes for: interphalangeal joint of pedal digit 4

Changes for: interphalangeal joint of pedal digit 5

Changes for: interphalangeal joint of manual digit 4

Changes for: interphalangeal joint of manual digit 3

Changes for: interphalangeal joint of manual digit 5

Changes for: metacarpophalangeal joint of manual digit 1

Changes for: metacarpophalangeal joint of manual digit 2

Changes for: blastopore

  • Deleted
    • - blastopore comment In protostome development, the first opening in development, the blastopore, becomes the animal’s mouth; In deuterostome development, the blastopore becomes the animal’s anus
  • Added
    • + blastopore taxon notes In protostome development, the first opening in development, the blastopore, becomes the animal’s mouth; In deuterostome development, the blastopore becomes the animal’s anus

Changes for: metacarpophalangeal joint of manual digit 5

Changes for: metacarpophalangeal joint of manual digit 4

Changes for: metacarpophalangeal joint of manual digit 3

Changes for: digit 6 plus metapodial segment

Changes for: digit 7 plus metapodial segment

Changes for: digit 8 plus metapodial segment

Changes for: sexually immature stage

  • Deleted
    • - sexually immature stage comment in mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother)
  • Added

Changes for: metatarsophalangeal joint of pedal digit 3

Changes for: metatarsophalangeal joint of pedal digit 4

Changes for: metatarsophalangeal joint of pedal digit 2

Changes for: facial nucleus

  • Deleted
    • - facial nucleus comment FMA has 3 subclasses - left, right and motor nucleus of facial nerve, but no defs. It’s not clear how facial nucleus is distinct from facial motor nucleus.
  • Added
    • + facial nucleus comment AO notes: FMA has 3 subclasses - left, right and motor nucleus of facial nerve, but no defs. It’s not clear how facial nucleus is distinct from facial motor nucleus.

Changes for: digit 6

Changes for: metatarsophalangeal joint of pedal digit 1

Changes for: digit 8

Changes for: digit 7

Changes for: intermediate nucleus of lateral lemniscus

Changes for: cloaca

  • Deleted
    • - cloaca comment . Editor notes: adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca
  • Added
    • + cloaca editor note adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca

Changes for: orifice

Changes for: intestine

  • Deleted
    • - intestine comment Taxon notes: In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type.
  • Added
    • + intestine taxon notes In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type.

Changes for: pleural effusion

Changes for: sagittal sinus

Changes for: intromittent organ

  • Deleted
    • - intromittent organ comment this is a broad grouping class connecting a number of different analagous organs by their function. We place the insect aedeagus here rather than penis, although this is somewhat arbitrary given the broadness of the current definition
  • Added
    • + intromittent organ curator notes this is a broad grouping class connecting a number of different analagous organs by their function. We place the insect aedeagus here rather than penis, although this is somewhat arbitrary given the broadness of the current definition

Changes for: mesentery of stomach

Changes for: presphenoid bone

Changes for: digit 6 digitopodial skeleton

Changes for: digit 8 digitopodial skeleton

Changes for: digit 7 digitopodial skeleton

Changes for: great auricular nerve

Changes for: cranial suspensory ligament

Changes for: digit 1 plus metapodial segment

Changes for: digit 2 plus metapodial segment

Changes for: epithelium of sublingual gland

Changes for: epithelium of parotid gland

Changes for: epithelium of submandibular gland

Changes for: blastodisc derived epiblast

Changes for: digit 3 plus metapodial segment

Changes for: digit 5 plus metapodial segment

Changes for: digit 4 plus metapodial segment

Changes for: epaxial musclulature

Changes for: hypaxial musclulature

Changes for: mesenchyme of knee

Changes for: mesenchyme of shoulder

Changes for: mesenchyme of hip

Changes for: mesenchyme of pinna

Changes for: mesenchyme of mammary gland

Changes for: mesenchyme of upper jaw

Changes for: mesenchyme of lower jaw

Changes for: mesenchyme of forearm

Changes for: mesenchyme of elbow

Changes for: proximal epiphysis of proximal phalanx of manual digit 1

Changes for: mesenchyme of ovary

Changes for: eye mesenchyme

Changes for: mesenchyme of testis

Changes for: proximal epiphysis of proximal phalanx of manual digit 3

Changes for: proximal epiphysis of proximal phalanx of manual digit 4

Changes for: proximal epiphysis of proximal phalanx of manual digit 5

Changes for: proximal epiphysis of distal phalanx of manual digit 1

Changes for: proximal epiphysis of proximal phalanx of manual digit 2

Changes for: proximal epiphysis of middle phalanx of manual digit 5

Changes for: proximal epiphysis of middle phalanx of manual digit 4

Changes for: proximal epiphysis of middle phalanx of manual digit 2

Changes for: proximal epiphysis of middle phalanx of manual digit 3

Changes for: proximal epiphysis of distal phalanx of manual digit 4

Changes for: mesoderm blood island

Changes for: proximal epiphysis of distal phalanx of manual digit 5

Changes for: proximal epiphysis of distal phalanx of manual digit 2

Changes for: proximal epiphysis of distal phalanx of manual digit 3

Changes for: proximal epiphysis of phalanx of manual digit 4

Changes for: proximal epiphysis of phalanx of manual digit 5

Changes for: nucleus of thalamus

Changes for: proximal epiphysis of phalanx of manual digit 3

Changes for: proximal epiphysis of phalanx of manual digit 2

Changes for: proximal epiphysis of phalanx of manual digit 1

Changes for: late embryo

  • Deleted
    • - late embryo comment TODO - check fetus/embryo. WP: An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination. In humans, it is called an embryo until about eight weeks after fertilization (i.e. ten weeks LMP), and from then it is instead called a fetus.
  • Added
    • + late embryo editor note TODO - check fetus/embryo. WP: An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination. In humans, it is called an embryo until about eight weeks after fertilization (i.e. ten weeks LMP), and from then it is instead called a fetus.

Changes for: portion of cartilage tissue in tibia

Changes for: blastula

  • Deleted
    • - blastula comment TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula
  • Added
    • + blastula editor note TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula

Changes for: body wall

Changes for: musculature of body wall

Changes for: tendon sheath

Changes for: capillary loop nephron

Changes for: maturing nephron

Changes for: musculature of thorax

Changes for: esophageal sphincter

  • Deleted
    • - esophageal sphincter comment editor note - check for specific subtypes across species. Note mammals have upper and lower, but lower is really part of cardia and thus is not classified under here
  • Added
    • + esophageal sphincter comment editor note: check for specific subtypes across species. Note mammals have upper and lower, but lower is really part of cardia and thus is not classified under here

Changes for: trunk or cervical vertebra

Changes for: tarsal region

  • Deleted
    • - tarsal region comment Usage notes: this term refers to the limb segment. See also: tarsal bones and tarsal skeleton. AO notes: MA has both tarsus (part of foot, has tarsal bone) and ankle (part of hindlimb, has joint, nerve, skin).
  • Added

Changes for: trigeminal nuclear complex

  • Deleted
    • - trigeminal nuclear complex comment In MA and FMA this is part of the pons / pontime tegmentum. We weaken this to overlaps to avoid inconsistency. In NIF this is a composite structure spanning multiple regions, which is more appropriate.
  • Added

Changes for: hippocampus alveus

Changes for: myoseptum

Changes for: median raphe nucleus

  • Deleted
    • - median raphe nucleus comment TODO: The term medial raphe nucleus refers to a composite structure that consists of the superior central nucleus and the inferior central nucleus of the pontine reticular formation ( Carpenter-1983 )[http://braininfo.rprc.washington.edu/centraldirectory.aspx?type=h&ID=1391]
  • Added
    • + median raphe nucleus editor note TODO - The term medial raphe nucleus refers to a composite structure that consists of the superior central nucleus and the inferior central nucleus of the pontine reticular formation ( Carpenter-1983 )[http://braininfo.rprc.washington.edu/centraldirectory.aspx?type=h&ID=1391]

Changes for: gastroesophageal sphincter

Changes for: ciliated columnar oviduct epithelium

Changes for: caudal region of vertebral column

Changes for: sacral region of vertebral column

Changes for: interdigital region between pedal digits 1 and 2

Changes for: interdigital region between manual digits 4 and 5

Changes for: interdigital region between manual digits 3 and 4

Changes for: interdigital region between pedal digits 4 and 5

Changes for: digit 1

Changes for: digit 2

Changes for: interdigital region between pedal digits 3 and 4

Changes for: interdigital region between pedal digits 2 and 3

Changes for: digit 5

Changes for: digit 3

Changes for: digit 4

Changes for: caudal region

  • Deleted
    • - caudal region comment We follow XAO is distinguishing the tail region from the tail; the tail bud is part of the tail region; the tail starts after the tail bud
  • Added

Changes for: zygapophysis

Changes for: periderm

  • Deleted
    • - periderm comment Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html)
  • Added
    • + periderm development notes Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html)

Changes for: ventricular zone

  • Deleted
    • - ventricular zone comment in BTO this is restricted to the 4th ventricle - however this class also represents the early ventricular zone as well as its post-natal remnants. The MA class is named ‘ventricular zon