2015-08-11 release

Minor release
2015-08-11 release image

Ontology Diff Report

  • Branching structures
    • NTs for veins
    • Axiomatized spinal plexuses and ganglia using innervates relationships
  • Ontolology alignment
    • Brought in select synonyms from ZFA
    • aligned with FMA 4.0.1 - this version of FMA has many more embryonic structures
    • Generalized classes from EHDAA2: embryonic capillary plexus, yolk sac cavities
  • Other
    • NT: submandibular region. Issue 1137
    • added logical definition for endothelium

~

Original Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2015-07-24/uberon.owl

New Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2015-08-11/uberon.owl

Report for classes

Class objects lost from source: 0

Class objects new in target: 25

New Class : deep facial vein

New Class : pulmonary capillary plexus

New Class : capillary plexus

New Class : embryonic capillary plexus

New Class : peritubular capillary plexus of kidney

New Class : systemic capillary plexus

New Class : capillary network of liver

New Class : cavity of cardiac chamber

New Class : capillary network of kidney

New Class : subsegmental lymph node

New Class : pulmonary lymph node

New Class : median lobe of prostate

New Class : intrapulmonary bronchus

New Class : coccygeal nerve plexus

New Class : mesenteric ganglion

New Class : submandibular region

New Class : thoracic aortic plexus

New Class : abdominal nerve plexus

New Class : aortic plexus

New Class : mesenteric plexus

New Class : inferior mesenteric nerve plexus

New Class : anterior facial vein

New Class : secondary yolk sac savity

New Class : primary yolk sac cavity

New Class : parotid vein

Changed Class objects: 1168

Changes for: base of crypt of Lieberkuhn

  • Deleted
    • - base of crypt of Lieberkuhn taxon notes Clearly defined prolifieration zones found in mammals. Not observed in agnathostomes, larval amphibians. Described in advanced species of fish and adult amphibians. { source=ISBN:9780521617147 }
  • Added
    • + base of crypt of Lieberkuhn taxon notes Clearly defined prolifieration zones found in mammals. Not observed in agnathostomes, larval amphibians. Described in advanced species of fish and adult amphibians. { source=ISBN:9780521617147 }

Changes for: dartos muscle

Changes for: ilio-marsupialis muscle

  • Deleted
    • - ilio-marsupialis muscle function notes In pouched marsupials, the ilio-marsupialis is less well developed, but may help in gland contraction to express milk during suckling (Griffiths & Slater, 1988) and it carries the genitofemoral nerve that innervates the mammary gland (Renfree, 1979) [doi:10.1046/j.1469-7580.2002.00087.x]
  • Added
    • + ilio-marsupialis muscle function notes In pouched marsupials, the ilio-marsupialis is less well developed, but may help in gland contraction to express milk during suckling (Griffiths & Slater, 1988) and it carries the genitofemoral nerve that innervates the mammary gland (Renfree, 1979) [doi:10.1046/j.1469-7580.2002.00087.x]

Changes for: fascia of Scarpa

Changes for: notochordal canal

Changes for: longissimus atlantis muscle

Changes for: supra-orbital ridge

Changes for: inner canthus of left eye

Changes for: pericranium

Changes for: inner canthus of right eye

Changes for: anatomical line between inner canthi

Changes for: posterior cingulate cortex

Changes for: medial orbital frontal cortex

Changes for: maxillary tooth

Changes for: dentary tooth

Changes for: lenticular process of incus bone

Changes for: gingiva of upper jaw

Changes for: gingiva of lower jaw

Changes for: sagulum nucleus

Changes for: embryonic cardiovascular system

Changes for: inferior horn of thyroid cartilage

Changes for: frontal process of maxilla

Changes for: ectopterygoid bone

Changes for: rostral anterior cingulate cortex

Changes for: nucleus of pudendal nerve

Changes for: corticobulbar tract

Changes for: epithelium of crypt of Lieberkuhn of small intestine

Changes for: tear film

  • Deleted
    • - tear film external definition the thin acellular fluid layer that adheres to the most superficial layer of the corneal epithelium and lubricates and protects the ocular surface; the film is generally composed of three layers: (i) an inner mucous layer, secreted largely by the conjunctival goblet cells with contributions from the lacrimal glands, which coats the cornea, provides a hydrophobic layer, and allows for even distribution of the tear film; (ii) a middle aqueous layer, secreted by the lacrimal glands, which keeps the corneal surface moist, and provides a mechanism for oxygenation and nutrient exchange with the avascular anterior corneal tissue; and (iii) an outer lipid layer, secreted principally by the Meibomian (tarsal) glands although lipid tear elements also are contributed by the Harderian glands; tear film lipids form a monolayer on the tear surface, and function by enhancing the surface tension which supports the integrity of the tear film against collapse due to gravity and also slows down the loss of the tear film by evaporation; in addition , the lipid layer provides a glassy, smooth interface between the air and the transparent cornea { source=MGI:anna }
  • Added
    • + tear film external definition the thin acellular fluid layer that adheres to the most superficial layer of the corneal epithelium and lubricates and protects the ocular surface; the film is generally composed of three layers: (i) an inner mucous layer, secreted largely by the conjunctival goblet cells with contributions from the lacrimal glands, which coats the cornea, provides a hydrophobic layer, and allows for even distribution of the tear film; (ii) a middle aqueous layer, secreted by the lacrimal glands, which keeps the corneal surface moist, and provides a mechanism for oxygenation and nutrient exchange with the avascular anterior corneal tissue; and (iii) an outer lipid layer, secreted principally by the Meibomian (tarsal) glands although lipid tear elements also are contributed by the Harderian glands; tear film lipids form a monolayer on the tear surface, and function by enhancing the surface tension which supports the integrity of the tear film against collapse due to gravity and also slows down the loss of the tear film by evaporation; in addition , the lipid layer provides a glassy, smooth interface between the air and the transparent cornea { source=MGI:anna }

Changes for: anterior thalamic peduncle

Changes for: posterior thalamic peduncle

Changes for: inferior thalamic peduncle

Changes for: superior thalamic peduncle

Changes for: subcallosal fasciculus

Changes for: ventral thalamic fasciculus

Changes for: medullary anterior horn

Changes for: cartilaginous projection

Changes for: motor nucleus of vagal nerve

Changes for: dentate gyrus molecular layer inner

Changes for: dentate gyrus molecular layer middle

Changes for: long ciliary nerve

Changes for: short ciliary nerve

Changes for: loose connective tissue

Changes for: muscle layer of esophagus

Changes for: angular bone

Changes for: annular ligament of stapes

Changes for: radiation of thalamus

Changes for: pars tensa of tympanic membrane

Changes for: pars flaccida of tympanic membrane

Changes for: medial olfactory stria

Changes for: anterior process of malleus

Changes for: transverse process of lumbar vertebra

Changes for: buccal vestibule

Changes for: primary auditory cortex

Changes for: margin of eyelid

Changes for: developing neuroepithelium

Changes for: inflow tract of right ventricle

Changes for: posterior fascicle of palatopharyngeus

Changes for: ampulla of uterine tube

Changes for: pineal tract

Changes for: medial forebrain bundle

Changes for: mammary gland

Changes for: ophthalmic plexus

Changes for: lunule of nail

Changes for: habenula

Changes for: optic tract

Changes for: lateral hypothalamic nucleus

Changes for: superficial part of masseter muscle

Changes for: submucosa of bronchus

Changes for: postfrontal bone

Changes for: submucosa of esophagus

Changes for: substantia nigra pars reticulata

Changes for: reticular layer of dermis

Changes for: papillary layer of dermis

Changes for: superior cervical ganglion

Changes for: superior tibiofibular joint

Changes for: crypt of Lieberkuhn

Changes for: post-cranial axial skeletal system

Changes for: anterior root of zygomatic arch

Changes for: meningeal vein

  • Deleted
    • - meningeal vein taxon notes In humans, any of several veins that accompany the meningeal arteries, communicate with the sinuses of the dura mater and diploic veins, and drain into the regional veins outside the cranial vault.
  • Added
    • + meningeal vein taxon notes In humans, any of several veins that accompany the meningeal arteries, communicate with the sinuses of the dura mater and diploic veins, and drain into the regional veins outside the cranial vault.

Changes for: jejunal artery

Changes for: premolar 1 hypoconoid

Changes for: spinalis cervicis muscle

Changes for: molar 1 posteroloph

Changes for: nucleus of medial eminence

Changes for: inferior central nucleus

Changes for: substantia nigra pars lateralis

Changes for: supramammillary commissure

Changes for: lumbosacral nerve plexus

Changes for: spinal nerve plexus

  • Added
    • + spinal nerve plexus homology notes To reach the muscles, dermatomes, and other structures of the limbs, some of the neurons in the spinal nerves come together in the plexus at the base of the limb. Such plexuses occur in all gnathostomes, and they reach their highest complexity among mammals and birds in which the cervical plexus supplies many ventral neck muscles, the brachial plexus supplies the pectoral appendage, a lumbosacral plexus supplies the pelvic appendage, and a coccygeal plexus supplies some of the pelvic muscles.[well established][VHOG] { date retrieved=2012-09-17 , external class=VHOG:0000926 , ontology=VHOG , source=http://bgee.unil.ch/ , source=ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.436 }

Changes for: brachial nerve plexus

Changes for: posterior segment of eyeball

Changes for: anterior segment of eyeball

Changes for: maxillary process ectoderm

Changes for: embryonic facial prominence

Changes for: incisive foramen

Changes for: rhombomere

Changes for: lobule of pinna

  • Deleted
    • - lobule of pinna structure notes The earlobe is composed of tough areolar and adipose (fatty) connective tissues, lacking the firmness and elasticity of the rest of the pinna. Since the earlobe does not contain cartilage the earlobe has a large blood supply and may help to warm the ears and maintain balance but generally earlobes are not considered to have any major biological function. { source=WP,unvetted }
  • Added
    • + lobule of pinna structure notes The earlobe is composed of tough areolar and adipose (fatty) connective tissues, lacking the firmness and elasticity of the rest of the pinna. Since the earlobe does not contain cartilage the earlobe has a large blood supply and may help to warm the ears and maintain balance but generally earlobes are not considered to have any major biological function. { source=WP,unvetted }

Changes for: cochlea

Changes for: carpometacarpal joint of digit 1

Changes for: dorsal trunk

  • Deleted
    • - dorsal trunk taxon notes In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA]
  • Added
    • + dorsal trunk taxon notes In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA]

Changes for: caudal-sacral region of vertebral column

  • Deleted
  • Added

Changes for: nail of pedal digit 1

Changes for: tendon of obturator internus

Changes for: outer limiting layer of retina

Changes for: photoreceptor layer of retina

Changes for: outer nuclear layer of retina

Changes for: pigmented layer of retina

Changes for: molar 3

Changes for: molar 1

Changes for: inner limiting layer of retina

Changes for: nerve fiber layer of retina

Changes for: outer plexiform layer of retina

Changes for: inner nuclear layer of retina

Changes for: zone of organ

Changes for: saccus vasculosus

  • Deleted
    • - saccus vasculosus function notes Although its function remains hypothetical, it may contain sensory receptors for depth chemical detection. Other probable functions are osmoregulation ionic transport skeletal growth and tooth regeneration, although other homeostatic functions are not excluded
  • Added
    • + saccus vasculosus function notes Although its function remains hypothetical, it may contain sensory receptors for depth chemical detection. Other probable functions are osmoregulation ionic transport skeletal growth and tooth regeneration, although other homeostatic functions are not excluded

Changes for: prismatic cartilage

  • Deleted
    • - prismatic cartilage definition cartilage arranged into tesserae, blocks of calcified cartilage that fit together as tiles on a floor form a mosaic. Found only in chondrichthyans. Reference: A. Peter Klimley. 2013. The Biology of Sharks and Rays. University of Chicago Press. { database cross reference=PHENOSCAPE:Wasila }
  • Added
    • + prismatic cartilage definition cartilage arranged into tesserae, blocks of calcified cartilage that fit together as tiles on a floor form a mosaic. Found only in chondrichthyans. Reference: A. Peter Klimley. 2013. The Biology of Sharks and Rays. University of Chicago Press. { database cross reference=PHENOSCAPE:Wasila }

Changes for: pharyngeal apophysis

  • Deleted
    • - pharyngeal apophysis definition Ventral process on the neurocranium for the articulation of upper pharyngeal bones. It is variably composed of the parasphenoid, basioccipital, and prootic depending on the species. From: Greenwood, PH (1978). A review of the pharyngeal hypophysis and its significance in the classification of African cichlid fishes. Bull. Br. Mus. Nat. Hist. (Zool.) 33: 297-323. { database cross reference=PHENOSCAPE:Wasila }
  • Added
    • + pharyngeal apophysis definition Ventral process on the neurocranium for the articulation of upper pharyngeal bones. It is variably composed of the parasphenoid, basioccipital, and prootic depending on the species. From: Greenwood, PH (1978). A review of the pharyngeal hypophysis and its significance in the classification of African cichlid fishes. Bull. Br. Mus. Nat. Hist. (Zool.) 33: 297-323. { database cross reference=PHENOSCAPE:Wasila }

Changes for: small intestine smooth muscle longitudinal layer

Changes for: nasal process of premaxilla

Changes for: oviduct mucosal fold

Changes for: small intestine smooth muscle circular layer

Changes for: medial condyle of quadrate

Changes for: intraramal joint

Changes for: flexor sesamoid

Changes for: extramural oviduct

Changes for: dorsal osteoderm

Changes for: cheek scale row

Changes for: post-axial region

Changes for: anatomical row

Changes for: subicular complex

Changes for: cloacal lumen

Changes for: dentine

Changes for: pinna

  • Deleted
    • - pinna function notes The purpose of the pinna is to collect sound. It does so by acting as a funnel, amplifying the sound and directing it to the ear canal. While reflecting from the pinna, sound also goes through a filtering process which adds directional information to the sound (see sound localization, head-related transfer function, pinna notch).
  • Added
    • + pinna function notes The purpose of the pinna is to collect sound. It does so by acting as a funnel, amplifying the sound and directing it to the ear canal. While reflecting from the pinna, sound also goes through a filtering process which adds directional information to the sound (see sound localization, head-related transfer function, pinna notch).

Changes for: lateral surface of mandible

Changes for: medial surface of mandible

Changes for: capsule of thyroid gland

Changes for: pupil

Changes for: substantia propria of cornea

Changes for: cranial lymph vasculature

Changes for: cranial blood vasculature

Changes for: male external urethral sphincter

Changes for: turbinate bone

  • Deleted
    • - turbinate bone taxon notes In humans, the turbinates divide the nasal airway into three groove-like air passages –and are responsible for forcing inhaled air to flow in a steady, regular pattern around the largest possible surface of cilia and climate controlling tissue. { source=WP,unvetted }
  • Added
    • + turbinate bone taxon notes In humans, the turbinates divide the nasal airway into three groove-like air passages –and are responsible for forcing inhaled air to flow in a steady, regular pattern around the largest possible surface of cilia and climate controlling tissue. { source=WP,unvetted }

Changes for: mesencephalic nucleus of trigeminal nerve

Changes for: facial modiolus

Changes for: eyelid

  • Deleted
    • - eyelid taxon notes In humans the upper and lower eyelid consists of the following layers, starting anteriorly: (1) skin, (2) a layer of subcutaneous connective tissue, (3) a layer of striated muscle fibres of the orbicularis muscle, (4) a layer of submuscular connective tissue, (5) a fibrous layer, including the tarsal plates, (6) a layer of smooth muscle, (7) the palpebral conjunctiva.
  • Added
    • + eyelid taxon notes In humans the upper and lower eyelid consists of the following layers, starting anteriorly: (1) skin, (2) a layer of subcutaneous connective tissue, (3) a layer of striated muscle fibres of the orbicularis muscle, (4) a layer of submuscular connective tissue, (5) a fibrous layer, including the tarsal plates, (6) a layer of smooth muscle, (7) the palpebral conjunctiva.

Changes for: female external urethral sphincter

Changes for: upper jaw region

Changes for: jaw skeleton

  • Deleted
    • - 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).
  • 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).

Changes for: obsolete viscerocranium

  • Deleted
    • - obsolete viscerocranium curator notes this class was made obsolete as it conflated the facial skeleton with the splanchnocranium. The facial skeleton includes: * Inferior nasal concha * Lacrimal bone * Mandible * Maxilla * Nasal bone * Palatine bone * Vomer * Zygomatic bone. The hyoid is sometimes included, and sometimes excluded (FMA includes it) (See also notes for ethmoid bone). The splanchoncranium is the endoskeleton derived from pharyngeal arches.
  • Added
    • + obsolete viscerocranium curator notes this class was made obsolete as it conflated the facial skeleton with the splanchnocranium. The facial skeleton includes: * Inferior nasal concha * Lacrimal bone * Mandible * Maxilla * Nasal bone * Palatine bone * Vomer * Zygomatic bone. The hyoid is sometimes included, and sometimes excluded (FMA includes it) (See also notes for ethmoid bone). The splanchoncranium is the endoskeleton derived from pharyngeal arches.

Changes for: neurocranium

  • Deleted
    • - neurocranium development notes The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP]. { source=WP }
  • Added
    • + neurocranium development notes The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP]. { source=WP }

Changes for: pharyngeal tonsil

Changes for: tongue

  • Deleted
    • - tongue editor note in MA the tongue is part of the oral region, which in uberon is treated as the oral opening. consider revising oral opening - oral region equivalence.
  • Added
    • + tongue editor note in MA the tongue is part of the oral region, which in uberon is treated as the oral opening. consider revising oral opening - oral region equivalence.

Changes for: insular cortex

Changes for: maxillary vein

  • Deleted
    • - maxillary vein definition The maxillary veins (internal maxillary vein in older sources) consist of a short trunk which accompanies the first part of the internal maxillary artery. It is formed by a confluence of the veins of the pterygoid plexus, and passes backward between the sphenomandibular ligament and the neck of the mandible, and unites with the superficial temporal vein to form the retromandibular vein. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Maxillary_vein }
  • Added
    • + maxillary vein definition A vein that consists of a short trunk which accompanies the first part of the internal maxillary artery. It is formed by a confluence of the veins of the pterygoid plexus, and passes backward between the sphenomandibular ligament and the neck of the mandible, and unites with the superficial temporal vein to form the retromandibular vein. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Maxillary_vein }

Changes for: temporal bone

  • Deleted
    • - temporal bone structure notes The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP]. { source=[WP] }
  • Added
    • + temporal bone structure notes The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP]. { source=[WP] }

Changes for: nasal bone

Changes for: mandible

  • Deleted
    • - mandible editor note consider merging with dentary - for now we make it a mammal-specific subclass.
  • Added
    • + mandible editor note consider merging with dentary - for now we make it a mammal-specific subclass.

Changes for: auditory ossicle bone

  • Deleted
    • - auditory ossicle bone editor note This should probably be restricted to mammals - the AAO/XAO structures may group non-homologous structures [Wikipedia:Evolution_of_mammalian_auditory_ossicles] see https://github.com/seger/aao/issues/5.
  • Added
    • + auditory ossicle bone editor note This should probably be restricted to mammals - the AAO/XAO structures may group non-homologous structures [Wikipedia:Evolution_of_mammalian_auditory_ossicles] see https://github.com/seger/aao/issues/5.

Changes for: stapes bone

  • Deleted
    • - stapes bone taxon notes ‘This structure [the hyomandibular], on ontogenic grounds alone, can be considered homologous with the amphibian and reptilian columella and the mammalian stapes.’ Gerrie J, The phylogeny of the mammalian tympanic cavity and auditory ossicles. The Journal of Laryngology and Otology (1948) 62:339-357?[VHOG].
  • Added
    • + stapes bone taxon notes ‘This structure [the hyomandibular], on ontogenic grounds alone, can be considered homologous with the amphibian and reptilian columella and the mammalian stapes.’ Gerrie J, The phylogeny of the mammalian tympanic cavity and auditory ossicles. The Journal of Laryngology and Otology (1948) 62:339-357?[VHOG].

Changes for: sensory root of facial nerve

Changes for: exoccipital bone

Changes for: foramen ovale of skull

Changes for: squamous part of temporal bone

Changes for: facial nerve canal

Changes for: ventral wall of dorsal aorta

Changes for: submucosa of pharynx

Changes for: sphincter of hepatopancreatic ampulla

Changes for: upper secondary canine tooth

Changes for: lower secondary canine tooth

Changes for: ventral tegmental area

Changes for: cuneate fasciculus of medulla

Changes for: upper third secondary molar tooth

Changes for: upper first secondary premolar tooth

Changes for: lower first secondary premolar tooth

Changes for: upper second secondary premolar tooth

Changes for: lower second secondary premolar tooth

Changes for: body of caudate nucleus

Changes for: lower third secondary molar tooth

Changes for: anterior horizontal limb of lateral sulcus

Changes for: lower primary canine tooth

Changes for: lower central primary incisor tooth

Changes for: upper primary canine tooth

Changes for: lower lateral primary incisor tooth

Changes for: upper primary incisor tooth

Changes for: posterior parahippocampal gyrus

Changes for: anterior horn of lateral ventricle

Changes for: body of lateral ventricle

Changes for: kidney arcuate artery

Changes for: digestive tract

Changes for: genioglossus muscle

Changes for: left subclavian artery

Changes for: vertebral endplate

Changes for: mesenchyme derived from neural crest

Changes for: abdominal segment skin

Changes for: cervical nerve plexus

Changes for: tubotympanic recess epithelium

Changes for: thoracic nerve

Changes for: collection of basal ganglia

Changes for: lumbar nerve

Changes for: sacral nerve

Changes for: extra-ocular muscle

Changes for: medial rectus extraocular muscle

Changes for: lateral rectus extra-ocular muscle

Changes for: 6th arch mesenchyme

Changes for: maxillary artery

Changes for: lumbar sympathetic nerve trunk

Changes for: pharyngotympanic tube epithelium

Changes for: forebrain midbrain boundary neural plate

Changes for: network of trabecular spaces in bone tissue

Changes for: supraorbital vein

Changes for: cardiovascular system endothelium

Changes for: cervical spinal cord

Changes for: paraaortic lymph node

Changes for: splanchnic layer of lateral plate mesoderm

Changes for: splanchnopleure

Changes for: vestibulocochlear nerve root

Changes for: somatic layer of lateral plate mesoderm

Changes for: urogenital fold

Changes for: somatopleure

Changes for: perinatal stage

  • Deleted
    • - 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
  • 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: posterior cingulate gyrus

Changes for: ileocolic lymph node

Changes for: intermediate periventricular nucleus

Changes for: ventral amygdalofugal projection

Changes for: endometrium epithelium

Changes for: oronasal membrane

Changes for: nasal fin

Changes for: respiratory velum

Changes for: frontal process of zygomatic bone

Changes for: dental lamina

Changes for: anterior median oculomotor nucleus

Changes for: intergluteal cleft

Changes for: medullary cavity of long bone

Changes for: external nucleus of inferior colliculus

Changes for: pericentral nucleus of inferior colliculus

Changes for: central nucleus of inferior colliculus

Changes for: intermediate hypothalamic region

  • Deleted
    • - intermediate hypothalamic region taxon notes In humans it contains the following nuclei: dorsal nucleus [TA] (nucleus dorsalis hypothalami [TA]), parts of the dorsomedial nucleus [TA] (nucleus dorsomedialis [TA]), arcuate nucleus [TA] (nucleus arcuatus [TA]), posterior periventricular nucleus [TA] (nucleus periventricularis posterior [TA]), retrochiasmatic area [TA] (area retrochiasmatica [TA]), lateral tuberal nuclei [TA] (nuclei tuberales laterales [TA]), and ventromedial nucleus [TA] (nucleus ventromedialis hypothalami { source=TA }
  • Added
    • + intermediate hypothalamic region taxon notes In humans it contains the following nuclei: dorsal nucleus [TA] (nucleus dorsalis hypothalami [TA]), parts of the dorsomedial nucleus [TA] (nucleus dorsomedialis [TA]), arcuate nucleus [TA] (nucleus arcuatus [TA]), posterior periventricular nucleus [TA] (nucleus periventricularis posterior [TA]), retrochiasmatic area [TA] (area retrochiasmatica [TA]), lateral tuberal nuclei [TA] (nuclei tuberales laterales [TA]), and ventromedial nucleus [TA] (nucleus ventromedialis hypothalami { source=TA }

Changes for: mesocolic lymph node

Changes for: upper secondary premolar tooth

Changes for: germ ring

  • Deleted
    • - 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)
  • 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: upper central secondary incisor tooth

Changes for: lower secondary premolar tooth

Changes for: pharyngeal arch

Changes for: superior ischial ramus

Changes for: epiblast (generic)

Changes for: lumbar lymph node

Changes for: pancreatic lymph node

Changes for: palmar branch of median nerve

Changes for: endochondral bone

Changes for: intramembranous bone

Changes for: precentral fissure of cerebellum

Changes for: postcentral fissure of cerebellum

Changes for: primary fissure of cerebellum

Changes for: visceral abdominal adipose tissue

Changes for: compact bone tissue

Changes for: carpal bone

  • Deleted
    • - carpal bone taxon notes In tetrapods, the carpals is the sole cluster of the bones in the wrist between the radius and ulna and the metacarpus. The bones of the carpus do not belong to individual fingers (or toes in quadrupeds), whereas those of the metacarpus do. The corresponding part of the foot is the tarsus. The carpal bones allow the wrist to move and rotate vertically, horizontally and laterally. In human anatomy, the main role of the carpus is to facilitate effective positioning of the hand and powerful use of the extensors and flexors of the forearm, but the mobility of individual carpal bones increase the freedom of movements at the wrist. { source=http://en.wikipedia.org/wiki/Carpus }
  • Added
    • + carpal bone taxon notes In tetrapods, the carpals is the sole cluster of the bones in the wrist between the radius and ulna and the metacarpus. The bones of the carpus do not belong to individual fingers (or toes in quadrupeds), whereas those of the metacarpus do. The corresponding part of the foot is the tarsus. The carpal bones allow the wrist to move and rotate vertically, horizontally and laterally. In human anatomy, the main role of the carpus is to facilitate effective positioning of the hand and powerful use of the extensors and flexors of the forearm, but the mobility of individual carpal bones increase the freedom of movements at the wrist. { source=http://en.wikipedia.org/wiki/Carpus }

Changes for: pectoral girdle region

Changes for: saphenous artery

Changes for: ansoparamedian fissure of cerebellum

Changes for: intermedium

  • Deleted
    • - intermedium taxon notes articulating with the ulnare and the radiale[VSAO]. human articulations: radius proximally capitate and hamate distally scaphoid laterally triangular medially
  • Added
    • + intermedium taxon notes articulating with the ulnare and the radiale[VSAO]. human articulations: radius proximally capitate and hamate distally scaphoid laterally triangular medially

Changes for: jugular lymphatic vessel

Changes for: elbow joint

  • Deleted
    • - elbow joint taxon notes In human anatomy, the elbow joint is a compound joint that actually comprises three separate joints: the joints connecting the upper and lower arm: 1) Articulatio humero-ulnaris and 2) Articulatio humero-radialis as well as the proximal joint connecting the forarm bones: 3) Articulatio radio-ulnaris proximalis { source=HP }
  • Added
    • + elbow joint taxon notes In human anatomy, the elbow joint is a compound joint that actually comprises three separate joints: the joints connecting the upper and lower arm: 1) Articulatio humero-ulnaris and 2) Articulatio humero-radialis as well as the proximal joint connecting the forarm bones: 3) Articulatio radio-ulnaris proximalis { source=HP }

Changes for: wrist joint

Changes for: vasa vasorum

Changes for: splenic vein

Changes for: bone element

Changes for: orbital operculum

Changes for: lateral medullary reticular complex

Changes for: intermediate reticular formation

Changes for: Guérin’s valve

Changes for: hemisphere of embryo

Changes for: gland of nasal mucosa

Changes for: head fold of embryonic disc

Changes for: visceral yolk sac cavity

Changes for: lymph node medullary sinus

Changes for: tail fold of embryonic disc

Changes for: lower jaw molar

Changes for: vertebral artery

Changes for: right subclavian artery

Changes for: entire pharyngeal arch endoderm

Changes for: internal carotid artery

Changes for: lumbrical muscle of manus

Changes for: lumbrical muscle of pes

Changes for: dorsal interosseous of manus

Changes for: intermaxillary process

Changes for: cupular organ

  • Deleted
    • - cupular organ taxon notes possible homologues of neuromasts in the inner ear (Bone & Ryan, 1978; Wada et al 1998). In the tunicate cupular organ, the sensory cell is a primary neuron sending an axon to the CNS. The sensory cilium is within a deep indentation of the cell and is surrounded by a collar of short microvilli.
  • Added
    • + cupular organ taxon notes possible homologues of neuromasts in the inner ear (Bone & Ryan, 1978; Wada et al 1998). In the tunicate cupular organ, the sensory cell is a primary neuron sending an axon to the CNS. The sensory cilium is within a deep indentation of the cell and is surrounded by a collar of short microvilli.

Changes for: larynx submucosa

Changes for: eyelid tarsus

  • Deleted
    • - eyelid tarsus taxon notes In most taxa (birds, mammals, lizards), the tarsal plate is described as a dense, fibrous connective tissue, possibly including cartilage, present within one or both of the upper and lower eyelids (Gau- thier et al., 1988; Rieppel, 2000). In humans, the tarsal plate of the upper eyelid is composed of collagens types I, III, and V, as well as glycosaminogly- cans (chondroitin sulphate 4 and 6), aggrecan, and cartilage oligomeric matrix proteins but lacks collagen type II as well as chondrocytes (Milz et al., 2005). Thus, for humans, the upper tarsal plate represents neither a truly fibrous nor a truly cartilagi- nous element but instead one that is composed of a unique transitional tissue (Milz et al., 2005). In many birds, lizards, and Sphenodon (the tuatara), the upper eyelid has lim- ited mobility and a putative tarsal plate is instead found within the lower eyelid (Underwood, 1970; Gau- thier et al., 1988). { source=http://www.ncbi.nlm.nih.gov/pubmed/16496288 }
  • Added
    • + eyelid tarsus taxon notes In most taxa (birds, mammals, lizards), the tarsal plate is described as a dense, fibrous connective tissue, possibly including cartilage, present within one or both of the upper and lower eyelids (Gau- thier et al., 1988; Rieppel, 2000). In humans, the tarsal plate of the upper eyelid is composed of collagens types I, III, and V, as well as glycosaminogly- cans (chondroitin sulphate 4 and 6), aggrecan, and cartilage oligomeric matrix proteins but lacks collagen type II as well as chondrocytes (Milz et al., 2005). Thus, for humans, the upper tarsal plate represents neither a truly fibrous nor a truly cartilagi- nous element but instead one that is composed of a unique transitional tissue (Milz et al., 2005). In many birds, lizards, and Sphenodon (the tuatara), the upper eyelid has lim- ited mobility and a putative tarsal plate is instead found within the lower eyelid (Underwood, 1970; Gau- thier et al., 1988). { source=http://www.ncbi.nlm.nih.gov/pubmed/16496288 }

Changes for: pedal digit 1 phalanx

Changes for: thoracic aorta

Changes for: limb joint

Changes for: gall bladder lamina propria

Changes for: lower central incisor tooth

Changes for: lower lateral incisor tooth

Changes for: upper central incisor tooth

Changes for: upper lateral incisor tooth

Changes for: pars postrema of ventral lateral nucleus

Changes for: molar 2

Changes for: medial part of ventral lateral nucleus

Changes for: epicondyle of humerus

Changes for: tendon of palmaris longus

Changes for: triangular part of inferior frontal gyrus

Changes for: orbital part of inferior frontal gyrus

Changes for: gastrula

Changes for: masticatory muscle

Changes for: zygomatic process of maxilla

Changes for: abdominal wall

Changes for: capsule of liver

Changes for: fasciolar gyrus

Changes for: supraoccipital bone

Changes for: precentral operculum

Changes for: kidney arcuate vein

Changes for: Brodmann (1909) area 29

Changes for: Brodmann (1909) area 26

Changes for: interlobular artery

Changes for: lower secondary incisor tooth

Changes for: cingulum of tooth

Changes for: lamina IV of gray matter of spinal cord

Changes for: lamina III of gray matter of spinal cord

Changes for: olfactory cortex

Changes for: muscle layer of spongiose part of urethra

Changes for: frontal lobe

  • Deleted
    • - frontal lobe editor note Many species don’t have lobes but they do have frontal cortex. Lobe isn’t a really well defined term though { source=MM }
  • Added
    • + frontal lobe editor note Many species don’t have lobes but they do have frontal cortex. Lobe isn’t a really well defined term though { source=MM }

Changes for: muscle of leg

Changes for: cortex of cerebral lobe

Changes for: parietal cortex

Changes for: temporal cortex

Changes for: occipital cortex

Changes for: limbic cortex

Changes for: external acoustic meatus

Changes for: gluteus maximus

  • Deleted
    • - gluteus maximus taxon notes In humans, it makes up a large portion of the shape and appearance of the buttocks. It is a broad and thick fleshy mass of a quadrilateral shape, and forms the prominence of the nates. Its large size is one of the most characteristic features of the muscular system in humans, connected as it is with the power of maintaining the trunk in the erect posture. The muscle is remarkably coarse in structure, being made up of fasciculi lying parallel with one another and collected together into large bundles separated by fibrous septa.
  • Added
    • + gluteus maximus taxon notes In humans, it makes up a large portion of the shape and appearance of the buttocks. It is a broad and thick fleshy mass of a quadrilateral shape, and forms the prominence of the nates. Its large size is one of the most characteristic features of the muscular system in humans, connected as it is with the power of maintaining the trunk in the erect posture. The muscle is remarkably coarse in structure, being made up of fasciculi lying parallel with one another and collected together into large bundles separated by fibrous septa.

Changes for: cavity of right ventricle

Changes for: inferior vesical vein

Changes for: spongiose part of urethra

Changes for: prepuce of penis

Changes for: lobe of prostate

  • Deleted
    • - lobe of prostate taxon notes Anatomically, the human prostate gland is located between the base of the bladder and the rectum, and it completely surrounds the proximal urethra (Fig. 1A). It is a single alobular structure with central (CZ), peripheral (PZ) and transitional (TZ) zones. In contrast, the mouse prostate is not merged into one compact anatomical structure. It comprises four paired lobes situated circumferentially around the urethra, immediately caudal to the urinary bladder—namely, anterior (AP), dorsal (DP), lateral (LP), and ventral (VP) prostate (Fig. 1B). Often, the dorsal and the lateral lobes are thought of in combination and referred to as the dorsolateral (DLP) lobe as they share a ductal system. The mouse AP is considered analogous to the human CZ, which is rarely a site of neoplastic transformation in humans. The mouse DLP is considered most similar to the human PZ, which is the zone in which most carcinomas arise (Xue et al. 1997). These analogies, however, are limited as they are based solely on descriptive data and need to be re-evaluated using molecular techniques before the relationship between specific mouse prostate lobes and the human prostate zones is definitively asserted (Abate-Shen & Shen 2000). The mouse VP does not have a human homologue, and the human TZ does not have a murine homologue { source=http://www.ncbi.nlm.nih.gov/pubmed/15163300 , source=https://github.com/obophenotype/uberon/issues/665 }
  • Added
    • + lobe of prostate taxon notes Anatomically, the human prostate gland is located between the base of the bladder and the rectum, and it completely surrounds the proximal urethra (Fig. 1A). It is a single alobular structure with central (CZ), peripheral (PZ) and transitional (TZ) zones. In contrast, the mouse prostate is not merged into one compact anatomical structure. It comprises four paired lobes situated circumferentially around the urethra, immediately caudal to the urinary bladder—namely, anterior (AP), dorsal (DP), lateral (LP), and ventral (VP) prostate (Fig. 1B). Often, the dorsal and the lateral lobes are thought of in combination and referred to as the dorsolateral (DLP) lobe as they share a ductal system. The mouse AP is considered analogous to the human CZ, which is rarely a site of neoplastic transformation in humans. The mouse DLP is considered most similar to the human PZ, which is the zone in which most carcinomas arise (Xue et al. 1997). These analogies, however, are limited as they are based solely on descriptive data and need to be re-evaluated using molecular techniques before the relationship between specific mouse prostate lobes and the human prostate zones is definitively asserted (Abate-Shen & Shen 2000). The mouse VP does not have a human homologue, and the human TZ does not have a murine homologue { source=http://www.ncbi.nlm.nih.gov/pubmed/15163300 , source=https://github.com/obophenotype/uberon/issues/665 }

Changes for: dorsolateral prefrontal cortex

Changes for: anterior cingulate cortex

Changes for: basilic vein

  • Deleted
    • - basilic vein taxon notes It originates on the medial (ulnar) side of the dorsal venous network of the manus, and it travels up the base of the forearm and arm. Most of its course is superficial; it generally travels in the subcutaneous fat and other fasciae that lie superficial to the muscles of the upper extremity. Because of this, it is usually visible through the skin. Near the region anterior to the cubital fossa, in the bend of the elbow joint, the basilic vein usually connects with the other large superficial vein of the upper extremity, the cephalic vein, via the median cubital vein. The layout of superficial veins in the forearm is highly variable from person to person, and there are generally a variety of other unnamed superficial veins that the basilic vein communicates with. About halfway up the arm proper (the part between the shoulder and elbow), the basilic vein goes deep, travelling under the muscles. There, around the lower border of the teres major muscle, the anterior and posterior circumflex humeral veins feed into it, just before it joins the brachial veins to form the axillary vein. Along with other superficial veins in the forearm, the basilic vein is a possible site for venipuncture. { source=WP,unvetted }
  • Added
    • + basilic vein taxon notes It originates on the medial (ulnar) side of the dorsal venous network of the manus, and it travels up the base of the forearm and arm. Most of its course is superficial; it generally travels in the subcutaneous fat and other fasciae that lie superficial to the muscles of the upper extremity. Because of this, it is usually visible through the skin. Near the region anterior to the cubital fossa, in the bend of the elbow joint, the basilic vein usually connects with the other large superficial vein of the upper extremity, the cephalic vein, via the median cubital vein. The layout of superficial veins in the forearm is highly variable from person to person, and there are generally a variety of other unnamed superficial veins that the basilic vein communicates with. About halfway up the arm proper (the part between the shoulder and elbow), the basilic vein goes deep, travelling under the muscles. There, around the lower border of the teres major muscle, the anterior and posterior circumflex humeral veins feed into it, just before it joins the brachial veins to form the axillary vein. Along with other superficial veins in the forearm, the basilic vein is a possible site for venipuncture. { source=WP,unvetted }

Changes for: tarsal skeleton

  • Deleted
    • - 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 }
  • 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: carotid sinus nerve

Changes for: facial mesenchyme

Changes for: secondary heart field

  • Deleted
    • - secondary heart field taxon notes In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11–14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested { source=http://www.ncbi.nlm.nih.gov/pubmed/17276708 }
  • Added
    • + secondary heart field taxon notes In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11–14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested { source=http://www.ncbi.nlm.nih.gov/pubmed/17276708 }

Changes for: ciliary stroma

Changes for: carpal skeleton

  • Deleted
  • Added

Changes for: marginal sulcus

Changes for: magnocellular part of red nucleus

Changes for: parvocellular part of red nucleus

Changes for: regional part of cerebellum

Changes for: anterior column of fornix

Changes for: dorsal hypothalamic area

  • Deleted
    • - dorsal hypothalamic area taxon notes In humans it contains the following nuclei: portions of the dorsomedial nucleus [TA] (nucleus dorsomedialis [TA]), endopeduncular nucleus [TA]) (nucleus endopeduncularis [TA]), and portions of the nucleus of the ansa lenticularis (nucleus ansae lenticularis { source=TA }
  • Added

Changes for: granular layer of cerebellar cortex

Changes for: central gray substance of pons

Changes for: molecular layer of cerebellar cortex

Changes for: first dorsal interosseous of manus

Changes for: ventral nucleus of medial geniculate body

Changes for: opercular part of inferior frontal gyrus

Changes for: internal medullary lamina of thalamus

Changes for: vestibulospinal tract

Changes for: distal epiphysis of phalanx of pes

Changes for: dorsal nucleus of medial geniculate body

Changes for: anterior cingulate gyrus

Changes for: superior phrenic artery

Changes for: inner medulla of kidney

Changes for: outer medulla of kidney

Changes for: blowhole ligament

Changes for: nephron

  • Deleted
    • - nephron editor note kidney terms require review for cross-vertebrate compatibility and developmental relationships.
  • Added
    • + nephron editor note kidney terms require review for cross-vertebrate compatibility and developmental relationships.

Changes for: renal column

Changes for: intralobular bile duct

Changes for: supplemental motor cortex

Changes for: isthmus of fallopian tube

Changes for: ilium

Changes for: innominate bone

  • Deleted
    • - innominate bone external ontology notes in FMA this is a paired structure. NCITA has ‘pelvic bone’ but this is the superclass of ilium/ischium/pubis. The MA class ‘pelvis bone’ is actually a superclass of ‘pelvic girdle bone’ and caudal/sacral vertebra. { external ontology=FMA }
  • Added
    • + innominate bone external ontology notes in FMA this is a paired structure. NCITA has ‘pelvic bone’ but this is the superclass of ilium/ischium/pubis. The MA class ‘pelvis bone’ is actually a superclass of ‘pelvic girdle bone’ and caudal/sacral vertebra. { external ontology=FMA }

Changes for: bony pelvis

Changes for: acetabular part of hip bone

Changes for: motor root of trigeminal nerve

Changes for: pancreas

  • Deleted
    • - pancreas taxon notes As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52) { source=http://www.ncbi.nlm.nih.gov/pubmed/20959416 }
  • Added
    • + pancreas taxon notes As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52) { source=http://www.ncbi.nlm.nih.gov/pubmed/20959416 }

Changes for: lumbar spinal cord

Changes for: adventitia of ureter

Changes for: nucleus proprius of spinal cord

Changes for: closed circulatory system

Changes for: muscularis mucosae of large intestine

Changes for: muscularis mucosae of small intestine

Changes for: duodenal gland

  • Deleted
    • - duodenal gland taxon notes Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds { source=ISBN:9780521617147 }
  • Added
    • + duodenal gland taxon notes Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds { source=ISBN:9780521617147 }

Changes for: left outer canthus

Changes for: right outer canthus

Changes for: submucosa of large intestine

Changes for: muscularis mucosae of stomach

Changes for: submucosa of stomach

Changes for: sensory root of trigeminal nerve

Changes for: ventrobronchus

Changes for: mesobronchus

Changes for: anatomical lobe

Changes for: renal lobe

Changes for: lobule

Changes for: hypothalamo-hypophyseal system

Changes for: renal lymph node

Changes for: superior branch of oculomotor nerve

Changes for: inferior branch of oculomotor nerve

Changes for: dentate gyrus subgranular zone

Changes for: medial gland of ocular region

Changes for: mesenchyme of nasal septum

Changes for: medial condyle of tibia

Changes for: lateral condyle of tibia

Changes for: cranial sensory ganglion

Changes for: medial condyle of femur

Changes for: lateral condyle of femur

Changes for: lateral epicondyle of femur

Changes for: horizontal fissure of cerebellum

Changes for: prepyramidal fissure of cerebellum

Changes for: superior part of vestibular ganglion

Changes for: inferior part of vestibular ganglion

Changes for: submucosa of urinary bladder

Changes for: sesamoid bone of gastrocnemius

Changes for: upper jaw incisor

Changes for: periventricular zone of hypothalamus

Changes for: hyaloid artery

Changes for: lateral zone of hypothalamus

Changes for: medial zone of hypothalamus

Changes for: metacarpus skeleton

Changes for: metatarsus skeleton

Changes for: reticular formation

Changes for: entepicondylar foramen

Changes for: superior transverse frontopolar gyrus

Changes for: accessory lacrimal gland

Changes for: proximal phalanx of manus

Changes for: tubercle of rib

Changes for: body of rib

Changes for: cerebellar hemisphere

Changes for: dorsal thoracic nucleus

Changes for: intercostal muscle

Changes for: quadrate lobe of liver

Changes for: caudate lobe of liver

Changes for: lobe of thyroid gland

Changes for: dorsal horn of spinal cord

Changes for: ventral horn of spinal cord

Changes for: parathyroid gland

Changes for: celiac ganglion

Changes for: common iliac vein

  • Deleted
    • - common iliac vein taxon notes In human anatomy, the common iliac veins are formed by the external iliac veins and internal iliac veins and together, in the abdomen at the level of the fifth lumbar vertebrae, form the inferior vena cava. They drain blood from the pelvis and lower limbs. Both common iliac veins are accompanied along their course by common iliac arteries. { source=http://en.wikipedia.org/wiki/Common_iliac_vein }
  • Added
    • + common iliac vein taxon notes In human anatomy, the common iliac veins are formed by the external iliac veins and internal iliac veins and together, in the abdomen at the level of the fifth lumbar vertebrae, form the inferior vena cava. They drain blood from the pelvis and lower limbs. Both common iliac veins are accompanied along their course by common iliac arteries. { source=http://en.wikipedia.org/wiki/Common_iliac_vein }

Changes for: xiphoid process

  • Deleted
    • - xiphoid process curator notes this class may represent a mixed bony-cartilage element, or it may be the superclass of either purely cartilage or purely ossified elements { source=WP,unvetted }
  • Added
    • + xiphoid process curator notes this class may represent a mixed bony-cartilage element, or it may be the superclass of either purely cartilage or purely ossified elements { source=WP,unvetted }

Changes for: medial pallium

Changes for: paleocortex

Changes for: right crus of diaphragm

Changes for: palpebral vein

Changes for: left crus of diaphragm

Changes for: macula of utricle of membranous labyrinth

Changes for: palpebral lobe of lacrimal gland

Changes for: orbital lobe of lacrimal gland

Changes for: levator cloacae

Changes for: transverse cloacal muscle

Changes for: periosteal dura mater

Changes for: prosomere

Changes for: midbrain neuromere

Changes for: tendon of quadriceps femoris

Changes for: pharyngeal membrane

Changes for: medial nasal process mesenchyme

Changes for: lateral nasal process mesenchyme

Changes for: lateral funiculus of spinal cord

Changes for: upper lobe of right lung

Changes for: lower lobe of right lung

Changes for: pulmonary alveolar duct

Changes for: substantia gelatinosa

Changes for: ventral funiculus of spinal cord

Changes for: segmental bronchus

Changes for: lobar bronchus

Changes for: main bronchus

Changes for: lateral reticular nucleus

Changes for: gray matter of hindbrain

Changes for: gray matter of forebrain

Changes for: respiratory airway

Changes for: hilus of dentate gyrus

Changes for: habenulo-interpeduncular tract

Changes for: renal system

  • Deleted
    • - renal system taxon notes In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels { source=GO }
  • Added
    • + renal system taxon notes In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels { source=GO }

Changes for: embryonic frontal process

Changes for: embryonic nasal process

Changes for: dorsal tegmental nucleus

Changes for: locus ceruleus

Changes for: thymus lobule

  • Deleted
    • - thymus lobule taxon notes in the mouse, the lobes of the thymus are not subdivided into lobules but only in the central medulla and a peripheral cortex (i.e. there is no distinct sublobulation). In humans, the two thymus lobes are composed of many lobules of various sizes which contain follicles, each comprising a medulla and a cortex. in the rat, the thymus is partially subdivided into lobules separated by thin bands of connective tissue which are continuous with the thin connective tissue capsule.[MP]
  • Added
    • + thymus lobule taxon notes in the mouse, the lobes of the thymus are not subdivided into lobules but only in the central medulla and a peripheral cortex (i.e. there is no distinct sublobulation). In humans, the two thymus lobes are composed of many lobules of various sizes which contain follicles, each comprising a medulla and a cortex. in the rat, the thymus is partially subdivided into lobules separated by thin bands of connective tissue which are continuous with the thin connective tissue capsule.[MP]

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: midgut

Changes for: neural tube

Changes for: yolk sac

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

  • Deleted
    • - spleen taxon notes Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96) { source=http://www.ncbi.nlm.nih.gov/pubmed/20959416 }
  • Added
    • + spleen taxon notes Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96) { source=http://www.ncbi.nlm.nih.gov/pubmed/20959416 }

Changes for: gemellus muscle

Changes for: inferior gemellus muscle

Changes for: mushroom body

  • Deleted
    • - mushroom body taxon notes Also in annelids. ‘Comparison to the vertebrate pallium reveals that the annelid mushroom bodies develop from similar molecular coordinates within a conserved overall molecular brain topology and that their development involves conserved patterning mechanisms and produces conserved neuron types that existed already in the proto- stome-deuterostome ancestors. These data indicate deep homology of pallium and mushroom bodies and date back the origin of higher brain centers to prebilaterian times’ { source=http://www.ncbi.nlm.nih.gov/pubmed/20813265 }
  • Added
    • + mushroom body taxon notes Also in annelids. ‘Comparison to the vertebrate pallium reveals that the annelid mushroom bodies develop from similar molecular coordinates within a conserved overall molecular brain topology and that their development involves conserved patterning mechanisms and produces conserved neuron types that existed already in the proto- stome-deuterostome ancestors. These data indicate deep homology of pallium and mushroom bodies and date back the origin of higher brain centers to prebilaterian times’ { source=http://www.ncbi.nlm.nih.gov/pubmed/20813265 }

Changes for: anterior leaflet of mitral valve

Changes for: tendon of triceps brachii

Changes for: tendon of biceps brachii

Changes for: posterior leaflet of mitral valve

Changes for: blood vessel layer of choroid

Changes for: postzygapophysis

Changes for: inferior transverse frontopolar gyrus

Changes for: vertebral bone 1

Changes for: vertebral bone 2

Changes for: flocculus

Changes for: brainstem white matter

Changes for: prezygapophysis

Changes for: neural spine

Changes for: thalamic eminence

Changes for: tooth bud

Changes for: lymph node primary follicle

Changes for: bone of hip region

Changes for: ventricular system choroidal fissure

Changes for: subcutaneous adipose tissue

Changes for: capsule of lymph node

Changes for: neurohypophysis

Changes for: dorsal nerve of penis

  • Added
    • + dorsal nerve of penis has exact synonym nervus dorsalis penis { [database cross reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref)=FMA:21869 , [database cross reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref)=FMA:TA , [has synonym type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType)=[latin term](http://purl.obolibrary.org/obo/uberon/core#LATIN) }

Changes for: cranial cavity

Changes for: orbitosphenoid

Changes for: cerebellar peduncular complex

  • Deleted
    • - 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.
  • 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: internal surface of frontal bone

Changes for: internal surface of cranial base

Changes for: hemispheric Lobule V

Changes for: hemispheric Lobule IV

Changes for: trabecular bone tissue

Changes for: bone tissue

Changes for: pulmonary lobule

Changes for: secondary pulmonary lobule

Changes for: ophryon

Changes for: region of conjunctiva

Changes for: CA3 alveus

Changes for: CA1 alveus

Changes for: gustatory gland

Changes for: neck of humerus

Changes for: scleral sesamoid bone

Changes for: pyramidal layer of CA2

Changes for: pyramidal layer of CA1

Changes for: sacral division of spinal cord central canal

Changes for: lumbar division of spinal cord central canal

Changes for: thoracic division of spinal cord central canal

Changes for: cervical division of cord spinal central canal

Changes for: prevertebral cervical fascia

Changes for: puboischiotibialis muscle

Changes for: precommissural fornix of forebrain

Changes for: superficial cervical fascia

Changes for: external medullary lamina of thalamus

Changes for: pericardium

Changes for: internal intercostal muscle

  • Deleted
    • - internal intercostal muscle structure notes The internal intercostals are responsible for the depression of the ribs decreasing the transverse dimensions of the thoracic cavity. the innermost intercostal muscle, the deep layers of the internal intercostal muscles which are separated from them by the neurovascular bundle. Both the external and internal muscles are innervated by the intercostal nerves, and are provided by the intercostal arteries and intercostal veins. Their fibers run in opposite directions
  • Added
    • + internal intercostal muscle structure notes The internal intercostals are responsible for the depression of the ribs decreasing the transverse dimensions of the thoracic cavity. the innermost intercostal muscle, the deep layers of the internal intercostal muscles which are separated from them by the neurovascular bundle. Both the external and internal muscles are innervated by the intercostal nerves, and are provided by the intercostal arteries and intercostal veins. Their fibers run in opposite directions

Changes for: pericardial sac

Changes for: abdominal segment of trunk

Changes for: lumbar vertebra

Changes for: cartilage tissue

Changes for: oral epithelium

Changes for: pyramidal layer of CA3

Changes for: cerebral hemisphere white matter

Changes for: cervicothoracic ganglion

Changes for: posterior limb of internal capsule

Changes for: anterior limb of internal capsule

Changes for: ethmoid sinus

Changes for: intersomitic artery

Changes for: inferior palpebral vein

Changes for: vesical vein

Changes for: inferior occipital gyrus

Changes for: celiac lymph node

Changes for: abdominal lymph node

Changes for: zygomatic arch

  • Deleted
    • - zygomatic arch taxon notes The zygomatic arch is significant in evolutionary biology, as it is part of the structures derived from the ancestral single temporal fenestra of the synapsid ancestor of mammals.
    • - zygomatic arch terminology notes The zygomatic arch is occasionally referred to as the zygoma, but this term usually refers to the zygomatic bone or occasionally the zygomatic process.
  • Added
    • + zygomatic arch taxon notes The zygomatic arch is significant in evolutionary biology, as it is part of the structures derived from the ancestral single temporal fenestra of the synapsid ancestor of mammals.
    • + zygomatic arch terminology notes The zygomatic arch is occasionally referred to as the zygoma, but this term usually refers to the zygomatic bone or occasionally the zygomatic process.

Changes for: scleral ossicle

  • Deleted
    • - scleral ossicle function notes The function of these elements is to support the eye from within the sclera; scleral ossicles play an additional important role during accommodation in terrestrial vertebrates (Lemmrich, 1931; Walls, 1942; King and McLelland, 1984).
  • Added
    • + scleral ossicle function notes The function of these elements is to support the eye from within the sclera; scleral ossicles play an additional important role during accommodation in terrestrial vertebrates (Lemmrich, 1931; Walls, 1942; King and McLelland, 1984).

Changes for: endochondral scleral ossicle

Changes for: substantia propria of sclera

Changes for: meningeal branch of spinal nerve

Changes for: anterior meningeal artery

Changes for: basiotic bone

Changes for: prevertebral ganglion

Changes for: cingulum of brain

Changes for: styloid process of temporal bone

Changes for: postsphenoidal bone

Changes for: fourth ventricle median aperture

Changes for: subarcuate fossa

Changes for: pharyngeal arch mesenchymal region

  • Deleted
    • - pharyngeal arch mesenchymal region editor note this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures. { source=MP:0011262 }
  • Added
    • + pharyngeal arch mesenchymal region database cross reference FMA:295694
    • + pharyngeal arch mesenchymal region editor note this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures. { source=MP:0011262 }

Changes for: hyoid bone greater horn

Changes for: cerebellum fissure

Changes for: midbrain basal plate

Changes for: scleral cartilage

Changes for: Brodmann (1909) area 20

Changes for: Brodmann (1909) area 19

Changes for: Brodmann (1909) area 25

Changes for: Brodmann (1909) area 23

Changes for: Brodmann (1909) area 22

Changes for: cerebellum anterior vermis

Changes for: placodal ectoderm

Changes for: Bruch’s membrane

Changes for: Brodmann (1909) area 10

Changes for: Brodmann (1909) area 9

Changes for: Brodmann (1909) area 12

Changes for: Brodmann (1909) area 14

Changes for: Brodmann (1909) area 13

Changes for: Brodmann (1909) area 15

Changes for: Brodmann (1909) area 16

Changes for: photoreceptor inner segment layer

Changes for: photoreceptor outer segment layer

Changes for: Brodmann (1909) area 2

Changes for: Brodmann (1909) area 8

Changes for: conducting system of heart

Changes for: Brodmann (1909) area 7

Changes for: Brodmann (1909) area 4

Changes for: atrioventricular node

Changes for: mesenchyme pectoral fin

Changes for: mesenchyme pelvic fin

Changes for: cranial cartilage

Changes for: transverse gyrus of Heschl

Changes for: Brodmann (1909) area 11

Changes for: bulbo-urethral gland

Changes for: tympanic membrane

Changes for: dorsal accessory nucleus of optic tract

Changes for: retinal neural layer

Changes for: nictitating membrane

  • Deleted
    • - nictitating membrane taxon notes in mice, the nictitating membrane is very small and composed of a very thin core of cartilage covered by loose connective tissue
  • Added
    • + nictitating membrane taxon notes in mice, the nictitating membrane is very small and composed of a very thin core of cartilage covered by loose connective tissue

Changes for: lacrimal caruncle

Changes for: Brodmann (1909) area 32

Changes for: Brodmann (1909) area 43

Changes for: layer of neocortex

Changes for: layer of hippocampus

Changes for: nucleus of brain

Changes for: hemisphere part of cerebellar posterior lobe

Changes for: hemisphere part of cerebellar anterior lobe

Changes for: basis modioli

Changes for: white matter of cerebellum

Changes for: white matter of spinal cord

Changes for: gray matter of spinal cord

Changes for: white matter

Changes for: periventricular nucleus

Changes for: lateral lingual swelling epithelium

Changes for: maxillary process mesenchyme

Changes for: mesenchyme of fronto-nasal process

Changes for: renal portal system

  • Deleted
    • - renal portal system taxon notes present in all classes of vertebrates except mammals; the mammalian kidney has a low pressure vascular network that may be its counterpart { source=ISBN10:0073040584 }
  • Added
    • + renal portal system taxon notes present in all classes of vertebrates except mammals; the mammalian kidney has a low pressure vascular network that may be its counterpart { source=ISBN10:0073040584 }

Changes for: lower primary incisor tooth

Changes for: obsolete coffin bone

Changes for: extraembryonic coelom

Changes for: moustache

Changes for: middle phalanx of manus

Changes for: distal phalanx of manus

Changes for: proximal phalanx of pes

Changes for: distal phalanx of pes

Changes for: middle phalanx of pes

Changes for: lumen of blood vessel

Changes for: coat of hair

Changes for: spinal cord neural plate

Changes for: medial accessory nucleus of optic tract

Changes for: parvocellular layer of dorsal nucleus of lateral geniculate body

Changes for: magnocellular layer of dorsal nucleus of lateral geniculate body

Changes for: lateral accessory nucleus of optic tract

Changes for: koniocellular layer of dorsal nucleus of lateral geniculate body

Changes for: cremaster muscle

Changes for: pronephric distal early tubule

Changes for: pronephric glomerular basement membrane

Changes for: sputum

Changes for: posterior arch of atlas

Changes for: ethmoid bone primordium

Changes for: cloacal membrane

Changes for: buccopharyngeal membrane

Changes for: future brain

Changes for: tetrapod frontal bone primordium

Changes for: nasolacrimal groove

Changes for: notochordal process

Changes for: pyramid of medulla oblongata

Changes for: tetrapod parietal bone primordium

Changes for: otic pit

Changes for: granulosa cell layer

Changes for: tooth enamel organ

Changes for: late embryonic stage

Changes for: 4 cell stage

Changes for: 2 cell stage

Changes for: 8 cell stage

Changes for: ventrolateral sulcus of medulla oblongata

Changes for: cerebellum posterior vermis

Changes for: presumptive neural plate

Changes for: presumptive segmental plate

Changes for: choroid plexus of tectal ventricle

Changes for: pectoral appendage musculature

Changes for: upper esophageal sphincter

Changes for: presumptive hindbrain

Changes for: presumptive midbrain hindbrain boundary

Changes for: intervertebral disk of sacral vertebra

Changes for: odontoid process of cervical vertebra 2

Changes for: ectodermal placode

  • Deleted
    • - ectodermal placode taxon notes With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates.
  • Added

Changes for: vertical limb of the diagonal band

Changes for: horizontal limb of the diagonal band

Changes for: forebrain-midbrain boundary

Changes for: superior colliculus superficial gray layer

Changes for: hemispheric lobule VIII

Changes for: lateral occipital cortex

Changes for: posterior column of fornix

Changes for: neural fold

Changes for: neural groove

Changes for: pontine cistern

Changes for: liver papillary process

Changes for: ectomesenchyme

Changes for: periocular mesenchyme

Changes for: dermatome

Changes for: mucosa of intermediate urethra

Changes for: cerebellum vermis lobule X

Changes for: genital labium

Changes for: cerebellum vermis lobule VII

Changes for: cerebellum vermis lobule VIII

Changes for: vena cava

Changes for: midface

Changes for: cerebellum vermis lobule

Changes for: cerebellum vermis lobule I

Changes for: cerebellum vermis lobule II

Changes for: cerebellum vermis lobule III

Changes for: cerebellum vermis lobule IX

Changes for: cerebellum vermis lobule VI

Changes for: frontonasal prominence

Changes for: lateral nasal prominence

Changes for: medial nasal prominence

Changes for: primitive pit

Changes for: primitive groove

Changes for: renal collecting system

Changes for: alveolar ridge

Changes for: hairline

Changes for: clivus of occipital bone

Changes for: pharyngeal pouch

Changes for: muscle of auditory ossicle

Changes for: midnasal cavity

Changes for: optic vesicle

Changes for: genitourinary system

Changes for: pharyngeal pouch 3

Changes for: pharyngeal pouch 2

Changes for: pharyngeal pouch 1

Changes for: pharyngeal pouch 4

Changes for: embryonic post-anal tail

Changes for: lumen of colon

Changes for: basisphenoid bone

Changes for: short head of biceps brachii

Changes for: long head of biceps brachii

Changes for: superior angle of scapula

Changes for: tracheobronchial tree

Changes for: Brodmann (1909) area 46

Changes for: Brodmann (1909) area 5

Changes for: external acoustic meatus osseus part

Changes for: interosseous muscle of pes

Changes for: dorsal pes interosseous muscle

Changes for: rostral middle frontal gyrus

Changes for: caudal middle frontal gyrus

Changes for: Harderian gland

  • Deleted
    • - Harderian gland taxon notes In mouse the HG appears in the posterior part of eye region, in the form of nonluminated tubules between the sixteenth and eighteenth days of gestation. At birth it is still not differentiated histologically. In birds the HG originates from the conjunctival epithelium at a late embryonic stage. In the English sparrow, Passer domesticus (incubation period of about 13 days), it appears between the seventh and the eighth days of incubation. In the chick embryo (incubation period of about 21 days) it originates between the eleventh and the twelfth days.[PMID:9156609]
  • Added
    • + Harderian gland taxon notes In mouse the HG appears in the posterior part of eye region, in the form of nonluminated tubules between the sixteenth and eighteenth days of gestation. At birth it is still not differentiated histologically. In birds the HG originates from the conjunctival epithelium at a late embryonic stage. In the English sparrow, Passer domesticus (incubation period of about 13 days), it appears between the seventh and the eighth days of incubation. In the chick embryo (incubation period of about 21 days) it originates between the eleventh and the twelfth days.[PMID:9156609]

Changes for: trigeminothalamic tract

Changes for: long nephron

Changes for: short nephron

Changes for: septum transversum

Changes for: orbitofrontal cortex

Changes for: arteriole smooth muscle

Changes for: iris smooth muscle

Changes for: lymphatic vessel smooth muscle

Changes for: glomerular capillary

Changes for: brain dura mater

Changes for: kidney pyramid

Changes for: renal vesicle

Changes for: viscus

Changes for: atrioventricular canal

Changes for: sinoatrial valve

Changes for: tunica vasculosa lentis

Changes for: cardiac mesoderm

Changes for: infrahyoid muscle

Changes for: labial commissure

Changes for: proximal deep inguinal lymph node

Changes for: pancreaticosplenic lymph node

Changes for: lymph node of epiploic foramen

Changes for: superior vesical vein

Changes for: vasa hyaloidea propria

Changes for: parietal pelvic lymph node

Changes for: stapedial artery

Changes for: nasal capsule

  • Deleted
    • - nasal capsule editor note consider splitting this class. Developing cartilage in mammals? { source=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.
  • Added
    • + nasal capsule database cross reference FMA:320527
    • + nasal capsule editor note consider splitting this class. Developing cartilage in mammals? { source=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.

Changes for: distal early tubule

Changes for: superior rectus extraocular muscle

Changes for: bodily fluid

Changes for: incisor dental pulp

Changes for: molar dental pulp

Changes for: endocardial cushion

Changes for: embryonic structure

Changes for: dermomyotome

Changes for: stratum basale of epidermis

Changes for: insula

Changes for: synovial membrane of synovial joint

Changes for: accessory XI nerve

Changes for: kidney capsule

Changes for: inferior hypogastric nerve plexus

Changes for: pulmonary artery

Changes for: celiac nerve plexus

  • Deleted
    • - celiac nerve plexus definition The celiac plexus, also known as the solar plexus, is a complex network of nerves located in the abdomen. The celiac plexus is located near where the celiac trunk, superior mesenteric artery, and renal arteries branch from the abdominal aorta. It is behind the stomach and the omental bursa and in front of the crura of the diaphragm, on the level of the first lumbar vertebra, L1. The plexus is formed (in part) by the greater and lesser splanchnic nerves of both sides, and also parts of the right vagus nerve. The celiac plexus proper consists of the celiac ganglia with a network of interconnecting fibers. The aorticorenal ganglia are often considered to be part of the celiac ganglia, and thus, part of the plexus. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Celiac_plexus }
  • Added
    • + celiac nerve plexus definition A complex network of nerves located in the abdomen behind the stomach. The celiac plexus is located near where the celiac trunk, superior mesenteric artery, and renal arteries branch from the abdominal aorta. It is behind the stomach and the omental bursa and in front of the crura of the diaphragm, on the level of the first lumbar vertebra, L1. The plexus is formed (in part) by the greater and lesser splanchnic nerves of both sides, and also parts of the right vagus nerve. The celiac plexus proper consists of the celiac ganglia with a network of interconnecting fibers. The aorticorenal ganglia are often considered to be part of the celiac ganglia, and thus, part of the plexus. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Celiac_plexus }

Changes for: cardiac nerve plexus

Changes for: pulmonary nerve plexus

Changes for: enteric nervous system

Changes for: stomach smooth muscle outer longitudinal layer

Changes for: stomach smooth muscle circular layer

  • Deleted
    • - stomach smooth muscle circular layer function notes This layer wraps in a circular orientation around the pylorus, and is held in a constricted state normally. The normal constriction of this muscle is what creates the pyloric sphincter, which controls the movement of chyme into the duodenum. This layer is concentric to the longitudinal axis of the stomach. (note: chyme is a thick and acidic mixture of acidic digestive fluids and partially digested food, which moves from the stomach to the small intestine as digestion moves along the digestive tract.)
  • Added

Changes for: visceral yolk sac

Changes for: parietal yolk sac

Changes for: pulmonary acinus

Changes for: tooth of lower jaw

Changes for: neural lobe of neurohypophysis

Changes for: splanchnocranium

Changes for: pharyngeal gill precursor

Changes for: fin

Changes for: phalanx

Changes for: limb bud

Changes for: primitive streak

Changes for: cerebellum culmen

Changes for: gyrus

Changes for: endothelial blood brain barrier

Changes for: Reichert’s membrane

Changes for: Reichert’s cartilage

Changes for: Descemet’s membrane

Changes for: pharyngeal arch artery

Changes for: pharyngeal arch 1

Changes for: tetrapod frontal bone

Changes for: apical ectodermal ridge

Changes for: interphalangeal joint of pedal digit 1

Changes for: anterior limiting lamina of cornea

Changes for: retroambiguus nucleus

Changes for: life cycle stage

Changes for: smooth muscle layer in fatty layer of subcutaneous tissue

Changes for: respiratory segment of nasal mucosa

Changes for: epiphysis of phalanx of manus

Changes for: metatarsophalangeal joint of pedal digit 1

Changes for: transverse foramen

Changes for: theca cell layer

Changes for: pelvic fin

Changes for: pectoral fin

Changes for: cloaca

Changes for: intestine

  • Deleted
    • - 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.
  • 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: amniotic fluid

Changes for: embryonic head

Changes for: pharyngeal arch system

Changes for: presphenoid bone

Changes for: epithelium of vomeronasal organ

Changes for: epithelium of tongue

Changes for: distal epiphysis of phalanx of manus

Changes for: cranial fossa

Changes for: ganglion of peripheral nervous system

Changes for: proximal epiphysis of fibula

Changes for: gustatory pore

Changes for: early pharyngeal endoderm

Changes for: proximal epiphysis of phalanx of manus

Changes for: gut wall

  • Deleted
    • - gut wall curator notes We model the digestive tract as consisting of two parts: the wall and the lumen.
  • Added
    • + gut wall curator notes We model the digestive tract as consisting of two parts: the wall and the lumen.

Changes for: breast

  • Deleted
    • - breast taxon notes The breasts of a female primate’s body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women’s breasts become more prominent than men’s. { source=WP,unvetted }
  • Added
    • + breast taxon notes The breasts of a female primate’s body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women’s breasts become more prominent than men’s. { source=WP,unvetted }

Changes for: musculature of pelvic girdle

Changes for: musculature of trunk

Changes for: lateral recess of fourth ventricle

Changes for: ligamentum arteriosum

Changes for: thoracic lymph node

Changes for: tarsal region

Changes for: hippocampus stratum lacunosum moleculare

Changes for: synovial cavity of joint

Changes for: skeletal muscle tissue of trapezius

Changes for: skeletal muscle tissue of biceps brachii

Changes for: skeletal muscle tissue of teres major

Changes for: skeletal muscle tissue of deltoid

Changes for: alveolar ridge of mandible

Changes for: anatomical projection

Changes for: alveolar process of maxilla

Changes for: skeletal muscle tissue of supraspinatus

Changes for: skeletal muscle tissue of pectoralis major

Changes for: lateral pes lemniscus

Changes for: alar central lobule

Changes for: postcommissural fornix of brain

Changes for: anterior quadrangular lobule

Changes for: posterior nucleus of thalamus

Changes for: thoracic spinal cord

Changes for: anterior commissure anterior part

Changes for: central lobule

Changes for: regenerating anatomical structure

Changes for: bony projection

Changes for: lymph vasculature

Changes for: cervical region of vertebral column

Changes for: inferior horn of the lateral ventricle

Changes for: body of corpus callosum

Changes for: posterior part of anterior commissure

Changes for: periderm

Changes for: ventricular zone

Changes for: ear vesicle

Changes for: olfactory placode

Changes for: pharyngeal arch 2

Changes for: otic placode

Changes for: pronephric duct

Changes for: primitive knot

Changes for: prechordal plate

Changes for: intermediate mesoderm

Changes for: ciliary marginal zone

Changes for: floor plate

  • Deleted
    • - floor plate description A structure integral to the developing nervous system of vertebrate organisms. Located on the ventral midline of the embryonic neural tube, the floor plate is a specialized glial structure that spans the anteroposterior axis from the midbrain to the tail regions. It has been shown that the floor plate is conserved among vertebrates with homologous structures in invertebrates such as the fruit fly Drosophila and the nematode C. elegans. Functionally, the structure serves as an organizer to ventralize tissues in the embryo as well as to guide neuronal positioning and differentiation along the dorsoventral axis of the neural tube. { source=http://en.wikipedia.org/wiki/Floor_plate }
  • Added
    • + floor plate description A structure integral to the developing nervous system of vertebrate organisms. Located on the ventral midline of the embryonic neural tube, the floor plate is a specialized glial structure that spans the anteroposterior axis from the midbrain to the tail regions. It has been shown that the floor plate is conserved among vertebrates with homologous structures in invertebrates such as the fruit fly Drosophila and the nematode C. elegans. Functionally, the structure serves as an organizer to ventralize tissues in the embryo as well as to guide neuronal positioning and differentiation along the dorsoventral axis of the neural tube. { source=http://en.wikipedia.org/wiki/Floor_plate }

Changes for: paraxial mesoderm

Changes for: epibranchial placode

Changes for: trigeminal placode complex

Changes for: neural plate

Changes for: lens placode

Changes for: heart primordium

Changes for: lateral plate mesoderm

Changes for: myotome

Changes for: sclerotome

Changes for: supraorbital lateral line

Changes for: optic stalk

Changes for: middle lateral line

Changes for: dorsal lateral line

Changes for: ultimobranchial body

  • Deleted
    • - ultimobranchial body taxon notes In humans, the ultimobranchial body is an embryological structure that gives rise to the calcitonin-producing cells - also called parafollicular cells or clear cells - of the thyroid gland. In humans, this body is a derivative of the ventral recess of the fourth pharyngeal pouch (or fifth) { source=WP,unvetted }
  • Added
    • + ultimobranchial body taxon notes In humans, the ultimobranchial body is an embryological structure that gives rise to the calcitonin-producing cells - also called parafollicular cells or clear cells - of the thyroid gland. In humans, this body is a derivative of the ventral recess of the fourth pharyngeal pouch (or fifth) { source=WP,unvetted }

Changes for: thyroid primordium

Changes for: esophagus muscularis mucosa

Changes for: pharyngeal arch 3

Changes for: pharyngeal arch 4

Changes for: pharyngeal arch 5

Changes for: pharyngeal arch 6

Changes for: spleen capsule

Changes for: renal efferent arteriole

Changes for: renal afferent arteriole

Changes for: Meckel’s cartilage

Changes for: surface structure

Changes for: mammalian cervical vertebra 7

Changes for: rib 1

Changes for: rib 2

Changes for: nucleus of cerebellar nuclear complex

Changes for: arthropod tibia

Changes for: trachea

Changes for: pes anserinus of tibia

Changes for: lieno-renal ligament

Changes for: apex of spinal cord dorsal horn

Changes for: dentate gyrus molecular layer

Changes for: spinal cord lateral horn

Changes for: spinal cord gray commissure

Changes for: facial nerve root

Changes for: hypoglossal nerve root

Changes for: posterior horn lateral ventricle

Changes for: trigeminal nerve root

Changes for: mandible temporal crest

Changes for: interventricular septum membranous part

Changes for: interventricular septum muscular part

Changes for: mandible condylar process

Changes for: temporal process of zygomatic bone

Changes for: zygomatic process of temporal bone

Changes for: secondary ovarian follicle

Changes for: lamina propria of trachea

Changes for: follicular fluid

  • Deleted
    • - follicular fluid taxon notes Generally, larger species such as ovine, equine, porcine, human, and bovine have larger follicles, with the fluid comprising a substantial proportion of the volume of the follicles at ovulation (estimated at >95% in bovine [3]). Smaller species such as rats and mice have smaller follicles with fractionally less follicular fluid[20164441]
  • Added
    • + follicular fluid taxon notes Generally, larger species such as ovine, equine, porcine, human, and bovine have larger follicles, with the fluid comprising a substantial proportion of the volume of the follicles at ovulation (estimated at >95% in bovine [3]). Smaller species such as rats and mice have smaller follicles with fractionally less follicular fluid[20164441]

Changes for: marginal ridge of tooth

Changes for: left hepatic artery

Changes for: right hepatic artery

Changes for: oblique ridge of tooth

Changes for: triangular ridge of tooth

Changes for: transverse ridge of tooth

Changes for: mucus body coating

  • Deleted
    • - mucus body coating function notes The epidermal mucus of fish regulates swimming speed by controlling the hydrodynamic resistance of the skin surface. The mucus is also presumed to serve as a defence against pathogenic organisms and is intimately associated with osmoregulation. { source=BTO:0005082 }
  • Added
    • + mucus body coating function notes The epidermal mucus of fish regulates swimming speed by controlling the hydrodynamic resistance of the skin surface. The mucus is also presumed to serve as a defence against pathogenic organisms and is intimately associated with osmoregulation. { source=BTO:0005082 }

Changes for: peripheral nervous system

Changes for: zone of skin

  • Deleted
    • - zone of skin curator notes Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee
  • Added
    • + zone of skin curator notes Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee

Changes for: endocrine pancreas

Changes for: cutaneous appendage

  • Deleted
    • - cutaneous appendage editor note Mammary glands develop by similar mechanisms, and there is an argument for including them here (e.g. http://www.ncbi.nlm.nih.gov/pubmed/20484386), but these structures do not fit the current definition (lactiferous glands are part of the integumentary system in FMA). Note the FMA class is a subdivision of epidermis, which may be too restrictive for our purposes here.
  • Added
    • + cutaneous appendage editor note Mammary glands develop by similar mechanisms, and there is an argument for including them here (e.g. http://www.ncbi.nlm.nih.gov/pubmed/20484386), but these structures do not fit the current definition (lactiferous glands are part of the integumentary system in FMA). Note the FMA class is a subdivision of epidermis, which may be too restrictive for our purposes here.

Changes for: frenulum of lip

Changes for: splenic lymph node

Changes for: blood vessel external elastic membrane

Changes for: upper lobe of left lung

Changes for: left lung lobe

Changes for: centrum semiovale

Changes for: somatosensory cortex

Changes for: bilaminar disc

Changes for: blastocele

Changes for: chondral bone

Changes for: proximo-distal subdivision of respiratory tract

Changes for: hypoblast (generic)

Changes for: morula

Changes for: inner cell mass

Changes for: fornix of brain

Changes for: lateral recess of third vetricle

Changes for: dermal bone

Changes for: respiratory tract

Changes for: fully formed stage

Changes for: embryo stage

Changes for: anterior surface of prostate

Changes for: posterior surface of kidney

Changes for: suspensory ligament of duodenum

Changes for: hilum of lymph node

Changes for: mediastinal pleura

Changes for: circumflex branch of left coronary artery

Changes for: cervical part of esophagus

Changes for: pectinate muscle

Changes for: Bachmann’s bundle

Changes for: left branch of atrioventricular bundle

Changes for: right branch of atrioventricular bundle

Changes for: urogenital diaphragm

Changes for: tricuspid valve cusp

Changes for: eye trabecular meshwork

Changes for: hair root sheath matrix

Changes for: primary choana

Changes for: hair root sheath

Changes for: outer root sheath companion layer

  • Deleted
    • - outer root sheath companion layer structure notes It contains cells that are morphologically and biochemically different from the inner root sheath and outer root sheath. The cells of the companion layer are more flattened than the other cells of the outer root sheath and do not contain glycogen. In addition, a novel human type II cytokeratin, K6hf, is specifically expressed in the companion layer of the hair follicle
  • Added
    • + outer root sheath companion layer structure notes It contains cells that are morphologically and biochemically different from the inner root sheath and outer root sheath. The cells of the companion layer are more flattened than the other cells of the outer root sheath and do not contain glycogen. In addition, a novel human type II cytokeratin, K6hf, is specifically expressed in the companion layer of the hair follicle

Changes for: retropharyngeal space

Changes for: head mesenchyme from mesoderm

Changes for: maxillary prominence

Changes for: mandibular prominence

Changes for: pharyngeal cleft

Changes for: undifferentiated genital tubercle

Changes for: periventricular pretectal nucleus

Changes for: olfactory pit

Changes for: post-hyoid pharyngeal arch skeleton

Changes for: gracile fasciculus of spinal cord

Changes for: mandible angular process

Changes for: caudal segment of spinal cord

Changes for: sacral spinal cord

Changes for: bone tissue of long bone

Changes for: cervical vertebra 1 anterior tubercle

Changes for: central carpal bone

Changes for: leptomeninx

Changes for: urinary bladder detrusor smooth muscle

Changes for: arachnoid barrier layer

Changes for: ventral intermediate nucleus of thalamus

Changes for: bone foramen

  • Deleted
    • - bone foramen external ontology notes in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper). { external ontology=FMA }
  • Added
    • + bone foramen external ontology notes in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper). { external ontology=FMA }

Changes for: optic canal

Changes for: visual cortex

Changes for: nephric ridge

Changes for: extraembryonic mesoderm

Changes for: olfactory system

  • Deleted
    • - olfactory system taxon notes In mammals, the main olfactory system detects odorants that are inhaled through the nose, where they contact the main olfactory epithelium, which contains various olfactory receptors. These olfactory receptors are membrane proteins of bipolar olfactory receptor neurons in the olfactory epithelium. Rather than binding specific ligands like most receptors, olfactory receptors display affinity for a range of odor molecules. Olfactory neurons transduce receptor activation into electrical signals in neurons. The signals travel along the olfactory nerve, which belongs to the peripheral nervous system. This nerve terminates in the olfactory bulb, which belongs to the central nervous system. The complex set of olfactory receptors on different olfactory neurons can distinguish a new odor from the background environmental odors and determine the concentration of the odor[WP].
  • Added
    • + olfactory system taxon notes In mammals, the main olfactory system detects odorants that are inhaled through the nose, where they contact the main olfactory epithelium, which contains various olfactory receptors. These olfactory receptors are membrane proteins of bipolar olfactory receptor neurons in the olfactory epithelium. Rather than binding specific ligands like most receptors, olfactory receptors display affinity for a range of odor molecules. Olfactory neurons transduce receptor activation into electrical signals in neurons. The signals travel along the olfactory nerve, which belongs to the peripheral nervous system. This nerve terminates in the olfactory bulb, which belongs to the central nervous system. The complex set of olfactory receptors on different olfactory neurons can distinguish a new odor from the background environmental odors and determine the concentration of the odor[WP].

Changes for: unilaminar epithelium

Changes for: solid compound organ

Changes for: reticular membrane of spiral organ

Changes for: anatomical space

Changes for: organism substance

Changes for: anatomical system

Changes for: membrane bone

Changes for: simple columnar epithelium

Changes for: atypical epithelium

Changes for: simple squamous epithelium

Changes for: multi-tissue structure

Changes for: simple cuboidal epithelium

Changes for: cavitated compound organ

Changes for: acellular anatomical structure

Changes for: simple organ

Changes for: compound organ component

Changes for: extraembryonic structure

Changes for: primary palate

Changes for: tubotympanic recess lumen

Changes for: extraembryonic membrane

Changes for: ultimobranchial body epithelium

  • Deleted
    • - ultimobranchial body epithelium external ontology notes in EHDAA2, develops_from ventral 4th arch branchial pouch endoderm. Kardong: develops from 5th pouch. http://www.ncbi.nlm.nih.gov/pubmed/16313389: the most posterior pouch generates the ultimobranchial bodies in most vertebrate classes, mammals do not form this structure. { external ontology=EHDAA2 }
  • Added
    • + ultimobranchial body epithelium external ontology notes in EHDAA2, develops_from ventral 4th arch branchial pouch endoderm. Kardong: develops from 5th pouch. http://www.ncbi.nlm.nih.gov/pubmed/16313389: the most posterior pouch generates the ultimobranchial bodies in most vertebrate classes, mammals do not form this structure. { external ontology=EHDAA2 }

Changes for: secondary palatal shelf epithelium

Changes for: primary palate epithelium

Changes for: 2nd arch mesenchyme

Changes for: 4th arch mesenchyme

Changes for: 3rd arch mesenchyme

Changes for: hyoid artery

Changes for: hyaloid vascular plexus

Changes for: hyaloid cavity

Changes for: secondary palatal shelf

Changes for: diencephalon lateral wall

Changes for: cerebellum vasculature

Changes for: lymph node secondary follicle

Changes for: bone of pectoral complex

Changes for: venous sinus

Changes for: tunica albuginea

Changes for: tectum synoticum

  • Deleted
    • - tectum synoticum taxon notes posterior tectum synoticum in humans - a skull roof element of the chondrocranium - temporarily exists in the territory of the interparietal during fetal life, and may be resposible for the sutura mendosa { source=PMC1259625 }
  • Added
    • + tectum synoticum taxon notes posterior tectum synoticum in humans - a skull roof element of the chondrocranium - temporarily exists in the territory of the interparietal during fetal life, and may be resposible for the sutura mendosa { source=PMC1259625 }

Changes for: corpus cavernosum

Changes for: musculo-phrenic vein

Changes for: cruciate ligament of knee

Changes for: tunica albuginea of ovary

Changes for: suspensory ligament of ovary

Changes for: coracoid process of scapula

Changes for: rhombomere 2

Changes for: telencephalon lateral wall

Changes for: rhombomere 7

Changes for: rhombomere 6

Changes for: rhombomere 4

Changes for: rhombomere 5

Changes for: rhombomere 3

Changes for: rhombomere floor plate

Changes for: subcapsular sinus of lymph node

Changes for: superior mesenteric ganglion

Changes for: superior mesenteric plexus

Changes for: non-neural ectoderm

Changes for: primitive heart tube

Changes for: rhombomere 1

Changes for: midbrain lateral wall

Changes for: pectinate line

Changes for: quadrate bone

  • Deleted
    • - quadrate bone taxon notes In snakes, the quadrate bone has become elongated and very mobile, and contributes greatly to their ability to swallow very large prey items. In mammals the articular and quadrate bones have migrated to the middle ear and are known as the malleus and incus. { source=TAO:0000621 }
  • Added

Changes for: palmar interosseous muscle of manus

Changes for: plantar interosseous muscle of pes

Changes for: calcarine artery

Changes for: posterior surface of prostate

Changes for: abdominal part of esophagus

Changes for: kidney calyx

Changes for: right lung lobe

Changes for: oblique extraocular muscle

Changes for: rectus extraocular muscle

Changes for: seminal fluid

Changes for: palatoethmoidal suture

Changes for: anterior nasal spine of maxilla

Changes for: pelvic appendage bud

Changes for: developing anatomical structure

Changes for: lens vesicle

Changes for: raphe of penis

Changes for: inferior mesenteric ganglion

Changes for: forelimb bud

Changes for: philtrum

Changes for: hippocampus stratum oriens

Changes for: hippocampus stratum radiatum

Changes for: spinal cord lateral column

Changes for: ansiform lobule

Changes for: lobule simplex

Changes for: Rathke’s pouch

Changes for: dentate gyrus granule cell layer

Changes for: brain arachnoid mater

Changes for: deep part of masseter muscle