2014-10-26 release

Random stuff
2014-10-26 release image

Ontology Diff Report

  • NTs: skin crease {palmar,plantar}. Fixes issue #591
  • NTs: digits1,5 and 2,3,4 of manus and pes - Fixes issue #592 #593 #594
  • subcapsular polar regions. Addresses #599. Requires expert input. It seems the subcapsular regions are not specifically part of the pole?
  • NT: chorioretinal region. drseb. Fixes issue #600
  • thyroid fixes - relationship to neck is species specific
  • merged false add of colorectal mucosa, added bto xref instead
  • bto and emapa xrefs
  • NTs: gemellus
  • NTs: skin of anterior chest; lateral chest. Fixes issue #588
  • added disjointness axiom between splenic and celiac arteries. Issue #268
  • Added definition of indirectly supplies. Fixes #587
  • syn for jugal bar. PHENOSCAPE:wd.\nFixed issue #586
  • EMAPA xrefs
  • NTs: dorsal nerve of penis/clitoris
  • improved multiple defs. Fixed otic capsule to use endochondral pattern
  • NT: nursing stage. Fixes issue #576
  • splanchnic nerve tidying

Original Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-09-23/uberon.owl

New Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-10-26/uberon.owl

Report for classes

Class objects lost from source: 1

Class objects new in target: 42

New Class : mesial region

New Class : labial region

New Class : posterolingual region

New Class : lingual region

New Class : upper jaw symphyseal tooth

New Class : lateral commissure

New Class : hindlimb feather

New Class : crural feather

New Class : glial limiting membrane

New Class : nursing stage

New Class : feather covering of ventral part of tail

New Class : dorsal side of post-anal tail

New Class : ventral side of post-anal tail

New Class : bladder organ

New Class : plantar skin crease

New Class : palmar skin crease

New Class : skin crease

New Class : pedal digit 2, 3 or 5

New Class : pedal digit 1 or 5

New Class : manual digit 1 or 5

New Class : manual digit 2, 3 or 5

New Class : digit 2, 3 or 4

New Class : digit 1 or 5

New Class : supcapsular region of posterior region of lens

New Class : pole of lens

New Class : supcapsular region of anterior region of lens

New Class : skin of anterior chest

New Class : gemellus muscle

New Class : gemellus inferior muscle

New Class : chorioretinal region

New Class : anterior pole of lens

New Class : gemellus superior muscle

New Class : skin epithelium

New Class : tongue papilla epithelium

New Class : mucous gland of lung

New Class : carotid artery endothelium

New Class : lateral side of chest

New Class : dorsal nerve of clitoris

New Class : dorsal nerve of penis

New Class : iliac artery endothelium

New Class : intramuscular adipose tissue

New Class : reproductive system mucosa

Changed Class objects: 322

Changes for: body proper

Changes for: upper jaw symphyseal region

Changes for: lumen of esophagus

Changes for: brain endothelium

Changes for: levator hyomandibulae muscle

Changes for: frontal process of maxilla

  • Deleted
    • - frontal process of maxilla definition The frontal process of the maxilla (nasal process) is a strong plate, which projects upward, medialward, and backward, by the side of the nose, forming part of its lateral boundary. Its lateral surface is smooth, continuous with the anterior surface of the body, and gives attachment to the Quadratus labii superioris, the Orbicularis oculi, and the medial palpebral ligament. Its medial surface forms part of the lateral wall of the nasal cavity; at its upper part is a rough, uneven area, which articulates with the ethmoid, closing in the anterior ethmoidal cells; below this is an oblique ridge, the ethmoidal crest, the posterior end of which articulates with the middle nasal concha, while the anterior part is termed the agger nasi; the crest forms the upper limit of the atrium of the middle meatus. The upper border articulates with the frontal bone and the anterior with the nasal; the posterior border is thick, and hollowed into a groove, which is continuous below with the lacrimal groove on the nasal surface of the body: by the articulation of the medial margin of the groove with the anterior border of the lacrimal a corresponding groove on the lacrimal is brought into continuity, and together they form the lacrimal fossa for the lodgement of the lacrimal sac. The lateral margin of the groove is named the anterior lacrimal crest, and is continuous below with the orbital margin; at its junction with the orbital surface is a small tubercle, the lacrimal tubercle, which serves as a guide to the position of the lacrimal sac. { database cross reference=http://en.wikipedia.org/wiki/Frontal_process_of_maxilla }
  • Added

Changes for: orbital part of frontal bone

Changes for: levator operculi

Changes for: epihyoidean

Changes for: feather follicle

Changes for: extensor carpi radialis muscle

Changes for: obturator muscle

Changes for: obturator internus

Changes for: flexor hallucis brevis muscle

Changes for: colorectum

Changes for: semen

Changes for: amygdala

Changes for: visceral fascia

  • Deleted
    • - visceral fascia definition Visceral fascia suspends the organs within their cavities and wraps them in layers of connective tissue membranes. Each of the organs is covered in a double layer of fascia; these layers are separated by a thin serous membrane. The outermost wall of the organ is known as the parietal layer The skin of the organ is known as the visceral layer. The organs have specialized names for their visceral fasciae. In the brain, they are known as meninges; in the heart they are known as pericardia; in the lungs, they are known as pleura; and in the abdomen, they are known as peritonea. { database cross reference=http://en.wikipedia.org/wiki/Visceral_fascia }
  • Added
    • + visceral fascia comment Visceral fascia suspends the organs within their cavities and wraps them in layers of connective tissue membranes. Each of the organs is covered in a double layer of fascia; these layers are separated by a thin serous membrane. The outermost wall of the organ is known as the parietal layer The skin of the organ is known as the visceral layer. The organs have specialized names for their visceral fasciae. In the brain, they are known as meninges; in the heart they are known as pericardia; in the lungs, they are known as pleura; and in the abdomen, they are known as peritonea. [Wikipedia:Visceral_fascia]
    • + visceral fascia definition Fascia that suspends a visceral organ. { database cross reference=UBERON:cjm }

Changes for: skin of chest

Changes for: nasal cavity mucosa

Changes for: gingiva

Changes for: oviduct mucosal fold

Changes for: metotic fissure

Changes for: jugal bar

Changes for: hyoid articular area

Changes for: dorsal part of neck

Changes for: cloacal epithelium

Changes for: optic choroid

Changes for: tibialis posterior

Changes for: flexor digitorum longus

Changes for: sphenoid bone

Changes for: occipital bone

  • Deleted
    • - occipital bone taxon notes formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the an- nexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII { source=http://www.ncbi.nlm.nih.gov/pubmed/11523816 }
  • Added

Changes for: squamous part of temporal bone

Changes for: right lung lobar bronchus mesenchyme

Changes for: right lung middle lobe lobar bronchus mesenchyme

Changes for: anteroventral nucleus

Changes for: anal sphincter

Changes for: ventral tegmental area

Changes for: midbrain reticular formation

Changes for: ventral anterior nucleus

Changes for: anterior nucleus of hypothalamus

Changes for: lateral septal nucleus

Changes for: digestive tract

Changes for: digastric muscle group

Changes for: adductor hallucis muscle

Changes for: internal jugular vein

Changes for: vertebral endplate

Changes for: flexor digitorum brevis muscle

Changes for: prostate bud

Changes for: mediastinum

Changes for: right lung accessory lobe lobar bronchus mesenchyme

Changes for: right lung cranial lobe lobar bronchus mesenchyme

Changes for: future diaphragm

Changes for: celiac artery

Changes for: basal forebrain

Changes for: lung hilus

Changes for: endometrium epithelium

Changes for: infraspinatus tendon

  • Deleted
    • - infraspinatus tendon definition The infraspinatus muscle inserts at this tendon to the distal greater tubercle of the humerus . This tendon stretches across the shoulder joint to attach to the humerus and in doing so acts as a very strong ligament to hold the joint surface in apposition. This structure restricts the movement of the shoulder joint to flexion and extension (together with the suscapularis tendon and the supraspinatus tendon). A bursa lies under this tendon at the greater tubercle of the humerus. The bursa is lined by a synovial membrance and filled with synovial fluid and protects the infraspinatus tendon and the shoulder joint by allowing the transmissions of tension and sheer forces around an angle. { database cross reference=MURDOCH:963 }
  • Added
    • + infraspinatus tendon definition The infraspinatus muscle inserts at this tendon to the distal greater tubercle of the humerus. This tendon stretches across the shoulder joint to attach to the humerus and in doing so acts as a very strong ligament to hold the joint surface in apposition. This structure restricts the movement of the shoulder joint to flexion and extension (together with the suscapularis tendon and the supraspinatus tendon). A bursa lies under this tendon at the greater tubercle of the humerus. The bursa is lined by a synovial membrance and filled with synovial fluid and protects the infraspinatus tendon and the shoulder joint by allowing the transmissions of tension and sheer forces around an angle. { database cross reference=MURDOCH:963 }

Changes for: dental lamina

Changes for: centrale

Changes for: posterior nuclear complex of thalamus

Changes for: anterior chest

Changes for: pontine reticular formation

Changes for: posterior pole of lens

Changes for: fibularis quartus

Changes for: distal tarsal bone 1

Changes for: navicular bone of pes

Changes for: distal tarsal bone 3

Changes for: distal tarsal bone 2

Changes for: cuboid bone

Changes for: metatarsal bone

Changes for: phalanx of pes

Changes for: distal carpal bone 3

Changes for: distal carpal bone 2

Changes for: distal carpal bone 4

Changes for: distal carpal bone 1

Changes for: phalanx of manus

Changes for: pisiform

Changes for: muscle of pelvic girdle

Changes for: muscle of pes

Changes for: muscle of arm

Changes for: proximal carpal bone

Changes for: distal carpal bone

Changes for: muscle of shoulder

Changes for: deltoid

Changes for: manual digit 1

Changes for: manual digit 4

Changes for: manual digit 5

Changes for: lateral medullary reticular complex

  • Added
    • + lateral medullary reticular complex comment The lateral reticular nucleus, of the funiculus, can be divided into three subnuclei, the parvocellular, magnocellular and the subtrigeminal. As is typical of the reticular formation, none of these are very distinct subnuclei, but rather blurred distinctions between cell types and location. The lateral reticular nucleus sends all of its projections to the cerebellum. The parvocellular portion of the LRN and the immediately adjacent magnocellular portion send most their projections to the vermis of the cerebellum. The rest of the magnocellular subnucleus sends its projections to the hemisphere regions of the cerebellum. The subtrigeminal nucleus sends its projections to the flocculonodular lobe. All of these efferent pathways are projected in an ipsilateral manner to the cerebellum, the most abundant of which are those to the vermis. This nucleus is also involved in the mediation of inspiration (in-breathing) with a part of the ventral r. nucleus. The afferent pathways to the LRN come from the spinal cord and higher brain structures. Most of the afferents come from the ipsilateral dorsal horn of the spinal cord and project exclusively to the parts of the LRN that do not receive input from the cortex. The spinal cord projections terminate mostly in the parvocellular region along with the adjacent magnocellular cells. This implies that most input from the spinal cord is relayed into the vermis[WP]
    • + lateral medullary reticular complex definition A nuclear complex of the medullary reticular formation that can be divided into three subnuclei: the parvocellular, magnocellular and the subtrigeminal[WP,modified]. { database cross reference=http://en.wikipedia.org/wiki/Lateral_reticular_nucleus }

Changes for: manual digit 3

Changes for: manual digit 2

Changes for: pedal digit 5

Changes for: pedal digit 2

Changes for: pedal digit 1

Changes for: pedal digit 4

Changes for: pedal digit 3

Changes for: pancreas mesenchyme

Changes for: proamniotic cavity

Changes for: abductor pollicis longus

Changes for: fascia lata

Changes for: extensor carpi radialis longus muscle

Changes for: extensor carpi ulnaris muscle

Changes for: extensor carpi radialis brevis muscle

Changes for: forelimb muscle

Changes for: pronator teres

Changes for: flexor carpi radialis muscle

Changes for: flexor carpi ulnaris muscle

Changes for: interosseous muscle of manus

Changes for: lumbrical muscle of manus

Changes for: lumbrical muscle of pes

Changes for: coracobrachialis muscle

Changes for: muscle of manus

Changes for: gastrointestinal system mucosa

Changes for: palmaris longus muscle

Changes for: auditory system

Changes for: diaphysis

Changes for: prootic bone

Changes for: jugular vein

Changes for: conceptus

Changes for: cervical mucosa

Changes for: nucleus of lateral olfactory tract

Changes for: popliteus muscle

Changes for: vastus medialis

Changes for: pectineus muscle

Changes for: semimembranosus muscle

Changes for: gastrocnemius

Changes for: fibularis longus

Changes for: colorectal mucosa

Changes for: vestibule

Changes for: vastus lateralis

Changes for: iliacus muscle

Changes for: umbilical ring

Changes for: obturator externus

Changes for: muscularis mucosae of fundus of stomach

Changes for: intertarsal sesamoid

Changes for: obsolete otic capsule endochondral element

Changes for: body of uterus

Changes for: facial mesenchyme

Changes for: ventral posteromedial nucleus of thalamus

Changes for: adductor pollicis muscle

Changes for: anconeus muscle

Changes for: serosa of uterus

Changes for: myometrium

  • Deleted
    • - myometrium SubClassOf organ component layer
    • - myometrium SubClassOf smooth muscle tissue
    • - myometrium comment The inner layer of the uterine wall is the endometrium or uterine lining, and the outer layer the serosa or perimetrium. The myometrium stretches (the smooth muscle cells expand in both size and number[1]) during pregnancy to allow for the harboring of the pregnancy, and contracts in a coordinated fashion during the process of labor. After delivery the myometrium contracts to expel the placenta and reduce blood loss.
  • Added
    • + myometrium SubClassOf composed primarily of some smooth muscle tissue
    • + myometrium SubClassOf layer of muscle tissue
    • + myometrium comment The inner layer of the uterine wall is the endometrium or uterine lining, and the outer layer the serosa or perimetrium. The myometrium stretches (the smooth muscle cells expand in both size and number) during pregnancy to allow for the harboring of the pregnancy, and contracts in a coordinated fashion during the process of labor. After delivery the myometrium contracts to expel the placenta and reduce blood loss.

Changes for: urothelium of ureter

Changes for: urinary bladder

Changes for: neck of urinary bladder

Changes for: endopiriform nucleus

Changes for: lobar bronchus of right lung middle lobe

Changes for: peroneus

Changes for: perineural vascular plexus

Changes for: obsolete thymic region

Changes for: dorsal cochlear nucleus

Changes for: mucosa of seminal vesicle

Changes for: mucosa of ejaculatory duct

Changes for: mucosa of deferent duct

Changes for: mucosa of vagina

Changes for: metacarpus skeleton

Changes for: body of rib

Changes for: sternothyroid muscle

Changes for: sternohyoid muscle

Changes for: clavicle bone

Changes for: descending colon

  • Deleted
    • - descending colon definition The descending colon of humans passes downward through the left hypochondrium and lumbar regions, along the lateral border of the left kidney. At the lower end of the kidney it turns medialward toward the lateral border of the psoas muscle, and then descends, in the angle between psoas and quadratus lumborum, to the crest of the ilium, where it ends in the sigmoid colon. The peritoneum covers its anterior surface and sides, and therefore the descending colon is described as retroperitoneal. (The transverse colon and sigmoid colon, which are immediately proximal and distal, are intraperitoneal). Its posterior surface is connected by areolar tissue with the lower and lateral part of the left kidney, the aponeurotic origin of the transversus abdominis, and the quadratus lumborum. It is smaller in caliber and more deeply placed than the ascending colon. It has a mesentery in 33% of people, and is therefore more frequently covered with peritoneum on its posterior surface than the ascending colon (which has a mesentery in 25% of people). However, it is less likely to undergo volvulus than the ascending colon. In front of it are some coils of small intestine. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Descending_colon }
    • - descending colon editor note This class was created automatically from a combination of ontologies
  • Added
    • + descending colon definition The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon. { database cross reference=BTO:0000641 }

Changes for: ascending colon

Changes for: transverse colon

  • Deleted
    • - transverse colon definition The transverse colon the longest and most movable part of the colon, passes with a downward convexity from the right hypochondrium region across the abdomen, opposite the confines of the epigastric and umbilical zones, into the left hypochondrium region, where it curves sharply on itself beneath the lower end of the spleen, forming the splenic or left colic flexure. The right colic flexure is adjacent to the liver. In its course, it describes an arch, the concavity of which is directed backward and a little upward; toward its splenic end there is often an abrupt U-shaped curve which may descend lower than the main curve. It is almost completely invested by peritoneum, and is connected to the inferior border of the pancreas by a large and wide duplicature of that membrane, the transverse mesocolon. It is in relation, by its upper surface, with the liver and gall-bladder, the greater curvature of the stomach, and the lower end of the spleen; by its under surface, with the small intestine; by its anterior surface, with the anterior layers of the greater omentum and the abdominal parietes; its posterior surface is in relation from right to left with the descending portion of the duodenum, the head of the pancreas, and some of the convolutions of the jejunum and ileum. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Transverse_colon }
    • - transverse colon editor note This class was created automatically from a combination of ontologies
  • Added

Changes for: colon

Changes for: caecum

Changes for: crus of diaphragm

Changes for: visceral peritoneum

Changes for: fibularis brevis

Changes for: fibularis tertius

Changes for: vastus intermedius

Changes for: teres minor muscle

Changes for: nephric duct

Changes for: lateral reticular nucleus

  • Deleted
    • - lateral reticular nucleus definition The lateral reticular nucleus, of the funiculus, can be divided into three subnuclei, the parvocellular, magnocellular and the subtrigeminal. As is typical of the reticular formation, none of these are very distinct subnuclei, but rather blurred distinctions between cell types and location. The lateral reticular nucleus sends all of its projections to the cerebellum. The parvocellular portion of the LRN and the immediately adjacent magnocellular portion send most their projections to the vermis of the cerebellum. The rest of the magnocellular subnucleus sends its projections to the hemisphere regions of the cerebellum. The subtrigeminal nucleus sends its projections to the flocculonodular lobe. All of these efferent pathways are projected in an ipsilateral manner to the cerebellum, the most abundant of which are those to the vermis. This nucleus is also involved in the mediation of inspiration (in-breathing) with a part of the ventral r. nucleus. The afferent pathways to the LRN come from the spinal cord and higher brain structures. Most of the afferents come from the ipsilateral dorsal horn of the spinal cord and project exclusively to the parts of the LRN that do not receive input from the cortex. The spinal cord projections terminate mostly in the parvocellular region along with the adjacent magnocellular cells. This implies that most input from the spinal cord is relayed into the vermis. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Lateral_reticular_nucleus }
  • Added

Changes for: parametrial fat pad

Changes for: urethral opening

Changes for: parvocellular oculomotor nucleus

Changes for: nervous system

Changes for: teres muscle

Changes for: gall bladder

Changes for: obsolete ureter

Changes for: vestibulo-auditory system

Changes for: visual system

Changes for: hypopharynx

Changes for: pneumatized bone

  • Deleted
  • Added
    • + pneumatized bone SubClassOf bone element
    • + pneumatized bone definition A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD]. { database cross reference=http://www.medilexicon.com/medicaldictionary.php?t=11303 }
    • + pneumatized bone taxon notes Skeletal pneumaticity is the presence of air spaces within bones. Skeletal pneumaticity exists only in synapsids and archosaurs. It is generally produced during development by excavation of bone by pneumatic diverticula (air sacs) from an air-filled space such as the lungs or nasal cavity. Pneumatization is highly variable between individuals, and bones not normally pneumatized can become pneumatized in pathological development. Pneumatization occurs in the skulls of mammals, crocodilians and birds among extant groups, as well as extinct archosaurs including the dinosaurs and pterosaurs. Pneumatic spaces include the paranasal sinuses and some of the mastoid cells[WP]. [Wikipedia:Skeletal_pneumaticity]

Changes for: parametrium

Changes for: pterygoid bone

  • Deleted
    • - pterygoid bone external definition In tetrapods, the pterygoid is a complex, but relatively stable, paired palatal bone with a number of parts. In many tetrapods, it is the largest palatal bone and serves as the main structural support. Most typically, the pterygoids meet extensively on the mid-line of the palate and jointly send a process, the palatal ramus, anteriorly, which may cover the parasphenoid more or less completely. Sometimes this term is used to include the main body of the pterygoid as well. More variably, there are one or two anterolateral processes which go by various names, such as ectopterygoid ramus. In many amniotes, the pterygoid develops a strong transverse process or transverse flange which forms a bar running laterally across the palate. The pterygoid also articulates with (where present) the dorsoventral supports for the palate: the epipterygoid (dorsal) and the basipterygoid process of the braincase. Finally, the pterygoid sends a long, robust quadrate ramus with complex curvature down (posteroventrally) to grasp the quadrate and support the jaw articulation. The pterygoid bone of tetrapods is, roughly speaking, derived from the middle entopterygoid portion of the palatoquadrate complex of fishes. The entopterygoid is not actually a part of the palatoquadrate. It is a dermal bone which has replaced the middle section of the primitively continuous endochondral bone of the palatoquadrate, the original upper jaw. In tetrapods, the pterygoid advances further, and also replaces the central part of the posterior, pterygoquadrate unit. This becomes the quadrate ramus. The upper part of this unit, the portion involved in the dorsal and basipterygoid articulations between jaw and braincase, is referred to as the metapterygoid. In tetrapods, most of this region is incorporated into the pterygoid as well, with the exception of the ascending process of the palatoquadrate, which becomes the epipterygoid. { date retrieved=2012-09-17 , source=http://palaeos.com/vertebrates/glossary/glossaryPte.html }
    • - pterygoid bone has related synonym pterygoid { database cross reference=AAO:0000521 }
  • Added

Changes for: integument

Changes for: stylopod

Changes for: otic capsule pre-cartilage condensation

Changes for: trabecular bone tissue

Changes for: oral epithelium

Changes for: ulnare

Changes for: extensor pollicis brevis muscle

Changes for: axilla

Changes for: interventricular foramen of CNS

Changes for: anal pterya

Changes for: thymus

Changes for: metacarpal bone

Changes for: muscle of neck

Changes for: sex gland

Changes for: neural crest

Changes for: somite

Changes for: paraurethral duct

Changes for: paraurethral gland

Changes for: psoas muscle

Changes for: hyperpallium

Changes for: arcopallium

  • Deleted
    • - arcopallium definition The arcopallium refers to regions of the avian brain which partially overlap regions homologous to the amygdala of mammals. These regions have formerly been referred to as archistriatum, and before this epistriatum or amygdaloid complex, and a recent change of nomenclature has divided the region into the arcopallium and posterior pallial amygdala. The new nomenclature, adopted in 2004, reflects a modern understanding that the avian brain is broadly similar to the mammalian brain, containing large regions homologous to the mammalian neocortex, claustrum, and pallial amygdala. The outdated nomenclature it replaced perceived the avian brain as consisting almost entirely of enlarged basal ganglia, to which more complex outer layers had been added during a progress toward mammalian intelligence. { database cross reference=http://en.wikipedia.org/wiki/Arcopallium }
  • Added
    • + arcopallium comment The arcopallium refers to regions of the avian brain which partially overlap regions homologous to the amygdala of mammals. These regions have formerly been referred to as archistriatum, and before this epistriatum or amygdaloid complex, and a recent change of nomenclature has divided the region into the arcopallium and posterior pallial amygdala. The new nomenclature, adopted in 2004, reflects a modern understanding that the avian brain is broadly similar to the mammalian brain, containing large regions homologous to the mammalian neocortex, claustrum, and pallial amygdala. The outdated nomenclature it replaced perceived the avian brain as consisting almost entirely of enlarged basal ganglia, to which more complex outer layers had been added during a progress toward mammalian intelligence. [Wikipedia:Arcopallium]
    • + arcopallium definition A pallial region found in avias that partially overlap regions homologous to the amygdala of mammals. { database cross reference=http://en.wikipedia.org/wiki/Arcopallium }

Changes for: paired fin radial bone

Changes for: outer epithelium

Changes for: future brain

Changes for: neural groove

Changes for: anterior visceral endoderm

Changes for: mucosa of uterine tube

Changes for: mucosa of infundibulum of uterine tube

Changes for: spongiotrophoblast layer

Changes for: egg cylinder

Changes for: mucosa of prostatic urethra

Changes for: mucosa of nasal septum

Changes for: interosseous muscle of pes

Changes for: proepicardium

Changes for: pedal digit bone

Changes for: manual digit bone

Changes for: quadratus femoris

Changes for: gluteus minimus

Changes for: piriformis muscle

Changes for: pterotic

Changes for: truncus arteriosus

Changes for: dermomyotome

Changes for: forelimb zeugopod muscle

Changes for: osteoid

Changes for: extensor pollicis longus muscle

Changes for: flexor digitorum superficialis

Changes for: supinator muscle

Changes for: limb bud

Changes for: paramedian reticular nucleus

  • Deleted
    • - paramedian reticular nucleus definition The paramedian reticular nucleus (in Terminologia Anatomica, or paramedian medullary reticular group in NeuroNames) sends its connections to the spinal cord in a mostly ipsilateral manner, although there is some decussation. It projects to the vermis in the anterior lobe, the pyramis and the uvula. The paramedian nucleus also projects to the contralateral PRN, the gigantocellular nucleus, and the nucleus ambiguous. The paramedian reticular formation is adjacent to the abducens (VI)nucleus in the pons and adjacent to the oculomotor nucleus(III) in the midbrain. The paramedian nucleus receives afferents mostly from the fastigial nucleus in the cerebellum and the cerebral cortex; however, the projections from the spinal cord are very sparse. The descending afferent connections come mostly from the frontal and parietal lobes; however the pontine reticular formation also sends projections to the paramedian reticular nucleus. There are also very sparse innervations from the superior colliculus. Lesions in the paramedian reticular nucleus have been shown to cause a stereotyped increase in the random patterns of motion in rats. The paramedian nuclei on either side of the brain stem have been shown to mediate the horizontal eye movements on their ipsilateral sides. It seems possible that that the random motion patterns of the above rats were caused by an inability to mediate their horizontal eye movements. { database cross reference=http://en.wikipedia.org/wiki/Paramedian_reticular_nucleus }
  • Added
    • + paramedian reticular nucleus comment A medullary nucleus that sends its connections to the spinal cord in a mostly ipsilateral manner, although there is some decussation. It projects to the vermis in the anterior lobe, the pyramis and the uvula. The paramedian nucleus also projects to the contralateral PRN, the gigantocellular nucleus, and the nucleus ambiguous. The paramedian reticular formation is adjacent to the abducens (VI)nucleus in the pons and adjacent to the oculomotor nucleus(III) in the midbrain. The paramedian nucleus receives afferents mostly from the fastigial nucleus in the cerebellum and the cerebral cortex; however, the projections from the spinal cord are very sparse. The descending afferent connections come mostly from the frontal and parietal lobes; however the pontine reticular formation also sends projections to the paramedian reticular nucleus. There are also very sparse innervations from the superior colliculus. Lesions in the paramedian reticular nucleus have been shown to cause a stereotyped increase in the random patterns of motion in rats. The paramedian nuclei on either side of the brain stem have been shown to mediate the horizontal eye movements on their ipsilateral sides. It seems possible that that the random motion patterns of the above rats were caused by an inability to mediate their horizontal eye movements
    • + paramedian reticular nucleus definition A medullary nucleus that sends its connections to the spinal cord in a mostly ipsilateral manner. { database cross reference=http://en.wikipedia.org/wiki/Paramedian_reticular_nucleus }

Changes for: induseum griseum

Changes for: smooth muscle tissue layer of ejaculatory duct

Changes for: mesenchyme of testis

Changes for: gut wall

Changes for: musculature of limb

Changes for: subarachnoid space

Changes for: adductor longus

Changes for: anatomical junction

Changes for: musculature of neck

Changes for: musculature of pharynx

Changes for: hippocampus stratum lucidum

Changes for: toilet claw

Changes for: extensor digitorum communis

Changes for: extensor digitorum lateralis muscle

Changes for: epiotic

Changes for: stylohyoid muscle

Changes for: median raphe nucleus

Changes for: central dorsal nucleus

Changes for: central lateral nucleus

Changes for: digit 1

Changes for: digit 2

Changes for: digit 5

Changes for: digit 3

Changes for: digit 4

Changes for: midbrain-hindbrain boundary

Changes for: optic cup

Changes for: sclerotome

Changes for: ultimobranchial body

Changes for: otic capsule

Changes for: blastocele

Changes for: external ectoderm

Changes for: inner cell mass

  • Deleted
    • - inner cell mass definition Mass of cells inside the primordial embryo that will eventually give rise to the definitive structures of the fetus. This structure forms in the earliest steps of development, before implantation into the endometrium of the uterus has occurred. The ICM lies within the blastocoele (more correctly termed ‘blastocyst cavity’, as it is not strictly homologous to the blastocoele of anamniote vertebrates) and is entirely surrounded by the single layer of cells called trophoblast. { database cross reference=http://en.wikipedia.org/wiki/Inner_cell_mass }
  • Added

Changes for: trophoblast

Changes for: external naris

Changes for: cartilaginous condensation

Changes for: protonephridium

  • Deleted
    • - protonephridium definition A network of dead-end tubules lacking internal openings found in the Phylums Platyhelminthes, kinorhyncha and Rotifera. The ends are called flame cells (if cilliated) or solenocytes (if flagellated); they function in osmoregulation and ionoregulation. The terminal cells are located at the blind end of the protonephridium. Each cell has one or more cilia and their beating inside the protonephridial tube creates an outward going current and hence a partial pressurization in the blind of the tube. Because of this pressurization drives waste fluids from the inside of the animal, they are pulled through small perforations in the terminal cells and into the protonephridium. The perforations in the terminal cell are large enough for small molecules to pass, but larger proteins are retained within the animal. From the bottom of the protonephridium the solutes are led through the tube, formed by the canal cells, and exits the animal from a small opening formed by the nephridiopore. Selective reabsorption of useful molecules by the canal cells occurs as the solutes pass down the tubule. Protonephridia are generally found in basal organisms such as flatworms. Protonephridia likely first arose as a way to cope with a hypotonic environment by removing excess water from the organism (osmoregulation). Their use as excretory/ionoregulatory structures likely arose secondarily. { database cross reference=Metanephridia }
  • Added
    • + protonephridium comment The ends are called flame cells (if cilliated) or solenocytes (if flagellated); they function in osmoregulation and ionoregulation. The terminal cells are located at the blind end of the protonephridium. Each cell has one or more cilia and their beating inside the protonephridial tube creates an outward going current and hence a partial pressurization in the blind of the tube. Because of this pressurization drives waste fluids from the inside of the animal, they are pulled through small perforations in the terminal cells and into the protonephridium. The perforations in the terminal cell are large enough for small molecules to pass, but larger proteins are retained within the animal. From the bottom of the protonephridium the solutes are led through the tube, formed by the canal cells, and exits the animal from a small opening formed by the nephridiopore. Selective reabsorption of useful molecules by the canal cells occurs as the solutes pass down the tubule. Protonephridia are generally found in basal organisms such as flatworms. Protonephridia likely first arose as a way to cope with a hypotonic environment by removing excess water from the organism (osmoregulation). Their use as excretory/ionoregulatory structures likely arose secondarily
    • + protonephridium definition A network of dead-end tubules lacking internal openings found in the Phylums Platyhelminthes, kinorhyncha and Rotifera. { database cross reference=Metanephridia }

Changes for: falciform carpal bone

Changes for: extensor digitorum brevis

Changes for: adductor magnus

Changes for: urothelium

Changes for: adductor brevis

Changes for: preputial gland

Changes for: blastocyst

Changes for: limbic system

  • Deleted
    • - limbic system definition A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn’t correspond closely to the anatomical meaning any longer. [BirnLex]. including the hippocampus, amygdala, anterior thalamic nuclei, and limbic cortex, which support a variety of functions including emotion, behavior, long term memory, and olfaction [Wikipedia]. { database cross reference=http://en.wikipedia.org/wiki/Limbic_system , database cross reference=BIRNLEX:Limbic_system }
    • - limbic system editor note obsoletion recommended. The current part_of children were chosen as the intersection of what is stated in wikipedia and in the FMA. NIF: We are including Limbic System because it is still used by neuroscientists and others, but as a data annotation term, it is very poor because it is not a clearly defined entity.
  • Added
    • + limbic system comment includes the hippocampus, amygdala, anterior thalamic nuclei, and limbic cortex, which support a variety of functions including emotion, behavior, long term memory, and olfaction [Wikipedia]
    • + limbic system definition A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn’t correspond closely to the anatomical meaning any longer. [BirnLex]. { database cross reference=http://en.wikipedia.org/wiki/Limbic_system , database cross reference=BIRNLEX:Limbic_system }
    • + limbic system editor note obsoletion proposes. The current part_of children were chosen as the intersection of what is stated in wikipedia and in the FMA. NIF: We are including Limbic System because it is still used by neuroscientists and others, but as a data annotation term, it is very poor because it is not a clearly defined entity.

Changes for: scapholunate

Changes for: extravillous trophoblast

Changes for: olfactory system

Changes for: synsacrum

Changes for: minor vestibular gland

Changes for: furcula

Changes for: organism subdivision

Changes for: vascular plexus

Changes for: lens anterior epithelium

  • Deleted
    • - lens anterior epithelium comment Cells of the subcapsular epithelium (or anterior lens cells) are mitotically active. In adult individuals they only cover the anterior “hemisphere” of the lens. As they divide, cells gradually move towards the equator of the lens where they tranform into lens fibres. The apical part of the gradually elongating cell extends between the subcapsular epithelium and adjacent lens fibres towards the anterior pole of the lens. The basal part extends towards the posterior pole. The nucleus remains close to the equatorial plane of the lens - http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm
  • Added
    • + lens anterior epithelium comment Histology notes: Cells of the subcapsular epithelium (or anterior lens cells) are mitotically active. In adult individuals they only cover the anterior “hemisphere” of the lens. As they divide, cells gradually move towards the equator of the lens where they tranform into lens fibres. The apical part of the gradually elongating cell extends between the subcapsular epithelium and adjacent lens fibres towards the anterior pole of the lens. The basal part extends towards the posterior pole. The nucleus remains close to the equatorial plane of the lens - http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm

Changes for: lung primordium

Changes for: pelvic complex

Changes for: pectoral complex

Changes for: prefrontal bone

Changes for: atrium auricular region

Changes for: thymus primordium

Changes for: hyoid muscle

Changes for: bony otic capsule

Changes for: cartilaginous otic capsule

Changes for: coronoid process of ulna

  • Deleted
    • - coronoid process of ulna definition The coronoid process is a triangular eminence projecting forward from the upper and front part of the ulna. Its base is continuous with the body of the bone, and of considerable strength. Its apex is pointed, slightly curved upward, and in flexion of the forearm is received into the coronoid fossa of the humerus. Its upper surface is smooth, concave, and forms the lower part of the semilunar notch. Its antero-inferior surface is concave, and marked by a rough impression for the insertion of the Brachialis muscle. At the junction of this surface with the front of the body is a rough eminence, the tuberosity of the ulna, which gives insertion to a part of the Brachialis; to the lateral border of this tuberosity the oblique cord is attached. Its lateral surface presents a narrow, oblong, articular depression, the radial notch. Its medial surface, by its prominent, free margin, serves for the attachment of part of the ulnar collateral ligament. At the front part of this surface is a small rounded eminence for the origin of one head of the Flexor digitorum superficialis muscle; behind the eminence is a depression for part of the origin of the Flexor digitorum profundus muscle; descending from the eminence is a ridge which gives origin to one head of the Pronator teres muscle. Frequently, the Flexor pollicis longus muscle arises from the lower part of the coronoid process by a rounded bundle of muscular fibers. { database cross reference=http://en.wikipedia.org/wiki/Coronoid_process_of_the_ulna }
  • Added

Changes for: muscle of digastric group

Changes for: thyropharyngeus muscle

Changes for: opisthotic

Changes for: cricopharyngeus muscle

Changes for: paraglossale

Changes for: swim bladder

Changes for: medial tibial tarsal bone

Changes for: epioccipital posterior process

Changes for: mammary bud

Changes for: mammary placode

Changes for: female preputial gland

Changes for: gastrocnemius lateralis

Changes for: plantaris

Changes for: gastrocnemius medialis

Changes for: pharyngeal muscle

Changes for: retina

Changes for: gracilis

Changes for: lamina

Changes for: germ layer

Changes for: abdomen

Changes for: neck

Changes for: sternum

  • Added
    • + sternum taxon notes in birds, either ratite (no keel or carina) or carinate (keel and carina present)

Changes for: female gonad

Report for properties

ObjectProperty objects lost from source: 0

ObjectProperty objects new in target: 2

New ObjectProperty : indirectly_supplies

New ObjectProperty : has_branching_part

Changed ObjectProperty objects: 2

Changes for: bounding layer of

  • Deleted
    • - bounding layer of definition X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y

has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000

Changes for: branching_part_of

October 26, 2014 |

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