releases/2014-04-23/uberon

Chris Mungall

releases/2014-04-23/uberon

Mostly fixes to definitions, synonyms and labels. Added new terms to represent the baleen feeding system in whales, including the lunge feeding organ

Skeletal
- Using zygapophysis as primary label issue 421
Neuro
- Added more NN xrefs
- Various NTs
Mammalian
- NT: baleen feeding system (whale)
- NT: lunge feeding organ
Misc
- High level xref for XAO. 422
- New Relation: has_component (from RO)
- Using RO IDs for composed_primarily_of
- Pharyngea Arch 2 def. Fixes 416 – ZFIN:yb
- classifying to more specific CARO classes
- Fixed typo. Fixes 418
- Removing stray CARO classes from composite builds. Issue 422
- Improving text defs for parts of renal system

Ontology Diff Report

Original Ontology

IRI: http://purl.obolibrary.org/obo/uberon.owl
VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-04-10/uberon.owl

New Ontology

IRI: http://purl.obolibrary.org/obo/uberon.owl
VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-04-23/uberon.owl

Report for classes

Class objects lost from source: 1

Class objects new in target: 27

subparafascicular nucleus database cross reference FMA:226239
subparafascicular nucleus has related synonym nucleus subparafascicularis thalami { database cross reference=NeuroNames:2253 , has synonym type=latin term }
subparafascicular nucleus has related synonym subparafascicular nucleus thalamus { database cross reference=NeuroNames:2253 }
subparafascicular nucleus SubClassOf part of some thalamic complex
subparafascicular nucleus SubClassOf diencephalic nucleus
subparafascicular nucleus definition The term subparafascicular nucleus refers to a cell group located ventral to the parafascicular nucleus in the thalamus. Identified by internal structure, it is present in the human ( Mai-1997 ), the macaque ( Paxinos-2009a ), the rat ( Swanson-1998 ), and the mouse ( Hof-2000 ). { database cross reference=NeuroNames:2253 }
subparafascicular nucleus database cross reference NeuroNames:2253
subparafascicular nucleus has obo namespace uberon
subparafascicular nucleus has related synonym subparafascicular nucleus { database cross reference=NeuroNames:2253 }
subparafascicular nucleus has related synonym subparafascicular thalamic nucleus { database cross reference=NeuroNames:2253 }
subparafascicular nucleus label subparafascicular nucleus
subparafascicular nucleus id UBERON:0016641
subparafascicular nucleus has related synonym subparafascicular nucleus of the thalamus { database cross reference=NeuroNames:2253 }

paratrigeminal nucleus has related synonym paratrigeminal nucleus { database cross reference=NeuroNames:761 }
paratrigeminal nucleus has related synonym nucleus paratrigeminalis { database cross reference=NeuroNames:761 , has synonym type=latin term }
paratrigeminal nucleus database cross reference BAMS:PAT
paratrigeminal nucleus id UBERON:0016832
paratrigeminal nucleus has related synonym lateral cervical nucleus, trigeminal extension { database cross reference=NeuroNames:761 }
paratrigeminal nucleus SubClassOf part of some medulla oblongata
paratrigeminal nucleus SubClassOf nucleus of medulla oblongata
paratrigeminal nucleus database cross reference NeuroNames:761
paratrigeminal nucleus database cross reference FMA:72599
paratrigeminal nucleus definition The term paratrigeminal nucleus refers to a group of cells located lateral to the spinal trigeminal tract of the medulla and medial to the spinocerebellar tracts at the level of the spinal trigeminal nucleus. The cells, identified by Nissl stain, are partially embedded in the adjacent tracts; their distribution varies by species. The paratrigeminal nucleus may represent an extension of the lateral cervical nucleus into the medulla ( Swanson-2004 ). It is found in the human ( Carpenter-1983 ), the macaque ( Paxinos-2009a ), the rat ( Swanson-2004 ) and the mouse ( Paxinos-2001 ). In the functional model of central nervous system organization it is classified as part of the subcortical somatosensory system ( Swanson-2004 ) { database cross reference=NeuroNames:761 }
paratrigeminal nucleus label paratrigeminal nucleus
paratrigeminal nucleus has obo namespace uberon

lateral paragigantocellular nucleus has obo namespace uberon
lateral paragigantocellular nucleus has exact synonym lateral paragigantocellular reticular nucleus { database cross reference=FMA:72577 }
lateral paragigantocellular nucleus has exact synonym paragigantocellular nucleus, lateral part { database cross reference=FMA:72577 }
lateral paragigantocellular nucleus database cross reference NeuroNames:731
lateral paragigantocellular nucleus has related synonym paragigantocellular reticular nucleus, lateral part { database cross reference=NeuroNames:731 }
lateral paragigantocellular nucleus label lateral paragigantocellular nucleus
lateral paragigantocellular nucleus database cross reference ABA:PGRNl
lateral paragigantocellular nucleus id UBERON:0016824
lateral paragigantocellular nucleus definition Nucleus located in the rostral ventrolateral medulla. The PGL was originally identified by cytoarchitectural criteria in the human medulla (Olszewski and Baxter, 1954). In humans, the PGL is located in the ventrolateral quadrant of the rostral medullary tegmentum between the nucleus subtrigeminalis caudally, trapezoid body and the superior olive rostrally, nucleus gigantocellularis medially, spinothalamic tract fibers laterally, inferior olive ventrally, and the nucleus ambiguous dorsally (Olszewski and Baxter, 1954). In the rat, the PGL has been further subdivided into retrofacial PGL (caudal to the facial nucleus), and more rostrally located juxtafacial PGL (medial to the facial nucleus), based upon different connectivity. { database cross reference=http://neurolex.org/wiki/Category:Lateral_paragigantocellular_nucleus }
lateral paragigantocellular nucleus has related synonym nucleus paragigantocellularis lateralis { database cross reference=NeuroNames:731 , has synonym type=latin term }
lateral paragigantocellular nucleus has related synonym paragigantocellular nucleus, lateral part { database cross reference=NeuroNames:731 }
lateral paragigantocellular nucleus SubClassOf paragigantocellular nucleus
lateral paragigantocellular nucleus has related synonym lateral paragigantocellular nucleus { database cross reference=NeuroNames:731 }
lateral paragigantocellular nucleus database cross reference FMA:72577

Changed Class objects: 390

Deleted
- - palatine bone SubClassOf connected to some maxilla
Added
- + palatine bone SubClassOf connected to some maxilla

Deleted
- - hyoglossus muscle definition The Hyoglossus, thin and quadrilateral, arises from the side of the body and from the whole length of the greater cornu of the hyoid bone, and passes almost vertically upward to enter the side of the tongue, between the Styloglossus and Longitudinalis inferior. The hyoglossus depresses and retracts the tongue makes the dorsum more convex The fibers arising from the body of the hyoid bone overlap those from the greater cornu. It is important in singing. Structures passing medially to the hyoglossus muscle are the lingual vein and lingual artery. Laterally, in between the hyoglossus muscle and the mylohyoid muscle lay several important structures (from superior in inferior): submandibular gland, submandibular duct, lingual nerve, vena comitans of hypoglossal nerve, and the hypoglossal nerve. Note, posteriorly, the lingual nerve is superior to the submandibular duct and a portion of the submandibular salivary gland protrudes into the space between the hyoglossus and mylohyoid muscles. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Hyoglossus_muscle }
Added
- + hyoglossus muscle EquivalentTo muscle organ and innervated by some hypoglossal nerve and attaches to some hyoid bone and attaches to some tongue
- + hyoglossus muscle SubClassOf attaches to some hyoid bone
- + hyoglossus muscle SubClassOf attaches to some tongue
- + hyoglossus muscle definition A muscle that attaches to the hyopid bone and to the tongue and is innervated by cranial nerve XII { database cross reference=FEED:rd }

Added
- + ventral patch of Leydig’s organ comment Gradation varies in species. In the stingray, two distinct lobes are seen, in the banded dogfish each lobe is divided into lobules [Homma et al 1984]
- + ventral patch of Leydig’s organ definition The ventralmost of the two bodies of the elasmopbranch hemopoietic organ betweean the esophageal mucosa and muscularis { database cross reference=UBERON:cjm }

Added
- + dorsal patch of Leydig’s organ comment Gradation varies in species. In the stingray, two distinct lobes are seen, in the banded dogfish each lobe is divided into lobules [Homma et al 1984]
- + dorsal patch of Leydig’s organ definition The dosralmost of the two bodies of the elasmopbranch hemopoietic organ betweean the esophageal mucosa and muscularis { database cross reference=UBERON:cjm }

Deleted
- - skeleton of pes comment here ‘pes’ includes both the ankle region and foot proper
Added
- + skeleton of pes comment here ‘pes’ includes both the ankle region, metatarsals and acropodial region

Deleted
- - skeleton of manus comment here ‘manus’ includes both the wrist region and hand proper
Added
- + skeleton of manus comment here ‘manus’ includes both the wrist region, metatarsal region and acropodial region

Deleted
- - dorsal motor nucleus of vagus nerve definition The dorsal nucleus of the vagus nerve (or posterior motor nucleus of vagus) is a cranial nerve nucleus for the vagus nerve that arises from the floor of the fourth ventricle. It mostly serves parasympathetic vagal functions in the heart, gastrointestinal tract, lungs, and other thoracic and abdominal vagal innervations. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Dorsal_nucleus_of_vagus_nerve }
Added
- + dorsal motor nucleus of vagus nerve comment AO notes: The FMA includes a separate sensoryt nucleus
- + dorsal motor nucleus of vagus nerve definition A cranial nerve nucleus for the vagus nerve in the medulla that lies under the floor of the fourth ventricle. It mostly serves parasympathetic vagal functions in the gastrointestinal tract, lungs, and other thoracic and abdominal vagal innervations. The cell bodies for the preganglionic parasympathetic vagal neurons that innervate the heart reside in the nucleus ambiguus.[WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Dorsal_nucleus_of_vagus_nerve }

Deleted
- - extensor digitorum longus SubClassOf muscle of leg
- - extensor digitorum longus SubClassOf part of some leg
- - extensor digitorum longus definition The Extensor digitorum longus is a pennate muscle, situated at the lateral part of the front of the leg. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Extensor_digitorum_longus_muscle }
Added
- + extensor digitorum longus SubClassOf hindlimb muscle
- + extensor digitorum longus SubClassOf part of some hindlimb
- + extensor digitorum longus definition A penniform muscle of the lateral front part of the hindlimb responsible for extension of the digits and dorsiflexion of the ankle. { database cross reference=MP:0004246 }

Deleted
- - distal convoluted tubule definition a portion of kidney nephron between the loop of Henle and the collecting duct system. { database cross reference=http://en.wikipedia.org/wiki/Distal_convoluted_tubule }
Added
- + distal convoluted tubule definition the first segment of the nephron lying just downstream from the loop of Henle, immediately after the macula densa. Among other functions, in humans it is responsible for the reabsorption of about 5% of filtered sodium via the thiazide-sensitive Na-Cl symporter. { database cross reference=GO:0072025 }
- + distal convoluted tubule external definition a portion of kidney nephron between the loop of Henle and the collecting duct system[Wikipedia:Distal_convoluted_tubule]. { source=http://en.wikipedia.org/wiki/Distal_convoluted_tubule }

Deleted
- - renal column comment This class was created automatically from a combination of ontologies
- - renal column definition The renal column (or Bertin column, or column of Bertin) is a medullary extension of the renal cortex in between the renal pyramids. It allows the cortex to be better anchored. Each column consists of lines of blood vessels and urinary tubes and a fibrous material. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Renal_column }
Added
- + renal column comment Editor notes: Check part_of location against textual definition
- + renal column definition A column of tissue that is histologically identical to tissue found in the renal cortex, but which is located in the medulla between the renal pyramids. { database cross reference=http://anatomy.uams.edu/anatomyhtml/kidney.html }

Deleted
- - cocoon SubClassOf composed primarily of some silk
Added
- + cocoon SubClassOf composed primarily of some silk

Deleted
- - renal papilla comment This class was created automatically from a combination of ontologies
- - renal papilla definition In the kidney, the renal papilla is the location where the Medullary pyramids empty urine into the renal pelvis. Histologically it is marked by medullary collecting ducts converging to channel the fluid. Transitional epithelium begins to be seen. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Renal_papilla }
Added
- + renal papilla definition Tip of renal pyramid projecting into a minor calyx. { database cross reference=http://anatomy.uams.edu/anatomyhtml/kidney.html }

Deleted
- - minor calyx comment This class was created automatically from a combination of ontologies
- - minor calyx definition The minor calyx, in the kidney, surrounds the apex of the malpighian pyramids. Urine formed in the kidney passes through a papilla at the apex into the minor calyx then into the major calyx. Peristalsis of the smooth muscle originating in pace-maker cells originating in the walls of the calyces propels urine through the pelvis and ureters to the bladder. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Minor_calyx }
Added
- + minor calyx SubClassOf drains some renal papilla
- + minor calyx comment one renal papilla projects into the lumen of one minor calyx; several minor calyces unite to form a major calyx
- + minor calyx definition portion of the urinary collecting system within the kidney that drains one renal papilla { database cross reference=http://anatomy.uams.edu/anatomyhtml/kidney.html }
- + minor calyx has exact synonym calices renales minores { database cross reference=http://en.wikipedia.org/wiki/Minor_calyx , has synonym type=latin term }

Deleted
- - major calyx comment This class was created automatically from a combination of ontologies
- - major calyx definition The major calyx, in the kidney, surrounds the apex of the malpighian pyramids. Urine formed in the kidney passes through a papilla at the apex into a minor calyx then into major calyx before passing through the renal pelvis into the ureter. Peristalsis of the smooth muscle originating in pace-maker cells originating in the walls of the calyces propels urine through the pelvis and ureters to the bladder. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Major_calyx }
Added
- + major calyx SubClassOf drains some minor calyx
- + major calyx comment major calyx collects urine from several renal papillae; all major calyces unite to form the renal pelvis
- + major calyx definition portion of the urinary collecting system within the kidney that drains several minor calyces { database cross reference=http://anatomy.uams.edu/anatomyhtml/kidney.html }
- + major calyx has exact synonym calices renales majores { database cross reference=http://en.wikipedia.org/wiki/Major_calyx , has synonym type=latin term }

Deleted
- - renal pelvis definition funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP]. { database cross reference=http://en.wikipedia.org/wiki/Renal_pelvis , database cross reference=MP:0004194 }
Added
- + renal pelvis definition A funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP]. { database cross reference=MP:0004194 }

Deleted
- - ventrobronchus SubClassOf connected to some parabronchus
Added
- + ventrobronchus SubClassOf connected to some parabronchus

Deleted
- - mesobronchus SubClassOf connected to some air sac
Added
- + mesobronchus SubClassOf connected to some air sac

Deleted
- - uterine spiral artery definition A corkscrew-like artery in premenstrual or progestational endometrium; uterine spiral arteries play a vital role in supplying nutrients to the placenta and fetus, and are thus remodeled into highly dilated inelastic vessels by the action of invading trophoblast (physiological change) { database cross reference=J:100668 , database cross reference=J:117841 , database cross reference=MGI:anna }
Added
- + uterine spiral artery definition A corkscrew-like artery in premenstrual or progestational endometrium; uterine spiral arteries play a vital role in supplying nutrients to the placenta and fetus, and are thus remodeled into highly dilated inelastic vessels by the action of invading trophoblast (physiological change) { database cross reference=J:100668 , database cross reference=J:117841 , database cross reference=MGI:anna , database cross reference=MP:0012726 }

Deleted
- - true rib EquivalentTo rib and connected to some sternum
- - true rib SubClassOf connected to some sternum
Added
- + true rib EquivalentTo rib and connected to some sternum
- + true rib SubClassOf connected to some sternum

Deleted
- - head of rib SubClassOf connected to some vertebra
Added
- + head of rib SubClassOf connected to some vertebra

Deleted
- - uterine horn SubClassOf connected to some fallopian tube
Added
- + uterine horn SubClassOf connected to some fallopian tube

Deleted
- - ovarian vein EquivalentTo vein and connected to some female gonad
- - ovarian vein SubClassOf connected to some female gonad
Added
- + ovarian vein EquivalentTo vein and connected to some female gonad
- + ovarian vein SubClassOf connected to some female gonad

Deleted
- - vertebral arch joint definition a synovial joint between the superior articular process of one vertebra and the inferior articular process of the vertebra directly above it. There are two facet joints in each spinal motion segment[WP]. { database cross reference=http://en.wikipedia.org/wiki/Zygapophysial_joint }
Added
- + vertebral arch joint definition a synovial joint between the prezygapophysis of one vertebra and the postzygapophysis of the vertebra directly above it. There are two facet joints in each spinal motion segment[WP]. { database cross reference=http://en.wikipedia.org/wiki/Zygapophysial_joint }

Deleted
- - patella EquivalentTo bone element and part of some knee and connected to some femur
- - patella SubClassOf connected to some femur
Added
- + patella EquivalentTo bone element and part of some knee and connected to some femur
- + patella SubClassOf connected to some femur

Deleted
- - uterine tube isthmus label uterine tube isthmus
Added
- + avian uterine tube isthmus label avian uterine tube isthmus

Deleted
- - purkinje fiber definition Conducting tissue of heart which consists of Purkinje myocytes.[FMA] { database cross reference=http://en.wikipedia.org/wiki/Purkinje_fiber , database cross reference=FMA:FMA }
Added
- + purkinje fiber SubClassOf part of some His-Purkinje system
- + purkinje fiber database cross reference BTO:0001735
- + purkinje fiber definition The cardiac Purkinje fiber is part of the cardiac conduction system that receives signals from the bundle of His and innervates the ventricular cardiac muscle { database cross reference=GO:0003165 }
- + purkinje fiber has alternative id UBERON:0004147
- + purkinje fiber has exact synonym cardiac Purkinje fiber { database cross reference=BTO:0001735 }
- + purkinje fiber has exact synonym subendocardial branch
- + purkinje fiber has related synonym heart Purkinje fiber { database cross reference=BTO:0001735 }

Deleted
- - adrenal gland comment Taxon notes: The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole
Added
- + adrenal gland comment Taxon notes: The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole. Function notes: suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n.

Deleted
- - talus SubClassOf connected to some tibia
Added
- + talus SubClassOf connected to some tibia

Deleted
- - interlobular duct EquivalentTo duct and part of some connective tissue and connected to some lobule
- - interlobular duct SubClassOf connected to some lobule
Added
- + interlobular duct EquivalentTo duct and part of some connective tissue and connected to some lobule
- + interlobular duct SubClassOf connected to some lobule

Deleted
- - thymus epithelium definition the supporting framework of the thymus. { database cross reference=MP:0009544 }
Added
- + thymus epithelium definition An epithelium that is part of a thymus, forming a supporting framework[MP,modified]. { database cross reference=MP:0009544 }

Deleted
- - radial bone SubClassOf endochondral bone
- - radial bone SubClassOf fin bone

Added
- + renal sinus definition A hollowed out area on the medial margin of the kidney. The renal sinus opens at the renal hilum; it contains the renal aa. and vv., major calyces and renal pelvis, perirenal fat { database cross reference=http://anatomy.uams.edu/anatomyhtml/kidney.html }

Added
- + genital labium SubClassOf zone of skin

Deleted
- - midface SubClassOf anatomical structure
Added
- + midface SubClassOf subdivision of head

Deleted
- - hairline SubClassOf adjacent to some strand of hair
- - hairline SubClassOf anatomical structure
- - hairline definition . { database cross reference=HP:0009553 }
Added
- + hairline EquivalentTo anatomical line and connects some scalp and connects some forehead
- + hairline SubClassOf anatomical line
- + hairline SubClassOf connects some forehead
- + hairline SubClassOf connects some scalp
- + hairline definition Anatomical line demarcating the boundary between forehead and scalp. { database cross reference=http://en.wikipedia.org/wiki/Hairline }

Deleted
- - visceral muculature label visceral muculature
Added
- + visceral musculature label visceral musculature

Deleted
- - kidney pyramid definition Kidney pyramids are the conical masses that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts[GO]. One of a number of pyramidal masses seen on longitudinal section of the kidney; collectively, they constitute the renal medulla, and contain part of the secreting tubules and the collecting tubules[BTO]. Renal pyramids (or malpighian pyramids) are cone-shaped tissues of the kidney. The renal medulla is made up of 8 to 18 of these conical subdivisions. The broad base of each pyramid faces the renal cortex, and its apex, or papilla, points internally. The pyramids appear striped because they are formed by straight parallel segments of nephrons. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Renal_pyramids , database cross reference=BTO:0003926 , database cross reference=GO:0072056 }
Added
- + kidney pyramid definition Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts. { database cross reference=http://anatomy.uams.edu/anatomyhtml/kidney.html , database cross reference=GO:0072056 }

Deleted
- - vasculature SubClassOf composed primarily of some vessel
Added
- + vasculature SubClassOf composed primarily of some vessel

Deleted
- - hilum of kidney definition A hilum that is part of a kidney. { database cross reference=OBOL:automatic }
Added
- + hilum of kidney definition An opening on medial margin of the kidney leading into the renal sinus. he renal vessels enter/leave the kidney at the hilum; the renal pelvis leaves the kidney at the hilum. { database cross reference=http://anatomy.uams.edu/anatomyhtml/kidney.html }
- + hilum of kidney has exact synonym hilar area of the kidney

Deleted
- - venous system SubClassOf composed primarily of some vein
Added
- + venous system SubClassOf composed primarily of some vein

Deleted
- - metoptic pilar definition posterior border of the optic nerve foramen. { database cross reference=MP:0010705 }
Added
- + metoptic pilar SubClassOf zone of bone organ
- + metoptic pilar definition the posterior border of the optic nerve foramen. { database cross reference=MP:0010705 }

Deleted
- - pharyngeal arch 2 definition assists in forming the side and front of the neck. { database cross reference=http://en.wikipedia.org/wiki/Second_pharyngeal_arch }
Added
- + pharyngeal arch 2 definition The second pharyngeal arch will form the hyoid apparatus. The cranial neural crest cells that populate the second pharyngeal arch emerge primarily from rhombomere 4 and will form skeletal elements. { database cross reference=http://www.ncbi.nlm.nih.gov/pubmed/12784288 , database cross reference=ZFIN:yb }

Deleted
- - interdigital region SubClassOf ObjectMinCardinality( connected to digit ) and ObjectMaxCardinality( connected to digit )
Added
- + interdigital region SubClassOf ObjectMinCardinality( connected to digit ) and ObjectMaxCardinality( connected to digit )

Deleted
- - organ SubClassOf anatomical structure
- - organ definition Anatomical structure that performs a specific function or group of functions [WP]. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions[GO]. { database cross reference=http://en.wikipedia.org/wiki/Organ_(anatomy) , database cross reference=GO:0048513 }
Added
- + organ SubClassOf has boundary some anatomical surface
- + organ SubClassOf multicellular anatomical structure
- + organ definition Anatomical structure that performs a specific function or group of functions [WP]. { database cross reference=http://en.wikipedia.org/wiki/Organ_(anatomy) }
- + organ external definition Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. { source=GO:0048513 }

Deleted
- - manus bone has exact synonym bone of hand proper or wrist

Added
- + crus commune SubClassOf tube
- + crus commune definition A region formed by non-ampulated ends of posterior and superior semicircular canals of vestibular apparatus in inner ear. { database cross reference=http://emedicine.medscape.com/article/883956-overview }
- + crus commune has exact synonym crus commune canalis semicircularis

Added
- + nephrostome SubClassOf orifice

Deleted
- - inter limb-segment region SubClassOf ObjectMinCardinality( connected to limb segment ) and ObjectMaxCardinality( connected to limb segment )
Added
- + inter limb-segment region SubClassOf ObjectMinCardinality( connected to limb segment ) and ObjectMaxCardinality( connected to limb segment )

Deleted
- - sternum SubClassOf connected to some pectoral girdle skeleton
- - sternum SubClassOf connected to some rib
Added
- + sternum SubClassOf connected to some pectoral girdle skeleton
- + sternum SubClassOf connected to some rib

Report for properties

ObjectProperty objects lost from source: 1

ObjectProperty objects new in target: 4

composed primarily of id composed_primarily_of
SubObjectPropertyOf( composed primarily of has part )
composed primarily of label composed_primarily_of
composed primarily of database cross reference RO:0002473
composed primarily of has obo namespace uberon
composed primarily of shorthand composed_primarily_of
composed primarily of definition x composed_primarily_of y iff: more than half of the mass of x is made from parts of y

Changed ObjectProperty objects: 8

Deleted
- - SubObjectPropertyOf( anteriorly connected to connected to )
Added
- + SubObjectPropertyOf( anteriorly connected to connected to )

Deleted
- - SubObjectPropertyOf( distally connected to connected to )
Added
- + SubObjectPropertyOf( distally connected to connected to )

Deleted
- - SubObjectPropertyOf( proximally connected to connected to )
Added
- + SubObjectPropertyOf( proximally connected to connected to )

Deleted
- - SubObjectPropertyOf( drains connected to )
Added
- + SubObjectPropertyOf( drains connected to )

Deleted
- - SubObjectPropertyOf( supplies connected to )
Added
- + SubObjectPropertyOf( supplies connected to )

Deleted
- - output of label output_of
Added
- + output of label output of

Deleted
- - SubObjectPropertyOf( composed primarily of has part )
- - composed primarily of database cross reference UBREL:0000002
- - composed primarily of definition x composed_primarily_of y iff: more than half of the mass of x is made from parts of y
- - composed primarily of has obo namespace uberon
- - composed primarily of id composed_primarily_of
- - composed primarily of label composed_primarily_of
- - composed primarily of shorthand composed_primarily_of

releases/2014-04-23/uberon

Ontology Diff Report

Original Ontology

New Ontology

Report for classes

Class objects lost from source: 1

Class objects new in target: 27

New Class : paragigantocellular nucleus

New Class : supplemental motor cortex

New Class : parvocellular reticular nucleus

New Class : premotor cortex

New Class : actinopterygian frontal-parietal joint

New Class : isthmus of fallopian tube

New Class : neurovascular bundle

New Class : lateral periolivary nucleus

New Class : subparafascicular nucleus

New Class : baleen feeding system

New Class : Y-shaped fibrocartilage skeleton of ventral pouch

New Class : stem of Y-shaped fibrocartilage skeleton of ventral pouch

New Class : branch of Y-shaped fibrocartilage skeleton of ventral pouch

New Class : lunge feeding organ

New Class : ventral throat pleat

New Class : lunge feeding vibrissa

New Class : lunge feeding organ papilla

New Class : lateral nucleus of trapezoid body

New Class : subparabrachial nucleus

New Class : retroambiguus nucleus

New Class : paratrigeminal nucleus

New Class : renal fascia

New Class : nucleus of phrenic nerve

New Class : lateral paragigantocellular nucleus

New Class : dorsal paragigantocellular nucleus

New Class : paramedian medullary reticular complex

New Class : dorsal paramedian reticular nucleus

Changed Class objects: 390

Changes for: basibranchial cartilage

Changes for: parabrachial pigmental nucleus

Changes for: dartos muscle of labia majora

Changes for: ilio-marsupialis muscle

Changes for: lateral ethmoid cartilage

Changes for: ring of oral cilia

Changes for: hyomandibular cartilage

Changes for: hyomandibular bone

Changes for: plastron-carapace bridge

Changes for: proximal tarsal bone

Changes for: left extraembryonic umbilical artery

Changes for: common crus of semicircular duct

Changes for: surangular bone

Changes for: dorsal head of rib

Changes for: ventral head of rib

Changes for: cartilaginous projection

Changes for: primary remex feather

Changes for: secondary remex feather

Changes for: tertial remex feather

Changes for: atrioventricular region

Changes for: radial cartilage

Changes for: supraoccipital cartilage element

Changes for: papillary layer of dermis

Changes for: paratenial nucleus

Changes for: pedal digitopodium bone

Changes for: manual digitopodium bone

Changes for: autopod bone

Changes for: row of scales

Changes for: sphenoid bone

Changes for: malleus bone

Changes for: incus bone

Changes for: palatine bone

Changes for: stapes bone

Changes for: exoccipital bone

Changes for: basioccipital bone

Changes for: cuneiform nucleus

Changes for: hyoglossus muscle

Changes for: glandular system

Changes for: respiratory muscle

Changes for: proximal mesopodial bone

Changes for: femur cartilage element

Changes for: skeleton of digitopodium

Changes for: skeleton of manual digitopodium

Changes for: skeleton of pedal digitopodium

Changes for: ventral patch of Leydig’s organ