Fixes for Phenoscape and BGee

This release tidies up the remaining terms generated by CharaParser for the Phenoscape project, and fixes a number of inter-ontology stage issues. It also marks the initial use of a new exploratory relation (not yet in RO) “conduit for”, which is used to connect conduits and bone foramens with the vessels and nerves that run through them.

• Nervous system
  • reticular formation overhaul. Obsoleted two classes (spinal cord and brainstem RF)
  • isa->po for superior reticular formation. Issue #527
• Stages
  • added xref to fly life stage. BGEE:an. Fixes issue #523
  • addex xref to fly cleavage stage. BGEE:an. Fixes issue #524
  • obsoleted tailbud stage. Issue #520
• Renal
  • kidney tubule fixes Fixed isa->part_of for renal tubule segments.
• Ontology coordination
  • Made isa/partof between GO aligned. Issue #527
  • latest MA xrefs. Various enhancements to Brodmann areas
  • Improvements to composite-metazoan build
• Relations
  • added conduit_for relationshipships to foramina and conduits
• Skeletal
  • interorbital septum: added part_of head (Phenoscape:WD)
  • Jakubowski’s organ: added is_a neuromast (Phenoscape:WD)
  • Added part_of pterygoid bone to vidian canal. This was lost from spreadsheet due to use of nonexact syn. Issue #516
  • enhanced logic and annotation axioms for vidian canal. Added vidian nerve. Issue #516

Ontology Diff Report

Original Ontology

• IRI: http://purl.obolibrary.org/obo/uberon.owl
• VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-07-11/uberon.owl

New Ontology

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

Report for classes

Class objects lost from source: 0

Class objects new in target: 13

New Class : petrosal foramen

• petrosal foramen label petrosal foramen
• petrosal foramen id UBERON:0018424
• petrosal foramen EquivalentTo foramen of skull and part of some petrosal bone
• petrosal foramen has exact synonym Foramen petrosum { database cross reference=FMA:53158 }
• petrosal foramen database cross reference FMA:53158
• petrosal foramen has obo namespace uberon
• petrosal foramen SubClassOf foramen of skull
• petrosal foramen SubClassOf part of some petrosal bone

New Class : facial nerve canal

• facial nerve canal id UBERON:0018413
• facial nerve canal SubClassOf conduit for some facial nerve
• facial nerve canal definition A Z-shaped canal running through the temporal bone from the internal acoustic meatus to the stylomastoid foramen . It is located within the middle ear region, according to its shape it is divided into three main segments: the labyrinthine, the tympanic, and the mastoidal segment . { database cross reference=http://en.wikipedia.org/wiki/Facial_canal }
• facial nerve canal SubClassOf part of some temporal bone
• facial nerve canal SubClassOf neural crest-derived structure
• facial nerve canal has obo namespace uberon
• facial nerve canal label facial nerve canal
• facial nerve canal has exact synonym facial canal { database cross reference=FMA:54952 }
• facial nerve canal database cross reference http://en.wikipedia.org/wiki/Facial_canal
• facial nerve canal has exact synonym fallopian canal { database cross reference=FMA:54952 }
• facial nerve canal EquivalentTo bone foramen and conduit for some facial nerve
• facial nerve canal database cross reference FMA:54952
• facial nerve canal SubClassOf foramen of skull

New Class : vidian nerve

• vidian nerve SubClassOf branching part of some facial nerve
• vidian nerve has exact synonym pterygoid canal nerve { database cross reference=FMA:67584 }
• vidian nerve label vidian nerve
• vidian nerve id UBERON:0018412
• vidian nerve has exact synonym nerve of pterygoid canal { database cross reference=FMA:67584 }
• vidian nerve external ontology notes FMA classifies as an anatomical junction { external ontology=FMA }
• vidian nerve database cross reference http://en.wikipedia.org/wiki/Nerve_of_pterygoid_canal
• vidian nerve has related synonym nerve of the pterygoid canal { database cross reference=http://en.wikipedia.org/wiki/Nerve_of_pterygoid_canal }
• vidian nerve has exact synonym vidian nerve { database cross reference=FMA:67584 }
• vidian nerve definition A nerve that is formed by the junction of the great petrosal nerve and the deep petrosal nerve in the cartilaginous substance which fills the foramen lacerum. It passes forward, through the pterygoid canal, with the corresponding artery, and is joined by a small ascending sphenoidal branch from the otic ganglion. Finally, it enters the pterygopalatine fossa, and joins the posterior angle of the pterygopalatine ganglion. It contains preganglionic parasympathetic fibers from the greater petrosal nerve, a branch of the facial nerve (CN VII), and postganglionic sympathetic fibers from the deep petrosal nerve. { database cross reference=http://en.wikipedia.org/wiki/Nerve_of_pterygoid_canal }
• vidian nerve SubClassOf facial nerve
• vidian nerve has related synonym vidian nerve { database cross reference=http://en.wikipedia.org/wiki/Nerve_of_pterygoid_canal }
• vidian nerve has obo namespace uberon
• vidian nerve database cross reference http://www.snomedbrowser.com/Codes/Details/280273005
• vidian nerve database cross reference FMA:67584

New Class : ligament of hip joint

• ligament of hip joint has obo namespace uberon
• ligament of hip joint label ligament of hip joint
• ligament of hip joint database cross reference http://www.snomedbrowser.com/Codes/Details/182435001
• ligament of hip joint database cross reference FMA:42868
• ligament of hip joint id UBERON:0018411
• ligament of hip joint SubClassOf part of some hip joint
• ligament of hip joint SubClassOf hip connective tissue
• ligament of hip joint has exact synonym hip joint ligament { database cross reference=FMA:42868 }
• ligament of hip joint EquivalentTo skeletal ligament and part of some hip joint
• ligament of hip joint SubClassOf skeletal ligament

New Class : ethmoid foramen

• ethmoid foramen has related synonym ethmoidal foramina { has synonym type=plural term }
• ethmoid foramen id UBERON:0018415
• ethmoid foramen has obo namespace uberon
• ethmoid foramen SubClassOf neural crest-derived structure
• ethmoid foramen label ethmoid foramen
• ethmoid foramen SubClassOf part of some ethmoid bone
• ethmoid foramen comment Taxon nodes: In humans, refers to anterior or posterior ethmoid foramina
• ethmoid foramen EquivalentTo anatomical conduit and part of some ethmoid bone
• ethmoid foramen database cross reference http://en.wikipedia.org/wiki/Ethmoidal_foramina
• ethmoid foramen definition An bone foramen in the ethmoid bone.
• ethmoid foramen SubClassOf mesoderm-derived structure
• ethmoid foramen has related synonym ethmoid foramina { has synonym type=plural term }
• ethmoid foramen SubClassOf foramen of skull

New Class : lacteal

• lacteal database cross reference http://en.wikipedia.org/wiki/Lacteals
• lacteal label lacteal
• lacteal SubClassOf part of some intestinal villus
• lacteal EquivalentTo lymphatic capillary and part of some intestinal villus and channel for some chyle
• lacteal id UBERON:0018410
• lacteal SubClassOf lymphatic capillary
• lacteal database cross reference FMA:68443
• lacteal definition a lymphatic capillary that absorbs dietary fats in the villi of the small intestine. { database cross reference=http://en.wikipedia.org/wiki/Lacteals }
• lacteal has obo namespace uberon
• lacteal database cross reference http://www.snomedbrowser.com/Codes/Details/282414002
• lacteal SubClassOf channel for some chyle

New Class : male inguinal ring

• male inguinal ring SubClassOf part of some male inguinal canal
• male inguinal ring label male inguinal ring
• male inguinal ring id UBERON:0018530
• male inguinal ring SubClassOf reproductive structure
• male inguinal ring SubClassOf male anatomical structure
• male inguinal ring has obo namespace uberon
• male inguinal ring EquivalentTo inguinal ring and part of some male reproductive system
• male inguinal ring database cross reference EMAPA:29307
• male inguinal ring SubClassOf part of some male reproductive system
• male inguinal ring SubClassOf inguinal ring

New Class : female superficial inguinal ring

• female superficial inguinal ring database cross reference EMAPA:19174
• female superficial inguinal ring SubClassOf part of some female reproductive system
• female superficial inguinal ring SubClassOf female inguinal ring
• female superficial inguinal ring has exact synonym female external inguinal ring { database cross reference=MA:0003252 }
• female superficial inguinal ring id UBERON:0018531
• female superficial inguinal ring EquivalentTo deep inguinal ring and part of some female reproductive system
• female superficial inguinal ring has obo namespace uberon
• female superficial inguinal ring database cross reference MA:0003252
• female superficial inguinal ring label female superficial inguinal ring
• female superficial inguinal ring SubClassOf deep inguinal ring

New Class : female deep inguinal ring

• female deep inguinal ring database cross reference EMAPA:19173
• female deep inguinal ring id UBERON:0018532
• female deep inguinal ring has exact synonym female internal inguinal ring { database cross reference=MA:0003251 }
• female deep inguinal ring SubClassOf part of some male reproductive system
• female deep inguinal ring label female deep inguinal ring
• female deep inguinal ring EquivalentTo deep inguinal ring and part of some male reproductive system
• female deep inguinal ring SubClassOf male inguinal ring
• female deep inguinal ring database cross reference MA:0003251
• female deep inguinal ring SubClassOf deep inguinal ring
• female deep inguinal ring has obo namespace uberon

New Class : crus of penis or clitoris

• crus of penis or clitoris SubClassOf part of some corpus cavernosum
• crus of penis or clitoris label crus of penis or clitoris
• crus of penis or clitoris definition the continuation of each corpus cavernosum of the penis or clitoris, diverging posteriorly to be attached to the pubic arch.
• crus of penis or clitoris has obo namespace uberon
• crus of penis or clitoris id UBERON:0018533
• crus of penis or clitoris SubClassOf organ part

New Class : obsolete spinal cord reticular formation

• obsolete spinal cord reticular formation has obo namespace uberon
• obsolete spinal cord reticular formation comment Obsoleted as NN retricts this to brainstem structures
• obsolete spinal cord reticular formation consider FMA:77455
• obsolete spinal cord reticular formation id UBERON:0018534
• obsolete spinal cord reticular formation deprecated true
• obsolete spinal cord reticular formation has exact synonym reticular formation of spinal cord { database cross reference=FMA:77455 }
• obsolete spinal cord reticular formation has exact synonym formatio reticularis spinalis { database cross reference=FMA:TA }
• obsolete spinal cord reticular formation label obsolete spinal cord reticular formation
• obsolete spinal cord reticular formation has exact synonym spinal reticular formation { database cross reference=FMA:77455 }
• obsolete spinal cord reticular formation consider SCTID:369268003

New Class : foramen of nasal bone

• foramen of nasal bone has related synonym nasal foramina { database cross reference=FMA:57653 , has synonym type=plural term }
• foramen of nasal bone label foramen of nasal bone
• foramen of nasal bone has exact synonym foramina nasalia { database cross reference=http://en.wikipedia.org/wiki/Nasal_foramina , has synonym type=latin term }
• foramen of nasal bone SubClassOf part of some nasal bone
• foramen of nasal bone database cross reference http://en.wikipedia.org/wiki/Nasal_foramina
• foramen of nasal bone SubClassOf neural crest-derived structure
• foramen of nasal bone SubClassOf conduit for some blood vessel
• foramen of nasal bone has related synonym foramen of nasal bone
• foramen of nasal bone SubClassOf mesoderm-derived structure
• foramen of nasal bone has obo namespace uberon
• foramen of nasal bone EquivalentTo foramen of skull and part of some nasal bone
• foramen of nasal bone has exact synonym nasal foramen
• foramen of nasal bone SubClassOf foramen of skull
• foramen of nasal bone definition A vascular foramen opening on the outer surface of a nasal bone. { database cross reference=http://medical-dictionary.thefreedictionary.com/nasal+foramina }
• foramen of nasal bone id UBERON:0018508
• foramen of nasal bone database cross reference FMA:57653

New Class : female inguinal ring

• female inguinal ring database cross reference MA:0003250
• female inguinal ring database cross reference EMAPA:19172
• female inguinal ring id UBERON:0018529
• female inguinal ring SubClassOf inguinal ring
• female inguinal ring EquivalentTo inguinal ring and part of some female reproductive system
• female inguinal ring SubClassOf reproductive structure
• female inguinal ring has obo namespace uberon
• female inguinal ring label female inguinal ring
• female inguinal ring SubClassOf part of some female reproductive system
• female inguinal ring SubClassOf female anatomical structure
• female inguinal ring SubClassOf part of some female inguinal canal

Changed Class objects: 131

Changes for: notochordal canal

• Added
  • + notochordal canal definition A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily. { database cross reference=http://medical-dictionary.thefreedictionary.com/notochordal+canal }
  • + notochordal canal has related synonym chordal canal

Changes for: anal fin basal cartilage

• Added
  • + anal fin basal cartilage has broad synonym anal fin base plate

Changes for: internal acoustic meatus

• Added
  • + internal acoustic meatus SubClassOf conduit for some facial nerve
  • + internal acoustic meatus SubClassOf conduit for some vestibulocochlear nerve

Changes for: mesorchium

• Added
  • + mesorchium database cross reference MA:0003238

Changes for: acoelous

• Added
  • + acoelous has broad synonym amphiplatyan

Changes for: bile

• Deleted
  • - bile definition A bitter-tasting, dark green to yellowish brown fluid, produced by the liver of most vertebrates, that aids the process of digestion of lipids in the small intestine. In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum. Bile is a composition of the following materials: water (85%), bile salts (10%), mucus and pigments (3%), fats (1%), inorganic salts (0.7%) and cholesterol (0.3%)[WP]. { database cross reference=http://en.wikipedia.org/wiki/Bile }
• Added
  • + bile definition A bodily fluid that is produced by the liver and aids the process of digestion of lipids in the small intestine[WP, modified]. { database cross reference=http://en.wikipedia.org/wiki/Bile }
  • + bile taxon notes In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum.

Changes for: lower pharyngobranchial toothplate

• Deleted
  • - lower pharyngobranchial toothplate comment Editor note: need to add relationship: UBERON:’pharyngeal tooth plate’ needs relationship part_of ‘splanchnocranium’
• Added
  • + lower pharyngobranchial toothplate editor note need to add relationship: UBERON:’pharyngeal tooth plate’ needs relationship part_of ‘splanchnocranium’

Changes for: epidermal egg tooth

• Deleted
  • - epidermal egg tooth comment Taxon notes: found in Archosaurs and monotreames
• Added
  • + epidermal egg tooth taxon notes found in Archosaurs and monotreames

Changes for: femoral canal

• Deleted
  • - femoral canal definition The compartment of the femoral sheaththat contains efferent lymphatic vessels and a lymph node embedded in a small amount of areolar tissue. It is conical in shape and is about 2 cm long. The femoral canal is bordered: Anteriorly by the inguinal ligament Posteriorly by the pectineal ligament Medially by the lacunar ligament Laterally by the femoral vein It contains the lymph nodes of Cloquet or Rosenmuller. It should not be confused with the nearby adductor canal. { database cross reference=http://en.wikipedia.org/wiki/Femoral_canal }
• Added
  • + femoral canal SubClassOf conduit for some efferent lymphatic vessel
  • + femoral canal definition The compartment of the femoral sheath that contains efferent lymphatic vessels and a lymph node embedded in a small amount of areolar tissue. It is conical in shape and is about 2 cm long. The femoral canal is bordered: Anteriorly by the inguinal ligament Posteriorly by the pectineal ligament Medially by the lacunar ligament Laterally by the femoral vein It contains the lymph nodes of Cloquet or Rosenmuller. It should not be confused with the nearby adductor canal. { database cross reference=http://en.wikipedia.org/wiki/Femoral_canal }

Changes for: vidian canal

• Deleted
  • - vidian canal SubClassOf anatomical conduit
• Added
  • + vidian canal EquivalentTo anatomical conduit and conduit for some vidian nerve
  • + vidian canal SubClassOf conduit for some vidian nerve
  • + vidian canal SubClassOf facial nerve canal
  • + vidian canal SubClassOf mixed ectoderm/mesoderm/endoderm-derived structure
  • + vidian canal SubClassOf part of some pterygoid bone
  • + vidian canal database cross reference FMA:54756
  • + vidian canal database cross reference http://en.wikipedia.org/wiki/Pterygoid_canal
  • + vidian canal has exact synonym pterygoid canal { database cross reference=FMA:54756 }
  • + vidian canal has related synonym canalis pterygoidei { database cross reference=http://en.wikipedia.org/wiki/Pterygoid_canal }
  • + vidian canal has related synonym canalis pterygoideus { database cross reference=http://en.wikipedia.org/wiki/Pterygoid_canal }

Changes for: sallet

• Deleted
  • - sallet definition v=onepage&q=sallet&f=false { database cross reference=PHENOSCAPE:Alex }
• Added
  • + sallet definition v=onepage&q=sallet&f=false { database cross reference=PHENOSCAPE:Alex }

Changes for: processus ventralis of thoracic vertebra

• Deleted
  • - processus ventralis of thoracic vertebra comment Taxon notes: found in some birds
• Added
  • + processus ventralis of thoracic vertebra taxon notes found in some birds

Changes for: processus ventrolateralis of thoracic vertebra

• Deleted
  • - processus ventrolateralis of thoracic vertebra comment Taxon notes: found in some birds
• Added
  • + processus ventrolateralis of thoracic vertebra taxon notes found in some birds

Changes for: petrosal bone

• Deleted
  • - petrosal bone comment Usage notes: distinct from UBERON:0001694 petrous part of temporal bone; [http://www.ncbi.nlm.nih.gov/pubmed/19438763]
• Added
  • + petrosal bone curator notes distinct from UBERON:0001694 petrous part of temporal bone; [http://www.ncbi.nlm.nih.gov/pubmed/19438763]

Changes for: interpterygoid region

• Deleted
  • - interpterygoid region comment Editor notes: propose changing palate bone to palate bone series[PHENOSCAPE:ad]
• Added
  • + interpterygoid region editor note propose changing palate bone to palate bone series[PHENOSCAPE:ad]

Changes for: cementum

• Deleted
  • - cementum comment Taxon notes: Cementum, the supporting tissue that anchors mammalian and crocodylian teeth into their sockets, differs among species and can have features of dentine, of bone, and of calcified cartilage, as well as unique features. Cementum is deposited by cementoblasts onto existing dentine. As in bone and dentine, cementoblasts produce an organic matrix, the main constituent of which is collagen type I (Bosshardt, 2005), but cementum, dentine, and bone also share a number of important noncollagenous matrix components such as osteopontin, osteocalcin, bone sialoprotein, a2-HS- glycoprotein, dentine matrix protein, dentine sialoprotein, and den- tine phosphoprotein (McKee et al., 1996; Bosshardt, 2005). it has been argued that in all rodents and ruminants, cementum is a form of calcified cartilage[H&W]
• Added
  • + cementum taxon notes Cementum, the supporting tissue that anchors mammalian and crocodylian teeth into their sockets, differs among species and can have features of dentine, of bone, and of calcified cartilage, as well as unique features. Cementum is deposited by cementoblasts onto existing dentine. As in bone and dentine, cementoblasts produce an organic matrix, the main constituent of which is collagen type I (Bosshardt, 2005), but cementum, dentine, and bone also share a number of important noncollagenous matrix components such as osteopontin, osteocalcin, bone sialoprotein, a2-HS- glycoprotein, dentine matrix protein, dentine sialoprotein, and den- tine phosphoprotein (McKee et al., 1996; Bosshardt, 2005). it has been argued that in all rodents and ruminants, cementum is a form of calcified cartilage[H&W]

Changes for: sensory root of facial nerve

• Deleted
  • - sensory root of facial nerve SubClassOf develops from some neural crest
• Added
  • + sensory root of facial nerve SubClassOf develops from some cranial neural crest
  • + sensory root of facial nerve has exact synonym sensory component of the VIIth (facial) nerve

Changes for: foramen ovale of skull

• Added
  • + foramen ovale of skull database cross reference http://www.snomedbrowser.com/Codes/Details/369441001
  • + foramen ovale of skull has exact synonym foramen ovale cranii
  • + foramen ovale of skull has exact synonym foramen ovale of cranium

Changes for: midbrain reticular formation

• Deleted
  • - midbrain reticular formation EquivalentTo reticular formation and part of some midbrain
  • - midbrain reticular formation SubClassOf brainstem reticular formation
  • - midbrain reticular formation SubClassOf part of some midbrain
  • - midbrain reticular formation SubClassOf regional part of midbrain tegmentum
• Added
  • + midbrain reticular formation SubClassOf brain grey matter
  • + midbrain reticular formation SubClassOf nuclear complex of neuraxis
  • + midbrain reticular formation SubClassOf part of some reticular formation
  • + midbrain reticular formation SubClassOf structure with developmental contribution from neural crest

Changes for: lower part of vagina

• Added
  • + lower part of vagina database cross reference MA:0003243
  • + lower part of vagina has exact synonym vagina lower part { database cross reference=MA:0003243 }

Changes for: extrastriate cortex

• Added
  • + extrastriate cortex SubClassOf part of some visual cortex
  • + extrastriate cortex SubClassOf regional part of cerebral cortex
  • + extrastriate cortex database cross reference BTO:0004704
  • + extrastriate cortex database cross reference http://en.wikipedia.org/wiki/Extrastriate_cortex
  • + extrastriate cortex has exact synonym peristriate cortex { database cross reference=http://en.wikipedia.org/wiki/Extrastriate_cortex }

Changes for: hindlimb zeugopod

• Deleted
  • - hindlimb zeugopod comment Terminology notes: Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here
• Added
  • + hindlimb zeugopod terminology notes Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here

Changes for: chorda tympani branch of facial nerve

• Deleted
  • - facial VII nerve chorda tympani branch label facial VII nerve chorda tympani branch
• Added
  • + chorda tympani branch of facial nerve database cross reference FMA:53228
  • + chorda tympani branch of facial nerve database cross reference http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1434
  • + chorda tympani branch of facial nerve database cross reference http://en.wikipedia.org/wiki/Chorda_tympani
  • + chorda tympani branch of facial nerve database cross reference http://www.snomedbrowser.com/Codes/Details/280274004
  • + chorda tympani branch of facial nerve definition The chorda tympani is a nerve that branches from the facial nerve (cranial nerve VII) inside the facial canal, just before the facial nerve exits the skull via the stylomastoid foramen. Chorda tympani is a branch of the facial nerve (the seventh cranial nerve) that serves the taste buds in the front of the tongue, runs through the middle ear, and carries taste messages to the brain. The chorda tympani is part of one of three cranial nerves that are involved in taste. The taste system involves a complicated feedback loop, with each nerve acting to inhibit the signals of other nerves. The chorda tympani appears to exert a particularly strong inhibitory influence on other taste nerves, as well as on pain fibers in the tongue. When the chorda tympani is damaged, its inhibitory function is disrupted, leading to less inhibited activity in the other nerves. { database cross reference=http://en.wikipedia.org/wiki/Chorda_tympani }
  • + chorda tympani branch of facial nerve has exact synonym chorda tympani { database cross reference=FMA:53228 }
  • + chorda tympani branch of facial nerve has exact synonym facial VII nerve chorda tympani branch { database cross reference=MA:0001092 }
  • + chorda tympani branch of facial nerve has exact synonym parasympathetic root of submandibular ganglion { database cross reference=FMA:53228 }
  • + chorda tympani branch of facial nerve has exact synonym radix parasympathica ganglii submandibularis { database cross reference=FMA:TA }
  • + chorda tympani branch of facial nerve has related synonym chorda tympani nerve { database cross reference=http://en.wikipedia.org/wiki/Chorda_tympani }
  • + chorda tympani branch of facial nerve has related synonym corda tympani nerve { database cross reference=http://en.wikipedia.org/wiki/Chorda_tympani }
  • + chorda tympani branch of facial nerve has related synonym nervus corda tympani { database cross reference=http://en.wikipedia.org/wiki/Chorda_tympani }
  • + chorda tympani branch of facial nerve has related synonym tympanic cord { database cross reference=http://en.wikipedia.org/wiki/Chorda_tympani }
  • + chorda tympani branch of facial nerve label chorda tympani branch of facial nerve

Changes for: nutrient foramen conduit

• Added
  • + nutrient foramen conduit SubClassOf conduit for some nutrient foramen artery
  • + nutrient foramen conduit SubClassOf conduit for some nutrient foramen vein

Changes for: bolus of food

• Deleted
  • - bolus of food definition Ingested food contained in the esophagus. { database cross reference=http://en.wikipedia.org/wiki/Bolus_(digestion) , database cross reference=FMA:78441 }
• Added
  • + bolus of food SubClassOf located in some esophagus
  • + bolus of food definition Ingested food has been chewed at the point of swallowing. { database cross reference=http://en.wikipedia.org/wiki/Bolus_(digestion) }

Changes for: ingested food

• Added
  • + ingested food SubClassOf located in some upper digestive tract

Changes for: postcentral gyrus

• Deleted
  • - postcentral gyrus has related synonym gyrus postcentralis { database cross reference=NeuroNames:105 , has synonym type=latin term }
• Added
  • + postcentral gyrus has exact synonym gyrus postcentralis { database cross reference=NeuroNames:105 , has synonym type=latin term }

Changes for: pontine reticular formation

• Deleted
  • - pontine reticular formation EquivalentTo reticular formation and part of some pons
  • - pontine reticular formation SubClassOf brainstem reticular formation
  • - pontine reticular formation SubClassOf part of some pons
  • - pontine reticular formation SubClassOf regional part of metencephalon
• Added
  • + pontine reticular formation SubClassOf brain grey matter
  • + pontine reticular formation SubClassOf nuclear complex of neuraxis
  • + pontine reticular formation SubClassOf part of some reticular formation
  • + pontine reticular formation SubClassOf structure with developmental contribution from neural crest

Changes for: medullary reticular formation

• Deleted
  • - medullary reticular formation EquivalentTo reticular formation and part of some medulla oblongata
  • - medullary reticular formation SubClassOf brainstem reticular formation
  • - medullary reticular formation SubClassOf regional part of medulla oblongata
• Added
  • + medullary reticular formation SubClassOf brain grey matter
  • + medullary reticular formation SubClassOf nuclear complex of neuraxis
  • + medullary reticular formation SubClassOf part of some reticular formation
  • + medullary reticular formation SubClassOf structure with developmental contribution from neural crest

Changes for: sciatic notch

• Added
  • + sciatic notch definition Either of two notches on the dorsal border of the hip bone on each side that when closed off by ligaments form the corresponding sciatic foramina. { database cross reference=http://www.merriam-webster.com/medical/sciatic+notch }

Changes for: lesser sciatic notch

• Added
  • + lesser sciatic notch SubClassOf conduit for some obturator internus
  • + lesser sciatic notch SubClassOf conduit for some obturator nerve

Changes for: acetabular notch

• Deleted
  • - acetabular notch definition The acetabulum presents below a deep notch, the acetabular notch, which is continuous with a circular non-articular depression, the acetabular fossa, at the bottom of the cavity: this depression is perforated by numerous apertures, and lodges a mass of fat. The notch is converted into a by the transverse ligament; through the foramen nutrient vessels and nerves enter the joint; the margins of the notch serve for the attachment of the ligament of the head of the femur. { database cross reference=http://en.wikipedia.org/wiki/Acetabular_notch }
• Added
  • + acetabular notch SubClassOf conduit for some ligament of hip joint
  • + acetabular notch definition The acetabulum presents below a deep notch, the acetabular notch, which is continuous with a circular non-articular depression, the acetabular fossa, at the bottom of the cavity: this depression is perforated by numerous apertures, and lodges a mass of fat. The notch is converted into a foramen by the transverse ligament; through the foramen nutrient vessels and nerves enter the joint; the margins of the notch serve for the attachment of the ligament of the head of the femur. { database cross reference=http://en.wikipedia.org/wiki/Acetabular_notch }

Changes for: greater sciatic notch

• Added
  • + greater sciatic notch SubClassOf conduit for some piriformis muscle

Changes for: postnasal wall

• Added
  • + postnasal wall has broad synonym posterior wall of nasal capsule

Changes for: elbow

• Deleted
  • - elbow comment Terminology notes: Naming conventions for pod terms under discussion within phenoscape group
• Added
  • + elbow terminology notes Naming conventions for pod terms under discussion within phenoscape group

Changes for: obsolete tailbud stage

• Deleted
  • - tailbud stage SubClassOf embryo stage
  • - tailbud stage database cross reference XAO:1000007
  • - tailbud stage definition Any of the developmental stages from Nieuwkoop and Faber stage 20 to stage 44 (feeding), including the beginning of hatching (NF stage 35/36). { database cross reference=ISBN:0815318960 }
  • - tailbud stage label tailbud stage
• Added
  • + obsolete tailbud stage comment Was made obsolete as it was xenopus specific
  • + obsolete tailbud stage consider XAO:1000007
  • + obsolete tailbud stage deprecated true
  • + obsolete tailbud stage label obsolete tailbud stage

Changes for: salt gland

• Deleted
  • - salt gland comment Taxon notes: In sharks, salt glands are found in the rectum, but in birds and reptiles, they are found in or on the skull, in the area of the eyes, nostrils or mouth. In crocodiles, the salt is excreted through the tongue. Such glands work by active transport via sodium-potassium pump that moves salt from the blood into the gland, where it can be excreted as a concentrated solution. Salt glands function to keep salt balance, and allow marine vertebrates to drink seawater
• Added
  • + salt gland taxon notes In sharks, salt glands are found in the rectum, but in birds and reptiles, they are found in or on the skull, in the area of the eyes, nostrils or mouth. In crocodiles, the salt is excreted through the tongue. Such glands work by active transport via sodium-potassium pump that moves salt from the blood into the gland, where it can be excreted as a concentrated solution. Salt glands function to keep salt balance, and allow marine vertebrates to drink seawater

Changes for: segmental subdivision of nervous system

• Added
  • + segmental subdivision of nervous system in subset non informative

Changes for: mesovarium

• Added
  • + mesovarium database cross reference MA:0003236

Changes for: Mullerian tubercle

• Added
  • + Mullerian tubercle database cross reference MA:0003239

Changes for: metapodium region

• Deleted
  • - metapodium region comment Terminology notes: Naming conventions for pod terms under discussion within phenoscape group. Editors note: considering adding ‘acropodial region’
• Added
  • + metapodium region editor note considering adding ‘acropodial region’
  • + metapodium region terminology notes Naming conventions for pod terms under discussion within phenoscape group

Changes for: anterior intestinal portal

• Added
  • + anterior intestinal portal SubClassOf part of some foregut-midgut junction

Changes for: interventricular foramen of heart

• Added
  • + interventricular foramen of heart SubClassOf embryonic structure
  • + interventricular foramen of heart SubClassOf part of some embryo
  • + interventricular foramen of heart comment Phenotype notes: In some individuals, the foramen fails to close, leading to an interventricular septal defect known as a patent interventricular foramen
  • + interventricular foramen of heart database cross reference http://en.wikipedia.org/wiki/Primary_interventricular_foramen
  • + interventricular foramen of heart definition A temporary opening between the developing ventricles of the heart. The ventricles arise as a single cavity is divided by the developing interventricular septum. Before the septum closes completely, the remaining opening between the two ventricles is termed the interventricular foramen. { database cross reference=http://en.wikipedia.org/wiki/Primary_interventricular_foramen }
  • + interventricular foramen of heart has related synonym interventricular foramen
  • + interventricular foramen of heart has related synonym primary interventricular foramen { database cross reference=EHDAA2:0004064 }

Changes for: proximal straight tubule

• Added
  • + proximal straight tubule SubClassOf renal straight tubule

Changes for: distal convoluted tubule

• Deleted
  • - distal convoluted tubule SubClassOf distal tubule
  • - distal convoluted tubule SubClassOf part of some region of nephron tubule
  • - distal convoluted tubule editor note This class was created automatically from a combination of ontologies
• Added
  • + distal convoluted tubule SubClassOf distal tubular epithelium
  • + distal convoluted tubule SubClassOf part of some distal tubule

Changes for: thick ascending limb of loop of Henle

• Deleted
  • - thick ascending limb of loop of Henle SubClassOf region of nephron tubule
  • - thick ascending limb of loop of Henle has exact synonym distal straight tubule
• Added
  • + thick ascending limb of loop of Henle SubClassOf renal straight tubule
  • + thick ascending limb of loop of Henle has exact synonym distal straight tubule { database cross reference=MA:0001677 }

Changes for: renal straight tubule

• Deleted
  • - renal straight tubule SubClassOf nephron tubule
  • - renal straight tubule editor note TODO - add relationships
• Added
  • + renal straight tubule SubClassOf region of nephron tubule
  • + renal straight tubule definition Any region of a nephron tubule that is straight. Examples: distal convoluted tubule, proximal convoluted tuble. { database cross reference=UBERON:cjm }
  • + renal straight tubule has exact synonym straight tubule

Changes for: reticular formation

• Deleted
  • - reticular formation SubClassOf regional part of nervous system
  • - reticular formation database cross reference http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2915
• Added
  • + reticular formation SubClassOf anatomical cluster
  • + reticular formation SubClassOf ectoderm-derived structure
  • + reticular formation SubClassOf part of some brainstem
  • + reticular formation database cross reference EMAPA:35188
  • + reticular formation database cross reference MA:0003185
  • + reticular formation database cross reference http://en.wikipedia.org/wiki/Reticular_formation
  • + reticular formation definition The term reticular formation (classical) denotes a composite substructure of the brainstem that consists of the midbrain reticular formation, the pontine reticular formation and the medullary reticular formation ( Carpenter-1983 ). { database cross reference=NeuroNames:1223 }
  • + reticular formation external ontology notes FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure { external ontology=FMA }
  • + reticular formation has exact synonym brain stem reticular formation { database cross reference=NeuroNames:1223 }
  • + reticular formation has exact synonym brainstem reticular formation { database cross reference=MA:0003185 }
  • + reticular formation has exact synonym brainstem reticular formation { database cross reference=NeuroNames:1223 }
  • + reticular formation has exact synonym reticular formation (classical) { database cross reference=NeuroNames:1223 }
  • + reticular formation has exact synonym reticular formation of the brainstem { database cross reference=NeuroNames:1223 }
  • + reticular formation taxon notes It is essential for governing some of the basic functions of higher organisms, and is one of the phylogenetically oldest portions of the brain.

Changes for: entepicondylar foramen

• Deleted
  • - entepicondylar foramen definition The entepicondylar foramen is an opening in the distal (far) end of the humerus (upper arm bone) present in some mammals. It is often present in primitive placentals, such as the enigmatic Madagascan Plesiorycteropus. In most Neotominae and all Tylomyinae among cricetid rodents, it is located above the medial epicondyle of the humerus, but it is absent in all Sigmodontinae and Arvicolinae and this trait has been suggested as a synapomorphy for the former subfamily. { database cross reference=http://en.wikipedia.org/wiki/Entepicondylar_foramen }
• Added
  • + entepicondylar foramen SubClassOf conduit for some brachial artery
  • + entepicondylar foramen SubClassOf conduit for some median nerve
  • + entepicondylar foramen definition A canal through the medial epicondyle at the distal end of the vertebrate humerus, usually traversed by the median nerve and brachial artery. { database cross reference=http://www.jstor.org/discover/10.2307/2422468 }
  • + entepicondylar foramen present in taxon http://purl.obolibrary.org/obo/NCBITaxon_376911
  • + entepicondylar foramen present in taxon http://purl.obolibrary.org/obo/NCBITaxon_37887
  • + entepicondylar foramen present in taxon http://purl.obolibrary.org/obo/NCBITaxon_38624
  • + entepicondylar foramen present in taxon http://purl.obolibrary.org/obo/NCBITaxon_9255
  • + entepicondylar foramen present in taxon http://purl.obolibrary.org/obo/NCBITaxon_9265
  • + entepicondylar foramen present in taxon http://purl.obolibrary.org/obo/NCBITaxon_9322
  • + entepicondylar foramen present in taxon http://purl.obolibrary.org/obo/NCBITaxon_9338
  • + entepicondylar foramen present in taxon http://purl.obolibrary.org/obo/NCBITaxon_9363
  • + entepicondylar foramen present in taxon http://purl.obolibrary.org/obo/NCBITaxon_9369
  • + entepicondylar foramen present in taxon http://purl.obolibrary.org/obo/NCBITaxon_9376
  • + entepicondylar foramen present in taxon http://purl.obolibrary.org/obo/NCBITaxon_9681
  • + entepicondylar foramen present in taxon http://purl.obolibrary.org/obo/NCBITaxon_9709
  • + entepicondylar foramen taxon notes It is often present in primitive placentals, such as the enigmatic Madagascan Plesiorycteropus. In most Neotominae and all Tylomyinae among cricetid rodents, it is located above the medial epicondyle of the humerus, but it is absent in all Sigmodontinae and Arvicolinae and this trait has been suggested as a synapomorphy for the former subfamily.[WP]
  • + entepicondylar foramen taxon notes Primitive amniote feature found in primitive reptil-like amphibians (Romeer) [http://www.jstor.org/discover/10.2307/2422468]

Changes for: central canal of spinal cord

• Added
  • + central canal of spinal cord SubClassOf channel for some cerebrospinal fluid

Changes for: foramen of Panizza

• Deleted
  • - foramen of Panizza comment Taxon notes: Crocodilians have a completely separated ventricle with deoxygenated blood from the body, or systemic circulation, in the right ventricle and oxygenated blood from the lungs, or pulmonary circulation, in the left ventricle, as in birds and mammals. Two vessels, the left aorta and the pulmonary artery, exit the right ventricle. Blood from the right ventricle goes to the lungs through the pulmonary artery, as in mammals and birds. However, when a unique active valve leading to the pulmonary artery contracts, pressure in the right ventricle can increase and blood can leave the right ventricle, enter the left aortic arch, and therefore bypass the pulmonary circulation. The foramen of panizza connects the left and right aorta. Deoxygenated blood from the right ventricle, sitting in the left aorta, can flow into the right aorta through the foramen of panizza. When the heart is relaxed, some oxygenated blood from the left ventricle, sitting in the right aorta, can flow into the left aorta across the foramen of panizza. However, some species of Crocodilians have regulatory sphincters that prevent unwanted flow of blood through the foramen of panizza during non-diving
• Added
  • + foramen of Panizza taxon notes Crocodilians have a completely separated ventricle with deoxygenated blood from the body, or systemic circulation, in the right ventricle and oxygenated blood from the lungs, or pulmonary circulation, in the left ventricle, as in birds and mammals. Two vessels, the left aorta and the pulmonary artery, exit the right ventricle. Blood from the right ventricle goes to the lungs through the pulmonary artery, as in mammals and birds. However, when a unique active valve leading to the pulmonary artery contracts, pressure in the right ventricle can increase and blood can leave the right ventricle, enter the left aortic arch, and therefore bypass the pulmonary circulation. The foramen of panizza connects the left and right aorta. Deoxygenated blood from the right ventricle, sitting in the left aorta, can flow into the right aorta through the foramen of panizza. When the heart is relaxed, some oxygenated blood from the left ventricle, sitting in the right aorta, can flow into the left aorta across the foramen of panizza. However, some species of Crocodilians have regulatory sphincters that prevent unwanted flow of blood through the foramen of panizza during non-diving

Changes for: haversian canal

• Added
  • + haversian canal SubClassOf conduit for some blood vessel

Changes for: vesicular appendage of epoophoron

• Added
  • + vesicular appendage of epoophoron database cross reference EMAPA:18978
  • + vesicular appendage of epoophoron database cross reference MA:0003241
  • + vesicular appendage of epoophoron has exact synonym female cystic vesicular appendage { database cross reference=MA:0003241 }

Changes for: gall bladder

• Deleted
  • - gallbladder definition A small organ that aids digestion and stores bile produced by the liver[WP]. Organ with organ cavity which is continuous proximally with the cystic duct and distally terminates in the fundus of the gallbladder[FMA]. { database cross reference=http://en.wikipedia.org/wiki/Gallbladder , database cross reference=FMA:7202 }
  • - gallbladder has related synonym vesica fellea; vesica biliaris { database cross reference=http://en.wikipedia.org/wiki/Gallbladder , has synonym type=latin term }
  • - gallbladder label gallbladder
• Added
  • + gall bladder definition An organ that aids digestion and stores bile produced by the liver[WP]. { database cross reference=http://en.wikipedia.org/wiki/Gallbladder }
  • + gall bladder has exact synonym gallbladder { database cross reference=FMA:7202 }
  • + gall bladder has related synonym vesica biliaris { database cross reference=http://en.wikipedia.org/wiki/Gallbladder , has synonym type=latin term }
  • + gall bladder has related synonym vesica fellea { database cross reference=http://en.wikipedia.org/wiki/Gallbladder , has synonym type=latin term }
  • + gall bladder label gall bladder

Changes for: esophagus

• Added
  • + esophagus SubClassOf part of some upper digestive tract

Changes for: pterygoid bone

• Added
  • + pterygoid bone database cross reference http://en.wikipedia.org/wiki/Pterygoid_bone

Changes for: stylopod

• Deleted
  • - stylopod comment Terminology notes: Naming conventions for pod terms under discussion within phenoscape group
• Added
  • + stylopod terminology notes Naming conventions for pod terms under discussion within phenoscape group

Changes for: autopod region

• Deleted
  • - autopod region comment Terminology notes: Naming conventions for pod terms under discussion within phenoscape group; note that this refers to the limb segment, not just the skeleton.
• Added
  • + autopod region terminology notes Naming conventions for pod terms under discussion within phenoscape group; note that this refers to the limb segment, not just the skeleton.

Changes for: intertarsale sesamoid

• Deleted
  • - os sesamoides tarsale label os sesamoides tarsale
• Added
  • + intertarsale sesamoid has broad synonym os sesamoides tarsale
  • + intertarsale sesamoid label intertarsale sesamoid

Changes for: subdivision of spinal cord central canal

• Added
  • + subdivision of spinal cord central canal EquivalentTo anatomical conduit and subdivision of some central canal of spinal cord
  • + subdivision of spinal cord central canal SubClassOf subdivision of some central canal of spinal cord

Changes for: primary visual cortex

• Deleted
  • - primary visual cortex SubClassOf part of some occipital lobe
  • - primary visual cortex database cross reference http://en.wikipedia.org/wiki/Visual_cortex
  • - primary visual cortex definition The term area 17 of Brodmann (human) refers to a subdivision of the cytoarchitecturally defined occipital region of cerebral cortex in the human. Defined by the band of Gennari, which gives it the name striate (furrowed) area, it occupies the banks of the calcarine sulcus which are located in the cuneus and the lingual gyrus of the occipital lobe. Cytoarchitecturally it is bounded by the area 18 of Brodmann (human) which surrounds it ( Brodmann-1909 ). In the mouse ( Paxinos-2001 ) and the rat ( Swanson-1998 ) it is located on the dorsolateral surface of the cerebral hemisphere[BrainInfo]. { database cross reference=http://en.wikipedia.org/wiki/Visual_cortex , database cross reference=BrainInfo:2102 }
  • - primary visual cortex has exact synonym area 17 of brodmann-1909 { database cross reference=NIF_GrossAnatomy:birnlex_1748 }
  • - primary visual cortex has exact synonym striate cortex { database cross reference=FMA:236871 }
  • - primary visual cortex has related synonym V1
• Added
  • + primary visual cortex SubClassOf part of some visual cortex
  • + primary visual cortex definition The term area 17 of Brodmann (human) refers to a subdivision of the cytoarchitecturally defined occipital region of cerebral cortex in the human. Defined by the band of Gennari, which gives it the name striate (furrowed) area, it occupies the banks of the calcarine sulcus which are located in the cuneus and the lingual gyrus of the occipital lobe. Cytoarchitecturally it is bounded by the area 18 of Brodmann (human) which surrounds it ( Brodmann-1909 ). In the mouse ( Paxinos-2001 ) and the rat ( Swanson-1998 ) it is located on the dorsolateral surface of the cerebral hemisphere[BrainInfo]. { database cross reference=BrainInfo:2102 }
  • + primary visual cortex external ontology notes We explicitly merge two FMA classes here, as BA17 is equivalent to V1 { external ontology=FMA }
  • + primary visual cortex has exact synonym area 17 of Brodmann-1909 { database cross reference=NIF_GrossAnatomy:birnlex_1748 }
  • + primary visual cortex has exact synonym striate cortex { database cross reference=http://en.wikipedia.org/wiki/Visual_cortex , database cross reference=FMA:236871 }
  • + primary visual cortex has related synonym V1 { database cross reference=http://en.wikipedia.org/wiki/Visual_cortex }
  • + primary visual cortex has related synonym visual area one { database cross reference=http://en.wikipedia.org/wiki/Visual_cortex }

Changes for: intestine secretion

• Deleted
  • - intestine secretion has exact synonym succus entericus
• Added
  • + intestine secretion has exact synonym succus entericus { database cross reference=http://en.wikipedia.org/wiki/Succus_entericus }
  • + intestine secretion has related synonym intestinal juice { database cross reference=BTO:0000644 }

Changes for: upper part of vagina

• Added
  • + upper part of vagina database cross reference MA:0003242
  • + upper part of vagina has exact synonym vagina upper part { database cross reference=MA:0003242 }

Changes for: interventricular foramen of CNS

• Added
  • + interventricular foramen of CNS SubClassOf channel for some cerebrospinal fluid

Changes for: motor root of facial nerve

• Added
  • + motor root of facial nerve has exact synonym motor component of the VIIth (facial) nerve

Changes for: Brodmann (1909) area 19

• Added
  • + Brodmann (1909) area 19 SubClassOf part of some extrastriate cortex
  • + Brodmann (1909) area 19 database cross reference http://en.wikipedia.org/wiki/Brodmann_area_19

Changes for: Brodmann (1909) area 10

• Added
  • + Brodmann (1909) area 10 SubClassOf part of some prefrontal cortex
  • + Brodmann (1909) area 10 database cross reference http://en.wikipedia.org/wiki/Brodmann_area_10

Changes for: Brodmann (1909) area 14

• Added
  • + Brodmann (1909) area 14 SubClassOf part of some prefrontal cortex
  • + Brodmann (1909) area 14 database cross reference http://en.wikipedia.org/wiki/Brodmann_area_14

Changes for: forelimb zeugopod

• Deleted
  • - forelimb zeugopod comment Terminology notes: Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here
• Added
  • + forelimb zeugopod terminology notes Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here

Changes for: pes

• Added
  • + pes has narrow synonym hindfeet { has synonym type=plural term }

Changes for: Brodmann (1909) area 2

• Added
  • + Brodmann (1909) area 2 database cross reference http://en.wikipedia.org/wiki/Brodmann_area_2
  • + Brodmann (1909) area 2 has related synonym postcentral gyrus { database cross reference=http://en.wikipedia.org/wiki/Brodmann_area_2 }

Changes for: Brodmann (1909) area 4

• Added
  • + Brodmann (1909) area 4 database cross reference http://en.wikipedia.org/wiki/Brodmann_area_4

Changes for: blood clot

• Deleted
  • - blood clot has related synonym thrombus { database cross reference=BTO:0000102 }
• Added
  • + blood clot has exact synonym coagulated blood
  • + blood clot has exact synonym fibrin clot
  • + blood clot has exact synonym hemostatic plug { database cross reference=http://en.wikipedia.org/wiki/Thrombus }
  • + blood clot has exact synonym thrombus { database cross reference=BTO:0000102 }
  • + blood clot has narrow synonym clot

Changes for: supraacetabular buttress

• Added
  • + supraacetabular buttress has broad synonym acetabular buttress

Changes for: manus

• Added
  • + manus has narrow synonym forefeet { has synonym type=plural term }

Changes for: rete ovarii

• Added
  • + rete ovarii database cross reference MA:0003237
  • + rete ovarii database cross reference http://en.wikipedia.org/wiki/Rete_ovarii
  • + rete ovarii definition A structure formed from the primary sex cords in females, counterpart of the rete testis in males. { database cross reference=http://en.wikipedia.org/wiki/Rete_ovarii }
  • + rete ovarii has exact synonym rete ovarii of ovary { database cross reference=MA:0003237 }

Changes for: transverse foramen of atlas

• Added
  • + transverse foramen of atlas SubClassOf conduit for some vertebral artery

Changes for: diencephalic part of interventricular foramen

• Added
  • + diencephalic part of interventricular foramen SubClassOf channel for some cerebrospinal fluid

Changes for: metanephric distal convoluted tubule

• Deleted
  • - metanephric distal convoluted tubule SubClassOf metanephric distal tubule
• Added
  • + metanephric distal convoluted tubule SubClassOf metanephric nephron tubule

Changes for: Brodmann (1909) area 24

• Added
  • + Brodmann (1909) area 24 database cross reference http://en.wikipedia.org/wiki/Brodmann_area_24

Changes for: Brodmann (1909) area 3

• Added
  • + Brodmann (1909) area 3 database cross reference http://en.wikipedia.org/wiki/Brodmann_area_3

Changes for: Brodmann (1909) area 36

• Deleted
  • - Brodmann (1909) area 36 has exact synonym area ectorhinalis { database cross reference=NIF_GrossAnatomy:birnlex_1769 }
• Added
  • + Brodmann (1909) area 36 SubClassOf part of some perirhinal cortex
  • + Brodmann (1909) area 36 database cross reference http://en.wikipedia.org/wiki/Brodmann_area_36
  • + Brodmann (1909) area 36 has exact synonym area ectorhinalis { database cross reference=NIF_GrossAnatomy:birnlex_1769 , has synonym type=latin term }

Changes for: Brodmann (1909) area 35

• Added
  • + Brodmann (1909) area 35 SubClassOf part of some perirhinal cortex
  • + Brodmann (1909) area 35 database cross reference http://en.wikipedia.org/wiki/Brodmann_area_35
  • + Brodmann (1909) area 35 taxon notes Brodmann found a cytoarchitecturally homologous area in the monkey (Cercopithecus), but it was so weakly developed that he omitted it from the cortical map of that species (Brodmann-1909).

Changes for: postganglionic parasympathetic nervous system

• Deleted
  • - postganglionic parasympathetic nervous system SubClassOf parasympathetic nervous system
• Added
  • + postganglionic parasympathetic nervous system SubClassOf autonomic nervous system
  • + postganglionic parasympathetic nervous system SubClassOf part of some parasympathetic nervous system
  • + postganglionic parasympathetic nervous system SubClassOf structure with developmental contribution from neural crest

Changes for: preganglionic parasympathetic nervous system

• Deleted
  • - preganglionic parasympathetic nervous system SubClassOf parasympathetic nervous system
• Added
  • + preganglionic parasympathetic nervous system SubClassOf autonomic nervous system
  • + preganglionic parasympathetic nervous system SubClassOf part of some parasympathetic nervous system

Changes for: mediastinum testis

• Added
  • + mediastinum testis database cross reference MA:0003240

Changes for: rectal diverticulum

• Added
  • + rectal diverticulum SubClassOf develops from some embryonic cloaca
  • + rectal diverticulum SubClassOf mesoderm-derived structure
  • + rectal diverticulum SubClassOf part of some pronephros
  • + rectal diverticulum SubClassOf urinary system structure

Changes for: Brodmann (1909) area 18

• Deleted
  • - Brodmann (1909) area 18 has exact synonym visual area ii { database cross reference=FMA:68615 }
• Added
  • + Brodmann (1909) area 18 SubClassOf part of some extrastriate cortex
  • + Brodmann (1909) area 18 function notes interpretation of images[WP]
  • + Brodmann (1909) area 18 has exact synonym visual area II { database cross reference=FMA:68615 }
  • + Brodmann (1909) area 18 has related synonym V2 { database cross reference=http://en.wikipedia.org/wiki/Brodmann_area_18 }
  • + Brodmann (1909) area 18 has related synonym visual area two { database cross reference=http://en.wikipedia.org/wiki/Visual_cortex }

Changes for: superior raphe nucleus

• Added
  • + superior raphe nucleus SubClassOf brainstem nucleus

Changes for: hemopoietic organ

• Deleted
  • - hemopoietic organ editor note consider splitting out lymph organ
• Added
  • + hemopoietic organ editor note consider splitting out lymph organ, compare with lymph node

Changes for: outflow tract

• Added
  • + outflow tract SubClassOf channel for some blood
  • + outflow tract SubClassOf channels from some heart
  • + outflow tract SubClassOf channels into some artery

Changes for: distal tubule

• Deleted
  • - distal tubule definition The distal tubule is a nephron tubule that consists of the convoluted and straight distal tubule segments { database cross reference=GO:0072017 }
• Added
  • + distal tubule definition The distal tubule is a nephron tubule that consists of the distal convoluted tubule and distal straight tubule segments { database cross reference=GO:0072017 }

Changes for: superior reticular formation

• Deleted
  • - superior reticular formation SubClassOf medullary reticular formation
  • - superior reticular formation SubClassOf regional part of medullary reticular formation
• Added
  • + superior reticular formation SubClassOf brain grey matter
  • + superior reticular formation SubClassOf nuclear complex of neuraxis
  • + superior reticular formation SubClassOf structure with developmental contribution from neural crest

Changes for: telencephalic part of interventricular foramen

• Added
  • + telencephalic part of interventricular foramen SubClassOf channel for some cerebrospinal fluid

Changes for: obsolete brainstem reticular formation

• Deleted
  • - brainstem reticular formation EquivalentTo reticular formation and part of some brainstem
  • - brainstem reticular formation SubClassOf part of some brainstem
  • - brainstem reticular formation SubClassOf regional part of brain
  • - brainstem reticular formation SubClassOf reticular formation
  • - brainstem reticular formation database cross reference EMAPA:35188
  • - brainstem reticular formation database cross reference MA:0003185
  • - brainstem reticular formation has related synonym brain stem reticular formation { database cross reference=NeuroNames:1223 }
  • - brainstem reticular formation has related synonym brainstem reticular formation { database cross reference=NeuroNames:1223 }
  • - brainstem reticular formation has related synonym reticular formation of the brainstem { database cross reference=NeuroNames:1223 }
  • - brainstem reticular formation label brainstem reticular formation
• Added
  • + obsolete brainstem reticular formation deprecated true
  • + obsolete brainstem reticular formation label obsolete brainstem reticular formation
  • + obsolete brainstem reticular formation term replaced by UBERON:0002275

Changes for: enteric nervous system

• Deleted
  • - enteric nervous system SubClassOf autonomic nervous system
  • - enteric nervous system definition The enteric nervous system is composed of two ganglionated neural plexuses in the gut wall which form one of the three major divisions of the autonomic nervous system. The enteric nervous system innervates the gastrointestinal tract, the pancreas, and the gall bladder. It contains sensory neurons, interneurons, and motor neurons. Thus the circuitry can autonomously sense the tension and the chemical environment in the gut and regulate blood vessel tone, motility, secretions, and fluid transport. The system is itself governed by the central nervous system and receives both parasympathetic and sympathetic innervation[GO]. { database cross reference=http://en.wikipedia.org/wiki/Enteric_nervous_system }
  • - enteric nervous system editor note This class was created automatically from a combination of ontologies
  • - enteric nervous system has exact synonym PNS - enteric
• Added
  • + enteric nervous system SubClassOf organ system subdivision
  • + enteric nervous system definition The enteric nervous system is composed of two ganglionated neural plexuses in the gut wall which form one of the three major divisions of the autonomic nervous system. The enteric nervous system innervates the gastrointestinal tract, the pancreas, and the gall bladder. It contains sensory neurons, interneurons, and motor neurons. Thus the circuitry can autonomously sense the tension and the chemical environment in the gut and regulate blood vessel tone, motility, secretions, and fluid transport. The system is itself governed by the central nervous system and receives both parasympathetic and sympathetic innervation[GO]. { database cross reference=GO:0048484 }
  • + enteric nervous system external ontology notes most sources classify this as autonomic, but in FMA it is placed directly under nervous system. { external ontology=FMA }
  • + enteric nervous system has exact synonym PNS - enteric { database cross reference=EFO:0000895 }
  • + enteric nervous system has exact synonym enteric PNS { database cross reference=EFO:0000895 }

Changes for: gubernaculum (male or female)

• Deleted
  • - gubernaculum label gubernaculum
• Added
  • + gubernaculum (male or female) has exact synonym gubernaculum { database cross reference=UBERON:cjm }
  • + gubernaculum (male or female) label gubernaculum (male or female)

Changes for: male inguinal canal

• Added
  • + male inguinal canal SubClassOf conduit for some spermatic cord
  • + male inguinal canal SubClassOf contributes to morphology of some male reproductive system
  • + male inguinal canal database cross reference MA:0003256
  • + male inguinal canal has exact synonym inguinal canal of male

Changes for: female inguinal canal

• Added
  • + female inguinal canal SubClassOf conduit for some round ligament of uterus
  • + female inguinal canal database cross reference MA:0003249
  • + female inguinal canal has exact synonym inguinal canal of female

Changes for: cleavage stage

• Added
  • + cleavage stage database cross reference FBdv:00000054

Changes for: life cycle stage

• Added
  • + life cycle stage database cross reference FBdv:00007012

Changes for: transverse foramen

• Added
  • + transverse foramen SubClassOf conduit for some sympathetic nerve plexus
  • + transverse foramen SubClassOf conduit for some vertebral vein

Changes for: anal canal

• Added
  • + anal canal SubClassOf channel for some feces

Changes for: gubernaculum testis

• Added
  • + gubernaculum testis database cross reference MA:0003248
  • + gubernaculum testis has broad synonym gubernaculum { database cross reference=MA:0003248 }

Changes for: mesentery of urinary system

• Added
  • + mesentery of urinary system database cross reference MA:0003233

Changes for: Brodmann (1909) area 1

• Added
  • + Brodmann (1909) area 1 database cross reference http://en.wikipedia.org/wiki/Brodmann_area_1

Changes for: nucleus of midbrain reticular formation

• Deleted
  • - nucleus of midbrain reticular formation EquivalentTo nucleus of midbrain tegmentum and part of some midbrain reticular formation
• Added
  • + nucleus of midbrain reticular formation EquivalentTo neural nucleus and part of some midbrain reticular formation

Changes for: raphe nuclei

• Deleted
  • - raphe nuclei SubClassOf regional part of nervous system
• Added
  • + raphe nuclei SubClassOf regional part of brain

Changes for: parasympathetic nervous system

• Deleted
  • - parasympathetic nervous system SubClassOf autonomic nervous system
• Added
  • + parasympathetic nervous system SubClassOf organ system subdivision

Changes for: sympathetic nervous system

• Deleted
  • - sympathetic nervous system SubClassOf autonomic nervous system
• Added
  • + sympathetic nervous system SubClassOf organ system subdivision

Changes for: vessel

• Added
  • + vessel SubClassOf channel for some bodily fluid

Changes for: parasphenoid flange

• Added
  • + parasphenoid flange has broad synonym parasphenoid wing

Changes for: urorectal septum

• Deleted
  • - urorectal septum database cross reference EMAPA:17212
• Added
  • + urorectal septum database cross reference MA:0003235

Changes for: visual cortex

• Deleted
  • - visual cortex definition Area of the occipital lobe concerned with vision. { database cross reference=MESH:A08.186.211.730.885.213.571.735 }
  • - visual cortex editor note merge with primary visual cortex? FMA and BTO treat as distinct
  • - visual cortex has related synonym V1 { database cross reference=http://en.wikipedia.org/wiki/Visual_cortex }
  • - visual cortex has related synonym striate cortex { database cross reference=MESH:A08.186.211.730.885.213.571.735 }
• Added
  • + visual cortex comment The visual cortex is made up of Brodmann area 17 (the primary visual cortex), and Brodmann area 18 and Brodmann area 19, the extrastriate cortical areas.
  • + visual cortex database cross reference http://en.wikipedia.org/wiki/Visual_cortex
  • + visual cortex definition the part of the cerebral cortex responsible for processing visual information. { database cross reference=http://en.wikipedia.org/wiki/Visual_cortex }

Changes for: vertebral canal

• Added
  • + vertebral canal SubClassOf conduit for some spinal cord

Changes for: inguinal ring

• Deleted
  • - inguinal ring database cross reference EMAPA:19172
• Added
  • + inguinal ring SubClassOf part of some inguinal canal

Changes for: hypoglossal canal

• Deleted
  • - hypoglossal canal SubClassOf anatomical conduit
• Added
  • + hypoglossal canal EquivalentTo anatomical conduit and conduit for some hypoglossal nerve
  • + hypoglossal canal SubClassOf conduit for some hypoglossal nerve
  • + hypoglossal canal SubClassOf foramen of skull
  • + hypoglossal canal SubClassOf mesoderm-derived structure
  • + hypoglossal canal SubClassOf part of some occipital bone
  • + hypoglossal canal database cross reference http://en.wikipedia.org/wiki/Hypoglossal_canal
  • + hypoglossal canal definition The hypoglossal canal is a bony canal in the occipital bone of the skull. { database cross reference=http://en.wikipedia.org/wiki/Hypoglossal_canal }
  • + hypoglossal canal has related synonym canalis nervi hypoglossi { database cross reference=http://en.wikipedia.org/wiki/Hypoglossal_canal , has synonym type=latin term }
  • + hypoglossal canal has related synonym hyperglossal canal { database cross reference=http://en.wikipedia.org/wiki/Hypoglossal_canal }

Changes for: appendix testis

• Deleted
  • - appendix testis comment ‘ is male and thus belongs here. See also ‘vesicular appendage of epoophoron’
  • - appendix testis editor note the label hydatid of morgagni is ambiguous w.r.t male vs female. The ncita structure ‘hydatic of morgani { source=sic }
• Added
  • + appendix testis comment See also ‘vesicular appendage of epoophoron’. TODO: check vesicular appendages
  • + appendix testis database cross reference EMAPA:29304
  • + appendix testis database cross reference MA:0003246
  • + appendix testis editor note the label hydatid of morgagni is ambiguous w.r.t male vs female. The ncita structure ‘hydatic of morgani’ is male and thus belongs here. { source=sic }

Changes for: tunica vaginalis testis

• Added
  • + tunica vaginalis testis database cross reference MA:0003253

Changes for: crus of clitoris

• Deleted
  • - crus of clitoris SubClassOf organ part
  • - crus of clitoris definition The clitoral crura are an internal portion of the clitoris. A single one is called a clitoral crus. They are shaped like an inverted ‘V’ with the vertex of the ‘V’ connecting to the clitoral body. They are near the vestibular bulbs, also known as the clitoral bulbs. They are to the left and right of the urethra, urethral sponge, and vagina and extend back toward the pubic bone. The clitoral crura contain muscles called the ischiocavernosi. ‘Crus’ basically translates as ‘leg’, thus ‘crura’ as ‘legs’. Each clitoral crus connects to the rami of the pubis and the ischium. The crura, like the rest of the clitoris, are composed of two corpus cavernosa muscles, which are made up of erectile tissue. { database cross reference=http://en.wikipedia.org/wiki/Crus_of_clitoris }
  • - crus of clitoris has exact synonym Clitoris crus { database cross reference=FMA:20175 }
• Added
  • + crus of clitoris EquivalentTo crus of penis or clitoris and part of some clitoris
  • + crus of clitoris SubClassOf crus of penis or clitoris
  • + crus of clitoris SubClassOf part of some clitoris
  • + crus of clitoris definition The continuation of the clitoris on each side of the corpus cavernosum, diverging from the body posteriorly and attached to the pubic arch. { database cross reference=http://dictionary.reference.com/browse/crus+of+clitoris }
  • + crus of clitoris has exact synonym clitoris crus { database cross reference=FMA:20175 }
  • + crus of clitoris has related synonym crus clitoris { database cross reference=http://en.wikipedia.org/wiki/Clitoral_crura }

Changes for: tunica albuginea of testis

• Added
  • + tunica albuginea of testis database cross reference MA:0003254

Changes for: appendix epididymis

• Added
  • + appendix epididymis database cross reference MA:0003245

Changes for: suspensory ligament of ovary

• Added
  • + suspensory ligament of ovary database cross reference MA:0003244

Changes for: crus of penis

• Deleted
  • - crus penis SubClassOf organ part
  • - crus penis definition For their anterior three-fourths the corpora cavernosa penis lie in intimate apposition with one another, but behind they diverge in the form of two tapering processes, known as the crura, which are firmly connected to the ischial rami. Traced from behind forward, each crus begins by a blunt-pointed process in front of the tuberosity of the ischium, along the perineal surface of the conjoined (ischiopubic) ramus. Just before it meets its fellow it presents a slight enlargement, named by Georg Ludwig Kobelt (1804-1857) the bulb of the corpus cavernosum penis. Beyond this point the crus undergoes a constriction and merges into the corpus cavernosum proper, which retains a uniform diameter to its anterior end. { database cross reference=http://en.wikipedia.org/wiki/Crus_of_penis }
  • - crus penis label crus penis
• Added
  • + crus of penis EquivalentTo crus of penis or clitoris and part of some penis
  • + crus of penis SubClassOf crus of penis or clitoris
  • + crus of penis SubClassOf part of some penis
  • + crus of penis database cross reference MA:0003255
  • + crus of penis definition the continuation of each corpus cavernosum of the penis, diverging posteriorly to be attached to the pubic arch. { database cross reference=http://medical-dictionary.thefreedictionary.com/crus }
  • + crus of penis label crus of penis

Changes for: renal convoluted tubule

• Added
  • + renal convoluted tubule definition Any region of a nephron tubule that is convoluted. Examples: distal convoluted tubule, proximal convoluted tuble. { database cross reference=UBERON:cjm }
  • + renal convoluted tubule in subset grouping class

Changes for: obturator foramen

• Added
  • + obturator foramen SubClassOf conduit for some obturator artery
  • + obturator foramen SubClassOf conduit for some obturator nerve

Changes for: mesopodium region

• Deleted
  • - mesopodium region comment Terminology notes: Naming conventions for pod terms under discussion within phenoscape group
• Added
  • + mesopodium region terminology notes Naming conventions for pod terms under discussion within phenoscape group

Changes for: autopodial skeleton

• Deleted
  • - autopodial skeleton comment Terminology notes: Naming conventions for pod terms under discussion within phenoscape group
• Added
  • + autopodial skeleton terminology notes Naming conventions for pod terms under discussion within phenoscape group

Changes for: chyme

• Deleted
  • - chyme definition Chyme is a bodily fluid consisting of a liquid substance found in the stomach before passing through the pyloric valve and entering the duodenum. It results from the mechanical and chemical breakdown of a bolus and consists of partially digested food, water, hydrochloric acid, and various digestive enzymes. { database cross reference=http://en.wikipedia.org/wiki/Chyme }
• Added
  • + chyme SubClassOf bodily fluid
  • + chyme SubClassOf located in some upper digestive tract
  • + chyme comment Chyme has a low pH that is countered by the production of bile, helping to further digest food. Chyme is also part liquid and part solid: a thick semifluid mass of partially digested food and digestive secretions that is formed in the stomach and intestine during digestion.
  • + chyme definition A semifluid mass of partly digested food expelled by the stomach into the duodenum. { database cross reference=http://en.wikipedia.org/wiki/Chyme }

Changes for: chyle

• Added
  • + chyle SubClassOf located in some small intestine
  • + chyle SubClassOf produced by some small intestine

Changes for: ejaculatory duct

• Added
  • + ejaculatory duct database cross reference MA:0003247

Report for properties

ObjectProperty objects lost from source: 0

ObjectProperty objects new in target: 1

New ObjectProperty : input of

• input of has obo namespace uberon
• input of database cross reference RO:0002352
• input of shorthand input_of
• input of id input_of
• SubObjectPropertyOf( input of functionally related to )
• input of label input of

Changed ObjectProperty objects: 0

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