2014-07-15 release

Fixes for Phenoscape and BGee
2014-07-15 release image

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

New Class : facial nerve canal

New Class : vidian nerve

New Class : ligament of hip joint

New Class : ethmoid foramen

New Class : lacteal

New Class : male inguinal ring

New Class : female superficial inguinal ring

New Class : female deep inguinal ring

New Class : crus of penis or clitoris

New Class : obsolete spinal cord reticular formation

New Class : foramen of nasal bone

New Class : female inguinal ring

Changed Class objects: 131

Changes for: notochordal canal

Changes for: anal fin basal cartilage

Changes for: internal acoustic meatus

Changes for: mesorchium

Changes for: acoelous

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

Changes for: lower pharyngobranchial toothplate

Changes for: epidermal egg tooth

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

Changes for: vidian canal

Changes for: sallet

Changes for: processus ventralis of thoracic vertebra

Changes for: processus ventrolateralis of thoracic vertebra

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

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

Changes for: foramen ovale of skull

Changes for: midbrain reticular formation

Changes for: lower part of vagina

Changes for: 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

Changes for: nutrient foramen conduit

Changes for: bolus of food

Changes for: ingested food

Changes for: postcentral gyrus

Changes for: pontine reticular formation

Changes for: medullary reticular formation

Changes for: sciatic notch

Changes for: lesser sciatic notch

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

Changes for: greater sciatic notch

Changes for: postnasal wall

Changes for: elbow

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

Changes for: 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

Changes for: mesovarium

Changes for: Mullerian tubercle

Changes for: metapodium region

Changes for: anterior intestinal portal

Changes for: interventricular foramen of heart

Changes for: proximal straight tubule

Changes for: distal convoluted tubule

Changes for: thick ascending limb of loop of Henle

Changes for: renal straight tubule

Changes for: reticular formation

Changes for: entepicondylar foramen

Changes for: central canal of spinal cord

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

Changes for: vesicular appendage of epoophoron

Changes for: gall bladder

Changes for: esophagus

Changes for: pterygoid bone

Changes for: stylopod

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

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

Changes for: subdivision of spinal cord central canal

Changes for: primary visual cortex

Changes for: intestine secretion

Changes for: upper part of vagina

Changes for: interventricular foramen of CNS

Changes for: motor root of facial nerve

Changes for: Brodmann (1909) area 19

Changes for: Brodmann (1909) area 10

Changes for: Brodmann (1909) 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

Changes for: Brodmann (1909) area 2

Changes for: Brodmann (1909) area 4

Changes for: blood clot

Changes for: supraacetabular buttress

Changes for: manus

Changes for: rete ovarii

Changes for: transverse foramen of atlas

Changes for: diencephalic part of interventricular foramen

Changes for: metanephric distal convoluted tubule

Changes for: Brodmann (1909) area 24

Changes for: Brodmann (1909) area 3

Changes for: Brodmann (1909) area 36

Changes for: Brodmann (1909) area 35

Changes for: postganglionic parasympathetic nervous system

Changes for: preganglionic parasympathetic nervous system

Changes for: mediastinum testis

Changes for: rectal diverticulum

Changes for: Brodmann (1909) area 18

Changes for: superior raphe nucleus

Changes for: hemopoietic organ

Changes for: outflow tract

Changes for: distal tubule

Changes for: superior reticular formation

Changes for: telencephalic part of interventricular foramen

Changes for: obsolete brainstem reticular formation

Changes for: enteric nervous system

Changes for: gubernaculum (male or female)

Changes for: male inguinal canal

Changes for: female inguinal canal

Changes for: cleavage stage

Changes for: life cycle stage

Changes for: transverse foramen

Changes for: anal canal

Changes for: gubernaculum testis

Changes for: mesentery of urinary system

Changes for: Brodmann (1909) area 1

Changes for: nucleus of midbrain reticular formation

Changes for: raphe nuclei

Changes for: parasympathetic nervous system

Changes for: sympathetic nervous system

Changes for: vessel

Changes for: parasphenoid flange

Changes for: urorectal septum

Changes for: visual cortex

Changes for: vertebral canal

Changes for: inguinal ring

Changes for: hypoglossal canal

Changes for: appendix testis

Changes for: tunica vaginalis testis

Changes for: crus of clitoris

Changes for: tunica albuginea of testis

Changes for: appendix epididymis

Changes for: suspensory ligament of ovary

Changes for: crus of penis

Changes for: renal convoluted tubule

Changes for: obturator foramen

Changes for: mesopodium region

Changes for: autopodial skeleton

Changes for: chyme

Changes for: chyle

Changes for: ejaculatory duct

Report for properties

ObjectProperty objects lost from source: 0

ObjectProperty objects new in target: 1

New ObjectProperty : input of

Changed ObjectProperty objects: 0

July 15, 2014 |

Comments Section

Feel free to comment on the post but keep it clean and on topic.

comments powered by Disqus

logo Uberon is an integrated cross-species ontology covering anatomical structures in animals. See the about page for more info.

github.com/obophenotype/uberon
 

Google+