2015-07-24 release

Improvements to branchy structures (nerves and vasculature), overhaul of image URLs
2015-07-24 release image

Ontology Diff Report

  • branching structures
    • Addition axiomatizing of nerves: new innervates and extends_fibers_into relationships
    • Improvements to veins and arteries
    • Added explicit classification in superficial and deep veins
    • vesical arteries
    • NTR: paraumbilical vein. Fixes 1134
  • images
    • multiple wikipedia images were 404 - see issue 720, drseb
    • these have been removed and in many cases new images manually selected
  • Taxon constraints and evolution
    • tagged homology grouping classes
    • New taxon constraints, emphasis on human subset. Issue 703
    • Added wing taxon constraints. Issue 721
  • Misc.
    • obsoleting NMJ (replaced_by the equivalent GO class)
    • placed reproductive structure in grouping_class anti-slim. Issue 1133
    • fixed synonym case. 720 - Changed label of pelvis to ‘pelvic region of trunk’, this better communicates the fact this is not the bony parts
    • NTR: ocular region. Added mereological sum axioms. Fixes 1132
    • axiomatizing breast quadrants
    • NTs: pharyngeal spaces. MGI:cs. Fixes 1131
    • relabeled cervical segments. Added prelim defs. Issue 725

Original Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2015-06-22/uberon.owl

New Ontology

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

Report for classes

Class objects lost from source: 1

Class objects new in target: 19

New Class : nerve of penis

New Class : anterior superior alveolar nerve

New Class : posterior auricular nerve

New Class : nerve innervating pinna

New Class : laryngeal nerve

New Class : middle vesical artery

New Class : paraumbilical vein

New Class : fibular nerve

New Class : glans

New Class : nerve of clitoris

New Class : lower quadrant of breast

New Class : inner quadrant of breast

New Class : quadrant of breast

New Class : upper quadrant of breast

New Class : outer quadrant of breast

New Class : ocular adnexa

New Class : retropharyngeal space

New Class : parapharyngeal space

New Class : peripharyngeal space

Changed Class objects: 165

Changes for: venom gland

Changes for: foramen of skull

Changes for: lateral pterygoid nerve

Changes for: buccal nerve

Changes for: paired limb/fin skeleton

Changes for: early premaxilla

Changes for: right recurrent laryngeal nerve

Changes for: left recurrent laryngeal nerve

Changes for: long ciliary nerve

Changes for: nasociliary nerve

Changes for: short ciliary nerve

Changes for: lacrimal nerve

Changes for: inferior ophthalmic vein

Changes for: superior ophthalmic vein

Changes for: ophthalmic vein

Changes for: infra-orbital canal of maxilla

Changes for: nerve to quadratus femoris

Changes for: sacral nerve plexus

Changes for: masseteric nerve

Changes for: mylohyoid nerve

Changes for: superior alveolar nerve

Changes for: pharyngeal nerve plexus

Changes for: deep temporal nerve

Changes for: superior laryngeal nerve

Changes for: digastric branch of facial nerve

Changes for: infra-orbital groove of maxilla

Changes for: infra-orbital nerve

Changes for: mental nerve

Changes for: infra-orbital foramen of maxilla

Changes for: pudendal nerve

Changes for: perineal nerve

Changes for: inferior cerebral vein

Changes for: central retinal vein

Changes for: vidian nerve

Changes for: medial marginal vein

Changes for: lateral marginal vein

Changes for: vertebral endplate

Changes for: musculocutaneous nerve

Changes for: lingual nerve

Changes for: anterior cerebral artery

Changes for: middle cerebral artery

Changes for: posterior cerebral artery

Changes for: nasion

Changes for: intergluteal cleft

Changes for: medullary cavity of long bone

Changes for: esophageal hiatus

Changes for: fibularis quartus

Changes for: palmar branch of median nerve

Changes for: radial nerve

Changes for: axillary nerve

Changes for: ulnar nerve

  • Deleted
    • - ulnar nerve definition In human anatomy, the ulnar nerve is a nerve which runs near the ulna bone. The ulnar nerve is the largest unprotected nerve in the human body (meaning, unprotected by muscle or bone), and the only unprotected nerve that does not serve a purely sensory function (those nerves specifically meant to perceive changes in the environment, such as nerves in the skin). This nerve is directly connected to the little finger, and the adjacent half of the ring finger, supplying the palmar side of these fingers, including both front and back of the tips, perhaps as far back as the fingernail beds. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Ulnar_nerve }
  • Added

Changes for: recurrent laryngeal nerve

Changes for: splanchnic nerve

Changes for: biceps brachii

Changes for: pectoral appendage

Changes for: interlobular artery

Changes for: paired limb/fin

Changes for: pelvic appendage

Changes for: pit

Changes for: vastus medialis

Changes for: femoral vein

Changes for: inferior vesical artery

Changes for: superior vesical artery

Changes for: common fibular nerve

Changes for: sciatic nerve

Changes for: basilic vein

Changes for: skin of limb

Changes for: skin of thorax

Changes for: skin of neck

Changes for: skin of abdomen

Changes for: skin of pelvis

Changes for: median basilic vein

Changes for: carotid sinus nerve

Changes for: anal column

Changes for: glans penis

Changes for: thick ascending limb of loop of Henle

Changes for: nephron

Changes for: proximal convoluted tubule

Changes for: descending limb of loop of Henle

Changes for: loop of Henle

Changes for: pancreas

Changes for: left outer canthus

Changes for: right outer canthus

Changes for: helicine artery

Changes for: iris nerve

Changes for: marsupium

Changes for: paired limb/fin segment

Changes for: future glans

Changes for: otic notch

  • Deleted
    • - otic notch definition Otic notches are invagination in the posterior margin of the skull roof, one behind each orbit. Such notches are found in labyrinthodonts and some of their immediate ancestors, but not their reptilian descendants. The presence or absence of the otic notches is one of the traits used to separate the amniotes from the amphibian grade tetrapods. The notches have been interpreted as part of an auditory structure, and are often shown holding a tympanum similar to those seen in modern anurans. Analysis of the columella (the stapes in amphibians and reptiles) of labyrinthodonts however indicate it did not function in transmitting low energy vibrations, thus rendering them effectively deaf to airborne sound. The otic notch instead functioned as a spiracle, at least in the early forms. { database cross reference=http://en.wikipedia.org/wiki/Otic_notch }
  • Added
    • + otic notch definition Otic notches are invagination in the posterior margin of the skull roof, one behind each orbit. Such notches are found in labyrinthodonts and some of their immediate ancestors, but not their reptilian descendants. The presence or absence of the otic notches is one of the traits used to separate the amniotes from the amphibian grade tetrapods. { database cross reference=http://en.wikipedia.org/wiki/Otic_notch }
    • + otic notch function notes The notches have been interpreted as part of an auditory structure, and are often shown holding a tympanum similar to those seen in modern anurans. Analysis of the columella (the stapes in amphibians and reptiles) of labyrinthodonts however indicate it did not function in transmitting low energy vibrations, thus rendering them effectively deaf to airborne sound. The otic notch instead functioned as a spiracle, at least in the early forms

Changes for: costal cartilage

Changes for: cephalic vein

Changes for: gall bladder

Changes for: inferior orbital fissure

Changes for: obsolete neuromuscular junction

Changes for: obsolete motor nerve

Changes for: sensory nerve

Changes for: pericardial cavity

Changes for: pouch sphincter

Changes for: dorsal nerve of clitoris

Changes for: dorsal nerve of penis

Changes for: saphenous nerve

Changes for: parietal pleura

Changes for: visceral pleura

Changes for: visceral serous pericardium

Changes for: lymphoid system

Changes for: eyeball of camera-type eye

Changes for: fibrous pericardium

Changes for: pelvic region of trunk

Changes for: serous pericardium

Changes for: superficial epigastric vein

Changes for: right gastric vein

Changes for: left gastric vein

Changes for: epicardium

Changes for: bona-fide anatomical boundary

Changes for: eyebrow

Changes for: saphenous vein

Changes for: paired limb/fin cartilage

Changes for: deferent duct artery

Changes for: reproductive structure

Changes for: orbital fissure

Changes for: renal interlobular vein

Changes for: descending thin limb

Changes for: renal connecting tubule

Changes for: renal collecting system

Changes for: venom

Changes for: C2 segment of cervical spinal cord

Changes for: C3 segment of cervical spinal cord

Changes for: C8 segment of cervical spinal cord

Changes for: C4 segment of cervical spinal cord

Changes for: C5 segment of cervical spinal cord

Changes for: C6 segment of cervical spinal cord

Changes for: C7 segment of cervical spinal cord

Changes for: C1 segment of cervical spinal cord

Changes for: loop of Henle ascending limb thin segment

Changes for: strand of vibrissa hair

Changes for: accessory XI nerve

Changes for: paired limb/fin bud

Changes for: bone of free limb or fin

Changes for: anal canal

Changes for: intertarsal-type crurotarsal joint

  • Deleted
    • - intertarsal-type crurotarsal joint comment The ankle joint of pseudosuchians (including crocodilians) and phytosaurs, passing between the astragalus and calcaneum, is also called crurotarsal joint in the literature.[5][6] In the skeletons of the phytosaurs and most of the pseudosuchians this joint bends around a peg on the astragalus which fits into a socket in the calcaneum (the “crocodile normal” tarsus); only in the skeletons of the ornithosuchid pseudosuchians a peg on the calcaneum fits into a socket in the astragalus (the “crocodile reversed” tarsus).[3] Strictly speaking this ankle isn’t a crurotarsal joint in the previously discussed sense, as it’s situated between the two proximal tarsal bones. However, while calcaneum isn’t fixed to the fibula, the astragalus is fixed to the tibia by a suture and thus in practice it functions as an extension of the crus.[7]
  • Added
    • + intertarsal-type crurotarsal joint taxon notes The ankle joint of pseudosuchians (including crocodilians) and phytosaurs, passing between the astragalus and calcaneum, is also called crurotarsal joint in the literature.[5][6] In the skeletons of the phytosaurs and most of the pseudosuchians this joint bends around a peg on the astragalus which fits into a socket in the calcaneum (the ‘crocodile normal’ tarsus); only in the skeletons of the ornithosuchid pseudosuchians a peg on the calcaneum fits into a socket in the astragalus (the ‘crocodile reversed’ tarsus).[3] Strictly speaking this ankle isn’t a crurotarsal joint in the previously discussed sense, as it’s situated between the two proximal tarsal bones. However, while calcaneum isn’t fixed to the fibula, the astragalus is fixed to the tibia by a suture and thus in practice it functions as an extension of the crus.[7]

Changes for: nasopalatine nerve

Changes for: great auricular nerve

Changes for: gastric vein

Changes for: renal efferent arteriole

Changes for: renal afferent arteriole

Changes for: dorsal root ganglion

Changes for: hypoblast (generic)

Changes for: simple eye with multiple lenses

Changes for: superficial fibular nerve

Changes for: lower inner quadrant of breast

Changes for: upper inner quadrant of breast

Changes for: insect leg

Changes for: chemosensory system

Changes for: paired limb/fin field

Changes for: inner canthus

Changes for: glans clitoris

Changes for: obturator nerve

Changes for: superior orbital fissure

Changes for: transverse palatine suture

Changes for: adrenal/interrenal gland

Changes for: deep fibular nerve

Changes for: efferent nerve

Changes for: outer canthus

Changes for: upper outer quadrant of breast

Changes for: lower outer quadrant of breast

Report for properties

ObjectProperty objects lost from source: 0

ObjectProperty objects new in target: 4

New ObjectProperty : in_innermost_side_of

New ObjectProperty : immediately_anterior_to

New ObjectProperty : immediately_posterior_to

New ObjectProperty : in_outermost_side_of

Changed ObjectProperty objects: 0

July 24, 2015 |

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