Bug fix release

Minor changes in this release.

• Other
  • NT: ventral wall of dorsal aorta
  • Fixed test def on sense organ. Fixes issue #549
  • added TODOs for issue #547 (genitals) - punted til next release
  • facial nerve fixes. Syn addition

Ontology Diff Report

Original Ontology

• IRI: http://purl.obolibrary.org/obo/uberon.owl
• VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-07-31/uberon.owl

New Ontology

• IRI: http://purl.obolibrary.org/obo/uberon.owl
• VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-08-18/uberon.owl

Report for classes

Class objects lost from source: 0

Class objects new in target: 1

New Class : ventral wall of dorsal aorta

• ventral wall of dorsal aorta SubClassOf tissue
• ventral wall of dorsal aorta id UBERON:0018549
• ventral wall of dorsal aorta label ventral wall of dorsal aorta
• ventral wall of dorsal aorta database cross reference EFO:0003699
• ventral wall of dorsal aorta has obo namespace uberon
• ventral wall of dorsal aorta has exact synonym DA-PCV joint { database cross reference=ZFA:0005028 }
• ventral wall of dorsal aorta has related synonym DP joint { database cross reference=ZFA:0005028 }
• ventral wall of dorsal aorta database cross reference ZFA:0005028
• ventral wall of dorsal aorta database cross reference TAO:0005028
• ventral wall of dorsal aorta has related synonym aorta gonad mesonephros region { database cross reference=ZFA:0005028 }
• ventral wall of dorsal aorta has related synonym AGM { database cross reference=ZFA:0005028 }
• ventral wall of dorsal aorta SubClassOf mesoderm-derived structure
• ventral wall of dorsal aorta definition Region where blood progenitor markers are expressed. Probable site of definitive hematopoiesis between 36hpf and 4dpf. { database cross reference=ZFA:0005028 , database cross reference=ZFA:curator }
• ventral wall of dorsal aorta has related synonym DA roof { database cross reference=ZFA:0005028 }
• ventral wall of dorsal aorta has exact synonym dorsal aorta - posterior cardinal vein joint { database cross reference=ZFIN:ZDB-PUB-061227-29 }
• ventral wall of dorsal aorta SubClassOf part of some hematopoietic system
• ventral wall of dorsal aorta SubClassOf part of some dorsal aorta

Changed Class objects: 19

Changes for: ramus hyomandibularis

• Added
  • + ramus hyomandibularis SubClassOf mixed endoderm/mesoderm-derived structure

Changes for: endolymphatic duct

• Deleted
  • - endolymphatic duct external definition Duct that is part of the inner ear and connects to the semicircular canals ending in a pouch.[TAO] { date retrieved=2012-08-14 , external class=TAO:0002194 , ontology=TAO , source=http:en.wikipedia.org/wiki/Endolymphatic_duct }
• Added
  • + endolymphatic duct external definition Duct that is part of the inner ear and connects to the semicircular canals ending in a pouch.[TAO] { date retrieved=2012-08-14 , external class=TAO:0002194 , ontology=TAO , source=http://en.wikipedia.org/wiki/Endolymphatic_duct }

Changes for: lip

• Deleted
  • - lip external definition Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO] { date retrieved=2012-08-14 , external class=TAO:0007006 , ontology=TAO , source=http:www.medterms.com/script/main/art.asp?articlekey=9458 , source=ZFIN:curator }
• Added
  • + lip external definition Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO] { date retrieved=2012-08-14 , external class=TAO:0007006 , ontology=TAO , source=http://purl.obolibrary.org/obo/uberon/http/:www.medterms.com/script/main/art.asp?articlekey=9458 , source=ZFIN:curator }

Changes for: optic choroid

• Added
  • + optic choroid comment AO notes: MP treats posterior uvea and optic choroid as distinct

Changes for: facial nerve

• Deleted
  • - facial nerve EquivalentTo nerve and part of some face
  • - facial nerve SubClassOf part of some face
• Added
  • + facial nerve EquivalentTo nerve and part of some facial muscle
  • + facial nerve SubClassOf mixed endoderm/mesoderm-derived structure
  • + facial nerve SubClassOf part of some facial muscle

Changes for: mouth floor

• Added
  • + mouth floor has exact synonym floor of the oval cavity

Changes for: iris nerve

• Deleted
  • - iris nerve SubClassOf facial nerve
• Added
  • + iris nerve SubClassOf nerve of head region

Changes for: eyelid nerve

• Deleted
  • - eyelid nerve SubClassOf facial nerve
• Added
  • + eyelid nerve SubClassOf nerve of head region

Changes for: gill filament

• Deleted
  • - gill filament definition Portion of tissue that projects outward from the gill and is a thread-like, soft, red respiratory and excretory structure. { database cross reference=http:www.briancoad.com/Dictionary/G.htm , database cross reference=ZFIN:ZDB-PUB-961014-576 }
• Added
  • + gill filament definition Portion of tissue that projects outward from the gill and is a thread-like, soft, red respiratory and excretory structure. { database cross reference=http://www.briancoad.com/Dictionary/G.htm , database cross reference=ZFIN:ZDB-PUB-961014-576 }

Changes for: internal female genitalia

• Added
  • + internal female genitalia comment TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547

Changes for: external female genitalia

• Added
  • + external female genitalia comment TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547

Changes for: external male genitalia

• Added
  • + external male genitalia comment TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547

Changes for: internal male genitalia

• Added
  • + internal male genitalia comment TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547

Changes for: internal genitalia

• Added
  • + internal genitalia comment TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547

Changes for: external genitalia

• Added
  • + external genitalia comment TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547

Changes for: dorsal lateral plate region

• Deleted
  • - dorsal lateral plate region database cross reference EFO:0003699
  • - dorsal lateral plate region database cross reference TAO:0005028
  • - dorsal lateral plate region database cross reference ZFA:0005028
  • - dorsal lateral plate region editor note This class was created automatically from a combination of ontologies
  • - dorsal lateral plate region has exact synonym DA-PCV joint { database cross reference=ZFA:0005028 }
  • - dorsal lateral plate region has exact synonym DLP
  • - dorsal lateral plate region has exact synonym DP joint { database cross reference=ZFA:0005028 }
  • - dorsal lateral plate region has exact synonym dorsal aorta - posterior cardinal vein joint { database cross reference=ZFA:0005028 }
  • - dorsal lateral plate region has exact synonym ventral wall of dorsal aorta
  • - dorsal lateral plate region has related synonym AGM
  • - dorsal lateral plate region has related synonym AGM region
  • - dorsal lateral plate region has related synonym DA roof { database cross reference=ZFA:0005028 }
  • - dorsal lateral plate region has related synonym aorta gonad mesonephros region
  • - dorsal lateral plate region has related synonym aorta-gonads-mesonephros region
• Added
  • + dorsal lateral plate region has exact synonym DLP { database cross reference=XAO:0003051 }
  • + dorsal lateral plate region has related synonym AGM region { database cross reference=XAO:0003051 }
  • + dorsal lateral plate region has related synonym aorta-gonads-mesonephros region { database cross reference=XAO:0003051 }

Changes for: sense organ

• Deleted
  • - sense organ definition An organ that is capable of detection of chemical stimulus involved in sensory perception. { database cross reference=https://orcid.org/0000-0002-6601-2165 }
• Added
  • + sense organ definition An organ that is capable of transducing sensory stimulus to the nervous system. { database cross reference=https://github.com/obophenotype/uberon/issues/549 , database cross reference=https://orcid.org/0000-0002-6601-2165 }

Changes for: swim bladder tunica externa

• Deleted
  • - swim bladder tunica externa definition Multi-tissue structure that is the external layer of the swim bladder that is covered by the peritoneum, and made of elastic fibres and ichthyocol (short needles of collagen). { database cross reference=http:www.briancoad.com/Dictionary/T.htm , database cross reference=ZFA:0001700 }
• Added
  • + swim bladder tunica externa definition Multi-tissue structure that is the external layer of the swim bladder that is covered by the peritoneum, and made of elastic fibres and ichthyocol (short needles of collagen). { database cross reference=http://www.briancoad.com/Dictionary/T.htm , database cross reference=ZFA:0001700 }

Changes for: swim bladder tunica interna

• Deleted
  • - swim bladder tunica interna definition Multi-tissue structure that is the internal layer of the swim bladder and is comprised of thin endoderm and a smooth muscle layer called the muscularis mucosa with longitudinal and circular fibres with some collagen. { database cross reference=http:www.briancoad.com/Dictionary/T.htm }
• Added
  • + swim bladder tunica interna definition Multi-tissue structure that is the internal layer of the swim bladder and is comprised of thin endoderm and a smooth muscle layer called the muscularis mucosa with longitudinal and circular fibres with some collagen. { database cross reference=http://www.briancoad.com/Dictionary/T.htm }

Report for properties

ObjectProperty objects lost from source: 0

ObjectProperty objects new in target: 0

Changed ObjectProperty objects: 0

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