2016-07-14 release

New release for BgeeDb and Phenoscape, multiple new species-specific stage ontologies included in composite-metazoan.
2016-07-14 release image

Ontology Diff Report

  • Composite-Metazoan
    • Addition of multiple new species-specific stage ontologies from Bgee
  • Lexical
    • Ensuring capitalization only used for proper nouns, see for https://github.com/cmungall/capital-offence/issues/1
  • Evo
    • added taxon GCI for platypus trigeminal electroreception.
    • relaxed TC on genital tubercle (undifferentiated). Fixes 1230
    • relaxed TC on pleura. Fixes 1231
    • Made clavicle-bone is-a shoulder-bone a tetrapod-specific axiom. Fixes 1227
    • duodenum never in danio
  • Xrefs
    • removing unused relation stanza, that has conflicting ID mapping. Fixes 1237 1236
    • Changed FMA xref for periodontium. Fixes 1233
    • xrefs for adult mammal kidney. 1232
    • xref for human zygote stage. Fixes 1238
  • New
    • NT diaphragmaticus muscle fixes 1229
    • NT: tracheoesophageal fold, septum
    • NT: suglottis
    • NT: larval pectoral fin

Original Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2016-06-12/uberon.owl

New Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2016-07-14/uberon.owl

Report for classes

Class objects lost from source: 0

Class objects new in target: 6

New Class : larval pectoral fin

New Class : larval pelvic fin

New Class : subglottis

New Class : tracheoesophageal fold

New Class : tracheoesophageal septum

New Class : diaphragmaticus muscle

Changed Class objects: 278

Changes for: clavicle bone

Changes for: ventral tegmental nucleus

Changes for: arm skin

Changes for: lateral globus pallidus

Changes for: medial globus pallidus

Changes for: metacarpal bone of digit 1

Changes for: axon tract

Changes for: submucosa of urinary bladder

Changes for: manual digit 1 phalanx

Changes for: cardiac Purkinje fiber

Changes for: pectoralis major

Changes for: hypopharynx

Changes for: forelimb zeugopod

Changes for: manual digit blood vessel

Changes for: pes blood vessel

Changes for: manus blood vessel

Changes for: hindlimb skin

Changes for: forelimb skin

Changes for: arm blood vessel

Changes for: forelimb blood vessel

Changes for: hindlimb blood vessel

Changes for: periventricular zone of hypothalamus

Changes for: medial zone of hypothalamus

Changes for: lateral zone of hypothalamus

Changes for: midbrain cerebral aqueduct

Changes for: telencephalic ventricle

Changes for: endopiriform nucleus

Changes for: arm connective tissue

Changes for: elbow connective tissue

Changes for: skin of forearm

Changes for: arm nerve

Changes for: limb

Changes for: pontine nuclear group

Changes for: gracile nucleus

Changes for: left hepatic artery

Changes for: right hepatic artery

Changes for: tail intervertebral disc

Changes for: manus nerve

Changes for: pes nerve

Changes for: duodenum

Changes for: forelimb nerve

Changes for: hindlimb nerve

Changes for: urethra urothelium

Changes for: inner renal medulla loop of Henle

Changes for: kidney pelvis urothelium

Changes for: arm bone

Changes for: forelimb zeugopod bone

Changes for: hindlimb bone

Changes for: parvocellular oculomotor nucleus

Changes for: dorsal tegmental nucleus

Changes for: oviduct epithelium

Changes for: nucleus intercalatus

Changes for: Brodmann (1909) area 2

Changes for: Brodmann (1909) area 8

Changes for: interpolar part of spinal trigeminal nucleus

Changes for: posterior leaflet of mitral valve

Changes for: intercalated amygdaloid nuclei

Changes for: Brodmann (1909) area 20

Changes for: Brodmann (1909) area 19

Changes for: Brodmann (1909) area 23

Changes for: Brodmann (1909) area 27

Changes for: olfactory nerve

Changes for: Brodmann (1909) area 10

Changes for: Brodmann (1909) area 9

Changes for: middle cerebral artery

Changes for: adductor longus

Changes for: caudal pontine reticular nucleus

Changes for: vestibulocochlear nerve

Changes for: cecum mucosa

Changes for: facial nerve

Changes for: duodenal mucosa

Changes for: hypoglossal nerve

Changes for: cerebellopontine angle

Changes for: magnocellular part of red nucleus

Changes for: parvocellular part of red nucleus

Changes for: genu of facial nerve

Changes for: frontal pole

Changes for: Hadjikhani et al. (1998) visuotopic partition scheme region

Changes for: theca interna

Changes for: muscle of pes

Changes for: Tootell and Hadjikhani (2001) LOC/LOP complex

Changes for: Press, Brewer, Dougherty, Wade and Wandell (2001) visuotopic area V7

Changes for: predorsal bundle

Changes for: zygote stage

Changes for: allocortex

Changes for: ventral pallidum

Changes for: crypt of Lieberkuhn of appendix

Changes for: crypt of Lieberkuhn of colon

Changes for: anteroventral cochlear nucleus

Changes for: muscle of manus

Changes for: skin of pes

Changes for: caudal part of spinal trigeminal nucleus

Changes for: ventral supraoptic decussation

Changes for: rhinal sulcus

Changes for: motor nucleus of trigeminal nerve

Changes for: dorsolateral fasciculus of medulla

Changes for: islet of Langerhans

Changes for: spongiose part of urethra

Changes for: auditory cortex

Changes for: renal glomerulus

Changes for: adult mammalian kidney

Changes for: metanephros

Changes for: ulnar artery

Changes for: isthmus of cingulate gyrus

Changes for: intralaminar nuclear group

Changes for: radial artery

Changes for: intermediate periventricular nucleus

Changes for: metathalamus

Changes for: renal corpuscle

Changes for: white matter lamina of cerebellum

Changes for: paraaortic body

Changes for: glomerular capsule

Changes for: dorsal tegmental nucleus pars dorsalis

Changes for: dorsal tegmental nucleus pars ventralis

Changes for: crypt of Lieberkuhn of small intestine

Changes for: pontine reticular formation

Changes for: decussation of superior cerebellar peduncle

Changes for: adventitia of ureter

Changes for: oral part of spinal trigeminal nucleus

Changes for: loop of Henle

Changes for: renal column

Changes for: Bowman’s space

Changes for: limbic lobe

Changes for: medial part of ventral lateral nucleus

Changes for: preoptic periventricular nucleus

Changes for: female external urethral sphincter

Changes for: male external urethral sphincter

Changes for: cleidocephalicus muscle

Changes for: lateral wall of nasopharynx

Changes for: superficial middle cerebral vein

Changes for: levator claviculae muscle

Changes for: lateral wall of oropharynx

Changes for: axillary tail of breast

Changes for: habenular commissure

Changes for: parafascicular nucleus

Changes for: tuberomammillary nucleus

Changes for: crypt of Lieberkuhn

Changes for: crypt of Lieberkuhn of large intestine

Changes for: papillary layer of dermis

Changes for: medial habenular nucleus

Changes for: substantia nigra pars compacta

Changes for: substantia nigra pars reticulata

Changes for: Sylvian cistern

Changes for: cavernous artery

Changes for: minor vestibular gland

Changes for: major vestibular gland

Changes for: calcarine artery

Changes for: cerebral hemisphere

Changes for: nucleus of diagonal band

Changes for: minor salivary gland

  • Deleted
    • - minor salivary gland comment There are over 600 minor salivary glands located throughout the oral cavity within the lamina propria of the oral mucosa. They are 1-2mm in diameter and unlike the other glands, they are not encapsulated by connective tissue only surrounded by it. The gland is usually a number of acini connected in a tiny lobule. A minor salivary gland may have a common excretory duct with another gland, or may have its own excretory duct. Their secretion is mainly mucous in nature (except for Von Ebner’s glands) and have many functions such as coating the oral cavity with saliva[WP].
  • Added
    • + minor salivary gland comment There are over 600 minor salivary glands located throughout the oral cavity within the lamina propria of the oral mucosa. They are 1-2mm in diameter and unlike the other glands, they are not encapsulated by connective tissue only surrounded by it. The gland is usually a number of acini connected in a tiny lobule. A minor salivary gland may have a common excretory duct with another gland, or may have its own excretory duct. Their secretion is mainly mucous in nature (except for von Ebner’s glands) and have many functions such as coating the oral cavity with saliva[WP].

Changes for: tracheal mucosa

Changes for: hindlimb stylopod

Changes for: epiglottis

Changes for: colonic epithelium

Changes for: oral pontine reticular nucleus

Changes for: substantia nigra pars lateralis

Changes for: malleus bone

Changes for: pharyngeal mucosa

Changes for: adductor brevis

Changes for: artery wall

Changes for: bronchial mucosa

Changes for: periodontium

Changes for: vagus nerve

Changes for: maxillary sinus

Changes for: septum of telencephalon

Changes for: wall of crypt of Lieberkuhn of large intestine

Changes for: base of crypt of Lieberkuhn of large intestine

Changes for: spinal nucleus of trigeminal nerve

Changes for: mesencephalic nucleus of trigeminal nerve

Changes for: nasopharynx

Changes for: medial vestibular nucleus

Changes for: oropharynx

Changes for: pharyngeal tonsil

Changes for: fascia of Scarpa

Changes for: periodontal ligament

Changes for: cardiac endomysium

Changes for: median lobe of prostate

Changes for: differentiated genital tubercle

Changes for: mentomeckelian

Changes for: operculum of brain

Changes for: anterior meningeal artery

Changes for: anterior commissure

Changes for: stomach

Changes for: pleura

Changes for: patagialis muscle

Changes for: circumflex branch of left coronary artery

Changes for: sphenoparietal suture

Changes for: sphenofrontal suture

Changes for: sensory root of trigeminal nerve

Changes for: pre-Botzinger complex

Changes for: hyaloid canal

Changes for: cleidooccipital muscle

Changes for: stria medullaris

Changes for: outer renal medulla loop of Henle

Changes for: renal medulla loop of Henle

Changes for: pole of cerebral hemisphere

Changes for: granular insular cortex

Changes for: agranular insular cortex

Changes for: short head of biceps brachii

Changes for: atretic follicle of ovary

Changes for: Hadjikhani et al. (1998) visuotopic area V2d

Changes for: os clitoris

  • Deleted
    • - os clitoris definition The ossified region of endochondral and membranous bone located in the clitoris of most mammals except humans;it is homologous to the penile bone (aka as baculum, penis bone or os penis) in male mammals { database cross reference=MP:0011849 }
  • Added
    • + os clitoris definition The ossified region of endochondral and membranous bone located in the clitoris of most mammals except humans; it is homologous to the penile bone (aka as baculum, penis bone or os penis) in male mammals { database cross reference=MP:0011849 }

Changes for: processus ventrolateralis of thoracic vertebra

Changes for: processus ventralis of thoracic vertebra

Changes for: ligamentum arteriosum

Changes for: descending thin limb

Changes for: subclavius

Changes for: horizontal limb of the diagonal band

Changes for: hemispheric lobule VIII

Changes for: vertical limb of the diagonal band

Changes for: nucleus of midbrain reticular formation

Changes for: sternal end of clavicle

Changes for: lower leg nerve

Changes for: upper leg nerve

Changes for: upper arm nerve

Changes for: lower arm nerve

Changes for: gastrointestinal system smooth muscle

Changes for: respiratory system smooth muscle

Changes for: muscular coat of vas deferens

Changes for: central vein of liver

Changes for: kidney pyramid

Changes for: upper leg skin

Changes for: lower leg skin

Changes for: upper arm skin

Changes for: definitive endoderm

Changes for: abdominal internal oblique muscle

Changes for: atrial septum primum

Changes for: atrial septum secundum

Changes for: lumbar artery

Changes for: accessory hemiazygos vein

Changes for: dentate gyrus granule cell layer

Changes for: cerebellum vermis lobule I

Changes for: lobule simplex

Changes for: interthalamic adhesion

Changes for: spinal vein

Changes for: outer medulla inner stripe loop of Henle

Changes for: outer medulla outer stripe loop of Henle

Changes for: left ventricle myocardium

Changes for: right ventricle myocardium

Changes for: superficial palmar arch

Changes for: thoracic vertebra 4

Changes for: thoracic vertebra 1

Changes for: sacral vertebra 4

Changes for: thoracic vertebra 3

Changes for: thoracic vertebra 2

Changes for: sacral vertebra 1

Changes for: sacral vertebra 3

Changes for: sacral vertebra 2

Changes for: thoracic vertebra 12

Changes for: thoracic vertebra 7

Changes for: thoracic vertebra 11

Changes for: thoracic vertebra 10

Changes for: thoracic vertebra 6

Changes for: thoracic vertebra 5

Changes for: saphenous artery

Changes for: mandible neck

Changes for: mandible head

Changes for: tricuspid valve cusp

Changes for: muscular coat of seminal vesicle

Changes for: mandible temporal crest

Changes for: aorta wall

Changes for: synovial membrane of synovial joint

Changes for: stratum spinosum of epidermis

Changes for: raphe nuclei

Changes for: cardiac atrium

Changes for: cuneate fasciculus

Changes for: epididymis epithelium

Changes for: undifferentiated genital tubercle

Changes for: Hadjikhani et al. (1998) visuotopic area V3

Changes for: Hadjikhani et al. (1998) visuotopic area V2v

Changes for: Hadjikhani et al. (1998) visuotopic area V8

Changes for: Hadjikhani et al. (1998) visuotopic area V4v

Changes for: Hadjikhani et al. (1998) visuotopic area VP

Changes for: Hadjikhani et al. (1998) visuotopic area V3A

Changes for: limitans nucleus

Changes for: Hadjikhani et al. (1998) visuotopic area V1d

Changes for: calcarine sulcus (ventral)

Changes for: Hadjikhani et al. (1998) visuotopic area V1v

Report for properties

ObjectProperty objects lost from source: 1

ObjectProperty objects new in target: 0

Changed ObjectProperty objects: 3

Changes for: develops_from

Changes for: has part

Changes for: has developmental contribution from

July 14, 2016 |

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