2015-01-01 release

This release encompasses multiple improvements in the representation of the nervous system, as well as improvements in textual definitions previously sourced from Wikipedia
2015-01-01 release image

Summary

This release encompasses multiple imrpovements in the representation of the nervous system. Many wikipedia-sourced definitions have been replaced with definitions from neurolex (632). We have defined and implemented a design pattern for cranial and spinal nerves, ganglia and nuclei (634). We made improvements to the mapping to Allen ontologies. Additionally, we now use the numeric identifiers for all Allen classes, rather than acronyms. Please note that the “ABA” prefix has been superseded by “MBA” (mouse brain atlas), to be consistent with the others (HBA, PBA, DMBA, DHBA). New terms were added from the HarvardOxford Cortical atlas based on work by Russ Poldrack and Trish Whetzel (630).

This release also ensures that every class from NIF_GrossAnatomy (but not its successor, neurolex) is represented in Uberon. Note that not all classes will be in the bridge file. Many of the region-part-of-X classes are present in Uberon as obsolete classes.

Changes

  • neuro
    • cranial nerve & ganglia improvements. Fixes issue 634
    • spinal nerves: nerve roots now neutral w.r.t. CNS/PNS
    • NTs for taste buds
    • Fixes to developing neural tube / CNS
    • NTs: forceps major & minor. Issue issue 630
    • Syn for basolateral amygdala. Issue issue 630
    • Replaced multiple wikipedia definitions with ones from neurolex
    • Realigned with nlx and allen atlases
    • added remaining nifstd classes. Note many may be obsoleted in future. See issue 632
    • Obsoleted multiple regional-part-of-X terms. issue 632
    • replaced all NIF_GrossAnatomy prefixes with NIFSTD. See issue issue 632
    • NT: palatal taste bud. Refined taste bud axioms. Merged some new nifstd predominant part terms
    • merging Vestibulocochlear nerve, root + nerve fiber bundle. Issue issue 300
    • NTs for rostral ACC and olfactory EC and primary OC
    • merging nifstd superior olive & SOC. Issue issue 300
    • Refactored SOC, fixes issue 631
    • entorhinal complex layers, ref doi:10.1155/2008/381243
    • NTs, cingula. Issue issue 630
    • NTs, corona radiata parts. Issue issue 630
    • new MBA alignment (was ABA). Issue issue 609.
    • NTs from HarvardOxford-Cortial atlas, via Russ Poldrack, Trish Whetzel. Rows 11-18. Issue issue 630
    • Mapped Allen Brain xrefs from acronyms to IDs. Issue issue 609
    • Fixed multiple incorrect BAMS xrefs
  • skeletal
    • added meckelian bone and meckelian foramen [adececchi]
    • added hypophysial region [adececchi]
  • embryonic/reproductive
    • removing taxon constraint on extra-embryonic membrane, as yolk sacs are found in anamniotes. Fixes issue 635
    • oviduct fixes
    • vitelline vasculature improvement
  • other
    • Using nlx and mp for definition sources replacing select WP defs issue 633
    • mandibular gland - improved defs sourced from MP, tax constr sourced from Bgee, more precise developmental lineage
    • Improvements to:
      • ligaments
      • vertebral arches
      • reproductive system development. NTs: gubernacular bulb parts
      • heart and veins. NTs: inflow tracts

Ontology Diff Report

Original Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2014-12-09/uberon.owl

New Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2015-01-01/uberon.owl

Report for classes

Class objects lost from source: 3

Class objects new in target: 546

New Class : obsolete regional part of trapezoid nuclear complex

New Class : obsolete predominantly gray regional part of pretectal region

New Class : obsolete superficial feature part of hypophysis

New Class : obsolete regional part of cingulate gyrus

New Class : obsolete regional part of outer ear

New Class : obsolete regional part of basilar membrane

New Class : obsolete predominantly gray regional part of temporal lobe

New Class : regional part of lumbar spinal cord white matter

New Class : obsolete predominantly gray regional part of pontine reticular formation

New Class : paravermic Lobule III

New Class : paravermic Lobule II

New Class : paravermic Lobule VII

New Class : paravermic Lobule VIII

New Class : paravermic Lobule IX

New Class : paravermic Lobule IV

New Class : paravermic Lobule VI

New Class : paravermic Lobule V

New Class : obsolete predominantly gray regional part of dentate nucleus

New Class : medial precentral sulcus

New Class : obsolete regional part of posterior superior frontal sulcus

New Class : inferior Parietal Sulcus

New Class : transverse parietal sulcus

New Class : superior parietal sulcus

New Class : angular sulcus

New Class : thalamic Fiber Tracts

New Class : obsolete regional part of hippocampal formation

New Class : intermediate frontal sulcus

New Class : obsolete predominantly gray regional part of hypothalamus

New Class : obsolete regional part of substantia nigra

New Class : Hadjikhani et al. (1998) visuotopic partition scheme region

New Class : regional part of cervical spinal cord white matter

New Class : inferior Sagittal Sulcus

New Class : superior Sagittal Sulcus

New Class : obsolete regional part of calcarine sulcus

New Class : obsolete regional part of anterior commissure

New Class : obsolete predominantly white regional part of fornix

New Class : Ongur, Price, and Ferry (2003) prefrontal cortical partition scheme region

New Class : Tootell and Hadjikhani (2001) LOC/LOP complex

New Class : Press, Brewer, Dougherty, Wade and Wandell (2001) Visuotopic area V7

New Class : obsolete predominantly gray regional part of intermediate hypothalamic region

New Class : obsolete regional part of organ cavity

New Class : obsolete superficial feature part of temporal lobe

New Class : obsolete regional part of solitary nucleus

New Class : sacral spinal cord ventral horn

New Class : pericalcarine cortex

New Class : regional part of a lobe of the cerebellum

New Class : obsolete regional part of septum

New Class : obsolete regional part of body system

New Class : posterior superior frontal sulcus

New Class : anterior parahippocampal gyrus

New Class : occipital fusiform gyrus

New Class : inferior lateral occipital cortex

New Class : superior lateral occipital cortex

New Class : obsolete predominantly gray part of basal amygdaloid nucleus

New Class : posterior temporal fusiform gyrus

New Class : paracingulate gyrus

New Class : temporal fusiform gyrus

New Class : anterior temporal fusiform gyrus

New Class : posterior parahippocampal white matter

New Class : regional part of sacral spinal cord white matter

New Class : obsolete predominantly gray regional part of basal nuclear complex

New Class : obsolete regional part of lateral amygdaloid nucleus

New Class : obsolete regional part of caudate nucleus

New Class : obsolete predominantly gray regional part of dentate gyrus

New Class : obsolete predominantly gray regional part of substantia nigra

New Class : obsolete predominantly white regional part of septum pellucidum

New Class : obsolete superficial feature part of posterior hypothalamic region

New Class : obsolete predominantly gray regional part of Preoptic area

New Class : obsolete predominantly white regional part of posterior hypothalamic region

New Class : temporal cortex cingulum

New Class : posterior corona radiata

New Class : cingulate cortex cingulum

New Class : anterior corona radiata

New Class : superior corona radiata

New Class : sagulum nucleus

New Class : supragenual nucleus

New Class : obsolete predominantly gray regional part of septal nuclear complex

New Class : obsolete predominantly gray regional part of limbic lobe

New Class : pontocerebellar tract

New Class : temporal part of superior longitudinal fasciculus

New Class : obsolete predominantly gray regional part of habenula

New Class : obsolete regional part of inferior frontal gyrus

New Class : obsolete predominantly white regional part of red nucleus

New Class : posterodorsal nucleus of medial geniculate body

New Class : obsolete predominantly white regional part of epithalamus

New Class : obsolete regional part of temporal lobe

New Class : obsolete predominantly gray regional part of red nucleus

New Class : primary olfactory cortex

New Class : regional part of lumbar spinal cord

New Class : olfactory entorhinal cortex

New Class : primary superior olive

New Class : dorsal periolivary nucleus

New Class : rostral anterior cingulate cortex

New Class : obsolete regional part of hypophysis

New Class : hippocampus cortex cingulum

New Class : obsolete simian fossa (macaque)

New Class : obsolete regional part of cerebral white matter

New Class : obsolete predominantly gray regional part of occipital lobe

New Class : obsolete regional part of neuraxis cavity

New Class : obsolete predominantly gray regional part of medial geniculate body

New Class : obsolete predominantly gray regional part of oculomotor nuclear complex

New Class : obsolete predominantly gray regional part of midbrain reticular formation

New Class : obsolete predominantly gray regional part of ventral nuclear group

New Class : cervical spinal cord gray commissure

New Class : obsolete predominantly white regional part of globus pallidus

New Class : obsolete regional part of globus pallidus

New Class : obsolete predominantly gray regional part of neostriatum

New Class : lumbar spinal cord gray matter

New Class : obsolete predominantly gray regional part of lateral nuclear group

New Class : obsolete predominantly gray regional part of medial dorsal nucleus

New Class : obsolete regional part of lateral ventricle

New Class : obsolete predominantly gray regional part of median eminence

New Class : obsolete predominantly gray regional part of metathalamus

New Class : caudal anterior cingulate cortex

New Class : obsolete regional part of substantia nigra pars reticulata

New Class : regional part of spinal cord gray commissure

New Class : obsolete predominantly white dorsal regional part of metathalamus

New Class : regional part of amygdala

New Class : lateral amygdaloid nucleus, ventrolateral part

New Class : lateral amygdaloid nucleus, dorsolateral part

New Class : lateral amygdaloid nucleus, ventromedial part

New Class : regional part of thoracic spinal cord gray matter

New Class : dorsomedial subnucleus of solitary tract

New Class : principal neuronal circuit

New Class : intrinsic neuronal circuit

New Class : obsolete regional part of cochlea

New Class : medullary anterior horn

New Class : obsolete predominantly gray part of medulla oblongata

New Class : regional part of spinal cord dorsal horn

New Class : medial subnucleus of solitary tract

New Class : obsolete regional part of cingulate cortex

New Class : obsolete regional part of inferior parietal cortex

New Class : obsolete predominantly gray regional part of ventral posterior nucleus

New Class : obsolete regional part of neurohypophysis

New Class : regional part of macula

New Class : vestibular canal

New Class : tympanic canal

New Class : obsolete regional part of cochlear duct

New Class : hemispheric parts of the cerebellar cortex

New Class : regional part of cerebellar white matter

New Class : obsolete superficial feature part of frontal lobe

New Class : obsolete predominantly gray regional part of medial mammillary nucleus

New Class : anterior superior frontal sulcus

New Class : obsolete predominantly gray regional part of superior olivary complex

New Class : part of neuraxis

New Class : obsolete regional part of paraventricular nucleus of hypothalamus magnocellular division

New Class : obsolete predominantly white regional part of superior olivary complex

New Class : obsolete predominantly gray regional part of anterior nuclear group

New Class : obsolete predominantly gray part of corticomedial nuclear complex

New Class : regional part of thoracic spinal cord dorsal horn

New Class : obsolete regional part of superior olive

New Class : suprachiasmatic nucleus dorsomedial part

New Class : suprachiasmatic nucleus ventrolateral part

New Class : obsolete regional part of ventral cochlear nucleus

New Class : dorsolateral subnucleus of solitary tract

New Class : parvicellular subnucleus of solitary tract

New Class : serotonergic system

New Class : glutamatergic system

New Class : gABAergic system

New Class : cholinergic system

New Class : sacral spinal cord dorsal horn

New Class : perirhinal cortex of primate of Burwell et al 1995

New Class : histaminergic system

New Class : catecholamine system

New Class : perirhinal cortex of rodent of Burwell et al 1995

New Class : obsolete regional part of Parahippocampal gyrus

New Class : obsolete regional part of tuberomammillary nucleus

New Class : ventral nerve root of lumbar spinal cord

New Class : obsolete regional part of transverse frontopolar gyri complex

New Class : spinal ganglion part of peripheral nervous system

New Class : sub-lobar region

New Class : proprioceptive system

New Class : sensorimotor

New Class : motor system

New Class : obsolete regional part of orbital gyri complex

New Class : obsolete cytoarchitectural part of cerebral cortex

New Class : obsolete predominantly white regional part of anterior hypothalamic region

New Class : obsolete predominantly gray regional part of anterior hypothalamic region

New Class : obsolete predominantly white regional part of cerebral peduncle

New Class : obsolete predominantly gray regional part of parietal lobe

New Class : obsolete regional part of basolateral nuclear complex

New Class : obsolete regional part of granular layer of cerebellar cortex

New Class : obsolete predominantly white regional part of hypothalamus

New Class : pyramidal layer of entorhinal cortex

New Class : obsolete predominantly gray regional part of tectum

New Class : obsolete predominantly white regional part of tectum

New Class : obsolete regional part of pons

New Class : obsolete regional part of anterior hypothalamic region

New Class : ventral nerve root of sacral spinal cord

New Class : internal spermatic fascia

New Class : gubernacular bulb, intra-abdominal part

New Class : cremasteric artery

New Class : fold of peritoneum

New Class : gubernacular bulb, extra-abdominal part

New Class : inflow tract of ventricle

New Class : inflow tract

New Class : external spermatic fascia

New Class : inflow tract of atrium

New Class : medial orbital sulcus

New Class : regional part of sacral spinal cord gray matter

New Class : obsolete regional part of paraventricular nucleus of hypothalamus magnocellular division - posterior magnocellular part

New Class : obsolete regional part of paraventricular nucleus of hypothalamus descending division

New Class : obsolete predominantly gray regional part of ventral anterior nucleus

New Class : obsolete predominantly gray regional part of hippocampal formation

New Class : medial olfactory stria

New Class : oviduct albumen gland

New Class : olfactory tract linking bulb to ipsilateral dorsal telencephalon

New Class : obsolete regional part of transverse temporal cortex

New Class : obsolete predominantly gray regional part of globus pallidus

New Class : lumbar spinal cord white matter

New Class : lateral orbital sulcus

New Class : inferior ramus of arcuate sulcus

New Class : cytoarchitectural part of dentate gyrus

New Class : obsolete regional part of stratum lacunosum moleculare

New Class : proliferating neuroepithelium

New Class : developing neuroepithelium

New Class : inflow tract of left ventricle

New Class : inflow tract of right ventricle

New Class : hindbrain marginal layer

New Class : cerebellum marginal layer

New Class : differentiating neuroepithelium

New Class : obsolete regional part of basal nuclear complex

New Class : obsolete predominantly gray regional part of inferior colliculus

New Class : head taste bud

New Class : esophageal taste bud

New Class : fin taste bud

New Class : mouth roof taste bud

New Class : pharyngeal taste bud

New Class : autonomic nerve

New Class : vestibular bulb artery

New Class : trunk taste bud

New Class : pterygopalatine nerve

New Class : sympathetic nerve

New Class : cortical preplate

New Class : spinal cord ventricular layer

New Class : cranial neuron projection bundle

New Class : yellow fibrocartilage

New Class : pineal tract

New Class : epiphyseal tract

New Class : integumental taste bud

New Class : rostral epiphyseal tract

New Class : lip taste bud

New Class : barbel taste bud

New Class : obsolete regional part of stratum radiatum

New Class : obsolete regional part of stratum oriens

New Class : obsolete regional part of stratum pyramidale hippocampi

New Class : conical papilla

New Class : regional part of tongue

New Class : sacral spinal cord lateral horn

New Class : sacral spinal cord gray matter

New Class : sacral spinal cord gray commissure

New Class : obsolete predominantly gray posterior regional part of thalamus

New Class : obsolete predominantly gray regional part of lateral geniculate body

New Class : obsolete predominantly gray ventral regional part of thalamus

New Class : spermatic fascia

New Class : laryngeal prominence

New Class : vocal organ

New Class : forceps minor of corpus callosum

New Class : arcuate sulcus

New Class : lateral eminence of fourth ventricle

New Class : palatal taste bud

New Class : forceps major of corpus callosum

New Class : amygdalohippocampal area

New Class : sulcus of limbic lobe

New Class : regional part of lumbar spinal cord dorsal horn

New Class : superficial feature part of occipital lobe

New Class : superficial feature part of forebrain

New Class : obsolete regional part of olfactory cortex

New Class : temporoparietal junction

New Class : commissural nucleus of the solitary tract

New Class : left sub-lobar region

New Class : right sub-lobar region

New Class : primary somatosensory cortex lamina VI

New Class : regional part of retina

New Class : hemisphere parts of cerebral cortex

New Class : obsolete regional part of corticomedial nuclear complex

New Class : superior calcarine sulcus

New Class : neural system

New Class : planum polare

New Class : hippocampal formation of GP94

New Class : body membrane

New Class : isla magna of Calleja

New Class : circuit part of central nervous system

New Class : medial ventral tegmental area

New Class : islands of Calleja of olfactory tubercle

New Class : regional part of thoracic spinal cord

New Class : regional part of cochlear canal

New Class : ganglion part of peripheral nervous system

New Class : obsolete regional part of paraventricular nucleus of hypothalamus

New Class : gross anatomical parts of the cerebellum

New Class : obsolete predominantly gray part of ventral cochlear nucleus

New Class : obsolete cytoarchitectural part of the cerebellum

New Class : obsolete regional part of frontal lobe

New Class : obsolete predominantly white regional part of inferior colliculus

New Class : duct part of cochlear canal

New Class : obsolete predominantly Gray regional part of inferior parietal cortex

New Class : obsolete regional part of neostriatum

New Class : annectant gyrus

New Class : obsolete predominantly white dorsal regional part of medial geniculate body

New Class : obsolete superficial feature part of cerebral peduncle

New Class : obsolete predominantly gray part of solitary nucleus

New Class : intermediate part of hypophysis

New Class : obsolete predominantly white regional part of thalamus

New Class : habenulo-interpeduncular tract of midbrain

New Class : regional part of gustatory epithelium

New Class : obsolete regional part of hindbrain

New Class : obsolete gross anatomical part of cerebral cortex

New Class : subicular complex

New Class : obsolete regional part of limbic lobe

New Class : obsolete predominantly gray regional part of ventral posterolateral nucleus

New Class : lumbar spinal cord gray commissure

New Class : obsolete regional part of fornix

New Class : obsolete predominantly gray regional part of cingulate gyrus

New Class : thoracic spinal cord gray commissure

New Class : obsolete regional part of Preoptic area

New Class : obsolete regional part of middle ear

New Class : obsolete predominantly gray anterior regional part of thalamus

New Class : regional part of cervical spinal cord gray matter

New Class : sacral spinal cord white matter

New Class : obsolete predominantly gray regional part of thalamus

New Class : obsolete regional part of longitudinal fissure

New Class : obsolete regional part of septal nuclear complex

New Class : inferior calcarine sulcus

New Class : ectocalcarine sulcus

New Class : inferior occipital sulcus

New Class : obsolete predominantly gray regional part of superior olive

New Class : obsolete superficial feature part of telencephalon

New Class : superficial feature part of parietal cortex

New Class : obsolete cytoarchitectural part of frontal lobe

New Class : obsolete cytoarchitectural part of occipital lobe

New Class : matrix compartment of caudate nucleus

New Class : matrix compartment of putamen

New Class : granular cell layer of dorsal cochlear nucleus

New Class : striosomal part of caudate nucleus

New Class : striosomal part of putamen

New Class : obsolete predominantly gray regional part of ventral lateral nucleus

New Class : obsolete predominantly gray part of rostral intralaminar nuclei

New Class : obsolete predominantly gray regional part of pulvinar

New Class : lumbar spinal cord ventral horn

New Class : superior transverse frontopolar gyrus

New Class : paravermis parts of the cerebellar cortex

New Class : obsolete regional part of deep cerebellar nuclear complex

New Class : obsolete predominantly gray regional part of frontal lobe

New Class : obsolete predominantly white regional part of cerebellar cortex

New Class : obsolete regional part of basal part of pons

New Class : obsolete regional part of autonomic nervous system

New Class : chemoarchitectural part of neostriatum

New Class : obsolete regional part of dorsal cochlear nucleus

New Class : posterior middle temporal sulcus

New Class : basis pontis

New Class : rostral sulcus

New Class : obsolete predominantly gray regional part of adenohypophysis

New Class : obsolete predominantly white regional part of basal part of pons

New Class : obsolete regional part of adenohypophysis

New Class : spur of arcuate sulcus

New Class : obsolete predominantly gray regional part of ventral posteromedial nucleus

New Class : tegmentum

New Class : obsolete regional part of pontine tegmentum

New Class : regional part orbital frontal cortex

New Class : obsolete regional part of inner ear