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Proposed PONS upper brain ontology

[edit] Common upper ontology of mammalian brain anatomical landmark structures

Brain

  Forebrain region
     Telencephalon region
       Corpus callosum
       Anterior Commissure
         Anterior part of anterior commissure
         Posterior part of anterior commissure
       Internal capsule
       External capsule
       Lamina terminalis
       Olfactory tract
       Fornix
         Crus of the fornix
         Body of the fornix
         Pre-commissural column of the fornix
       Lateral ventricle
       Claustrum      
       Basal nuclei
         Striatum
         Nucleus accumbens
         Septum
           Septal nuclear complex
         Amygdala (amygdaloid nuclear complex)
         Globus pallidus
           External segment of globus pallidus
           Internal segment of globus pallidus
       Substantia innominata (basal forebrain???)
           Ventral pallidum
           Basal nucleus
           Islands of Calleja
           Nucleus of the diagonal band       
       Cerebral cortex
         Isocortex = Neocortex
           Neocortex Layer 1
           Neocortex Layer 2
           Neocortex Layer 3
           Neocortex Layer 4
           Neocortex Layer 5
           Neocortex Layer 6
         Mesocortex (do we need this or is this only relevant in rodent?)
         Allocortex (is this a useful designation?)
             Olfactory bulb
             Piriform cortex
             Induseum griseum (R) = supracallosal gyrus (P)
             Hippocampal formation
               Dentate gyrus
               Hippocampus
                  Alveus
                  Fimbria of the fornix 
               Subiculum
               Presubiculum
               Entorhinal cortex
     Diencephalon region
          Mammillothalamic tract 
          Post-commissural fornix
          Stria Medullaris
          Optic chiasm
          Optic tract
       3rd ventricle 
       Thalamus
         Epithalamus
         Anterior nuclear group
         Midline nuclear group
         Medial dorsal nucleus
         Intralaminar nuclear group
         Lateral nuclear group
         Ventral nuclear group
         Lateral geniculate body
         Medial geniculate body
         Posterior nuclear complex
         External medullary lamina
         Internal medullary lamina       
       Hypothalamus
       Pineal gland
       Hypophysis
          Pituitary gland
          Median eminence
          Infundibulum
       Subthalamic nucleus
       Zona incerta
       Ansa lenticularis
       Fields of Forel
  Midbrain region
     Cerebral aqueduct
     Tectum
       Pretectal region
       Superior colliculus
       Inferior colliculus
     Tegmentum
       Oculomotor nuclear complex
       Midbrain reticular formation
       Substantia nigra
       Red nucleus
     White matter structures of midbrain
       Crus cerebri
       Decussation of superior cerebellar peduncle
  Hindbrain region
     Fourth ventricle
     Cerebellum
        Cerebellar cortex
        Deep cerebellar nuclei
          Dentate nucleus
          Interposed nuclear complex
        Arbor vitae (Q:  does this refer to the entirety of the white matter?)   
     Pons
        Pontine tegmentum
          Locus coeruleus
          abducens nucleus
          facial motor nucleus
          medial parabrachial nucleus
          pontine raphe nuclear complex
          Nucleus of the lateral lemniscus
          Mesencephalic tract of trigeminal nerve
          Superior medullary velum
          Abducens nerve fibers
          Medial longitudinal 
          Trigeminal nuclear complex
          Pontine reticular formation
          Superior olivary complex
            Superior olive
          Facial nerve fibers
        Basal part of pons
          Pontine nuclear complex
          Middle cerebellar peduncle
     Medulla
        Vestibular nuclear complex
        Cochlear nuclear complex
        Raphe nuclei of the medulla
        Solitary nucleus
        Inferior olive
        Dorsal motor nucleus of the vagus
        Hypoglossal nucleus
        nucleus prepositus
        nucleus gracilis
        nucleus cuneatus
        nucleus ambiguus
        central canal
        tectospinal tract
        area postrema
        inferior cerebellar pduncle
        medial lemniscus of medulla
          decussation of medial lemniscus
        cuneate fasciculus
        gracilis fasciculus
        medullary reticular formation         
        pyramidal tract
           decussation of pyramidal tract
        olivocerebellar tract
        anterior spinocerebellar tract
        vestibulospinal tract

Spinal cord


Other categories to be defined:

Cerebrum Brainstem Fornix

Contributors

Memartone


*Note: Neurolex imports many terms and their ids from existing community ontologies, e.g., the Gene Ontology. Neurolex, however, is a dynamic site and any content beyond the identifier should not be presumed to reflect the content or views of the source ontology. Users should consult with the authoritative source for each ontology for current information.