uberon-to-mbo.obo

[Term]
! The Sympathetic Nervous System (SNS) is a branch of the autonomic nervous system along with the enteric nervous system and parasympathetic nervous system. It is always active at a basal level (called sympathetic tone) and becomes more active during times of stress. Its actions during the stress response comprise the fight-or-flight response [Wikipedia]. he sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO].
id: UBERON:0000013 ! sympathetic nervous system
relationship: has_function_in MBO:0000088  {source="obol"} !  fight-or-flight response

[Term]
! specialized claw or nail on the foot of certain primates, used for personal grooming.
id: UBERON:0000212 ! toilet claw
relationship: has_function_in MBO:0000451  {source="obol"} !  personal grooming

[Term]
! A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex]. including the hippocampus, amygdala, anterior thalamic nuclei, and limbic cortex, which support a variety of functions including emotion, behavior, long term memory, and olfaction [Wikipedia].
id: UBERON:0000349 ! limbic system
relationship: has_function_in MBO:0000191  {source="obol"} !  emotional memory

[Term]
! The prefrontal cortex (PFC) is the anterior part of the frontal lobes of the brain, lying in front of the motor and premotor areas. This brain region has been implicated in planning complex cognitive behaviors, personality expression, decision making and moderating correct social behavior. The basic activity of this brain region is considered to be orchestration of thoughts and actions in accordance with internal goals. The most typical psychological term for functions carried out by the pre-frontal cortex area is executive function. Executive function relates to abilities to differentiate among conflicting thoughts, determine good and bad, better and best, same and different, future consequences of current activities, working toward a defined goal, prediction of outcomes, expectation based on actions, and social 'control' (the ability to suppress urges that, if not suppressed, could lead to socially-unacceptable outcomes). Many authors have indicated an integral link between a person's personality and the functions of the prefrontal cortex. [WP,unvetted].
id: UBERON:0000451 ! prefrontal cortex
relationship: has_function_in MBO:0000607  {source="obol"} !  cognition

[Term]
! Rounded band of white fibers crossing the middle line on the dorsal aspect of the upper end of the cerebral aqueduct. It is important in the bilateral pupillary light reflex. Its fibers acquire their medullary sheaths early, but their connections have not been definitely determined. Most of them have their origin in a nucleus, the nucleus of the posterior commissure (nucleus of Darkschewitsch), which lies in the central gray substance of the upper end of the cerebral aqueduct, in front of the nucleus of the oculomotor nerve. Some are probably derived from the posterior part of the thalamus and from the superior colliculus, whereas others are believed to be continued downward into the medial longitudinal fasciculus. The posterior commissure interconnects the pretectal nuclei, mediating the consensual pupillary light reflex[WP].Diencephalic tract which is located in the vicinity of the dorsal diencephalon and mesencephalon and connects the pretectal nuclei. From Neuroanatomy of the Zebrafish Brain[ZFA].
id: UBERON:0000936 ! posterior commissure
relationship: has_function_in MBO:0000412  {source="obol"} !  pupillary light reflex

[Term]
! The penis (plural penises, penes) is an external sexual organ of certain biologically male organisms, in both vertebrates and invertebrates. The penis is a reproductive organ, technically an intromittent organ, and for placental mammals, additionally serves as the external organ of urination. The penis is generally found on mammals and reptiles. [WP,unvetted].
id: UBERON:0000989 ! penis
relationship: has_function_in MBO:0000040  {source="obol"} !  urination
relationship: has_function_in MBO:0000060  {source="obol"} !  copulation

[Term]
! he excretory system is the system of an organism that mainly performs the function of excretion, the bodily process of discharging wastes. It is responsible for the elimination of wastes produced by the processes that maintain homeostasis.
id: UBERON:0001008 ! excretory system
relationship: has_function_in MBO:0000038  {source="obol"} !  excretion

[Term]
! The part of the nervous system which in vertebrates consists of the brain and spinal cord, to which sensory impulses are transmitted and from which motor impulses pass out, and which supervises and coordinates the activity of the entire nervous system[XAO]. Neuraxis plus retina[INCF].
id: UBERON:0001017 ! central nervous system
relationship: has_function_in MBO:0000339  {source="obol"} !  motor coordination

[Term]
! In human anatomy, the sternocleidomastoid muscle, also known as sternomastoid and commonly abbreviated as SCM, is a paired muscle in the superficial layers of the anterior portion of the neck. It acts to flex and rotate the head. It also acts as an accessory muscle of inspiration, along with the scalene muscles of the neck. [WP,unvetted].
id: UBERON:0001128 ! sternocleidomastoid
relationship: has_function_in MBO:0000026  {source="obol"} !  head rotation

[Term]
! The gluteus maximus (or glutC&us maximus) is the largest and most superficial of the three gluteal muscles. It makes up a large portion of the shape and appearance of the buttocks. It is a broad and thick fleshy mass of a quadrilateral shape, and forms the prominence of the nates. Its large size is one of the most characteristic features of the muscular system in humans, connected as it is with the power of maintaining the trunk in the erect posture. The muscle is remarkably coarse in structure, being made up of fasciculi lying parallel with one another and collected together into large bundles separated by fibrous septa. [WP,unvetted].
id: UBERON:0001370 ! gluteus maximus
relationship: has_function_in MBO:0000355  {source="obol"} !  posture

[Term]
! The scaphoid Bone is situated at the radial (radius bone) side of the carpus, or laterally between the hand and the forearm in standard medical posture (thumbs pointing outwards). The scaphoid bone is the largest bone of the proximal row of wrist bones, its long axis being from above downward, lateralward, and forward. It is approximately the size and shape of a medium sized cashew. The bone takes a semi-similar form of a boat. In reptiles, birds, and amphibians, this bone is instead commonly referred to as the radiale, because of its articulation with the radius. [WP,unvetted].
id: UBERON:0001427 ! scaphoid
relationship: has_function_in MBO:0000355  {source="obol"} !  posture

[Term]
! In human anatomy, hip (or 'coxa' in medical terminology) refer to either an anatomical region or a joint. The hip region is located lateral to the gluteal region (i.e. the buttock), inferior to the iliac crest, and overlying the greater trochanter of the thigh bone. In adults, three of the bones of the pelvis have fused into the hip bone which forms part of the hip region. The hip joint, scientifically referred to as the acetabulofemoral joint (art. coxae), is the joint between the femur and acetabulum of the pelvis and its primary function is to support the weight of the body in both static (e.g. standing) and dynamic (e.g. walking or running) postures. [WP,unvetted].
id: UBERON:0001464 ! hip
relationship: has_function_in MBO:0000356  {source="obol"} !  body posture

[Term]
! In human anatomy, the masseter is one of the muscles of mastication. In the animal kingdom, it is particularly powerful in herbivores to facilitate chewing of plant matter. [WP,unvetted].
id: UBERON:0001597 ! masseter
relationship: has_function_in MBO:0000073  {source="obol"} !  mastication

[Term]
! The temporal muscle is one of the muscles of mastication. [WP,unvetted].
id: UBERON:0001598 ! temporalis
relationship: has_function_in MBO:0000073  {source="obol"} !  mastication

[Term]
! the larger of the two muscles of the tympanic cavity, is contained in the bony canal above the osseous portion of the auditory tube. Its role is to dampen sounds produced from chewing. It arises from the cartilaginous portion of the auditory tube and the adjoining part of the great wing of the sphenoid, as well as from the osseous canal in which it is contained. Passing backward through the canal, it ends in a slender tendon which enters the tympanic cavity, makes a sharp bend around the extremity of the septum, known as the processus cochleariformis[1], and is inserted into the manubrium of the malleus, near its root[WP].
id: UBERON:0001600 ! tensor tympani
relationship: acts_in MBO:0000073  {source="obol"} !  chewing

[Term]
! Skeletal muscle derived from cranial mesoderm and controls eye movements.
id: UBERON:0001601 ! extra-ocular muscle
relationship: has_function_in MBO:0000444  {source="obol"} !  eye movement

[Term]
! For the muscle of the neck, see Rectus capitis lateralis muscle The lateral rectus muscle is a muscle in the orbit. It is one of six extraocular muscles that control the movements of the eye (abduction in this case) and the only muscle innervated by the abducens nerve, cranial nerve VI. [WP,unvetted].
id: UBERON:0001603 ! lateral rectus
relationship: has_function_in MBO:0000444  {source="obol"} !  eye movement

[Term]
! The iris dilator muscle (pupil dilator muscle, pupillary dilator, radial muscle of iris, radiating fibers), is a smooth muscle of the eye, running radially in the iris and therefore fit as a dilator. It is innervated by the sympathetic system, which acts by releasing noradrenaline, which acts on N11-receptors.. Thus, when presented with a threatening stimuli that activates the fight-or-flight response, this innervation dilates the iris, thus temporarily letting more light reach the retina. [WP,unvetted].
id: UBERON:0001608 ! dilatator pupillae
relationship: acts_during MBO:0000088  {source="obol"} !  fight-or-flight response

[Term]
! The incus or anvil is the anvil-shaped small bone or ossicle in the middle ear. It connects the malleus to the stapes. It was first described by Alessandro Achillin of Bologna. The incus transmits sound vibrations from the malleus to the stapes. The incus only exists in mammals, and is derived from a reptilian upper jaw bone, the quadrate bone. Embryologically it is derived from the first pharyngeal arch along with the rest of the bones of mastication, such as the maxilla and mandible. [WP,unvetted].
id: UBERON:0001688 ! incus
relationship: has_function_in MBO:0000073  {source="obol"} !  mastication

[Term]
! The malleus or hammer is a hammer-shaped small bone or ossicle of the middle ear which connects with the incus and is attached to the inner surface of the eardrum. The word is Latin for hammer. It transmits the sound vibrations from the eardrum to the incus. The malleus is unique to mammals, and evolved from a lower jaw bone in basal amniotes called the articular, which still forms part of the jaw joint in reptiles. Embryologically it is derived from the first pharyngeal arch along with the rest of the bones of mastication, such as the maxilla and mandible. [WP,unvetted].
id: UBERON:0001689 ! malleus
relationship: has_function_in MBO:0000073  {source="obol"} !  mastication

[Term]
! An eyelid is a thin fold of skin that covers and protects an eye. With the exception of the prepuce and the labia minora, it has the thinnest skin of the whole body. The levator palpebrae superioris muscle retracts the eyelid to 'open' the eye. This can be either voluntarily or involuntarily. The human eyelid features a row of eyelashes which serve to heighten the protection of the eye from dust and foreign debris, as well as from perspiration. 'Palpebral' (and 'blepharo') means relating to the eyelids. Its key function is to regularly spread the tears and other secretion on the eye surface to keep it moist, since the cornea must be continuously moist. They keep the eyes from drying out when asleep. Moreover, the blink reflex protects the eye from foreign bodies. [WP,unvetted].
id: UBERON:0001711 ! eyelid
relationship: has_function_in MBO:0000042  {source="obol"} !  tear secretion

[Term]
! The spinal trigeminal nucleus is a nucleus in the medulla that receives information about deep/crude touch, pain, and temperature from the ipsilateral face. The facial, glossopharyngeal, and vagus nerves also convey pain information from their areas to the spinal trigeminal nucleus. [WP,unvetted].
id: UBERON:0001717 ! spinal nucleus of trigeminal nerve
relationship: has_function_in MBO:0000331  {source="obol"} !  nociceptive behaviour

[Term]
! The mesencephalic nucleus is involved with proprioception of the face, that is, the feeling of position of the muscles. Unlike many nuclei within the CNS, the mesencephalic nucleus contains no chemical synapses but are electrically coupled. Instead, neurons of this nucleus are pseudounipolar cells receiving proprioceptive information from the jaw, and sending projections to the motor trigeminal nucleus to mediate monosynaptic jaw reflexes. It is also the only structure in the CNS to contain the cell bodies of a primary afferent, which are usually contained within ganglia. [WP,unvetted].
id: UBERON:0001718 ! mesencephalic nucleus of trigeminal nerve
relationship: has_function_in MBO:0000317  {source="obol"} !  proprioception

[Term]
! The tongue is the movable, muscular organ on the floor of the mouth of most vertebrates, in many other mammals is the principal organ of taste, aids in the prehension of food, in swallowing, and in modifying the voice as in speech[GO].
id: UBERON:0001723 ! tongue
relationship: has_function_in MBO:0000545  {source="obol"} !  swallowing

[Term]
! Conic projection from the posterior edge of the middle of the soft palate, composed of connective tissue containing a number of racemose glands, and some muscular fibers. The uvula, hanging from the end of the soft palate, is responsible for the sound of snoring. Touching the uvula or the end of the soft palate evokes a strong gag reflex in most people.
id: UBERON:0001734 ! uvula
relationship: has_function_in MBO:0000495  {source="obol"} !  snoring

[Term]
! the most superior of the laryngeal cartilages, which is found at the root of the tongue and folds back over the entrance to the larynx during swallowing.
id: UBERON:0001742 ! epiglottic cartilage
relationship: has_function_in MBO:0000545  {source="obol"} !  swallowing

[Term]
! The lacrimal apparatus is the physiologic system containing the orbital structures for tear production and drainage. It consists of: (a) the lacrimal gland, which secretes the tears, and its excretory ducts, which convey the fluid to the surface of the eye; (b) the lacrimal canaliculi, the lacrimal sac, and the nasolacrimal duct, by which the fluid is conveyed into the cavity of the nose. [WP,unvetted].
id: UBERON:0001750 ! lacrimal apparatus
relationship: has_function_in MBO:0000042  {source="obol"} !  lacrimation

[Term]
! Visible part of the ear that resides outside of the head. The purpose of the pinna is to collect sound. It does so by acting as a funnel, amplifying the sound and directing it to the ear canal. While reflecting from the pinna, sound also goes through a filtering process which adds directional information to the sound (see sound localization, head-related transfer function, pinna notch). The filtering effect of the human pinna preferentially selects sounds in the frequency range of human speech. In various species, the pinna can also signal mood and radiate heat.
id: UBERON:0001757 ! pinna
relationship: has_function_in MBO:0000003  {source="obol"} !  mood

[Term]
! The lacrimal canaliculi, also known as the lacrimal canals or lacrimal ducts, are the small channels in each eyelid that commence at minute orifices, termed puncta lacrimalia, on the summits of the papillae lacrimales, seen on the margins of the lids at the lateral extremity of the lacus lacrimalis. The superior duct, the smaller and shorter of the two, at first ascends, and then bends at an acute angle, and passes medialward and downward to the lacrimal sac. The inferior duct at first descends, and then runs almost horizontally to the lacrimal sac. At the angles they are dilated into ampullC&. Microscopically, they are lined by nonkeratinizing stratified squamous epithelium surrounded by fibrous tissue. Outside the latter is a layer of striped muscle, continuous with the lacrimal part of the Orbicularis oculi; at the base of each lacrimal papilla the muscular fibers are circularly arranged and form a kind of sphincter. [WP,unvetted].
id: UBERON:0001770 ! lacrimal canaliculus
relationship: has_function_in MBO:0000042  {source="obol"} !  lacrimation

[Term]
! Sympathetic ganglia are the ganglia of the sympathetic nervous system. They deliver information to the body about stress and impending danger, and are responsible for the familiar fight-or-flight response. They contain approximately 20000–30000 nerve cell bodies and are located close to and on either side of the spinal cord in long chains. [WP,unvetted].
id: UBERON:0001806 ! sympathetic ganglion
relationship: has_function_in MBO:0000088  {source="obol"} !  fight-or-flight response

[Term]
! The parotid gland is the largest of the salivary glands. It is found wrapped around the mandibular ramus, and it secretes saliva through Stensen's duct into the oral cavity, to facilitate mastication and swallowing. [WP,unvetted].
id: UBERON:0001831 ! parotid gland
relationship: has_function_in MBO:0000073  {source="obol"} !  mastication

[Term]
! Organ with organ cavity which connects the vestibule of the conjunctival sac to the nasal cavity. Examples: There are only two lacrimal ducts, the right and the left lacrimal ducts.
id: UBERON:0001850 ! lacrimal duct
relationship: has_function_in MBO:0000042  {source="obol"} !  lacrimation

[Term]
! one of the two otolith organs located in the vertebrate inner ear. These use small stones and a viscous fluid to stimulate hair cells to detect motion and orientation. The utricle is larger than the saccule and is of an oblong form, compressed transversely, and occupies the upper and back part of the vestibule, lying in contact with the recessus ellipticus and the part below it. The utricle contains mechanoreceptors called hair cells that distinguish between degrees of tilting of the head, thanks to their apical cilia set-up. These are covered by otolith which, due to gravity, pull on the cilia and tilt them. Depending on whether the tilt is in the direction of the kinocilium or not, the resulting hair cell polarisation is excitatory (depolarising) or inhibitory (hyperpolarisation), respectively. This signal to the vestibular nerve (which takes it to the brainstem) does not adapt with time. The effect of this is that, for example, an individual lying down to sleep will continue to detect that they are lying down hours later when they awaken[WP].
id: UBERON:0001853 ! utricle of membranous labyrinth
relationship: has_function_in MBO:0000070  {source="obol"} !  tilting

[Term]
! A bed of sensory cells situated in the inner ear. The saccule translates head movements into neural impulses which the brain can interpret. The saccule is sensitive to linear translations of the head, specifically movements up and down (think about moving on an elevator). When the head moves vertically, the sensory cells of the saccule are disturbed and the neurons connected to them begin transmitting impulses to the brain. These impulses travel along the vestibular portion of the eighth cranial nerve to the vestibular nuclei in the brainstem. is the smaller of the two vestibular sacs. It is globular in form and lies in the recessus sphC&ricus near the opening of the scala vestibuli of the cochlea. Its cavity does not directly communicate with that of the utricle. The anterior part of the saccule exhibits an oval thickening, the macula acustica sacculi, or macula, to which are distributed the saccular filaments of the vestibular branch of the vestibulocochlear nerve, also known as the acoustic nerve or cranial nerve VIII[WP].
id: UBERON:0001854 ! saccule of membranous labyrinth
relationship: has_function_in MBO:0000020  {source="obol"} !  head movement

[Term]
! The semicircular canals are three half-circular, interconnected tubes located inside each ear. The three canals are the horizontal semicircular canal (also known as the lateral semicircular canal), superior semicircular canal (also known as the anterior semicircular canal), and the posterior semicircular canal. The canals are aligned approximately orthogonally to one another. The horizontal canal is aligned roughly horizontally in the head. The superior and anterior canals are aligned roughly at a 45 degree angle to a vertical plane drawn from the nose to the back of the skull. Thus, the horizontal canal detects horizontal head movements (such as when doing a pirouette), while the superior and posterior canals detect vertical head movements. Each canal is filled with a fluid called endolymph and contains a motion sensor with little hairs whose ends are embedded in a gelatinous structure called the cupula. As the skull twists in any direction, the endolymph is thrown into different sections of the canals. The cilia detect when the endolymph rushes past, and a signal is then sent to the brain. The semicircular canals are a component of the Labyrinth. Among species of mammals, the size of the semicircular canals is correlated with their type of locomotion. Specifically, species that are agile and have fast, jerky locomotion have larger canals relative to their body size than those that move more cautiously. [WP,unvetted].
id: UBERON:0001858 ! posterior semicircular duct
relationship: has_function_in MBO:0000020  {source="obol"} !  head movement

[Term]
! The lateral or horizontal canal (external semicircular canal) is the shortest of the three canals. Movement of fluid within this canal corresponds to rotation of the head around a vertical axis (i.e. the neck). [WP,unvetted].
id: UBERON:0001859 ! lateral semicircular duct
relationship: has_function_in MBO:0000020  {source="obol"} !  head movement

[Term]
! A midline paired symmetrical structure within the brains of vertebrates, including humans. It is situated between the cerebral cortex and midbrain, both in terms of location and neurological connections. Its function includes relaying sensation, special sense and motor signals to the cerebral cortex, along with the regulation of consciousness, sleep and alertness. The thalamus surrounds the third ventricle. It is the main product of the embryonic diencephalon.
id: UBERON:0001897 ! thalamus
relationship: has_function_in MBO:0000312  {source="obol"} !  regulation of sleep

[Term]
! The zona incerta is a horizontally elongated region of gray matter cells in the subthalamus below the thalamus. Its connections project extensively over the brain from the cerebral cortex down into the spinal cord. Its function is unknown though several have been proposed related to blimbicbmotor integrationb such as controlling visceral activity and pain; gating sensory input and synchronizing cortical and subcortical brain rhythms. Its dysfunction may play a role in central pain syndrome. It is also been identified as a promising deep brain stimulation therapy target for treating Parkinsons Disease. Its existence was first described by Auguste Forel in 1877 as a bregion of which nothing certain can be saidb. A hundred and thirty years later in 2007, Nadia Urbain and Martin DeschC*nes of UniversitC) Laval noted that the bzona incerta is among the least studied regions of the brain; its name does not even appear in the index of many textbooks. b [WP,unvetted].
id: UBERON:0001907 ! zona incerta
relationship: has_function_in MBO:0000331  {source="obol"} !  nociceptive behaviour

[Term]
! The Medial forebrain bundle (MFB), is a complex bundle of axons coming from the basal olfactory regions, the periamygdaloid region, and the septal nuclei, and passing to the lateral hypothalamus, with some carrying on into the tegmentum. It contains both ascending and descending fibers. It also represents a part of the mesolimbic pathway, carrying information between the ventral tegmentum and the nucleus accumbens. It is commonly accepted that the MFB is a part of the reward system, involved in the integration of reward and pleasure. Electrical stimulation of the medial forebrain bundle is believed to cause sensations of pleasure. This hypothesis is based upon intracranial self-stimulation (ICSS) studies. Animals will work for MFB ICSS, and humans report that MFB ICSS is intensely pleasurable. This is most likely because the medial forebrain bundle carries information from the ventral tegmental area (VTA) to the nucleus accumbens (nAcc or Acb). The nAcc is a recognized reward center, and activation of the pathway from the VTA to the nAcc is believed to be rewarding, which is why it is sometimes referred to as the hedonic highway. [WP,unvetted].
id: UBERON:0001910 ! medial forebrain bundle
relationship: has_function_in MBO:0000230  {source="obol"} !  pleasure

[Term]
! The Medial Geniculate Nucleus (MGN) or Medial Geniculate Body (MGB) is part of the auditory thalamus and represents the thalamic relay between the inferior colliculus (IC) and the auditory cortex (AC). It is made up of a number of sub-nuclei that are distinguished by their neuronal morphology and density, by their afferent and efferent connections, and by the coding properties of their neurons. It is thought that the MGB influences the direction and maintenance of attention. [WP,unvetted].
id: UBERON:0001927 ! medial geniculate body
relationship: has_function_in MBO:0000455  {source="obol"} !  attention

[Term]
! The tuberomammillary nucleus is a subnucleus of the posterior third of the hypothalamus. It consists of, largely, histaminergic and is involved with the control of arousal, sleep and circadian rhythm. Axons of the tuberomammillary nucleus project primarily to the cerebral cortex, thalamus, basal ganglia, basal forebrain, and hypothalamus. The projections to the cerebral cortex directly increase cortical activation and arousal, and projections to acetylcholinergic neurons of the basal forebrain and dorsal pons do so indirectly, by increasing the release of acetylcholine in the cerebral cortex. [WP,unvetted].
id: UBERON:0001936 ! tuberomammillary nucleus
relationship: has_function_in MBO:0000166  {source="obol"} !  circadian rhythm

[Term]
! Region between dorsal thalamus and optic tectum[pub]. It receives binocular sensory input from retinal ganglion cells of the eyes, and is the region responsible for maintaining the pupillary light reflex. [WP,unvetted].
id: UBERON:0001944 ! pretectal region
relationship: has_function_in MBO:0000412  {source="obol"} !  pupillary light reflex

[Term]
! The red nucleus is a structure in the rostral midbrain involved in motor coordination. It comprises a caudal magnocellular and a rostral parvocellular part. [WP,unvetted].
id: UBERON:0001947 ! red nucleus
relationship: has_function_in MBO:0000339  {source="obol"} !  motor coordination

[Term]
! The neocortex is a part of the brain of mammals. It is the outer layer of the cerebral hemispheres, and made up of six layers, labelled I to VI (with VI being the innermost and I being the outermost). The neocortex is part of the cerebral cortex (along with the archicortex and paleocortex, which are cortical parts of the limbic system). It is involved in higher functions such as sensory perception, generation of motor commands, spatial reasoning, conscious thought and, in humans, language. Other names for the neocortex include neopallium and isocortex ('equal rind'). [WP,unvetted].
id: UBERON:0001950 ! neocortex
relationship: has_function_in MBO:0000454  {source="obol"} !  perception

[Term]
! The suprachiasmatic nucleus, or nuclei, (SCN), a tiny region on the brain's midline in a shallow impression of the optic chiasm, is responsible for controlling endogenous circadian rhythms. The neuronal and hormonal activities it generates regulate many different body functions over a 24-hour period. The SCN, pine cone shaped and the size of a grain of rice, interacts with many other regions of the brain. It contains several cell types and several different peptides and neurotransmitters. [WP,unvetted].
id: UBERON:0002034 ! suprachiasmatic nucleus
relationship: has_function_in MBO:0000167  {source="obol"} !  circadian period

[Term]
! Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA].
id: UBERON:0002037 ! cerebellum
relationship: has_function_in MBO:0000339  {source="obol"} !  motor coordination

[Term]
! The zona fasciculata constitutes the middle zone of the adrenal cortex, sitting directly beneath the zona glomerulosa. Constituent cells are organized into bundles or 'fascicles'. The zona fasciculata chiefly produces glucocorticoids (mainly cortisol in the human), which regulates the metabolism of glucose, especially in times of stress (e.g. , part of the fight-or-flight response). This tissue also generates a small amount of weak androgens. In certain animals such as rodents, the lack of 17alpha-hydroxylase results in the synthesis of corticosterone instead of cortisol. Steroid-producing adrenal tumours and hyperplasias of the zona fasciculata result in excess cortisol production and are the cause for adrenal Cushing's syndrome. The genetic disorder McCune-Albright syndrome can also present Cushing's syndrome in affected patients. [WP,unvetted].
id: UBERON:0002054 ! zona fasciculata of adrenal gland
relationship: has_function_in MBO:0000088  {source="obol"} !  fight-or-flight response

[Term]
! A paired organ which has the production of urine as its primary function.
id: UBERON:0002113 ! kidney
relationship: has_function_in MBO:0000040  {source="obol"} !  urination

[Term]
! In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO]. // The first kidney in all vertebrates - it is transitional and disappears soon after it has formed. // Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis. // The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.<a href='http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-PUB-961014-576'>Kimmel et al, 1995.</a>
id: UBERON:0002120 ! pronephros
relationship: has_function_in MBO:0000038  {source="obol"} !  excretion

[Term]
! largest nucleus situated in the olivary body, part of the medulla oblongata. It is closely associated with the cerebellum, but its specific function is voluntary body movements.
id: UBERON:0002127 ! inferior olivary complex
relationship: has_function_in MBO:0000001  {source="obol"} !  body part movement

[Term]
! The superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound[GO].
id: UBERON:0002128 ! superior olivary complex
relationship: has_function_in MBO:0000454  {source="obol"} !  perception

[Term]
! The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function[GO].
id: UBERON:0002129 ! cerebellar cortex
relationship: has_function_in MBO:0000454  {source="obol"} !  perception

[Term]
! The anterior lobe of cerebellum is the portion of the cerebellum responsible for mediating unconscious proprioception. In alcoholics, it can deteriorate. It is sometimes equated to the 'paleocerebellum'. [WP,unvetted].
id: UBERON:0002131 ! anterior lobe of cerebellum
relationship: has_function_in MBO:0000317  {source="obol"} !  proprioception

[Term]
! The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic[GO]. Bluish region in the superior angle of the fourth ventricle floor, corresponding to melanin-like pigmented nerve cells which lie lateral to the ponto-mesencephalic central gray (griseum centrale). It is also known as nucleus pigmentosus pontis[GAID].
id: UBERON:0002148 ! locus ceruleus
relationship: has_function_in MBO:0000247  {source="obol"} !  panic

[Term]
! The pontine nuclei are a part of the pons which store the memory of intention during motor activity. Corticopontine fibres carry information from the primary motor cortex to the ipsilateral pontine nucleus in the ventral pons, and the pontocerebellar projection then carries that information to the contralateral cerebellum via the middle cerebellar peduncle. They therefore allow modification of actions in the light of their outcome, or error correction, and are hence important in learning motor skills. [WP,unvetted].
id: UBERON:0002151 ! pontine nuclear group
relationship: has_function_in MBO:0000190  {source="obol"} !  motor memory

[Term]
! The gigantocellular nucleus, as the name indicates, is mainly composed of the so called giant neuronal cells. This nucleus has been known to innervate the caudal hypoglossal nucleus, and responds to glutamateric stimuli. The gigantocellular nucleus excites the hypoglossal nucleus, and can play a role in the actions of the said nerve . This nucleus receives connections from the periaqueductal gray, the paraventricular hypothalamic nucleus, central nucleus of the amygdala, lateral hypothalamic area, and parvocellular reticular nucleus. Retrograde studies have shown that the deep mesencephalic reticular formation and oral pontine reticular nucleus project to the nucleus gigantocellularis. The dorsal rostral section of the nucleus reticularis gigantocellularis is also involved mediating in expiration (or out-breathing) along with the parvocellular nucleus. [WP,unvetted].
id: UBERON:0002155 ! gigantocellular nucleus
relationship: has_function_in MBO:0000231  {source="obol"} !  excitement

[Term]
! The nucleus raphe magnus, located directly rostral to the raphe obscurus, is afferently stimulated from axons in the spinal cord and cerebellum. This makes the magnus a likely candidate for part of the motor system; however, it seems to participate in the endogenous analgesia system. The magnus receives descending afferents from the periaqueductal gray, the paraventricular hypothalamic nucleus, central nucleus of the amygdala, lateral hypothalamic area, parvocellular reticular nucleus and the prelimbic, infralimbic, medial and lateral precentral cortices . All of these brain areas influence the main function of the raphe magnus. The main function of the magnus is mostly pain mediation; in fact it sends projections to the dorsal horn of the spinal cord to directly inhibit pain. The periaquiductal gray, the epicenter of analgesia, sends efferent connections to the nucleus raphe magnus in when it is stimulated by opiates (endogenous or otherwise). Electrical stimulation of the PAG produces analgesia, as well as administration of morphine to the PAG or n.r. magnus. The antinociceptic effects of electrical stimulation of the PAG can be blocked by administering naloxone, an opiate antagonist, to the n.r. magnus. All of this seems to indicate that the magnus is part of the endogenous opiate system, and acts to inhibit pain in the spinal cord. [WP,unvetted].
id: UBERON:0002156 ! nucleus raphe magnus
relationship: has_function_in MBO:0000331  {source="obol"} !  nociceptive behaviour

[Term]
! The nucleus raphe pallidus receives afferent connections from the periaqueductal gray, the paraventricular hypothalamic nucleus, central nucleus of the amygdala, lateral hypothalamic area, and parvocellular reticular nucleus. Also, the pallidus receives afferents from the medial preoptic area, median preoptic nucleus and lateral paragigantocellular reticular nuclei . The pallidus has recently been shown to be involved in the activation of a fever as an immunoreaction. It has been implied that the preoptic area is constantly inhibiting the raphe pallidus, especially the rostral portion, with GABA. When the preoptic area receives immune signals from the body, the inhibition stops and the rostral portion of the raphe pallidus excites the intermediolateral cell column, which induces a fever . The raphe pallidus has also been known to mediate the tachycardia response, an extremely high heart rate known to be incited by emotional or psychological stress. Microinjections of a GABA-a antagonist into the raphe pallidus, induces an increased heart rate. Conversely, microinjections of muscimol, a GABA-a agonist, inhibit tachycardia in rats under air-stress stimuli. In both of these cases, GABA is mediating two different sympathetic responses, so clearly the nucleus raphe pallidus is a far more a complex nucleus than previously thought. [WP,unvetted].
id: UBERON:0002157 ! nucleus raphe pallidus
relationship: has_function_in MBO:0000231  {source="obol"} !  excitement

[Term]
! Located in the medulla oblongata, the gracile nucleus is one of the dorsal column nuclei that participate in the sensation of fine touch and proprioception of the lower body (legs and trunk). It contains second-order neurons of the dorsal column-medial lemniscus system, which receive inputs from sensory neurons of the dorsal root ganglia and send axons that synapse in the thalamus. The neurons contained within the nucleus form a visible bump called the gracile tubercle on the posterior side of the closed medulla at the floor of the fourth ventricle. The gracile nucleus and fasciculus carry epicritic, kinesthetic, and conscious proprioceptive information from the lower part of the body (below the level of T6 in the spinal cord). The counterpart to the gracile nucleus and fasciculus is the cuneate nucleus and fasciculus, which carries the same type of information, but from the upper body (above T6, excepting the face and ear - the information from the face and ear is carried by the primary sensory trigeminal nucleus). [WP,unvetted].
id: UBERON:0002161 ! gracile nucleus
relationship: has_function_in MBO:0000317  {source="obol"} !  proprioception

[Term]
! the pronounced, dorsolaterally oriented ridge of grey matter in each lateral half of the spinal cord[MP]. the dorsal (more towards the back) grey matter of the spinal cord. It receives several types of sensory information from the body, including light touch, proprioception, and vibration. This information is sent from receptors of the skin, bones, and joints through sensory neurons whose cell bodies lie in the dorsal root ganglion[WP]. The dorsal region of the mature spinal cord contains neurons that process and relay sensory input[GO].
id: UBERON:0002256 ! dorsal horn of spinal cord
relationship: has_function_in MBO:0000317  {source="obol"} !  proprioception

[Term]
! In the brain, the corpora quadrigemina (Latin for 'quadruplet bodies') are the four colliculibtwo inferior, two superiorblocated on the tectum the dorsal aspect of the midbrain. The corpora quadrigemina are reflex centers involving vision and hearing. [WP,unvetted]. Two pairs of colliculi on the dorsal surface of the midbrain composed of white matter externally and gray matter within, the superior pair containing correlation centers for optic reflexes and the inferior pair containing correlation centers for auditory reflexes[BTO].
id: UBERON:0002259 ! corpora quadrigemina
relationship: has_function_in MBO:0000435  {source="obol"} !  auditory reflex

[Term]
! In anatomy and neurology, the dorsal root (or posterior root) is the afferent sensory root of a spinal nerve. At the distal end of the dorsal root is the dorsal root ganglion, which contains the neuron cell bodies of the nerve fibres conveyed by the root. If the dorsal root of a spinal nerve were severed it would lead to numbness in certain areas of the body. The lateral division of the dorsal root contains lightly myelinated and unmyelinated axons of small diameter. These transmit pain and temperature sensation from the body. These fibers cross through the anterior white commissure to form the Anterior lateral system in the lateral funiculus. The medial division of the dorsal root contains myelinated axons of larger diameter. These transmit information of discriminative touch, pressure, vibration, and conscious proprioception originating from spinal levels C2 through S5. These fibers are pushed in towards the posterior medial sulcus to form the fasciculus gracilis and the fasciculus cuneatus. [WP,unvetted].
id: UBERON:0002261 ! dorsal root of spinal cord
relationship: has_function_in MBO:0000331  {source="obol"} !  nociceptive behaviour

[Term]
! The brainstem (or brain stem) is the lower part of the brain, adjoining and structurally continuous with the spinal cord. The brain stem provides the main motor and sensory innervation to the face and neck via the cranial nerves. Though small, this is an extremely important part of the brain as the nerve connections of the motor and sensory systems from the main part of the brain to the rest of the body pass through the brain stem. This includes the corticospinal tract (motor), the posterior column-medial lemniscus pathway (fine touch, vibration sensation and proprioception) and the spinothalamic tract (pain, temperature, itch and crude touch). The brain stem also plays an important role in the regulation of cardiac and respiratory function. It also regulates the central nervous system, and is pivotal in maintaining consciousness and regulating the sleep cycle. Some taxonomies describe the brain stem as the medulla oblongata (myelencephalon) and pons (part of metencephalon), whereas others include the midbrain (mesencephalon). [WP,unvetted].
id: UBERON:0002298 ! brainstem
relationship: has_function_in MBO:0000312  {source="obol"} !  regulation of sleep

[Term]
! The nasolacrimal duct (sometimes called tear duct) carries tears from the lacrimal sac into the nasal cavity. Excess tears flow through nasolacrimal duct which opens in the nose. This is the reason the nose starts to run when a person is crying or has watery eyes from an allergy, and why one can sometimes taste eye drops. Like the lacrimal sac, the duct is lined by stratified columnar epithelium containing mucus-secreting goblet cells, and is surrounded by connective tissue. Obstruction of the nasolacrimal duct leads to the excess overflow of tears called epiphora. A congenital obstruction can cause cystic expansion of the duct and is called a dacrocystocele or Timo cyst. Persons with dry eye conditions can be fitted with punctal plugs that seal the ducts to limit the amount of fluid drainage and retain moisture. The canal containing the nasolacrimal duct is called the nasolacrimal canal. [WP,unvetted].
id: UBERON:0002392 ! nasolacrimal duct
relationship: has_function_in MBO:0000042  {source="obol"} !  tear secretion

[Term]
! a gelatinous membrane located in the vestibular apparatus of the inner ear, and plays an essential role in the brain's interpretation of equilibrium. Both the saccular macula and utricular macula are covered by an otolithic membrane. The membrane is composed of crystalline particles of calcium carbonate called otoliths. When the head is moved the otoliths shift, causing cilia in the nearby saccule and utricle to distort. This produces nerve signals which are sent to the brain, which then uses them to establish its sense of balance. The embedded crystals are very and dense and make the density of the otolithic membrane higher than that of the endolymph surrounding it. When the head accelerates along a line or tilts to change its orientation to gravity, the otolithic membrane shifts relative to the bone supporting the maculae. This shift bends the hair cells whose processes are embedded in the otolithic membrane.[WP].
id: UBERON:0002519 ! otolithic membrane
relationship: has_function_in MBO:0000070  {source="obol"} !  tilting

[Term]
! Anatomical surface structure found in many aquatic organisms. It is a respiration organ whose function is the extraction of oxygen from water and the excretion of carbon dioxide. The microscopic structure of a gill is such that it presents a very large surface area to the external environment. Gills usually consist of thin filaments of tissue, branches, or slender tufted processes which have a highly folded surface to increase surface area. A high surface area is crucial to the gas exchange of aquatic organisms as water contains only 1/20 parts dissolved Oxygen compared to air. With the exception of some aquatic insects, the filaments and lamellae (folds) contain blood or coelomic fluid, from which gases are exchanged through the thin walls. Oxygen is carried by the blood to other parts of the body. Carbon dioxide passes from the blood through the thin gill tissue into the water. Gills or gill-like organs, located in different parts of the body, are found in various groups of aquatic animals, including mollusks, crustaceans, insects, fish, and amphibians.
id: UBERON:0002535 ! gill
relationship: has_function_in MBO:0000038  {source="obol"} !  excretion

[Term]
! The ventral trigeminothalamic tract serves as pain, temperature, and light touch pathway from the face, head and neck. It receives input from trigeminal nerve, facial nerve, glossopharyngeal nerve and vagus nerve. It receives discriminative tactile and pressure input from the contralateral principal sensory nucleus of CN V, which terminates in the ventral posteromedial nucleus of the thalamus. It then ascends to the contralateral sensory cortex via three neurons . [WP,unvetted].
id: UBERON:0002549 ! ventral trigeminal tract
relationship: has_function_in MBO:0000331  {source="obol"} !  nociceptive behaviour

[Term]
! The pretectum, also known as the pretectal area, is a region of neurons found between the thalamus and midbrain. It receives binocular sensory input from retinal ganglion cells of the eyes, and is the region responsible for maintaining the pupillary light reflex. [WP,unvetted].
id: UBERON:0002565 ! olivary pretectal nucleus
relationship: has_function_in MBO:0000412  {source="obol"} !  pupillary light reflex

[Term]
! The reticular formation is a part of the brain that is involved in actions such as awaking/sleeping cycle, and filtering incoming stimuli to discriminate irrelevant background stimuli. It is essential for governing some of the basic functions of higher organisms, and is one of the phylogenetically oldest portions of the brain. [WP,unvetted].
id: UBERON:0002573 ! pontine reticular formation
relationship: has_function_in MBO:0000277  {source="obol"} !  discrimination

[Term]
! The principal sensory nucleus (or chief sensory nucleus of V) is a group of second order neurons which have cell bodies in the dorsal Pons. It receives information about discriminative sensation and light touch of the face as well as conscious proprioception of the jaw via first order neurons of CN V. Most of the sensory information crosses the midline and travels to the contralateral ventral posteriomedial (VPM) of the thalamus via the Ventral Trigeminothalamic Tract, but information of the oral cavity travels to the ipsilateral Ventral Posteriomedial (VPM) of the thalamus via the Dorsal Trigeminothalamic Tract. [WP,unvetted].
id: UBERON:0002597 ! principal sensory nucleus of trigeminal nerve
relationship: has_function_in MBO:0000277  {source="obol"} !  discrimination

[Term]
! The trigeminal motor nucleus contains motor neurons that innervate muscles of the first branchial arch, namely the muscles of mastication, the tensor tympani, tensor veli palatini, mylohyoid, and anterior belly of the digastric.
id: UBERON:0002633 ! motor nucleus of trigeminal nerve
relationship: has_function_in MBO:0000073  {source="obol"} !  mastication

[Term]
! The angular gyrus is a region of the brain in the parietal lobe, that lies near the superior edge of the temporal lobe, and immediately posterior to the supramarginal gyrus; it is involved in a number of processes related to language, mathematics and cognition. It is Brodmann area 39 of the human brain. [WP,unvetted].
id: UBERON:0002686 ! angular gyrus
relationship: has_function_in MBO:0000607  {source="obol"} !  cognition

[Term]
! The ventral tegmentum (tegmentum is Latin for covering), better known as the ventral tegmental area (VTA), is a group of neurons located close to the midline on the floor of the midbrain. The VTA, the origin of dopaminergic cell bodies that comprise the mesocorticolimbic dopamine system, is widely implicated in the drug and natural reward circuitry of the brain, cognition, motivation, drug addiction, and several psychiatric disorders. The VTA contains neurons that project to numerous areas of the brain, from the prefrontal cortex (PFC) to the caudal brainstem and everywhere in between. [WP,unvetted].
id: UBERON:0002691 ! ventral tegmental area
relationship: has_function_in MBO:0000607  {source="obol"} !  cognition

[Term]
! The spino-olivary tract is located in the ventral funiculus of the spinal cord. This tract carries proprioception information from muscles and tendons as well as cutaneous impulses to the olivary nucleus. [WP,unvetted].
id: UBERON:0002719 ! spino-olivary tract
relationship: has_function_in MBO:0000317  {source="obol"} !  proprioception

[Term]
! The medial dorsal nucleus (or dorsomedial nucleus of thalamus) is a large nucleus in the thalamus. It receives inputs from the Pre-Frontal Cortex and the Limbic System and in turn relays them to the Pre-Frontal Association Cortex. As a result, it plays a crucial role in attention, planning, organization, abstract thinking, multi-tasking and active memory. The connections of the medial dorsal nucleus have even been used to delineate the prefrontal cortex of the GC6ttingen minipig brain. By stereology the number of brain cells in the region has been estimated to around 6.43 million neurons in the adult human brain and 36.3 million glial cells, and with the newborn having quite different numbers: around 11.2 million neurons and 10.6 million glial cells. Lesions of the medial dorsal nucleus have been associated with Wernicke's encephalopathy [WP,unvetted].
id: UBERON:0002739 ! medial dorsal nucleus
relationship: has_function_in MBO:0000455  {source="obol"} !  attention

[Term]
! The basal forebrain is a collection of structures located ventrally to the striatum. It is considered to be the major cholinergic output of the CNS. It includes a group of structures that lie near the bottom of the front of the brain, including the nucleus basalis, diagonal band of Broca, and medial septal nuclei. These structures are important in the production of acetylcholine, which is then distributed widely throughout the brain. Acetylcholine affects the ability of brain cells to transmit information to one another, and also encourages plasticity, or learning. Thus, damage to the basal forebrain can reduce the amount of acetylcholine in the brain and impair learning. This may be one reason why basal forebrain damage can result in memory impairments such as amnesia and confabulation. One common cause of basal forebrain damage is aneurysm of the anterior communicating artery. Research, conducted by investigators from Children's Hospital Boston and the University of Helsinki, ties together previous observations about sleep and finds that nitric oxide production in the basal forebrain is both necessary and sufficient to produce sleep. This structure is defined, in part, as the place where adenosine acts on A1 receptors of cholinergic neurons. This results in hyperpolarization of cholinergic neurons, which inhibits the release of acetylcholine. Acetylcholine is known to promote wakefulness in the basal forebrain. Inhibition of acetylcholine release in the basal forebrain by adenosine causes slow wave sleep. The basal forebrain and adjacent areas are a focus for sleep research. Stimulating the basal forebrain gives rise to EEG sychrony and sleep. [WP,unvetted].
id: UBERON:0002743 ! basal forebrain
relationship: has_function_in MBO:0000215  {source="obol"} !  observational learning

[Term]
! The inferior temporal gyrus is placed below the middle temporal sulcus, and is connected behind with the inferior occipital gyrus; it also extends around the infero-lateral border on to the inferior surface of the temporal lobe, where it is limited by the inferior sulcus. This region is one of the higher levels of the ventral stream of visual processing, associated with the representation of complex object features, such as global shape. It may also be involved in face perception. [WP,unvetted].
id: UBERON:0002751 ! inferior temporal gyrus
relationship: has_function_in MBO:0000454  {source="obol"} !  perception

[Term]
! The dorsal spinocerebellar tract (posterior spinocerebellar tract, Flechsig's fasciculus, Flechsig's tract) conveys proprioceptive information from the body to the cerebellum. It is part of the somatosensory system and runs in parallel with the ventral spinocerebellar tract. Proprioceptive information is taken to the via central processes of dorsal root ganglia (first order neurons). These central processes travel through the dorsal horn where they synapse with second order neurons of Clarke's nucleus. Axon fibers from Clarke's Nucleus convey this proprioceptive information in the spinal cord in the peripheral region of the posteriolateral funiculus ipsilaterally until it reaches the cerebellum, where unconscious proprioceptive information is processed. This tract involves two neurons and ends up on the same side of the body. [WP,unvetted].
id: UBERON:0002753 ! posterior spinocerebellar tract
relationship: has_function_in MBO:0000317  {source="obol"} !  proprioception

[Term]
! The Anterior cingulate cortex (ACC) is the frontal part of the cingulate cortex, that resembles a 'collar' form around the corpus callosum, the fibrous bundle that relays neural signals between the right and left cerebral hemispheres of the brain. It includes both the ventral and dorsal areas of the cingulate cortex, and appears to play a role in a wide variety of autonomic functions, such as regulating blood pressure and heart rate, as well as rational cognitive functions, such as reward anticipation, decision-making, empathy and emotion. [WP,unvetted].
id: UBERON:0002756 ! anterior cingulate gyrus
relationship: has_function_in MBO:0000607  {source="obol"} !  cognition

[Term]
! The cupula is a structure in the vestibular system, sensing proprioception. The cupula is located within the ampullae of each of the three semicircular canals. As fluid rushes by the cupula, hair cells within it sense rotational acceleration, and transmit the corresponding signal to the brain through the vestibulocochlear nerve (CN VIII) In their natural orientation within the head, the cupulae are located on the medial aspect of the semicircular canals. In this orientation, the kinocilia rest on the posterior aspect of the cupula. [WP,unvetted].
id: UBERON:0002819 ! apex of cochlea
relationship: has_function_in MBO:0000317  {source="obol"} !  proprioception

[Term]
! The olfactory cortex is involved in the perception of smell. It receives input from the olfactory bulb and is responsible for the identification of odors[GO].
id: UBERON:0002894 ! olfactory cortex
relationship: has_function_in MBO:0000454  {source="obol"} !  perception

[Term]
! a long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in the spinal cord towards target cells in the thalamus. This axonal process is a member of those that make up the spinothalamic tract, one of the major routes of nociceptive signaling[GO].
id: UBERON:0002944 ! spinothalamic tract of medulla
relationship: has_function_in MBO:0000331  {source="obol"} !  nociception

[Term]
! A portion of the cerebral cortex that, with the paleocortex, develops in association with the olfactory system, and which is phylogenetically older than the neocortex and lacks its layered structure. The embryonic archicortex corresponds to the cortex of the dentate gyrus and hippocampus in mature mammals. Being part of the limbic system, it has functions related to emotions and formation of memory. Signals being sent from the limbic lobe to the hippocampal formations can go via the archicortex as an intermediate.
id: UBERON:0002961 ! archicortex
relationship: has_function_in MBO:0000191  {source="obol"} !  emotional memory

[Term]
! The caudal pontine reticular nucleus is composed of gigantocellular neurons. In rabbits and cats it is exclusively giant cells, however in humans there are normally sized cells as well. The pontis caudalis is rostral to the gigantocellular nucleus and is located in the caudal pons, as the name would indicate. The pontis caudalis has been known to mediate head movement, in concert with the nucleus gigantocellularis and the superior colliculus. The neurons in the dorsal half of this nuclei fire rhythmically during mastication, and in an anesthetized animal it is possible to induce mastication via electrical stimulation of the PC or adjacent areas of the gigantocellular nucleus. The pontis caudalis is also thought to play a role in the grinding of teeth during sleep. [WP,unvetted].
id: UBERON:0002963 ! caudal pontine reticular nucleus
relationship: has_function_in MBO:0000020  {source="obol"} !  head movement

[Term]
! A gyrus in the medial part of the brain. It partially wraps around the corpus callosum and is limited above by the cingulate sulcus. The cortical part of the cingulate gyrus is referred to as cingulate cortex.[Wikipedia]. The cingulate gyrus receives inputs from the anterior nucleus of the thalamus and the neocortex, as well as from somatosensory areas of the cerebral cortex. It projects to the entorhinal cortex via the cingulum. It functions as an integral part of the limbic system, which is involved with emotion formation and processing, learning, and memory. Also, executive control needed to suppress inappropriate unconscious priming is known to involve the anterior cingulate gyrus. It is also involved in respiratory control.
id: UBERON:0002967 ! cingulate gyrus
relationship: has_function_in MBO:0000191  {source="obol"} !  emotional memory

[Term]
! The ventral spinocerebellar tract conveys proprioceptive information from the body to the cerebellum. It is part of the somatosensory system and runs in parallel with the dorsal spinocerebellar tract. Both these tracts involve two neurons and end up on the same side of the body. The ventral tract (under L2/L3) gets its proprioceptive/fine touch/vibration information from a first order neuron, with its cell body in a dorsal ganglion. The axon runs via the fila radicularia to the dorsal horn of the grey matter. There it makes a synapse with the dendrites of two neurons: they send their axons bilaterally to the ventral border of the lateral funiculi. The ventral spinocerebellar tract then enters the cerebellum via the superior cerebellar peduncle. This is in contrast with the dorsal spinocerebellar tract (C8 - L2/L3), which only has 1 unilateral axon that has its cell body in the Clarke's nuclei (only at the level of C8 - L2/L3). The fibers of the ventral spinocerebellar tract then eventually enter the cerebellum via the superior cerebellar peduncle. This is one of the few afferent tracts through the superior cerebellar peduncle. Originates from ventral horn at lumbosacral spinal levels. Axons first cross midline in the spinal cord and run in the ventral border of the lateral funiculi. These axons ascend up to the pons where they join the superior cerebellar peduncle to enter the cerebellum. Once in the deep white matter of the cerebellum, the axons recross the midline, give off collaterals to the globose and emboliform nuclei, and terminate in the cortex of the anterior lobe and vermis of the posterior lobe. [WP,unvetted].
id: UBERON:0002987 ! anterior spinocerebellar tract
relationship: has_function_in MBO:0000317  {source="obol"} !  proprioception

[Term]
! The oral pontine reticular nucleus is delineated from its caudal brother, with which it shares its first three names. This nucleus tapers into the lower mesencephalic reticular formation and contains sporadic giant cells. Different populations of the pontis oralis have displayed discharge patterns which coordinate with phasic movements to and from paradoxical sleep. From this information it has been implied that the n.r. pontis oralis is involved in the mediation of changing to and from REM sleep. [WP,unvetted].
id: UBERON:0002999 ! oral pontine reticular nucleus
relationship: has_function_in MBO:0000158  {source="obol"} !  sleep pattern

[Term]
! The pontine tegmentum is a part of the pons of the brain involved in the initiation of REM sleep. It includes the pedunculopontine nucleus and the laterodorsal tegmental nucleus, among others, and is located near the raphe nucleus and the locus ceruleus. The trapezoid body is part of the pontine tegmentum. [WP,unvetted].
id: UBERON:0003023 ! pontine tegmentum
relationship: has_function_in MBO:0000159  {source="obol"} !  REM sleep

[Term]
! any of the muscles responsible for the movement of the jaws during mastication, including the masseter, temporal, and medial and lateral pterygoid muscles.
id: UBERON:0003681 ! masticatory muscle
relationship: has_function_in MBO:0000073  {source="obol"} !  mastication

[Term]
! A joint of the jaw. There are two TMJs, one on either side, working in unison. The name is derived from the two bones which form the joint: the upper temporal bone which is part of the cranium (skull), and the lower jaw bone called the mandible. The unique feature of the TMJs is the articular disc. The disc is composed of fibrocartilagenous tissue (like the firm and flexible elastic cartilage of the ear) which is positioned between the two bones that form the joint. The TMJs are one of the only synovial joints in the human body with an articular disc, another being the sternoclavicular joint. The disc divides each joint into two. The lower joint compartment formed by the mandible and the articular disc is involved in rotational movement -- this is the initial movement of the jaw when the mouth opens. The upper joint compartment formed by the articular disk and the temporal bone is involved in translational movement -- this is the secondary gliding motion of the jaw as it is opened widely. The part of the mandible which mates to the under-surface of the disc is the condyle and the part of the temporal bone which mates to the upper surface of the disk is the glenoid (or mandibular) fossa[WP].
id: UBERON:0003700 ! temporomandibular joint
relationship: has_function_in MBO:0000001  {source="obol"} !  body part movement

[Term]
! the sensory organs in muscle that are involved in the stretch reflex.
id: UBERON:0003718 ! muscle spindle
relationship: has_function_in MBO:0000404  {source="obol"} !  stretch reflex

[Term]
! hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food.
id: UBERON:0003913 ! tooth-like structure
relationship: has_function_in MBO:0000073  {source="obol"} !  mastication

[Term]
! the paired regions of the cerebellar hemisphere that lie adjacent to the vermis and are between the vermis and lateral regions of the hemispheres; it receives input from the corticopontocerebellar fibers that originate from the motor cortex, and also receives sensory feedback from the muscles; these signals are integrated by this region, to coordinate muscle activity with motor inputs
id: UBERON:0004006 ! cerebellum intermediate hemisphere
relationship: has_function_in MBO:0000339  {source="obol"} !  motor coordination

[Term]
! the sensory organ in muscle; involved in the stretch reflex and sensitive to stretch velocity
id: UBERON:0004010 ! primary muscle spindle
relationship: has_function_in MBO:0000404  {source="obol"} !  stretch reflex

[Term]
! the sensory organ in muscle; involved in the stretch reflex and not sensitive to stretch velocity
id: UBERON:0004011 ! secondary muscle spindle
relationship: has_function_in MBO:0000404  {source="obol"} !  stretch reflex

[Term]
! The collecting duct system of the kidney consists of a series of tubules and ducts that connect the nephrons to the ureter. It participates in electrolyte and fluid balance through reabsorption and excretion, processes regulated by the hormones aldosterone and antidiuretic hormone.
id: UBERON:0004100 ! renal collecting system
relationship: has_function_in MBO:0000038  {source="obol"} !  excretion

[Term]
! the trigeminothalamic tract is one of the major routes of nociceptive and temperature signaling from the face
id: UBERON:0004171 ! trigeminothalamic tract
relationship: has_function_in MBO:0000331  {source="obol"} !  nociception

[Term]
! The vestibular system, which contributes to our balance and our sense of spatial orientation, is the sensory system that provides the dominant input about movement and equilibrioception. Together with the cochlea, a part of the auditory system, it constitutes the labyrinth of the inner ear, situated in the vestibulum in the inner ear. As our movements consist of rotations and translations, the vestibular system comprises two components: the semicircular canal system, which indicate rotational movements; and the otoliths, which indicate linear accelerations. The vestibular system sends signals primarily to the neural structures that control our eye movements, and to the muscles that keep us upright. The projections to the former provide the anatomical basis of the vestibulo-ocular reflex, which is required for clear vision; and the projections to the muscles that control our posture are necessary to keep us upright.
id: UBERON:0004681 ! vestibular system
relationship: has_function_in MBO:0000444  {source="obol"} !  eye movement

[Term]
! The septum pellucidum is made up of two thin sheets of mostly glial-like elements that abut each other in the midline and have a potential space between them. Those sheets also separate the left and right lateral ventricles from each other. At the base of the sheets rostrally, however, are the septal nuclei, which are important components of the limbic system.a thin, triangular, vertical membrane separating the lateral ventricles of the brain. It separates the anterior horn of the left and right lateral ventricles. It runs as a sheet from the corpus callosum down to the fornix. When the hemispheres are cut apart, the septum remains on one hemisphere, usually the left. The septum pellucidum is implicated in pleasure, mood, rage, sexual gratification and more. Lesions of the septum lead to sham rage. Stimulation of the medial forebrain bundle (primary efferent of the septum) restores normal behavior.
id: UBERON:0004714 ! septum pellucidum
relationship: has_function_in MBO:0000230  {source="obol"} !  pleasure

[Term]
! an organ for excreting excess salts. It is found in elasmobranchs, seabirds, and some reptiles. In sharks, salt glands are found in the rectum, but in birds and reptiles, they are found in or on the skull, in the area of the eyes, nostrils or mouth. In crocodiles, the salt is excreted through the tongue. Such glands work by active transport via sodium-potassium pump that moves salt from the blood into the gland, where it can be excreted as a concentrated solution. Salt glands function to keep salt balance, and allow marine vertebrates to drink seawater[WP].
id: UBERON:0004758 ! salt gland
relationship: has_function_in MBO:0000038  {source="obol"} !  excretion

[Term]
! a urethral sphincter muscle which constricts the internal urethral orifice. It is the junction of the urethra with the urinary bladder. The muscle is made of smooth muscle, so therefore it is under involuntary control. It is kept tonically contracted by the sympathetic nervous system and during micturition, is relaxed via the parasympathetic nervous system. This is the primary muscle for preventing the release of urine[WP].
id: UBERON:0004918 ! internal urethral sphincter
relationship: has_function_in MBO:0000040  {source="obol"} !  micturition

[Term]
! The avian beak is an external anatomical structure, in the head region, that is adapted for feeding self and young, catching prey, probing, etc. It encompasses, but is not restricted to, the maxilla, mandible, maxillary ramaphotheca, mandibular ramaphotheca, nostril, nasal fossa, nasal bones, egg tooth and rictus[GO]. The beak, bill or rostrum is an external anatomical structure of birds which is used for eating and for grooming, manipulating objects, killing prey, probing for food, courtship and feeding young. The term beak is also used to refer to a similar mouthpart in some Ornithischian dinosaurs, monotremes, cephalopods, cetaceans, pufferfishes, turtles, Anuran tadpoles and sirens[WP].
id: UBERON:0005094 ! beak
relationship: has_function_in MBO:0000451  {source="obol"} !  self-grooming

[Term]
! area of white matter in the dorsomedial side of the spinal cord. It is made up of the fasciculus gracilis and fasciculus cuneatus and itself is part of the dorsal funiculus. It is part of an ascending pathway that is important for well-localized fine touch and conscious proprioception called the posterior column-medial lemniscus pathway[WP]. The dorsal portion of the gray substance of the spinal cord, in transverse section seen as a horn[TFD]. The dorsal column is a part of the spinal cord which is responsible for transporting sensory input from the body to the cerebral cortex. This part of the spinal cord is key in perceiving fine touch, such as that used to distinguish textures, along with vibration. The dorsal column also contributes to the body's system of proprioception, used to orient the body in space and to coordinate muscle movements, given information about the body's position.
id: UBERON:0005373 ! spinal cord dorsal column
relationship: has_function_in MBO:0000001  {source="obol"} !  body part movement

[Term]
! Those portions of the caudate nucleus and especially the putamen located generally superior to a plane representing the anterior commissure; also called the dorsal basal ganglia; may function in motor activities with cognitive origins.
id: UBERON:0005382 ! dorsal striatum
relationship: has_function_in MBO:0000607  {source="obol"} !  cognition

[Term]
! Control of blood pressure is crucially dependent on the integrity of a small region of the brainstem called the ventrolateral medulla. Within this part of the brain are the cells that control the heart, blood vessels, swallowing, breathing and many other functions of the body that are not noticed at a conscious level; such unconscious activities are known as 'Autonomic'. One of these regions is the Rostral Ventrolateral Medulla (RVLM) is also known as the pressor area of the medulla (medulla pressor). It receives inhibitory GABAergic input from the caudal ventrolateral medulla (CVLM). The RVLM is the primary regulator of the sympathetic nervous system, sending excitatory fibers (catecholaminergic) to the sympathetic preganglionic neurons in the spinal cord, via reticulospinal tract[WP].
id: UBERON:0005807 ! rostral ventrolateral medulla
relationship: has_function_in MBO:0000545  {source="obol"} !  swallowing

[Term]
! a group of axons that are from neurons involved in proprioception from the lower trunk and lower limb[GO]. The fasciculus gracilis (tract of Goll) is a bundle of axon fibres in the dorsomedial spinal cord that carries information about fine touch, vibrations, and conscious proprioception from the lower part of the body to the brain stem. It is part of the posterior column of the spinal cord, which also contains the fasciculus cuneatus, which carries the same information from the upper part of the body. This tract and its continuation in the brain stem is often referred to as the posterior column-medial lemniscus pathway. The fasciculus gracilis is wedge-shaped on transverse section and lies next the posterior median septum, its base being at the surface of the medulla spinalis, and its apex directed toward the posterior gray commissure. It increases in size from below upward, and consists of long thin fibers that are derived from the posterior nerve roots, and ascend as far as the medulla oblongata, where they end in the nucleus gracilis. The tract of Goll was named after Swiss neuroanatomist Friedrich Goll[WP].
id: UBERON:0005821 ! gracile fasciculus
relationship: has_function_in MBO:0000317  {source="obol"} !  proprioception

[Term]
! A jointed or prehensible appendage used for locomotion or manipulation. Examples: human arm, human leg, octopus tentacle, insect limb[Wikipedia]. A limb is an appendage of an animal used for locomotion or grasping. For example a leg, arm or some types of fin[GO].
id: UBERON:0005896 ! jointed/prehensile appendage
relationship: has_function_in MBO:0000584  {source="obol"} !  limb grasping

[Term]
! The medial pterygoid (or internal pterygoid muscle), is a thick, quadrilateral muscle of mastication. The mandibular branch of the fifth cranial nerve, the trigeminal nerve, innervates the medial pterygoid muscle.
id: UBERON:0006718 ! medial pterygoid muscle
relationship: has_function_in MBO:0000073  {source="obol"} !  mastication

[Term]
! The lateral pterygoid (or external pterygoid) is a muscle of mastication with two heads.
id: UBERON:0006719 ! lateral pterygoid muscle
relationship: has_function_in MBO:0000073  {source="obol"} !  mastication

[Term]
! The swim bladder is a double-chambered organ located in the coelom and used to maintain buoyancy and may function as an acoustic resonator. The zebrafish does not appear to have a gas gland, but it is not yet clear if there are gas producing cells distributed more widely.
id: UBERON:0006860 ! swim bladder
relationship: has_function_in MBO:0000371  {source="obol"} !  swimming

[Term]
! The premolar teeth or bicuspids are transitional teeth located between the canine and molar teeth. In humans, there are two premolars per quadrant, making eight premolars total in the mouth. They have at least two cusps. Premolars can be considered as a 'transitional tooth' during chewing, or mastication. It has properties of both the anterior canines and posterior molars, and so food can be transferred from the canines to the premolars and finally to the molars for grinding, instead of directly from the canines to the molars. The premolars in humans are the maxillary first premolar, maxillary second premolar, mandibular first premolar, and the mandibular second premolar. There is always one large buccal cusp, especially so in the mandibular first premolar. The lower second premolar almost always presents with two lingual cusps. Premolar teeth by definition are permanent teeth distal to the canines preceded by deciduous molars. In primitive mammals there are four premolars per quadrant. The most mesial two have been lost in Catarrhines. Paleontologists refer to human premolars as Pm3 and Pm4.
id: UBERON:0007120 ! premolar tooth
relationship: has_function_in MBO:0000420  {source="obol"} !  teeth grinding

[Term]
! A dermatome is an area of skin that is mainly supplied by a single spinal nerve. There are eight cervical nerves, twelve thoracic nerves, five lumbar nerves and five sacral nerves. Each of these nerves relays sensation (including pain) from a particular region of skin to the brain[WP].
id: UBERON:0007121 ! dermatome segment of skin
relationship: has_function_in MBO:0000331  {source="obol"} !  nociceptive behaviour

[Term]
! The upper esophageal sphincter (UES) (also called the Pharyngoesophageal sphincter) refers to the superior portion of the esophagus. Unlike the lower esophageal sphincter, it consists of striated muscle and is under conscious control. The primary muscle of the UES is the cricopharyngeus portion of the inferior pharyngeal constrictor. During swallowing the upper esophageal sphincter opens so the bolus can pass into the esophagus. A secondary role of the UES is to reduce backflow from the esophagus into the pharynx.
id: UBERON:0007268 ! upper esophageal sphincter
relationship: has_function_in MBO:0000545  {source="obol"} !  swallowing

[Term]
! The nidopallium, meaning nested pallium, is the region of the avian brain that is used mostly for some types of executive functions but also other higher cognitive tasks. The region was renamed to nidopallium in 2002 during the Avian Brain Nomenclature Consortium because the prior name suggested that the region was used for more primitive functions.
id: UBERON:0007334 ! nidopallium
relationship: has_function_in MBO:0000607  {source="obol"} !  cognition