replace neuro defs with those from nifstd #300

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cmungall opened this Issue Jul 9, 2013 · 11 comments

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cmungall commented Jul 9, 2013

Replace any from Wikipedia, Obol

Other sources considered individually

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cmungall commented Jul 9, 2013

Leaving ganglion as is, NIFSTD too vertebrate specific. To be revisited.

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cmungall commented Jul 9, 2013

current:
def: "pia mater or arachnoid mater." [Wikipedia:Leptomeninges]

NIFSTD:
def: "Delicate meningeal covering of the brain and spinal cord, consisting of an outer arachnoid membrane that sits beneath the dura and an inner pial membrane that lies on the surface of the brain and spinal cord." [NIF_GrossAnatomy:nlx_anat_090207]

Leaving as is, as the def better matches the current modeling (class union rather than mereological sum)

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cmungall commented Jul 9, 2013

We need a good cross-metazoan definition for brain. See also 'ganglion' above.

The wikipedia def, whilst not perfect, is not vert-centric unlike the NIFSTD one

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cmungall commented Jul 9, 2013

gustatory system: do we need a superclass sensory system?

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cmungall commented Jul 9, 2013

Uberon:
def: "Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified]." [Wikipedia:Metencephalon]

NIFGA:
"Anterior part of the hindbrain ventral to the cerebellum[NIF_GrossAnatomy:birnlex_965]."

Currently uberon includes cerebellum as part of the metencephalon (consistent with FMA and MA). Requires further discussion

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cmungall commented Jul 9, 2013
id: UBERON:0001906
name: subthalamic nucleus
def: "Lens shaped nucleus lying in the subthalamus" [NIF_GrossAnatomy:nlx_anat_1010002]
def: "The subthalamic nucleus is the lens-shaped nucleus located in the ventral part of the subthalamus on the inner aspect of the internal capsule that is concerned with the integration of somatic motor function[GO]." [GO:0021763]

is the GO one too specific?

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cmungall commented Jul 9, 2013

I think we need a more compact def of the subventricular zone. Of the 3 below, the MP is the most precise and succinct?

id: UBERON:0004922
name: postnatal subventricular zone
def: "A mitotically active layer of cells surrounding the brain ventricles in the adult that consists of migrating neuroblasts, astrocytes and transitory amplifying progenitor cells[MP]." [MP:0004275]
def: "The subventricular zone (SVZ) is one of two sources of adult-born neurons in the mammalian brain, the other being the subgranular zone (SGZ) of the hippocampus. In most adult mammals, the SVZ is a three-layered sheath that lies along the lateral wall of the lateral ventricle and consists of type A, B, and C cells. Type A rest along the ventricle wall and are neuronal precursor cells, Type B are adjacent astrocytes, and Type C are immature precursors to the Type A neuroblasts. The neuronal precursor cells travel along the rostral migratory stream ensheathed in a tube of Type B astrocytes, until they reach the olfactory bulb. There they integrate into the existing cellular network and mature into local interneurons. While the majority become adult-born granule cells, a subset become periglomerular cells. Interestingly, the human SVZ differs from other mammals' in several ways. It consists of four layers rather than three: ependymal cells (layer I), a hypo cellular gap (layer II), a ribbon of astrocytes (layer III), and a transitional zone (layer IV). The astrocytes are capable of differentiating into many kinds of tissue including new neurons. However, there is no evidence that the proliferating neurons travel along the rostral migratory stream in a chain to populate the olfactory bulb with new interneurons, as is the case for other mammals." [NIF_GrossAnatomy:nlx_144262]
def: "A paired brain structure situated throughout the lateral walls of the lateral ventricles. It has been associated with having four distinct layers of variable thickness and cell density, as well as cellular composition[WP]." [Wikipedia:Subventricular_zone]

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We retain the uberon def here as it is less mammal specific (some amniotes have two meninges; zebrafish has a single meninx)

[Term]
id: UBERON:0002360 ! meninx
-def: "Membrane organ that surrounds the brain and the spinal cord." [http://www.shsu.edu/~bio_mlt/Chap15.html,Wikipedia:Meninx,FMA:9589]
+def: "One of three membranous coverings that surrounds the brain and spinal cord" [NIF_GrossAnatomy:nlx_anat_090204]
@cmungall
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Need a CUMBO decision on this:

id: UBERON:0001020
name: white matter commissure
def: "White matter fiber bundle that crosses the midline of the brain or spinal cord[NIF]. In the context of Drosophila refers to a broad band of axons connecting the same neuropils each side of the brain[FBbt]." [NIF_GrossAnatomy:nlx_anat_20090513, UBERON:cjm]

We want either the def to be applicable to inverts OR to split the class

@cmungall
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I don't think either is perfect. The NIFSTD one doesn't reflect how the structure is modeled (as a structure rather than a cavity - there is a separate class for the lumen). Also needs checked for cross-vert applicability

[Term]
id: UBERON:0004086 ! brain ventricle
-def: "one of the system of communicating cavities in the brain that are continuous with the central canal of the spinal cord, that like it are derived from the medullary canal of the embryo, that are lined with an epithelial ependyma, and that contain a serous fluid" []
+def: "Organ cavity of the brain which consists of the lateral ventricles, the third and fourth ventricles and the cerebral aqueduct." [NIF_GrossAnatomy:birnlex_1356]
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This item is ready to be closed pending approval of NIFSTD curators on decisions made

@cmungall cmungall added a commit that referenced this issue Jul 12, 2013
@cmungall cmungall * Added UMLS xrefs for neuro subset using NCIT and NIFGA. Fixes issue
…#302

     * Replaced multiple text defs with those from NIFSTD. Fixes issue #300
     * Adding pons relationships for pontine tracts. Addresses issue #299
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@cmungall cmungall closed this Aug 22, 2014
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