- Author:
- David Brooks <dave@bcs.co.nz>
- Date:
- 2021-07-03 13:39:00+12:00
- Desc:
- Add missing path for `neuron_8`.
- Permanent Source URI:
- https://models.cellml.org/workspace/693/rawfile/78cc9437fb3a783a1db462679999f3d8fce35a2d/apinatomy.json
{
"publications": [],
"nodes": [],
"links": [
{
"id": "lnk-vag_spn",
"name": "soma in spinal trigeminal nucleus",
"source": "ns1",
"target": "ns2",
"conveyingLyph": "vag_spn"
},
{
"id": "lnk-vag_nts",
"name": "soma in nucleus tractus solitarius",
"source": "ns3",
"target": "ns4",
"conveyingLyph": "vag_nts"
},
{
"id": "lnk-vag_dmn",
"name": "soma in dorsal motor nucleus of vagus",
"source": "ns5",
"target": "ns6",
"conveyingLyph": "vag_dmn"
},
{
"id": "lnk-vag_na",
"name": "soma in nucleus ambiguus",
"source": "ns7",
"target": "ns8",
"conveyingLyph": "vag_na"
}
],
"lyphs": [
{
"id": "nseg",
"name": "Segment of nerve (vag)",
"external": [
"FMA:74941"
],
"subtypes": [
"TUBE"
],
"isTemplate": true,
"materials": [
"vm_3",
"vm_9"
]
},
{
"id": "vag",
"name": "vagus nerve(n_5)",
"external": [
"UBERON:0001759"
],
"supertype": "nseg"
},
{
"id": "med",
"name": "medulla (brain_27)",
"external": [
"UBERON:0001896"
],
"internalLyphs": [
"stn",
"nts",
"dmn",
"sg"
],
"internalLyphsInLayers": [
0,
0,
0,
0
]
},
{
"id": "stn",
"name": "spinal trigeminal nucleus (brain_40)",
"external": [
"UBERON:0001717"
],
"internalLyphs": [
"vag_spn"
]
},
{
"id": "nts",
"name": "nucleus tractus solitarius (brain_12)",
"external": [
"UBERON:0009050"
],
"internalLyphs": [
"vag_nts"
]
},
{
"id": "dmn",
"name": "dorsal motor nucleus of vagus (brain_39)",
"external": [
"UBERON:0002870"
],
"supertype": "nseg",
"internalLyphs": [
"vag_dmn"
]
},
{
"id": "na",
"name": "nucleus ambiguus (brain_33)",
"external": [
"UBERON:0001719"
],
"internalLyphs": [
"vag_na"
]
},
{
"id": "sg",
"name": "superior ganglion of vagus nerve (ganglion_1)",
"external": [
"UBERON:0005364"
]
},
{
"id": "jf",
"name": "jugular foramen (skull_1)",
"external": [
"UBERON:0005456"
]
},
{
"id": "dm_crafos",
"name": "dura mater in the posterior cranial fossa (skull_2)",
"external": [
"UBERON:0008788"
]
},
{
"id": "fl_eam",
"name": "floor of external acoustic meatus (body_9)",
"external": [
"UBERON:0001352"
]
},
{
"id": "ear",
"name": "ear (body_5)",
"external": [
"UBERON:0001690"
],
"internalLyphsInLayers": [
null,
null,
null
]
},
{
"id": "poswall_eam",
"name": "posterior wall of external acoustic meatus (body_10)",
"external": [
"UBERON:0001352"
]
},
{
"id": "os_tm",
"name": "outer surface of the tympanic membrane (body_11)",
"external": [
"FMA:56819"
]
},
{
"id": "cp_aurglo",
"name": "communicating point of auricular branch of vagus nerve and glossopharyngeal nerve 1 (point_2)",
"external": [
"FMA:53485"
],
"supertype": "nseg"
},
{
"id": "men",
"name": "meningeal branch of vagus nerve (n_6)",
"external": [
"FMA:6231"
],
"supertype": "nseg"
},
{
"id": "aur",
"name": "auricular branch of vagus nerve(n_7)",
"external": [
"FMA:6232"
],
"supertype": "nseg"
},
{
"id": "vag_spn",
"name": "soma in spinal trigeminal nucleus",
"external": [
"NLX:154731"
],
"supertype": "nseg"
},
{
"id": "vag_nts",
"name": "soma in nucleus tractus solitarius",
"external": [
"NLX:154731"
],
"supertype": "nseg"
},
{
"id": "vag_dmn",
"name": "soma in dorsal motor nucleus of vagus",
"external": [
"NLX:154731"
],
"supertype": "nseg"
},
{
"id": "vag_na",
"name": "soma in nucleus ambiguus",
"external": [
"NLX:154731"
],
"supertype": "nseg"
},
{
"id": "vag_sg",
"name": "soma in superior ganglion",
"external": [
"NLX:154731"
],
"supertype": "nseg"
},
{
"id": "unk",
"name": "posterior auricular nerve",
"external": [
"UBERON:0035647"
]
},
{
"id": "229",
"name": "Segment of neuron (fcolon)",
"external": [
"CL:0000540"
],
"isTemplate": true
}
],
"materials": [
{
"id": "vm_1",
"name": "endoneurium",
"external": [
"UBERON:0000123"
],
"materials": [
"vm_4",
"vm_6",
"vm_7"
]
},
{
"id": "vm_2",
"name": "perineurium",
"external": [
"UBERON:0000121"
],
"materials": [
"vm_4"
]
},
{
"id": "vm_3",
"name": "epineurium",
"external": [
"UBERON:0000124"
],
"materials": [
"vm_4"
]
},
{
"id": "vm_4",
"name": "connective tissue",
"external": [
"NCIT:C32367"
]
},
{
"id": "vm_5",
"name": "blood vessels",
"external": [
"UBERON:0001981"
]
},
{
"id": "vm_6",
"name": "lymphocyte",
"external": [
"FMA:62863"
]
},
{
"id": "vm_7",
"name": "fibroblasts",
"external": [
"FMA:63877"
]
},
{
"id": "vm_8",
"name": "collagen fibers",
"external": [
"FMA:63891"
]
},
{
"id": "vm_9",
"name": "endoneurial fluid",
"external": [
"UBERON:0011893"
]
},
{
"id": "vm_10",
"name": "Blood",
"external": [
"UBERON:0000178"
],
"materials": [
"vm_9"
]
},
{
"id": "vm_11",
"name": "Aqueous solution",
"external": [
"FMA:85815"
],
"materials": [
"vm_12",
"vm_13",
"vm_14",
"vm_15",
"vm_16",
"vm_17",
"vm_18",
"vm_19",
"vm_20",
"vm_21"
]
},
{
"id": "vm_12",
"name": "Water",
"external": [
"CHEBI:15377"
]
},
{
"id": "vm_13",
"name": "Sodium ion",
"external": [
"CHEBI:29101"
]
},
{
"id": "vm_14",
"name": "Potassium ion",
"external": [
"CHEBI:29103"
]
},
{
"id": "vm_15",
"name": "Calcium ion",
"external": [
"CHEBI:29108"
]
},
{
"id": "vm_16",
"name": "Chloride ion",
"external": [
"CHEBI:17996"
]
},
{
"id": "vm_17",
"name": "Hydrogen ion",
"external": [
"CHEBI:24636"
]
},
{
"id": "vm_18",
"name": "Hydroxide ion",
"external": [
"CHEBI:16234"
]
},
{
"id": "vm_19",
"name": "Bicarbonate ion",
"external": [
"CHEBI:17544"
]
},
{
"id": "vm_20",
"name": "Liquid",
"external": [
"FMA:85815"
]
},
{
"id": "vm_21",
"name": "Fluid",
"external": [
"UBERON:0006314"
]
},
{
"id": "vm_22",
"name": "Wall of vessel",
"external": [
"UBERON:0035965"
],
"materials": [
"vm_4"
]
},
{
"id": "vm_23",
"name": "Cytosol",
"external": [
"GO:0005829"
]
},
{
"id": "vm_24",
"name": "Plasma membrane",
"external": [
"GO:0005886"
]
},
{
"id": "vm_25",
"name": "Extracellular fluid",
"external": [
"GO:0005615"
]
}
],
"chains": [
{
"id": "dc-stn",
"name": "dendrite chain in spinal trigeminal nucleus",
"external": [
"SAO:1211023249"
],
"lyphTemplate": "nseg",
"root": "ns1",
"housingLyphs": [
"stn"
]
},
{
"id": "n_1",
"name": "axon chain in spinal trigeminal nucleus",
"external": [
"SAO:1770195789"
],
"lyphTemplate": "nseg",
"root": "ns2",
"leaf": "ns9",
"housingLayers": [
0,
0,
0
],
"housingLyphs": [
"stn",
"med",
"jf"
]
},
{
"id": "dc-nts",
"name": "dendrite chain in nucleus tractus solitarius",
"external": [
"SAO:1211023249"
],
"lyphTemplate": "nseg",
"root": "ns3",
"housingLyphs": [
"nts"
]
},
{
"id": "n_2",
"name": "axon chain in nucleus tractus solitarius",
"external": [
"SAO:1770195789"
],
"lyphTemplate": "nseg",
"root": "ns4",
"leaf": "ns9",
"housingLayers": [
0,
0,
0
],
"housingLyphs": [
"nts",
"med",
"jf"
]
},
{
"id": "dc-dmn",
"name": "dendrite chain in dorsal motor nucleus of vagus",
"external": [
"SAO:1211023249"
],
"lyphTemplate": "nseg",
"root": "ns5",
"housingLyphs": [
"dmn"
]
},
{
"id": "n_3",
"name": "axon chain in dorsal motor nucleus of vagus",
"external": [
"SAO:1770195789"
],
"lyphTemplate": "nseg",
"root": "ns6",
"leaf": "ns9",
"housingLayers": [
0,
0,
0
],
"housingLyphs": [
"dmn",
"med",
"jf"
]
},
{
"id": "dc-na",
"name": "dendrite chain in nucleus ambiguus",
"external": [
"SAO:1211023249"
],
"lyphTemplate": "nseg",
"root": "ns7",
"housingLyphs": [
"na"
]
},
{
"id": "n_4",
"name": "axon chain in nucleus ambiguus",
"external": [
"SAO:1770195789"
],
"lyphTemplate": "nseg",
"root": "ns8",
"leaf": "ns9",
"housingLayers": [
0,
0,
0
],
"housingLyphs": [
"na",
"med",
"jf"
]
},
{
"id": "n_5",
"name": "vagus nerve from jugular forman to superior ganglion of vagus nerve (point_1)",
"external": [
"SAO:1770195789"
],
"lyphTemplate": "nseg",
"root": "ns9",
"leaf": "ns11",
"housingLayers": [
0,
0
],
"housingLyphs": [
"jf",
"sg"
]
},
{
"id": "n_6",
"name": "meningeal branch of vagus nerve",
"external": [
"SAO:1770195789"
],
"lyphTemplate": "nseg",
"root": "ns11",
"leaf": "ns12",
"housingLayers": [
0,
0
],
"housingLyphs": [
"sg",
"dm_crafos"
]
},
{
"id": "n_7",
"name": "auricular branch of vagus nerve",
"external": [
"SAO:1770195789"
],
"lyphTemplate": "nseg",
"root": "ns11",
"leaf": "ns13",
"housingLayers": [
0,
0
],
"housingLyphs": [
"sg",
"cp_aurglo"
]
},
{
"id": "n_8",
"name": "communicating branch of auricular branch of vagus nerve with posterior auricular nerve",
"external": [
"SAO:1770195789"
],
"lyphTemplate": "nseg",
"root": "ns13",
"leaf": "ns14",
"housingLayers": [
0,
0
],
"housingLyphs": [
"cp_aurglo",
"unk"
]
},
{
"id": "n_9",
"name": "branch of auricular branch of vagus nerve to floor of external acoustic meatus",
"external": [
"SAO:1770195789"
],
"lyphTemplate": "nseg",
"root": "ns13",
"leaf": "ns15",
"housingLayers": [
0,
0
],
"housingLyphs": [
"cp_aurglo",
"fl_eam"
]
},
{
"id": "n_10",
"name": "branch of auricular branch of vagus nerve to posterior wall of external acoustic meatus",
"external": [
"SAO:1770195789"
],
"lyphTemplate": "nseg",
"root": "ns13",
"leaf": "ns16",
"housingLayers": [
0,
0
],
"housingLyphs": [
"cp_aurglo",
"poswall_eam"
]
},
{
"id": "n_11",
"name": "branch of auricular branch of vagus nerve to tympanic membrane",
"external": [
"SAO:1770195789"
],
"lyphTemplate": "nseg",
"root": "ns13",
"leaf": "ns17",
"housingLayers": [
0,
0
],
"housingLyphs": [
"cp_aurglo",
"os_tm"
]
},
{
"id": "md",
"name": "medulla",
"external": [
"UBERON:0001896"
],
"lyphs": [
"med",
"stn",
"nts",
"dmn",
"na"
],
"root": "node1",
"leaf": "node2"
},
{
"id": "skull_1",
"name": "jugular foramen",
"external": [
"UBERON:0005456"
],
"lyphs": [
"jf"
],
"root": "node3",
"leaf": "node5"
},
{
"id": "skull_2",
"name": "posterior cranial fossa",
"external": [
"UBERON:0001352"
],
"lyphs": [
"dm_crafos"
],
"root": "node5",
"leaf": "node8"
},
{
"id": "ganglion_1",
"name": "superior ganglion of vagus nerve",
"external": [
"UBERON:0005364"
],
"lyphs": [
"sg"
],
"root": "node7",
"leaf": "node11"
},
{
"id": "body_5",
"name": "ear",
"external": [
"UBERON:0001690"
],
"lyphs": [
"ear"
],
"root": "node9",
"leaf": "node14"
}
],
"groups": [
{
"id": "vag_ner",
"name": "vagus nerve",
"links": [
"lnk-vag_spn",
"lnk-vag_nts",
"lnk-vag_dmn",
"lnk-vag_na"
],
"nodes": [
"ns1",
"ns2",
"ns3",
"ns4",
"ns5",
"ns6",
"ns7",
"ns8",
"ns9",
"ns10",
"ns11",
"ns12",
"ns13",
"ns14"
]
}
],
"localConventions": [
{
"prefix": "UBERON",
"namespace": "http://purl.obolibrary.org/obo/UBERON_"
},
{
"prefix": "CHEBI",
"namespace": "http://purl.obolibrary.org/obo/CHEBI_"
},
{
"prefix": "FMA",
"namespace": "http://purl.org/sig/ont/fma/fma"
},
{
"prefix": "GO",
"namespace": "http://purl.obolibrary.org/obo/GO_"
},
{
"prefix": "ILX",
"namespace": "http://uri.interlex.org/base/ilx_"
},
{
"prefix": "NLX",
"namespace": "http://uri.neuinfo.org/nif/nifstd/nlx_"
},
{
"prefix": "SAO",
"namespace": "http://uri.neuinfo.org/nif/nifstd/sao"
},
{
"prefix": "PMID",
"namespace": "http://www.ncbi.nlm.nih.gov/pubmed/"
},
{
"prefix": "EMAPA",
"namespace": "http://purl.obolibrary.org/obo/EMAPA_"
},
{
"prefix": "CL",
"namespace": "http://purl.obolibrary.org/obo/CL_"
},
{
"prefix": "NCBITaxon",
"namespace": "http://purl.obolibrary.org/obo/NCBITaxon_"
}
],
"id": "vagus-nerve",
"name": "Vagus Nerve model"
}
