Permalink
Browse files

some terms required for MP definitions

  • Loading branch information...
1 parent 08004ca commit 6865a3c6ee3ccef663b2ba30c2555a303c9aa070 @cmungall cmungall committed Apr 18, 2012
Showing with 482 additions and 116 deletions.
  1. +482 −116 uberon_edit.obo
View
598 uberon_edit.obo
@@ -119,8 +119,6 @@ xref: AAO:0000311 ! naris
xref: EHDAA:9083 ! naris
xref: VHOG:0000663 ! naris
xref: MA:0000282 ! naris
-xref: TAO:0000550 ! naris
-xref: ZFA:0000550 ! naris
xref: galen:Naris ! naris
xref: EHDAA2:0001225 ! naris
xref: EMAPA:17847 ! naris
@@ -134,17 +132,18 @@ xref: SCTID:272650008 ! Naris, entire, anterior or posterior
id: UBERON:0005928 ! external naris
name: external naris
def: "Surface structure that provides one of the small external openings of the head that give passage to air for breathing." [OMD:nostril, Wikipedia:Nostril]
-comment: Fish have two pairs of external nostrils. There is a case for classifying ZFA:0001427 here as well as anterior naris.
+comment: Fish have two pairs of external nostrils.
subset: vertebrate_core
synonym: "external nares" EXACT PLURAL []
synonym: "anterior naris" EXACT [ZFA:0001427]
synonym: "nostril" EXACT [XAO:0003033, FMA:59645]
synonym: "blowhole" NARROW [Wikipedia:Blowhole_(anatomy)]
-xref: TAO:0001427
+synonym: "naris" BROAD [ZFA:0000550]
+xref: TAO:0000550 ! naris
+xref: ZFA:0000550 ! naris
xref: FMA:59645 ! External naris
xref: MA:0001320 ! external naris
xref: XAO:0003033 ! nostril
-xref: ZFA:0001427 ! anterior naris
xref: ncithesaurus:Nostril ! Nostril
xref: AAO:0000024 ! apertura_nasalis_externa
xref: OpenCyc:Mx4rvViCLpwpEbGdrcN5Y29ycA ! nostril
@@ -163,7 +162,7 @@ xref: SCTID:276165005 ! Entire anterior naris
id: UBERON:0004771 ! posterior nasal aperture
name: posterior nasal aperture
def: "Opening/conduit between the nasal cavity and the nasopharynx[AAO] The choanae are separated by the vomer[WP]." [AAO:0000093, Wikipedia:Posterior_nasal_apertures]
-comment: Fish don't have choanae, instead they have two pairs of external nostrils[WP] In addition to tetrapods, the lungfish has internal nostrils too. TODO: check part_of vs adjacent_to nasal cavity. In tetrapods the exhalant nostril (choana) empties into the buccal cavity
+comment: Fish don't have choanae, instead they have two pairs of external nostrils[WP] In addition to tetrapods, the lungfish has internal nostrils too. TODO: check part_of vs adjacent_to nasal cavity. In tetrapods the exhalant nostril (choana) empties into the buccal cavity. Edit: TODO - birds (palatal choanae)
synonym: "choana" EXACT [XAO:0000277, Wikipedia:Choane]
synonym: "internal naris" EXACT [MA:0001323]
xref: AAO:0000093 ! choana
@@ -553,10 +552,11 @@ intersection_of: capable_of GO:0007606 ! sensory perception of chemical stimulus
id: UBERON:0001728
name: nasopharynx
alt_id: UBERON:FMA_54878-MA_0000443
-def: "uppermost part of the pharynx. It extends from the base of the skull to the upper surface of the soft palate;[1] it differs from the oral and laryngeal parts of the pharynx in that its cavity always remains patent (open)[WP]. In front it communicates through the choanae with the nasal cavities. On its lateral wall is the pharyngeal ostium of the auditory tube, somewhat triangular in shape, and bounded behind by a firm prominence, the torus tubarius or cushion, caused by the medial end of the cartilage of the tube which elevates the mucous membrane." [Wikipedia:Nasopharynx]
+def: "uppermost part of the pharynx. It extends from the base of the skull to the upper surface of the soft palate; it differs from the oral and laryngeal parts of the pharynx in that its cavity always remains patent (open)[WP]. In front it communicates through the choanae with the nasal cavities. On its lateral wall is the pharyngeal ostium of the auditory tube, somewhat triangular in shape, and bounded behind by a firm prominence, the torus tubarius or cushion, caused by the medial end of the cartilage of the tube which elevates the mucous membrane." [Wikipedia:Nasopharynx]
subset: uberon_slim
synonym: "nasal part of pharynx" EXACT []
synonym: "rhinopharynx" EXACT []
+synonym: "epipharynx" RELATED [Wikipedia:Pharynx]
synonym: "Nasenrachenraum" RELATED [BTO:0000662]
xref: BTO:0000662
xref: EHDAA:7086 ! nasopharynx
@@ -577,6 +577,7 @@ is_a: UBERON:0000477 ! anatomical cluster
relationship: part_of UBERON:0001042 ! chordate pharynx
relationship: part_of UBERON:0001557 ! upper respiratory tract
xref: SCTID:181200003 ! Entire nasopharynx
+disjoint_from: FBbt:00005750 ! epipharynx
[Term]
id: UBERON:0001729
@@ -585,6 +586,7 @@ alt_id: UBERON:FMA_54879-MA_0000351
def: "The Oropharynx (oral part of the pharynx) reaches from the Uvula to the level of the hyoid bone. It opens anteriorly, through the isthmus faucium, into the mouth, while in its lateral wall, between the two palatine arches, is the palatine tonsil. [WP,unvetted]." [Wikipedia:Oropharynx]
subset: uberon_slim
synonym: "oral part of pharynx" EXACT []
+synonym: "mesopharynx" RELATED [Wikipedia:Pharynx]
xref: FMA:54879 ! Oropharynx
xref: GAID:340 ! oropharynx
xref: VHOG:0000457 ! oropharynx
@@ -615,6 +617,7 @@ synonym: "oropharyngeal cavity" EXACT [EHDAA2:0004556]
is_a: UBERON:0000464 ! anatomical space
relationship: surrounded_by UBERON:0001729 {source="FMA"} ! oropharynx
relationship: develops_from UBERON:0006272 {source="EHDAA2"} ! oronasal cavity
+relationship: part_of UBERON:0001731 ! cavity of pharynx
xref: FMA:55095 ! lumen of oropharynx
xref: EHDAA2:0004556 ! oropharyngeal cavity
@@ -623,7 +626,6 @@ id: UBERON:0001051
name: hypopharynx
alt_id: UBERON:FBbt_00005751-FMA_54880-MA_0001796
def: "Bottom part of the pharynx, and is the part of the throat that connects to the esophagus." [Wikipedia:Hypopharynx]
-comment: This class was created automatically from a combination of ontologies
subset: uberon_slim
synonym: "laryngeal pharynx" EXACT [FMA:54877]
synonym: "laryngopharynx" EXACT [FMA:54877]
@@ -644,6 +646,15 @@ xref: EHDAA2:0004574 ! laryngopharynx
xref: SCTID:281490009 ! Entire hypopharynx
[Term]
+id: UBERON:0010384
+name: lumen of laryngopharynx
+synonym: "laryngopharynx lumen" EXACT [FMA:55096]
+is_a: UBERON:0000464 ! anatomical space
+relationship: surrounded_by UBERON:0001051 ! hypopharynx
+relationship: part_of UBERON:0001731 ! cavity of pharynx
+xref: FMA:55096 ! Lumen of laryngopharynx
+
+[Term]
id: UBERON:0000006
name: islet of Langerhans
def: "Regions of the pancreas that contain its endocrine (i.e., hormone-producing) cells." [Wikipedia:Islet_of_Langerhans]
@@ -1464,7 +1475,7 @@ def: "Appendage that protrudes from the skin." [UBERON:cjm]
synonym: "skin appendage" EXACT [FMA:71012]
synonym: "epidermal appendage" NARROW []
synonym: "epidermal growth" RELATED []
-comment: examples: hair, nail (FMA); feather, claw, hoof, horn, wattle, spur, beak, scale(?), antler, bristle. Mammary glands develop by similar mechanisms, and their is an argument for including them here (e.g. PMID:20484386), but they don't fit the current definition.
+comment: Examples: hair, nail (FMA); feather, claw, hoof, horn, wattle, spur, beak, scale(?), antler, bristle. Editors note: Mammary glands develop by similar mechanisms, and there is an argument for including them here (e.g. PMID:20484386), but these structures do not fit the current definition. TODO: revise after definition of appendage is finalized in CARO2; in addition, verify subtypes w.r.t definition - e.g. beaks may overlap with skin of body rather than being part of it - rhamphotheca may be more appropriate
subset: uberon_slim
is_a: UBERON:0000026 ! appendage
relationship: part_of UBERON:0002097 ! skin of body
@@ -2285,6 +2296,14 @@ xref: SCTID:302513006 ! Entire urethra
subset: organ_slim
[Term]
+id: UBERON:0010390
+name: lumen of urethra
+synonym: "urethral lumen" EXACT [FMA:19709]
+intersection_of: UBERON:0002558 ! organ cavity
+intersection_of: part_of UBERON:0000057 ! urethra
+xref: FMA:19709 ! lumen of urethra
+
+[Term]
id: UBERON:0000025
name: tube
def: "Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues including lung and trachea, kidney, the mammary gland, the vascular system and the gastrointestinal and urinary-genital tracts. with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system" [GO:0035295, PMID:12526790]
@@ -6955,7 +6974,7 @@ xref: FMA:55222 ! Nodular lymphoid tissue
xref: MA:0000742 ! lymph node follicle
xref: ncithesaurus:Lymphoid_Follicle ! Lymphoid Follicle
is_a: UBERON:0001744 ! lymphoid tissue
-relationship: part_of UBERON:0000029 ! lymph node
+relationship: part_of UBERON:0000029 {source="MA"} ! lymph node
xref: SCTID:64626006 ! Lymphoid nodule
[Term]
@@ -9784,13 +9803,12 @@ xref: MAT:0000206 ! abdominal sensillum
xref: MIAA:0000206 ! abdominal sensillum
is_a: UBERON:0002536 ! arthropod sensillum
-
[Term]
id: UBERON:0000972
name: antenna
alt_id: UBERON:FBbt_00004511-MIAA_0000086
def: "The paired, usually multiple jointed, sensory organs articulating on the procephalic region of the head capsule; its highly versatile sensory structures are capable to detect the various environmental stimuli. In the context of Drosophila refers to they are the most anterior segmented sensory appendage of the head." [FB:gg, ISBN:3110148986, Wikipedia:Antenna_(biology)]
-comment: This class was created automatically from a combination of ontologies
+comment: Editor notes: this term should be ceded to the arthropod anatomy ontology
subset: uberon_slim
synonym: "feeler" RELATED [BTO:0000074]
xref: BTO:0000074
@@ -9816,6 +9834,7 @@ is_obsolete: true
id: UBERON:0005905
name: insect labrum
def: "A mouthpart of insects." [Wikipedia:Insect_mouthparts#Labrum]
+comment: Editor notes: this term should be ceded to the arthropod anatomy ontology
synonym: "labium" RELATED [BTO:0004104]
synonym: "labrum" RELATED [BTO:0004104]
synonym: "insect labium" EXACT [BTO:0004104]
@@ -10191,16 +10210,6 @@ xref: ncithesaurus:Tarsal_Plate ! Tarsal Plate
xref: SCTID:362529005 ! Entire tarsal plate
subset: organ_slim
-[Term]
-id: UBERON:0010309
-name: palpebral bone
-def: "An ossified element investing the upper eyelid." [Wikipedia:Palpebral_(bone), PMID:16496288]
-comment: Taxon notes: The most extreme development of the palpebral is found in the armored dino- saur Euoplocephalus tutus, where the bone forms a quarter-sphere and adducts to completely occlude the or- bit (Coombs, 1972; Vickaryous and Russell, 2003). Notwithstanding the superficially similar position, palpe- brals and tarsal plates differ both anatomically and developmentally and are not considered homologous (Gauthier et al., 1988). Editor notes PMID:16496288 says 'invests' the eyelid, is this consistent across taxa?
-synonym: "palpebral" EXACT []
-intersection_of: UBERON:0001474 ! bone
-intersection_of: part_of UBERON:0001712 ! upper eyelid
-relationship: only_in_taxon NCBITaxon:8457 ! Sauropsida
-
[Term]
id: UBERON:0004773
@@ -10235,6 +10244,30 @@ synonym: "tarsus inferior" EXACT [FMA:TA, FMA:59088]
xref: SCTID:368774005 ! Entire inferior tarsal plate
[Term]
+id: UBERON:0010379
+name: superior tarsal muscle
+def: "The superior tarsal muscle is a smooth muscle adjoining the levator palpebrae superioris muscle that helps to raise the upper eyelid." [Wikipedia:Superior_tarsal_muscle]
+synonym: "mueller muscle" RELATED [Wikipedia:Superior_tarsal_muscle]
+synonym: "Muller's muscle" RELATED [Wikipedia:Superior_tarsal_muscle]
+synonym: "Müller's muscle" RELATED [Wikipedia:Superior_tarsal_muscle]
+synonym: "the superior tarsal muscle" RELATED [Wikipedia:Superior_tarsal_muscle]
+synonym: "Mueller's muscle" EXACT [FMA:49058]
+is_a: UBERON:0001135 ! smooth muscle tissue
+relationship: part_of UBERON:0001604 {source="FMA"} ! levator palpebrae superioris
+xref: FMA:49058 ! superior tarsal muscle
+
+[Term]
+id: UBERON:0010309
+name: palpebral bone
+def: "An ossified element investing the upper eyelid." [Wikipedia:Palpebral_(bone), PMID:16496288]
+comment: Taxon notes: The most extreme development of the palpebral is found in the armored dino- saur Euoplocephalus tutus, where the bone forms a quarter-sphere and adducts to completely occlude the or- bit (Coombs, 1972; Vickaryous and Russell, 2003). Notwithstanding the superficially similar position, palpe- brals and tarsal plates differ both anatomically and developmentally and are not considered homologous (Gauthier et al., 1988). Editor notes PMID:16496288 says 'invests' the eyelid, is this consistent across taxa?
+synonym: "palpebral" EXACT []
+intersection_of: UBERON:0001474 ! bone
+intersection_of: part_of UBERON:0001712 ! upper eyelid
+relationship: only_in_taxon NCBITaxon:8457 ! Sauropsida
+
+
+[Term]
id: UBERON:0000984
name: imaginal disc-derived wing
alt_id: UBERON:FBbt_00004729-MIAA_0000202
@@ -10280,7 +10313,7 @@ id: UBERON:0000987
name: haltere
alt_id: UBERON:FBbt_00004783-MIAA_0000203
def: "The capitate stalk on both sides of the thorax having developed from the dorsal metathoracic wing-buds, it is freely movable and capable of vibration, representing the hind wing of Diptera; used for flight balance." [FB:gg, ISBN:3110148986, Wikipedia:Haltere]
-comment: This class was created automatically from a combination of ontologies
+comment: Editor notes: this term should be ceded to the arthropod anatomy ontology
subset: uberon_slim
synonym: "balancer organ" RELATED []
xref: EFO:0000886 ! haltere
@@ -12412,12 +12445,21 @@ id: UBERON:0001992
name: papillary layer of dermis
alt_id: UBERON:FMA_64776-MA_0000800
def: "Dense irregular connective tissue of the skin that consists of fibroblasts, various connective tissue cell types, and collagen, predominantly type III.[FMA]" [Wikipedia:Papillary_dermis, FMA:FMA]
-comment: This class was created automatically from a combination of ontologies
-subset: uberon_slim
+comment: AO notes: check AO
+subset: uberon_slim
+synonym: "corpus papillary" EXACT [MP:0009545]
+synonym: "papillary layer" EXACT [MP:0009545]
+synonym: "stratum papillare corii" EXACT [MP:0009545]
+synonym: "stratum papillare" EXACT [MP:0009545]
+synonym: "superficial dermis" EXACT [MP:0009545]
+synonym: "papillary layer of dermis" EXACT [FMA:64776]
synonym: "dermis papillary layer" EXACT []
synonym: "papillary dermis" EXACT []
+synonym: "superficial dermis" EXACT [MA:0000802]
+synonym: "dermis papillary layer" EXACT [MA:0000800]
xref: FMA:64776 ! Papillary layer of dermis
xref: MA:0000800 ! dermis papillary layer
+xref: MA:0000802 ! superficial dermis
is_a: UBERON:0004923 ! organ component layer
relationship: part_of UBERON:0002067 ! dermis
@@ -13134,6 +13176,7 @@ subset: early_development
[Term]
id: UBERON:0004879
name: marginal zone of embryo
+def: "Belt-like region of presumptive mesoderm at the equator of the late blastula." [XAO:0000068]
comment: todo - check
synonym: "marginal zone" BROAD [XAO:0000068]
synonym: "margin" BROAD [ZFA:0000038]
@@ -20220,30 +20263,6 @@ synonym: "hilum splenicum" EXACT [FMA:TA, FMA:15841]
xref: SCTID:245377005 ! Entire hilum of spleen
[Term]
-id: UBERON:0001249
-name: lymphoid nodule of spleen
-alt_id: UBERON:FMA_15843-MA_0002672
-def: "A lymphoid nodule that is part_of a spleen" [GOC:Obol]
-synonym: "lymphatic follicle of spleen" EXACT []
-synonym: "lymphoid follicle of spleen" EXACT []
-synonym: "malpighian body" EXACT []
-synonym: "spleen lymphoid follicle" EXACT []
-synonym: "spleen lymphoid nodule" RELATED []
-synonym: "splenic lymphatic follicle" EXACT []
-synonym: "lymphoid nodule of spleen" EXACT [OBOL:automatic]
-synonym: "spleen Lymphoid nodule" EXACT [OBOL:automatic]
-synonym: "splenic Lymphoid nodule" EXACT [OBOL:automatic]
-xref: FMA:15843 ! Lymphoid nodule of spleen
-xref: MA:0002672 ! spleen lymphoid follicle
-xref: ncithesaurus:Splenic_Lymphoid_Follicle ! Splenic Lymphoid Follicle
-is_a: UBERON:0001744 ! lymphoid tissue
-intersection_of: UBERON:0000444 ! lymphoid follicle
-intersection_of: part_of UBERON:0002106 ! spleen
-relationship: part_of UBERON:0001959 ! white pulp of spleen
-relationship: part_of UBERON:0006561 {source="FMA"} ! non-lymphatic part of lymphoid system
-xref: SCTID:35845000 ! Lymphatic follicle of spleen
-
-[Term]
id: UBERON:0001251
name: marginal zone of spleen
alt_id: UBERON:FMA_15852-MA_0000755
@@ -32386,7 +32405,9 @@ relationship: part_of UBERON:0000166 ! oral opening
id: UBERON:0007250
name: lingual tonsil
def: "The lingual tonsils are rounded masses of lymphatic tissue that cover the posterior region of the tongue. They are on the dorsal surface at the base of the tongue. Their lymphatic tissue are dense and nodular, their surface is covered with stratified squamous epithelium which invaginates as a single crypt into each lingual tonsil. They are partially surrounded by connective tissue placing them in the group of Partially-Encapsulated Lymphatic Organs, tonsils, the only one of its kind. They have associated mucous glands which are drained by ducts directly into the single tonsillar crypt." [Wikipedia:Lingual_tonsils]
+synonym: "lingual tonsillar tissue" EXACT [MA:0000773]
xref: FMA:54836 ! lingual tonsil
+xref: MA:0000773 ! lingual tonsillar tissue
is_a: UBERON:0002372 ! tonsil
xref: ncithesaurus:Lingual_Tonsil ! Lingual Tonsil
xref: SCTID:276957006 ! Entire lingual tonsil
@@ -32724,6 +32745,7 @@ xref: MESH:A.02.165.507.411 ! epiglottis
is_a: UBERON:0000477 ! anatomical cluster
relationship: part_of UBERON:0001051 ! hypopharynx
relationship: has_developmental_contribution_from UBERON:0003115 {source="EHDAA2"} ! pharyngeal arch 4
+relationship: never_in_taxon NCBITaxon:8782 ! Aves
xref: EHDAA2:0004081 ! epiglottis
xref: SCTID:245502004 ! Entire epiglottis
@@ -33030,7 +33052,6 @@ id: UBERON:0001757
name: pinna
alt_id: UBERON:FMA_56580-MA_0000259
def: "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." [Wikipedia:Pinna_(anatomy)]
-comment: This class was created automatically from a combination of ontologies
subset: uberon_slim
synonym: "auricle" EXACT []
synonym: "auricula" EXACT [Wikipedia:Auricula]
@@ -38212,6 +38233,7 @@ xref: MA:0000797 ! thoracic mammary gland
xref: EHDAA:6524 ! mammary gland
xref: FMA:62088 ! Lactiferous gland
xref: EHDAA2:0001056 ! mammary gland
+xref: SCTID:31448001 ! Caudal thoracic mammary gland
intersection_of: UBERON:0001911 ! mammary gland
intersection_of: part_of UBERON:0000915 ! throax
relationship: part_of UBERON:0000310 {source="BTO"} ! breast
@@ -38230,14 +38252,16 @@ synonym: "lobe of breast of abdomen" EXACT [OBOL:automatic]
synonym: "lobe of mammary gland of abdomen" EXACT [OBOL:automatic]
synonym: "mammary gland of abdomen" EXACT [OBOL:automatic]
xref: MA:0000787 ! abdominal mammary gland
+xref: SCTID:68037003 ! Cranial abdominal mammary gland
+xref: SCTID:113191002 ! Caudal abdominal mammary gland
intersection_of: UBERON:0001911 ! lactiferous gland
intersection_of: part_of UBERON:0000916 ! abdomen
[Term]
id: UBERON:0008424
name: inguinal mammary gland
-is_a: UBERON:0001911 {source="MA"} ! mammary gland
-is_a: UBERON:0005398 {source="MA"} ! female reproductive gland
+intersection_of: UBERON:0001911 ! mammary gland
+intersection_of: part_of UBERON:0008337 ! inguinal part of abdomen
xref: MA:0000790 ! inguinal mammary gland
xref: SCTID:66519003 ! Inguinal mammary gland
@@ -39934,19 +39958,6 @@ synonym: "pulpa rubra" EXACT [FMA:TA, FMA:15844]
xref: SCTID:27579002 ! Splenic red pulp
[Term]
-id: UBERON:0001960
-name: periarterial lymphatic sheath
-alt_id: UBERON:FMA_62810-MA_0000765
-comment: This class was created automatically from a combination of ontologies
-synonym: "PALS" EXACT []
-synonym: "periarterial lymphoid sheath" EXACT []
-synonym: "spleen periarteriolar lymphatic sheath" EXACT []
-xref: FMA:62810 ! Periarterial lymphatic sheath
-xref: MA:0000765 ! spleen periarteriolar lymphatic sheath
-is_a: UBERON:0000064 ! organ part
-relationship: part_of UBERON:0001959 ! white pulp of spleen
-
-[Term]
id: UBERON:0001961
name: mucosa-associated lymphoid tissue
alt_id: UBERON:FMA_62819-MA_0000140
@@ -48181,6 +48192,16 @@ disjoint_from: WBbt:0005834 ! RIB
relationship: develops_from UBERON:0006288 {evidence="definitional"} ! rib cartilage condensation
[Term]
+id: UBERON:0010388
+name: proximal segment of rib
+def: "The segment of the rib that connects to a vertebra" [MP:0000152]
+comment: TODO: add distal, sternal
+synonym: "proximal rib" EXACT [MA:0001400]
+is_a: UBERON:0005913 ! zone of bone organ
+relationship: part_of UBERON:0002228 {source="MA"} ! rib
+xref: MA:0001400 ! proximal rib
+
+[Term]
id: UBERON:0007843
name: uncinate process of ribs
def: "Extensions of bone that in birds project caudally from the vertical segment of each rib[WP]. Posteriorly directed process (occasionally directed anteriorly) usually associated with the rib (sometimes with the transverse process) of the third vertebra; they provide the origin of the mm serratus superior, medius, and inferior[AAO]. " [AAO:Pugener_2002, Wikipedia:Uncinate_processes_of_ribs]
@@ -65884,6 +65905,16 @@ synonym: "somatomere" RELATED [Wikipedia:Somitomere]
xref: FMA:85523 ! somitomere
is_obsolete: true
+
+[Term]
+id: UBERON:0007282
+name: presumptive segmental plate
+xref: ZFA:0000053 ! presumptive segmental plate
+xref: EFO:0003421 ! presumptive segmental plate
+intersection_of: UBERON:0006598 ! presumptive structure
+intersection_of: develops_into UBERON:0003059 ! presomitic mesoderm
+relationship: develops_from UBERON:0009618 {source="EDHAA2", consistent_with="RCN:2012"} ! trunk paraxial mesenchyme
+
[Term]
id: UBERON:0003059
name: presomitic mesoderm
@@ -65892,23 +65923,24 @@ def: "Unsegmented field of paraxial mesoderm present posterior to the most recen
synonym: "PSM" RELATED []
synonym: "segmental plate" EXACT []
synonym: "somitogenic mesoderm" RELATED []
+synonym: "presumptive somite mesoderm" RELATED []
synonym: "unsegmented paraxial mesoderm" EXACT [UBERON:cjm]
xref: VHOG:0000559 ! presomitic mesoderm
xref: TAO:0000279 ! segmental plate
xref: XAO:0000057 ! presomitic mesoderm
xref: ZFA:0000279 ! segmental plate
xref: EFO:0001982 ! presomitic mesoderm
xref: AAO:0011086 ! presomitic mesoderm
-is_a: UBERON:0000061 ! anatomical structure
+is_a: UBERON:0005423 ! developing anatomical structure
relationship: part_of UBERON:0003077 ! paraxial mesoderm
-relationship: develops_from UBERON:0009618 {source="EDHAA2", consistent_with="RCN:2012"} ! trunk paraxial mesenchyme
relationship: develops_from UBERON:0007282 {evidence="definitional"} ! presumptive segmental plate
[Term]
id: UBERON:0002329
name: somite
alt_id: UBERON:FMA_85522-MIAA_0000068-XAO_0000058-ZFA_0000155
def: "A segmental mass of mesoderm in the vertebrate embryo, occurring in pairs along the notochord and developing into muscles and vertebrae[BTO]. Portion of mesoderm distributed along the two sides of the neural tube and that will eventually become dermis (dermatome), skeletal muscle (myotome), and vertebrae (sclerotome)[WP]. In Zebrafish: Any of the approximately 45 bilaterally paired blocks of mesoderm cells, lying on either side of the notochord and neural tube, and forming sequentially starting at the head during development of the embryo. Together they give rise to the axial skeleton (from the sclerotome), associated musculature (from the myotome), and dermis (from the dermatome). // Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. <a href='http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-PUB-961014-576'>Kimmel et al, 1995.</a>" [OMD:somite, Wikipedia:Somite, XB:curator, ZFIN:curator, BTO:0001558]
+comment: Editor notes: currently classified as an epithelial sac, consistent with EHDAA2 and RCN:2012. Consider making "somitic mesoderm" a separate term and correlate with regionalization processes. // When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248]
subset: uberon_slim
subset: vertebrate_core
synonym: "somites" RELATED PLURAL []
@@ -65933,7 +65965,8 @@ xref: EHDAA2:0003436 ! somite
is_a: UBERON:0005423 ! developing anatomical structure
is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle
relationship: part_of UBERON:0000926 ! mesoderm
-relationship: develops_from UBERON:0003059 ! presomitic mesoderm
+relationship: develops_from UBERON:0003059 {source="ZFA"} ! presomitic mesoderm
+relationship: part_of UBERON:0002100 {source="ZFA"} ! trunk
relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata
relationship: never_in_taxon NCBITaxon:7712 {source="PMID:17237766"} ! Tunicata
xref: AAO:0010569 ! somite
@@ -66005,6 +66038,7 @@ id: UBERON:0003089 ! sclerotome
name: sclerotome
alt_id: UBERON:XAO_0000397-ZFA_0001080
def: "Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]." [Wikipedia:Sclerotome, XB:curator]
+comment: AO notes: part_of somite in XAO
subset: uberon_slim
subset: vertebrate_core
xref: VHOG:0000680 ! sclerotome
@@ -66013,9 +66047,8 @@ xref: XAO:0000397 ! sclerotome
xref: ZFA:0001080 ! sclerotome
xref: ncithesaurus:Sclerotome ! Sclerotome
xref: http://upload.wikimedia.org/wikipedia/commons/thumb/9/96/Gray65.png/200px-Gray65.png
-is_a: UBERON:0002050 {source="XAO"} ! embryonic structure
-is_a: UBERON:0000479 {source="ZFA"} ! tissue
-relationship: part_of UBERON:0002329 ! somite
+is_a: UBERON:0005856 {source="EHDAA2"} ! mesenchymal condensation
+is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population
relationship: develops_from UBERON:0002329 {source="ZFA"} ! somite
xref: AAO:0010571 ! sclerotome
xref: EHDAA2:0003439 ! sclerotome
@@ -72099,14 +72132,6 @@ intersection_of: UBERON:0001134 ! skeletal muscle tissue
intersection_of: part_of UBERON:0003104 ! mesenchyme
[Term]
-id: UBERON:0003386
-name: smooth muscle of eye
-def: "A portion of smooth muscle tissue that is part of a eye [Obol]." [OBOL:automatic]
-xref: EMAPA:18807 ! smooth muscle of eye
-intersection_of: UBERON:0001135 ! smooth muscle tissue
-intersection_of: part_of UBERON:0000019 ! camera-type eye
-
-[Term]
id: UBERON:0003387
name: smooth muscle of trachea
alt_id: UBERON:0004244
@@ -73283,46 +73308,72 @@ id: UBERON:0001211
name: Peyer's patch
alt_id: UBERON:FMA_15054-MA_0000137
def: "aggregations of lymphoid tissue that are usually found in the lowest portion of the small intestine ileum in humans; as such, they differentiate the ileum from the duodenum and jejunum // nodular lymphoid structures on the serosal surface of the small intestine." [Wikipedia:Peyer's_patch]
-comment: This class was created automatically from a combination of ontologies
+comment: AO notes: FMA has [set of?] [aggregated,small] lymphoid [follice,nodule] of [colon, SI, I, etc] - Pp is a syn for Aggregated lymphoid follicle of small intestine; but MA uses Pp as covering both SI and LI. MA also includes follicle as a part
+synonym: "aggregated lymphoid follicle of intestine" RELATED []
+synonym: "aggregated lymphoid nodule" RELATED []
subset: uberon_slim
-synonym: "aggregated lymphoid nodules of small intestine" EXACT [FMA:76466]
-synonym: "peyer's patches" EXACT [FMA:76466]
xref: GAID:950 ! peyer's patch
xref: MA:0000137 ! peyer's patch
xref: EFO:0001381 ! Peyer's patch
-xref: FMA:76466 ! Set of aggregated lymphoid nodules of small intestine
xref: BTO:0001784 ! Peyer's gland
xref: EMAPA:19028 ! Peyer's patches
xref: MESH:A.10.549.598 ! peyer's patch
+xref: ncithesaurus:Mouse_Peyer_s_Patches ! Murine Peyer's Patches
is_a: UBERON:0001962 ! gut-associated lymphoid tissue
relationship: part_of UBERON:0000160 ! intestine
synonym: "noduli lymphoidei aggregati intestini tenuis" EXACT [FMA:TA, FMA:76466]
[Term]
+id: UBERON:0010386
+name: peyer's patch follicle
+is_a: UBERON:0000444 ! lymphoid follicle
+relationship: part_of UBERON:0001211 {source="MA"} ! Peyer's patch
+xref: MA:0000732 ! peyer's patch follicle
+
+[Term]
id: UBERON:0003453
name: large intestine Peyer's patch
-def: "A Peyer ' s patch that is part of a large intestine [Obol]." [OBOL:automatic]
+comment: Edtor notes: requires expert attention
synonym: "Peyer's patch of large intestine" EXACT [OBOL:automatic]
synonym: "large intestine Peyer's patch" EXACT [OBOL:automatic]
xref: MA:0001550 ! large intestine peyer's patch
+xref: FMA:15658 ! solitary lymphoid follicle of subdivision of large intestine
intersection_of: UBERON:0001211 !
intersection_of: part_of UBERON:0000059 ! large intestine
[Term]
id: UBERON:0003454
name: small intestine Peyer's patch
def: "nodular lymphoid structures on the serosal surface of the small intestine." []
-synonym: "Aggregated lymphoid follicle of small intestine" EXACT []
+synonym: "aggregated lymphoid follicle of small intestine" EXACT [FMA:15054]
+synonym: "Peyer's patch" BROAD [FMA:15054]
synonym: "Peyer's patch of small bowel" EXACT [OBOL:automatic]
synonym: "Peyer's patch of small intestine" EXACT [OBOL:automatic]
synonym: "small bowel Peyer's patch" EXACT [OBOL:automatic]
synonym: "small intestine Peyer's patch" EXACT [OBOL:automatic]
xref: MA:0001557 ! small intestine peyer's patch
-xref: FMA:15054 ! Aggregated lymphoid follicle of small intestine
+xref: FMA:15054 ! aggregated lymphoid follicle of small intestine
intersection_of: UBERON:0001211 !
intersection_of: part_of UBERON:0002108 ! small intestine
[Term]
+id: UBERON:0004697
+name: Peyer's patch germinal center
+def: "area of the Peyer's patch where B cells proliferate and differentiate into plasma cells" [MP:0002391]
+xref: MA:0000734 ! peyer's patch germinal center
+intersection_of: UBERON:0001745 ! secondary nodular lymphoid tissue
+intersection_of: part_of UBERON:0001211 ! part_of Peyer's patch
+relationship: site_of GO:0002317 ! plasma cell differentiation
+relationship: site_of GO:0042100 ! B cell proliferation
+
+[Term]
+id: UBERON:0010387
+name: Peyer's patch T cell area
+def: "the Peyer's patch area normally occupied by T lymphocytes" [MP:0002392]
+is_a: UBERON:0001744 ! lymphoid tissue
+relationship: part_of UBERON:0001211 ! Peyer's patch
+
+[Term]
id: UBERON:0003455
name: inner renal medulla loop of henle
def: "A loop of Henle that is part of a inner medulla of kidney [Obol]." [OBOL:automatic]
@@ -79645,11 +79696,12 @@ xref: SCTID:325510007 ! Fetal membranes
id: UBERON:0005631 ! extraembryonic membrane
name: extraembryonic membrane
def: "Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo." [ISBN10:0073040584 "Vertebrates\, Kardong"]
-comment: Taxon notes: stuctures homologous to the four extraembryonic membranes appear in mammals [ISBN10:0073040584 "Vertebrates\, Kardong"]
+comment: AO notes: EHDAA2 is a mereological sum. Taxon notes: stuctures homologous to the four extraembryonic membranes appear in mammals [ISBN10:0073040584 "Vertebrates\, Kardong"]
is_a: UBERON:0000478 ! extraembryonic structure
is_a: UBERON:0000158 ! membranous layer
relationship: only_in_taxon NCBITaxon:32524 ! Amniota
xref: SCTID:362840007 ! extraembryonic membranes
+xref: EHDAA2:0004714 ! embryonic membranes
[Term]
id: UBERON:0005335
@@ -80395,14 +80447,17 @@ xref: NIF_GrossAnatomy:birnlex_1702 ! Rostral migratory stream
[Term]
id: UBERON:0004922
-name: subventricular zone
-def: "A paired brain structure situated throughout the lateral walls of the lateral ventricles. Along with the subgranular zone of dentate gyrus, subventricular zone serves as a source of neural stem cells in the process of adult neurogenesis. It harbors the largest population of proliferating cells in the adult brain of rodents, monkeys and humans. Neurons generated in SVZ travel to the olfactory bulb via the rostral migratory stream[BTO]. 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]
+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]. 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]
comment: todo - add layers
synonym: "postnatal subventricular zone" EXACT [MP:0004275]
synonym: "adult subventricular zone" EXACT [MP:0004275]
synonym: "subependymal zone" RELATED [MP:0004275]
+synonym: "subependymal layer" RELATED [MP:0004275]
+synonym: "subependymal plate" RELATED [MP:0004275]
synonym: "brain subventricular zone" EXACT [MA:0000817]
synonym: "subventricular zone of brain" EXACT []
+synonym: "subventricular zone" EXACT [MA:0000817]
synonym: "SVZ" EXACT []
xref: MA:0000817 ! brain subventricular zone
xref: BTO:0003090 ! subventricular zone
@@ -82337,8 +82392,11 @@ xref: FMA:54979 ! pharyngeal opening of pharyngotympanic tube
id: UBERON:0010061 ! lumen of nasopharynx
name: lumen of nasopharynx
synonym: "nasopharynx lumen" EXACT [FMA:55094]
+synonym: "nasopharynx cavity" EXACT []
+synonym: "nasopharyngeal luman" EXACT []
is_a: UBERON:0000464 ! anatomical space
relationship: surrounded_by UBERON:0001728 {source="FMA"} ! nasopharynx
+relationship: part_of UBERON:0001731 ! cavity of pharynx
xref: FMA:55094 ! lumen of nasopharynx
[Term]
@@ -89343,12 +89401,15 @@ xref: SCTID:57789003 ! Urothelium
[Term]
id: UBERON:0001254
name: urothelium of ureter
+def: "the luminal epithelium of the tube that conducts the urine from the renal pelvis to the bladder" [MP:0000535]
+comment: TODO - check MP
alt_id: UBERON:FMA_15897-MA_0002655
synonym: "ureter transitional epithelium" EXACT []
synonym: "ureter urothelium" EXACT []
synonym: "transitional epithelium of ureter" EXACT []
xref: FMA:15897 ! Transitional epithelium of ureter
xref: MA:0002655 ! ureter urothelium
+xref: MA:0002656 ! ureter luminal urothelium
intersection_of: UBERON:0000365 ! urothelium
intersection_of: part_of UBERON:0000056 ! ureter
@@ -89510,6 +89571,22 @@ xref: AAO:0010086 ! pterygoid process
xref: SCTID:140390001 ! Entire pterygoid process of sphenoid bone
[Term]
+id: UBERON:0010389
+name: pterygoid bone
+def: "a bone which corresponds to the inner plate of the pterygoid process of the human skull, but which, in all vertebrates below mammals, is not connected with the posterior nares, but serves to connect the palatine bones with the point of suspension of the lower jaw" [http://www.websters-online-dictionary.org/definitions/Pterygoid+bone]
+synonym: "inner plate of pterygoid process" RELATED [MA:0001471]
+synonym: "lamina lateralis (processus pterygoideus)" EXACT [FMA:54687, MP:0004452]
+synonym: "lamina lateralis processi pterygoideus ossis sphenoidalis" EXACT [FMA:TA, MP:0004452]
+synonym: "lateral lamina of pterygoid process" EXACT [FMA:54687, MP:0004452]
+synonym: "lateral plate of sphenoid" EXACT [FMA:54687, MP:0004452]
+synonym: "lateral plate of pterygoid process" EXACT [FMA:54687, MP:0004452]
+comment: AO notes: FMA dividers pterygoid process into medial and lateral plates
+is_a: UBERON:0003465 {source="MA"} ! chondrocranium bone
+relationship: part_of UBERON:0004649 {source="MA"} ! sphenoid bone pterygoid process
+xref: MA:0001471 ! pterygoid bone
+xref: FMA:54687 ! lateral plate of pterygoid process
+
+[Term]
id: UBERON:0004651
name: scapula spine
def: "a prominent plate of bone, which crosses obliquely the medial four-fifths of the scapula at its upper part, and separates the supra- from the infraspinatous fossa." [Wikipedia:Spine_of_scapula]
@@ -90076,13 +90153,6 @@ intersection_of: part_of UBERON:0004582 ! part_of venous system
relationship: part_of UBERON:0004237 ! blood vessel smooth muscle
[Term]
-id: UBERON:0004697
-name: peyer's patch germinal center
-xref: MA:0000734 ! peyer's patch germinal center
-intersection_of: UBERON:0001745 ! secondary nodular lymphoid tissue
-intersection_of: part_of UBERON:0001211 ! part_of Peyer's patch
-
-[Term]
id: UBERON:0004698
name: vena cava endothelium
def: "An endothelium that is part of a vena cava [Obol]." [OBOL:automatic]
@@ -91634,8 +91704,7 @@ def: "A gland that is part of a eye [Obol]." [OBOL:automatic]
synonym: "gland of eye" EXACT [OBOL:automatic]
xref: MA:0000267 ! eye gland
intersection_of: UBERON:0002530 ! gland
-intersection_of: part_of UBERON:0000970 ! part_of eye
-relationship: part_of UBERON:0000019 ! camera-type eye
+intersection_of: part_of UBERON:0000019 ! camera-type eye
subset: organ_slim
[Term]
@@ -94303,8 +94372,10 @@ name: rhamphotheca
def: "thin keratinized layer of epidermis projecting from outer surface of beak[WP]." [Wikipedia:Beak#Rhamphotheca]
comment: Development notes: This covering arises from the Malpighian cells of the bird's epidermis,[9] growing from plates at the base of each mandible[WP]
synonym: "horny sheath" RELATED []
-is_a: UBERON:0000061 ! anatomical structure
+synonym: "outer keratin layer of beak" RELATED []
+is_a: UBERON:0003102 ! surface structure
relationship: part_of UBERON:0005094 ! beak
+relationship: part_of UBERON:0001003 ! epidermis
[Term]
id: UBERON:0007331
@@ -97307,13 +97378,14 @@ is_a: UBERON:0001482 ! muscle of shoulder
[Term]
id: UBERON:0005463
-name: marginal sinus
+name: marginal sinus of lymph node
def: "The subcapsular sinus (lymph path, lymph sinus, marginal sinus) is a region within the lymph node immediately deep to the capsule that contains relatively sparse lymphocytes. It thus allows lymph to flow freely through it. The lymph node contains lymphoid tissue, i.e. , a meshwork or fibers called reticulum with white blood cells enmeshed in it. The regions where there are few cells within the meshwork are known lymph sinus. It is lined by reticular cells, fibroblasts and fixed macrophages. Thus, subcapsular (sub=below) sinus lies immediately deep to the capsule of the lymph node and immediately above the cortex. It is continuous with the similar lymph sinuses that flank the trabeculae (the extensions of capsule within the substance of the lymph node). The subcapsular sinus is of clinical importance as it is the most likely location where the earliest manifestations of a metastatic carcinoma in a lymph node would be found." [Wikipedia:Subcapsular_sinus]
comment: todo - add syns to disambiguate from rodent speen marginal sinus
synonym: "subcapsular sinus" RELATED [Wikipedia:Subcapsular_sinus]
synonym: "lymph path" RELATED [Wikipedia:Subcapsular_sinus]
synonym: "lymph sinus" RELATED [Wikipedia:Subcapsular_sinus]
-xref: FMA:50766 ! Marginal sinus
+synonym: "marginal sinus" EXACT [FMA:50766]
+xref: FMA:50766 ! marginal sinus
xref: EHDAA2:0001064 ! marginal sinus
xref: EHDAA:8693 ! marginal sinus
is_a: UBERON:0001638 ! vein
@@ -102050,7 +102122,7 @@ xref: EMAPA:17420 ! radius-ulna pre-cartilage condensation
xref: EHDAA2:0001587 ! radius-ulna pre-cartilage condensation
xref: VHOG:0000949 ! radius-ulna pre-cartilage condensation
xref: EHDAA:4178 ! radius-ulna pre-cartilage condensation
-is_a: UBERON:0005423 ! developing anatomical structure
+is_a: UBERON:0005866 ! pre-cartilage condensation
relationship: part_of UBERON:0000922 ! embryo
relationship: part_of UBERON:0003327 ! mesenchyme of forearm
@@ -102062,14 +102134,12 @@ xref: EMAPA:17678 ! rib cartilage condensation
xref: EHDAA2:0001716 ! rib cartilage condensation
xref: VHOG:0001122 ! rib cartilage condensation
xref: EHDAA:8347 ! rib cartilage condensation
-is_a: UBERON:0005423 ! developing anatomical structure
-is_a: UBERON:0005863 ! cartilagenous condensation
+is_a: UBERON:0005863 {source="EHDAA2"} ! cartilaginous condensation
+relationship: develops_from UBERON:0006289 {source="EHDAA2"} ! rib pre-cartilage condensation
relationship: part_of UBERON:0000922 ! embryo
relationship: part_of UBERON:0005482 ! thoracic region
relationship: part_of UBERON:0006073 ! thoracic region of vertebral column
relationship: develops_into UBERON:0002228 ! rib
-relationship: part_of UBERON:0005482 ! thoracic region
-relationship: part_of UBERON:0006073 ! thoracic region of vertebral column
[Term]
id: UBERON:0006289
@@ -102079,12 +102149,12 @@ xref: EMAPA:17397 ! rib pre-cartilage condensation
xref: EHDAA2:0001717 ! rib pre-cartilage condensation
xref: VHOG:0000681 ! rib pre-cartilage condensation
xref: EHDAA:6026 ! rib pre-cartilage condensation
-is_a: UBERON:0005423 ! developing anatomical structure
-is_a: UBERON:0005866 ! pre-cartilage condensation
+is_a: UBERON:0005866 {source="EHDAA2"} ! pre-cartilage condensation
relationship: part_of UBERON:0000922 ! embryo
relationship: part_of UBERON:0005482 ! thoracic region
relationship: part_of UBERON:0006073 ! thoracic region of vertebral column
relationship: develops_into UBERON:0002228 ! rib
+relationship: develops_from UBERON:0003089 ! sclerotome
[Term]
id: UBERON:0006290
@@ -104036,6 +104106,15 @@ disjoint_from: UBERON:0008847 ! ovarian ligament
xref: SCTID:279917007 ! Entire suspensory ligament of ovary
[Term]
+id: UBERON:0010391 ! parametrium
+name: parametrium
+def: "In women, the supravaginal portion of the cervix is separated in front from the bladder by fibrous tissue, the parametrium, which extends also on to its sides and laterally between the layers of the broad ligaments. The uterine artery and ovarian ligament are located in the parametrium. Inflammation causes Parametritis." [Wikipedia:Parametrium]
+comment: subserous coat of the uterus laterally between the layers of the broad ligament[MP] - todo - check relationships
+is_a: UBERON:0002095 {source="FMA"} ! mesentery
+xref: FMA:77061 ! parametrium
+xref: SCTID:280455005 ! Entire parametrium
+
+[Term]
id: UBERON:0008847 ! ovarian ligament
def: "a fibrous ligament that connects the ovary to the lateral surface of the uterus." [Wikipedia:Ovarian_ligament]
comment: The ligament runs in the broad ligament of the uterus, which is a fold of peritoneum rather than a fibrous ligament. Specifically, it is located in the parametrium
@@ -106530,14 +106609,6 @@ xref: ZFA:0000148 ! presumptive midbrain
[Term]
-id: UBERON:0007282
-name: presumptive segmental plate
-xref: ZFA:0000053 ! presumptive segmental plate
-xref: EFO:0003421 ! presumptive segmental plate
-intersection_of: UBERON:0006598 ! presumptive structure
-intersection_of: develops_into UBERON:0003059 ! presomitic mesoderm
-
-[Term]
id: UBERON:0007283
name: presumptive shield
xref: ZFA:0001121 ! presumptive shield
@@ -108884,6 +108955,7 @@ subset: organ_slim
id: UBERON:0008930 ! somatosensory cortex
name: somatosensory cortex
def: "Area of the parietal lobe concerned with receiving general sensations. It lies posterior to the central sulcus." [MESH:A.08.186.211.730.885.213.670.675]
+comment: TODO - add layers
synonym: "somesthetic area" RELATED [BTO:0004353]
is_a: UBERON:0002616 ! regional part of brain
relationship: part_of UBERON:0002581 {source="BTO"} ! postcentral gyrus
@@ -108903,6 +108975,7 @@ xref: MA:0000908 ! primary somatosensory cortex
[Term]
id: UBERON:0008934
name: secondary somatosensory cortex
+comment: TODO - check brodmann
is_a: UBERON:0008930 ! somatosensory cortex
relationship: part_of UBERON:0001872 {source="MA"} ! parietal lobe
xref: MA:0000918 ! secondary somatosensory cortex
@@ -110907,6 +110980,299 @@ intersection_of: UBERON:0000483 ! epithelium
intersection_of: develops_from UBERON:0000924 ! ectoderm
xref: FMA:69064 ! ecto-epithelium
+[Term]
+id: UBERON:0010380
+name: enteric nerve
+intersection_of: UBERON:0001021 ! nerve
+intersection_of: part_of UBERON:0002005 ! enteric nervous system
+xref: MA:0001145 ! enteric nerve
+
+[Term]
+id: UBERON:0010394 ! lymphocyte domain
+name: lymphocyte domain
+is_a: UBERON:0000477 ! anatomical cluster
+relationship: has_part CL:0000542 ! lymphocyte
+
+[Term]
+id: UBERON:0010392 ! B cell domain
+name: B cell domain
+intersection_of: UBERON:0010394 ! lymphocyte domain
+intersection_of: has_part CL:0000236 ! B cell
+
+[Term]
+id: UBERON:0010393 ! T cell domain
+name: T cell domain
+intersection_of: UBERON:0010394 ! lymphocyte domain
+intersection_of: has_part CL:0000084 ! T cell
+
+[Term]
+id: UBERON:0001960
+name: periarterial lymphatic sheath
+alt_id: UBERON:FMA_62810-MA_0000765
+def: "the area of the spleen in which T cells surround the central arteriole" [MP:0002358]
+synonym: "PALS" EXACT [MP:0002358]
+synonym: "T cell domain of the splenic white pulp" EXACT [MP:0002358]
+synonym: "periarteriolar sheath" EXACT [MP:0002358]
+synonym: "splenic periarteriolar lymphoid sheath" EXACT [MP:0002358]
+synonym: "periarterial lymphoid sheath" EXACT []
+synonym: "spleen periarteriolar lymphatic sheath" EXACT []
+xref: FMA:62810 ! Periarterial lymphatic sheath
+xref: MA:0000765 ! spleen periarteriolar lymphatic sheath
+intersection_of: UBERON:0010393 ! T cell domain
+intersection_of: part_of UBERON:0001959 ! white pulp of spleen
+
+[Term]
+id: UBERON:0010395
+name: lymph node primary follicle
+is_a: UBERON:0000444 ! lymphoid follicle
+xref: MA:0000743 ! lymph node primary follicle
+
+[Term]
+id: UBERON:0010396
+name: afferent lymphatic vessel
+def: "Lymphatic vessel that enters the lymph node. The afferent lymph vessels enter at all parts of the periphery of the lymph node, and after branching and forming a dense plexus in the substance of the capsule, open into the lymph sinuses of the cortical part. In doing this they lose all their coats except their endothelial lining, which is continuous with a layer of similar cells lining the lymph paths" [UBERON:0010388]
+synonym: "vasa afferentia lymphoglandulae" EXACT [Wikipedia:Afferent_lymphatic_vessels]
+synonym: "vasa afferentia lymphoglandula" EXACT [Wikipedia:Afferent_lymphatic_vessels]
+is_a: UBERON:0001473 ! lymphatic vessel
+relationship: part_of UBERON:0000029 ! lymph node
+xref: MA:0000748 ! afferent lymphatic vessel
+xref: http://en.wikipedia.org/wiki/File:Illu_lymph_node_structure.png
+
+[Term]
+id: UBERON:0010397
+name: efferent lymphatic vessel
+def: "Lymphatic vessel that exits the lymph node. The efferent lymphatic vessel commences from the lymph sinuses of the medullary portion of the lymph nodes and leave the lymph nodes either to veins or greater nodes. Efferent lymphatic vessels are also found in the thymus and spleen. This is in contrast to afferent lymphatic vessels, which are found only in lymph nodes." [UBERON:0010388]
+synonym: "efferent lymphatic vessel" RELATED [Wikipedia:Efferent_lymph_vessel]
+synonym: "efferent lymphatic vessels" RELATED [Wikipedia:Efferent_lymph_vessel]
+is_a: UBERON:0001473 ! lymphatic vessel
+xref: MA:0000749 ! efferent lymphatic vessel
+
+[Term]
+id: UBERON:0010398
+name: spleen marginal sinus
+def: "the border region surrounding the spleen B cell follicles and the periarteriolar lymphoid sheath (PALS) that separates it from the marginal zone that mediates lymphocyte entry into the white pulp from the blood" [UBERON:0010388]
+comment: Note that there is no consensus in the literature about which compartments constitute the white pulp or the ramifications of the microvasculature. In addition, notable differences exist between humans and rodents. In this ontology, the marginal sinus (which may not exist in human) has been included as part of the white pulp. The perifollicular zone, which is present in human and not rodents, may be the functional equivalent of the marginal sinus in rodents.[MP:0002363]
+synonym: "splenic marginal sinus" EXACT [MP:0002363]
+is_a: UBERON:0001959 ! white pulp of spleen
+xref: MA:0000754 ! spleen marginal sinus
+
+[Term]
+id: UBERON:0010399
+name: spleen trabecular artery
+intersection_of: UBERON:0001637 ! artery
+intersection_of: part_of UBERON:0001265 ! trabecula of spleen
+xref: MA:0000759 ! spleen trabecular artery
+
+[Term]
+id: UBERON:0010400
+name: spleen trabecular vein
+intersection_of: UBERON:0001638 ! vein
+intersection_of: part_of UBERON:0001265 ! trabecula of spleen
+xref: MA:0000760 ! spleen trabecular vein
+
+[Term]
+id: UBERON:0010401
+name: spleen central arteriole
+def: "A blood vessel surrounded by the periarteriolar lymphoid sheath that connects the trabecular artery to the trabecular vein" [UBERON:0010388]
+synonym: "follicular arteriole" EXACT [MP:0002361]
+synonym: "splenic central arteriole" EXACT [MP:0002361]
+is_a: UBERON:0001981 ! blood vessel
+relationship: part_of UBERON:0001959 ! white pulp of spleen
+xref: MA:0000763 ! spleen central arteriole
+
+[Term]
+id: UBERON:0010402
+name: epidermis suprabasal layer
+synonym: "suprabasal layer" BROAD [MP:0001233]
+is_a: UBERON:0004923 ! organ component layer
+relationship: part_of UBERON:0001003 ! epidermis
+xref: MA:0000808 ! epidermis suprabasal layer
+
+[Term]
+id: UBERON:0010403
+name: cortical marginal zone
+def: "developing superficial cortical layer located just under the pia matter." [UBERON:0010388]
+comment: TODO; add other marginal zones; determine correct developmental relationships
+synonym: "MZ" EXACT [MP:0000792]
+synonym: "cortical marginal zone" EXACT [MP:0000792]
+synonym: "brain marginal zone" BROAD [MA:0000812]
+is_a: UBERON:0002301 ! layer of neocortex
+relationship: adjacent_to UBERON:0002361 ! pia mater
+xref: MA:0000812 ! brain marginal zone
+
+[Term]
+id: UBERON:0010404
+name: lateral ventricle subependymal layer
+intersection_of: UBERON:0004922 ! postnatal subventricular zone
+intersection_of: part_of UBERON:0002285 ! lateral ventricle
+xref: MA:0000965 ! lateral ventricle subependymal layer
+
+[Term]
+id: UBERON:0010405
+name: spinal cord lateral motor column
+def: "Column of motor neurons which innervate muscles in the limb; motor neurons in the lateral motor column are further organized into pools, each of which innervates a specific muscle in the limb" [UBERON:0010388]
+is_a: UBERON:0000073 ! regional part of nervous system
+relationship: part_of UBERON:0002240 ! spinal cord
+xref: MA:0001129 ! spinal cord lateral motor column
+
+[Term]
+id: UBERON:0010406
+name: cholinergic enteric nerve
+is_a: UBERON:0010380 ! enteric nerve
+! no mapping (CL:0000108) -- relationship: overlaps CL:0000108 ! cholinergic neuron
+xref: MA:0001146 ! cholinergic enteric nerve
+
+[Term]
+id: UBERON:0003386
+name: smooth muscle of eye
+def: "A portion of smooth muscle tissue that is part of a eye [Obol]." [OBOL:automatic]
+xref: EMAPA:18807 ! smooth muscle of eye
+xref: MA:0001268 ! ocular smooth muscle
+synonym: "ocular smooth muscle" EXACT [MA:0001268]
+intersection_of: UBERON:0001135 ! smooth muscle tissue
+intersection_of: part_of UBERON:0000019 ! camera-type eye
+
+[Term]
+id: UBERON:0010408
+name: ocular angle artery
+def: "The angular artery is the terminal part of the facial artery; it ascends to the medial angle of the eye's orbit, imbedded in the fibers of the angular head of the Quadratus labii superioris, and accompanied by the angular vein." [UBERON:0010388]
+is_a: UBERON:0001637 ! artery
+relationship: branch_of UBERON:0001612 ! facial artery
+synonym: "angular artery" EXACT [FMA:49583]
+xref: FMA:49583 ! angular artery
+xref: MA:0002010 ! ocular angle artery
+
+[Term]
+id: UBERON:0010409
+name: eye surface
+comment: TODO - subparts
+relationship: part_of UBERON:0000019 ! camera-type eye
+xref: MA:0002486 ! eye surface
+
+[Term]
+id: UBERON:0010410
+name: inguinal fat pad
+def: "encapsulated adipose tissue found in the groin" [UBERON:0010388]
+intersection_of: UBERON:0003916 ! fat pad
+intersection_of: part_of UBERON:0008337 ! inguinal part of abdomen
+xref: MA:0002548 ! inguinal fat pad
+
+[Term]
+id: UBERON:0010411
+name: retroperitoneal fat pad
+def: "encapsulated adipose tissue found on the dorsal side of the peritoneum" [UBERON:0010388]
+intersection_of: UBERON:0003916 ! fat pad
+intersection_of: part_of UBERON:0002358 ! peritoneum
+relationship: surrounded_by UBERON:0003693 ! retroperitoneal space
+xref: MA:0002549 ! retroperitoneal fat pad
+
+[Term]
+id: UBERON:0010412
+name: epididymal fat pad
+comment: TODO - other fat pad types
+def: "encapsulated adipose tissue associated with the epididymis" [UBERON:0010388]
+synonym: "periepididymal fat pad" EXACT [MP:0009288]
+intersection_of: UBERON:0003916 ! fat pad
+intersection_of: part_of UBERON:0001301 ! epididymis
+xref: MA:0002550 ! epididymal fat pad
+
+[Term]
+id: UBERON:0010413
+name: parametrial fat pad
+def: "encapsulated adipose tissue associated with the extension of the subserous coat of the uterus laterally between the layers of the broad ligament" [UBERON:0010388]
+synonym: "parametrial fat depot" EXACT [MP:0009301]
+intersection_of: UBERON:0003916 ! fat pad
+intersection_of: part_of UBERON:0010391 ! parametrium
+xref: MA:0002953 ! parametrial fat pad
+
+[Term]
+id: UBERON:0010414
+name: omental fat pad
+def: "encapsulated adipose tissue associated with the fold of peritoneal tissue that extends from the stomach to the posterior abdominal wall after associating with the transverse colon" [UBERON:0010388]
+synonym: "omental fat depot" EXACT [MP:0010044]
+intersection_of: UBERON:0003427 ! abdominal fat pad
+intersection_of: part_of UBERON:0003688 ! omentum
+xref: MA:0002956 ! omental fat pad
+
+[Term]
+id: UBERON:0010415
+name: barrel cortex
+def: "dark-staining regions of layer four of the somatosensory cortex where somatosensory inputs from the contralateral side of the body come in from the thalamus. Barrels are found in some species of rodents and species of at least two other orders." [UBERON:0010388]
+is_a: UBERON:0002616 ! regional part of brain
+relationship: part_of UBERON:0008933 ! primary somatosensory cortex
+relationship: only_in_taxon NCBITaxon:9989 ! Rodenti
+xref: MA:0002712 ! barrel cortex
+
+[Term]
+id: UBERON:0010416
+name: lymph node B cell domain
+def: "A part of the lymph node cortex in which B lymphocytes home to primary follicles to survey follicular dendritic cells (FDCs); antigen stimulated B cells proliferate and differentiate within the follicles forming distinctive germinal centers" [UBERON:0010388]
+synonym: "lymph node B cell dependent cortex" EXACT [MP:0002344]
+synonym: "lymph node B-cell domain" EXACT [MP:0002344]
+synonym: "nodular lymph node cortex" EXACT [MP:0002344]
+intersection_of: UBERON:0010392 ! B cell domain
+intersection_of: part_of UBERON:0000029 ! lymph node
+xref: MA:0002851 ! lymph node B cell domain
+
+[Term]
+id: UBERON:0001249
+name: lymphoid nodule of spleen
+alt_id: UBERON:FMA_15843-MA_0002672
+def: "A lymphoid nodule that is part_of a spleen" [GOC:Obol]
+synonym: "lymphatic follicle of spleen" EXACT []
+synonym: "lymphoid follicle of spleen" EXACT []
+synonym: "malpighian body" EXACT []
+synonym: "spleen lymphoid follicle" EXACT []
+synonym: "spleen lymphoid nodule" RELATED []
+synonym: "splenic lymphatic follicle" EXACT []
+synonym: "lymphoid nodule of spleen" EXACT [OBOL:automatic]
+synonym: "spleen Lymphoid nodule" EXACT [OBOL:automatic]
+synonym: "splenic Lymphoid nodule" EXACT [OBOL:automatic]
+synonym: "B cell domain of the spleen" BROAD [MP:0002360]
+synonym: "follicle mantle" EXACT [MP:0002360]
+synonym: "lymphocytic corona" BROAD [MP:0002360]
+synonym: "mantle zone" EXACT [MP:0002360]
+synonym: "spleen B-cell corona" EXACT [MP:0002360]
+synonym: "splenic B cell corona" EXACT [MP:0002360]
+xref: FMA:15843 ! Lymphoid nodule of spleen
+xref: MA:0002672 ! spleen lymphoid follicle
+xref: ncithesaurus:Splenic_Lymphoid_Follicle ! Splenic Lymphoid Follicle
+is_a: UBERON:0010392 ! B cell domain
+intersection_of: UBERON:0000444 ! lymphoid follicle
+intersection_of: part_of UBERON:0002106 ! spleen
+relationship: part_of UBERON:0001959 ! white pulp of spleen
+relationship: part_of UBERON:0006561 {source="FMA"} ! non-lymphatic part of lymphoid system
+xref: SCTID:35845000 ! Lymphatic follicle of spleen
+
+[Term]
+id: UBERON:0010417
+name: lymph node T cell domain
+intersection_of: UBERON:0010393 ! T cell domain
+intersection_of: part_of UBERON:0000029 ! lymph node
+xref: MA:0002852 ! lymph node T cell domain
+
+[Term]
+id: UBERON:0010418
+name: urethral opening
+intersection_of: UBERON:0000161 ! orifice
+intersection_of: part_of UBERON:0001556 ! lower urinary tract
+xref: MA:0002867 ! urethral opening
+
+[Term]
+id: UBERON:0010419
+name: vibrissa follicle
+intersection_of: UBERON:0002073 ! hair follicle
+intersection_of: part_of UBERON:0006378 ! vibrissa
+xref: MA:0002910 ! vibrissa follicle
+
+[Term]
+id: UBERON:0010420
+name: lymph node follicular mantle
+def: "A part of the secondary follicle in which naive B cells reside along with some helper T cells, macrophages and follicular dendritic cells; these are displaced by the expanding germinal centre and form a 'mantle' around it" [UBERON:0010388]
+synonym: "lymph node follicular corona" EXACT [MP:0010774]
+relationship: part_of UBERON:0001745 ! secondary nodular lymphoid tissue
+xref: MA:0002990 ! lymph node follicular mantle
+
[Typedef]
id: adjacent_to
name: adjacent_to

0 comments on commit 6865a3c

Please sign in to comment.