Merge pull request #29436 from geneontology/issue-29415

added term and moved children for #29265, fixed term and defintion fo…

src/ontology/go-edit.obo

@@ -53345,7 +53345,7 @@ namespace: cellular_component
 def: "A collagen heterotrimer containing type VIII alpha chains; [alpha1(VIII)2]alpha2(VIII) and alpha1(VIII)[alpha2(VIII)]2 trimers have been observed; type VIII collagen triple helices associate to form regular hexagonal nets." [ISBN:0721639976, PMID:21421911]
 is_a: GO:0005598 ! short-chain collagen trimer
 relationship: part_of GO:0005604 ! basement membrane
-relationship: part_of GO:0098646 ! collagen sheet
+relationship: part_of GO:0098646 ! interstitial hexagonal collagen network
 
 [Term]
 id: GO:0005592
@@ -53405,11 +53405,12 @@ is_a: GO:0005581 ! collagen trimer
 id: GO:0005599
 name: collagen type X trimer
 namespace: cellular_component
-def: "A collagen homotrimer of alpha1(X) chains; type X collagen triple helices form hexagonal networks (sheets)." [ISBN:0721639976, PMID:21421911]
+def: "A collagen homotrimer of alpha1(X) chains; type X collagen triple helices form hexagonal networks (sheets)." [PMID:21421911]
 comment: Collagen X trimers have been observed to form hexagonal lattices in vitro, but in vivo they have been found in a fibril associated form (PMID:19693541).
 is_a: GO:0005581 ! collagen trimer
 is_a: GO:0005598 ! short-chain collagen trimer
-relationship: part_of GO:0098646 ! collagen sheet
+relationship: part_of GO:0098646 ! interstitial hexagonal collagen network
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29415" xsd:anyURI
 
 [Term]
 id: GO:0005600
@@ -91998,7 +91999,7 @@ name: middle lamella
 namespace: cellular_component
 def: "Layer of intercellular material, chiefly pectic substances, cementing together the primary walls of contiguous cells." [ISBN:0471245208]
 xref: Wikipedia:Middle_lamella
-is_a: GO:0031012 ! extracellular matrix
+is_a: GO:0140047 ! specialized extracellular matrix
 
 [Term]
 id: GO:0009521
@@ -166831,7 +166832,7 @@ namespace: cellular_component
 def: "A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers assemble into a sheet." [PMID:7188361]
 synonym: "hexagonal network-forming collagen" EXACT [ISBN:0815316194]
 intersection_of: GO:0005581 ! collagen trimer
-intersection_of: part_of GO:0098646 ! collagen sheet
+intersection_of: part_of GO:0098646 ! interstitial hexagonal collagen network
 relationship: part_of GO:0031012 ! extracellular matrix
 relationship: part_of GO:0062023 ! collagen-containing extracellular matrix
 
@@ -190232,6 +190233,7 @@ name: interphotoreceptor matrix
 namespace: cellular_component
 def: "A specialized extracellularc matrix that surrounds the photoreceptors of the retina and lies between them and the apical surface of the retinal pigment epithelium. The IPM has been implicated in several important activities required for photoreceptor function and maintenance." [PMID:1862095, PMID:2194288]
 is_a: GO:0062023 ! collagen-containing extracellular matrix
+is_a: GO:0140047 ! specialized extracellular matrix
 
 [Term]
 id: GO:0033166
@@ -218313,7 +218315,7 @@ namespace: cellular_component
 def: "A specialized extracellular matrix that surrounds the plasma membrane of the ovum of animals. The egg coat provides structural support and can play an essential role in oogenesis, fertilization and early development." [PMID:16944418, PMID:17163408]
 synonym: "vitelline membrane" NARROW [PMID:16944418, PMID:17163408]
 synonym: "zona pellucida" NARROW [PMID:16944418, PMID:17163408]
-intersection_of: GO:0031012 ! extracellular matrix
+intersection_of: GO:0140047 ! specialized extracellular matrix
 intersection_of: part_of CL:0000025 ! egg cell
 created_by: bf
 creation_date: 2011-04-19T02:07:23Z
@@ -343229,11 +343231,15 @@ relationship: negatively_regulates GO:0006897 {http://purl.obolibrary.org/obo/IA
 
 [Term]
 id: GO:0060102
-name: collagen and cuticulin-based cuticle extracellular matrix
+name: cuticular extracellular matrix
 namespace: cellular_component
-def: "A collagen and cuticulin-based noncellular, multilayered structure that is synthesized by an underlying ectodermal (hypodermal) cell layer. The cuticle serves essential functions in body morphology, locomotion, and environmental protection. An example of this component is found in Caenorhabditis elegans." [GOC:dph, GOC:kmv, ISSN:15518507]
+def: "A collagen and cuticulin-based noncellular, multilayered structure that is synthesized by an underlying ectodermal (hypodermal) cell layer. The cuticle serves essential functions in body morphology, locomotion, and environmental protection. An example of this component is found in Caenorhabditis elegans." [GOC:dph, GOC:kmv, ISSN:15518507, PMID:12619137]
+synonym: "collagen and cuticulin-based cuticle extracellular matrix" EXACT []
 synonym: "collagen and cuticulin-based exoskeleton extracellular matrix" RELATED []
+synonym: "cuticular ECM" EXACT []
 is_a: GO:0062023 ! collagen-containing extracellular matrix
+is_a: GO:0140047 ! specialized extracellular matrix
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29265" xsd:anyURI
 
 [Term]
 id: GO:0060103
@@ -343251,7 +343257,7 @@ namespace: cellular_component
 def: "An electron dense, amorphous envelope that comprises the outermost layer of the cuticle. The surface coat is loosely apposed to the epicuticle, has distinct biochemical properties, is synthesized by cells other than the underlying hypodermis, and is labile. In addition to serving as a lubricant to protect against abrasion and dehydration, the surface coat may also play important roles in infection and immune evasion. An example of this component is found in Caenorhabditis elegans." [GOC:dph, GOC:kmv, ISSN:15518507]
 synonym: "surface coat of collagen and cuticulin-based exoskeleton extracellular matrix" RELATED []
 is_a: GO:0110165 ! cellular anatomical structure
-relationship: part_of GO:0060102 ! collagen and cuticulin-based cuticle extracellular matrix
+relationship: part_of GO:0060102 ! cuticular extracellular matrix
 
 [Term]
 id: GO:0060105
@@ -343260,15 +343266,15 @@ namespace: cellular_component
 def: "A lipid-containing layer of cuticle that lies between the cortical layer and the surface coat. An example of this component is found in Caenorhabditis elegans." [GOC:dph, GOC:kmv, ISSN:15518507]
 synonym: "epicuticle of collagen and cuticulin-based exoskeleton extracellular matrix" RELATED []
 is_a: GO:0110165 ! cellular anatomical structure
-relationship: part_of GO:0060102 ! collagen and cuticulin-based cuticle extracellular matrix
+relationship: part_of GO:0060102 ! cuticular extracellular matrix
 
 [Term]
 id: GO:0060106
 name: cortical layer of collagen and cuticulin-based cuticle extracellular matrix
 namespace: cellular_component
 def: "The cuticle layer that lies directly beneath the lipid-containing epicuticle. The cortical layer contains collagens and insoluble, non-collagenous cuticulins and is characterized by a distinct annular pattern consisting of regularly spaced annular ridges delineated by annular furrows. An example of this component is found in Caenorhabditis elegans." [GOC:dph, GOC:kmv, ISSN:15518507]
 is_a: GO:0110165 ! cellular anatomical structure
-relationship: part_of GO:0060102 ! collagen and cuticulin-based cuticle extracellular matrix
+relationship: part_of GO:0060102 ! cuticular extracellular matrix
 
 [Term]
 id: GO:0060107
@@ -343280,7 +343286,7 @@ synonym: "annular rings" RELATED []
 synonym: "annule(s)" RELATED []
 synonym: "annulus" RELATED []
 is_a: GO:0110165 ! cellular anatomical structure
-relationship: part_of GO:0060102 ! collagen and cuticulin-based cuticle extracellular matrix
+relationship: part_of GO:0060102 ! cuticular extracellular matrix
 relationship: part_of GO:0060106 ! cortical layer of collagen and cuticulin-based cuticle extracellular matrix
 
 [Term]
@@ -343289,7 +343295,7 @@ name: annular furrow extracellular matrix
 namespace: cellular_component
 def: "The extracellular matrix part that is a regularly spaced indentation in the outer cortical layer of the cuticle. The pattern of annular furrows corresponds to sites of invaginations in hypodermal cell membranes that, in turn, correspond to submembranous regions where actin microfilament bundles assemble early in lethargus, the first phase of the molting cycle in which activity and feeding decline." [GOC:dph, GOC:kmv, ISSN:15518507]
 is_a: GO:0110165 ! cellular anatomical structure
-relationship: part_of GO:0060102 ! collagen and cuticulin-based cuticle extracellular matrix
+relationship: part_of GO:0060102 ! cuticular extracellular matrix
 relationship: part_of GO:0060106 ! cortical layer of collagen and cuticulin-based cuticle extracellular matrix
 
 [Term]
@@ -343299,7 +343305,7 @@ namespace: cellular_component
 def: "The fluid-filled cuticle layer that lies between the cortical and basal layers and is characterized by the presence of regularly spaced columnar struts that lie on either side of the annular furrows and link the two surrounding layers. In C. elegans, a defined medial layer is found only in adult animals." [GOC:dph, GOC:kmv, ISSN:15518507]
 synonym: "medial layer struts" RELATED []
 is_a: GO:0110165 ! cellular anatomical structure
-relationship: part_of GO:0060102 ! collagen and cuticulin-based cuticle extracellular matrix
+relationship: part_of GO:0060102 ! cuticular extracellular matrix
 
 [Term]
 id: GO:0060110
@@ -343308,7 +343314,7 @@ namespace: cellular_component
 def: "The layer of cuticle most closely apposed to the hypodermal cells. The morphology of the basal layer varies with life stage. In adult C. elegans animals, the basal layers is comprised of three sublayers: two fibrous layers whose fibers run in clockwise and counter-clockwise directions meeting one another at a 60 degree angle, and an amorphous basal layer that lies underneath the fibrous layers and directly contacts the hypodermis. In C. elegans dauer and L1 larval stage animals, the basal layer is characterized by a striated pattern that appears to derive from interwoven laminae. An example of this component is found in Caenorhabditis elegans." [GOC:dph, GOC:kmv, ISSN:15518507]
 synonym: "basal layer of collagen and cuticulin-based exoskeleton extracellular matrix" RELATED []
 is_a: GO:0110165 ! cellular anatomical structure
-relationship: part_of GO:0060102 ! collagen and cuticulin-based cuticle extracellular matrix
+relationship: part_of GO:0060102 ! cuticular extracellular matrix
 
 [Term]
 id: GO:0060111
@@ -343317,7 +343323,7 @@ namespace: cellular_component
 def: "Raised, thickened cuticular ridges that run longitudinally, and in parallel, along the left and right sides of the animal. The alae lie above the hypodermal cells known as the lateral seam cells. In C. elegans, alae are produced in L1 larvae, dauer larvae and adult stage animals, where they consist of three, five, and three ridges of distinct morphology, respectively." [GOC:dph, GOC:kmv, ISSN:15518507]
 synonym: "alae of collagen and cuticulin-based exoskeleton extracellular matrix" RELATED []
 is_a: GO:0110165 ! cellular anatomical structure
-relationship: part_of GO:0060102 ! collagen and cuticulin-based cuticle extracellular matrix
+relationship: part_of GO:0060102 ! cuticular extracellular matrix
 
 [Term]
 id: GO:0060112
@@ -363702,6 +363708,7 @@ id: GO:0062023
 name: collagen-containing extracellular matrix
 namespace: cellular_component
 def: "An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells." [GOC:BHF, GOC:rph, PMID:21123617]
+synonym: "collagen-containing ECM" EXACT []
 is_a: GO:0031012 ! extracellular matrix
 created_by: dph
 creation_date: 2018-04-13T12:47:21Z
@@ -363856,7 +363863,7 @@ name: biofilm matrix
 namespace: cellular_component
 def: "A type of extracellular matrix that surrounds the cells within a microbial biofilm. The matrix is composed of extracellular polymeric substances including exopolysaccharides, proteins, nucleic acids, lipids, and other biomolecules." [PMID:22571672, PMID:27129222, PMID:28516088, PMID:32663461]
 subset: gocheck_do_not_annotate
-is_a: GO:0031012 ! extracellular matrix
+is_a: GO:0140047 ! specialized extracellular matrix
 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22176" xsd:anyURI
 created_by: dph
 creation_date: 2018-05-04T12:49:17Z
@@ -364732,7 +364739,7 @@ name: chitin-based extracellular matrix
 namespace: cellular_component
 def: "Any constituent part of a chitin-based noncellular, hardened, or membranous extracellular matrix secreted from the apical surface of an epithelial sheet." [PMID:23955854]
 synonym: "chitin-based ECM" EXACT [GOC:dph]
-is_a: GO:0031012 ! extracellular matrix
+is_a: GO:0140047 ! specialized extracellular matrix
 created_by: dph
 creation_date: 2019-06-13T12:57:13Z
 
@@ -371107,7 +371114,7 @@ namespace: cellular_component
 def: "A layer of extracellular matrix deposited onto the surface of the pollen wall upon disintegration of the tapetal layer of the anther wall in the late stages of pollen development. The composition of this material is highly heterogeneous and includes waxes, lipid droplets, small aromatic molecules, and proteins. The pollen coat is proposed to have many functions, such as holding pollen in the anther until dispersal, facilitation of pollen dispersal, protection of pollen from water loss and UV radiation, and facilitation of adhesion of pollen to the stigma." [GOC:mah, GOC:rph, PMID:12930826, PMID:15012271]
 synonym: "pollenkitt" EXACT [PMID:15012271]
 synonym: "tryphine" EXACT [PMID:15012271]
-is_a: GO:0031012 ! extracellular matrix
+is_a: GO:0140047 ! specialized extracellular matrix
 
 [Term]
 id: GO:0070506
@@ -372701,7 +372708,7 @@ namespace: cellular_component
 def: "A small, granular structure that is found in the extracellular matrix of cell of the secretory tapetal layer that surrounds developing pollen grains. Ubisch bodies have a sporopollenin coat, are attached to the peritapetal wall, and may play a role in pollen development." [GOC:ecd, GOC:mah, PMID:14612572, PMID:16524248]
 synonym: "orbicule" EXACT [PMID:14612572]
 is_a: GO:0110165 ! cellular anatomical structure
-relationship: part_of GO:0031012 ! extracellular matrix
+relationship: part_of GO:0140047 ! specialized extracellular matrix
 created_by: mah
 creation_date: 2009-05-11T11:35:33Z
 
@@ -421524,11 +421531,13 @@ relationship: bearer_of PATO:0015006 ! polymeric
 
 [Term]
 id: GO:0098646
-name: collagen sheet
+name: interstitial hexagonal collagen network
 namespace: cellular_component
-def: "A protein complex that consists of collagen triple helices associated to form a sheet-like network." [GOC:dos, PMID:21421911]
+def: "A hexagonal shaped collagen network formed by collagen type X trimer, mostly found in the cartilage hyaline matrix, which located in the interstitial area." [PMID:21421911, PMID:34948124]
 synonym: "collagen hexagonal network" EXACT [PMID:21421911]
+synonym: "collagen sheet" EXACT []
 is_a: GO:0098645 ! collagen network
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29415" xsd:anyURI
 
 [Term]
 id: GO:0098647
@@ -427569,7 +427578,9 @@ namespace: cellular_component
 def: "The extracellular matrix of the perisynaptic space (the extracellular space adjacent to the synapse) and the synaptic cleft." [GOC:dos]
 subset: goslim_synapse
 synonym: "extra-synaptic extracellular matrix" EXACT []
+synonym: "synapse-associated ECM" EXACT []
 is_a: GO:0062023 ! collagen-containing extracellular matrix
+is_a: GO:0140047 ! specialized extracellular matrix
 relationship: adjacent_to GO:0043083 ! synaptic cleft
 relationship: adjacent_to GO:0099544 ! perisynaptic space
 
@@ -450707,6 +450718,17 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i
 created_by: pg
 creation_date: 2024-12-06T15:53:35Z
 
+[Term]
+id: GO:0140047
+name: specialized extracellular matrix
+namespace: cellular_component
+def: "Species or cell-type specific extracellular matrices that are different from the two main types of extracellular matrices: the interstitial ECM and the basement membrane ECM in metazoa." [PMID:33605520]
+synonym: "specialized ECM" EXACT []
+is_a: GO:0031012 ! extracellular matrix
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29265" xsd:anyURI
+created_by: pg
+creation_date: 2024-12-13T08:19:31Z
+
 [Term]
 id: GO:0140048
 name: manganese ion export across plasma membrane
@@ -578612,7 +578634,7 @@ name: organomineral extracellular matrix
 namespace: cellular_component
 def: "An extracellular matrix consisting of a densely packed organomineral assembly in which the mineral phase represents the majority of the material by weight." [GOC:jh2, PMID:15994301]
 comment: An example is found in shell calcitic prisms of the Mediterranean fan mussel Pinna nobilis (PMID:15994301), but the term may also be useful to annotate bone and eggshell proteins.
-is_a: GO:0031012 ! extracellular matrix
+is_a: GO:0140047 ! specialized extracellular matrix
 created_by: pr
 creation_date: 2014-05-07T10:02:28Z