Term name and definition update: collagen sheet (GO:0098646) to interstitial hexagonal collagen network

[DaiqingChen]

• GO term ID and label for which you request a definition update
  collagen sheet (GO:0098646)

• New proposed definition (genus-differentia pattern, plus additional information if needed)

• A hexagonal shaped collagen network formed by collagen type X trimer, mostly found in the cartilage hyaline matrix, which located in the interstitial area.

• Reference(s)
  collagen type X trimers forms Hexagonal supramolecular structure: PMID: 21421911
  collagen type X trimers occurs in interstitial matrix: PMID: 34948124

• Parent term(s)

• Collagenous component of interstitial matrix,
• Collagen network

• Children terms (if applicable)
  collagen type X trimer (GO:0005599)

• Remove gene product

• remove COL8A1(UniProtKB:P27658, 9606 Homo sapiens) from the annotation

• Additional information
  The network-forming collagen forms two types of supramolecular structures(chicken-wire and hexagonal), the hexagonal collagen network is formed by collagen type VIII trimers in the basement membrane and collagen type X trimers in the interstitial matrix.
  However, the collagen type X trimer is not in the same area of interstitial matrix that composed of collagen types I, III, and V, but specifically localized to the cartilage matrix that's closer to the chondrocytes.

[pgaudet]

collagen type X trimer (GO:0005599) is already part_of collagen sheet (GO:0098646), is this OK ? (I dont think it should be is_a? )

[pgaudet]

Hi @DaiqingChen

I dont see COL8A1(UniProtKB:P27658, 9606 Homo sapiens annotated to collagen sheet (GO:0098646); which annotation do you want to change?

Thanks, Pascale

[pgaudet]

Term now looks like this:

[Term]
id: GO:0098646
name: interstitial hexagonal collagen network
namespace: cellular_component
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

[DaiqingChen]

collagen type X trimer (GO:0005599) is already part_of collagen sheet (GO:0098646), is this OK ? (I dont think it should be is_a? )

Yes, collagen type X trimer(GO:0005599) should be part_of collagen sheet(GO:0098646).

[DaiqingChen]

Hi @DaiqingChen

I dont see COL8A1(UniProtKB:P27658, 9606 Homo sapiens annotated to collagen sheet (GO:0098646); which annotation do you want to change?

Thanks, Pascale

Hi Pascale,
I found COL8A1 in one of the 67 annotations of collagen sheet (GO:0098646) from QuickGO, on page 3, with 1 record out of the 67 annotations.

I'm not sure why collagen sheet(GO:0098646) is not showing up in the parental list, looks like it's assigned by "PINC".

Best,
Daiqing

[pgaudet]

OK, I think it's because of the ontology:
'collagen type VIII trimer' is a grand-child of collagen sheet (now called interstitial hexagonal collagen network), via its relation to sheet-forming collagen trimer

It seems like something is not right there?