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Term name and definition update: collagen sheet (GO:0098646) to interstitial hexagonal collagen network #29415

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DaiqingChen opened this issue Dec 10, 2024 · 9 comments
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@DaiqingChen
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DaiqingChen commented Dec 10, 2024

  • GO term ID and label for which you request a definition update
    collagen sheet (GO:0098646)
    Note: "collagen sheet" is NOT synonyms of interstitial hexagonal collagen network, requesting "definition update" instead of obsoleting and adding new term because the annotations are the same(collagen type X trimer).

  • 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(GO:0098645)
  • 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.

Frame work in slide page 1 for localization information, slide page 3 for supramolecular complex information, and slide page 7 for the overview of relationships.https://docs.google.com/presentation/d/1zxL0gt5vOynmJsS8BP-Xqs_0sTaEB8Zo/edit?usp=sharing&ouid=109267399050361021326&rtpof=true&sd=true

Screen shot of slide page 7, interstitial hexagonal collagen network is pointed with arrows
Image

@pgaudet
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pgaudet commented Dec 13, 2024

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
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pgaudet commented Dec 13, 2024

Hi @DaiqingChen

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

image

Thanks, Pascale

@pgaudet
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pgaudet commented Dec 13, 2024

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
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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
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Hi @DaiqingChen

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

image 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.
Image
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
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pgaudet commented Dec 13, 2024

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

image

It seems like something is not right there?

@DaiqingChen
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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

image It seems like something is not right there?

Yes, while we would like to obsolete term "sheet-forming collagen trimer(GO:0030935)", #29416

@DaiqingChen
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Hi @pgaudet ,
I realized that the term definition is already up on QuickGO, thank you for the quick update! In the synonyms you put "collagen sheet" as exact, but it's wrong. Collagen sheet is the synonyms of collagen IV(#29401 ), not collagen X(this requested term). The reason I requested name change instead of obsoleting & creating new term is only because the annotation of the old term is almost the same(collagen X) as the new term.
Sorry for the misleading request, could you remove the synonym "collagen sheet"? Thanks!

@pgaudet
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pgaudet commented Dec 20, 2024

Thanks @DaiqingChen
I removed "collagen sheet" as a synonyms for interstitial hexagonal collagen network

Thanks, Pascale

pgaudet added a commit that referenced this issue Dec 20, 2024
pgaudet added a commit that referenced this issue Dec 20, 2024
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