Obsoletion request: basement membrane collagen trimer (GO:0098651)

[DaiqingChen]

Please provide as much information as you can:

• GO term ID and Label
  basement membrane collagen trimer (GO:0098651)

• Reason for deprecation Put an x in the appropriate box:

• The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent.
• The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
• The reason for obsoletion is that this term represent an assay and not a GO process.
• The reason for obsoletion is that this represents a phenotype.
• The reason for obsoletion is that the data from the paper for which the term was requested can be accurately described using [appropriate GO term].
• The reason for obsoletion is that this term represents a molecular function.
• The reason for obsoletion is that this term represents a gene product.
• The reason for obsoletion is that this term refers to a class of proteins.
• The reason for obsoletion is that this term was added in error.
• The reason for obsoletion is that more specific terms were created.
• The reason for obsoletion is that this term was an unnecessary grouping term.
• The reason for obsoletion is that the meaning of the term is ambiguous.
• The reason for obsoletion is that is not known to be catalyzed by any gene product.
• The reason for obsoletion is that it more specific than the specificity of any known gene product.
• The reason for obsoletion is that there is no evidence that this function/process/component exists.

• "Replace by" term (ID and label)
  Same as collagenous component of basement membrane Add term Collagenous component of basement membrane #29472 . collagenous component of basement membrane should include all child terms and annotations already.(Except collagen type XIX trimer, discussed in next section)

• "Consider" term(s) (ID and label)
  For the child term of basement membrane collagen trimer:

• collagen type XVIII trimer (GO:0030938) will be under multiplexin collagen trimer Add term multiplexin collagen trimer #29469
• collagen type XV trimer (GO:0005582) will be under multiplexin collagen trimer Add term multiplexin collagen trimer #29469
• collagen type IV trimer (GO:0005587) will be under chicken-wire like collagen network Add term Chicken-wire like collagen network  #29401
• collagen type VIII trimer (GO:0005591) will be under Basement membrane hexagonal collagen network Add term Basement membrane hexagonal collagen network #29402
• collagen type XIX trimer (GO:1990318) is a FACIT collagen, multiple evidence(PMID: 9403723, PMID: 35346795) showing that this is in basement membrane.

PMID: 31823868:
The amino acid sequence of type XIX collagen shares strong similarities to other FACIT members....Considering that it(collagen XIX) contains a thrombospondin like N-terminal domain in NC6 and it is not associated with fibres, type XIX collagen has also been described as a member of the multiplexin family, to which types XV and XVIII collagens belongs to (Myers et al., 1997; Sumiyoshi et al., 2001; Ricard et al., 2011). Additionally, the localization of type XIX collagen in the basement membrane zone of different organs resembles the one observed in other multiplexins. Albeit these similarities, type XIX collagen as a whole is a unique collagen member that can play different roles depending on its localization.

@Matrisome shall we classify collagen XIX as multiplexin, or add another arrow from collagen XIX to basement membrane?

• Are there annotations to this term?
  1194 annotations

• Are there mappings and cross references to this term? (InterPro, Keywords; check QuickGO cross-references section)

• Is this term in a subset? (check the AmiGO page for that term)

• Any other information

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Checklist for ontology editor

Check term usage and metadata in Protégé

• check term usage in the ontology
• check internal mappings: RHEA, EC, MetaCyc
• check subset usage
• check taxon constraints

Check annotations

• create Annotation Review spreadsheet
• • Annotation Review template: https://docs.google.com/spreadsheets/d/1izV3q1jnq_Ybg5MJ53O_b5BCTkGtjl_Fi-cOg3-7eBE/edit#gid=0
• • Instructions: https://wiki.geneontology.org/Annotation_Review_Request
• create annotation review ticket: https://github.com/geneontology/go-annotation/issues/new?assignees=&labels=annotation+review&template=annotation-review-for-obsoletion.md&title=Review+annotations+to+%5BINSERT+GO+TERM%5D
• find external mappings (via IEAS), include in obsoletion notice
• tag curators in Annotation Review ticket. Responsible annotator for each group: https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv

Notification

• create obsoletion announcement
• announce to GO friends ([email protected])
• paste the text in the ontology ticket