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 (NTR Add term Collagenous component of basement membrane #29472).
  Collagenous component of basement membrane should include all child terms and annotations already, except for 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 IV trimer (GO:0005587) will be under Chicken-wire-like collagen network (NTR Add term Chicken-wire-like collagen network  #29401)
• Collagen type VIII trimer (GO:0005591) will be under Hexagonal collagen network of basement membrane (NTR Add term Hexagonal collagen network of basement membrane #29402)
• Collagen type XV trimer (GO:0005582) will be under Multiplexin collagen trimer (NTR Add term multiplexin collagen trimer #29469)
• Collagen type XVIII trimer (GO:0030938) will be under Multiplexin collagen trimer (NTR Add term multiplexin collagen trimer #29469)
• Collagen type XIX trimer (GO:1990318) will be under Collagenous component of basement membrane (NTR Add term Collagenous component of basement membrane #29472) (Term child term update: Remove Collagen type XIX trimer (GO:1990318) from FACIT collagen trimer (GO:0005593) #29569 )

• 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

[Matrisome]

@DaiqingChen @pgaudet I have asked collagen expert Dr. Sylvie Ricard-Blum to provide details on collagen XIX to help classify it.