Obsoletion request: [GO 0030935: sheet-forming collagen trimer]

[DaiqingChen]

Please provide as much information as you can:

• GO term ID and Label
  sheet-forming collagen trimer (GO:0030935)

• 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)
  basement membrane hexagonal collagen network (NTR Add term Hexagonal collagen network of basement membrane #29402) and Interstitial hexagonal collagen network (requested name change Term name and definition update: collagen sheet (GO:0098646) to interstitial hexagonal collagen network #29415)

• "Consider" term(s) (ID and label)
  Suggestions for reannotation: This term becomes redundant given that we are separating it into hexagonal network in basement membrane (NTR Add term Hexagonal collagen network of basement membrane #29402) and interstitial matrix (NTR Term name and definition update: collagen sheet (GO:0098646) to interstitial hexagonal collagen network #29415). Sheet-forming collagen was a combination of both, separated to better annotate the respective localization of these collagens in the basement membrane (GO:0005604 and NTR Add term Collagenous component of basement membrane #29472) and the interstitial matrix (GO:0005614 and NTR Add term Collagenous component of interstitial matrix #29473).

• Are there annotations to this term?
  67 annotations were assigned to this term, same as collagen sheet (GO:0098646)

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

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

• Any other information
  NA

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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

[pgaudet]

No direct annotations.

[pgaudet]

Dear all,

The proposal has been made to obsolete GO 0030935: sheet-forming collagen trimer. The reason for obsoletion is that this is an unnecessary grouping term. There are no direct annotations to this term. This term is not present in any subsets.

You can comment on the ticket: #29416

Thanks,