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 (go-friends@mailman.stanford.edu)
• paste the text in the ontology ticket