Obsoletion request: collagen-containing extracellular matrix (GO:0062023)

[DaiqingChen]

Please provide as much information as you can:

• GO term ID and Label
  collagen-containing extracellular matrix (GO:0062023)

• 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)
  child terms are re-assigned to different parents

• "Consider" term(s) (ID and label)
  The new parent for child terms are as follow:

  • Child term moving to specialized ECM (Re-organize the child term of extracellular matrix (GO:0031012) #29267, NTR: Add term Specialized extracellular matrix #29265 )

    • interphotoreceptor matrix (GO:0033165)
    • cuticular ECM (GO:0060102)
    • synapse-associated extracellular matrix (GO:0099535)
    • extracellular matrix of synaptic cleft (GO:0098965) and perisynaptic extracellular matrix (GO:0098966) stay under synapse-associated extracellular matrix (GO:0099535) as they are

  • Child term moving to non-collagenous component of interstitial matrix (Re-organize the child term of extracellular matrix (GO:0031012) #29267 )

    • hyaline layer (GO:0033166)
    • matrilin complex (GO:0120216)
    • tenascin complex (GO:0090733)
    • transforming growth factor beta complex (GO:0099126)

  • Child term moving to non-collagenous component of basement membrane (Re-organize the child term of extracellular matrix (GO:0031012) #29267 )

    • EMILIN complex (GO:1990971)

  • Child term moving to extracellular matrix (GO:0031012)(Re-organize the child term of extracellular matrix (GO:0031012) #29267 )

    • Basement membrane (GO: 0005604)
    • Interstitial matrix (GO:0005614)
    • multimerin complex (GO:1990972) haven't tackle this part, not sure about localization, put under ECM for now.
    • all the other annotations, if not being specified, move to extracellular matrix (GO:0031012)
      @Matrisome shall we keep those we haven't tackled under extracellular matrix (GO:0031012) for now?

  • Other child terms

    • anchoring collagen complex (GO:0030934) obsoleted (Obsoletion request: anchoring collagen complex (GO:0030934) #29457 )
    • collagen type XXVI trimer (GO:1990324) move to collagenous component of interstitial matrix(NTR: Add term Collagenous component of interstitial matrix #29473 )
    • collagen type XXVIII trimer (GO:1990326) move to collagenous component of basement membrane (NTR: Add term Collagenous component of basement membrane #29472 )
    • complex of collagen trimer (GO:0098644) keep under Supramolecular complex (GO:0099080) as it is

• Are there annotations to this term?
  226,563 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
  Re-assignment of child terms in slide page 11: https://docs.google.com/presentation/d/1zxL0gt5vOynmJsS8BP-Xqs_0sTaEB8Zo/edit?usp=sharing&ouid=109267399050361021326&rtpof=true&sd=true

screen shot:

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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