Obsoletion request: GO:0046350:galactosaminoglycan metabolic process

[rozaru]

Please provide as much information as you can:

• GO term ID and Label galactosaminoglycan metabolic process GO:0046350 galactosaminoglycan catabolic process GO:0006028 galactosaminoglycan biosynthetic process GO:0006025

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

• [x] The reason for obsoletion is that the term is not clearly defined and ~usage has been inconsistent.~ (not used)

• [x] The reason for obsoletion is that this term was an unnecessary grouping term.

• Are there annotations to this term? There is no annotation to these terms

• Any other information According to the literature so far there are 3 types, chondroitin sulfate, dermatan sulfate and fucosylated chondroitin sulfate (PMID: 17239763), that would be part of galactosaminoglycans. Their corresponding GO terms are not children of GO:0046350 at the moment. This term seems to be an unnecessary grouping term. There is already a grouping term (mucopolysaccharide metabolic process) for all the GAG that are not bacterial proteoglycan.

Related to ticket #28977 (Review of glycosaminoglycan metabolic process (GO:0030203) and proteoglycan metabolic process (GO:0006029) branches)

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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

[deustp01]

@ukemi does this fit with your work on mouse glycoprotein metabolism pathways (most of which are on hold because of annotation obstacles)?

[ukemi]

I haven't used these terms in any models and if I did, I would use the specific types, so I guess yes.

[pgaudet]

No annotations, see https://github.com/geneontology/go-annotation/issues/5543