Textual definition update for proteoglycan metabolic process and glycosaminoglycan metabolic process children #29745
Comments
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Thanks @rozaru I made some comments on the task list for point 1 - see above. For the new defs, we should add good references, so not use ISBN:0192800981 (Oxford Dictionary of Science) or '[GOC:go_curators]'. PMID: 38500384 (from 2024) might be a good source for all/most defs, and there are other refs noted on the related tickets . Can you check and provide a good ref for each new def? Thanks. |
@rozaru ChEBI also lacks 'heparin proteoglycan', I think. If you agree, can you also request that on your ticket? |
I updated the ticket to add heparin proteoglycan.
I added references for all the GO terms apart from the regulatory terms where I left the original ref. |
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I've updated all the textual defs, and addressed most of the points raised in the original ticket. |
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@sjm41 |
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OK, now I just need to wait for ChEBI to make a new public release and for GO to be updated with it, so that the new terms are available to use within Protege! |
GO:0015014:heparan sulfate proteoglycan biosynthetic process, chain elongation
This term was supposed to have been made obsolete and annotation merged to GO:0015012:heparan sulfate proteoglycan biosynthetic process.
This is already noted here Review of glycosaminoglycan metabolic process (GO:0030203) and proteoglycan metabolic process (GO:0006029) branches #28977 (comment) (Steven)
GO:0050654 chondroitin sulfate proteoglycan metabolic process
In quickGO and Amigo appear as a child of glycosaminoglycan metabolic process (this link is not in the logical definition file)
This is because of incorrect relations in ChEBI, already corrected in CHEBI:26349 - proteochondroitin sulfate ebi-chebi/ChEBI#4635 but not yet incorporated into the GO (Steven)
GO:0120532: glycosaminoglycan-protein linkage region biosynthetic process
Currently, a direct child of protein glycosylation, but should be a child of O-glycosylation
ChEBI terms retrieved form the ChEBI ontology for proteoglycans:
CHEBI:37396 proteoglycan
CHEBI:64602 dermatan sulfate proteoglycan
CHEBI:26349 chondroitin sulfate proteoglycan
CHEBI:24499 heparan sulfate proteoglycan
CHEBI:26349 ! proteochondroitin sulfate
When searching ChEBI with CHEBI:26349 it return no results but the entry exists.
Why does it display proteochondroitin sulfate instead of the ChEBI name chondroitin sulfate proteoglycan
I can't explain the search behaviour, but I see the correct name here: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:26349, which is also the result of ebi-chebi/ChEBI#4635 (Steven)
Could heparin be used as an output as the chain is cleaved off the protein?
There is a keratan sulfate term but no keratan sulfate proteoglycan
Have requested term to ChEBI: New term request: keratan sulfate proteoglycan #4638
GO:0030203: glycosaminoglycan metabolic process
Def: The chemical reactions and pathways involving glycosaminoglycans, any of a group of linear polysaccharides composed of repeating disaccharide units. [PMID: 38500384]
GO:0006024: glycosaminoglycan biosynthetic process
Def: The chemical reactions and pathways resulting in the breakdown of glycosaminoglycans, any one of a group of linear polysaccharides composed of repeating disaccharide units. [PMID: 38500384]
GO:0006027: glycosaminoglycan catabolic process
Def: The chemical reactions and pathways resulting in the breakdown of glycosaminoglycans, any one of a group of linear polysaccharides composed of repeating disaccharide units. [PMID: 38500384]
GO:0030212: hyaluronan metabolic process
Def: The chemical reactions and pathways involving hyaluronan, the naturally occurring anionic form of hyaluronic acid. Hyaluronan is a type of non-sulfated glycosaminoglycans composed of the repeating disaccharide unit beta-1,4 linked D-glucuronic acid-beta-(1,3)-N-acetyl-D-glucosamine. [PMID: [33171800(https://pubmed.ncbi.nlm.nih.gov/33171800/), PMID: 35536932]
GO:0030213: hyaluronan biosynthetic process
Def: The chemical reactions and pathways resulting in the formation of hyaluronan, the naturally occurring anionic form of hyaluronic acid. Hyaluronan is a type of non-sulfated glycosaminoglycans composed of the repeating disaccharide unit beta-1,4 linked D- glucuronic acid -beta-(1,3)-N-acetyl-D-glucosamine. [PMID: [33171800(https://pubmed.ncbi.nlm.nih.gov/33171800/), PMID: 35536932]
GO:0030214: hyaluronan catabolic process
Def: The chemical reactions and pathways resulting in the breakdown of hyaluronan, the naturally occurring anionic form of hyaluronic acid. Hyaluronan is a type of non-sulfated glycosaminoglycans composed of the repeating disaccharide unit beta-1,4 linked D- glucuronic acid -beta-(1,3)-N-acetyl-D-glucosamine. [PMID: [33171800(https://pubmed.ncbi.nlm.nih.gov/33171800/), PMID: 35536932]
GO:0000270: peptidoglycan metabolic process
Def: The chemical reactions and pathways involving peptidoglycans, any of a class of glycoconjugates found only in bacterial cell walls and consisting of long glycan strands of alternating residues of β-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid cross-linked by short peptides. [ISBN:0198506732, PMID:33139480]
GO:0009252: peptidoglycan biosynthetic process
Def: The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of β-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid cross-linked by short peptides. [ISBN:0198506732, PMID:18266853]
GO:0009253: peptidoglycan catabolic process
Def: The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of β-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid cross-linked by short peptides. [ISBN:0198506732, PMID:9158729]
GO:0009254: peptidoglycan turnover
Def: The continual breakdown and regeneration of peptidoglycan required to maintain the bacterial cell wall. Peptidoglycans consist in long glycan strands of alternating residues of β-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid cross-linked by short peptides. [PMID: 31296364]
GO:0006029: proteoglycan metabolic process
Def: The chemical reactions and pathways involving proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans, a group of linear polysaccharides composed of repeating disaccharide units. [PMID: 35536939]
GO:0030166: proteoglycan biosynthetic process
Def: The chemical reactions and pathways resulting in the formation of proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans, a group of linear polysaccharides composed of repeating disaccharide units. [PMID: 35536939]
GO:1902729: negative regulation of proteoglycan biosynthetic process
Def: Any process that stops, prevents or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans, a group of linear polysaccharides composed of repeating disaccharide units. [GO_REF:0000058, GOC:TermGenie, PMID:23212449]
GO:1902730: positive regulation of proteoglycan biosynthetic process
Def: Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans, a group of linear polysaccharides composed of repeating disaccharide units. [GO_REF:0000058, GOC:TermGenie, PMID:23212449]
GO:0030167: proteoglycan catabolic process
Def: The chemical reactions and pathways resulting in the breakdown of proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans, a group of linear polysaccharides composed of repeating disaccharide units. [PMID: 35536982]
GO:0030201: heparan sulfate proteoglycan metabolic process
Def: The chemical reactions and pathways involving heparan sulfate proteoglycans which consist of a core protein linked to a heparan sulfate glycosaminoglycan. The heparan sulfate chain is composed of the repeating disaccharide unit beta-(1,4)-linked N-acetyl-D-glucosamine-alpha-(1,4)- hexuronic acid, the former being either sulfated or deacetylated on its amino group as well as sulfated on one of its hydroxyl groups and the latter can be a mixture of sulfated and nonsulfated D-glucuronic and L-iduronic acids. [PMID: 27241222
GO:0015012: heparan sulfate proteoglycan biosynthetic process
Def: The chemical reactions and pathways resulting in the formation of heparan sulfate proteoglycans which consist of a core protein linked to a heparan sulfate glycosaminoglycan. The heparan sulfate chain is composed of the repeating disaccharide unit beta-(1,4)-linked N-acetyl-D-glucosamine-alpha-(1,4)- hexuronic acid, the former being either sulfated or deacetylated on its amino group as well as sulfated on one of its hydroxyl groups and the latter can be a mixture of sulfated and nonsulfated D-glucuronic and L-iduronic acids. Heparan sulfate chains are covalently linked to serine/threonine residues (O-linked) of the core protein via a tetrasaccharide linker sequence (xylose-galactose-galactose-glucuronate). [PMID: 27241222
GO:0010908: regulation of heparan sulfate proteoglycan biosynthetic process
Def: Any process that modulates the rate, frequency or extent of heparan sulfate proteoglycan biosynthesis. Heparan sulfate proteoglycan biosynthetic processes are the chemical reactions and pathways resulting in the formation of the heparan sulfate proteoglycan which consist of a core protein linked to a heparan sulfate glycosaminoglycan. The heparan sulfate chain is composed of the repeating disaccharide unit beta-(1,4)-linked N-acetyl-D-glucosamine-alpha-(1,4)- hexuronic acid. [GOC:dph, GOC:tb]
GO:0010909: positive regulation of heparan sulfate proteoglycan biosynthetic process
Def: Any process that increases the rate, frequency or extent of heparan sulfate proteoglycan biosynthesis. Heparan sulfate proteoglycan biosynthetic processes are the chemical reactions and pathways resulting in the formation of the heparan sulfate proteoglycan which consist of a core protein linked to a heparan sulfate glycosaminoglycan. The heparan sulfate chain is composed of the repeating disaccharide unit beta-(1,4)-linked N-acetyl-D-glucosamine-alpha-(1,4)- hexuronic acid. [GOC:dph, GOC:tb]
GO:0030200: heparan sulfate proteoglycan catabolic process
Def: The chemical reactions and pathways resulting in the breakdown of heparan sulfate proteoglycans which consist of a core protein linked to a heparan sulfate glycosaminoglycan. The heparan sulfate chain is composed of the repeating disaccharide unit beta-(1,4)-linked N-acetyl-D-glucosamine-alpha-(1,4)- hexuronic acid, the former being either sulfated or deacetylated on its amino group as well as sulfated on one of its hydroxyl groups and the latter can be a mixture of sulfated and nonsulfated D-glucuronic and L-iduronic acids. [PMID: 35536982]
GO:0030202: heparin proteoglycan metabolic process
Def: The chemical reactions and pathways involving heparin proteoglycans which consist of a core protein linked to a heparin glycosaminoglycan. The heparin chain is composed of the repeating disaccharide unit beta-(1,4)-linked N-acetyl-D-glucosamine-alpha-(1,4)- hexuronic acid, the former being either sulfated or deacetylated on its amino group as well as sulfated on one of its hydroxyl groups and the latter can be a mixture of sulfated and nonsulfated D-glucuronic and L-iduronic acids. Heparin is similar to heparan sulfate but it contains more N-sulfate and O-sulfate groups. Heparin proteoglycans are stored selectively in the secretory granules of mammalian mast cells. [PMID: 22566225]
GO:0030210: heparin proteoglycan biosynthetic process
Def: The chemical reactions and pathways resulting in the formation of heparin proteoglycans which consist of a core protein linked to a heparin glycosaminoglycan. The heparin chain is composed of the repeating disaccharide unit beta-(1,4)-linked N-acetyl-D-glucosamine-alpha-(1,4)- hexuronic acid, the former being either sulfated or deacetylated on its amino group as well as sulfated on one of its hydroxyl groups and the latter can be a mixture of sulfated and nonsulfated D-glucuronic and L-iduronic acids. Heparin is similar to heparan sulfate but it contains more N-sulfate and O-sulfate groups. Heparin chains are covalently linked to serine/threonine residues (O-linked) of the core protein via a tetrasaccharide linker sequence (xylose-galactose-galactose-glucuronate). [PMID: 22566225]
GO:0030211: heparin proteoglycan catabolic process
Def: The chemical reactions and pathways resulting in the breakdown of heparin proteoglycans which consist of a core protein linked to a heparin glycosaminoglycan. The heparin chain is composed of the repeating disaccharide unit beta-(1,4)-linked N-acetyl-D-glucosamine-alpha-(1,4)- hexuronic acid, the former being either sulfated or deacetylated on its amino group as well as sulfated on one of its hydroxyl groups and the latter can be a mixture of sulfated and nonsulfated D-glucuronic and L-iduronic acids. Heparin is similar to heparan sulfate but it contains more N-sulfate and O-sulfate groups. [PMID: 35536982]
GO:0050654: chondroitin sulfate proteoglycan metabolic process
Def: The chemical reactions and pathways involving chondroitin sulfate proteoglycans which consist of a core protein linked to a chondroitin sulfate glycosaminoglycan. The chondroitin sulfate chain is composed of the repeating disaccharide unit beta-(1,4)-linked D-glucuronic acid beta-(1,3)-N-acetyl-D-galactosamine, the latter can be O-sulfated. [PMID: 17239763]
GO:0050650: chondroitin sulfate proteoglycan biosynthetic process
Def: The chemical reactions and pathways resulting in the formation of chondroitin sulfate proteoglycans which consist of a core protein linked to a chondroitin sulfate glycosaminoglycan. The chondroitin sulfate chain is composed of the repeating disaccharide unit beta-(1,4)-linked D-glucuronic acid beta-(1,3)-N-acetyl-D-galactosamine, the latter can be O-sulfated. Chondroitin sulfate chains are covalently linked to serine/threonine residues (O-linked) of the core protein via a tetrasaccharide linker sequence (xylose-galactose-galactose-glucuronate). [PMID: 17239763]
GO:0030207: chondroitin sulfate proteoglycan catabolic process
Def: The chemical reactions and pathways resulting in the breakdown of chondroitin sulfate proteoglycans which consist of a core protein linked to a chondroitin sulfate glycosaminoglycan. The chondroitin sulfate chain is composed of the repeating disaccharide unit beta-(1,4)-linked D-glucuronic acid beta-(1,3)-N-acetyl-D-galactosamine, the latter can be O-sulfated. [PMID: 17239763]
GO:0050655: dermatan sulfate proteoglycan metabolic process
Def: The chemical reactions and pathways involving dermatan sulfate proteoglycans which consist of a core protein linked to a dermatan sulfate glycosaminoglycan. The dermatan sulfate chain is composed of the repeating disaccharide unit beta-(1,4)-linked D-hexuronic acid beta-(1,3)-N-acetyl-D-galactosamine, the former can be a mixture of sulfated and nonsulfated D-glucuronic and L-iduronic acids and the latter can be O-sulfated. [PMID: 17239763]
GO:0050651: dermatan sulfate proteoglycan biosynthetic process
Def: The chemical reactions and pathways resulting in the formation of dermatan sulfate proteoglycans which consist of a core protein linked to a dermatan sulfate glycosaminoglycan. The dermatan sulfate chain is composed of the repeating disaccharide unit beta-(1,4)-linked D-hexuronic acid beta-(1,3)-N-acetyl-D-galactosamine, the former can be a mixture of sulfated and nonsulfated D-glucuronic and L-iduronic acids and the latter can be O-sulfated. Dermatan sulfate chains are covalently linked to serine/threonine residues (O-linked) of the core protein via a tetrasaccharide linker sequence (xylose-galactose-galactose-glucuronate). [PMID: 17239763]
GO:0030209: dermatan sulfate proteoglycan catabolic process
Def: The chemical reactions and pathways resulting in the breakdown of dermatan sulfate proteoglycans which consist of a core protein linked to a dermatan sulfate glycosaminoglycan. The dermatan sulfate chain is composed of the repeating disaccharide unit beta-(1,4)-linked D-hexuronic acid beta-(1,3)-N-acetyl-D-galactosamine, the former can be a mixture of sulfated and nonsulfated D-glucuronic and L-iduronic acids and the latter can be O-sulfated. [PMID: 17239763]
GO:0042339: keratan sulfate proteoglycan metabolic process
Def: The chemical reactions and pathways involving keratan sulfate proteoglycans which consist of a core protein linked to a keratan sulfate glycosaminoglycan. The keratan sulfate chain is composed of the repeating disaccharide unit beta-(1,4)-linked N-acetyl-D-glucosamine beta-(1,3)-galactose, both can be sulfated. [PMID: 29340594]
GO:0018146: keratan sulfate proteoglycan biosynthetic process
Def: The chemical reactions and pathways resulting in the formation of keratan sulfate proteoglycans which consist of a core protein linked to a keratan sulfate glycosaminoglycan. The keratan sulfate chain is composed of the repeating disaccharide unit beta-(1,4)-linked N-acetyl-D-glucosamine beta-(1,3)-galactose, both can be sulfated. Keratan sulfate chains can be covalently linked either to an asparagine residue (N-linked) of the core protein via a high mannose oligasacccharide linker or to serine/threonine residues (O-linked) of the core protein via a core 2 type-linker. [PMID: 29340594]
GO:0042340: keratan sulfate proteoglycan catabolic process
Def:The chemical reactions and pathways resulting in the breakdown of keratan sulfate proteoglycans which consist of a core protein linked to a keratan sulfate glycosaminoglycan. The keratan sulfate chain is composed of the repeating disaccharide unit beta-(1,4)-linked N-acetyl-D-glucosamine beta-(1,3)-galactose, both can be sulfated. [PMID: 35536982]
@sjm41
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