Carbbank Mapping Instructions

[ubhuiyan]

Source file: downloads/carbbank/current/carbbank.csv

Mapping files: downloads/glytoucan/current/export/carbbank.tsv

Output file: *_proteoform_glyosylation_sites_carbbank.csv

The output file should have the following headers:

"uniprotkb_canonical_ac","saccharide","glycosylation_type","xref_key","xref_id"

Organism Mapping:

• "BS" has organism, look for: "(CN) human","(CN) mouse","(CN) rat","(CN) pig","(CN) chicken","(GS) Saccharomyces cerevisiae","(GS) Dictyostelium discoideum","(GS) Drosophila melanogaster","(CN) fruit fly" --> Don't use "(CN) yeast", as this will result in many other types of yeast --> Use regex when parsing species and watch out for instances such as "(CN) human cytomegalovirus", "(CN) mouse-ear chickweed", or "(CN) human, mouse," (the later is a human-mouse xenograft)

See the chart below for instructions on mapping source fields to output (if any required fields are missing here, add them in with blank values):

Source field	Output field	Instructions
DB	uniprotkb_canonical_ac	Accessions starting with SwissProt
CC	saccharide	Map to glytoucan ac using carbbank.tsv
MT	glycosylation_type	N-linked if "N-linked glycopeptide" or "N-linked glycoprotein" O-linked if "O-linked glycopeptide" or "O-linked glycoprotein"
	xref_key	All rows: "protein_xref_pubmed"
DB	xref_id	Accessions starting with PMID

Example:

Input file

"CCSD:42830","Irie F; Murakoshi H; Suzuki T; Suzuki Y; Kon K; Ando S; Yoshida K;Hirabayashi Y","Characterization of four monosialo and a novel disialo Asn N-glycosides from the urine of a patient with aspartylglycosaminuria","Glycoconj J (1995) 12: 290-297","AG-1","(CN) human, (OT) urine, (disease) aspartylglycosaminuria","Shough NJ","19-09-1995","944504e4","CBank:14042","","N-linked glycopeptide","","","","","","","","PMID:7496144","","",""
"CCSD:5474","Carlsson SR; Lycksell PO; Fukuda M","Assignment of O-glycan attachment sites to the hinge-like regions ofhuman lysosomal membrane glycoproteins lamp-1 and lamp-2","Arch Biochem Biophys (1993) 304: 65-73","","(CN) human, (OT) lysosome membrane","Doubet S","06-10-1993","cb86e782","CBank:2116","","O-linked glycoprotein","","","","lamp-2","","desialylated","","SwissProt:P13473 -- lamp-2","","",""

Output file

"uniprotkb_canonical_ac","saccharide","glycosylation_type","xref_key","xref_id"
"", "G00065MO", "N-linked", "protein_xref_pubmed", "7496144" 
"P13473", "G00032MO", "O-linked", "protein_xref_pubmed", ""
...

[rykahsay]

I have tried to create the datasets -- please check.

Here are some points:

• PMID/DOI is a required to make any glycosylation row, and only 4 organisms (human, mouse, rat and yeast) have rows with PMIDs. This means there will not be carbbank datasets for other organisms.
• You will need to edit misc/ds2bco.json and enter the correct BCO mapping the the four carbbank datasets
• You need to maintain the misc/carbbank_species.json file to allow us to map organism names as they come in the source file to GlyGen short names ("human", "fruitfly" ...)

Please assign the ticket back to me after you edit misc/ds2bco.json so that I can update the datasets

[ubhuiyan]

I have updated the misc/ds2bco.json. Please let me know if there's any issues.

[rykahsay]

I have updated the datasets, please check

[ubhuiyan]

[sbhuiyan28@glygen-vm-dev unreviewed]$ awk -F, '{print $1, $4, $5, $6, $7, $8, $9}' human_proteoform_glycosylation_sites_carbbank.csv | head -2
"uniprotkb_canonical_ac" "saccharide" "glycosylation_type" "xref_key" "xref_id" "src_xref_key" "src_xref_id"
"Q6P1J9-1" "G36855WW" "O-linked" "protein_xref_pubmed" "93364082" "protein_xref_glygen_ds" "GLY_001113"
[sbhuiyan28@glygen-vm-dev unreviewed]$ awk -F, '{print $1, $4, $5, $6, $7, $8, $9}' rat_proteoform_glycosylation_sites_carbbank.csv | head -2
"uniprotkb_canonical_ac" "saccharide" "glycosylation_type" "xref_key" "xref_id" "src_xref_key" "src_xref_id"
"A6JX65-1" "G36855WW" "O-linked" "protein_xref_pubmed" "93364082" "protein_xref_glygen_ds" "GLY_001115"
[sbhuiyan28@glygen-vm-dev unreviewed]$ awk -F, '{print $1, $4, $5, $6, $7, $8, $9}' mouse_proteoform_glycosylation_sites_carbbank.csv | head 
-2
"uniprotkb_canonical_ac" "saccharide" "glycosylation_type" "xref_key" "xref_id" "src_xref_key" "src_xref_id"
"Q3UD01-1" "G99229VQ" "N-linked" "protein_xref_pubmed" "7496147" "protein_xref_glygen_ds" "GLY_001114"
[sbhuiyan28@glygen-vm-dev unreviewed]$ awk -F, '{print $1, $4, $5, $6, $7, $8, $9}' yeast_proteoform_glycosylation_sites_carbbank.csv | head 
-2
"uniprotkb_canonical_ac" "saccharide" "glycosylation_type" "xref_key" "xref_id" "src_xref_key" "src_xref_id"
"P0CW41-1" "G46565HP" "N-linked" "protein_xref_pubmed" "7496153" "protein_xref_glygen_ds" "GLY_001116"