New dataset: human_proteoform_glycosylation_sites_embl.csv and mouse_proteoform_glycosylation_sites_embl.csv

ubhuiyan commented 2 weeks ago

Source = glygen_upload.csv Output = *_proteoform_glycosylation_sites_embl.csv

Mapping Files: unreviewed/human_protein_masterlist.csv and unreviewed/mouse_protein_masterlist.csv misc/n_sequon_info.csv unreviewed/*_protein_glycosylation_motifs.csv glytoucan/current/export/names.tsv

"uniprotkb_canonical_ac","glycosylation_site_uniprotkb","amino_acid","saccharide","glycosylation_type","source_glycan_type","xref_key","xref_id","source_gene_name","start_pos","end_pos","start_aa","end_aa","site_seq","composition","composition_mass","source_tissue_id","source_tissue_name","source_cell_line_cellosaurus_id","source_cell_line_cellosaurus_name","n_sequon","n_sequon_type"

Output Files: human_proteoform_glycosylation_sites_embl.csv mouse_proteoform_glycosylation_sites_embl.csv

The output file should have the following headers: Source Field	Output Field	Notes
uniprotkb_ac (or gene_name if uniprotkb_ac can't be mapped)	uniprotkb_cannonical_ac	Map to canonical ac using *_protein_masterlist.csv field "uniprotkb_canonical_ac" (or use "gene_name" if uniprotkb_ac can't be mapped)
glycosylation_site_uniprotkb	glycosylation_site_uniprotkb	Copy directly from Source
amino_acid	amino_acid	Copy directly from source
composition	saccharide	Map from Byonic composition string to GlyTouCan accession using names.tsv
glycosylation_type	glycosylation_type	Copy directly from Source
glycan_type	source_glycan_type	Copy directly from source
	xref_key	All rows: "protein_xref_doi"
	xref_id	All rows: "10.1101/2023.09.13.557529v1"
gene_name	source_gene_name	Copy directly from Source
glycosylation_site_uniprotkb	start_pos	Copy directly from Source
glycosylation_site_uniprotkb	end_pos	Copy directly from Source
amino_acid	start_aa	Copy directly from Source
amino_acid	end_aa	Copy directly from Source
peptide	site_seq	Copy directly from Source
composition	composition	Extract comp string before " %" Ex. HexNAc(2)Hex(8) % 1702.5814
glycan_mass	composition_mass	Copy directly from Source
source_tissue_id	source_tissue_id	Copy directly from Source
source_tissue	source_tissue_name	Copy directly from Source
source_cell_line_cellosaurus_id	source_cell_line_cellosaurus_id	copy directly from Source
source_cell_line_cellosaurus_name	source_cell_line_cellosaurus_name	copy directly from Source
	n_sequon	Map using *_protein_glycosylation_motifs.csv
	n_sequon_type	Map using misc/n_sequon_info.csv

Example:

Input File:

$ head -2 /data/projects/glygen/downloads/embl/current/glygen_upload.csv
"uniprotkb_ac","gene_name","glycosylation_site_uniprotkb","amino_acid","glycosylation_type","start_pos","end_pos","peptide","taxonomy_id","taxonomy_species","composition","glycan_mass","glycan_type","abundance","source_tissue_id","source_tissue","source_cell_line_cellosaurus_id","source_cell_line_cellosaurus_name","evidence"
"Q5JTV8","TOR1AIP1","399","Asn","N-linked","397","404","HLNSSHPR","9606","homo sapiens","HexNAc(2)Hex(8) % 1702.5814","1702.5814","high mannose","","UBERON:0002113","kidney","CVCL_0063","HEK293T","https://www.biorxiv.org/content/10.1101/2023.09.13.557529v1.full"

Output File:

uniprotkb_canonical_ac","glycosylation_site_uniprotkb","amino_acid","saccharide","glycosylation_type","source_glycan_type","xref_key","xref_id","source_gene_name","start_pos","end_pos","start_aa","end_aa","site_seq","composition","composition_mass","source_tissue_id","source_tissue_name","source_cell_line_cellosaurus_id","source_cell_line_cellosaurus_name","n_sequon","n_sequon_type"
"Q5JTV8-1", "399", "Asn", "G62765YT", "N-linked", "high mannose", "protein_xref_doi", "10.1101/2023.09.13.557529v1", "TOR1AIP1", "397", "397", "Asn", "Asn", "HLNSSHPR", "HexNAc(2)Hex(8)", "1702.5814", "UBERON:0002113", "kidney", "CVCL_0063", "HEK293T", "NSS", "NXS"

rykahsay commented 2 weeks ago

@kmartinez834 --- passing reported glycosylation at the composition level to glytoucan level seems to be problematic to me? There are many glytoucans that have the same composition and this propagation of information is problematic.

We have similar data in unreviewed/human_proteoform_glycosylation_sites_unicarbkb.csv where saccharide="" and composition has value, and I don't think we are passing this glycosylation record to any glytoucan. Please look into this carefully.

$ cat unreviewed/human_proteoform_glycosylation_sites_unicarbkb.csv | awk -F"\",\"" '{print $4","$18}'  |grep ^, |sort -u |head
,
,comp_HexNAc0Hex0dHex0NeuAc0NeuGc0Pent0S0P0KDN0HexA0
,comp_HexNAc1HexdHex0NeuAc1NeuGc0Pent0S0P0KDN0HexA0
,comp_HexNAc2Hex3dHex0NeuAc0Gc0Pent0S0P0KDN0HexA0
,comp_HexNAc2Hex3dHex1NeuAc0Gc0Pent0S0P0KDN0HexA0
,comp_HexNAc2Hex4dHex1NeuAc0Gc0Pent0S0P0KDN0HexA0
,comp_HexNAc2Hex5dHex0NeuAc0Gc0Pent0S0P0KDN0HexA0
,comp_HexNAc2Hex5dHex1NeuAc0Gc0Pent0S0P0KDN0HexA0
,comp_HexNAc2Hex6dHex0NeuAc0Gc0Pent0S0P0KDN0HexA0
,comp_HexNAc2Hex7dHex0NeuAc0Gc0Pent0S0P0KDN0HexA0

kmartinez834 commented 2 weeks ago

@rykahsay I can confirm that Glytoucan to Byonic name is 1:1 in names.tsv

kmartinez834 commented 1 week ago

Update the "src_xref_key" and "src_xref_id" values for all rows:

human_proteoform_glycosylation_sites_embl.csv:

"src_xref_key","src_xref_id"
"protein_xref_glygen_ds","GLY_000888"

mouse_proteoform_glycosylation_sites_embl.csv:

"src_xref_key","src_xref_id"
"protein_xref_glygen_ds","GLY_000889"

rykahsay commented 1 week ago

done, check the datasets for now and the effect will propagate after I make and push json objects to tst

glygener / glygen-issues

New dataset: human_proteoform_glycosylation_sites_embl.csv and mouse_proteoform_glycosylation_sites_embl.csv #1287

Example: