Process Glycan Structure Dictionary datasets

kmartinez834 commented 1 year ago

Process the following datasets:

unreviewed/glycan_dictionary.csv
unreviewed/glycan_xref_dictionary.csv

src_file	changes
downloads/glycan_dictionary/current/glycan_dictionary.csv	"best_match" field removed
unreviewed/glycan_masterlist.csv	N/A

rykahsay commented 1 year ago

done --> please check

kmartinez834 commented 1 year ago

Some of the rows in unreviewed/glycan_dictionary.csv have pipes in the "glytoucan_ac" field:

"glytoucan_ac","term","term_in_sentence","publication","definition","term_xref","synonymns","function","disease_associations","wikipedia","essentials_of_glycobiology","xref_key","xref_id"
"G00058MO|G46055MA","i antigen","Inasmuch as the hybridoma was established by hybridization of lymphocytes derived from regional lymph nodes of lung cancer, and the antigen was found in the patient's lung cancer tissue, the i antigen in lung cancer is probably recognized as a tumor-associated antigen by the host's immune cell system.[PMID:2422274]","2422274|15679458|21912254|12468428|28508465|6203982|30728302|8449405|9122902|10360315|6159787|6183759|518539|6715951|21933024","","GlycoMotif:GGM.000004|GlycoMotif:GGM.000002|GTC:G46055MA|GTC:G00058MO","Type 2 LN2","","","","","glycan_xref_dictionary","GSD000111"
"G46677TE | G45714BQ","GD1a","Exclusive exposure of rat oligodendrocytes to GD1a, but not other gangliosides, overcomes aggregated fibronectin-induced inhibition of myelin membrane formation, in vitro, and OPC differentiation in fibronectin aggregate containing cuprizone-induced demyelinated lesions in male mice. [PMID: 28899916]","28899916|26860251|21930390|32906699|26054879|29951721|11745410|17653976|26119566|21554929|18435913|15342262|26865725|21151139|15716397|21492147|16942752|26973195|24449473|14999485|22735313|20589721|10521808|22929125|7827024|16897174|25062498|17227759","A branched amino hexasaccharide consisting of the linear sequence α-Neu5Ac-(2→3)-β-D-Gal-(1→3)-β-D-GalNAc-(1→4)-β-D-Gal-(1→4)-β-D-Glc having a Neu5Ac residue attached to a galactose via an α-(2→3) linkage. The oligosaccharide of ganglioside GD1a.[CHEBI:59209]","GlycoMotif:GGM.000106|GlycoMotif:GGM.000107|GTC:G46677TE|GTC:G45714BQ|CID:45266861|CHEBI:59209|GlycoEpitope:EP0056|SugarBind_Ligand:22|KEGG:G00111","GD1alpha","","Gastroenteritis[SugarBind_Ligand:22]|Actinomycosis[SugarBind_Ligand:22]|Lazy leukocyte syndrome[SugarBind_Ligand:22]|Toxoplasmosis[SugarBind_Ligand:22]|Lyme disease[SugarBind_Ligand:22]|Botulism[SugarBind_Ligand:22]|Keratoconjunctivitis[SugarBind_Ligand:22]|Influenza[SugarBind_Ligand:22]","","","glycan_xref_dictionary","GSD000083"

Split into separate rows for each glytoucan_ac:

"glytoucan_ac","term","term_in_sentence","publication","definition","term_xref","synonymns","function","disease_associations","wikipedia","essentials_of_glycobiology","xref_key","xref_id"
"G00058MO","i antigen","Inasmuch as the hybridoma was established by hybridization of lymphocytes derived from regional lymph nodes of lung cancer, and the antigen was found in the patient's lung cancer tissue, the i antigen in lung cancer is probably recognized as a tumor-associated antigen by the host's immune cell system.[PMID:2422274]","2422274|15679458|21912254|12468428|28508465|6203982|30728302|8449405|9122902|10360315|6159787|6183759|518539|6715951|21933024","","GlycoMotif:GGM.000004|GlycoMotif:GGM.000002|GTC:G46055MA|GTC:G00058MO","Type 2 LN2","","","","","glycan_xref_dictionary","GSD000111"
"G46055MA","i antigen","Inasmuch as the hybridoma was established by hybridization of lymphocytes derived from regional lymph nodes of lung cancer, and the antigen was found in the patient's lung cancer tissue, the i antigen in lung cancer is probably recognized as a tumor-associated antigen by the host's immune cell system.[PMID:2422274]","2422274|15679458|21912254|12468428|28508465|6203982|30728302|8449405|9122902|10360315|6159787|6183759|518539|6715951|21933024","","GlycoMotif:GGM.000004|GlycoMotif:GGM.000002|GTC:G46055MA|GTC:G00058MO","Type 2 LN2","","","","","glycan_xref_dictionary","GSD000111"
"G46677TE","GD1a","Exclusive exposure of rat oligodendrocytes to GD1a, but not other gangliosides, overcomes aggregated fibronectin-induced inhibition of myelin membrane formation, in vitro, and OPC differentiation in fibronectin aggregate containing cuprizone-induced demyelinated lesions in male mice. [PMID: 28899916]","28899916|26860251|21930390|32906699|26054879|29951721|11745410|17653976|26119566|21554929|18435913|15342262|26865725|21151139|15716397|21492147|16942752|26973195|24449473|14999485|22735313|20589721|10521808|22929125|7827024|16897174|25062498|17227759","A branched amino hexasaccharide consisting of the linear sequence α-Neu5Ac-(2→3)-β-D-Gal-(1→3)-β-D-GalNAc-(1→4)-β-D-Gal-(1→4)-β-D-Glc having a Neu5Ac residue attached to a galactose via an α-(2→3) linkage. The oligosaccharide of ganglioside GD1a.[CHEBI:59209]","GlycoMotif:GGM.000106|GlycoMotif:GGM.000107|GTC:G46677TE|GTC:G45714BQ|CID:45266861|CHEBI:59209|GlycoEpitope:EP0056|SugarBind_Ligand:22|KEGG:G00111","GD1alpha","","Gastroenteritis[SugarBind_Ligand:22]|Actinomycosis[SugarBind_Ligand:22]|Lazy leukocyte syndrome[SugarBind_Ligand:22]|Toxoplasmosis[SugarBind_Ligand:22]|Lyme disease[SugarBind_Ligand:22]|Botulism[SugarBind_Ligand:22]|Keratoconjunctivitis[SugarBind_Ligand:22]|Influenza[SugarBind_Ligand:22]","","","glycan_xref_dictionary","GSD000083"
"G45714BQ","GD1a","Exclusive exposure of rat oligodendrocytes to GD1a, but not other gangliosides, overcomes aggregated fibronectin-induced inhibition of myelin membrane formation, in vitro, and OPC differentiation in fibronectin aggregate containing cuprizone-induced demyelinated lesions in male mice. [PMID: 28899916]","28899916|26860251|21930390|32906699|26054879|29951721|11745410|17653976|26119566|21554929|18435913|15342262|26865725|21151139|15716397|21492147|16942752|26973195|24449473|14999485|22735313|20589721|10521808|22929125|7827024|16897174|25062498|17227759","A branched amino hexasaccharide consisting of the linear sequence α-Neu5Ac-(2→3)-β-D-Gal-(1→3)-β-D-GalNAc-(1→4)-β-D-Gal-(1→4)-β-D-Glc having a Neu5Ac residue attached to a galactose via an α-(2→3) linkage. The oligosaccharide of ganglioside GD1a.[CHEBI:59209]","GlycoMotif:GGM.000106|GlycoMotif:GGM.000107|GTC:G46677TE|GTC:G45714BQ|CID:45266861|CHEBI:59209|GlycoEpitope:EP0056|SugarBind_Ligand:22|KEGG:G00111","GD1alpha","","Gastroenteritis[SugarBind_Ligand:22]|Actinomycosis[SugarBind_Ligand:22]|Lazy leukocyte syndrome[SugarBind_Ligand:22]|Toxoplasmosis[SugarBind_Ligand:22]|Lyme disease[SugarBind_Ligand:22]|Botulism[SugarBind_Ligand:22]|Keratoconjunctivitis[SugarBind_Ligand:22]|Influenza[SugarBind_Ligand:22]","","","glycan_xref_dictionary","GSD000083"

Update unreviewed/glycan_xref_dictionary.csv to include the above glytoucan accessions

rykahsay commented 1 year ago

check

kmartinez834 commented 1 year ago

glycan_dictionary.csv Remove trailing/leading spaces in "glytoucan_ac":

"glytoucan_ac","term","term_in_sentence","publication","definition","term_xref","synonymns","function","disease_associations","wikipedia","essentials_of_glycobiology","xref_key","xref_id"
"G46677TE ","GD1a","Exclusive exposure of rat oligodendrocytes to GD1a, but not other gangliosides, overcomes aggregated fibronectin-induced inhibition of myelin membrane formation, in vitro, and OPC differentiation in fibronectin aggregate containing cuprizone-induced demyelinated lesions in male mice. [PMID: 28899916]","28899916|26860251|21930390|32906699|26054879|29951721|11745410|17653976|26119566|21554929|18435913|15342262|26865725|21151139|15716397|21492147|16942752|26973195|24449473|14999485|22735313|20589721|10521808|22929125|7827024|16897174|25062498|17227759","A branched amino hexasaccharide consisting of the linear sequence α-Neu5Ac-(2→3)-β-D-Gal-(1→3)-β-D-GalNAc-(1→4)-β-D-Gal-(1→4)-β-D-Glc having a Neu5Ac residue attached to a galactose via an α-(2→3) linkage. The oligosaccharide of ganglioside GD1a.[CHEBI:59209]","GlycoMotif:GGM.000106|GlycoMotif:GGM.000107|GTC:G46677TE|GTC:G45714BQ|CID:45266861|CHEBI:59209|GlycoEpitope:EP0056|SugarBind_Ligand:22|KEGG:G00111","GD1alpha","","Gastroenteritis[SugarBind_Ligand:22]|Actinomycosis[SugarBind_Ligand:22]|Lazy leukocyte syndrome[SugarBind_Ligand:22]|Toxoplasmosis[SugarBind_Ligand:22]|Lyme disease[SugarBind_Ligand:22]|Botulism[SugarBind_Ligand:22]|Keratoconjunctivitis[SugarBind_Ligand:22]|Influenza[SugarBind_Ligand:22]","","","glycan_xref_dictionary","GSD000083"
" G45714BQ","GD1a","Exclusive exposure of rat oligodendrocytes to GD1a, but not other gangliosides, overcomes aggregated fibronectin-induced inhibition of myelin membrane formation, in vitro, and OPC differentiation in fibronectin aggregate containing cuprizone-induced demyelinated lesions in male mice. [PMID: 28899916]","28899916|26860251|21930390|32906699|26054879|29951721|11745410|17653976|26119566|21554929|18435913|15342262|26865725|21151139|15716397|21492147|16942752|26973195|24449473|14999485|22735313|20589721|10521808|22929125|7827024|16897174|25062498|17227759","A branched amino hexasaccharide consisting of the linear sequence α-Neu5Ac-(2→3)-β-D-Gal-(1→3)-β-D-GalNAc-(1→4)-β-D-Gal-(1→4)-β-D-Glc having a Neu5Ac residue attached to a galactose via an α-(2→3) linkage. The oligosaccharide of ganglioside GD1a.[CHEBI:59209]","GlycoMotif:GGM.000106|GlycoMotif:GGM.000107|GTC:G46677TE|GTC:G45714BQ|CID:45266861|CHEBI:59209|GlycoEpitope:EP0056|SugarBind_Ligand:22|KEGG:G00111","GD1alpha","","Gastroenteritis[SugarBind_Ligand:22]|Actinomycosis[SugarBind_Ligand:22]|Lazy leukocyte syndrome[SugarBind_Ligand:22]|Toxoplasmosis[SugarBind_Ligand:22]|Lyme disease[SugarBind_Ligand:22]|Botulism[SugarBind_Ligand:22]|Keratoconjunctivitis[SugarBind_Ligand:22]|Influenza[SugarBind_Ligand:22]","","","glycan_xref_dictionary","GSD000083"

glycan_xref_dictionary.csv Add these GlyTouCan accessions: G00058MO G46055MA G46677TE G45714BQ

rykahsay commented 1 year ago

Great job catching all these issues, I am really impressed!

I have fixed these issues now -- please check

kmartinez834 commented 1 year ago

👍 Looks good

glygener / glygen-issues

Process Glycan Structure Dictionary datasets #91