Instructions for TableMaker datasets

[ubhuiyan]

Source = /tablemaker/current/TD10901054.txt

Output = [please determine the naming for these files]

Output Headers:

saccharide, xref_key, xref_id, src_xref_key, src_xref_id, taxonomy_species, taxonomy_id

Organism Mapping:

Map the organism using the TaxID provided in the Species column using species_info.csv

Mapping Files:

1. glytoucan/current/export/allgtcxrefs.tsv
2. /generated/misc/species_info.csv

Source Field	Output Field	Notes
GlyTouCan ID	saccharide	Map to allgtcxrefs.tsv
-	xref_key	All rows "glycan_xref_pubmed"
Evidence	xref_id	Copy directly from Source
-	src_xref_key	"glycan_xref_tablemaker" for all rows
GlyTouCan ID	src_xref_id	Copy directly from source.
-	taxonomy_species	Map to species_info.csv using Species column.
Species	taxonomy_id	Copy directly from source

Source File:

"GlyTouCan ID","Evidence","Species","Strain","Cell line ID",,"Disease","Glycan dictionary term ID","has_abundance","has_expression","Functional annotation/Keyword","Experimental technique","Variant (Fly, yeast, mouse)","Organismal/cellular Phenotype","Molecular Phenotype","Contributor","Comment"
"G64780OA","17264077","7227","Oregon-R",,,,,"Yes","No","differentiation","HPLC","WT",,,"createdBy:melody porterfield ([email protected], UGA)|createdWith:GlyTableMaker (https://glygen.ccrc.uga.edu/tablemaker)|createdWith:GRITS Toolbox (http://www.grits-toolbox.org/)",

Output File:

saccharide, xref_key, xref_id, src_xref_key, src_xref_id, taxonomy_species, taxonomy_id
G64780OA, glycan_xref_pubmed, 17264077, glycan_xref_tablemaker, G64780OA, Drosophila melanogaster, 7227

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Source = /tablemaker/current/TD1127346.txt

Output = [please determine the naming for these files]

Output Headers:

saccharide, xref_key, xref_id, src_xref_key, src_xref_id, source_tissue_id, taxonomy_species, taxonomy_id

Organism Mapping:

Map the organism using the TaxID provided in the Species column using species_info.csv

Mapping Files:

1. glytoucan/current/export/allgtcxrefs.tsv
2. /generated/misc/species_info.csv

Source Field	Output Field	Notes
GlyTouCan ID	saccharide	Map to allgtcxrefs.tsv
-	xref_key	All rows "glycan_xref_pubmed"
Evidence	xref_id	Copy directly from Source
-	src_xref_key	"glycan_xref_tablemaker" for all rows
GlyTouCan ID	src_xref_id	Copy directly from source.
Tissue ID	source_tissue_id	Copy directly from source.
-	taxonomy_species	Map to species_info.csv using the Species column
Species	taxonomy_id	Copy directly from source

Source File:

"GlyTouCan ID","Evidence","Species","Strain","Cell line ID",,"Disease","Glycan dictionary term ID","has_abundance","has_expression","Functional annotation/Keyword","Experimental technique","Variant (Fly, yeast, mouse)","Organismal/cellular Phenotype","Molecular Phenotype","Contributor","Comment"
"G72404VA","37998752","7955",,,,,,"Yes","No",,"LC-MS/MS",,,,"createdBy:Sergei Shalygin ([email protected], undefined)|createdWith:GlyTableMaker (https://glygen.ccrc.uga.edu/tablemaker)",

Output File:

saccharide, xref_key, xref_id, src_xref_key, src_xref_id, taxonomy_species, taxonomy_id
G72404VA, glycan_xref_pubmed, 37998752, glycan_xref_tablemaker, G72404VA, Danio rerio, 7955