{ "bcoid": "GLY_000703", "title": "Glycan Pathway GlycoTree", "description": "The dataset contains pathway data for all N-glycans which are fully mapped to the GlycoTree framework. ...", "filename": "glycan_pathway_glycotree.csv", "filetype": "csv", "categories": { "molecule": [ "Glycan" ], "tag": [ "Pathway GlycoTree" ], "status": [ "Reviewed" ], "file_type": [ "csv" ], "scope": [ "internal" ], "species": [ "Homo sapiens", "Rattus norvegicus", "Rattus", "Mus musculus", "Sus scrofa", "Drosophila melanogaster" ] }, "minitable": { "content": [ [ "G00017IP...", "G59741XZ..." ], [ "G00017IP...", "G61751GZ..." ] ], "headers": [ "glytoucan_ac...", "source..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "glytoucan_ac" }, { "type": "string", "label": "source" }, { "type": "string", "label": "target" }, { "type": "string", "label": "residue_id" }, { "type": "string", "label": "residue_name" }, { "type": "string", "label": "enzyme_uniprotkb_ac" }, { "type": "string", "label": "enzyme_tax_name" } ], [ "G00017IP", "G59741XZ", "G56271TF", "N469", "-n-sulfate", "", "" ], [ "G00017IP", "G61751GZ", "G59741XZ", "N29", "β-D-GalpNAc", "Q6L9W6", "Homo sapiens" ], [ "G00017IP", "G61751GZ", "G59741XZ", "N29", "β-D-GalpNAc", "Q76KP1", "Homo sapiens" ], [ "G00017IP", "G61751GZ", "G59741XZ", "N29", "β-D-GalpNAc", "A0A1D5RMF7", "Mus musculus" ], [ "G00017IP", "G61751GZ", "G59741XZ", "N29", "β-D-GalpNAc", "Q766D5", "Mus musculus" ], [ "G00176HZ", "G20030CU", "G00176HZ", "N15", "α-L-Fucp", "Q9BYC5", "Homo sapiens" ], [ "G00176HZ", "G20030CU", "G00176HZ", "N15", "α-L-Fucp", "Q9WTS2", "Mus musculus" ], [ "G00176HZ", "G10219AA", "G20030CU", "N7", "β-D-GlcpNAc", "Q9UBM8", "Homo sapiens" ], [ "G00176HZ", "G10219AA", "G20030CU", "N7", "β-D-GlcpNAc", "Q9UM21", "Homo sapiens" ], [ "G00176HZ", "G10219AA", "G20030CU", "N7", "β-D-GlcpNAc", "Q9UQ53", "Homo sapiens" ], [ "G00176HZ", "G10219AA", "G20030CU", "N7", "β-D-GlcpNAc", "Q812F8", "Mus musculus" ], [ "G00176HZ", "G10219AA", "G20030CU", "N7", "β-D-GlcpNAc", "Q812G0", "Mus musculus" ], [ "G00176HZ", "G10219AA", "G20030CU", "N7", "β-D-GlcpNAc", "Q9D306", "Mus musculus" ], [ "G00176HZ", "G39213VZ", "G10219AA", "N9", "β-D-GlcpNAc", "Q09328", "Homo sapiens" ], [ "G00176HZ", "G39213VZ", "G10219AA", "N9", "β-D-GlcpNAc", "Q3V5L5", "Homo sapiens" ], [ "G00176HZ", "G39213VZ", "G10219AA", "N9", "β-D-GlcpNAc", "Q765H6", "Mus musculus" ], [ "G00176HZ", "G39213VZ", "G10219AA", "N9", "β-D-GlcpNAc", "Q8R4G6", "Mus musculus" ], [ "G00176HZ", "G61751GZ", "G39213VZ", "N5", "β-D-GlcpNAc", "Q10469", "Homo sapiens" ], [ "G00176HZ", "G61751GZ", "G39213VZ", "N5", "β-D-GlcpNAc", "Q921V5", "Mus musculus" ], [ "G00212RH", "G11929SN", "G55479DB", "N52", "α-D-Galp", "P16442", "Homo sapiens" ], [ "G00212RH", "G11929SN", "G55479DB", "N52", "α-D-Galp", "P38649", "Mus musculus" ], [ "G00212RH", "G80294GH", "G11929SN", "N39", "α-D-Galp", "P16442", "Homo sapiens" ], [ "G00212RH", "G80294GH", "G11929SN", "N39", "α-D-Galp", "P38649", "Mus musculus" ], [ "G00212RH", "G86357DX", "G80294GH", "N50", "α-D-Galp", "P16442", "Homo sapiens" ], [ "G00212RH", "G86357DX", "G80294GH", "N50", "α-D-Galp", "P38649", "Mus musculus" ], [ "G00212RH", "G10691MJ", "G86357DX", "N8", "β-D-Galp", "O60512", "Homo sapiens" ], [ "G00212RH", "G10691MJ", "G86357DX", "N8", "β-D-Galp", "O60909", "Homo sapiens" ], [ "G00212RH", "G10691MJ", "G86357DX", "N8", "β-D-Galp", "P15291", "Homo sapiens" ], [ "G00212RH", "G10691MJ", "G86357DX", "N8", "β-D-Galp", "P15535", "Mus musculus" ], [ "G00212RH", "G10691MJ", "G86357DX", "N8", "β-D-Galp", "Q91YY2", "Mus musculus" ], [ "G00212RH", "G10691MJ", "G86357DX", "N8", "β-D-Galp", "Q9Z2Y2", "Mus musculus" ], [ "G00212RH", "G32305RZ", "G10691MJ", "N6", "β-D-Galp", "O60512", "Homo sapiens" ], [ "G00212RH", "G32305RZ", "G10691MJ", "N6", "β-D-Galp", "O60909", "Homo sapiens" ], [ "G00212RH", "G32305RZ", "G10691MJ", "N6", "β-D-Galp", "P15291", "Homo sapiens" ], [ "G00212RH", "G32305RZ", "G10691MJ", "N6", "β-D-Galp", "P15535", "Mus musculus" ], [ "G00212RH", "G32305RZ", "G10691MJ", "N6", "β-D-Galp", "Q91YY2", "Mus musculus" ], [ "G00212RH", "G32305RZ", "G10691MJ", "N6", "β-D-Galp", "Q9Z2Y2", "Mus musculus" ], [ "G00212RH", "G42672MA", "G32305RZ", "N5", "β-D-GlcpNAc", "Q10469", "Homo sapiens" ], [ "G00212RH", "G42672MA", "G32305RZ", "N5", "β-D-GlcpNAc", "Q921V5", "Mus musculus" ], [ "G00212RH", "G12398HZ", "G42672MA", "N7", "β-D-GlcpNAc", "Q9UBM8", "Homo sapiens" ], [ "G00212RH", "G12398HZ", "G42672MA", "N7", "β-D-GlcpNAc", "Q9UM21", "Homo sapiens" ], [ "G00212RH", "G12398HZ", "G42672MA", "N7", "β-D-GlcpNAc", "Q9UQ53", "Homo sapiens" ], [ "G00212RH", "G12398HZ", "G42672MA", "N7", "β-D-GlcpNAc", "Q812F8", "Mus musculus" ], [ "G00212RH", "G12398HZ", "G42672MA", "N7", "β-D-GlcpNAc", "Q812G0", "Mus musculus" ], [ "G00212RH", "G12398HZ", "G42672MA", "N7", "β-D-GlcpNAc", "Q9D306", "Mus musculus" ], [ "G00212RH", "G07483YN", "G12398HZ", "N3", "β-D-Galp", "O60512", "Homo sapiens" ], [ "G00212RH", "G07483YN", "G12398HZ", "N3", "β-D-Galp", "O60909", "Homo sapiens" ], [ "G00212RH", "G07483YN", "G12398HZ", "N3", "β-D-Galp", "P15291", "Homo sapiens" ], [ "G00212RH", "G07483YN", "G12398HZ", "N3", "β-D-Galp", "P15535", "Mus musculus" ], [ "G00212RH", "G07483YN", "G12398HZ", "N3", "β-D-Galp", "Q91YY2", "Mus musculus" ], [ "G00212RH", "G07483YN", "G12398HZ", "N3", "β-D-Galp", "Q9Z2Y2", "Mus musculus" ], [ "G00212RH", "G61751GZ", "G07483YN", "N15", "α-L-Fucp", "Q9BYC5", "Homo sapiens" ], [ "G00212RH", "G61751GZ", "G07483YN", "N15", "α-L-Fucp", "Q9WTS2", "Mus musculus" ], [ "G00231WL", "G92574YO", "G19469VZ", "N471", "-n-sulfate", "", "" ], [ "G00231WL", "G32287FD", "G92574YO", "N38", "α-D-NeupNAc", "Q11203", "Homo sapiens" ], [ "G00231WL", "G32287FD", "G92574YO", "N38", "α-D-NeupNAc", "Q11206", "Homo sapiens" ], [ "G00231WL", "G32287FD", "G92574YO", "N38", "α-D-NeupNAc", "Q9Y274", "Homo sapiens" ], [ "G00231WL", "G32287FD", "G92574YO", "N38", "α-D-NeupNAc", "P97325", "Mus musculus" ], [ "G00231WL", "G32287FD", "G92574YO", "N38", "α-D-NeupNAc", "Q8VIB3", "Mus musculus" ], [ "G00231WL", "G32287FD", "G92574YO", "N38", "α-D-NeupNAc", "Q91Y74", "Mus musculus" ], [ "G00231WL", "G76842ZR", "G32287FD", "N17", "α-D-NeupNAc", "Q11203", "Homo sapiens" ], [ "G00231WL", "G76842ZR", "G32287FD", "N17", "α-D-NeupNAc", "Q11206", "Homo sapiens" ], [ "G00231WL", "G76842ZR", "G32287FD", "N17", "α-D-NeupNAc", "Q9Y274", "Homo sapiens" ], [ "G00231WL", "G76842ZR", "G32287FD", "N17", "α-D-NeupNAc", "P97325", "Mus musculus" ], [ "G00231WL", "G76842ZR", "G32287FD", "N17", "α-D-NeupNAc", "Q8VIB3", "Mus musculus" ], [ "G00231WL", "G76842ZR", "G32287FD", "N17", "α-D-NeupNAc", "Q91Y74", "Mus musculus" ], [ "G00231WL", "G63889NK", "G76842ZR", "N16", "α-D-NeupNAc", "Q11203", "Homo sapiens" ], [ "G00231WL", "G63889NK", "G76842ZR", "N16", "α-D-NeupNAc", "Q11206", "Homo sapiens" ], [ "G00231WL", "G63889NK", "G76842ZR", "N16", "α-D-NeupNAc", "Q9Y274", "Homo sapiens" ], [ "G00231WL", "G63889NK", "G76842ZR", "N16", "α-D-NeupNAc", "P97325", "Mus musculus" ], [ "G00231WL", "G63889NK", "G76842ZR", "N16", "α-D-NeupNAc", "Q8VIB3", "Mus musculus" ], [ "G00231WL", "G63889NK", "G76842ZR", "N16", "α-D-NeupNAc", "Q91Y74", "Mus musculus" ], [ "G00231WL", "G73492AT", "G63889NK", "N10", "β-D-Galp", "O60512", "Homo sapiens" ], [ "G00231WL", "G73492AT", "G63889NK", "N10", "β-D-Galp", "O60909", "Homo sapiens" ], [ "G00231WL", "G73492AT", "G63889NK", "N10", "β-D-Galp", "P15291", "Homo sapiens" ], [ "G00231WL", "G73492AT", "G63889NK", "N10", "β-D-Galp", "P15535", "Mus musculus" ], [ "G00231WL", "G73492AT", "G63889NK", "N10", "β-D-Galp", "Q91YY2", "Mus musculus" ], [ "G00231WL", "G73492AT", "G63889NK", "N10", "β-D-Galp", "Q9Z2Y2", "Mus musculus" ], [ "G00231WL", "G98809PE", "G73492AT", "N8", "β-D-Galp", "O60512", "Homo sapiens" ], [ "G00231WL", "G98809PE", "G73492AT", "N8", "β-D-Galp", "O60909", "Homo sapiens" ], [ "G00231WL", "G98809PE", "G73492AT", "N8", "β-D-Galp", "P15291", "Homo sapiens" ], [ "G00231WL", "G98809PE", "G73492AT", "N8", "β-D-Galp", "P15535", "Mus musculus" ], [ "G00231WL", "G98809PE", "G73492AT", "N8", "β-D-Galp", "Q91YY2", "Mus musculus" ], [ "G00231WL", "G98809PE", "G73492AT", "N8", "β-D-Galp", "Q9Z2Y2", "Mus musculus" ] ] }, "readme": "Name\n - Glycan Pathway GlycoTree\n\nVersion\n - v-2.2.1\n\nCreated on\n - 2022-09-14T12:37:04.198762\n\nModified on\n - 2022-09-26T09:08:12.656288\n\nCreated by\n - Karina Martinez [karinamartinez@gwu.edu], Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - Will York [will@ccrc.uga.edu]\n\nChecksum\n - \n\nUsability Domain\n - The dataset contains pathway data for all N-glycans which are fully mapped to the GlycoTree framework. Each pathway specifies details for a particular reaction catalyzed by enzymes (UniProtKB Accession) which effect the associated glycan structures (GlyTouCan Accessions).\n\nDescription Domain\n Keywords\n - Glycan\n - GlyTouCan Accession\n - Pathway\n - Glycotree\n\n Pipeline Steps\n - Step-1: The input file was downloaded from the source author and a python script was used to extract the following keys: glytoucan_ac,source,target,residue_id,residue_name,enzyme_uniprotkb_ac,enzyme_tax_name. The script also assigned the recommended enzyme taxonomy name based on the UniProtKB accession. \n\nExecution Domain\n Scripts\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: glycan_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/glycan_masterlist.csv\n Name: allPaths.json\n URI: https:/data.glygen.org/ln2downloads/sandbox/08_17_2023/allPaths.json\n Output Subdomain\n Name: glycan_pathway_glycotree.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/glycan_pathway_glycotree.csv\n Name: glycan_pathway_glycotree.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/glycan_pathway_glycotree.stat.csv\n\nFields\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"3296\"\n Name: \"source\"\n Description: \"Source for the data\"\n Unique Values: \"546\"\n Name: \"target\"\n Description: \"\"\n Unique Values: \"1275\"\n Name: \"residue_id\"\n Description: \"residue id associated with the glycan\"\n Unique Values: \"126\"\n Name: \"residue_name\"\n Description: \"Residue name of the glycan\"\n Unique Values: \"19\"\n Name: \"enzyme_uniprotkb_ac\"\n Description: \"\"\n Unique Values: \"68\"\n Name: \"enzyme_tax_name\"\n Description: \"\"\n Unique Values: \"4\"", "downloadurl": "/ln2data/releases/data/v-2.2.1/reviewed/glycan_pathway_glycotree.csv" }