{ "bcoid": "GLY_000304", "title": "Glycan Xref PDB", "description": "The dataset provides cross-references to PDB ID(s) for the associated glycan (GlyTouCan Accession). The ...", "filename": "glycan_xref_pdb.csv", "filetype": "csv", "categories": { "molecule": [ "Glycan" ], "tag": [ "PDB cross-references" ], "status": [ "Reviewed" ], "file_type": [ "csv" ], "scope": [ "internal" ], "species": [ "Saccharomyces cerevisiae", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Sus scrofa domesticus", "Rattus norvegicus", "Rattus", "Severe acute respiratory syndrome coronavirus 2", "Sus scrofa", "Dictyostelium discoideum" ] }, "minitable": { "content": [ [ "G00024MO...", "2cl8..." ], [ "G00024MO...", "2w52..." ] ], "headers": [ "glytoucan_ac...", "xref_id..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "glytoucan_ac" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "xref_key" } ], [ "G00024MO", "2cl8", "glycan_xref_pdb" ], [ "G00024MO", "2w52", "glycan_xref_pdb" ], [ "G00024MO", "2w63", "glycan_xref_pdb" ], [ "G00024MO", "3n9k", "glycan_xref_pdb" ], [ "G00024MO", "4gzi", "glycan_xref_pdb" ], [ "G00024MO", "4gzj", "glycan_xref_pdb" ], [ "G00025MO", "1ece", "glycan_xref_pdb" ], [ "G00025MO", "1f9d", "glycan_xref_pdb" ], [ "G00025MO", "1j84", "glycan_xref_pdb" ], [ "G00025MO", "1uu6", "glycan_xref_pdb" ], [ "G00025MO", "1w2u", "glycan_xref_pdb" ], [ "G00025MO", "2bof", "glycan_xref_pdb" ], [ "G00025MO", "2bvw", "glycan_xref_pdb" ], [ "G00025MO", "2bwc", "glycan_xref_pdb" ], [ "G00025MO", "2rg0", "glycan_xref_pdb" ], [ "G00025MO", "2z1s", "glycan_xref_pdb" ], [ "G00025MO", "3ach", "glycan_xref_pdb" ], [ "G00025MO", "3amm", "glycan_xref_pdb" ], [ "G00025MO", "3f5j", "glycan_xref_pdb" ], [ "G00025MO", "3pfz", "glycan_xref_pdb" ], [ "G00025MO", "3qhm", "glycan_xref_pdb" ], [ "G00025MO", "3qhn", "glycan_xref_pdb" ], [ "G00025MO", "3qho", "glycan_xref_pdb" ], [ "G00025MO", "3sct", "glycan_xref_pdb" ], [ "G00025MO", "3scv", "glycan_xref_pdb" ], [ "G00025MO", "3scw", "glycan_xref_pdb" ], [ "G00025MO", "4a05", "glycan_xref_pdb" ], [ "G00025MO", "4afd", "glycan_xref_pdb" ], [ "G00025MO", "4b4f", "glycan_xref_pdb" ], [ "G00025MO", "4fg2", "glycan_xref_pdb" ], [ "G00025MO", "4hu0", "glycan_xref_pdb" ], [ "G00025MO", "5cel", "glycan_xref_pdb" ], [ "G00025MO", "6cel", "glycan_xref_pdb" ], [ "G00031MO", "1jot", "glycan_xref_pdb" ], [ "G00031MO", "1lti", "glycan_xref_pdb" ], [ "G00031MO", "1m26", "glycan_xref_pdb" ], [ "G00031MO", "1ugx", "glycan_xref_pdb" ], [ "G00031MO", "1y2v", "glycan_xref_pdb" ], [ "G00031MO", "1y2w", "glycan_xref_pdb" ], [ "G00031MO", "1y2x", "glycan_xref_pdb" ], [ "G00031MO", "2dva", "glycan_xref_pdb" ], [ "G00031MO", "3afk", "glycan_xref_pdb" ], [ "G00031MO", "3aya", "glycan_xref_pdb" ], [ "G00031MO", "3nk3", "glycan_xref_pdb" ], [ "G00031MO", "3qdt", "glycan_xref_pdb" ], [ "G00031MO", "3qdx", "glycan_xref_pdb" ], [ "G00031MO", "3qdy", "glycan_xref_pdb" ], [ "G00031MO", "3qum", "glycan_xref_pdb" ], [ "G00031MO", "4akc", "glycan_xref_pdb" ], [ "G00035MO", "2w1u", "glycan_xref_pdb" ], [ "G00048MO", "1led", "glycan_xref_pdb" ], [ "G00048MO", "4gwj", "glycan_xref_pdb" ], [ "G00049MO", "2z8f", "glycan_xref_pdb" ], [ "G00050MO", "2zl6", "glycan_xref_pdb" ], [ "G00050MO", "3sln", "glycan_xref_pdb" ], [ "G00051MO", "1uz8", "glycan_xref_pdb" ], [ "G00051MO", "2ox9", "glycan_xref_pdb" ], [ "G00052MO", "1gsl", "glycan_xref_pdb" ], [ "G00052MO", "2j1t", "glycan_xref_pdb" ], [ "G00052MO", "2wmg", "glycan_xref_pdb" ], [ "G00052MO", "3leg", "glycan_xref_pdb" ], [ "G00052MO", "3pa2", "glycan_xref_pdb" ], [ "G00052MO", "4gwi", "glycan_xref_pdb" ], [ "G00054MO", "1g1r", "glycan_xref_pdb" ], [ "G00054MO", "1g1t", "glycan_xref_pdb" ], [ "G00054MO", "2kmb", "glycan_xref_pdb" ], [ "G00054MO", "2r61", "glycan_xref_pdb" ], [ "G00054MO", "2z8l", "glycan_xref_pdb" ], [ "G00055MO", "1a3k", "glycan_xref_pdb" ], [ "G00055MO", "1gx4", "glycan_xref_pdb" ], [ "G00055MO", "1kjl", "glycan_xref_pdb" ], [ "G00055MO", "1v84", "glycan_xref_pdb" ], [ "G00055MO", "1vzx", "glycan_xref_pdb" ], [ "G00055MO", "2d6n", "glycan_xref_pdb" ], [ "G00055MO", "2vs3", "glycan_xref_pdb" ], [ "G00055MO", "2vs4", "glycan_xref_pdb" ], [ "G00055MO", "2wt0", "glycan_xref_pdb" ], [ "G00055MO", "2xrs", "glycan_xref_pdb" ], [ "G00055MO", "3ehn", "glycan_xref_pdb" ], [ "G00056MO", "2ll4", "glycan_xref_pdb" ], [ "G00056MO", "2z8d", "glycan_xref_pdb" ], [ "G00056MO", "4h04", "glycan_xref_pdb" ], [ "G00057MO", "1e6x", "glycan_xref_pdb" ], [ "G00058MO", "2d6o", "glycan_xref_pdb" ] ] }, "readme": "Name\n - Glycan Xref PDB\n\nVersion\n - v-2.2.1\n\nCreated on\n - 2019-11-14T11:38:02.465398\n\nModified on\n - 2022-09-26T09:05:27.674247\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - Nathan Edwards [nje5@georgetown.edu]\n\nChecksum\n - \n\nUsability Domain\n - The dataset provides cross-references to PDB ID(s) for the associated glycan (GlyTouCan Accession). The listed GlyTouCan Accessions are derived from the GlyTouCan accession master list (https://data.glygen.org/GLYDS000281). Source database: https://glytoucan.org/;http://www.glycome-db.org/; https://www.rcsb.org/\n\nDescription Domain\n Keywords\n - Glycan\n - GlyTouCan Accession\n - PDB\n - Cross-references\n - ID/Accession Mapping\n\n Pipeline Steps\n - Step-1: The input file was downloaded from the author and a python script is used to extract the data for the GlyTouCan accessions based on the acession master list. Refer to the usability domain for more information on master list.\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-species-agnostic-dataset.py\n\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: pdb.tsv\n URI: https:/data.glygen.org/ln2downloads/glytoucan/gtc_08_17_2023/export/pdb.tsv\n Output Subdomain\n Name: glycan_xref_pdb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/glycan_xref_pdb.csv\n Name: glycan_xref_pdb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/glycan_xref_pdb.stat.csv\n\nFields\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"629\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"4753\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.2.1/reviewed/glycan_xref_pdb.csv" }