{ "bcoid": "GLY_000341", "title": "Glycan Species ", "description": "The dataset provides species annotation for the associated glycan (GlyTouCan Accession) generated from ...", "filename": "glycan_species.csv", "filetype": "csv", "categories": { "molecule": "Glycan", "tags": "NCBI TaxID", "status": "Reviewed", "file_type": "csv", "scope": "internal" }, "minitable": { "content": [ [ "G00002CF...", "10114..." ], [ "G00002CF...", "9606..." ] ], "headers": [ "glytoucan_ac...", "tax_id..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "glytoucan_ac" }, { "type": "string", "label": "tax_id" }, { "type": "string", "label": "tax_name" }, { "type": "string", "label": "annotation_category" }, { "type": "string", "label": "source" }, { "type": "string", "label": "source_id" }, { "type": "string", "label": "original_source_id" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "is_motif" } ], [ "G00002CF", "10114", "Rattus", "Subsumption", "GNOme", "G84891DZ", "", "glycan_xref_gnome", "G84891DZ", "False" ], [ "G00002CF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G84891DZ", "", "glycan_xref_gnome", "G84891DZ", "False" ], [ "G00012MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G57710SU", "", "glycan_xref_gnome", "G57710SU", "False" ], [ "G00012MO", "10090", "Mus musculus", "Subsumption", "GNOme", "G57710SU", "", "glycan_xref_gnome", "G57710SU", "False" ], [ "G00012MO", "10114", "Rattus", "Subsumption", "GNOme", "G57710SU", "", "glycan_xref_gnome", "G57710SU", "False" ], [ "G00016MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G62763GO", "", "glycan_xref_gnome", "G62763GO", "False" ], [ "G00016MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G67988RO", "", "glycan_xref_gnome", "G67988RO", "False" ], [ "G00016MO", "10090", "Mus musculus", "Subsumption", "GNOme", "G67988RO", "", "glycan_xref_gnome", "G67988RO", "False" ], [ "G00017MO", "9606", "Homo sapiens", "Direct", "GlyTouCan", "G00017MO", "", "glycan_xref_glytoucan", "G00017MO", "False" ], [ "G00018MO", "10114", "Rattus", "Direct", "GlyTouCan", "G00018MO", "", "glycan_xref_glytoucan", "G00018MO", "False" ], [ "G00025AJ", "9606", "Homo sapiens", "Direct", "GlyTouCan", "G00025AJ", "", "glycan_xref_glytoucan", "G00025AJ", "False" ], [ "G00025YC", "9606", "Homo sapiens", "Subsumption", "GNOme", "G13583BZ", "", "glycan_xref_gnome", "G13583BZ", "False" ], [ "G00026MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G20624LQ", "", "glycan_xref_gnome", "G20624LQ", "False" ], [ "G00026MO", "10090", "Mus musculus", "Subsumption", "GNOme", "G20624LQ", "", "glycan_xref_gnome", "G20624LQ", "False" ], [ "G00026MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G22768VO", "", "glycan_xref_gnome", "G22768VO", "False" ], [ "G00026MO", "10090", "Mus musculus", "Subsumption", "GNOme", "G22768VO", "", "glycan_xref_gnome", "G22768VO", "False" ], [ "G00026MO", "10116", "Rattus norvegicus", "Subsumption", "GNOme", "G22768VO", "", "glycan_xref_gnome", "G22768VO", "False" ], [ "G00027MO", "10090", "Mus musculus", "Direct", "GlyConnect", "1555", "", "glycan_xref_glytoucan", "G00027MO", "False" ], [ "G00027MO", "10114", "Rattus", "Direct", "GlyTouCan", "G00027MO", "", "glycan_xref_glytoucan", "G00027MO", "False" ], [ "G00027MO", "10116", "Rattus norvegicus", "Direct", "GlyTouCan", "G00027MO", "", "glycan_xref_glytoucan", "G00027MO", "False" ], [ "G00028MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G03652TR", "", "glycan_xref_gnome", "G03652TR", "False" ], [ "G00028MO", "10090", "Mus musculus", "Subsumption", "GNOme", "G03652TR", "", "glycan_xref_gnome", "G03652TR", "False" ], [ "G00028MO", "10114", "Rattus", "Subsumption", "GNOme", "G03652TR", "", "glycan_xref_gnome", "G03652TR", "False" ], [ "G00028MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G55220VL", "", "glycan_xref_gnome", "G55220VL", "False" ], [ "G00028MO", "10090", "Mus musculus", "Subsumption", "GNOme", "G55220VL", "", "glycan_xref_gnome", "G55220VL", "False" ], [ "G00028MO", "10116", "Rattus norvegicus", "Subsumption", "GNOme", "G55220VL", "", "glycan_xref_gnome", "G55220VL", "False" ], [ "G00029MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G04445KN", "", "glycan_xref_gnome", "G04445KN", "False" ], [ "G00029MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G53168IY", "", "glycan_xref_gnome", "G53168IY", "False" ], [ "G00029MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G75896PD", "", "glycan_xref_gnome", "G75896PD", "False" ], [ "G00029MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G87320GN", "", "glycan_xref_gnome", "G87320GN", "False" ], [ "G00030MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G39213VZ", "", "glycan_xref_gnome", "G39213VZ", "False" ], [ "G00030MO", "10090", "Mus musculus", "Subsumption", "GNOme", "G39213VZ", "", "glycan_xref_gnome", "G39213VZ", "False" ], [ "G00030MO", "10116", "Rattus norvegicus", "Subsumption", "GNOme", "G39213VZ", "", "glycan_xref_gnome", "G39213VZ", "False" ], [ "G00030MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G42679AH", "", "glycan_xref_gnome", "G42679AH", "False" ], [ "G00030MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G56175ED", "", "glycan_xref_gnome", "G56175ED", "False" ], [ "G00030MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G84678BK", "", "glycan_xref_gnome", "G84678BK", "False" ], [ "G00030MO", "10090", "Mus musculus", "Subsumption", "GNOme", "G84678BK", "", "glycan_xref_gnome", "G84678BK", "False" ], [ "G00030MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G88876JQ", "", "glycan_xref_gnome", "G88876JQ", "False" ], [ "G00030MO", "10090", "Mus musculus", "Subsumption", "GNOme", "G88876JQ", "", "glycan_xref_gnome", "G88876JQ", "False" ], [ "G00030MO", "10116", "Rattus norvegicus", "Subsumption", "GNOme", "G88876JQ", "", "glycan_xref_gnome", "G88876JQ", "False" ], [ "G00031MO", "9606", "Homo sapiens", "Direct", "GlyConnect", "1947", "", "glycan_xref_glytoucan", "G00031MO", "True" ], [ "G00031MO", "9606", "Homo sapiens", "Direct", "GlyTouCan", "G00031MO", "", "glycan_xref_glytoucan", "G00031MO", "True" ], [ "G00031MO", "9606", "Homo sapiens", "Direct", "UniCarbKB", "4", "", "glycan_xref_glytoucan", "G00031MO", "True" ], [ "G00031MO", "10090", "Mus musculus", "Direct", "GlyConnect", "1947", "", "glycan_xref_glytoucan", "G00031MO", "True" ], [ "G00031MO", "10090", "Mus musculus", "Direct", "GlyTouCan", "G00031MO", "", "glycan_xref_glytoucan", "G00031MO", "True" ], [ "G00031MO", "10090", "Mus musculus", "Direct", "UniCarbKB", "4", "", "glycan_xref_glytoucan", "G00031MO", "True" ], [ "G00031MO", "10116", "Rattus norvegicus", "Direct", "GlyConnect", "1947", "", "glycan_xref_glytoucan", "G00031MO", "True" ], [ "G00031MO", "10114", "Rattus", "Direct", "GlyTouCan", "G00031MO", "", "glycan_xref_glytoucan", "G00031MO", "True" ], [ "G00031MO", "10116", "Rattus norvegicus", "Direct", "GlyTouCan", "G00031MO", "", "glycan_xref_glytoucan", "G00031MO", "True" ], [ "G00031MO", "10116", "Rattus norvegicus", "Direct", "UniCarbKB", "4", "", "glycan_xref_glytoucan", "G00031MO", "True" ], [ "G00032MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G00031MO", "", "glycan_xref_gnome", "G00031MO", "False" ], [ "G00032MO", "10090", "Mus musculus", "Subsumption", "GNOme", "G00031MO", "", "glycan_xref_gnome", "G00031MO", "False" ], [ "G00032MO", "10116", "Rattus norvegicus", "Subsumption", "GNOme", "G00031MO", "", "glycan_xref_gnome", "G00031MO", "False" ], [ "G00032MO", "10114", "Rattus", "Subsumption", "GNOme", "G00031MO", "", "glycan_xref_gnome", "G00031MO", "False" ], [ "G00032MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G01534TU", "", "glycan_xref_gnome", "G01534TU", "False" ], [ "G00032MO", "10090", "Mus musculus", "Subsumption", "GNOme", "G78436BB", "", "glycan_xref_gnome", "G78436BB", "False" ], [ "G00032MO", "10114", "Rattus", "Subsumption", "GNOme", "G78436BB", "", "glycan_xref_gnome", "G78436BB", "False" ], [ "G00033MO", "9606", "Homo sapiens", "Direct", "GlyConnect", "3318", "", "glycan_xref_glytoucan", "G00033MO", "False" ], [ "G00033MO", "9606", "Homo sapiens", "Direct", "GlyTouCan", "G00033MO", "", "glycan_xref_glytoucan", "G00033MO", "False" ], [ "G00033MO", "10090", "Mus musculus", "Direct", "GlyConnect", "3318", "", "glycan_xref_glytoucan", "G00033MO", "False" ], [ "G00033MO", "10116", "Rattus norvegicus", "Direct", "GlyConnect", "3318", "", "glycan_xref_glytoucan", "G00033MO", "False" ], [ "G00034MO", "9606", "Homo sapiens", "Direct", "GlyTouCan", "G00034MO", "", "glycan_xref_glytoucan", "G00034MO", "False" ], [ "G00034MO", "10090", "Mus musculus", "Subsumption", "GNOme", "G00033MO", "", "glycan_xref_gnome", "G00033MO", "False" ], [ "G00034MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G00033MO", "", "glycan_xref_gnome", "G00033MO", "False" ], [ "G00034MO", "10116", "Rattus norvegicus", "Subsumption", "GNOme", "G00033MO", "", "glycan_xref_gnome", "G00033MO", "False" ], [ "G00034MO", "10114", "Rattus", "Direct", "GlyTouCan", "G00034MO", "", "glycan_xref_glytoucan", "G00034MO", "False" ], [ "G00035MO", "9606", "Homo sapiens", "Direct", "GlyConnect", "2294", "", "glycan_xref_glytoucan", "G00035MO", "False" ], [ "G00035MO", "9606", "Homo sapiens", "Direct", "GlyTouCan", "G00035MO", "", "glycan_xref_glytoucan", "G00035MO", "False" ], [ "G00035MO", "10116", "Rattus norvegicus", "Direct", "GlyConnect", "2294", "", "glycan_xref_glytoucan", "G00035MO", "False" ], [ "G00036MO", "9606", "Homo sapiens", "Direct", "GlyTouCan", "G00036MO", "", "glycan_xref_glytoucan", "G00036MO", "False" ], [ "G00036MO", "10116", "Rattus norvegicus", "Subsumption", "GNOme", "G00035MO", "", "glycan_xref_gnome", "G00035MO", "False" ], [ "G00036MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G00035MO", "", "glycan_xref_gnome", "G00035MO", "False" ], [ "G00036MO", "10116", "Rattus norvegicus", "Subsumption", "GNOme", "G85714GY", "", "glycan_xref_gnome", "G85714GY", "False" ], [ "G00036MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G85714GY", "", "glycan_xref_gnome", "G85714GY", "False" ], [ "G00037MO", "9606", "Homo sapiens", "Direct", "GlyTouCan", "G00037MO", "", "glycan_xref_glytoucan", "G00037MO", "False" ], [ "G00038MO", "9606", "Homo sapiens", "Direct", "GlyTouCan", "G00038MO", "", "glycan_xref_glytoucan", "G00038MO", "False" ], [ "G00038MO", "10116", "Rattus norvegicus", "Subsumption", "GNOme", "G18892PE", "", "glycan_xref_gnome", "G18892PE", "False" ], [ "G00038MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G18892PE", "", "glycan_xref_gnome", "G18892PE", "False" ], [ "G00039MO", "9606", "Homo sapiens", "Direct", "GlyConnect", "500", "", "glycan_xref_glytoucan", "G00039MO", "False" ], [ "G00039MO", "9606", "Homo sapiens", "Direct", "GlyTouCan", "G00039MO", "", "glycan_xref_glytoucan", "G00039MO", "False" ], [ "G00040MO", "9606", "Homo sapiens", "Direct", "GlyTouCan", "G00040MO", "", "glycan_xref_glytoucan", "G00040MO", "False" ], [ "G00040MO", "10090", "Mus musculus", "Subsumption", "GNOme", "G45388GV", "", "glycan_xref_gnome", "G45388GV", "False" ], [ "G00040MO", "9606", "Homo sapiens", "Subsumption", "GNOme", "G45388GV", "", "glycan_xref_gnome", "G45388GV", "False" ], [ "G00040MO", "10114", "Rattus", "Subsumption", "GNOme", "G97834OQ", "", "glycan_xref_gnome", "G97834OQ", "False" ] ] }, "readme": "Name\n - Glycan Species \n\nVersion\n - 1.7.13\n\nCreated on\n - 2020-03-02T13:55:30.488616\n\nModified on\n - 2020-06-25T13:32:13.597601\n\nCreated by\n - Rahi Navelkar [rsn13@gwu.edu], Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu]\n\nAuthors\n - Nathan Edwards [nje5@georgetown.edu]\n\nChecksum\n - \n\nUsability Domain\n - The dataset provides species annotation for the associated glycan (GlyTouCan Accession) generated from direct TaxID annotation and/or inferred via subsumption. The listed GlyTouCan Accessions are derived from the GlyTouCan accession master list (https://data.glygen.org/GLYDS000281). Source database: https://glytoucan.org/; https://www.ncbi.nlm.nih.gov/taxonomy.\n\nDescription Domain\n Keywords\n - Glycan\n - GlyTouCan Accession\n - NCBI TaxID\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/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/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: species.tsv\n URI: https://data.glygen.org/ln2wwwdata/source/species.tsv\n Output Subdomain\n Name: glycan_species.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/glycan_species.csv\n Name: glycan_species.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/glycan_species.stat.csv\n\nFields\n Name: \"original_source_id\"\n Description: \"Original source id of the species annoation for the glycan. This columns contains values where the source id is not a valid database id. \"\n Unique Values: \"223\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"6336\"\n Name: \"source\"\n Description: \"Source for the data\"\n Unique Values: \"6\"\n Name: \"tax_name\"\n Description: \"NCBI Taxonomy name\"\n Unique Values: \"7\"\n Name: \"is_motif\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"annotation_category\"\n Description: \"Species annotation category of the glycan. Category could be either direct or subsumption\"\n Unique Values: \"2\"\n Name: \"source_id\"\n Description: \"source database id of the species annoation for the glycan.\"\n Unique Values: \"8630\"\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"17333\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"tax_id\"\n Description: \"NCBI Taxonomy database Identifier\"\n Unique Values: \"7\"", "downloadurl": "/ln2data/releases/data/v-1.7.13/reviewed/glycan_species.csv" }