{ "bcoid": "GLY_000342", "title": "Glycans with NeuAc (Customized table)", "description": "The dataset provides glycans that have at least one \"NeuAc\" residue in the current GlyGen dataset (https://data.glygen.org/GLYDS000281). ...", "filename": "glycan_species_customized_neuac_neugc.csv", "filetype": "csv", "categories": { "molecule": [ "Glycan" ], "tag": [ "NeuAc", "Mammalian species annotation" ], "status": [ "Reviewed" ], "file_type": [ "csv" ], "scope": [ "internal" ], "species": [ "Sus scrofa", "Rattus", "Homo sapiens", "Mus musculus", "Severe acute respiratory syndrome coronavirus 2", "Rattus norvegicus", "Drosophila melanogaster", "Saccharomyces cerevisiae", "Hepacivirus C" ] }, "minitable": { "content": [ [ "G00002CF...", "9823..." ], [ "G00002CF...", "10114..." ] ], "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", "9823", "Sus scrofa", "Subsumption", "GNOme", "G84891DZ", "", "glycan_xref_gnome", "G84891DZ", "False" ], [ "G00002CF", "10114", "Rattus", "Subsumption", "GNOme", "G84891DZ", "", "glycan_xref_gnome", "G84891DZ", "False" ], [ "G00025HU", "9606", "Homo sapiens", "Subsumption", "GNOme", "G07392QY", "", "glycan_xref_gnome", "G07392QY", "False" ], [ "G00025HU", "9606", "Homo sapiens", "Subsumption", "GNOme", "G30460NZ", "", "glycan_xref_gnome", "G30460NZ", "False" ], [ "G00025HU", "10090", "Mus musculus", "Subsumption", "GNOme", "G30460NZ", "", "glycan_xref_gnome", "G30460NZ", "False" ], [ "G00025HU", "9606", "Homo sapiens", "Subsumption", "GNOme", "G30797DS", "", "glycan_xref_gnome", "G30797DS", "False" ], [ "G00025HU", "10090", "Mus musculus", "Subsumption", "GNOme", "G30797DS", "", "glycan_xref_gnome", "G30797DS", "False" ], [ "G00025HU", "9606", "Homo sapiens", "Subsumption", "GNOme", "G70382WT", "", "glycan_xref_gnome", "G70382WT", "False" ], [ "G00025HU", "9823", "Sus scrofa", "Subsumption", "GNOme", "G70382WT", "", "glycan_xref_gnome", "G70382WT", "False" ], [ "G00025HU", "9606", "Homo sapiens", "Subsumption", "GNOme", "G88068QT", "", "glycan_xref_gnome", "G88068QT", "False" ], [ "G00025HU", "9606", "Homo sapiens", "Subsumption", "GNOme", "G88242BL", "", "glycan_xref_gnome", "G88242BL", "False" ], [ "G00025HU", "10090", "Mus musculus", "Subsumption", "GNOme", "G88242BL", "", "glycan_xref_gnome", "G88242BL", "False" ], [ "G00025HU", "9823", "Sus scrofa", "Subsumption", "GNOme", "G88242BL", "", "glycan_xref_gnome", "G88242BL", "False" ], [ "G00041IL", "9606", "Homo sapiens", "Subsumption", "GNOme", "G19749DC", "", "glycan_xref_gnome", "G19749DC", "False" ], [ "G00053MO", "9606", "Homo sapiens", "Direct", "GlyCosmos", "G00053MO", "", "glycan_xref_glycosmos", "G00053MO", "True" ], [ "G00053MO", "10090", "Mus musculus", "Direct", "GlyCosmos", "G00053MO", "", "glycan_xref_glycosmos", "G00053MO", "True" ], [ "G00054MO", "9606", "Homo sapiens", "Direct", "GlyCosmos", "G00054MO", "", "glycan_xref_glycosmos", "G00054MO", "True" ], [ "G00054MO", "10090", "Mus musculus", "Direct", "GlyCosmos", "G00054MO", "", "glycan_xref_glycosmos", "G00054MO", "True" ], [ "G00054MO", "9823", "Sus scrofa", "Direct", "GlyCosmos", "G00054MO", "", "glycan_xref_glycosmos", "G00054MO", "True" ], [ "G00054MO", "10114", "Rattus", "Direct", "GlyCosmos", "G00054MO", "", "glycan_xref_glycosmos", "G00054MO", "True" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G01670UQ", "", "glycan_xref_gnome", "G01670UQ", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G04909DG", "", "glycan_xref_gnome", "G04909DG", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G07995VK", "", "glycan_xref_gnome", "G07995VK", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G08646YJ", "", "glycan_xref_gnome", "G08646YJ", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G09811YI", "", "glycan_xref_gnome", "G09811YI", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G26164VG", "", "glycan_xref_gnome", "G26164VG", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G36598FV", "", "glycan_xref_gnome", "G36598FV", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G37591JC", "", "glycan_xref_gnome", "G37591JC", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G37868ZX", "", "glycan_xref_gnome", "G37868ZX", "False" ], [ "G00057LF", "2697049", "Severe acute respiratory syndrome coronavirus 2", "Subsumption", "GNOme", "G37868ZX", "", "glycan_xref_gnome", "G37868ZX", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G42846BO", "", "glycan_xref_gnome", "G42846BO", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G44826KU", "", "glycan_xref_gnome", "G44826KU", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G45560HM", "", "glycan_xref_gnome", "G45560HM", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G46754UW", "", "glycan_xref_gnome", "G46754UW", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G50739NP", "", "glycan_xref_gnome", "G50739NP", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G57413FT", "", "glycan_xref_gnome", "G57413FT", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G58236FD", "", "glycan_xref_gnome", "G58236FD", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G62785VB", "", "glycan_xref_gnome", "G62785VB", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G65835SY", "", "glycan_xref_gnome", "G65835SY", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G66377OH", "", "glycan_xref_gnome", "G66377OH", "False" ], [ "G00057LF", "10090", "Mus musculus", "Subsumption", "GNOme", "G66377OH", "", "glycan_xref_gnome", "G66377OH", "False" ], [ "G00057LF", "10116", "Rattus norvegicus", "Subsumption", "GNOme", "G66377OH", "", "glycan_xref_gnome", "G66377OH", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G68318SH", "", "glycan_xref_gnome", "G68318SH", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G71269BI", "", "glycan_xref_gnome", "G71269BI", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G72368JX", "", "glycan_xref_gnome", "G72368JX", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G73455AR", "", "glycan_xref_gnome", "G73455AR", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G75850OP", "", "glycan_xref_gnome", "G75850OP", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G76675AB", "", "glycan_xref_gnome", "G76675AB", "False" ], [ "G00057LF", "10116", "Rattus norvegicus", "Subsumption", "GNOme", "G76675AB", "", "glycan_xref_gnome", "G76675AB", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G77177HT", "", "glycan_xref_gnome", "G77177HT", "False" ], [ "G00057LF", "10090", "Mus musculus", "Subsumption", "GNOme", "G77177HT", "", "glycan_xref_gnome", "G77177HT", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G81282CC", "", "glycan_xref_gnome", "G81282CC", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G84553QQ", "", "glycan_xref_gnome", "G84553QQ", "False" ], [ "G00057LF", "10090", "Mus musculus", "Subsumption", "GNOme", "G84553QQ", "", "glycan_xref_gnome", "G84553QQ", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G87433AX", "", "glycan_xref_gnome", "G87433AX", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G91365ZQ", "", "glycan_xref_gnome", "G91365ZQ", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G93284HQ", "", "glycan_xref_gnome", "G93284HQ", "False" ], [ "G00057LF", "10090", "Mus musculus", "Subsumption", "GNOme", "G93284HQ", "", "glycan_xref_gnome", "G93284HQ", "False" ], [ "G00057LF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G94239KE", "", "glycan_xref_gnome", "G94239KE", "False" ], [ "G00057LF", "10090", "Mus musculus", "Subsumption", "GNOme", "G13257IK", "", "glycan_xref_gnome", "G13257IK", "False" ], [ "G00057LF", "10090", "Mus musculus", "Subsumption", "GNOme", "G19914RN", "", "glycan_xref_gnome", "G19914RN", "False" ], [ "G00057LF", "10090", "Mus musculus", "Subsumption", "GNOme", "G58370UT", "", "glycan_xref_gnome", "G58370UT", "False" ], [ "G00057LF", "10116", "Rattus norvegicus", "Subsumption", "GNOme", "G21823MR", "", "glycan_xref_gnome", "G21823MR", "False" ], [ "G00057LF", "10116", "Rattus norvegicus", "Subsumption", "GNOme", "G71309WZ", "", "glycan_xref_gnome", "G71309WZ", "False" ], [ "G00063MO", "9606", "Homo sapiens", "Direct", "GlyCosmos", "G00063MO", "", "glycan_xref_glycosmos", "G00063MO", "False" ], [ "G00065MO", "9606", "Homo sapiens", "Direct", "GlyConnectStructure", "2804", "", "glycan_xref_glyconnectstructure", "2804", "False" ], [ "G00065MO", "9606", "Homo sapiens", "Direct", "GlyCosmos", "G00065MO", "", "glycan_xref_glycosmos", "G00065MO", "False" ], [ "G00073MO", "10090", "Mus musculus", "Subsumption", "GNOme", "G07508HQ", "", "glycan_xref_gnome", "G07508HQ", "False" ], [ "G00087BY", "9606", "Homo sapiens", "Subsumption", "GNOme", "G24812WY", "", "glycan_xref_gnome", "G24812WY", "False" ], [ "G00087BY", "9606", "Homo sapiens", "Subsumption", "GNOme", "G25423CA", "", "glycan_xref_gnome", "G25423CA", "False" ], [ "G00087BY", "9606", "Homo sapiens", "Subsumption", "GNOme", "G27983PC", "", "glycan_xref_gnome", "G27983PC", "False" ], [ "G00087BY", "9606", "Homo sapiens", "Subsumption", "GNOme", "G32659RY", "", "glycan_xref_gnome", "G32659RY", "False" ], [ "G00087BY", "9606", "Homo sapiens", "Subsumption", "GNOme", "G38217AM", "", "glycan_xref_gnome", "G38217AM", "False" ], [ "G00087BY", "9606", "Homo sapiens", "Subsumption", "GNOme", "G72406BE", "", "glycan_xref_gnome", "G72406BE", "False" ], [ "G00087BY", "9606", "Homo sapiens", "Subsumption", "GNOme", "G96932XT", "", "glycan_xref_gnome", "G96932XT", "False" ], [ "G00089VH", "9606", "Homo sapiens", "Direct", "GlyCosmos", "G00089VH", "", "glycan_xref_glycosmos", "G00089VH", "False" ], [ "G00091UN", "9606", "Homo sapiens", "Subsumption", "GNOme", "G48954CA", "", "glycan_xref_gnome", "G48954CA", "False" ], [ "G00091UN", "9606", "Homo sapiens", "Subsumption", "GNOme", "G84852GW", "", "glycan_xref_gnome", "G84852GW", "False" ], [ "G00105XF", "9606", "Homo sapiens", "Subsumption", "GNOme", "G85136IQ", "", "glycan_xref_gnome", "G85136IQ", "False" ], [ "G00106LE", "9606", "Homo sapiens", "Subsumption", "GNOme", "G08961VV", "", "glycan_xref_gnome", "G08961VV", "False" ], [ "G00106LE", "10090", "Mus musculus", "Subsumption", "GNOme", "G00672PE", "", "glycan_xref_gnome", "G00672PE", "False" ], [ "G00109SL", "9606", "Homo sapiens", "Subsumption", "GNOme", "G25416CE", "", "glycan_xref_gnome", "G25416CE", "False" ], [ "G00113FP", "9606", "Homo sapiens", "Subsumption", "GNOme", "G95260HV", "", "glycan_xref_gnome", "G95260HV", "False" ], [ "G00116QX", "9606", "Homo sapiens", "Subsumption", "GNOme", "G07689ET", "", "glycan_xref_gnome", "G07689ET", "False" ] ] }, "readme": "Name\n - Glycans with NeuAc (Customized table)\n\nVersion\n - v-2.3.1\n\nCreated on\n - 2020-03-02T14:23:10.848312\n\nModified on\n - 2022-09-26T09:05:27.762294\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 glycans that have at least one \"NeuAc\" residue in the current GlyGen dataset (https://data.glygen.org/GLYDS000281). The GlyTouCan accessions included in this list have mammalian species annotation (human/mouse/rat) through direct TaxID annotation and/or inferred via subsumption. This table was customized based on a GlyGen user query submitted through GlyGen help on Feb 17th 2020.\n\nDescription Domain\n Keywords\n - Glycan\n - GlyTouCan Accession\n - NeuAc\n - Mammalian species annotation \n\n Pipeline Steps\n - Step-1: Based on the submitted user query (different sialic acid-containing mammalian glycan structures reported in your database), the list of glycans that have \"NeuAc\" were from input file 1 (monocomp.tsv;column:5 ;filter:not \"0\"). The selected GlyTouCan accessions were mapped to input file 2 (glycan_species.tsv) where the value is \"true\". \n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/A\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_monosaccharide_composition.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/glycan_monosaccharide_composition.csv\n Name: glycan_species.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/glycan_species.csv\n Output Subdomain\n Name: glycan_species_customized_neuac_neugc.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/glycan_species_customized_neuac_neugc.csv\n Name: glycan_species_customized_neuac_neugc.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/glycan_species_customized_neuac_neugc.stat.csv\n\nFields\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"9662\"\n Name: \"tax_id\"\n Description: \"NCBI Taxonomy database Identifier\"\n Unique Values: \"9\"\n Name: \"tax_name\"\n Description: \"NCBI Taxonomy name\"\n Unique Values: \"9\"\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\"\n Description: \"Source for the data\"\n Unique Values: \"6\"\n Name: \"source_id\"\n Description: \"source database id of the species annoation for the glycan.\"\n Unique Values: \"4532\"\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: \"129\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"6\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"4030\"\n Name: \"is_motif\"\n Description: \"\"\n Unique Values: \"2\"", "downloadurl": "/ln2data/releases/data/v-2.3.1/reviewed/glycan_species_customized_neuac_neugc.csv" }