{ "bcoid": "GLY_000342", "title": "Glycans with NeuAc (Customized table)", "description": "The dataset provides glycans that have atleast 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", "tags": "Mammalian species annotation", "status": "Reviewed", "file_type": "csv", "scope": "internal" }, "minitable": { "content": [ [ "G79026TT...", "10090..." ], [ "G79026TT...", "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" } ], [ "G79026TT", "10090", "Mus musculus", "Subsumption", "Subsumption", "via G45209NR", "", "glycan_xref_subsumption", "G45209NR" ], [ "G79026TT", "9606", "Homo sapiens", "Direct", "GlyConnect", "3255", "", "glycan_xref_glyconnect", "3255" ], [ "G96934US", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G08465VN", "", "glycan_xref_subsumption", "G08465VN" ], [ "G96934US", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G09859LE", "", "glycan_xref_subsumption", "G09859LE" ], [ "G09173AD", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G60542VK", "", "glycan_xref_subsumption", "G60542VK" ], [ "G07051YW", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G13282WA", "", "glycan_xref_subsumption", "G13282WA" ], [ "G59345UT", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G16150CJ", "", "glycan_xref_subsumption", "G16150CJ" ], [ "G24634JN", "10090", "Mus musculus", "Subsumption", "Subsumption", "via G40012WS", "", "glycan_xref_subsumption", "G40012WS" ], [ "G24634JN", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G03984TW", "", "glycan_xref_subsumption", "G03984TW" ], [ "G24634JN", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G30939HN", "", "glycan_xref_subsumption", "G30939HN" ], [ "G24634JN", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G38349VC", "", "glycan_xref_subsumption", "G38349VC" ], [ "G24634JN", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G54956ME", "", "glycan_xref_subsumption", "G54956ME" ], [ "G24634JN", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G59821FL", "", "glycan_xref_subsumption", "G59821FL" ], [ "G39632CM", "10090", "Mus musculus", "Subsumption", "Subsumption", "via G23347CS", "", "glycan_xref_subsumption", "G23347CS" ], [ "G39632CM", "10090", "Mus musculus", "Subsumption", "Subsumption", "via G70647TI", "", "glycan_xref_subsumption", "G70647TI" ], [ "G39632CM", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G04676YO", "", "glycan_xref_subsumption", "G04676YO" ], [ "G39632CM", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G23347CS", "", "glycan_xref_subsumption", "G23347CS" ], [ "G39632CM", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G34797BZ", "", "glycan_xref_subsumption", "G34797BZ" ], [ "G39632CM", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G35879BG", "", "glycan_xref_subsumption", "G35879BG" ], [ "G39632CM", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G38710SX", "", "glycan_xref_subsumption", "G38710SX" ], [ "G39632CM", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G70647TI", "", "glycan_xref_subsumption", "G70647TI" ], [ "G39632CM", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G96709CX", "", "glycan_xref_subsumption", "G96709CX" ], [ "G24823MG", "10090", "Mus musculus", "Subsumption", "Subsumption", "via G89877QI", "", "glycan_xref_subsumption", "G89877QI" ], [ "G24823MG", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G89877QI", "", "glycan_xref_subsumption", "G89877QI" ], [ "G18574CV", "10090", "Mus musculus", "Subsumption", "Subsumption", "via G01614ZM", "", "glycan_xref_subsumption", "G01614ZM" ], [ "G18574CV", "10090", "Mus musculus", "Subsumption", "Subsumption", "via G86130AV", "", "glycan_xref_subsumption", "G86130AV" ], [ "G18574CV", "9606", "Homo sapiens", "Direct", "GlyConnect", "1513", "", "glycan_xref_glyconnect", "1513" ], [ "G17593CN", "10090", "Mus musculus", "Subsumption", "Subsumption", "via G60230OQ", "", "glycan_xref_subsumption", "G60230OQ" ], [ "G17593CN", "10090", "Mus musculus", "Subsumption", "Subsumption", "via G97489LK", "", "glycan_xref_subsumption", "G97489LK" ], [ "G99580PT", "10090", "Mus musculus", "Direct", "GlyTouCan", "G99580PT", "", "glycan_xref_glytoucan", "G99580PT" ], [ "G99580PT", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G01767JJ", "", "glycan_xref_subsumption", "G01767JJ" ], [ "G99580PT", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G83513YI", "", "glycan_xref_subsumption", "G83513YI" ], [ "G72011DH", "10090", "Mus musculus", "Subsumption", "Subsumption", "via G42295MA", "", "glycan_xref_subsumption", "G42295MA" ], [ "G72011DH", "10090", "Mus musculus", "Subsumption", "Subsumption", "via G58063ME", "", "glycan_xref_subsumption", "G58063ME" ], [ "G72011DH", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G29884LW", "", "glycan_xref_subsumption", "G29884LW" ], [ "G72011DH", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G33947BV", "", "glycan_xref_subsumption", "G33947BV" ], [ "G72011DH", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G42295MA", "", "glycan_xref_subsumption", "G42295MA" ], [ "G72011DH", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G72905QH", "", "glycan_xref_subsumption", "G72905QH" ], [ "G72011DH", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G91023GB", "", "glycan_xref_subsumption", "G91023GB" ], [ "G84852GW", "9606", "Homo sapiens", "Direct", "GlyTouCan", "G84852GW", "", "glycan_xref_glytoucan", "G84852GW" ], [ "G84852GW", "9606", "Homo sapiens", "Direct", "UniCarbKB", "7737", "", "glycan_xref_unicarbkb", "7737" ], [ "G50911BZ", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G65449BO", "", "glycan_xref_subsumption", "G65449BO" ], [ "G50911BZ", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G69170UT", "", "glycan_xref_subsumption", "G69170UT" ], [ "G80207ET", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G55922CA", "", "glycan_xref_subsumption", "G55922CA" ], [ "G80207ET", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G93899AU", "", "glycan_xref_subsumption", "G93899AU" ], [ "G75660JH", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G13282WA", "", "glycan_xref_subsumption", "G13282WA" ], [ "G20100CF", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G56516KW", "", "glycan_xref_subsumption", "G56516KW" ], [ "G20100CF", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G68892PJ", "", "glycan_xref_subsumption", "G68892PJ" ], [ "G79852UE", "9606", "Homo sapiens", "Direct", "GlyTouCan", "G79852UE", "", "glycan_xref_glytoucan", "G79852UE" ], [ "G27004VA", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G33608TH", "", "glycan_xref_subsumption", "G33608TH" ], [ "G27004VA", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G48527XN", "", "glycan_xref_subsumption", "G48527XN" ], [ "G00927ER", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G69794GX", "", "glycan_xref_subsumption", "G69794GX" ], [ "G63078AB", "9606", "Homo sapiens", "Direct", "GlyTouCan", "G63078AB", "", "glycan_xref_glytoucan", "G63078AB" ], [ "G83257QY", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G44339YF", "", "glycan_xref_subsumption", "G44339YF" ], [ "G09442VX", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G80068SW", "", "glycan_xref_subsumption", "G80068SW" ], [ "G93692RJ", "9606", "Homo sapiens", "Direct", "GlyConnect", "312", "", "glycan_xref_glyconnect", "312" ], [ "G90974OV", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G03542TR", "", "glycan_xref_subsumption", "G03542TR" ], [ "G90974OV", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G55126WZ", "", "glycan_xref_subsumption", "G55126WZ" ], [ "G43159UR", "10090", "Mus musculus", "Subsumption", "Subsumption", "via G46774NB", "", "glycan_xref_subsumption", "G46774NB" ], [ "G00800WJ", "9606", "Homo sapiens", "Direct", "GlyConnect", "2590", "", "glycan_xref_glyconnect", "2590" ], [ "G00800WJ", "9606", "Homo sapiens", "Direct", "UniCarbKB", "7151", "", "glycan_xref_unicarbkb", "7151" ], [ "G13024PC", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G55184IL", "", "glycan_xref_subsumption", "G55184IL" ], [ "G13024PC", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G85721WE", "", "glycan_xref_subsumption", "G85721WE" ], [ "G13024PC", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G90221FQ", "", "glycan_xref_subsumption", "G90221FQ" ], [ "G05951JM", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G98961TI", "", "glycan_xref_subsumption", "G98961TI" ], [ "G70507DZ", "9606", "Homo sapiens", "Direct", "GlyTouCan", "G70507DZ", "", "glycan_xref_glytoucan", "G70507DZ" ], [ "G15355KC", "9606", "Homo sapiens", "Direct", "GlyTouCan", "G15355KC", "", "glycan_xref_glytoucan", "G15355KC" ], [ "G23611BU", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G24539CG", "", "glycan_xref_subsumption", "G24539CG" ], [ "G79761XY", "10090", "Mus musculus", "Subsumption", "Subsumption", "via G23616ZX", "", "glycan_xref_subsumption", "G23616ZX" ], [ "G79761XY", "10090", "Mus musculus", "Subsumption", "Subsumption", "via G28330DZ", "", "glycan_xref_subsumption", "G28330DZ" ], [ "G79761XY", "10090", "Mus musculus", "Subsumption", "Subsumption", "via G89877QI", "", "glycan_xref_subsumption", "G89877QI" ], [ "G79761XY", "10090", "Mus musculus", "Subsumption", "Subsumption", "via G93638BI", "", "glycan_xref_subsumption", "G93638BI" ], [ "G79761XY", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G02760XH", "", "glycan_xref_subsumption", "G02760XH" ], [ "G79761XY", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G04273XP", "", "glycan_xref_subsumption", "G04273XP" ], [ "G79761XY", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G05098FE", "", "glycan_xref_subsumption", "G05098FE" ], [ "G79761XY", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G11479AN", "", "glycan_xref_subsumption", "G11479AN" ], [ "G79761XY", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G13291XJ", "", "glycan_xref_subsumption", "G13291XJ" ], [ "G79761XY", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G14438ZT", "", "glycan_xref_subsumption", "G14438ZT" ], [ "G79761XY", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G17168RO", "", "glycan_xref_subsumption", "G17168RO" ], [ "G79761XY", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G17441MI", "", "glycan_xref_subsumption", "G17441MI" ], [ "G79761XY", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G19537TS", "", "glycan_xref_subsumption", "G19537TS" ], [ "G79761XY", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G23296IL", "", "glycan_xref_subsumption", "G23296IL" ], [ "G79761XY", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G23616ZX", "", "glycan_xref_subsumption", "G23616ZX" ], [ "G79761XY", "9606", "Homo sapiens", "Subsumption", "Subsumption", "via G28330DZ", "", "glycan_xref_subsumption", "G28330DZ" ] ] }, "readme": "Name\n - Glycans with NeuAc (Customized table)\n\nVersion\n - 1.7.13\n\nCreated on\n - 2020-03-02T14:23:10.848312\n\nModified on\n - 2020-05-01T15:18:30.118777\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 glycans that have atleast 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 - N/A\n\n\n Software Prerequisites\n Name: LINUX\n Version: -\n URI: \n\nI/O Domain\n Input Subdomain\n Name: monocomp.tsv\n URI: https://data.glygen.org/ln2wwwdata/source/monocomp.tsv\n Output Subdomain\n Name: glycan_species_customized_neuac_neugc.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/glycan_species_customized_neuac_neugc.csv\n Name: glycan_species_customized_neuac_neugc.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/glycan_species_customized_neuac_neugc.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: \"108\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"3643\"\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: \"6\"\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: \"5087\"\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"6603\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"7\"\n Name: \"tax_id\"\n Description: \"NCBI Taxonomy database Identifier\"\n Unique Values: \"6\"", "downloadurl": "/ln2data/releases/data/v-1.7.13/reviewed/glycan_species_customized_neuac_neugc.csv" }