{ "bcoid": "GLY_000060", "title": "Human Glycome Accessions", "description": "List of Glycans identified by GlyTouCan Accessions mapped to different databases.", "filename": "human_glycan_idmapping.csv", "filetype": "csv", "categories": { "status": "Reviewed" }, "minitable": { "content": [ [ "G95617FJ...", "7752..." ], [ "G95617FJ...", "7752..." ] ], "headers": [ "glytoucan_ac...", "glycomedb_id..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "glytoucan_ac" }, { "type": "string", "label": "glycomedb_id" }, { "type": "string", "label": "glyco_id" }, { "type": "string", "label": "pubchem_id" }, { "type": "string", "label": "taxid" }, { "type": "string", "label": "unicarbkb_id" }, { "type": "string", "label": "uniprotkb_id" }, { "type": "string", "label": "unicarbdb_id" }, { "type": "string", "label": "pdb_id" } ], [ "G95617FJ", "7752", "GOG186", "CID91849043", "9606", "", "", "", "" ], [ "G95617FJ", "7752", "GOG186", 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"10564", "", "", "9606", "", "", "", "" ], [ "G29081NM", "10564", "", "", "10029", "", "", "", "" ], [ "G97083VO", "24504", "", "CID71298105", "9606", "", "", "", "" ], [ "G97083VO", "24504", "", "SID252294114", "9606", "", "", "", "" ], [ "G09173AD", "40440", "", "", "", "", "P14210", "", "" ], [ "G23647WB", "8807", "", "CID91856602", "9606", "", "", "", "" ], [ "G23647WB", "8807", "", "SID252289655", "9606", "", "", "", "" ], [ "G19490AF", "968", "", "", "9606", "", "", "", "" ], [ "G19490AF", "968", "", "", "10141", "", "", "", "" ], [ "G19490AF", "968", "", "", "10090", "", "", "", "" ], [ "G19490AF", "968", "", "", "9823", "", "", "", "" ], [ "G59345UT", "19593", "", "CID71297866", "", "", "", "", "" ], [ "G59345UT", "19593", "", "SID252278314", "", "", "", "", "" ], [ "G63474NY", "3183", "", "CID91852450", "9606", "", "", "", "" ], [ "G63474NY", "3183", "", "SID252284681", "9606", "", "", "", "" ], [ "G59456VR", "32290", "", "CID91860338", "9913", "", "", "", "" ], [ "G59456VR", "32290", "", "SID252294112", "9913", "", "", "", "" ], [ "G71919QK", "", "", "", "", "7812", "", "", "" ], [ "G55786MG", "10297", "", "CID91845340", "4932", "", "", "", "2qc1" ], [ "G55786MG", "10297", "", "SID252276215", "4932", "", "", "", "2qc1" ], [ "G24791UN", "13507", "", "CID91860418", "", "", "", "", "" ], [ "G24791UN", "13507", "", "SID252294215", "", "", "", "", "" ], [ "G47870LR", "28925", "", "", "9606", "", "", "", "" ], [ "G83716SQ", "2501", "", "", "9606", "", "", "", "" ], [ "G38979OV", "23880", "", "", "9606", "7645", "P08709", "", "" ], [ "G38979OV", "23880", "", "", "9913", "7645", "P08709", "", "" ], [ "G80161SF", "17544", "", "CID91856688", "32644", "", "", "", "" ], [ "G80161SF", "17544", "", "SID252289754", "9606", "", "", "", "" ], [ "G97765TT", "14235", "", "CID91853046", "", "4346", "P08861", "", "" ], [ "G97765TT", "14235", "", "SID252285389", "", "7672", "P00533", "", "" ], [ "G97765TT", "14235", "", "SID252285389", "", "7672", "P04275", "", "" ], [ "G97765TT", "14235", "", "SID252285389", "", "7672", "P08861", "", "" ], [ "G96919WB", "13626", "GOG349", "CID91852137", "", "", "", "", "" ], [ "G96919WB", "13626", "GOG349", "SID252284299", "", "", "", "", "" ], [ "G25953KD", "10389", "", "CID91859289", "9606", "", "", "", "" ], [ "G25953KD", "10389", "", "SID252292854", "9606", "", "", "", "" ], [ "G42731RJ", "14572", "GOG565", "CID91848307", "", "", "", "", "" ], [ "G42731RJ", "14572", "GOG565", "SID252279772", "", "", "", "", "" ], [ "G41974MG", "2050", "", "CID91856796", "10090", "", "", "", "" ], [ "G41974MG", "2050", "", "SID252289881", "10090", "", "", "", "" ], [ "G44137YR", "39274", "", "CID71298056", "", "", "", "", "" ], [ "G44137YR", "39274", "", "SID252293869", "", "", "", "", "" ], [ "G13583BZ", "24674", "", "CID71297727", "9606", "", "", "", "" ], [ "G13583BZ", "24674", "", "SID252279061", "11309", "", "", "", "" ], [ "G13583BZ", "24674", "", "SID252279061", "9823", "", "", "", "" ], [ "G13583BZ", "24674", "", "SID252279061", "9031", "", "", "", "" ], [ "G16437LH", "13322", "", "CID91856516", "", "", "", "", "" ], [ "G16437LH", "13322", "", "SID252289555", "", "", "", "", "" ], [ "G03414KZ", "18396", "", "CID71297846", "", "", "", "", "" ], [ "G03414KZ", "18396", "", "SID252294459", "", "", "", "", "" ], [ "G18905AN", "32475", "", "CID91857395", "", "", "", "", "" ], [ "G18905AN", "32475", "", "SID252290587", "", "", "", "", "" ], [ "G53667CH", "2066", "GOG139", "CID91846789", "10090", "", "", "", "" ], [ "G53667CH", "2066", "GOG139", "SID252277934", "10090", "", "", "", "" ], [ "G84852GW", "2114", "GOG148", "CID91860758", "9606", "7737", "P10253", "", "1lgc" ], [ "G84852GW", "2114", "GOG148", "SID252294627", "9606", "7737", "P10253", "", "1lgc" ], [ "G49963IQ", "17416", "", "CID53262369", "9606", "", "", "", "" ], [ "G49963IQ", "17416", "", "SID252284308", "9606", "", "", "", "" ], [ "G37745TJ", "16486", "", "", "9606", "", "", "", "" ], [ "G63160NR", "17568", "", "CID71297634", "151740", "", "", "", "" ], [ "G63160NR", "17568", "", "SID252281920", "32644", "", "", "", "" ], [ "G63160NR", "17568", "", "SID252281920", "9606", "", "", "", "" ], [ "G35455OM", "38337", "GOG846", "CID91846002", "", "", "", "", "" ], [ "G35455OM", "38337", "GOG846", "SID252276994", "", "", "", "", "" ], [ "G18612LP", "1963", "", "", "9606", "", "", "", "" ], [ "G29011JC", "1646", "GOG38", "CID91858077", "9606", "", "P01579", "", "" ], [ "G29011JC", "1646", "GOG38", "SID252291401", "9913", "", "P01579", "", "" ] ] }, "readme": "Name\n - Human Glycome Accessions\n\nVersion\n - 1.0.13\n\nCreated on\n - 2019-01-23T17:21:05.928353\n\nModified on\n - 2019-04-12T13:49:54.302994\n\nCreated by\n - Rahi Navelkar [rsn13@gwu.edu], Jeet Vora [jeetvora@gwu.edu], Brian Fochtman [bfochtman@email.gwu.edu]\n\nAuthors\n - Nathan Edwards [nje5@georgetown.edu]\n\nChecksum\n - \n\nUsability Domain\n - List of Glycans identified by GlyTouCan Accessions mapped to different databases.\n\nDescription Domain\n Keywords\n - GlyTouCan\n - Glycan\n\n Pipeline Steps\n - Step-1: The input file(s) were downloaded from the source link and were seperated into individual 2 column input files (glytoucan_acc, database_id) if required and the individual input file(s) were processed based on the compiled glycan list using a python script[make-glycan-csv.py] to generate the final output csv file. a) If the glycan has source/taxonomy annotation[taxid:9606] in GlyTouCan b) If the glycan is listed on human[taxid:9606] glycan webpage at UniCarbKB c) If the glycan is listed on a human [taxid:9606] protein webpage at UniCarbKB d) If the glycan is synthesized by a human[taxid:9606] protein [http://data.glygen.org/GLYDS00064] e) If the glycan is known to be attached to a human[taxid:9606] protein [http://data.glygen.org/GLYDS00040] f) If the glycan is a motif of the glycan mentioned under criteria a-f \n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend/blob/master/integration/ \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: gdb.txt \n URI: https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/gdb.txt \n Name: glycomedb.txt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/glycomedb.txt\n Name: glyco.txt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/glyco.txt\n Name: pbch.txt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/pbch.txt\n Name: taxa.txt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/taxa.txt\n Name: uckb.txt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/uckb.txt\n Name: humanprot.txt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/humanprot.txt\n Name: ucdb.txt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/ucdb.txt\n Name: pdb.txt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/pdb.txt\n Output Subdomain\n Name: human_glycan_idmapping.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.0.13/reviewed/human_glycan_idmapping.csv\n Name: human_glycan_idmapping.stat.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.0.13/reviewed/human_glycan_idmapping.stat.csv\n\nFields\n Name: \"glyco_id\"\n Description: \"GlycO database identifier\"\n Unique Values: \"780\"\n Name: \"unicarbkb_id\"\n Description: \"\"\n Unique Values: \"845\"\n Name: \"glycomedb_id\"\n Description: \"GlycomeDB database identifier\"\n Unique Values: \"5363\"\n Name: \"taxid\"\n Description: \"\"\n Unique Values: \"355\"\n Name: \"pdb_id\"\n Description: \"4-character id assigned to each protein structure in Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)\"\n Unique Values: \"3262\"\n Name: \"pubchem_id\"\n Description: \"\"\n Unique Values: \"8012\"\n Name: \"uniprotkb_id\"\n Description: \"The entry name or mnemonic identifier assigned to the protein accession that consists of up to 11 uppercase alphanumeric characters for UniProtKB/Swiss-Prot entry and up to 16 uppercase alphanumeric characters for UniProtKB/TrEMBL entry with a defined naming convention\"\n Unique Values: \"114\"\n Name: \"unicarbdb_id\"\n Description: \"\"\n Unique Values: \"239\"\n Name: \"glytoucan_ac\"\n Description: \"\"\n Unique Values: \"5840\"", "downloadurl": "/ln2data/releases/data/v-1.0.13/reviewed/human_glycan_idmapping.csv" }