{ "bcoid": "GLY_000296", "title": "Glycan Xref ChEBI", "description": " The dataset provides cross-references to ChEBI Id's for the associated glycan (GlyTouCan Accession). ...", "filename": "glycan_xref_chebi.csv", "filetype": "csv", "categories": { "molecule": [ "Glycan" ], "tags": [ "ChEBI cross-references" ], "status": [ "Reviewed" ], "file_type": [ "csv" ], "scope": [ "internal" ], "species": [ "Homo sapiens", "Mus musculus", "Rattus", "Rattus norvegicus", "Drosophila melanogaster", "Severe acute respiratory syndrome coronavirus 2", "Hepatitis C virus (isolate H)", "Severe acute respiratory syndrome-related coronavirus" ] }, "minitable": { "content": [ [ "G68137PO...", "27387..." ], [ "G29057GU...", "138712..." ] ], "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" } ], [ "G68137PO", "27387", "glycan_xref_chebi" ], [ "G29057GU", "138712", "glycan_xref_chebi" ], [ "G26097PL", "138714", "glycan_xref_chebi" ], [ "G98814RL", "138715", "glycan_xref_chebi" ], [ "G69038UV", "138717", "glycan_xref_chebi" ], [ "G97423JA", "138716", "glycan_xref_chebi" ], [ "G57710SU", "140819", "glycan_xref_chebi" ], [ "G82576YO", "2181", "glycan_xref_chebi" ], [ "G14783GG", "4191", "glycan_xref_chebi" ], [ "G47203JO", "6182", "glycan_xref_chebi" ], [ "G08545ST", "17765", "glycan_xref_chebi" ], [ "G74407MX", "4093", "glycan_xref_chebi" ], [ "G68158BT", "4139", "glycan_xref_chebi" ], [ "G00055MO", "16153", "glycan_xref_chebi" ], [ "G88438YV", "16789", "glycan_xref_chebi" ], [ "G81533KY", "17012", "glycan_xref_chebi" ], [ "G83119OD", "37740", "glycan_xref_chebi" ], [ "G74621DY", "17716", "glycan_xref_chebi" ], [ "G41915IH", "17979", "glycan_xref_chebi" ], [ "G58161NS", "17925", "glycan_xref_chebi" ], [ "G70323CJ", "4208", "glycan_xref_chebi" ], [ "G71142DF", "15903", "glycan_xref_chebi" ], [ "G01550VL", "15936", "glycan_xref_chebi" ], [ "G19038KD", "25164", "glycan_xref_chebi" ], [ "G14987PW", "37746", "glycan_xref_chebi" ], [ "G27025MB", "28037", "glycan_xref_chebi" ], [ "G78317QO", "28085", "glycan_xref_chebi" ], [ "G82562YG", "27442", "glycan_xref_chebi" ], [ "G51535NO", "27586", "glycan_xref_chebi" ], [ "G65889KE", "27667", "glycan_xref_chebi" ], [ "G04616ST", "27707", "glycan_xref_chebi" ], [ "G51060EL", "27476", "glycan_xref_chebi" ], [ "G64863OF", "28385", "glycan_xref_chebi" ], [ "G19577LJ", "28393", "glycan_xref_chebi" ], [ "G88980IR", "17535", "glycan_xref_chebi" ], [ "G15305CQ", "29111", "glycan_xref_chebi" ], [ "G09546QO", "28061", "glycan_xref_chebi" ], [ "G95233PP", "28480", "glycan_xref_chebi" ], [ "G98006LH", "28772", "glycan_xref_chebi" ], [ "G07982RO", "28681", "glycan_xref_chebi" ], [ "G15021LG", "4167", "glycan_xref_chebi" ], [ "G38999IM", "27907", "glycan_xref_chebi" ], [ "G97146EI", "28014", "glycan_xref_chebi" ], [ "G61491DK", "28729", "glycan_xref_chebi" ], [ "G37615KF", "6178", "glycan_xref_chebi" ], [ "G84224TW", "36218", "glycan_xref_chebi" ], [ "G88362QR", "36219", "glycan_xref_chebi" ], [ "G78926JO", "36224", "glycan_xref_chebi" ], [ "G48027TR", "36226", "glycan_xref_chebi" ], [ "G73578JC", "17725", "glycan_xref_chebi" ], [ "G49108TO", "28009", "glycan_xref_chebi" ], [ "G03144EF", "28518", "glycan_xref_chebi" ], [ "G26478JK", "28543", "glycan_xref_chebi" ], [ "G87251UV", "36230", "glycan_xref_chebi" ], [ "G42865BX", "16177", "glycan_xref_chebi" ], [ "G09165XB", "28053", "glycan_xref_chebi" ], [ "G55958KV", "35930", "glycan_xref_chebi" ], [ "G64007OP", "28272", "glycan_xref_chebi" ], [ "G93924TT", "17118", "glycan_xref_chebi" ], [ "G17475NE", "40656", "glycan_xref_chebi" ], [ "G27798EJ", "18217", "glycan_xref_chebi" ], [ "G35170ES", "39610", "glycan_xref_chebi" ], [ "G49736TE", "36231", "glycan_xref_chebi" ], [ "G05939SX", "37741", "glycan_xref_chebi" ], [ "G10338IN", "37744", "glycan_xref_chebi" ], [ "G96370VA", "27931", "glycan_xref_chebi" ], [ "G57321FI", "40356", "glycan_xref_chebi" ], [ "G61418DU", "28497", "glycan_xref_chebi" ], [ "G45827GY", "30248", "glycan_xref_chebi" ], [ "G44688AW", "17631", "glycan_xref_chebi" ], [ "G16579HJ", "28161", "glycan_xref_chebi" ], [ "G95531HX", "37675", "glycan_xref_chebi" ], [ "G48232PN", "37677", "glycan_xref_chebi" ], [ "G30086RR", "37680", "glycan_xref_chebi" ], [ "G10899AB", "37686", "glycan_xref_chebi" ], [ "G38427JR", "37701", "glycan_xref_chebi" ], [ "G76432BK", "37704", "glycan_xref_chebi" ], [ "G62164YY", "37706", "glycan_xref_chebi" ], [ "G36445ON", "37617", "glycan_xref_chebi" ], [ "G75623HL", "37619", "glycan_xref_chebi" ], [ "G76622SI", "37620", "glycan_xref_chebi" ], [ "G06186NU", "37626", "glycan_xref_chebi" ], [ "G16038XU", "37627", "glycan_xref_chebi" ], [ "G15768VA", "37630", "glycan_xref_chebi" ] ] }, "readme": "Name\n - Glycan Xref ChEBI\n\nVersion\n - v-2.1.1\n\nCreated on\n - 2019-11-13T16:58:52.830892\n\nModified on\n - 2022-09-26T09:04:47.924861\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 - Gareth Owen [gowen@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The dataset provides cross-references to ChEBI Id's for the associated glycan (GlyTouCan Accession). The mapping is produced using the direct download files(database_accession.tsv) from the ChEBI-EBI FTP (ftp://ftp.ebi.ac.uk/pub/databases/chebi/). The glycans are mapped/registered into the ChEBI database as follows: 1) GlyTouCan accession is mapped directly to ChEBI ID through PubChem CID (if the PubChem CID has a ChEBI cross-reference) 2) glycans with PubChem CID (which lack a ChEBI cross-reference) are integrated into ChEBI through applications like KNIME (https://europepmc.org/article/med/28757290) and ClassyFire (https://pubmed.ncbi.nlm.nih.gov/27867422/). 2) glycans without a PubChem CID are registered manually into the CHEBI database.\n\nDescription Domain\n Keywords\n - Glycan\n - GlyTouCan Accession\n - ChEBI\n - Cross-references\n - ID/Accession Mapping\n\n Pipeline Steps\n - Step-1: The input file (database_accession) was downloaded directly from the CHEBI-EBI FTP dowloads (ftp://ftp.ebi.ac.uk/pub/databases/chebi/). The following rules were applied to generate the final output file: 1) rows where \"SOURCE\" column = GlyTouCan were filtered out. 2) for such rows \"COMPOUND_ID\" is chebi_id and \"ACCESSION_NUMBER\" is glytoucan_ac. 2) the extracted glytoucan_ac were checked against the GlyGen glycan masterlist (https://data.glygen.org/GLY_000281 or input file glycan_masterlist.csv) and the GlyTouCan accessions not included in the GlyGen glycan masterlist were excluded to generate the final output file. The glycans are submitted into the ChEBI database as follows: 1) GlyTouCan accession is mapped directly to ChEBI ID through PubChem CID (if the PubChem CID has a ChEBI cross-reference) 2) glycans with PubChem CID (which lack a ChEBI cross-reference) are integrated into ChEBI through applications like KNIME (https://europepmc.org/article/med/28757290) and ClassyFire (https://pubmed.ncbi.nlm.nih.gov/27867422/). 2) glycans without a PubChem CID are registered manually into the CHEBI database.\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-2.1.1/reviewed/glycan_masterlist.csv\n Name: database_accession.tsv\n URI: /data/shared/glyds/downloads/chebi/2023_05_19/database_accession.tsv\n Output Subdomain\n Name: glycan_xref_chebi.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/glycan_xref_chebi.csv\n Name: glycan_xref_chebi.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/glycan_xref_chebi.stat.csv\n\nFields\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"10541\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"10532\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.1.1/reviewed/glycan_xref_chebi.csv" }