{ "bcoid": "GLY_000290", "title": "Glycan Sequences IUPAC Extended", "description": "The dataset provides the glycan sequences in IUPAC extended format for the associated glycans (GlyTouCan ...", "filename": "glycan_sequences_iupac_extended.csv", "filetype": "csv", "categories": { "molecule": "Glycan", "tags": "IUPAC Extended format", "status": "Reviewed", "file_type": "csv", "scope": "internal" }, "minitable": { "content": [ [ "G00002CF...", "?-D-NeupGc-(..." ], [ "G00009BX...", "alpha-L-Fucp..." ] ], "headers": [ "glytoucan_ac...", "sequence_iup..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "glytoucan_ac" }, { "type": "string", "label": "sequence_iupac_extended" } ], [ "G00002CF", "?-D-NeupGc-(2->?)-?-D-NeupGc-(2->?)-?-D-Galp-(1->?)-?-D-Glcp-(1->" ], [ "G00009BX", "alpha-L-Fucp-(1->2)-beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->3)-beta-D-Galp-(1->4)-?-D-GlcNAc-(?->" ], [ "G00012MO", "beta-D-GalpNAc-(1->3)-alpha-D-Galp-(1->3)-beta-D-Galp-(1->4)-?-D-Glc-(?->" ], [ "G00013MO", "beta-D-Galp-(1->3)-beta-D-Galp-(1->4)-beta-D-Galp-(1->4)-?-D-Glc-(?->" ], [ "G00014MO", "beta-D-GalpNAc-(1->4)-beta-D-GlcpNAc-(1->3)-beta-D-Manp-(1->4)-?-D-Glc-(?->" ], [ "G00015MO", "beta-D-GlcpNAc-(1->2)-alpha-D-Manp-(1->3)-beta-D-Manp-(1->4)-?-D-Glc-(?->" ], [ "G00016MO", "alpha-D-Galp-(1->4)-?-D-Gal-(?->" ], [ "G00017MO", "beta-D-GlcpA-(1->3)-beta-D-GlcpNAc-(1->4)-beta-D-GlcpA-(1->3)-?-D-GlcNAc-(?->" ], [ "G00018MO", "beta-D-GlcpA-(1->3)-beta-D-GalpNAc4S-(1->4)-beta-D-GlcpA-(1->3)-?-D-GalNAc4S-(?->" ], [ "G00019MO", "beta-D-IdopA-(1->3)-beta-D-GalpNAc4S-(1->4)-beta-D-IdopA-(1->3)-?-D-GalNAc4S-(?->" ], [ "G00020MO", "beta-D-Galp-(1->4)-beta-D-GlcpNAc6S-(1->3)-beta-D-Galp-(1->4)-?-D-GlcNAc6S-(?->" ], [ "G00023MO", "beta-D-GlcpNAc3lRLac-(1->4)-beta-D-GlcpNAc-(1->4)-beta-D-GlcpNAc3lRLac-(1->4)-?-D-GlcpNAc-(1->" ], [ "G00024MO", "beta-D-Glcp-(1->3)-beta-D-Glcp-(1->3)-beta-D-Glcp-(1->" ], [ "G00025AJ", "beta-D-Galp-(1->4)[alpha-L-Fucp-(1->3)]-?-D-Glc-(?->" ], [ "G00025MO", "beta-D-Glcp-(1->4)-beta-D-Glcp-(1->4)-beta-D-Glcp-(1->4)-beta-D-Glcp-(1->" ], [ "G00026MO", "alpha-D-Manp-(1->3)[alpha-D-Manp-(1->6)]-beta-D-Manp-(1->4)-beta-D-GlcpNAc-(1->4)-?-D-GlcNAc-(?->" ], [ "G00027JG", "alpha-L-Fucp-(1->2)-beta-D-Galp-(1->3)[alpha-L-Fucp-(1->2)-beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->6)]-beta-D-Gal?NAc-(1->" ], [ "G00027MO", "alpha-D-Manp-(1->3)[alpha-D-Manp-(1->6)]-beta-D-Manp-(1->4)-beta-D-GlcpNAc-(1->" ], [ "G00028MO", "alpha-D-Manp-(1->3)[alpha-D-Manp-(1->3)[alpha-D-Manp-(1->6)]-alpha-D-Manp-(1->6)]-beta-D-Manp-(1->4)-beta-D-GlcpNAc-(1->4)-?-D-GlcNAc-(?->" ], [ "G00029MO", "beta-D-GlcpNAc-(1->2/4)-alpha-D-Manp-(1->3)[alpha-D-Manp-(1->3/6)-alpha-D-Manp-(1->6)]-beta-D-Manp-(1->4)-beta-D-GlcpNAc-(1->4)-?-D-GlcpNAc-(1->" ], [ "G00030MO", "beta-D-GlcpNAc-(1->2/4)-alpha-D-Manp-(1->3)[beta-D-GlcpNAc-(1->2/4)-alpha-D-Manp-(1->6)]-beta-D-Manp-(1->4)-beta-D-GlcpNAc-(1->4)-?-D-GlcNAc-(?->" ], [ "G00031MO", "beta-D-Galp-(1->3)-alpha-D-GalpNAc-(1->" ], [ "G00032MO", "beta-D-Galp-(1->3)-?-D-GalNAc-(?->" ], [ "G00033MO", "beta-D-Galp-(1->3)[beta-D-GlcpNAc-(1->6)]-alpha-D-GalpNAc-(1->" ], [ "G00034MO", "beta-D-Galp-(1->3)[beta-D-GlcpNAc-(1->6)]-?-D-GalNAc-(?->" ], [ "G00034WH", "alpha-D-Glcp-(1->6)-alpha-D-Glcp-(1->6)-alpha-D-Glcp-(1->6)-alpha-D-Glcp-(1->4)-alpha-D-Glcp-(1->4)-?-D-Glc-(?->" ], [ "G00035MO", "beta-D-GlcpNAc-(1->3)-alpha-D-GalpNAc-(1->" ], [ "G00036MO", "beta-D-GlcpNAc-(1->3)-?-D-GalNAc-(?->" ], [ "G00037MO", "beta-D-GlcpNAc-(1->3)[beta-D-GlcpNAc-(1->6)]-alpha-D-GalpNAc-(1->" ], [ "G00038MO", "beta-D-GlcpNAc-(1->3)[beta-D-GlcpNAc-(1->6)]-?-D-GalNAc-(?->" ], [ "G00039MO", "alpha-D-GalpNAc-(1->3)-alpha-D-GalpNAc-(1->" ], [ "G00040MO", "alpha-D-GalpNAc-(1->3)-?-D-GalNAc-(?->" ], [ "G00041IL", "beta-D-Galp-(1->3)-?-D-GlcpNAc-(1->3)[alpha-D-NeupAc-(2->6)]-alpha-D-GalpNAc-(1->" ], [ "G00041MO", "beta-D-GlcpNAc-(1->6)-alpha-D-GalpNAc-(1->" ], [ "G00042MO", "beta-D-GlcpNAc-(1->6)-?-D-GalNAc-(?->" ], [ "G00043MO", "alpha-D-GalpNAc-(1->6)-alpha-D-GalpNAc-(1->" ], [ "G00044MO", "alpha-D-GalpNAc-(1->6)-?-D-GalNAc-(?->" ], [ "G00045MO", "alpha-D-Manp-(1->2)-alpha-D-Manp-(1->6)-alpha-D-Manp-(1->4)-?-D-GlcN-(?->" ], [ "G00046MO", "alpha-D-Galp-(1->3)-?-D-Gal-(?->" ], [ "G00047MO", "beta-D-Galp-(1->3)[alpha-L-Fucp-(1->4)]-?-D-GlcpNAc-(1->" ], [ "G00048MO", "alpha-L-Fucp-(1->2)-beta-D-Galp-(1->3)[alpha-L-Fucp-(1->4)]-beta-D-GlcpNAc-(1->" ], [ "G00049MO", "beta-D-Galp-(1->3)-beta-D-GlcpNAc-(1->3)-beta-D-Galp-(1->4)-beta-D-Glcp-(1->" ], [ "G00050MO", "alpha-L-Fucp-(1->2)-beta-D-Galp-(1->3)-beta-D-GlcpNAc-(1->3)-beta-D-Galp-(1->4)-beta-D-Glcp-(1->" ], [ "G00051MO", "beta-D-Galp-(1->4)[alpha-L-Fucp-(1->3)]-beta-D-GlcpNAc-(1->" ], [ "G00052MO", "alpha-L-Fucp-(1->2)-beta-D-Galp-(1->4)[alpha-L-Fucp-(1->3)]-beta-D-GlcpNAc-(1->" ], [ "G00053MO", "alpha-D-NeupAc-(2->3)-beta-D-Galp-(1->3)[alpha-L-Fucp-(1->4)]-beta-D-GlcpNAc-(1->" ], [ "G00054MO", "alpha-D-NeupAc-(2->3)-beta-D-Galp-(1->4)[alpha-L-Fucp-(1->3)]-beta-D-GlcpNAc-(1->" ], [ "G00055MO", "beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->" ], [ "G00056HH", "beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->2)[beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->6)]-alpha-D-Manp-(1->?)[beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->2)-alpha-D-Manp-(1->?)]-beta-D-Manp-(1->4)-beta-D-GlcpNAc-(1->4)[?-L-Fucp-(1->?)]-?-D-GlcpNAc-(1->" ], [ "G00056MO", "beta-D-Galp-(1->3)-beta-D-GlcpNAc-(1->" ], [ "G00057MO", "beta-D-GalpNAc-(1->4)-beta-D-GlcpNAc-(1->" ], [ "G00058MO", "beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->3)-beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->" ], [ "G00059MO", "alpha-D-Galp-(1->4)-beta-D-Galp-(1->4)-beta-D-Glcp-(1->" ], [ "G00060BT", "alpha-D-Manp-(1->3)[alpha-D-Manp-(1->3)-beta-D-Manp-(1->6)]-beta-D-Manp-(1->4)-?-D-GlcNAc-(?->" ], [ "G00060MO", "alpha-D-Galp-(1->4)-beta-D-Galp-(1->4)-beta-D-GalpNAc-(1->3)-beta-D-Galp-(1->4)-beta-D-Glcp-(1->" ], [ "G00061MO", "beta-D-GalpNAc-(1->3)-alpha-D-Galp-(1->4)-beta-D-Galp-(1->4)-beta-D-Glcp-(1->" ], [ "G00062MO", "alpha-D-NeupAc-(2->3)[beta-D-GalpNAc-(1->4)]-beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->3)-beta-D-Galp-(1->" ], [ "G00063MO", "alpha-D-NeupAc-(2->3)[beta-D-GalpNAc-(1->4)]-beta-D-Galp-(1->3)[alpha-D-NeupAc-(2->6)]-beta-D-GalpNAc-(1->" ], [ "G00064MO", "alpha-D-GlcpNAc-(1->3)-beta-D-GalpNAc-(1->3)-alpha-D-Galp-(1->4)-beta-D-Galp-(1->4)-beta-D-Glcp-(1->" ], [ "G00065MO", "alpha-D-NeupAc-(2->3)-beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->" ], [ "G00066MO", "alpha-D-GalpNAc-(1->3)[alpha-L-Fucp-(1->2)]-beta-D-Galp-(1->" ], [ "G00067MO", "beta-D-Galp-(1->3)[alpha-L-Fucp-(1->2)]-beta-D-Galp-(1->" ], [ "G00068MO", "alpha-L-Fucp-(1->2)-beta-D-Galp-(1->" ], [ "G00069MO", "beta-D-Galp-(1->3)-beta-D-GlcpNAc-(1->3)-beta-D-Galp-(1->4)-?-D-Glc-(?->" ], [ "G00070MO", "beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->3)-beta-D-Galp-(1->4)-?-D-Glc-(?->" ], [ "G00071MO", "beta-D-Galp-(1->3)-beta-D-GalpNAc-(1->4)-beta-D-Galp-(1->4)-?-D-Glc-(?->" ], [ "G00072MO", "beta-D-GalpNAc-(1->3)-beta-D-Galp-(1->4)-beta-D-Galp-(1->4)-?-D-Glc-(?->" ], [ "G00076PK", "alpha-D-Galp-(1->4)-beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->" ], [ "G00089VH", "alpha-D-NeupAc-(2->6)-beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->2)-beta-D-Manp-(1->3)[alpha-D-NeupAc-(2->6)-beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->2)-beta-D-Manp-(1->6)]-alpha-D-Manp-(1->4)-?-D-GlcNAc-(?->" ], [ "G00090SL", "alpha-D-Manp-(1->6)-?-D-Man-(?->" ], [ "G00091RT", "alpha-D-Manp-(1->2)-alpha-D-Manp-(1->3)[alpha-D-Manp-(1->2)-alpha-D-Manp-(1->6)]-alpha-D-Manp-(1->" ], [ "G00094SE", "alpha-D-Galp-(1->3)-alpha-D-GalpNAc-(1->3)[alpha-L-Fucp-(1->2)]-beta-D-Galp-(1->3)[beta-D-GlcpNAc-(1->3)-beta-D-GlcpNAc-(1->6)]-alpha-D-GalpNAc-(1->" ], [ "G00106LE", "?-D-NeupAc-(2->?)-?-D-Galp6S-(1->?)[?-L-Fucp-(1->?)]-?-D-GlcNAc-(?->" ], [ "G00112IO", "alpha-D-GalpNAc-(1->3)-beta-D-Galp-(1->3)-beta-D-GlcpNAc-(1->3)[beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->6)]-beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->3)-?-D-GalNAc-(?->" ], [ "G00120QS", "alpha-D-Manp-(1->6)-?-D-Manp-(1->4)-beta-D-GlcpNAc-(1->4)-?-D-GlcpNAc-(1->" ], [ "G00123JF", "beta-D-Xylf-(1->" ], [ "G00133UK", "alpha-D-NeupGc-(2->3)[beta-D-Galp-(1->4)]-alpha-D-Galp-(1->" ], [ "G00140XB", "alpha-D-Galp-(1->3)-?-D-Manp-(1->" ], [ "G00140YZ", "beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->3/6)[alpha-L-Fucp-(1->2)-beta-D-Galp-(1->3/6)]-?-D-GalNAc-(?->" ], [ "G00141ZD", "alpha-D-Glcp-(1->4)[alpha-D-Galp-(1->6)]-?-D-Glc-(?->" ], [ "G00152LK", "beta-D-Glcp-(1->3)-beta-D-Glcp-(1->3)-beta-D-Glcp-(1->3)-alpha-D-Glcp-(1->3)-beta-D-Glcp-(1->3)-beta-D-Glcp-(1->" ], [ "G00153LJ", "beta-D-Galp-(1->2)-beta-D-Galp-(1->2)-beta-D-Galp-(1->" ], [ "G00157WT", "alpha-D-NeupAc-(2->3)-beta-D-Galp-(1->3)[alpha-L-Fucp-(1->4)]-beta-D-GlcpNAc-(1->3)[beta-D-Galp-(1->3)[alpha-L-Fucp-(1->4)]-beta-D-GlcpNAc-(1->3)-beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->6)]-beta-D-Galp-(1->4)-beta-D-Glcp-(1->" ], [ "G00167VE", "beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->2)[beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->6)]-alpha-D-Manp-(1->3/6)[beta-D-GalpNAc-(1->4)-beta-D-GlcpNAc-(1->2)-alpha-D-Manp-(1->3/6)]-beta-D-Manp-(1->4)-beta-D-GlcpNAc-(1->4)[alpha-L-Fucp-(1->6)]-?-D-GlcpNAc-(1->" ] ] }, "readme": "Name\n - Glycan Sequences IUPAC Extended\n\nVersion\n - 1.8.25\n\nCreated on\n - 2019-11-13T16:31:31.525156\n\nModified on\n - 2020-05-01T15:05:00.162142\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 the glycan sequences in IUPAC extended format for the associated glycans (GlyTouCan Accession). The listed GlyTouCan Accessions are derived from the GlyTouCan accession master list (https://data.glygen.org/GLYDS000281). Source database: https://glytoucan.org/\n\nDescription Domain\n Keywords\n - Glycan\n - GlyTouCan Accession\n - IUPAC Extended\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: iupac_extended.zip\n URI: https://data.glygen.org/ln2wwwdata/source/iupac_extended.zip\n Output Subdomain\n Name: glycan_sequences_iupac_extended.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/glycan_sequences_iupac_extended.csv\n Name: glycan_sequences_iupac_extended.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/glycan_sequences_iupac_extended.stat.csv\n\nFields\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"119\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"119\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"120\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"49\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"118\"\n Name: \"publication_date\"\n Description: \"Contains the full date on which the issue of the journal was published. Sourced from MEDLINE/PubMed data element(fields) description.\"\n Unique Values: \"117\"\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"115\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.8.25/reviewed/glycan_sequences_iupac_extended.csv" }