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"", "", "", "" ], [ "", "", "", "G54021WX", "Free", "protein_xref_pubmed", "26613816", "glycan_xref_glyconnect", "212", "None", "9606", "Homo sapiens", "212", "G54021WX", "Lactose", "Free", "4,2,0,0,0,0,0,0,0,0,0,0,0,0", "H4N2", "HexNAc(2)Hex(4)", "1072.3806", "1072.9749", "Hex:4 HexNAc:2", "G66538GV", "milk", "UBERON:0001913", "", "", "", "", "", "", "", "", "", "", "", "" ], [ "", "", "", "G66538GV", "Free", "protein_xref_pubmed", "26613816", "glycan_xref_glyconnect", "212", "None", "9606", "Homo sapiens", "212", "G54021WX", "Lactose", "Free", "4,2,0,0,0,0,0,0,0,0,0,0,0,0", "H4N2", "HexNAc(2)Hex(4)", "1072.3806", "1072.9749", "Hex:4 HexNAc:2", "G66538GV", "milk", "UBERON:0001913", "", "", "", "", "", "", "", "", "", "", "", "" ], [ "", "", "", "G15531AF", "N-linked", "glycan_xref_glyconnect", "213", "glycan_xref_glyconnect", "213", "None", "9606", "Homo sapiens", "213", "G02622IU", "No-core", "N-Linked", "3,2,0,1,0,0,0,0,0,0,0,0,0,0", "H3N2S1", "HexNAc(2)Hex(3)NeuAc(1)", "1201.4232", "1202.0904", "Hex:3 HexNAc:2 NeuAc:1", "G15531AF", "urine", "UBERON:0001088", "", "", "", "", "", "", "", "", "", "", "", "" ], [ "", "", "", "G02622IU", "N-linked", "glycan_xref_glyconnect", "213", "glycan_xref_glyconnect", "213", "None", "9606", "Homo sapiens", "213", "G02622IU", "No-core", "N-Linked", "3,2,0,1,0,0,0,0,0,0,0,0,0,0", "H3N2S1", "HexNAc(2)Hex(3)NeuAc(1)", "1201.4232", "1202.0904", "Hex:3 HexNAc:2 NeuAc:1", "G15531AF", "urine", "UBERON:0001088", "", "", "", "", "", "", "", "", "", "", "", "" ], [ "", "", "", "G15531AF", "N-linked", "protein_xref_pubmed", "1779619", "glycan_xref_glyconnect", "213", "None", "9606", "Homo sapiens", "213", "G02622IU", "No-core", "N-Linked", "3,2,0,1,0,0,0,0,0,0,0,0,0,0", "H3N2S1", "HexNAc(2)Hex(3)NeuAc(1)", "1201.4232", "1202.0904", "Hex:3 HexNAc:2 NeuAc:1", "G15531AF", "urine", "UBERON:0001088", "", "", "", "", "", "", "", "", "", "", "", "" ] ] }, "readme": "Name\n - Human Glycosylation Sites (GlyConnect) \n\nVersion\n - v-2.1.1\n\nCreated on\n - 2020-02-10T10:16:50.152756\n\nModified on\n - 2022-09-26T09:05:27.721392\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 - Frederique Lisacek [frederique.lisacek@sib.swiss], Julien Mariethoz [julien.mariethoz@sib.swiss]\n\nChecksum\n - \n\nUsability Domain\n - The Human Glycosylation Sites (GlyConnect) dataset contains human [taxid:9606] UniProtKB canonical accessions with information on reported glycosylation sites in GlyConnect database (https://glyconnect.expasy.org/; PMID: 30574787).A json file was derived through GlyConnect API (https://glyconnect.expasy.org/api/docs/index.html?url=/api/assets/swagger.json#/Glycosylation/listGlycosylationsAsJson) (Query: taxonomy:Homo sapiens). If you use this dataset please provide proper attribution to GlyConnect and GlyGen.\n\nDescription Domain\n Keywords\n - glycosylation\n - reported glycosylation\n\n Pipeline Steps\n - Step-1: The script loads the glycosylation information from the input JSON file and extracts the data. The QC checks filter out: 1) any rows where the UniProtKB accession is not included in the GlyGen protein list (https://data.glygen.org/GLYDS000001) and/or 2) if the given glycosylation position and amino acid does not match to the amino acid on the .fasta sequence provided in the 2019-09 UniProtKB release for that protein (However it does pass if the amino acid +glyco-site is empty (as these records correspond to the \"not reported\" glyco-sites and/or 3) If the glycosylation type does not associate to the glycostlation based on amino acid (i.e if a N-linked is associated with Ser/Thr residue, etc). 4) If the glyco-site is not reported and the glycosylation type is ambigious (c-Linked/o-linked) and/or 5) if the saccharide (GlyTouCan) is not present in the GlyGen glycan masterlist. All the flagged entries are added in the log file (human_proteoform_glycosylation_sites_glyconnect.1.log)\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-proteoform-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: n_sequon_info.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/misc/n_sequon_info.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/misc/sample_mapping.csv\n Name: cellosaurus.txt\n URI: /data/shared/glyds/downloads/cellosaurus/2023-03-21/cellosaurus.txt\n Name: glycosylations?taxonomy=Homo sapiens\n URI: /data/shared/glyds/downloads/glyconnect/2023_05_18/glycosylations?taxonomy=Homo sapiens\n Output Subdomain\n Name: human_proteoform_glycosylation_sites_glyconnect.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/human_proteoform_glycosylation_sites_glyconnect.csv\n Name: human_proteoform_glycosylation_sites_glyconnect.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/human_proteoform_glycosylation_sites_glyconnect.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"1241\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"1156\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"5\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"2046\"\n Name: \"glycosylation_type\"\n Description: \"Type of glycosylation (N/O/C/S linked glycosylation)\"\n Unique Values: \"4\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"3\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"2243\"\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"2\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"1825\"\n Name: \"protein_id\"\n Description: \"ID of the protein\"\n Unique Values: \"1306\"\n Name: \"taxonomy_taxonomy_id\"\n Description: \"Taxonomy ID associated with species name \"\n Unique Values: \"1\"\n Name: \"taxonomy_species\"\n Description: \"Taxonomy species name\"\n Unique Values: \"1\"\n Name: \"structure_id\"\n Description: \"Structure ID\"\n Unique Values: \"2966\"\n Name: \"structure_glytoucan_id\"\n Description: \"GlyTouCan Ac. Assocaiated with the structure\"\n Unique Values: \"1569\"\n Name: \"structure_glycan_core\"\n Description: \"Glycan core associated to glytoucan_ac_struture\"\n Unique Values: \"22\"\n Name: \"structure_glycan_type\"\n Description: \"Glycan type associated to glytoucan_ac_struture\"\n Unique Values: \"4\"\n Name: \"composition_format_numeric\"\n Description: \"glycan composition in a numeric format\"\n Unique Values: \"596\"\n Name: \"composition_format_condensed\"\n Description: \"condensed format of the glycan description\"\n Unique Values: \"596\"\n Name: \"composition_format_byonic\"\n Description: \"byonic format of the glycan description\"\n Unique Values: \"596\"\n Name: \"composition_mass_monoisotopic\"\n Description: \"Monoisotopic mass of the glycan\"\n Unique Values: \"579\"\n Name: \"composition_mass\"\n Description: \"Mass of the glycan\"\n Unique Values: \"579\"\n Name: \"composition_format_glyconnect\"\n Description: \"composition format of the glyconnect\"\n Unique Values: \"596\"\n Name: \"composition_glytoucan_id\"\n Description: \"GlyTouCan Ac. Associated with the glycan composition.\"\n Unique Values: \"479\"\n Name: \"source_tissue_name\"\n Description: \"Tissue NAME from GlyConnect\"\n Unique Values: \"47\"\n Name: \"source_tissue_id\"\n Description: \"Tissue ID from GlyConnect\"\n Unique Values: \"47\"\n Name: \"source_cell_line_cellosaurus_name\"\n Description: \"\"\n Unique Values: \"68\"\n Name: \"source_cell_line_cellosaurus_id\"\n Description: \"cellosaurus ID of the cell line\"\n Unique Values: \"68\"\n Name: \"source_cell_component_id\"\n Description: \"Cell component IF from GlyConnect\"\n Unique Values: \"5\"\n Name: \"source_cell_component_go_id\"\n Description: \"Cell component GO ID from GlyConnect\"\n Unique Values: \"5\"\n Name: \"source_cell_component_name\"\n Description: \"Cell Component name from GlyConnect\"\n Unique Values: \"5\"\n Name: \"n_sequon\"\n Description: \"\"\n Unique Values: \"72\"\n Name: \"n_sequon_type\"\n Description: \"\"\n Unique Values: \"7\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"1156\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"1156\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"5\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"5\"\n Name: \"site_seq\"\n Description: \"\"\n Unique Values: \"5\"", "downloadurl": "/ln2data/releases/data/v-2.1.1/reviewed/human_proteoform_glycosylation_sites_glyconnect.csv" }