{ "bcoid": "GLY_000530", "title": "SARS-CoV2 Glycosylation sites", "description": "The SARS-CoV2 Glycosylation Sites (GlyConnect) dataset contains Severe acute respiratory syndrome coronavirus ...", "filename_list": "sarscov2_proteoform_glycosylation_sites_glyconnect.csv", "filename": "sarscov2_proteoform_glycosylation_sites_glyconnect.csv", "filetype": "csv", "categories": { "species": [ "Severe acute respiratory syndrome coronavirus 2" ], "molecule": [ "Proteoform" ], "tag": [ "Glycosylation Sites" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ], "file_category": [ "glycosylation_sites_" ] }, "minitable": { "content": [ [ "P0DTC2-1...", "1074..." ], [ "P0DTC2-1...", "1074..." ] ], "headers": [ "uniprotkb_ca...", "glycosylatio..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "glycosylation_site_uniprotkb" }, { "type": "string", "label": "amino_acid" }, { "type": "string", "label": "saccharide" }, { "type": "string", "label": "glycosylation_type" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "src_xref_key" }, { "type": "string", "label": "src_xref_id" }, { "type": "string", "label": "protein_id" }, { "type": "string", "label": "taxonomy_taxonomy_id" }, { "type": "string", "label": "taxonomy_species" }, { "type": "string", "label": "structure_id" }, { "type": "string", "label": "structure_glytoucan_id" }, { "type": "string", "label": "structure_glycan_core" }, { "type": "string", "label": "structure_glycan_type" }, { "type": "string", "label": "composition_format_numeric" }, { "type": "string", "label": "composition_format_condensed" }, { "type": "string", "label": "composition_format_byonic" }, { "type": "string", "label": "composition_mass_monoisotopic" }, { "type": "string", "label": "composition_mass" }, { "type": "string", "label": "composition_format_glyconnect" }, { "type": "string", "label": "composition_glytoucan_id" }, { "type": "string", "label": "source_tissue_name" }, { "type": "string", "label": "source_tissue_id" }, { "type": "string", "label": "source_cell_line_cellosaurus_name" }, { "type": "string", "label": "source_cell_line_cellosaurus_id" }, { "type": "string", "label": "source_cell_component_id" }, { "type": "string", "label": "source_cell_component_go_id" }, { "type": "string", "label": "source_cell_component_name" }, { "type": "string", "label": "n_sequon" }, { "type": "string", "label": "n_sequon_type" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "start_aa" }, { "type": "string", "label": "end_aa" }, { "type": "string", "label": "site_seq" }, { "type": "string", "label": "isoform_mapping_notes" } ], [ "P0DTC2-1", "1074", "Asn", "G10256JP", "N-linked", "protein_xref_pubmed", "32363391", "protein_xref_glyconnect", "2838", "2838", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "1289", "", "Undefined core", "N-Linked", "3,5,1,0,0,0,0,0,0,0,0,0,0,0", "H3N5F1", "HexNAc(5)Hex(3)dHex(1)", "1665.6239", "1666.5605", "Hex:3 HexNAc:5 dHex:1", "G10256JP", "", "", "HEK293", "CVCL_0045", "", "", "", "NFT", "NXT", "1074", "1074", "Asn", "Asn", "N", "" ], [ "P0DTC2-1", "1074", "Asn", "G23863VK", "N-linked", "protein_xref_pubmed", "32363391", "protein_xref_glyconnect", "2838", "2838", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "2287", "", "Undefined core", "N-Linked", "5,4,1,0,0,0,0,0,0,0,0,0,0,0", "H5N4F1", "HexNAc(4)Hex(5)dHex(1)", "1786.6501", "1787.6503", "Hex:5 HexNAc:4 dHex:1", "G23863VK", "", "", "HEK293", "CVCL_0045", "", "", "", "NFT", "NXT", "1074", "1074", "Asn", "Asn", "N", "" ] ] }, "readme": "Name\n - SARS-CoV2 Glycosylation sites\n\nVersion\n - v-2.12.1\n\nCreated on\n - 2020-09-24T13:36:00.724463\n\nModified on\n - 2024-05-17T11:24:03.671Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Kate Warner [k.warner1@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 SARS-CoV2 Glycosylation Sites (GlyConnect) dataset contains Severe acute respiratory syndrome coronavirus 2 [taxid:2697049] 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:Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)). 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 UniProtKB 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 (sarscov2_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-2.12.1/misc/n_sequon_info.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/misc/sample_mapping.csv\n Name: cellosaurus.txt\n URI: https:/data.glygen.org/ln2downloads/cellosaurus/2026_06_02/cellosaurus.txt\n Name: glyconnect_sarscov2.json\n URI: https:/data.glygen.org/ln2downloads/glyconnect/2026_05_28/glyconnect_sarscov2.json\n Output Subdomain\n Name: sarscov2_proteoform_glycosylation_sites_glyconnect.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/sarscov2_proteoform_glycosylation_sites_glyconnect.csv\n Name: sarscov2_proteoform_glycosylation_sites_glyconnect.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/sarscov2_proteoform_glycosylation_sites_glyconnect.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\"\n Description: \"\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.12.1/reviewed/sarscov2_proteoform_glycosylation_sites_glyconnect.csv" }