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"HEK293", "CVCL_0045", "", "", "", "NAT", "NXT", "122", "122", "Asn", "Asn", "N" ], [ "P0DTC2-1", "122", "Asn", "G39188ZX", "N-linked", "protein_xref_glyconnect", "2838", "protein_xref_glyconnect", "2838", "2838", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "1530", "", "Undefined core", "N-Linked", "6,2,0,0,0,0,0,0,0,0,0,0,0,0", "H6N2", "HexNAc(2)Hex(6)", "1396.4862", "1397.2597", "Hex:6 HexNAc:2", "G39188ZX", "", "", "HEK293", "CVCL_0045", "", "", "", "NAT", "NXT", "122", "122", "Asn", "Asn", "N" ], [ "P0DTC2-1", "122", "Asn", "G39188ZX", "N-linked", "protein_xref_pubmed", "32363391", "protein_xref_glyconnect", "2838", "2838", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "1530", "", "Undefined core", "N-Linked", "6,2,0,0,0,0,0,0,0,0,0,0,0,0", "H6N2", "HexNAc(2)Hex(6)", "1396.4862", "1397.2597", "Hex:6 HexNAc:2", "G39188ZX", "", "", "HEK293", "CVCL_0045", "", "", "", "NAT", "NXT", "122", "122", "Asn", "Asn", "N" ], [ 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"protein_xref_glyconnect", "2838", "2838", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "219", "", "Undefined core", "N-Linked", "5,4,1,2,0,0,0,0,0,0,0,0,0,0", "H5N4F1S2", "HexNAc(4)Hex(5)dHex(1)NeuAc(2)", "2368.8409", "2370.1661", "Hex:5 HexNAc:4 dHex:1 NeuAc:2", "G22310AV", "", "", "HEK293", "CVCL_0045", "", "", "", "NAT", "NXT", "122", "122", "Asn", "Asn", "N" ], [ "P0DTC2-1", "122", "Asn", "G22310AV", "N-linked", "protein_xref_pubmed", "32363391", "protein_xref_glyconnect", "2838", "2838", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "219", "", "Undefined core", "N-Linked", "5,4,1,2,0,0,0,0,0,0,0,0,0,0", "H5N4F1S2", "HexNAc(4)Hex(5)dHex(1)NeuAc(2)", "2368.8409", "2370.1661", "Hex:5 HexNAc:4 dHex:1 NeuAc:2", "G22310AV", "", "", "HEK293", "CVCL_0045", "", "", "", "NAT", "NXT", "122", "122", "Asn", "Asn", "N" ], [ "P0DTC2-1", "122", "Asn", "G23863VK", "N-linked", "protein_xref_glyconnect", "2838", "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", "", "", "", "NAT", "NXT", "122", "122", "Asn", "Asn", "N" ], [ "P0DTC2-1", "122", "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", "", "", "", "NAT", "NXT", "122", "122", "Asn", "Asn", "N" ], [ "P0DTC2-1", "122", "Asn", "G49874UX", "N-linked", "protein_xref_glyconnect", "2838", "protein_xref_glyconnect", "2838", "2838", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "3097", "", "Undefined core", "N-Linked", "3,4,1,0,0,0,0,0,0,0,0,0,0,0", "H3N4F1", "HexNAc(4)Hex(3)dHex(1)", "1462.5445", "1463.3655", "Hex:3 HexNAc:4 dHex:1", "G49874UX", "", "", "HEK293", "CVCL_0045", "", "", "", "NAT", "NXT", "122", "122", "Asn", "Asn", "N" ], [ "P0DTC2-1", "122", "Asn", "G49874UX", "N-linked", "protein_xref_pubmed", "32363391", "protein_xref_glyconnect", "2838", "2838", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "3097", "", "Undefined core", "N-Linked", "3,4,1,0,0,0,0,0,0,0,0,0,0,0", "H3N4F1", "HexNAc(4)Hex(3)dHex(1)", "1462.5445", "1463.3655", "Hex:3 HexNAc:4 dHex:1", "G49874UX", "", "", "HEK293", "CVCL_0045", "", "", "", "NAT", "NXT", "122", "122", "Asn", "Asn", "N" ], [ "P0DTC2-1", "122", "Asn", "G06110VR", "N-linked", "protein_xref_glyconnect", "2838", "protein_xref_glyconnect", "2838", "2838", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "3115", "", "Undefined core", "N-Linked", "5,2,0,0,0,0,0,0,0,0,0,0,0,0", "H5N2", "HexNAc(2)Hex(5)", "1234.4334", "1235.1173", "Hex:5 HexNAc:2", "G06110VR", "", "", "HEK293", "CVCL_0045", "", "", "", "NAT", "NXT", "122", "122", "Asn", "Asn", "N" ], [ "P0DTC2-1", "122", "Asn", "G06110VR", "N-linked", "protein_xref_pubmed", "32363391", "protein_xref_glyconnect", "2838", "2838", "2697049", "Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)", "3115", "", "Undefined core", "N-Linked", "5,2,0,0,0,0,0,0,0,0,0,0,0,0", "H5N2", "HexNAc(2)Hex(5)", "1234.4334", "1235.1173", "Hex:5 HexNAc:2", "G06110VR", "", "", "HEK293", "CVCL_0045", "", "", "", "NAT", "NXT", "122", "122", "Asn", "Asn", "N" ] ] }, "readme": "Name\n - SARS-CoV2 Glycosylation sites\n\nVersion\n - v-2.2.1\n\nCreated on\n - 2020-09-24T13:36:00.724463\n\nModified on\n - 2022-09-26T09:08:12.455012\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 SARS-CoV2 Glycosylation Sites (GlyConnect) dataset contains SARS-CoV2 [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 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 (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-2.2.1/misc/n_sequon_info.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/misc/sample_mapping.csv\n Name: cellosaurus.txt\n URI: https:/data.glygen.org/ln2downloads/cellosaurus/2023_07_13/cellosaurus.txt\n Name: glycosylations?taxonomy=Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)\n URI: https:/data.glygen.org/ln2downloads/glyconnect/2023_07_13/glycosylations?taxonomy=Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)\n Output Subdomain\n Name: sarscov2_proteoform_glycosylation_sites_glyconnect.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/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-2.2.1/reviewed/sarscov2_proteoform_glycosylation_sites_glyconnect.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"48\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"4\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"206\"\n Name: \"glycosylation_type\"\n Description: \"Type of glycosylation (N/O/C/S linked glycosylation)\"\n Unique Values: \"3\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"15\"\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"8\"\n Name: \"protein_id\"\n Description: \"ID of the protein\"\n Unique Values: \"8\"\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: \"303\"\n Name: \"structure_glytoucan_id\"\n Description: \"GlyTouCan Ac. Assocaiated with the structure\"\n Unique Values: \"52\"\n Name: \"structure_glycan_core\"\n Description: \"Glycan core associated to glytoucan_ac_struture\"\n Unique Values: \"9\"\n Name: \"structure_glycan_type\"\n Description: \"Glycan type associated to glytoucan_ac_struture\"\n Unique Values: \"3\"\n Name: \"composition_format_numeric\"\n Description: \"glycan composition in a numeric format\"\n Unique Values: \"159\"\n Name: \"composition_format_condensed\"\n Description: \"condensed format of the glycan description\"\n Unique Values: \"159\"\n Name: \"composition_format_byonic\"\n Description: \"byonic format of the glycan description\"\n Unique Values: \"159\"\n Name: \"composition_mass_monoisotopic\"\n Description: \"Monoisotopic mass of the glycan\"\n Unique Values: \"159\"\n Name: \"composition_mass\"\n Description: \"Mass of the glycan\"\n Unique Values: \"159\"\n Name: \"composition_format_glyconnect\"\n Description: \"composition format of the glyconnect\"\n Unique Values: \"159\"\n Name: \"composition_glytoucan_id\"\n Description: \"GlyTouCan Ac. Associated with the glycan composition.\"\n Unique Values: \"157\"\n Name: \"source_tissue_name\"\n Description: \"Tissue NAME from GlyConnect\"\n Unique Values: \"1\"\n Name: \"source_tissue_id\"\n Description: \"Tissue ID from GlyConnect\"\n Unique Values: \"1\"\n Name: \"source_cell_line_cellosaurus_name\"\n Description: \"\"\n Unique Values: \"6\"\n Name: \"source_cell_line_cellosaurus_id\"\n Description: \"cellosaurus ID of the cell line\"\n Unique Values: \"6\"\n Name: \"source_cell_component_id\"\n Description: \"Cell component IF from GlyConnect\"\n Unique Values: \"1\"\n Name: \"source_cell_component_go_id\"\n Description: \"Cell component GO ID from GlyConnect\"\n Unique Values: \"1\"\n Name: \"source_cell_component_name\"\n Description: \"Cell Component name from GlyConnect\"\n Unique Values: \"1\"\n Name: \"n_sequon\"\n Description: \"\"\n Unique Values: \"15\"\n Name: \"n_sequon_type\"\n Description: \"\"\n Unique Values: \"3\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"48\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"48\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"4\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"4\"\n Name: \"site_seq\"\n Description: \"\"\n Unique Values: \"4\"", "downloadurl": "/ln2data/releases/data/v-2.2.1/reviewed/sarscov2_proteoform_glycosylation_sites_glyconnect.csv" }