{ "bcoid": "GLY_000479", "title": "Glycosylation Sites - UniCarbKB [SARS CoV 2 proteins]", "description": "List of SARS coronavirus (SARS-CoV-2 or 2019-nCoV) [taxid:2697049] proteins with information on glycosylation ...", "filename": "sarscov2_proteoform_glycosylation_sites_unicarbkb.csv", "filetype": "csv", "categories": { "status": [ "Reviewed" ], "molecule": [ "Proteoform" ], "species": [ "Severe acute respiratory syndrome coronavirus 2" ], "tag": [ "UniCarbKB glycosylation sites" ], "file_type": [ "csv" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P0DTC2-1...", "61..." ], [ "P0DTC2-1...", "61..." ] ], "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": "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": "site_type" }, { "type": "string", "label": "src_file_name" }, { "type": "string", "label": "uckb_id" }, { "type": "string", "label": "composition" }, { "type": "string", "label": "curation_notes" }, { "type": "string", "label": "additional_notes" }, { "type": "string", "label": "pdb" }, { "type": "string", "label": "swiss_model" }, { "type": "string", "label": "abundance" }, { "type": "string", "label": "source_tissue_id" }, { "type": "string", "label": "source_tissue_name" }, { "type": "string", "label": "source_cell_line_cellosaurus_id" }, { "type": "string", "label": "source_cell_line_cellosaurus_name" }, { "type": "string", "label": "n_sequon" }, { "type": "string", "label": "n_sequon_type" } ], [ "P0DTC2-1", "61", "Asn", "G02815KT", "N-linked", "protein_xref_pubmed", "34004174", "protein_xref_unicarbkb_ds", "GLY_000479", "61", "61", "Asn", "Asn", "N", "known_site", "known_34004174_glygen", "G02815KT", "", "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "Ultimate 3000 HPLC system coupled to a high field Q-Exactive (HFX) Orbitrap mass spectrometer. Data analysis Byonic v3.8.13.", "", "", "", "", "", "CVCL_0045", "HEK293", "NVT", "NXT" ], [ "P0DTC2-1", "61", "Asn", "G02815KT", "N-linked", "protein_xref_doi", "10.1016/j.celrep.2021.109179", "protein_xref_unicarbkb_ds", "GLY_000479", "61", "61", "Asn", "Asn", "N", "known_site", "known_34004174_glygen", "G02815KT", "", "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "Ultimate 3000 HPLC system coupled to a high field Q-Exactive (HFX) Orbitrap mass spectrometer. Data analysis Byonic v3.8.13.", "", "", "", "", "", "CVCL_0045", "HEK293", "NVT", "NXT" ] ] }, "readme": "Name\n - Glycosylation Sites - UniCarbKB [SARS CoV 2 proteins]\n\nVersion\n - v-2.5.1\n\nCreated on\n - 2020-04-20T16:02:18.234465\n\nModified on\n - 2024-05-17T11:24:02.094Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@email.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 - Matthew Campbell [m.campbell2@griffith.edu.au], Nathan Edwards [Georgetown University]\n\nChecksum\n - \n\nUsability Domain\n - List of SARS coronavirus (SARS-CoV-2 or 2019-nCoV) [taxid:2697049] proteins with information on glycosylation sites and associated glycans (if available) from UniCarbKB database [https://academic.oup.com/nar/article/42/D1/D215/1052197 ,https://doi.org/10.1093/nar/gkt1128]. The listed protein (UniProtKB) accessions are part of the GlyGen UniProtKB canonical list (https://data.glygen.org/GLYDS000434)\n\nDescription Domain\n Keywords\n - proteins\n - canonical\n - glycosylation sites\n - glycan\n - UniCarbKB\n - GlyTouCan\n\n Pipeline Steps\n - Step-1: The input file was received directly from the provider (Matthew Campbell). A python script along with additional inputs was used to process data and generate a final dataset object. The script checks the GlyTouCan accessions against the existing accessions from GlyTouCan. (Input file 3). The missing accessions are added in log 2 file (sarscov2_proteoform_glycosylation_sites_unicarbkb.2.log) for validation purposes but are not eliminated during the processing. The unicarbkb id's which are glycan compostion strings, are mapped to GlyTouCan accession using input file 7, generated by Nathan Edwards. The script additionally implements 10 QC checks. Any row that fails for one or more checks is eliminated. All eliminated rows can be accessed from the log 1 (sarscov2_proteoform_glycosylation_sites_unicarbkb.1.log) file along the QC tags. QC tags and description: 1) no_canon: The given protein accession cannot be mapped to a canonical accession. (input file 2) 2) bad_pos: The given amino-acid position is invalid or exceeds the length of the protein sequence. 3) aa_mismatch: Bad amino acid reported (input file 6) 4) invalid_aa: The given amino acid is invalid. 5) glycan_without_glytype: glycan is not in the glycan classification file (Glycan classification file is generated by Author Nathan Edwards; input file 3). 6) bad_glytype: A bad glycan type is detected 7) n_glycan_aa_mismatch: An N glycan is associated with a ser/thr residue 8) o_glycan_aa_mismatch: An O glycan is associated with a Asn residue. 9) no_glycan_invalid_aa: row has no glycan and amino acid is invalid.\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-2.5.1/misc/n_sequon_info.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/misc/sample_mapping.csv\n Name: cellosaurus.txt\n URI: https:/data.glygen.org/ln2downloads/cellosaurus/2024_04_02/cellosaurus.txt\n Name: fuzzy_legacy_cph_start_end_positions.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/fuzzy_legacy_cph_start_end_positions.csv\n Name: fuzzy_legacy_human_proteoform_glycosylation_sites_unicarbkb_qin_isoforms.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/fuzzy_legacy_human_proteoform_glycosylation_sites_unicarbkb_qin_isoforms.csv\n Name: fuzzy_legacy_qin_oglanac.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/fuzzy_legacy_qin_oglanac.csv\n Name: fuzzy_simplecell_all_glygen_qc.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/fuzzy_simplecell_all_glygen_qc.csv\n Name: known_33064451_glygen.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/known_33064451_glygen.csv\n Name: known_33167210_glygen.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/known_33167210_glygen.csv\n Name: known_33806155_glygen.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/known_33806155_glygen.csv\n Name: known_34004174_glygen.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/known_34004174_glygen.csv\n Name: known_34106099_glygen.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/known_34106099_glygen.csv\n Name: known_legacy_cph_single_positions.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/known_legacy_cph_single_positions.csv\n Name: known_legacy_dbogap_dbogap2_glygen.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/known_legacy_dbogap_dbogap2_glygen.csv\n Name: known_legacy_human_mouse_rat_glygen.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/known_legacy_human_mouse_rat_glygen.csv\n Name: known_legacy_larsson_xyl.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/known_legacy_larsson_xyl.csv\n Name: known_legacy_reis_gastric_ags.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/known_legacy_reis_gastric_ags.csv\n Name: known_legacy_sarscov2_glygen.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/known_legacy_sarscov2_glygen.csv\n Name: known_unicarbkb_glycomics_study.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/known_unicarbkb_glycomics_study.csv\n Name: mixed_34089345_glygen.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/mixed_34089345_glygen.csv\n Name: unknown_20131323_glygen.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/unknown_20131323_glygen.csv\n Name: unknown_33993882_glygen.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/unknown_33993882_glygen.csv\n Name: unknown_34083726_glygen.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/unknown_34083726_glygen.csv\n Name: unknown_34191522_glygen.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/unknown_34191522_glygen.csv\n Name: unknown_34327564_glygen.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/unknown_34327564_glygen.csv\n Name: unknown_legacy_human_proteoform_glycosylation_sites_unicarbkb_ogalnac_data.csv\n URI: https:/data.glygen.org/ln2downloads/unicarbkb/01_11_2022/unknown_legacy_human_proteoform_glycosylation_sites_unicarbkb_ogalnac_data.csv\n Output Subdomain\n Name: sarscov2_proteoform_glycosylation_sites_unicarbkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/sarscov2_proteoform_glycosylation_sites_unicarbkb.csv\n Name: sarscov2_proteoform_glycosylation_sites_unicarbkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/sarscov2_proteoform_glycosylation_sites_unicarbkb.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: \"3\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"143\"\n Name: \"glycosylation_type\"\n Description: \"Type of glycosylation (N/O/C/S linked glycosylation)\"\n Unique Values: \"2\"\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: \"14\"\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: \"1\"\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: \"3\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"3\"\n Name: \"site_seq\"\n Description: \"\"\n Unique Values: \"6\"\n Name: \"site_type\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"src_file_name\"\n Description: \"\"\n Unique Values: \"4\"\n Name: \"uckb_id\"\n Description: \"\"\n Unique Values: \"76\"\n Name: \"composition\"\n Description: \"Composition of glycan\"\n Unique Values: \"3\"\n Name: \"curation_notes\"\n Description: \"GlycoSuiteDB curation notes\"\n Unique Values: \"39\"\n Name: \"additional_notes\"\n Description: \"\"\n Unique Values: \"21\"\n Name: \"pdb\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"swiss_model\"\n Description: \"SWISS-MODEL ID.\"\n Unique Values: \"2\"\n Name: \"abundance\"\n Description: \" Abundance ratio of the glycan.\"\n Unique Values: \"337\"\n Name: \"source_tissue_id\"\n Description: \"Tissue ID from GlyConnect\"\n Unique Values: \"2\"\n Name: \"source_tissue_name\"\n Description: \"Tissue NAME from GlyConnect\"\n Unique Values: \"2\"\n Name: \"source_cell_line_cellosaurus_id\"\n Description: \"cellosaurus ID of the cell line\"\n Unique Values: \"5\"\n Name: \"source_cell_line_cellosaurus_name\"\n Description: \"\"\n Unique Values: \"5\"\n Name: \"n_sequon\"\n Description: \"\"\n Unique Values: \"16\"\n Name: \"n_sequon_type\"\n Description: \"\"\n Unique Values: \"3\"", "downloadurl": "/ln2data/releases/data/v-2.5.1/reviewed/sarscov2_proteoform_glycosylation_sites_unicarbkb.csv" }