{ "bcoid": "GLY_000479", "title": "Glycosylation Sites - UniCarbKB [SARS CoV 2 proteins]", "description": "List of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or 2019-nCoV) [taxid:2697049] proteins ...", "filename_list": "sarscov2_proteoform_glycosylation_sites_unicarbkb.csv", "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" ], "file_category": [ "glycosylation_sites_" ] }, "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" }, { "type": "string", "label": "isoform_mapping_notes" } ], [ "P0DTC2-1", "61", "Asn", "G59937CP", "N-linked;o-linked", "protein_xref_pubmed", "33064451", "protein_xref_unicarbkb_ds", "GLY_000479", "61", "61", "Asn", "Asn", "N", "known_site", "known_33064451_glygen", "G59937CP", "", "S2P-AC", "The S2P sample was sequentially digested by Asp-N and chymotrypsin.Mass spectrometric data acquisition was performed using a signature ion-triggered EThcD method. MS/MS data were processed using PMiByonic (version 3.7) and PMi-Byologic (version 3.7, Protein Metrics, Inc.). Data were searched using the Protein Metrics 182 human N-glycan library (for proteins expressed in HEK cells) or 38 insect N-glycan library (for proteins expressed in insect cells)", "", "", "", "", "", "", "", "NVT", "NXT", "" ], [ "P0DTC2-1", "61", "Asn", "G59937CP", "N-linked;o-linked", "protein_xref_doi", "10.1021/acs.analchem.0c03301", "protein_xref_unicarbkb_ds", "GLY_000479", "61", "61", "Asn", "Asn", "N", "known_site", "known_33064451_glygen", "G59937CP", "", "S2P-AC", "The S2P sample was sequentially digested by Asp-N and chymotrypsin.Mass spectrometric data acquisition was performed using a signature ion-triggered EThcD method. MS/MS data were processed using PMiByonic (version 3.7) and PMi-Byologic (version 3.7, Protein Metrics, Inc.). Data were searched using the Protein Metrics 182 human N-glycan library (for proteins expressed in HEK cells) or 38 insect N-glycan library (for proteins expressed in insect cells)", "", "", "", "", "", "", "", "NVT", "NXT", "" ] ] }, "readme": "Name\n - Glycosylation Sites - UniCarbKB [SARS CoV 2 proteins]\n\nVersion\n - v-2.12.1\n\nCreated on\n - 2020-04-20T16:02:18.234465\n\nModified on\n - 2024-12-05T19:03:31.064Z\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 Severe acute respiratory syndrome coronavirus 2 (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-2.12.1/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: 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-2.12.1/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-2.12.1/reviewed/sarscov2_proteoform_glycosylation_sites_unicarbkb.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_unicarbkb.csv" }