{ "bcoid": "GLY_000628", "title": "SARS-CoV1 Glycosylation Sites (UniCarbKB)", "description": "This is a SARS-CoV-1 Glycosylation Sites (UniCarbKB) dataset. It contains a list of Severe acute respiratory ...", "filename_list": "sarscov1_proteoform_glycosylation_sites_unicarbkb.csv", "filename": "sarscov1_proteoform_glycosylation_sites_unicarbkb.csv", "filetype": "csv", "categories": { "status": [ "Reviewed" ], "molecule": [ "Proteoform" ], "species": [ "Severe acute respiratory syndrome-related coronavirus" ], "tag": [ "UniCarbKB glycosylation sites" ], "file_type": [ "csv" ], "scope": [ "internal" ], "file_category": [ "glycosylation_sites_" ] }, "minitable": { "content": [ [ "P59594-1...", "589..." ], [ "P59594-1...", "589..." ] ], "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" } ], [ "P59594-1", "589", "Asn", "G20956ZV", "N-linked;o-linked", "protein_xref_pubmed", "33064451", "protein_xref_unicarbkb_ds", "GLY_000628", "589", "589", "Asn", "Asn", "N", "known_site", "known_33064451_glygen", "G20956ZV", "", "SN-AC", "The SN 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)", "", "", "", "", "", "", "", "NAS", "NXS", "" ], [ "P59594-1", "589", "Asn", "G20956ZV", "N-linked;o-linked", "protein_xref_doi", "10.1021/acs.analchem.0c03301", "protein_xref_unicarbkb_ds", "GLY_000628", "589", "589", "Asn", "Asn", "N", "known_site", "known_33064451_glygen", "G20956ZV", "", "SN-AC", "The SN 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)", "", "", "", "", "", "", "", "NAS", "NXS", "" ] ] }, "readme": "Name\n - SARS-CoV1 Glycosylation Sites (UniCarbKB)\n\nVersion\n - v-2.12.1\n\nCreated on\n - 2022-03-31T15:05:49.377202\n\nModified on\n - 2024-12-05T19:05:06.063Z\n\nCreated by\n - Karina Martinez [karinamartinez@gwu.edu], Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@email.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]\n\nChecksum\n - \n\nUsability Domain\n - This is a SARS-CoV-1 Glycosylation Sites (UniCarbKB) dataset. It contains a list of Severe acute respiratory syndrome-related coronavirus (SARS-CoV-1) [taxonomy:694009] proteins with information on glycosylation sites and associated glycans (if available) from UniCarbKB. The listed proteins (UniProtKB accession) are part of the GlyGen UniProtKB SARS CoV1 Proteome Masterlist (https://data.glygen.org/GLY_000467). If you use this dataset, please provide proper attribution to UniCarbKB, EMBL-EBI-UniProtKB, and GlyGen. Cite: PMID:24234447, PMID:33237286, and PMID:31616925. This dataset can be used for obtaining a list of glycosylation sites for canonical glycoproteins from the UnicarbKB database.\n\nDescription Domain\n Keywords\n - proteins\n - canonical\n - glycosylation sites\n - glycan\n - UniCarbKB\n - GlyTouCan\n\n Pipeline Steps\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: sarscov1_proteoform_glycosylation_sites_unicarbkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/sarscov1_proteoform_glycosylation_sites_unicarbkb.csv\n Name: sarscov1_proteoform_glycosylation_sites_unicarbkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/sarscov1_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/sarscov1_proteoform_glycosylation_sites_unicarbkb.csv" }