{ "bcoid": "GLY_000221", "title": "Glycosylation sites - UniCarbKB [Rat proteins]", "description": "List of Rattus norvegicus [taxid:10116] proteins with information on glycosylation sites and associated ...", "filename_list": "rat_proteoform_glycosylation_sites_unicarbkb.csv", "filename": "rat_proteoform_glycosylation_sites_unicarbkb.csv", "filetype": "csv", "categories": { "status": [ "Reviewed" ], "molecule": [ "Proteoform" ], "species": [ "Rattus norvegicus" ], "tag": [ "UniCarbKB glycosylation sites" ], "file_type": [ "csv" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P06687-1...", "473..." ], [ "P06687-1...", "473..." ] ], "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" } ], [ "P06687-1", "473", "Asn", "G45504EY", "N-linked;o-linked", "protein_xref_pubmed", "34106099", "protein_xref_unicarbkb_ds", "GLY_000221", "473", "473", "Asn", "Asn", "N", "known_site", "known_34106099_glygen", "G45504EY", "HexNAc4Hex4dHex0NeuAc1NeuGc0Pent0S0P0KDN0HexA0", "", "467", "", "", "", "OMIT:0014437", "Synaptosomes", "", "", "NST", "NXT" ], [ "P06687-1", "473", "Asn", "G45504EY", "N-linked;o-linked", "protein_xref_doi", "10.1039/D0MO00044B", "protein_xref_unicarbkb_ds", "GLY_000221", "473", "473", "Asn", "Asn", "N", "known_site", "known_34106099_glygen", "G45504EY", "HexNAc4Hex4dHex0NeuAc1NeuGc0Pent0S0P0KDN0HexA0", "", "467", "", "", "", "OMIT:0014437", "Synaptosomes", "", "", "NST", "NXT" ] ] }, "readme": "Name\n - Glycosylation sites - UniCarbKB [Rat proteins]\n\nVersion\n - v-2.10.1\n\nCreated on\n - 2019-09-05T14:34:59.005886\n\nModified on\n - 2024-12-05T19:02:39.985Z\n\nCreated by\n - Jeet Vora [jeetvora@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], Robel Kahsay [rykahsay@email.gwu.edu], Nathan Edwards [Georgetown University]\n\nChecksum\n - \n\nUsability Domain\n - List of Rattus norvegicus [taxid:10116] 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/GLYDS000244).\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-2.10.1/misc/n_sequon_info.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/misc/sample_mapping.csv\n Name: cellosaurus.txt\n URI: https:/data.glygen.org/ln2downloads/cellosaurus/2025_09_18/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: rat_proteoform_glycosylation_sites_unicarbkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/rat_proteoform_glycosylation_sites_unicarbkb.csv\n Name: rat_proteoform_glycosylation_sites_unicarbkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/rat_proteoform_glycosylation_sites_unicarbkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"160\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"249\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"2\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"178\"\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: \"9\"\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: \"249\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"249\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"site_seq\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"site_type\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"src_file_name\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"uckb_id\"\n Description: \"\"\n Unique Values: \"127\"\n Name: \"composition\"\n Description: \"Composition of glycan\"\n Unique Values: \"130\"\n Name: \"curation_notes\"\n Description: \"GlycoSuiteDB curation notes\"\n Unique Values: \"256\"\n Name: \"additional_notes\"\n Description: \"\"\n Unique Values: \"84\"\n Name: \"pdb\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"swiss_model\"\n Description: \"SWISS-MODEL ID.\"\n Unique Values: \"1\"\n Name: \"abundance\"\n Description: \" Abundance ratio of the glycan.\"\n Unique Values: \"1\"\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: \"1\"\n Name: \"source_cell_line_cellosaurus_name\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"n_sequon\"\n Description: \"\"\n Unique Values: \"39\"\n Name: \"n_sequon_type\"\n Description: \"\"\n Unique Values: \"4\"", "downloadurl": "/ln2data/releases/data/v-2.10.1/reviewed/rat_proteoform_glycosylation_sites_unicarbkb.csv" }