{ "bcoid": "GLY_000143", "title": "Human Protein Glycosylation (Literature)", "description": "The dataset provides information on N-glycosylation sites on Human proteins. The data has been processed ...", "filename_list": "human_proteoform_glycosylation_sites_literature.csv", "filename": "human_proteoform_glycosylation_sites_literature.csv", "filetype": "csv", "categories": { "species": [ "Homo sapiens" ], "molecule": [ "Proteoform" ], "tag": [ "UniCarbKB publications" ], "status": [ "Reviewed" ], "file_type": [ "csv" ], "scope": [ "internal" ], "file_category": [ "glycosylation_sites_" ] }, "minitable": { "content": [ [ "O60911-1...", "221..." ], [ "Q08174-1...", "305..." ] ], "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": "uniprotkb_ac" }, { "type": "string", "label": "evidence" }, { "type": "string", "label": "n_sequon" }, { "type": "string", "label": "n_sequon_type" }, { "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": "isoform_mapping_notes" } ], [ "O60911-1", "221", "Asn", "", "N-linked", "protein_xref_pubmed", "23090970", "protein_xref_glygen_ds", "GLY_000143", "O60911", "23090970", "NDT", "NXT", "221", "221", "Asn", "Asn", "N", "" ], [ "Q08174-1", "305", "Asn", "", "N-linked", "protein_xref_pubmed", "23090970", "protein_xref_glygen_ds", "GLY_000143", "Q08174-1", "23090970", "NDS", "NXS", "305", "305", "Asn", "Asn", "N", "" ] ] }, "readme": "Name\n - Human Protein Glycosylation (Literature)\n\nVersion\n - v-2.12.1\n\nCreated on\n - 2019-06-14T14:54:26.195339\n\nModified on\n - 2024-12-10T16:47:37.700Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@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 - Not Applicable []\n\nChecksum\n - \n\nUsability Domain\n - The dataset provides information on N-glycosylation sites on Human proteins. The data has been processed from the supplementary material from 2 publications (1. \"Deeb, S. J., Cox, J., Schmidt-Supprian, M., & Mann, M. (2013). N-linked Glycosylation Enrichment for In-depth Cell Surface Proteomics of Diffuse Large B-cell Lymphoma Subtypes. Molecular & Cellular Proteomics, 13(1), 240-251. doi:10.1074/mcp.m113.033977\" 2. \"Boersema, P. J., Geiger, T., Winiewski, J. R., & Mann, M. (2012). Quantification of the N-glycosylated Secretome by Super-SILAC During Breast Cancer Progression and in Human Blood Samples. Molecular & Cellular Proteomics, 12(1), 158-171. doi:10.1074/mcp.m112.023614\"). The listed proteins (UniProtKB) accessions are part of the GlyGen UniProtKB canonical list (https://data.glygen.org/GLY_000001). \n\nDescription Domain\n Keywords\n - proteins\n - canonical\n - glycosylation\n - literature\n - publications\n\n Pipeline Steps\n - Step-1: The supplementary tables from two publications were downloaded and columns \"protein\" and \"site\" were extracted, and additional column evidence where values=\"the respective PMIDs\" was added to produce the input files. A python script was developed process input files 1. to map the UniProtKB accessions to UniProtKB canonical accessions 2. Check position+amino acid with the canonical fasta sequences (https://data.glygen.org/GLY_000002) to generate the output files.\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: glycosylation_sites_lit_23090970_s2.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/compiled/glycosylation_sites_lit_23090970_s2.csv\n Name: glycosylation_sites_lit_23090970_s5.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/compiled/glycosylation_sites_lit_23090970_s5.csv\n Name: glycosylation_sites_lit_24190977_s5.cs\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/compiled/glycosylation_sites_lit_24190977_s5.cs\n Name: glycosylation_sites_lit_x_sx.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/compiled/glycosylation_sites_lit_x_sx.csv\n Name: hcv1a_proteoform_glycosylation_sites_literature.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/compiled/hcv1a_proteoform_glycosylation_sites_literature.csv\n Name: sarscov1_proteoform_glycosylation_sites_literature.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/compiled/sarscov1_proteoform_glycosylation_sites_literature.csv\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 Output Subdomain\n Name: human_proteoform_glycosylation_sites_literature.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/human_proteoform_glycosylation_sites_literature.csv\n Name: human_proteoform_glycosylation_sites_literature.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/human_proteoform_glycosylation_sites_literature.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\"\n Description: \"\"\n Unique Values: \"1330\"", "downloadurl": "/ln2data/releases/data/v-2.12.1/reviewed/human_proteoform_glycosylation_sites_literature.csv" }