{
    "bcoid": "GLY_000888",
    "title": "Human Glycosylation Sites (EMBL)",
    "description": "The Human Glycosylation Sites (EMBL) dataset contains glycosylation information (mainly for N-glycosylation) ...",
    "filename_list": "human_proteoform_glycosylation_sites_embl.csv",
    "filename": "human_proteoform_glycosylation_sites_embl.csv",
    "filetype": "csv",
    "categories": {
        "species": [
            "Homo sapiens"
        ],
        "molecule": [
            "Proteoform"
        ],
        "tag": [
            "Glycosylation Sites"
        ],
        "file_type": [
            "csv"
        ],
        "status": [
            "Reviewed"
        ],
        "scope": [
            "internal"
        ],
        "file_category": [
            "glycosylation_sites_"
        ]
    },
    "minitable": {
        "content": [
            [
                "Q5JTV8-1...",
                "399..."
            ],
            [
                "Q13563-1...",
                "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": "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": "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": "source_glycan_type"
                },
                {
                    "type": "string",
                    "label": "source_gene_name"
                },
                {
                    "type": "string",
                    "label": "composition"
                },
                {
                    "type": "string",
                    "label": "composition_mass"
                },
                {
                    "type": "string",
                    "label": "n_sequon"
                },
                {
                    "type": "string",
                    "label": "n_sequon_type"
                },
                {
                    "type": "string",
                    "label": "isoform_mapping_notes"
                }
            ],
            [
                "Q5JTV8-1",
                "399",
                "Asn",
                "G62765YT",
                "N-linked",
                "protein_xref_doi",
                "10.1101/2023.09.13.557529",
                "protein_xref_data_submission",
                "GLY_000888",
                "UBERON:0002113",
                "kidney",
                "CVCL_0063",
                "HEK293T",
                "399",
                "399",
                "Asn",
                "Asn",
                "HLNSSHPR",
                "high mannose",
                "TOR1AIP1",
                "HexNAc(2)Hex(8)",
                "1702.5814",
                "NSS",
                "NXS",
                ""
            ],
            [
                "Q13563-1",
                "305",
                "Asn",
                "G63332OE",
                "N-linked",
                "protein_xref_doi",
                "10.1101/2023.09.13.557529",
                "protein_xref_data_submission",
                "GLY_000888",
                "UBERON:0002113",
                "kidney",
                "CVCL_0063",
                "HEK293T",
                "305",
                "305",
                "Asn",
                "Asn",
                "MQPSNQTEADNR",
                "sialylated",
                "PKD2",
                "HexNAc(6)Hex(8)NeuAc(2)",
                "3097.0898",
                "NRS",
                "NXS",
                ""
            ]
        ]
    },
    "readme": "Name\n   - Human Glycosylation Sites (EMBL)\n\nVersion\n   - v-2.12.1\n\nModified on\n   - 2024-05-21T13:23:51.724Z\n\nCreated by\n   - Jeet Vora [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Robel Kahsay [rykahsay@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   - Clement Potel [clement.potel@embl.de], Mira Burtscher [mira.burtscher@embl.de], Martin Garrido [martin.garrido@embl.de]\n\nChecksum\n   - \n\nUsability Domain\n   - The Human Glycosylation Sites (EMBL) dataset contains glycosylation information (mainly for N-glycosylation) on Homo sapiens (taxid:9606) cell line (HelaK and HEK293T) proteins. The data is submitted by Dr. Clement Potel, Dr. Mira Burtscher and Dr. Martin Garrido, of the Genome Biology Unit, EMBL based on the publication 'Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome.' GlyTouCan accessions were mapped by the GlyGen team to the glycan compositions provided by the authors. If you use this dataset please provide proper attribution to the data source [1], EMBL and GlyGen.\n   - References: 1) Potel C, Burtscher ML, Garrido-Rodriguez M, Brauer-Nikonow A, Becher I, Typas A, Zimmermann M, Savitski M. Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome. bioRxiv 2023.09.13.557529; doi:10.1101/2023.09.13.557529.\n\nDescription Domain\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: glygen_upload.csv\n      URI: https:/data.glygen.org/ln2downloads/embl/2024_02_09/glygen_upload.csv\n      Name: names.tsv\n      URI: https:/data.glygen.org/ln2downloads/glytoucan/2026_07_27/export/names.tsv\n   Output Subdomain\n      Name: human_proteoform_glycosylation_sites_embl.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/human_proteoform_glycosylation_sites_embl.csv\n      Name: human_proteoform_glycosylation_sites_embl.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/human_proteoform_glycosylation_sites_embl.stat.csv\n\nFields\n      Name: \"uniprotkb_canonical_ac\"\"\n     Description: \"\"\n      Unique Values: \"2751\"",
    "downloadurl": "/ln2data/releases/data/v-2.12.1/reviewed/human_proteoform_glycosylation_sites_embl.csv"
}