{
    "bcoid": "GLY_000460",
    "title": "Mouse Germline Mutation",
    "description": "The Mouse Germline Mutation dataset contains Mus musculus [taxid:10090] germline mutation data from EBI ...",
    "filename_list": "mouse_protein_mutation_germline.csv",
    "filename": "mouse_protein_mutation_germline.csv",
    "filetype": "csv",
    "categories": {
        "species": [
            "Mus musculus"
        ],
        "molecule": [
            "Protein"
        ],
        "tag": [
            "Germline Mutations"
        ],
        "file_type": [
            "csv"
        ],
        "status": [
            "Reviewed"
        ],
        "scope": [
            "internal"
        ],
        "file_category": [
            "mutation_"
        ]
    },
    "minitable": {
        "content": [
            [
                "Q9R0X5-1...",
                "394..."
            ],
            [
                "Q9R0X5-1...",
                "394..."
            ]
        ],
        "headers": [
            "uniprotkb_ca...",
            "aa_pos..."
        ],
        "colwidth": [
            "40%",
            "20%"
        ]
    },
    "sampledata": {
        "type": "table",
        "data": [
            [
                {
                    "type": "string",
                    "label": "uniprotkb_canonical_ac"
                },
                {
                    "type": "string",
                    "label": "aa_pos"
                },
                {
                    "type": "string",
                    "label": "dbsnp_id"
                },
                {
                    "type": "string",
                    "label": "cosmic_id"
                },
                {
                    "type": "string",
                    "label": "description"
                },
                {
                    "type": "string",
                    "label": "cytogenic_band"
                },
                {
                    "type": "string",
                    "label": "chr_id"
                },
                {
                    "type": "string",
                    "label": "chr_pos"
                },
                {
                    "type": "string",
                    "label": "ref_nt"
                },
                {
                    "type": "string",
                    "label": "alt_nt"
                },
                {
                    "type": "string",
                    "label": "ref_aa"
                },
                {
                    "type": "string",
                    "label": "alt_aa"
                },
                {
                    "type": "string",
                    "label": "begin_aa_pos"
                },
                {
                    "type": "string",
                    "label": "end_aa_pos"
                },
                {
                    "type": "string",
                    "label": "minor_allelic_frequency"
                },
                {
                    "type": "string",
                    "label": "mutation_type"
                },
                {
                    "type": "string",
                    "label": "polyphen_score"
                },
                {
                    "type": "string",
                    "label": "polyphen_prediction"
                },
                {
                    "type": "string",
                    "label": "sift_score"
                },
                {
                    "type": "string",
                    "label": "sift_prediction"
                },
                {
                    "type": "string",
                    "label": "somatic_status"
                },
                {
                    "type": "string",
                    "label": "disease"
                },
                {
                    "type": "string",
                    "label": "disease_description"
                },
                {
                    "type": "string",
                    "label": "disease_xrefs"
                },
                {
                    "type": "string",
                    "label": "xref_key"
                },
                {
                    "type": "string",
                    "label": "xref_id"
                },
                {
                    "type": "string",
                    "label": "mim_id"
                },
                {
                    "type": "string",
                    "label": "do_id"
                },
                {
                    "type": "string",
                    "label": "filter_flags"
                },
                {
                    "type": "string",
                    "label": "glyco_annotation"
                },
                {
                    "type": "string",
                    "label": "protein_class"
                }
            ],
            [
                "Q9R0X5-1",
                "394",
                "rs229541962",
                "",
                "",
                "Xq",
                "X",
                "10062273",
                "T",
                "null",
                "D",
                "N",
                "394",
                "394",
                "",
                "missense",
                "",
                "",
                "0.27",
                "tolerated",
                "0",
                "",
                "",
                "",
                "protein_xref_dbsnp",
                "rs229541962",
                "",
                "",
                "Germline mutation passed 1 filters: n-glyco-sequon-gain (DLS->NLS).",
                "glycancount:0, pmidcount:0",
                "none"
            ],
            [
                "Q9R0X5-1",
                "394",
                "rs229541962",
                "",
                "",
                "Xq",
                "X",
                "10062273",
                "T",
                "null",
                "D",
                "N",
                "394",
                "394",
                "",
                "missense",
                "",
                "",
                "0.27",
                "tolerated",
                "0",
                "",
                "",
                "",
                "protein_xref_eva",
                "rs229541962",
                "",
                "",
                "Germline mutation passed 1 filters: n-glyco-sequon-gain (DLS->NLS).",
                "glycancount:0, pmidcount:0",
                "none"
            ]
        ]
    },
    "readme": "Name\n   - Mouse Germline Mutation\n\nVersion\n   - v-2.12.1\n\nCreated on\n  - 2020-04-03T17:22:53.520266\n\nModified on\n   - 2024-06-03T20:59:24.013Z\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   - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n   - \n\nUsability Domain\n   - The Mouse Germline Mutation dataset contains Mus musculus [taxid:10090] germline mutation data from EBI Variant Data API. Only nonsynonymous single-nucleotide variations (nsSNVs) germline mutations are integrated. If you use this dataset provide proper attribution to GlyGen and EBI-EMBL-UniProtKB.\n\nDescription Domain\n   Keywords\n   - single-nucleotide variations (nsSNVs)\n   - germline mutations\n   - dbSNP\n   - disease\n   - ClinVar\n\n   Pipeline Steps\n   - Step-1: The script extracts the gernline (somatic_staus = 0) mutation data from the input file and maps the UniProtKB accession to the UniProtKB canonical accessions\n\nExecution Domain\n   Scripts   - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-protein-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: glycan_masterlist.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/glycan_masterlist.csv\n      Name: mouse_protein_gene_groups.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/mouse_protein_gene_groups.csv\n      Name: protein_disease_idmap.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/protein_disease_idmap.csv\n      Name: aadict.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/misc/aadict.csv\n      Name: dbSNP-mus-musculus.tsv\n      URI: https:/data.glygen.org/ln2downloads/ebi/2026_01_31/dbSNP-mus-musculus.tsv\n   Output Subdomain\n      Name: mouse_protein_mutation_germline.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/mouse_protein_mutation_germline.csv\n      Name: mouse_protein_mutation_germline.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/mouse_protein_mutation_germline.stat.csv\n\nFields\n      Name: \"uniprotkb_canonical_ac\"\"\n     Description: \"\"\n      Unique Values: \"4588\"",
    "downloadurl": "/ln2data/releases/data/v-2.12.1/reviewed/mouse_protein_mutation_germline.csv"
}