{
    "bcoid": "GLY_000024",
    "title": "Human Cancer Mutation",
    "description": "The Human Cancer Mutation dataset contains human [taxid:9606] mutation data from BioMuta database (https://hive.biochemistry.gwu.edu/biomuta). ...",
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                "2394",
                "DOID:2394 / ovarian cancer"
            ],
            [
                "P19320-1",
                "355",
                "L",
                "V",
                "1",
                "101194797",
                "C",
                "G",
                "1",
                "38",
                "0.0263",
                "icgc",
                "1324",
                "DOID:1324 / lung cancer"
            ],
            [
                "P19320-1",
                "402",
                "S",
                "T",
                "1",
                "101194938",
                "T",
                "A",
                "1",
                "50",
                "0.0200",
                "icgc",
                "1781",
                "DOID:1781 / thyroid cancer"
            ],
            [
                "P19320-1",
                "493",
                "E",
                "Q",
                "1",
                "101197026",
                "G",
                "C",
                "1",
                "44",
                "0.0227",
                "icgc",
                "11934",
                "DOID:11934 / head and neck cancer"
            ],
            [
                "P19320-1",
                "542",
                "P",
                "L",
                "1",
                "101198073",
                "C",
                "T",
                "1",
                "94",
                "0.0106",
                "icgc",
                "9256",
                "DOID:9256 / colorectal cancer"
            ],
            [
                "P19320-1",
                "664",
                "G",
                "E",
                "1",
                "101200256",
                "G",
                "A",
                "1",
                "66",
                "0.0152",
                "icgc",
                "1324",
                "DOID:1324 / lung cancer"
            ],
            [
                "Q9UBQ6-1",
                "187",
                "S",
                "*",
                "1",
                "101339931",
                "G",
                "C",
                "1",
                "72",
                "0.0139",
                "icgc",
                "1612",
                "DOID:1612 / breast cancer"
            ],
            [
                "Q8NEW0-1",
                "243",
                "A",
                "E",
                "1",
                "101387283",
                "C",
                "A",
                "1",
                "50",
                "0.0200",
                "icgc",
                "1781",
                "DOID:1781 / thyroid cancer"
            ],
            [
                "Q8NEW0-1",
                "255",
                "A",
                "T",
                "1",
                "101387318",
                "G",
                "A",
                "1",
                "50",
                "0.0200",
                "icgc",
                "1781",
                "DOID:1781 / thyroid cancer"
            ],
            [
                "Q9H2P9-1",
                "207",
                "R",
                "Q",
                "1",
                "101458207",
                "C",
                "T",
                "1",
                "50",
                "0.0200",
                "icgc",
                "1612",
                "DOID:1612 / breast cancer"
            ],
            [
                "Q9H2P9-1",
                "207",
                "R",
                "*",
                "1",
                "101458208",
                "G",
                "A",
                "1",
                "94",
                "0.0106",
                "icgc",
                "9256",
                "DOID:9256 / colorectal cancer"
            ],
            [
                "Q9H2P9-1",
                "205",
                "R",
                "I",
                "1",
                "101458213",
                "C",
                "A",
                "1",
                "94",
                "0.0106",
                "icgc",
                "9256",
                "DOID:9256 / colorectal cancer"
            ],
            [
                "Q9H2P9-1",
                "180",
                "K",
                "N",
                "1",
                "101458287",
                "C",
                "A",
                "1",
                "94",
                "0.0106",
                "icgc",
                "9256",
                "DOID:9256 / colorectal cancer"
            ],
            [
                "Q9H2P9-1",
                "177",
                "K",
                "E",
                "1",
                "101460667",
                "T",
                "C",
                "1",
                "50",
                "0.0200",
                "icgc",
                "1612",
                "DOID:1612 / breast cancer"
            ],
            [
                "Q9H2P9-1",
                "154",
                "Q",
                "L",
                "1",
                "101467052",
                "T",
                "A",
                "1",
                "50",
                "0.0200",
                "icgc",
                "1781",
                "DOID:1781 / thyroid cancer"
            ],
            [
                "O95155-1",
                "90",
                "S",
                "P",
                "1",
                "10155575",
                "T",
                "C",
                "1",
                "50",
                "0.0200",
                "icgc",
                "1781",
                "DOID:1781 / thyroid cancer"
            ],
            [
                "O95155-1",
                "117",
                "M",
                "I",
                "1",
                "10161169",
                "G",
                "T",
                "1",
                "50",
                "0.0200",
                "icgc",
                "1781",
                "DOID:1781 / thyroid cancer"
            ],
            [
                "O95155-1",
                "146",
                "E",
                "*",
                "1",
                "10163006",
                "G",
                "T",
                "1",
                "50",
                "0.0200",
                "icgc",
                "1781",
                "DOID:1781 / thyroid cancer"
            ]
        ]
    },
    "readme": "Name\n   - Human Cancer Mutation\n\nVersion\n   - 1.5.12\n\nCreated on\n  - 2019-01-23T17:21:05.891293\n\nModified on\n   - 2019-11-28T10:58:39.643598\n\nCreated by\n   - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@email.gwu.edu]\n\nAuthors\n   - \n\nChecksum\n   - \n\nUsability Domain\n   - The Human Cancer Mutation dataset contains human [taxid:9606] mutation data from BioMuta database (https://hive.biochemistry.gwu.edu/biomuta). The current version of BioMuta contains only nonsynonymous single-nucleotide variations (nsSNVs) associated with cancer. BioMuta is a single-nucleotide variation (SNV) and disease association database where variations are mapped to genomes and NCBI RefSeq nucleotide entries, and unified through UniProtKB/Swiss-Prot positional coordinates. The dataset is imported and contributed by BioMuta and processed by GlyGen. If you use this dataset please provide proper attribution to BioMuta and GlyGen. Note GlyGen only integrates and displays the data that has cancer mutation frequency of greater than of 0.01(1%)\n\nDescription Domain\n   Keywords\n   - single-nucleotide variations (nsSNVs)\n   - cancer mutations\n   - BioMuta\n   - disease\n\n   Pipeline Steps\n   - Step-1: The script extracts the mutation data that has cancer mutation frequency of greater than of 0.01(1%) and maps the UniProtKB accession to the UniProtKB canonical accessions\n\nExecution Domain\n   Scripts   - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/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: mutid-map.final.csv\n      URI: https://data.glygen.org/ln2data/releases/data/v-1.5.12/source/mutid-map.final.csv\n      Name: human_protein_masterlist.csv\n      URI: https://data.glygen.org/ln2data/releases/data/v-1.5.12/reviewed/human_protein_masterlist.csv\n   Output Subdomain\n      Name: human_protein_mutation.csv\n      URI: https://data.glygen.org/ln2data/releases/data/v-1.5.12/reviewed/human_protein_mutation.csv\n      Name: human_protein_mutation.stat.csv\n      URI: https://data.glygen.org/ln2data/releases/data/v-1.5.12/reviewed/human_protein_mutation.stat.csv\n\nFields\n      Name: \"do_id\"\n     Description: \"\"\n      Unique Values: \"21\"\n      Name: \"uniprotkb_canonical_ac\"\n     Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n      Unique Values: \"17178\"\n      Name: \"data_source\"\n     Description: \"\"\n      Unique Values: \"2\"\n      Name: \"alt_nt\"\n     Description: \"\"\n      Unique Values: \"4\"\n      Name: \"patients_positive\"\n     Description: \"\"\n      Unique Values: \"62\"\n      Name: \"chromosome_id\"\n     Description: \"\"\n      Unique Values: \"24\"\n      Name: \"ref_nt\"\n     Description: \"\"\n      Unique Values: \"4\"\n      Name: \"chr_pos\"\n     Description: \"\"\n      Unique Values: \"126501\"\n      Name: \"aa_pos\"\n     Description: \"Position of the amino acid in canonical sequence of protein in the UniProtKB database\"\n      Unique Values: \"4633\"\n      Name: \"alt_aa\"\n     Description: \"Altered amino acid residue\"\n      Unique Values: \"21\"\n      Name: \"ref_aa\"\n     Description: \"Reference amino acid residue\"\n      Unique Values: \"20\"\n      Name: \"mut_freq\"\n     Description: \"Frequency count of mutations across datasets\"\n      Unique Values: \"340\"\n      Name: \"do_name\"\n     Description: \"\"\n      Unique Values: \"21\"\n      Name: \"patients_tested\"\n     Description: \"\"\n      Unique Values: \"64\"",
    "downloadurl": "/ln2data/releases/data/v-1.5.12/reviewed/human_protein_mutation.csv"
}