{
    "bcoid": "GLY_000024",
    "title": "Human Cancer Mutation",
    "description": "The Human Cancer Mutation dataset contains Homo sapiens [taxid:9606] mutation data from the BioMuta database ...",
    "filename_list": "human_protein_mutation_cancer.csv",
    "filename": "human_protein_mutation_cancer.csv",
    "filetype": "csv",
    "categories": {
        "species": [
            "Homo sapiens"
        ],
        "molecule": [
            "Protein"
        ],
        "tag": [
            "Somatic Cancer Mutations"
        ],
        "file_type": [
            "csv"
        ],
        "status": [
            "Reviewed"
        ],
        "scope": [
            "internal"
        ]
    },
    "minitable": {
        "content": [
            [
                "O14497-1...",
                "2087..."
            ],
            [
                "P46531-1...",
                "1636..."
            ]
        ],
        "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": "ref_aa"
                },
                {
                    "type": "string",
                    "label": "alt_aa"
                },
                {
                    "type": "string",
                    "label": "chr_id"
                },
                {
                    "type": "string",
                    "label": "chr_start_pos"
                },
                {
                    "type": "string",
                    "label": "chr_end_pos"
                },
                {
                    "type": "string",
                    "label": "ref_nt"
                },
                {
                    "type": "string",
                    "label": "alt_nt"
                },
                {
                    "type": "string",
                    "label": "patients_positive"
                },
                {
                    "type": "string",
                    "label": "patients_tested"
                },
                {
                    "type": "string",
                    "label": "mut_freq"
                },
                {
                    "type": "string",
                    "label": "data_source"
                },
                {
                    "type": "string",
                    "label": "do_id"
                },
                {
                    "type": "string",
                    "label": "do_name"
                },
                {
                    "type": "string",
                    "label": "xref_key"
                },
                {
                    "type": "string",
                    "label": "xref_id"
                },
                {
                    "type": "string",
                    "label": "filter_flags"
                },
                {
                    "type": "string",
                    "label": "glyco_annotation"
                },
                {
                    "type": "string",
                    "label": "mim_id"
                },
                {
                    "type": "string",
                    "label": "somatic_status"
                },
                {
                    "type": "string",
                    "label": "minor_allelic_frequency"
                }
            ],
            [
                "O14497-1",
                "2087",
                "G",
                "R",
                "1",
                "26780157",
                "26780157",
                "G",
                "A",
                "1",
                "2617",
                "0.0",
                "cbioportal",
                "1793",
                "DOID:1793 / pancreatic cancer",
                "protein_xref_biomuta",
                "O14497",
                "Somatic mutation passed 1 out of 6 filters: num. of cancers (11).",
                "glycancount:0, pmidcount:0",
                "",
                "1",
                ""
            ],
            [
                "P46531-1",
                "1636",
                "E",
                "K",
                "9",
                "136504785",
                "136504785",
                "C",
                "T",
                "2",
                "4484",
                "0.0",
                "cbioportal",
                "1612",
                "DOID:1612 / breast cancer",
                "protein_xref_biomuta",
                "P46531",
                "Somatic mutation passed 1 out of 6 filters: num. of cancers (5).",
                "glycancount:0, pmidcount:0",
                "",
                "1",
                ""
            ]
        ]
    },
    "readme": "Name\n   - Human Cancer Mutation\n\nVersion\n   - v-2.9.1\n\nCreated on\n  - 2019-01-23T17:21:05.891293\n\nModified on\n   - 2025-03-12T04:24:06.339Z\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], Mariia Kim [maria.kim@gwu.edu]\n\nAuthors\n   - \n\nChecksum\n   - \n\nUsability Domain\n   - The Human Cancer Mutation dataset contains Homo sapiens [taxid:9606] mutation data from the BioMuta database (https://hive.biochemistry.gwu.edu/biomuta). The BioMuta pipeline documentation can be found on the HIVE Lab Wiki: https://hivelab.biochemistry.gwu.edu/wiki/BioMuta_pipeline_README.\n   - The current version of BioMuta contains only nonsynonymous single-nucleotide variations (nsSNVs) associated with cancer.\n   - 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.\n   - 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.\n   - Note that the mutations shown in GlyGen are annotated based on passing of one or more filter criteria.\n   - Filter criterion 1 - Positive Patients Frequency Ratio \u2265 1.0%\n   - Filter criterion 2 - Presence of mutation in \u2265 3 cancer types\n   - Filter criterion 3 - Positive Patients count \u2265 10 patients\n   - Filter criterion 4 - Mutation reported and annotated in number of databases\n   - Filter criterion 5 - Mutation mined from literature using literaure mining tools (human_protein_mutation_literature.csv)\n   - If there is also a germline mutation reported in dbSNP, the rsid is also shown\n   - These filter criteria annotations are shown on the front end under the column Annotation Name\n   - Two different DO child terms are merged into one single entry showing the parent cancer DO term from the DO cancer slim.\n   - On the GlyGen interface in the Mutations section, the mutations that have passed the highest number of filter criteria are displayed first irrespective of their amio acid positions. E.g. the mutation entry that has passed 5 filter criteria will be shown first.\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 from the BioMuta and maps the UniProtKB accession to the UniProtKB canonical accessions as per the criterias\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-2.9.1/reviewed/glycan_masterlist.csv\n      Name: human_protein_masterlist.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/human_protein_masterlist.csv\n      Name: human_protein_mutation_literature.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/human_protein_mutation_literature.csv\n      Name: protein_disease_idmap.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/protein_disease_idmap.csv\n      Name: aadict.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/misc/aadict.csv\n      Name: biomuta.csv\n      URI: https:/data.glygen.org/ln2downloads/biomuta/2025_05_27/biomuta.csv\n      Name: clinical_information.csv\n      URI: https:/data.glygen.org/ln2downloads/biomuta/2025_05_27/clinical_information.csv\n      Name: dbSNP-homo-sapiens.tsv\n      URI: https:/data.glygen.org/ln2downloads/ebi/2025_05_20/dbSNP-homo-sapiens.tsv\n   Output Subdomain\n      Name: human_protein_mutation_cancer.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/human_protein_mutation_cancer.csv\n      Name: human_protein_mutation_cancer.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/human_protein_mutation_cancer.stat.csv\n\nFields\n      Name: \"uniprotkb_canonical_ac\"\n     Description: \"\"\n      Unique Values: \"16740\"\n      Name: \"aa_pos\"\n     Description: \"Position of the amino acid in canonical sequence of protein in the UniProtKB database\"\n      Unique Values: \"5354\"\n      Name: \"ref_aa\"\n     Description: \"Reference amino acid residue\"\n      Unique Values: \"20\"\n      Name: \"alt_aa\"\n     Description: \"Altered amino acid residue\"\n      Unique Values: \"21\"\n      Name: \"chr_id\"\n     Description: \"\"\n      Unique Values: \"24\"\n      Name: \"chr_start_pos\"\n     Description: \"\"\n      Unique Values: \"154484\"\n      Name: \"chr_end_pos\"\n     Description: \"\"\n      Unique Values: \"154484\"\n      Name: \"ref_nt\"\n     Description: \"Reference nucleotide\"\n      Unique Values: \"4\"\n      Name: \"alt_nt\"\n     Description: \"Alternative nucleotide\"\n      Unique Values: \"4\"\n      Name: \"patients_positive\"\n     Description: \"The number of the patients having the cancer mutation\"\n      Unique Values: \"146\"\n      Name: \"patients_tested\"\n     Description: \"The total number of patients tested for the given cancer mutation\"\n      Unique Values: \"21\"\n      Name: \"mut_freq\"\n     Description: \"Frequency count of mutations across datasets\"\n      Unique Values: \"96\"\n      Name: \"data_source\"\n     Description: \"The source database for the data\"\n      Unique Values: \"2\"\n      Name: \"do_id\"\n     Description: \"Disease Ontology identifier\"\n      Unique Values: \"19\"\n      Name: \"do_name\"\n     Description: \"Disease Ontology term or name for the disease assigned to the Disease Ontology identifier\"\n      Unique Values: \"19\"\n      Name: \"xref_key\"\n     Description: \"Source key associated to the  xref_id\"\n      Unique Values: \"1\"\n      Name: \"xref_id\"\n     Description: \"ID of the X-ref\"\n      Unique Values: \"16740\"\n      Name: \"filter_flags\"\n     Description: \"Filter tags/flags assigned to the mutation entries that have passed the mutation filter criteria\"\n      Unique Values: \"3486\"\n      Name: \"glyco_annotation\"\n     Description: \"\"\n      Unique Values: \"340\"\n      Name: \"mim_id\"\n     Description: \"Disease ID from the OMIM database\"\n      Unique Values: \"1\"\n      Name: \"somatic_status\"\n     Description: \"The status of the variant whether it is germline (somatic status =0) or somatic (somatic status =1) variant\"\n      Unique Values: \"1\"\n      Name: \"minor_allelic_frequency\"\n     Description: \"\"\n      Unique Values: \"1\"",
    "downloadurl": "/ln2data/releases/data/v-2.9.1/reviewed/human_protein_mutation_cancer.csv"
}