{
    "object_id": "https://biocomputeobject.org/GLY_001537/v-2.11.1",
    "spec_version": "1.3.0",
    "etag": "41edd36b5844b3b53e2fed2ad223389c",
    "provenance_domain": {
        "name": "All Human Cancer Mutations",
        "version": "v-2.11.1",
        "license": "https://creativecommons.org/licenses/by/4.0/",
        "modified": "2026-03-23T18:39:07.978Z",
        "contributors": [
            {
                "name": "Jeet Vora",
                "affiliation": "The George Washington University",
                "email": "jeetvora@gwu.edu",
                "contribution": [
                    "createdBy"
                ]
            },
            {
                "name": "Robel Kahsay",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "rykahsay@gwu.edu"
            },
            {
                "name": "Robel Kahsay",
                "affiliation": "BioMuta - The George Washington University",
                "contribution": [
                    "importedFrom"
                ],
                "email": "rykahsay@gwu.edu"
            },
            {
                "name": "Karina Martinez",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "karinamartinez@gwu.edu"
            },
            {
                "name": "Luke Johnson",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "luke.johnson@email.gwu.edu"
            },
            {
                "name": "Urnisha Bhuiyan",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "sbhuiyan28@email.gwu.edu"
            },
            {
                "name": "Cyrus Au-Yeung",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "cyruschauyeung@gwu.edu"
            },
            {
                "name": "Kate Warner",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "k.warner1@gwu.edu"
            },
            {
                "name": "Mariia Kim",
                "affiliation": "The George Washington University",
                "email": "maria.kim@gwu.edu",
                "contribution": [
                    "createdBy"
                ]
            }
        ]
    },
    "usability_domain": [
        "The Human Cancer Mutation dataset contains all 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.",
        "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 that the mutations shown in GlyGen are annotated based on passing of one or more filter criteria.",
        "Filter criterion 1 - Positive Patients Frequency Ratio \u2265 1.0%",
        "Filter criterion 2 - Presence of mutation in \u2265 3 cancer types",
        "Filter criterion 3 - Positive Patients count \u2265 10 patients",
        "Filter criterion 4 - Mutation reported and annotated in number of databases",
        "Filter criterion 5 - Mutation mined from literature using literaure mining tools (human_protein_mutation_literature.csv)",
        "If there is also a germline mutation reported in dbSNP, the rsid is also shown",
        "These filter criteria annotations are shown on the front end under the column Annotation Name",
        "Two different DO child terms are merged into one single entry showing the parent cancer DO term from the DO cancer slim.",
        "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."
    ],
    "description_domain": {
        "pipeline_steps": [
            {
                "name": "make-protein-dataset.py",
                "step_number": 1,
                "input_list": [],
                "description": "The script extracts the mutation data from the BioMuta and maps the UniProtKB accession to the UniProtKB canonical accessions as per the criterias",
                "prerequisite": [],
                "output_list": []
            }
        ],
        "keywords": [
            "single-nucleotide variations (nsSNVs)",
            "cancer mutations",
            "BioMuta",
            "disease"
        ]
    },
    "parametric_domain": [
        {
            "value": ""
        }
    ],
    "io_domain": {
        "output_subdomain": [
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.11.1/reviewed/human_protein_mutation_cancer_all.csv",
                    "filename": "human_protein_mutation_cancer_all.csv"
                }
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.11.1/reviewed/human_protein_mutation_cancer_all.stat.csv",
                    "filename": "human_protein_mutation_cancer_all.stat.csv"
                }
            }
        ],
        "input_subdomain": [
            {
                "uri": {
                    "filename": "glycan_masterlist.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.11.1/reviewed/glycan_masterlist.csv"
                }
            },
            {
                "uri": {
                    "filename": "human_protein_glycohydrolase.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.11.1/reviewed/human_protein_glycohydrolase.csv"
                }
            },
            {
                "uri": {
                    "filename": "human_protein_glycosyltransferase.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.11.1/reviewed/human_protein_glycosyltransferase.csv"
                }
            },
            {
                "uri": {
                    "filename": "human_protein_masterlist.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.11.1/reviewed/human_protein_masterlist.csv"
                }
            },
            {
                "uri": {
                    "filename": "human_protein_mutation_literature.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.11.1/reviewed/human_protein_mutation_literature.csv"
                }
            },
            {
                "uri": {
                    "filename": "protein_disease_idmap.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.11.1/reviewed/protein_disease_idmap.csv"
                }
            },
            {
                "uri": {
                    "filename": "aadict.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.11.1/misc/aadict.csv"
                }
            },
            {
                "uri": {
                    "filename": "biomuta.csv",
                    "uri": "https:/data.glygen.org/ln2downloads/biomuta/2025_05_27/biomuta.csv"
                }
            },
            {
                "uri": {
                    "filename": "clinical_information.csv",
                    "uri": "https:/data.glygen.org/ln2downloads/biomuta/2025_05_27/clinical_information.csv"
                }
            },
            {
                "uri": {
                    "filename": "dbSNP-homo-sapiens.tsv",
                    "uri": "https:/data.glygen.org/ln2downloads/ebi/2026_01_31/dbSNP-homo-sapiens.tsv"
                }
            }
        ]
    },
    "execution_domain": {
        "script": [
            {
                "uri": {
                    "uri": "https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-protein-dataset.py",
                    "filename": "make-protein-dataset.py"
                }
            }
        ],
        "script_driver": "manual",
        "software_prerequisites": [
            {
                "version": "2.7.5",
                "name": "Python",
                "uri": {
                    "uri": "https://www.python.org/download/releases/2.7.5/"
                }
            }
        ],
        "external_data_endpoints": [],
        "environment_variables": {}
    },
    "extension_domain": [
        {
            "extension_schema": "https://www.w3id.org/biocompute/extension_domain/1.2.0/dataset/dataset_extension.json",
            "dataset_extension": {
                "additional_license": {
                    "data_license": "https://creativecommons.org/licenses/by/4.0/",
                    "script_license": "https://www.gnu.org/licenses/gpl-3.0.en.html"
                },
                "dataset_categories": [
                    {
                        "category_value": "Homo sapiens",
                        "category_name": "species"
                    },
                    {
                        "category_value": "Protein",
                        "category_name": "molecule"
                    },
                    {
                        "category_value": "Somatic Cancer Mutations",
                        "category_name": "tag"
                    },
                    {
                        "category_value": "csv",
                        "category_name": "file_type"
                    },
                    {
                        "category_value": "Reviewed",
                        "category_name": "status"
                    },
                    {
                        "category_value": "internal",
                        "category_name": "scope"
                    }
                ]
            }
        }
    ],
    "error_domain": {}
}