{
    "object_id": "https://biocomputeobject.org/GLY_000737/v-2.2.1",
    "spec_version": "1.3.0",
    "etag": "e59643329cdf885d89a81424d1cc5827",
    "provenance_domain": {
        "name": "Glycan Biomarkers (Biomarker Database)",
        "version": "v-2.2.1",
        "created": "2023-03-14T20:00:08.127Z",
        "modified": "2023-03-14T20:07:25.567Z",
        "embargo": {
            "start_time": "",
            "end_time": ""
        },
        "contributors": [
            {
                "name": "Jeet Vora",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "jeetvora@gwu.edu"
            },
            {
                "name": "Karina Martinez",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy",
                    "curatedBy"
                ],
                "email": "karinamartinez@gwu.edu"
            },
            {
                "name": "Robel Kahsay",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "rykahsay@gwu.edu"
            },
            {
                "name": "Dan Lyman",
                "contribution": [
                    "createdBy",
                    "curatedBy"
                ],
                "affiliation": "The George Washington University",
                "email": "danlyman@gwu.edu",
                "orcid": ""
            },
            {
                "name": "Jingyue Wu",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "jingyue.wu@email.gwu.edu"
            }
        ],
        "license": "https://creativecommons.org/licenses/by/4.0/"
    },
    "usability_domain": [
        "The Glycan Biomarkers dataset contains glycan biomarker information,  including cross-mapped GlyTouCan accessions, assessed biomarker entity, biomarker type, specimen type, LOINC code, disease name, and source evidence from the biomarker portal (https://data.oncomx.org/allbiomarkers). If you use this dataset, please provide proper attribution to OncoMX and GlyGen. Cite: PMID:32142370, PMID:34015823, and PMID:31616925."
    ],
    "description_domain": {
        "keywords": [
            "biomarker",
            "cancer"
        ],
        "platform": [],
        "pipeline_steps": [
            {
                "name": "",
                "version": "",
                "step_number": 1,
                "input_list": [],
                "output_list": [],
                "prerequisite": [],
                "description": ""
            }
        ]
    },
    "execution_domain": {
        "script": [
            {
                "uri": {
                    "uri": "https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/",
                    "filename": ""
                }
            }
        ],
        "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": {}
    },
    "io_domain": {
        "input_subdomain": [
            {
                "uri": {
                    "filename": "glycan_masterlist.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/glycan_masterlist.csv"
                }
            },
            {
                "uri": {
                    "filename": "doid2uberonid_mapping_v5.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.2.1/misc/doid2uberonid_mapping_v5.csv"
                }
            },
            {
                "uri": {
                    "filename": "sample_mapping.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.2.1/misc/sample_mapping.csv"
                }
            },
            {
                "uri": {
                    "filename": "allbiomarkers-all.csv",
                    "uri": "https:/data.glygen.org/ln2downloads/biomarkerdb/2023_08_11/allbiomarkers-all.csv"
                }
            }
        ],
        "output_subdomain": [
            {
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/glycan_biomarkers.csv",
                    "filename": "glycan_biomarkers.csv"
                },
                "mediatype": "csv"
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/glycan_biomarkers.stat.csv",
                    "filename": "glycan_biomarkers.stat.csv"
                }
            }
        ]
    },
    "parametric_domain": [
        {
            "step": "",
            "param": "",
            "value": ""
        }
    ],
    "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": "Glycan",
                        "category_name": "molecule"
                    },
                    {
                        "category_value": "Glycan Biomarker (BiomarkerDB)",
                        "category_name": "tag"
                    },
                    {
                        "category_value": "csv",
                        "category_name": "file_type"
                    },
                    {
                        "category_value": "Reviewed",
                        "category_name": "status"
                    },
                    {
                        "category_value": "internal",
                        "category_name": "scope"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Drosophila melanogaster"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Homo sapiens"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Mus musculus"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Sus scrofa"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Rattus"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Rattus norvegicus"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Severe acute respiratory syndrome coronavirus 2"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Saccharomyces cerevisiae"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Dictyostelium discoideum"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Hepacivirus C"
                    }
                ]
            }
        }
    ]
}
