{
    "object_id": "https://biocomputeobject.org/GLY_000028/v-2.9.1",
    "spec_version": "1.3.0",
    "etag": "5ff00c6bdc58fc9ed85ab34b4d043328",
    "provenance_domain": {
        "name": "Gene Expression (Normal)",
        "version": "v-2.9.1",
        "license": "https://creativecommons.org/licenses/by/4.0/",
        "created": "2019-01-23T17:21:05.895453",
        "modified": "2024-12-10T16:54:49.405Z",
        "contributors": [
            {
                "name": "Jeet Vora",
                "affiliation": "The George Washington University",
                "email": "jeetvora@gwu.edu",
                "contribution": [
                    "createdBy"
                ]
            },
            {
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Robel Kahsay",
                "email": "rykahsay@gwu.edu"
            },
            {
                "affiliation": "BioXpress - The George Washington University",
                "contribution": [
                    "importedFrom"
                ],
                "name": "Hayley Dingerdissen",
                "email": "hmhamilt@gwmail.gwu.edu"
            },
            {
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Karina Martinez",
                "email": "karinamartinez@gwu.edu"
            },
            {
                "contribution": [
                    "contributedBy"
                ],
                "name": "Not Applicable"
            },
            {
                "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"
            }
        ]
    },
    "usability_domain": [
        "The Gene Expression (Normal) dataset contains the normal expression information of Homo sapiens [taxid:9606] genes from BioXpress database. The GlyGen Interface shows the normal gene expression information for select UBERON ids only which are mapped to corresponding DOIDs and have gene expression in cancer information for those DOID. For more gene expression information of other UBERON IDs (tissues) for a given gene, please refer to BioXpress - https://hive.biochemistry.gwu.edu/bioxpress. BioXpress is a gene/miRNA expression and disease association database with expression levels mapped to genes or miRNAs. The current version of BioXpress contains only genes associated with cancer. If you are using this dataset please give proper attribution to GlyGen and BioXpress"
    ],
    "description_domain": {
        "pipeline_steps": [
            {
                "name": "make-protein-dataset.py",
                "step_number": 1,
                "input_list": [],
                "description": "The script extracts the expression information and maps the UniProtKB accession/gene symbol to UniProtKB canonical expression",
                "prerequisite": [],
                "output_list": []
            }
        ],
        "keywords": [
            "normal gene expression",
            "BioXpress",
            "UBERON",
            "tissue",
            "Bgee"
        ]
    },
    "parametric_domain": [
        {
            "value": ""
        }
    ],
    "io_domain": {
        "output_subdomain": [
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/human_protein_expression_normal.csv",
                    "filename": "human_protein_expression_normal.csv"
                }
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/human_protein_expression_normal.stat.csv",
                    "filename": "human_protein_expression_normal.stat.csv"
                }
            }
        ],
        "input_subdomain": [
            {
                "uri": {
                    "filename": "human_protein_masterlist.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/human_protein_masterlist.csv"
                }
            },
            {
                "uri": {
                    "filename": "human_normal_expression_custom_filtered.csv",
                    "uri": "https:/data.glygen.org/ln2downloads/bioxpress/2021_08/human_normal_expression_custom_filtered.csv"
                }
            }
        ]
    },
    "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": "Normal Gene Expression",
                        "category_name": "tag"
                    },
                    {
                        "category_value": "csv",
                        "category_name": "file_type"
                    },
                    {
                        "category_value": "Reviewed",
                        "category_name": "status"
                    },
                    {
                        "category_value": "internal",
                        "category_name": "scope"
                    }
                ]
            }
        }
    ],
    "error_domain": {}
}