{
    "object_id": "https://biocomputeobject.org/GLY_000559/v-2.8.1",
    "spec_version": "1.3.0",
    "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": "byonic sequence format",
                        "category_name": "tag"
                    },
                    {
                        "category_value": "Reviewed",
                        "category_name": "status"
                    },
                    {
                        "category_value": "csv",
                        "category_name": "file_type"
                    },
                    {
                        "category_value": "internal",
                        "category_name": "scope"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Sus scrofa"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Rattus"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Homo sapiens"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Mus musculus"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Saccharomyces cerevisiae"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Drosophila melanogaster"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Rattus norvegicus"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Severe acute respiratory syndrome coronavirus 2"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Sus scrofa domesticus"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Dictyostelium discoideum"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Hepatitis C virus (isolate H77)"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Severe acute respiratory syndrome-related coronavirus"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Hepacivirus C"
                    }
                ]
            }
        }
    ],
    "provenance_domain": {
        "license": "https://creativecommons.org/licenses/by/4.0/",
        "name": "Glycan sequences Byonic",
        "contributors": [
            {
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Jeet Vora",
                "email": "jeetvora@gwu.edu"
            },
            {
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Robel Kahsay",
                "email": "rykahsay@gwu.edu"
            },
            {
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Karina Martinez",
                "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"
            }
        ],
        "created": "2021-06-02T12:48:41.483014",
        "modified": "2024-05-17T11:24:04.621Z",
        "version": "v-2.8.1"
    },
    "description_domain": {
        "keywords": [
            "Glycan",
            "GlyTouCan Accession",
            "Byonic"
        ],
        "pipeline_steps": [
            {
                "name": "make-species-agnostic-dataset.py",
                "step_number": 1,
                "version": "",
                "input_list": [],
                "output_list": [],
                "prerequisite": [],
                "description": "A python script is used to generate the byonic format based on the compositioon for the GlyTouCan accessions based on the acession master list. Refer to the usability domain for more information on master list."
            }
        ]
    },
    "execution_domain": {
        "external_data_endpoints": [],
        "environment_variables": {},
        "script_driver": "manual",
        "software_prerequisites": [
            {
                "version": "2.7.5",
                "name": "Python",
                "uri": {
                    "uri": "https://www.python.org/download/releases/2.7.5/"
                }
            }
        ],
        "script": [
            {
                "uri": {
                    "uri": "https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-species-agnostic-dataset.py",
                    "filename": "make-species-agnostic-dataset.py"
                }
            }
        ]
    },
    "parametric_domain": [
        {
            "step": "",
            "param": "",
            "value": ""
        }
    ],
    "usability_domain": [
        "The dataset provides the glycan sequences in Byonic format for the associated glycans (GlyTouCan Accession). The listed GlyTouCan Accessions are derived from the GlyTouCan accession master list (https://data.glygen.org/GLYDS000281). Source database: https://dev.glycam.org/"
    ],
    "etag": "23270be46258c0eb41e965940ac5373c",
    "io_domain": {
        "input_subdomain": [
            {
                "uri": {
                    "filename": "glycan_masterlist.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/glycan_masterlist.csv"
                }
            },
            {
                "uri": {
                    "filename": "names.tsv",
                    "uri": "https:/data.glygen.org/ln2downloads/glytoucan/2025_02_10/export/names.tsv"
                }
            },
            {
                "uri": {
                    "filename": "subsumption.tsv",
                    "uri": "https:/data.glygen.org/ln2downloads/glytoucan/2025_02_10/export/subsumption.tsv"
                }
            }
        ],
        "output_subdomain": [
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/glycan_sequences_byonic.csv",
                    "filename": "glycan_sequences_byonic.csv"
                }
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/glycan_sequences_byonic.stat.csv",
                    "filename": "glycan_sequences_byonic.stat.csv"
                }
            }
        ]
    },
    "error_domain": {
        "empirical_error": {},
        "algorithmic_error": {}
    }
}