{
    "object_id": "https://biocomputeobject.org/GLY_000556/v-2.4.1",
    "spec_version": "1.3.0",
    "etag": "c607988b395589238441ec15e8ad5e52",
    "provenance_domain": {
        "name": "Glycan Citations (GlycoMotif)",
        "version": "v-2.4.1",
        "created": "2021-03-16T15:44:18.145789",
        "modified": "2023-03-14T16:51:16.564Z",
        "embargo": {
            "start_time": "",
            "end_time": ""
        },
        "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": "Georgetown University",
                "contribution": [
                    "contributedBy",
                    "authoredBy"
                ],
                "name": "Nathan Edwards",
                "email": "nje5@georgetown.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": "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 dataset provides citations for the associated glycan (GlyTouCan Accession) from GlycoMotif (https://glycomotif.glyomics.org/). The listed GlyTouCan Accessions are derived from the GlyTouCan accession master list (https://data.glygen.org/GLY_000281) and the associated PMIDs are derived from the Glycan Motif dataset (https://data.glygen.org/GLY_000283)."
    ],
    "description_domain": {
        "keywords": [
            "Glycan",
            "GlyTouCan Accession",
            "Citations",
            "Motif"
        ],
        "platform": [],
        "pipeline_steps": [
            {
                "name": "make-species-agnostic-dataset.py",
                "step_number": 1,
                "version": "",
                "input_list": [],
                "output_list": [],
                "prerequisite": [],
                "description": "The input file was downloaded from the author and a python script is used to extract the associated PMIDs for the GlyTouCan accessions based on the acession master list. Refer to the usability domain for more information on master list. The MEDLINE format is used to add Journal, Author, Title detail associated with the publications. "
            }
        ]
    },
    "execution_domain": {
        "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"
                }
            }
        ],
        "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-2.4.1/reviewed/glycan_masterlist.csv"
                }
            },
            {
                "uri": {
                    "filename": "glycan_motif.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/glycan_motif.csv"
                }
            }
        ],
        "output_subdomain": [
            {
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/glycan_citations_motif.csv",
                    "filename": "glycan_citations_motif.csv"
                },
                "mediatype": "csv"
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/glycan_citations_motif.stat.csv",
                    "filename": "glycan_citations_motif.stat.csv"
                }
            }
        ]
    },
    "parametric_domain": [
        {
            "step": "",
            "param": "",
            "value": ""
        }
    ],
    "error_domain": {
        "empirical_error": {},
        "algorithmic_error": {}
    },
    "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": "Citations(GlycoMotif)",
                        "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": "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": "Drosophila melanogaster"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Sus scrofa domesticus"
                    },
                    {
                        "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"
                    }
                ]
            }
        }
    ]
}