{
    "object_id": "https://biocomputeobject.org/GLY_001644/v-2.12.1",
    "etag": "acb9820602c6bd01851c1c71cde2d6da",
    "spec_version": "1.3.0",
    "provenance_domain": {
        "name": "Glycan Xref GlyTableMaker",
        "version": "v-2.12.1",
        "license": "https://creativecommons.org/licenses/by/4.0/",
        "created": "2019-11-13T16:55:11.149043",
        "modified": "2024-05-17T11:23:55.326Z",
        "contributors": [
            {
                "name": "Jeet Vora",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "jeetvora@gwu.edu"
            },
            {
                "name": "Robel Kahsay",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "rykahsay@gwu.edu"
            },
            {
                "name": "Urnisha Bhuiyan",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "sbhuiyan28@email.gwu.edu"
            },
            {
                "name": "Kate Warner",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "k.warner1@gwu.edu"
            }
        ]
    },
    "usability_domain": [
        "This dataset provides cross-references to GlyTableMaker entries for the associated glycans (GlyTouCan Accession) that were manually curated on GlyTableMaker (https://glygen.ccrc.uga.edu/tablemaker)"
    ],
    "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": "GlyTableMaker cross-references",
                        "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": "Arabidopsis thaliana"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Sus scrofa"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Drosophila melanogaster"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Rattus norvegicus"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Danio rerio"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Dictyostelium discoideum"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Zaire ebolavirus (strain Mayinga-76)"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Bundibugyo virus"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Bos taurus"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Gallus gallus"
                    },
                    {
                        "category_name": "species",
                        "category_value": "Cricetulus griseus"
                    },
                    {
                        "category_name": "file_category",
                        "category_value": "xref_"
                    }
                ]
            }
        }
    ],
    "description_domain": {
        "keywords": [
            "Glycan",
            "GlyTouCan Accession",
            "GlyTableMaker",
            "Cross-references"
        ],
        "pipeline_steps": [
            {
                "name": "make-species-agnostic-dataset.py",
                "version": "",
                "step_number": 1,
                "input_list": [],
                "output_list": [],
                "prerequisite": [],
                "description": "The input file was downloaded from the author and a python script is used to extract the data 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": ""
        }
    ],
    "io_domain": {
        "input_subdomain": [
            {
                "uri": {
                    "filename": "bdbv_proteoform_glycosylation_sites_tablemaker.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/bdbv_proteoform_glycosylation_sites_tablemaker.csv"
                }
            },
            {
                "uri": {
                    "filename": "bovine_proteoform_glycosylation_sites_tablemaker.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/bovine_proteoform_glycosylation_sites_tablemaker.csv"
                }
            },
            {
                "uri": {
                    "filename": "chicken_proteoform_glycosylation_sites_tablemaker.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/chicken_proteoform_glycosylation_sites_tablemaker.csv"
                }
            },
            {
                "uri": {
                    "filename": "dicty_proteoform_glycosylation_sites_tablemaker.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/dicty_proteoform_glycosylation_sites_tablemaker.csv"
                }
            },
            {
                "uri": {
                    "filename": "ebov_proteoform_glycosylation_sites_tablemaker.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/ebov_proteoform_glycosylation_sites_tablemaker.csv"
                }
            },
            {
                "uri": {
                    "filename": "fruitfly_proteoform_glycosylation_sites_tablemaker.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/fruitfly_proteoform_glycosylation_sites_tablemaker.csv"
                }
            },
            {
                "uri": {
                    "filename": "glycan_masterlist.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/glycan_masterlist.csv"
                }
            },
            {
                "uri": {
                    "filename": "hamster_proteoform_glycosylation_sites_tablemaker.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/hamster_proteoform_glycosylation_sites_tablemaker.csv"
                }
            },
            {
                "uri": {
                    "filename": "human_proteoform_glycosylation_sites_tablemaker.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/human_proteoform_glycosylation_sites_tablemaker.csv"
                }
            },
            {
                "uri": {
                    "filename": "pig_proteoform_glycosylation_sites_tablemaker.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/pig_proteoform_glycosylation_sites_tablemaker.csv"
                }
            },
            {
                "uri": {
                    "filename": "zebrafish_proteoform_glycosylation_sites_tablemaker.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/zebrafish_proteoform_glycosylation_sites_tablemaker.csv"
                }
            }
        ],
        "output_subdomain": [
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/glycan_xref_tablemaker.csv",
                    "filename": "glycan_xref_tablemaker.csv"
                }
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/glycan_xref_tablemaker.stat.csv",
                    "filename": "glycan_xref_tablemaker.stat.csv"
                }
            }
        ]
    },
    "error_domain": {
        "empirical_error": {},
        "algorithmic_error": {}
    }
}