{
    "object_id": "https://biocomputeobject.org/GLY_000707/v-2.9.1",
    "spec_version": "1.3.0",
    "etag": "e32c4aa9425b09360d77ed4e893aeb4d",
    "provenance_domain": {
        "name": "Glycan Tool Support",
        "version": "v-2.9.1",
        "created": "2023-02-16T02:48:48.291Z",
        "modified": "2024-05-17T11:24:10.105Z",
        "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": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Karina Martinez",
                "email": "karinamartinez@gwu.edu"
            },
            {
                "name": "Nathan Edwards",
                "contribution": [
                    "contributedBy",
                    "authoredBy"
                ],
                "affiliation": "Georgetown University",
                "email": "nje5@georgetown.edu",
                "orcid": ""
            },
            {
                "name": "Will York",
                "contribution": [
                    "authoredBy"
                ],
                "affiliation": "University of Georgia",
                "email": "will@ccrc.uga.edu",
                "orcid": ""
            },
            {
                "name": "Robert Woods",
                "contribution": [
                    "contributedBy"
                ],
                "affiliation": "University of Georgia",
                "email": "rwoods.glycam@gmail.com",
                "orcid": ""
            },
            {
                "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"
            }
        ],
        "license": "https://creativecommons.org/licenses/by/4.0/"
    },
    "usability_domain": [
        "This dataset indicates the tool support status of each GlyTouCan accession. The status is required for the GlyCan Detail API. The tools are sandbox, gnome, pdb, gnome_glygen, gnome_glygen_nglycans, gnome_glygen_oglycans, gnome_glycotree_nglycans, and gnome_glycotree_oglycans. PDB support for glycam 3D structures was provided by Rob Woods (Glycam/UGA). Sandbox support was provided by Will York (UGA) and Nathan Edwards (Georgetown). All other tool support data was provided by Nathan Edwards (Georgetown)."
    ],
    "description_domain": {
        "keywords": [
            "Glycan",
            "Tool Support",
            "Gnome",
            "PDB",
            "Sandbox",
            "GlycoTree"
        ],
        "platform": [],
        "pipeline_steps": [
            {
                "name": "make-species-agnostic-dataset.py",
                "step_number": 1,
                "version": "",
                "input_list": [],
                "output_list": [],
                "prerequisite": [],
                "description": ""
            }
        ]
    },
    "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-2.9.1/reviewed/glycan_masterlist.csv"
                }
            },
            {
                "uri": {
                    "filename": "2022_05_24",
                    "uri": "https:/data.glygen.org/ln2downloads/glycam_3d/glycan/2022_05_24"
                }
            },
            {
                "uri": {
                    "filename": "GlycoTree_NGlycans.valid-accessions.txt",
                    "uri": "https:/data.glygen.org/ln2downloads/gnome/02_11_2025/GlycoTree_NGlycans.valid-accessions.txt"
                }
            },
            {
                "uri": {
                    "filename": "GlycoTree_OGlycans.valid-accessions.txt",
                    "uri": "https:/data.glygen.org/ln2downloads/gnome/02_11_2025/GlycoTree_OGlycans.valid-accessions.txt"
                }
            },
            {
                "uri": {
                    "filename": "GlyGen_NGlycans.valid-accessions.txt",
                    "uri": "https:/data.glygen.org/ln2downloads/gnome/02_11_2025/GlyGen_NGlycans.valid-accessions.txt"
                }
            },
            {
                "uri": {
                    "filename": "GlyGen_OGlycans.valid-accessions.txt",
                    "uri": "https:/data.glygen.org/ln2downloads/gnome/02_11_2025/GlyGen_OGlycans.valid-accessions.txt"
                }
            },
            {
                "uri": {
                    "filename": "GlyGen.valid-accessions.txt",
                    "uri": "https:/data.glygen.org/ln2downloads/gnome/02_11_2025/GlyGen.valid-accessions.txt"
                }
            },
            {
                "uri": {
                    "filename": "accessionlist.csv",
                    "uri": "https:/data.glygen.org/ln2downloads/sandbox/02_11_2025/accessionlist.csv"
                }
            }
        ],
        "output_subdomain": [
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/glycan_toolsupport.csv",
                    "filename": "glycan_toolsupport.csv"
                }
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/glycan_toolsupport.stat.csv",
                    "filename": "glycan_toolsupport.stat.csv"
                }
            }
        ]
    },
    "parametric_domain": [
        {
            "step": "",
            "value": "",
            "param": ""
        }
    ],
    "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": "",
                        "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"
                    }
                ]
            }
        }
    ]
}