{
    "object_id": "https://biocomputeobject.org/GLY_000284/1.11.2",
    "spec_version": "1.3.0",
    "extension_domain": [
        {
            "extension_schema": "http://www.w3id.org/biocompute/extension_domain/1.1.0/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": "",
                        "category_name": "species"
                    },
                    {
                        "category_value": "Glycan",
                        "category_name": "molecule"
                    },
                    {
                        "category_value": "Biosynthetic Enzyme",
                        "category_name": "tags"
                    },
                    {
                        "category_value": "Reviewed",
                        "category_name": "status"
                    },
                    {
                        "category_value": "csv",
                        "category_name": "file_type"
                    },
                    {
                        "category_value": "internal",
                        "category_name": "scope"
                    }
                ]
            }
        }
    ],
    "provenance_domain": {
        "license": "https://creativecommons.org/licenses/by/4.0/",
        "name": "Glycan Enzyme",
        "contributors": [
            {
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Rahi Navelkar",
                "email": "rsn13@gwu.edu"
            },
            {
                "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": "University of Georgia",
                "contribution": [
                    "contributedBy"
                ],
                "name": "Will York",
                "email": "will@ccrc.uga.edu"
            },
            {
                "affiliation": "University of Georgia",
                "contribution": [
                    "contributedBy"
                ],
                "name": "Allison Nairn",
                "email": "avnairn@uga.edu"
            },
            {
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Karina Martinez",
                "email": "karinamartinez@gwu.edu"
            },
            {
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Amanda Bell",
                "email": "amandab2140@gwu.edu"
            },
            {
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Jonathon Keeney",
                "email": "keeneyjg@gwu.edu"
            },
            {
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Millicent Quartey",
                "email": "mquartey@email.gwu.edu"
            }
        ],
        "created": "2019-11-13T13:19:08.883378",
        "modified": "2022-01-12T16:20:52.337922",
        "version": "1.11.2"
    },
    "description_domain": {
        "keywords": [
            "Glycan",
            "GlyTouCan Accession",
            "Enzyme"
        ],
        "pipeline_steps": [
            {
                "name": "make-species-agnostic-dataset.py",
                "step_number": 1,
                "version": "",
                "input_list": [
                    {
                        "uri": "https://data.glygen.org/ln2wwwdata/source/annotated_glycans.csv",
                        "filename": "annotated_glycans.csv"
                    },
                    {
                        "uri": "https://data.glygen.org/ln2wwwdata/source/human_protein_recnames.csv",
                        "filename": "human_protein_recnames.csv"
                    },
                    {
                        "uri": "https://data.glygen.org/ln2wwwdata/source/mouse_protein_recnames.csv",
                        "filename": "mouse_protein_recnames.csv"
                    }
                ],
                "output_list": [
                    {
                        "uri": "https://data.glygen.org/ln2wwwdata/source/glycan_enzyme.csv",
                        "filename": "glycan_enzyme.csv"
                    }
                ],
                "prerequisite": [],
                "description": "The input file was downloaded from the source authors and a python script was used to extract columns: glytoucan_ac,residue_name,residue_id,uniprot,gene_name,gene_id,parent_residue_id,type,species. The script also assigned protein recommended name based on the UniProtKB accession. "
            }
        ]
    },
    "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/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/make-species-agnostic-dataset.py",
                    "filename": "make-species-agnostic-dataset.py"
                }
            }
        ]
    },
    "error_domain": {
        "empirical_error": {},
        "algorithmic_error": {},
        "emperical_error": {}
    },
    "parametric_domain": [
        {
            "step": "",
            "param": "",
            "value": ""
        }
    ],
    "usability_domain": [
        "The dataset provides information on biosynthetic enzymes (UniProtKB Ac.) associated to the glycan structures (GlyTouCan Accessions). The enzymes listed are human or mouse proteins that are associated with the canonical monosaccharides. The association of a glycan structure to the canonical monosaccharides are based on the Glyco tree model. The glycans listed in the database may or may not have a human (TaxID:9606) or mouse (TaxID:10090) species annotation from the source (GlyTouCan or UniCarbKB) database. Please note that a human or mouse biosynthetic enzyme association should not be considered as a human or mouse species annotation for that glycan."
    ],
    "etag": "670be3192b913fc525ecb2d4b011d8f8",
    "io_domain": {
        "input_subdomain": [
            {
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-x.x.x/reviewed/human_protein_recnames.csv",
                    "filename": "human_protein_recnames.csv"
                }
            },
            {
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-x.x.x/reviewed/mouse_protein_recnames.csv",
                    "filename": "mouse_protein_recnames.csv"
                }
            },
            {
                "uri": {
                    "uri": "https:/data.glygen.org/ln2downloads/uga/v-x.x.x/annotated_glycans.csv",
                    "filename": "annotated_glycans.csv"
                }
            }
        ],
        "output_subdomain": [
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-x.x.x/reviewed/glycan_enzyme.csv",
                    "filename": "glycan_enzyme.csv"
                }
            }
        ]
    }
}