{
    "object_id": "https://biocomputeobject.org/GLY_000330/v-2.3.1",
    "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": "Mus musculus",
                        "category_name": "species"
                    },
                    {
                        "category_value": "Proteoform",
                        "category_name": "molecule"
                    },
                    {
                        "category_value": "Glycosylation Sites",
                        "category_name": "tag"
                    },
                    {
                        "category_value": "csv",
                        "category_name": "file_type"
                    },
                    {
                        "category_value": "Reviewed",
                        "category_name": "status"
                    },
                    {
                        "category_value": "internal",
                        "category_name": "scope"
                    }
                ]
            }
        }
    ],
    "provenance_domain": {
        "license": "https://creativecommons.org/licenses/by/4.0/",
        "name": "Mouse Glycosylation Sites (GlyConnect) ",
        "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": "GlyConnect",
                "contribution": [
                    "authoredBy"
                ],
                "name": "Frederique Lisacek",
                "email": "frederique.lisacek@sib.swiss"
            },
            {
                "affiliation": "GlyConnect",
                "contribution": [
                    "authoredBy"
                ],
                "name": "Julien Mariethoz",
                "email": "julien.mariethoz@sib.swiss"
            },
            {
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Karina Martinez",
                "email": "karinamartinez@gwu.edu"
            },
            {
                "name": "Jingyue Wu",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "jingyue.wu@email.gwu.edu"
            }
        ],
        "created": "2020-02-10T12:16:18.548585",
        "modified": "2022-09-26T09:05:27.645592",
        "version": "v-2.3.1"
    },
    "description_domain": {
        "keywords": [
            "glycosylation",
            "reported glycosylation"
        ],
        "pipeline_steps": [
            {
                "name": "make-proteoform-dataset.py",
                "step_number": 1,
                "version": "",
                "input_list": [],
                "output_list": [],
                "prerequisite": [],
                "description": "The script loads the glycosylation information from the input JSON file and extracts the data. The QC checks filter out: 1) any rows where the UniProtKB accession is not included in the GlyGen protein list (https://data.glygen.org/GLYDS000001) and/or 2) if the given glycosylation position and amino acid does not match to the amino acid on the .fasta sequence for that protein (However it does pass if the amino acid +glyco-site is empty (as these records correspond to the \"not reported\" glyco-sites and/or 3) If the glycosylation type does not associate to the glycosylation based on amino acid (i.e., if a N-linked is associated with Ser/Thr residue, etc.,). 4) If the glyco-site is not reported and the glycosylation type is ambiguous (c-Linked/o-linked) and/or 5) if the saccharide (GlyTouCan) is not present in the GlyGen glycan master list. All the flagged entries are added in the log file (mouse_proteoform_glycosylation_sites_glyconnect.1.log)"
            }
        ]
    },
    "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-proteoform-dataset.py",
                    "filename": "make-proteoform-dataset.py"
                }
            }
        ]
    },
    "error_domain": {
        "empirical_error": {},
        "algorithmic_error": {}
    },
    "parametric_domain": [
        {
            "step": "",
            "param": "",
            "value": ""
        }
    ],
    "usability_domain": [
        "The Mouse Glycosylation Sites (GlyConnect) dataset contains mouse [taxid:10090] UniProtKB canonical accessions with information on reported glycosylation sites in GlyConnect database (https://glyconnect.expasy.org/; PMID: 30574787).A json file was derived through GlyConnect API (https://glyconnect.expasy.org/api/docs/index.html?url=/api/assets/swagger.json#/Glycosylation/listGlycosylationsAsJson) (Query: taxonomy:Mus musculus). If you use this dataset please provide proper attribution to GlyConnect and GlyGen."
    ],
    "etag": "28e0c87e5c84a8ca94e0866c1ecc78ce",
    "io_domain": {
        "input_subdomain": [
            {
                "uri": {
                    "filename": "n_sequon_info.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.3.1/misc/n_sequon_info.csv"
                }
            },
            {
                "uri": {
                    "filename": "sample_mapping.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.3.1/misc/sample_mapping.csv"
                }
            },
            {
                "uri": {
                    "filename": "cellosaurus.txt",
                    "uri": "https:/data.glygen.org/ln2downloads/cellosaurus/2023_10_11/cellosaurus.txt"
                }
            },
            {
                "uri": {
                    "filename": "glyconnect_mouse.json",
                    "uri": "https:/data.glygen.org/ln2downloads/glyconnect/2023_12_05/glyconnect_mouse.json"
                }
            }
        ],
        "output_subdomain": [
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/mouse_proteoform_glycosylation_sites_glyconnect.csv",
                    "filename": "mouse_proteoform_glycosylation_sites_glyconnect.csv"
                }
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/mouse_proteoform_glycosylation_sites_glyconnect.stat.csv",
                    "filename": "mouse_proteoform_glycosylation_sites_glyconnect.stat.csv"
                }
            }
        ]
    }
}