{
    "object_id": "https://biocomputeobject.org/GLY_000822/v-2.8.1",
    "etag": "f0cb4606233f84196da12fad38109539",
    "spec_version": "1.3.0",
    "provenance_domain": {
        "name": "Dictyostelium Glycosylation Sites (GlyConnect)",
        "version": "v-2.8.1",
        "license": "https://creativecommons.org/licenses/by/4.0/",
        "created": "",
        "modified": "2024-05-17T11:24:14.598Z",
        "derived_from": [],
        "contributors": [
            {
                "name": "Jeet Vora",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "jeetvora@gwu.edu"
            },
            {
                "name": "Karina Martinez",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "karinamartinez@gwu.edu"
            },
            {
                "name": "Robel Kahsay",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "rykahsay@gwu.edu"
            },
            {
                "name": "Frederique Lisacek",
                "affiliation": "GlyConnect",
                "email": "frederique.lisacek@sib.swiss",
                "contribution": [
                    "contributedBy"
                ],
                "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"
            }
        ],
        "review": []
    },
    "usability_domain": [
        "The Dictyostelium Glycosylation Sites (GlyConnect) dataset contains dictyostelium [taxid:44689] 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/glycosylations?taxonomy=Dictyostelium%20discoideum)."
    ],
    "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": "Proteoform",
                        "category_name": "molecule"
                    },
                    {
                        "category_value": "",
                        "category_name": "tag"
                    },
                    {
                        "category_value": "csv",
                        "category_name": "file_type"
                    },
                    {
                        "category_value": "Reviewed",
                        "category_name": "status"
                    },
                    {
                        "category_value": "internal",
                        "category_name": "scope"
                    }
                ]
            }
        }
    ],
    "description_domain": {
        "keywords": [
            "glycosylation",
            "reported glycosylation"
        ],
        "pipeline_steps": [
            {
                "name": "make-proteoform-dataset.py",
                "version": "",
                "step_number": 1,
                "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 dictyostelium protein masterlist and/or 2) if the given glycosylation position and amino acid does not match to the amino acid on the .fasta sequence provided in the UniProtKB release 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 glycostlation 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 ambigious (c-Linked/o-linked) and/or 5) if the saccharide (GlyTouCan) is not present in the GlyGen glycan masterlist (https://data.glygen.org/GLY_000281)."
            }
        ]
    },
    "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/",
                    "filename": ""
                }
            }
        ]
    },
    "parametric_domain": [
        {
            "step": "",
            "param": "",
            "value": ""
        }
    ],
    "io_domain": {
        "input_subdomain": [
            {
                "uri": {
                    "filename": "n_sequon_info.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.8.1/misc/n_sequon_info.csv"
                }
            },
            {
                "uri": {
                    "filename": "sample_mapping.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.8.1/misc/sample_mapping.csv"
                }
            },
            {
                "uri": {
                    "filename": "cellosaurus.txt",
                    "uri": "https:/data.glygen.org/ln2downloads/cellosaurus/2025_01_13/cellosaurus.txt"
                }
            },
            {
                "uri": {
                    "filename": "glyconnect_dicty.json",
                    "uri": "https:/data.glygen.org/ln2downloads/glyconnect/2025_01_14/glyconnect_dicty.json"
                }
            }
        ],
        "output_subdomain": [
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/dicty_proteoform_glycosylation_sites_glyconnect.csv",
                    "filename": "dicty_proteoform_glycosylation_sites_glyconnect.csv"
                }
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/dicty_proteoform_glycosylation_sites_glyconnect.stat.csv",
                    "filename": "dicty_proteoform_glycosylation_sites_glyconnect.stat.csv"
                }
            }
        ]
    }
}