{
    "object_id": "https://biocomputeobject.org/GLY_001026/v-2.5.1",
    "spec_version": "1.3.0",
    "provenance_domain": {
        "name": "Chicken Proteoform Phosphorylation Citations (iPTMnet)",
        "version": "v-2.5.1",
        "license": "https://creativecommons.org/licenses/by/4.0/",
        "modified": "2024-05-17T11:24:22.427Z",
        "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": "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": "Jingyue Wu",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "jingyue.wu@email.gwu.edu"
            },
            {
                "name": "Kate Warner",
                "affiliation": "The George Washington University",
                "email": "k.warner1@gwu.edu",
                "contribution": [
                    "createdBy"
                ]
            }
        ]
    },
    "usability_domain": [
        "The Chicken Proteoform Citations (iPTMNet) contains Gallus gallus [taxid:9031] publication information of phosphorylated proteins from iPTMnet. The script accesses the NCBI ENTREZ infrastructure to retrieve the publication information of the given PMID from iPTMnet. If you use this dataset please provide proper attribution to iPTMnet and GlyGen."
    ],
    "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": "Gallus gallus",
                        "category_name": "species"
                    },
                    {
                        "category_value": "Proteoform",
                        "category_name": "molecule"
                    },
                    {
                        "category_value": "Phosphorylation Citations (iPTMnet)",
                        "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": [
            "PMID",
            "journal",
            "citations",
            "authors",
            "iPTMnet",
            "PubMed",
            "Phosphorylation"
        ],
        "pipeline_steps": [
            {
                "name": "make-proteoform-dataset.py",
                "step_number": 1,
                "description": "The script parses the input file for PMIDs and accesses the NCBI Entrez infrastructure to download the publication information of the corresponding PMIDs",
                "input_list": [],
                "prerequisite": [],
                "output_list": []
            }
        ]
    },
    "execution_domain": {
        "script": [
            {
                "uri": {
                    "uri": "https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-proteoform-dataset.py",
                    "filename": "make-proteoform-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": {}
    },
    "parametric_domain": [
        {
            "value": ""
        }
    ],
    "io_domain": {
        "output_subdomain": [
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/chicken_proteoform_citations_phosphorylation_sites_iptmnet.csv",
                    "filename": "chicken_proteoform_citations_phosphorylation_sites_iptmnet.csv"
                }
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/chicken_proteoform_citations_phosphorylation_sites_iptmnet.stat.csv",
                    "filename": "chicken_proteoform_citations_phosphorylation_sites_iptmnet.stat.csv"
                }
            }
        ],
        "input_subdomain": [
            {
                "uri": {
                    "filename": "chicken_proteoform_phosphorylation_sites_iptmnet.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/chicken_proteoform_phosphorylation_sites_iptmnet.csv"
                }
            }
        ]
    },
    "error_domain": {},
    "etag": "03257609022cadf901e5d51178ce1a5b"
}
