{
    "object_id": "https://biocomputeobject.org/GLY_000427/v-2.0.2",
    "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": "SARS coronavirus (SARS-CoV-1)",
                        "category_name": "species"
                    },
                    {
                        "category_value": "Protein",
                        "category_name": "molecule"
                    },
                    {
                        "category_value": "N-Glycosylation Sequon",
                        "category_name": "tags"
                    },
                    {
                        "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": "SARS-CoV1 N-Glycosylation Sequon",
        "contributors": [
            {
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Jeet Vora",
                "email": "jeetvora@gwu.edu"
            },
            {
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Rahi Navelkar",
                "email": "rsn13@gwu.edu"
            },
            {
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Robel Kahsay",
                "email": "rykahsay@gwu.edu"
            },
            {
                "affiliation": "EMBL-EBI-UniProt",
                "contribution": [
                    "contributedBy"
                ],
                "name": "Maria Martin",
                "email": "martin@ebi.ac.uk"
            },
            {
                "affiliation": "EMBL-EBI-UniProt",
                "contribution": [
                    "contributedBy"
                ],
                "name": "Preethi Vasudev",
                "email": "pvasudev@ebi.ac.uk"
            },
            {
                "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": "2020-04-03T00:35:31.181876",
        "modified": "2020-04-09T18:43:07.886517",
        "version": "v-2.0.2"
    },
    "description_domain": {
        "keywords": [
            "n-glycosylation sequon",
            "NXS/T",
            "n-glycosylation motif",
            "n-glycosylation consensus sequence"
        ],
        "pipeline_steps": [
            {
                "name": "make-protein-dataset.py",
                "step_number": 1,
                "version": "",
                "input_list": [
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-2.0.2/reviewed/sarscov1_protein_canonicalsequences.fasta",
                        "filename": "sarscov1_protein_canonicalsequences.fasta"
                    }
                ],
                "output_list": [
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-2.0.2/reviewed/sarscov1_protein_glycosylation_motifs.csv",
                        "filename": "sarscov1_protein_glycosylation_motifs.csv"
                    }
                ],
                "prerequisite": [],
                "description": "The script uses the PS Scan tool (accession- PS00001) from ProSite to extracts the N-glycosylation pattern/sequon/motif N-{P}-[ST]-{P} where P is not a proline from the UniProtKB canonical sequences. More info -  https://prosite.expasy.org/PDOC00001, https://prosite.expasy.org/PS00001 and extracts as a csv."
            }
        ]
    },
    "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-protein-dataset.py",
                    "filename": "make-protein-dataset.py"
                }
            }
        ]
    },
    "usability_domain": [
        "The SARS coronavirus (SARS-CoV-1) N-Glycosylation Sequon dataset contains N-glycosylation sequon or motif or consensus sequence for sarscov1 [taxid:694009] UniProtKB canonical sequences identified by the script. The script identifies the N-glycosylation sequon pattern - Asn-X-Ser/Thr , where X is any amino acid except proline (Pro) for UniProtKB accessions. The dataset is derived form 2020_01 UniprotKB release."
    ],
    "etag": "25c43d2db63729f7ff3d1933df6f15bb",
    "io_domain": {
        "input_subdomain": [
            {
                "uri": {
                    "filename": "sarscov1_protein_canonicalsequences.fasta",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.0.2/reviewed/sarscov1_protein_canonicalsequences.fasta"
                }
            },
            {
                "uri": {
                    "filename": "prosite.dat",
                    "uri": "https:/data.glygen.org/ln2downloads/prosite/prosite.dat"
                }
            }
        ],
        "output_subdomain": [
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.0.2/reviewed/sarscov1_protein_glycosylation_motifs.csv",
                    "filename": "sarscov1_protein_glycosylation_motifs.csv"
                }
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.0.2/reviewed/sarscov1_protein_glycosylation_motifs.stat.csv",
                    "filename": "sarscov1_protein_glycosylation_motifs.stat.csv"
                }
            }
        ]
    }
}