{
    "io_domain": {
        "input_subdomain": [
            {
                "uri": {
                    "uri": "https://data.glygen.org/ln2data/releases/data/v-1.5.18/source/glycosylation_sites_24190977_s5.csv",
                    "filename": "glycosylation_sites_24190977_s5.csv"
                }
            },
            {
                "uri": {
                    "uri": "https://data.glygen.org/ln2data/releases/data/v-1.5.18/source/glycosylation_sites_23090970_s5.csv",
                    "filename": "glycosylation_sites_23090970_s5.csv"
                }
            },
            {
                "uri": {
                    "uri": "https://data.glygen.org/ln2data/releases/data/v-1.5.18/source/glycosylation_sites_23090970_s2.csv",
                    "filename": "glycosylation_sites_23090970_s2.csv"
                }
            }
        ],
        "output_subdomain": [
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "http://data.glygen.org/ln2data/releases/data/v-1.5.18/reviewed/human_proteoform_glycosylation_sites_literature.csv",
                    "filename": "human_proteoform_glycosylation_sites_literature.csv"
                }
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "http://data.glygen.org/ln2data/releases/data/v-1.5.18/reviewed/human_proteoform_glycosylation_sites_literature.stat.csv",
                    "filename": "human_proteoform_glycosylation_sites_literature.stat.csv"
                }
            }
        ]
    },
    "spec_version": "1.3.0",
    "object_id": "https://biocomputeobject.org/GLY_000143/v-1.5.18",
    "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": "Homo sapiens",
                        "category_name": "species"
                    },
                    {
                        "category_value": "Proteoform",
                        "category_name": "molecule"
                    },
                    {
                        "category_value": "UniCarbKB publications",
                        "category_name": "tags"
                    },
                    {
                        "category_value": "Reviewed",
                        "category_name": "status"
                    },
                    {
                        "category_value": "csv",
                        "category_name": "file_type"
                    },
                    {
                        "category_value": "external",
                        "category_name": "scope"
                    }
                ]
            }
        }
    ],
    "provenance_domain": {
        "license": "https://creativecommons.org/licenses/by/4.0/",
        "name": "Human Protein Glycosylation (Literature)",
        "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": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Xavier Holmes",
                "email": "xavierh@email.gwu.edu"
            }
        ],
        "created": "2019-06-14T14:54:26.195339",
        "modified": "2019-09-12T16:37:13.572422",
        "version": "v-1.5.18"
    },
    "description_domain": {
        "keywords": [
            "proteins",
            "canonical",
            "glycosylation",
            "literature",
            "publications"
        ],
        "pipeline_steps": [
            {
                "name": "make-proteoform-dataset.py",
                "step_number": 1,
                "version": "",
                "input_list": [
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-1.5.18/source/glycosylation_sites_24190977_s5.csv",
                        "filename": "glycosylation_sites_24190977_s5.csv"
                    },
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-1.5.18/source/glycosylation_sites_23090970_s5",
                        "filename": "glycosylation_sites_23090970_s5"
                    },
                    {
                        "uri": ",https://data.glygen.org/ln2data/releases/data/v-1.5.18/source/glycosylation_sites_23090970_s2.csv",
                        "filename": "glycosylation_sites_23090970_s2.csv"
                    }
                ],
                "output_list": [
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-1.5.18/reviewed/human_proteoform_glycosylation_sites_literature.csv",
                        "filename": "human_proteoform_glycosylation_sites_literature.csv"
                    }
                ],
                "prerequisite": [],
                "description": "The supplementary tables from two publications were downloaded and columns \"protein\" and \"site\" were extracted, and additional column evidence where values=\"the respective PMIDs\" was added to produce the input files. A python script was developed process input files 1. to map the UniProtKB accessions to UniProtKB canonical accessions 2. Check position+amino acid with the canonical fasta sequences (https://data.glygen.org/GLYDS000002)to generate the output files."
            }
        ]
    },
    "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-proteoform-dataset.py",
                    "filename": "make-proteoform-dataset.py"
                }
            }
        ]
    },
    "parametric_domain": [
        {
            "step": "",
            "value": "",
            "param": ""
        }
    ],
    "usability_domain": [
        "The dataset provides information on N-glycosylation sites on Human proteins. The data has been processed from the supplementary material from 2 publications (1. \"Deeb, S. J., Cox, J., Schmidt-Supprian, M., & Mann, M. (2013). N-linked Glycosylation Enrichment for In-depth Cell Surface Proteomics of Diffuse Large B-cell Lymphoma Subtypes. Molecular & Cellular Proteomics, 13(1), 240-251. doi:10.1074/mcp.m113.033977\" 2. \"Boersema, P. J., Geiger, T., Wi?niewski, J. R., & Mann, M. (2012). Quantification of theN-glycosylated Secretome by Super-SILAC During Breast Cancer Progression and in Human Blood Samples. Molecular & Cellular Proteomics, 12(1), 158-171. doi:10.1074/mcp.m112.023614\").  The listed protein (UniProtKB) accessions are part of the GlyGen UniProtKB canonical list (https://data.glygen.org/GLYDS000001). "
    ],
    "etag": "",
    "_id": {
        "$oid": "5d03ed62f5c47b17575f69c5"
    }
}