{
    "object_id": "https://biocomputeobject.org/GLY_000068/v-1.0.13",
    "license": "https://creativecommons.org/licenses/by/4.0/",
    "contributors": [
        {
            "orcid": "",
            "affiliation": "George Washington University",
            "contribution": [
                "createdBy"
            ],
            "name": "Rahi Navelkar",
            "email": "rsn13@gwu.edu"
        },
        {
            "orcid": "",
            "affiliation": "George Washington University",
            "contribution": [
                "authoredBy"
            ],
            "name": "Brian Fochtman ",
            "email": "bfochtman@email.gwu.edu"
        },
        {
            "orcid": "",
            "affiliation": "Georgetown University",
            "contribution": [
                "contributedBy"
            ],
            "name": "Nathan Edwards",
            "email": "nje5@georgetown.edu"
        },
        {
            "orcid": "",
            "affiliation": "George Washington University",
            "contribution": [
                "contributedBy"
            ],
            "name": "Reza Mousavi",
            "email": "rezamousavi@gwmail.gwu.edu"
        }
    ],
    "created": "2019-01-23T17:21:05.936736",
    "spec_version": "1.3.0",
    "modified": "2019-01-30T14:44:34.677598",
    "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": "Reviewed",
                        "category_name": "status"
                    }
                ]
            }
        }
    ],
    "io_domain": {
        "input_subdomain": [
            {
                "uri": {
                    "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/allmotif.txt",
                    "filename": "allmotif.txt"
                }
            },
            {
                "uri": {
                    "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/glycan_type.txt",
                    "filename": "glycan_type.txt"
                }
            },
            {
                "uri": {
                    "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/glycan_subtype.txt",
                    "filename": "glycan_subtype.txt"
                }
            }
        ],
        "output_subdomain": [
            {
                "mediatype": "",
                "uri": {
                    "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/reviewed/human_glycan_classification.csv",
                    "filename": "human_glycan_classification.csv"
                }
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/reviewed/human_glycan_classification.stat.csv",
                    "filename": "human_glycan_classification.stat.csv"
                }
            }
        ]
    },
    "provenance_domain": {
        "license": "https://creativecommons.org/licenses/by/4.0/",
        "name": "Human Glycan Classification",
        "contributors": [
            {
                "affiliation": "George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Rahi Navelkar",
                "email": "rsn13@gwu.edu"
            },
            {
                "affiliation": "George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Jeet Vora",
                "email": "jeetvora@gwu.edu"
            },
            {
                "affiliation": "George Washington University",
                "contribution": [
                    "authoredBy"
                ],
                "name": "Brian Fochtman ",
                "email": "bfochtman@email.gwu.edu"
            },
            {
                "affiliation": "Georgetown University",
                "contribution": [
                    "contributedBy"
                ],
                "name": "Nathan Edwards",
                "email": "nje5@georgetown.edu"
            },
            {
                "affiliation": "George Washington University",
                "contribution": [
                    "contributedBy"
                ],
                "name": "Reza Mousavi",
                "email": "rezamousavi@gwmail.gwu.edu"
            }
        ],
        "created": "2019-01-23T17:21:05.936736",
        "modified": "2019-04-12T14:22:16.241444",
        "version": "v-1.0.13"
    },
    "description_domain": {
        "keywords": [
            "GlyTouCan",
            "Glycan",
            "Classification",
            "Motifs"
        ],
        "pipeline_steps": [
            {
                "name": "python",
                "step_number": 1,
                "version": "",
                "input_list": [
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/allmotif.txt",
                        "filename": "allmotif.txt"
                    },
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/glycan_type.txt",
                        "filename": "glycan_type.txt"
                    },
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/glycan_subtype.txt",
                        "filename": "glycan_subtype.txt"
                    }
                ],
                "output_list": [
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/human_glycan_classification.csv",
                        "filename": "human_glycan_classification.csv"
                    }
                ],
                "prerequisite": [
                    {
                        "name": "",
                        "uri": {
                            "uri": "",
                            "filename": ""
                        }
                    }
                ],
                "description": "The input file was downloaded from the source link and the column 'Label' was filtered for specific values. (N-Glycan complex, N-Glycan core basic ,N-Glycan high mannose ,N-Glycan hybrid,N-Glycan truncated motif. First GlcpNAC cut off, O-Glycan core 1, O-Glycan core 1 fuzzy, O-Glycan core 2, O-Glycan core 2 fuzzy, O-Glycan core 3, O-Glycan core 3 fuzzy,             O-Glycan core 4, O-Glycan core 4 fuzzy, O-Glycan core 5, O-Glycan core 5 fuzzy, O-Glycan core 6, O-Glycan core 6 Fuzzy, O-Glycan core 7, O-Glycan core 7 fuzzy)"
            },
            {
                "name": "python",
                "step_number": 1,
                "version": "",
                "input_list": [],
                "output_list": [],
                "prerequisite": [],
                "description": "The values were separated into two column individual input text files (glytoucan_acc|glycan_type/glycan_subtype) using a python script [make-glycan_classification-txt.py]. Following rules were applied to GlyTouCan accessions which had one of the following scenarios for subtypes: a) high mannose |hybrid = hybrid b) complex | hybrid = hybrid c) core basic = no subtype d) core x | core x fuzzy = core x  [where x= 1-7]  e) core x fuzzy = no subtype [where x= 1-7] f) core 1| core 2| core 6 = core 2  g) core 3| core 4 | core 6 = core 6"
            },
            {
                "name": "",
                "step_number": 1,
                "version": "",
                "input_list": [],
                "output_list": [],
                "prerequisite": [],
                "description": "The individual input file(s) were processed based on the compiled glycan list using a python script[make-glycan-csv.py] to generate the final output csv file."
            }
        ]
    },
    "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/blob/master/integration/ ",
                    "filename": "make-glycan_classification-txt.py"
                }
            },
            {
                "uri": {
                    "uri": "https://github.com/glygener/glygen-backend/blob/master/integration/ ",
                    "filename": "make-glycan-csv.py"
                }
            }
        ]
    },
    "version": "1.0.5",
    "error_domain": {
        "empirical_error": {},
        "algorithmic_error": {},
        "emperical_error": {}
    },
    "parametric_domain": [
        {
            "step": "",
            "value": "",
            "param": ""
        }
    ],
    "usability_domain": [
        "List of Glycans identified by GlyTouCan Accessions with infomation on the the glycan type and glycan sub-type."
    ],
    "etag": "35ee2827bf4b2ec4e03602a687ca6c1c",
    "_id": {
        "$oid": "5c48e8d1f5c47b65ae4b5d2f"
    },
    "name": "Human Glycan Classification"
}