{
    "object_id": "https://biocomputeobject.org/GLY_000062/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": [
                "createdBy"
            ],
            "name": "Brian Fochtman ",
            "email": "bfochtman@email.gwu.edu"
        },
        {
            "orcid": "",
            "affiliation": "Georgetown University",
            "contribution": [
                "contributedBy"
            ],
            "name": "Nathan Edwards",
            "email": "nje5@georgetown.edu"
        }
    ],
    "created": "2019-01-23T17:21:05.928353",
    "spec_version": "1.3.0",
    "modified": "2019-01-30T14:39:23.400652",
    "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/gdb.txt ",
                    "filename": "gdb.txt "
                }
            },
            {
                "uri": {
                    "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/glycomedb.txt",
                    "filename": "glycomedb.txt"
                }
            },
            {
                "uri": {
                    "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/glyco.txt",
                    "filename": "glyco.txt"
                }
            },
            {
                "uri": {
                    "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/pbch.txt",
                    "filename": "pbch.txt"
                }
            },
            {
                "uri": {
                    "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/taxa.txt",
                    "filename": "taxa.txt"
                }
            },
            {
                "uri": {
                    "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/uckb.txt",
                    "filename": "uckb.txt"
                }
            },
            {
                "uri": {
                    "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/mouseprot.txt",
                    "filename": "mouseprot.txt"
                }
            },
            {
                "uri": {
                    "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/ucdb.txt",
                    "filename": "ucdb.txt"
                }
            },
            {
                "uri": {
                    "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/pdb.txt",
                    "filename": "pdb.txt"
                }
            }
        ],
        "output_subdomain": [
            {
                "mediatype": "",
                "uri": {
                    "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/reviewed/mouse_glycan_idmapping.csv",
                    "filename": "mouse_glycan_idmapping.csv"
                }
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/reviewed/mouse_glycan_idmapping.stat.csv",
                    "filename": "mouse_glycan_idmapping.stat.csv"
                }
            }
        ]
    },
    "provenance_domain": {
        "license": "https://creativecommons.org/licenses/by/4.0/",
        "name": "Mouse Glycome Accessions",
        "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": "Georgetown University",
                "contribution": [
                    "contributedBy"
                ],
                "name": "Nathan Edwards",
                "email": "nje5@georgetown.edu"
            },
            {
                "affiliation": "George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Brian Fochtman ",
                "email": "bfochtman@email.gwu.edu"
            }
        ],
        "created": "2019-01-23T17:21:05.928353",
        "modified": "2019-04-12T13:57:36.819312",
        "version": "v-1.0.13"
    },
    "description_domain": {
        "keywords": [
            "GlyTouCan",
            "Glycan"
        ],
        "pipeline_steps": [
            {
                "name": "python",
                "step_number": 1,
                "version": "",
                "input_list": [
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/gdb.txt",
                        "filename": "gdb.txt"
                    },
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/glycomedb.txt",
                        "filename": "glycomedb.txt"
                    },
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/glyco.txt",
                        "filename": "glyco.txt"
                    },
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/pbch.txt",
                        "filename": "pbch.txt"
                    },
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/taxa.txt",
                        "filename": "taxa.txt"
                    },
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/uckb.txt",
                        "filename": "uckb.txt"
                    },
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/mouseprot.txt",
                        "filename": "mouseprot.txt"
                    },
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/ucdb.txt",
                        "filename": "ucdb.txt"
                    },
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/pdb.txt",
                        "filename": "pdb.txt"
                    }
                ],
                "output_list": [
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-1.0.13/reviewed/mouse_glycan_idmapping.csv",
                        "filename": "mouse_glycan_idmapping.csv"
                    }
                ],
                "prerequisite": [],
                "description": "The input file(s) were downloaded from the source link and were seperated into individual 2 column input files (glytoucan_acc, database_id) if required and 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. The List of GlyTouCans(glycan list) is compiled when the GlyTouCan accession is observed underone or more following criteria:  a) If the glycan has source/taxonomy annotation[taxid:10090] in GlyTouCan b) If the glycan is listed on mouse[taxid:10090] glycan webpage at UniCarbKB c) If the glycan is listed on a mouse[taxid:10090] protein webpage at UniCarbKB d) If the glycan is synthesized by a mouse[taxid:10090] protein [http://data.glygen.org/GLYDS00065] e) If the glycan is known to be attached to a mouse[taxid:10090] protein [http://data.glygen.org/GLYDS00041] f) If the glycan is a motif of the glycan mentioned under criteria a-f "
            }
        ]
    },
    "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-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 mapped to different databases."
    ],
    "etag": "bde11dd895a6a424ec656f4ad79683aa",
    "_id": {
        "$oid": "5c48e8d1f5c47b65ae4b5d29"
    },
    "name": "Mouse Glycome Accessions"
}