{
    "bcoid": "GLY_000342",
    "title": "Glycans with NeuAc (Customized table)",
    "description": "The dataset provides glycans that have at least one \"NeuAc\" residue in the current GlyGen dataset (https://data.glygen.org/GLY_000281). ...",
    "filename_list": "glycan_species_customized_neuac_neugc.csv",
    "filename": "glycan_species_customized_neuac_neugc.csv",
    "filetype": "csv",
    "categories": {
        "molecule": [
            "Glycan"
        ],
        "tag": [
            "NeuAc",
            "Mammalian species annotation"
        ],
        "status": [
            "Reviewed"
        ],
        "file_type": [
            "csv"
        ],
        "scope": [
            "internal"
        ],
        "species": [
            "Sus scrofa",
            "Rattus",
            "Homo sapiens",
            "Mus musculus",
            "Severe acute respiratory syndrome coronavirus 2",
            "Rattus norvegicus",
            "Drosophila melanogaster",
            "Saccharomyces cerevisiae",
            "Hepacivirus C"
        ]
    },
    "minitable": {
        "content": [
            [
                "G00002CF...",
                "9913..."
            ],
            [
                "G00002CF...",
                "9606..."
            ]
        ],
        "headers": [
            "glytoucan_ac...",
            "tax_id..."
        ],
        "colwidth": [
            "40%",
            "20%"
        ]
    },
    "sampledata": {
        "type": "table",
        "data": [
            [
                {
                    "type": "string",
                    "label": "glytoucan_ac"
                },
                {
                    "type": "string",
                    "label": "tax_id"
                },
                {
                    "type": "string",
                    "label": "tax_name"
                },
                {
                    "type": "string",
                    "label": "annotation_category"
                },
                {
                    "type": "string",
                    "label": "source"
                },
                {
                    "type": "string",
                    "label": "source_id"
                },
                {
                    "type": "string",
                    "label": "original_source_id"
                },
                {
                    "type": "string",
                    "label": "xref_key"
                },
                {
                    "type": "string",
                    "label": "xref_id"
                },
                {
                    "type": "string",
                    "label": "is_motif"
                }
            ],
            [
                "G00002CF",
                "9913",
                "Bos taurus",
                "Subsumption",
                "GNOme",
                "G84891DZ",
                "",
                "glycan_xref_gnome",
                "G84891DZ",
                "False"
            ],
            [
                "G00002CF",
                "9606",
                "Homo sapiens",
                "Subsumption",
                "GNOme",
                "G84891DZ",
                "",
                "glycan_xref_gnome",
                "G84891DZ",
                "False"
            ]
        ]
    },
    "readme": "Name\n   - Glycans with NeuAc (Customized table)\n\nVersion\n   - v-2.10.1\n\nCreated on\n  - 2020-03-02T14:23:10.848312\n\nModified on\n   - 2024-08-02T15:46:32.188Z\n\nCreated by\n   - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Kate Warner [k.warner1@gwu.edu]\n\nAuthors\n   - Nathan Edwards [nje5@georgetown.edu]\n\nChecksum\n   - \n\nUsability Domain\n   - The dataset provides glycans that have at least one \"NeuAc\" residue in the current GlyGen dataset (https://data.glygen.org/GLY_000281). The GlyTouCan accessions included in this list have mammalian species annotation (human/mouse/rat) through direct TaxID annotation and/or inferred via subsumption. This table was customized based on a GlyGen user query submitted through GlyGen help on Feb 17th 2020.\n\nDescription Domain\n   Keywords\n   - Glycan\n   - GlyTouCan Accession\n   - NeuAc\n   - Mammalian species annotation \n\n   Pipeline Steps\n   - Step-1: Based on the submitted user query (different sialic acid-containing mammalian glycan structures reported in your database), the  list of glycans that have \"NeuAc\" were from input file 1 (monocomp.tsv;column:5 ;filter:not \"0\"). The selected GlyTouCan accessions were mapped to input file 2 (glycan_species.tsv) where the value is \"true\".  \n\nExecution Domain\n   Scripts   - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/A\n\n\n   Software Prerequisites\n      Name: Python\n      Version: 2.7.5\n      URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n   Input Subdomain\n      Name: glycan_monosaccharide_composition.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/glycan_monosaccharide_composition.csv\n      Name: glycan_species.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/glycan_species.csv\n   Output Subdomain\n      Name: glycan_species_customized_neuac_neugc.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/glycan_species_customized_neuac_neugc.csv\n      Name: glycan_species_customized_neuac_neugc.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.10.1/reviewed/glycan_species_customized_neuac_neugc.stat.csv\n\nFields\n      Name: \"glytoucan_ac\"\n     Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n      Unique Values: \"13004\"\n      Name: \"tax_id\"\n     Description: \"NCBI Taxonomy database Identifier\"\n      Unique Values: \"13\"\n      Name: \"tax_name\"\n     Description: \"NCBI Taxonomy name\"\n      Unique Values: \"13\"\n      Name: \"annotation_category\"\n     Description: \"Species annotation category of the glycan. Category could be either direct or subsumption\"\n      Unique Values: \"2\"\n      Name: \"source\"\n     Description: \"Source for the data\"\n      Unique Values: \"15\"\n      Name: \"source_id\"\n     Description: \"source database id of the species annoation for the glycan.\"\n      Unique Values: \"6429\"\n      Name: \"original_source_id\"\n     Description: \"Original source id of the species annoation for the glycan. This columns contains values where the source id is not a valid database id. \"\n      Unique Values: \"131\"\n      Name: \"xref_key\"\n     Description: \"Source key associated to the  xref_id\"\n      Unique Values: \"10\"\n      Name: \"xref_id\"\n     Description: \"ID of the X-ref\"\n      Unique Values: \"5935\"\n      Name: \"is_motif\"\n     Description: \"\"\n      Unique Values: \"2\"",
    "downloadurl": "/ln2data/releases/data/v-2.10.1/reviewed/glycan_species_customized_neuac_neugc.csv"
}