{
    "bcoid": "GLY_000333",
    "title": "Mouse Glycan Interaction Data (MatrixDB)",
    "description": "The Mouse Glycan Interaction Data (MatrixDB) dataset contains interaction data between Mus musculus [taxid:10090] ...",
    "filename_list": "mouse_protein_matrixdb.csv",
    "filename": "mouse_protein_matrixdb.csv",
    "filetype": "csv",
    "categories": {
        "species": [
            "Mus musculus"
        ],
        "molecule": [
            "Protein"
        ],
        "tag": [
            "MatrixDB"
        ],
        "file_type": [
            "csv"
        ],
        "status": [
            "Reviewed"
        ],
        "scope": [
            "internal"
        ]
    },
    "minitable": {
        "content": [
            [
                "P01587-1...",
                "GAG_1..."
            ],
            [
                "P01587-1...",
                "GAG_1..."
            ]
        ],
        "headers": [
            "uniprotkb_ca...",
            "matrix_db_id..."
        ],
        "colwidth": [
            "40%",
            "20%"
        ]
    },
    "sampledata": {
        "type": "table",
        "data": [
            [
                {
                    "type": "string",
                    "label": "uniprotkb_canonical_ac"
                },
                {
                    "type": "string",
                    "label": "matrix_db_id"
                },
                {
                    "type": "string",
                    "label": "matrix_db_label"
                },
                {
                    "type": "string",
                    "label": "chebi_id"
                },
                {
                    "type": "string",
                    "label": "gag_interactor_biological_role"
                },
                {
                    "type": "string",
                    "label": "protein_interactor_biological_role"
                },
                {
                    "type": "string",
                    "label": "evidence"
                },
                {
                    "type": "string",
                    "label": "saccharide"
                },
                {
                    "type": "string",
                    "label": "interaction_type"
                },
                {
                    "type": "string",
                    "label": "source"
                },
                {
                    "type": "string",
                    "label": "source_id"
                },
                {
                    "type": "string",
                    "label": "xref_key"
                },
                {
                    "type": "string",
                    "label": "xref_id"
                },
                {
                    "type": "string",
                    "label": "src_xref_key"
                },
                {
                    "type": "string",
                    "label": "src_xref_id"
                }
            ],
            [
                "P01587-1",
                "GAG_1",
                "matrixdb:Heparin(short label)",
                "CHEBI:28304",
                "psi-mi:MI:0499(unspecified role)",
                "psi-mi:MI:0499(unspecified role)",
                "pubmed:16027123",
                "",
                "Glycosaminoglycan",
                "MatrixDB",
                "matrixdb:GAG_1",
                "glycan_xref_matrixdb",
                "GAG_1",
                "glycan_xref_matrixdb",
                "GAG_1"
            ],
            [
                "P01587-1",
                "GAG_1",
                "matrixdb:Heparin(short label)",
                "CHEBI:28304",
                "psi-mi:MI:0499(unspecified role)",
                "psi-mi:MI:0499(unspecified role)",
                "pubmed:16027123",
                "",
                "Glycosaminoglycan",
                "MatrixDB",
                "matrixdb:GAG_1",
                "protein_xref_pubmed",
                "16027123",
                "glycan_xref_matrixdb",
                "GAG_1"
            ]
        ]
    },
    "readme": "Name\n   - Mouse Glycan Interaction Data (MatrixDB)\n\nVersion\n   - v-2.7.1\n\nCreated on\n  - 2020-02-10T14:02:01.224476\n\nModified on\n   - 2024-05-21T16:19:31.828Z\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   - Sylvie Ricard-Blum [sylvie.ricard-blum@univ-lyon1.fr]\n\nChecksum\n   - \n\nUsability Domain\n   - The Mouse Glycan Interaction Data (MatrixDB) dataset contains interaction data between Mus musculus [taxid:10090] proteins and Glycosaminoglycans (GAGs) from MatrixDB database (http://matrixdb.univ-lyon1.fr/ ;PMID:19147664). If you use this dataset please provide proper attribution to MatrixDB and GlyGen.\n\nDescription Domain\n   Keywords\n   - protein-GAGs interaction\n   - MatrixDB\n\n   Pipeline Steps\n   - Step-1: The tab file (matrixdb_CORE.tab (labeled as \u201cCore MatrixDB dataset as PSI-MI TAB 2.7 file\u201d) was downloaded directly from the MatrixDB database. Following rules were applied to extract specific data from the file. The rules were also verified by the author. 1)Rule 1: where column \"Alt. ID(s) interactor A\" has \"GAG\" AND column \"ID(s) interactor B\" has \"uniprotkb\" as prefixs. 2)Rule 2: where column \"Alt. ID(s) interactor B\" has \"GAG\" AND column \"#ID(s) interactor A\" has \"uniprotkb\" as prefixes. 3)for Rule 1: 3a) Add values from column \"Biological role(s) interactor A\" to new column \"gag_interactor_biological_role\". 3b)Add from column \"Biological role(s) interactor B\" to new column \"protein_interactor_biological_role\".3c)Add  from column \"Publication Identifier(s)\" to new column \"evidence\". 4)for Rule 2: 4a)Add values from\"Biological role(s) interactor A\" to column \"protein_interactor_biological_role\". 4b)Add  from \"Biological role(s) interactor B\" to column gag_interactor_biological_role\". 4c)Add from \"Publication Identifier(s)\" to column \"evidence\". 5) finally the UniProtKB accessions were mapped to UniProtKB canonical accessions based on the GlyGen protein master list (https://data.glygen.org/GLY_000007).\n\nExecution Domain\n   Scripts   - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-protein-dataset.py\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_masterlist.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/glycan_masterlist.csv\n      Name: matrix_db_label.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/misc/matrix_db_label.csv\n      Name: matrixdb.tsv\n      URI: https:/data.glygen.org/ln2downloads/glytoucan/2024_10_01/export/matrixdb.tsv\n      Name: matrixdb_CORE.tab\n      URI: https:/data.glygen.org/ln2downloads/matrixdb/2024_09_05/matrixdb_CORE.tab\n   Output Subdomain\n      Name: mouse_protein_matrixdb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/mouse_protein_matrixdb.csv\n      Name: mouse_protein_matrixdb.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/mouse_protein_matrixdb.stat.csv\n\nFields\n      Name: \"uniprotkb_canonical_ac\"\n     Description: \"\"\n      Unique Values: \"16\"\n      Name: \"matrix_db_id\"\n     Description: \"Entity identifier from MatrixDB database \"\n      Unique Values: \"5\"\n      Name: \"matrix_db_label\"\n     Description: \"Name of the entity associated with a MatrixDB ID\"\n      Unique Values: \"6\"\n      Name: \"chebi_id\"\n     Description: \"Entity identifier from ChEBI  database \"\n      Unique Values: \"5\"\n      Name: \"gag_interactor_biological_role\"\n     Description: \"Biological role of the Glycosylaminoglycan from MatrixDB\"\n      Unique Values: \"1\"\n      Name: \"protein_interactor_biological_role\"\n     Description: \"Biological role of the protein from MatrixDB\"\n      Unique Values: \"1\"\n      Name: \"evidence\"\n     Description: \"NCBI PubMed Id (PMID) or DOI (Digital Object Identifier) as evidence for the entry/annotation\"\n      Unique Values: \"15\"\n      Name: \"saccharide\"\n     Description: \"Sugar\"\n      Unique Values: \"3\"\n      Name: \"interaction_type\"\n     Description: \"Type of interaction\"\n      Unique Values: \"1\"\n      Name: \"source\"\n     Description: \"Source for the data\"\n      Unique Values: \"2\"\n      Name: \"source_id\"\n     Description: \"source database id of the species annoation for the glycan.\"\n      Unique Values: \"5\"\n      Name: \"xref_key\"\n     Description: \"Source key associated to the  xref_id\"\n      Unique Values: \"2\"\n      Name: \"xref_id\"\n     Description: \"ID of the X-ref\"\n      Unique Values: \"18\"\n      Name: \"src_xref_key\"\n     Description: \"Source Xref  key\"\n      Unique Values: \"1\"\n      Name: \"src_xref_id\"\n     Description: \"Source X-ref ID\"\n      Unique Values: \"5\"",
    "downloadurl": "/ln2data/releases/data/v-2.7.1/reviewed/mouse_protein_matrixdb.csv"
}