{
    "bcoid": "GLY_000332",
    "title": "Human Interaction data (MatrixDB)",
    "description": "The Human Interaction data (MatrixDB) dataset contains interaction data between Human [taxid:9606] proteins ...",
    "filename": "human_protein_matrixdb.csv",
    "filetype": "csv",
    "categories": {
        "species": "Homo sapiens",
        "molecule": "Protein",
        "tags": "MatrixDB",
        "file_type": "csv",
        "status": "Reviewed",
        "scope": "internal"
    },
    "minitable": {
        "content": [
            [
                "Q9BY76-1...",
                "matrixdb:GAG..."
            ],
            [
                "P00441-1...",
                "matrixdb:GAG..."
            ]
        ],
        "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": "chebi_id"
                },
                {
                    "type": "string",
                    "label": "gag_interactor_biological_role"
                },
                {
                    "type": "string",
                    "label": "protein_interactor_biological_role"
                },
                {
                    "type": "string",
                    "label": "evidence"
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                    "type": "string",
                    "label": "saccharide"
                }
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        ]
    },
    "readme": "Name\n   - Human Interaction data (MatrixDB)\n\nVersion\n   - 1.5.30\n\nCreated on\n  - 2020-02-10T12:42:38.432328\n\nModified on\n   - 2020-05-01T15:23:10.031133\n\nCreated by\n   - Rahi Navelkar [rsn13@gwu.edu], Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu]\n\nAuthors\n   - Sylvie Ricard-Blum [sylvie.ricard-blum@univ-lyon1.fr]\n\nChecksum\n   - \n\nUsability Domain\n   - The Human Interaction data (MatrixDB) dataset contains interaction data between Human [taxid:9606] 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/GLYDS000001).\n\nExecution Domain\n   Scripts   - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/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: matrixdb_CORE.csv\n      URI: https://data.glygen.org/ln2data/releases/data/v-1.5.30/source/matrixdb_CORE.csv\n      Name: human_protein_masterlist.csv\n      URI: https://data.glygen.org/ln2data/releases/data/v-1.5.30/reviewed/human_protein_masterlist.csv\n   Output Subdomain\n      Name: human_protein_matrixdb.csv\n      URI: http://data.glygen.org/ln2data/releases/data/v-1.5.30/reviewed/human_protein_matrixdb.csv\n      Name: human_protein_matrixdb.stat.csv\n      URI: http://data.glygen.org/ln2data/releases/data/v-1.5.30/reviewed/human_protein_matrixdb.stat.csv\n\nFields\n      Name: \"protein_interactor_biological_role\"\n     Description: \"Biological role of the protein from MatrixDB\"\n      Unique Values: \"2\"\n      Name: \"uniprotkb_canonical_ac\"\n     Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n      Unique Values: \"62\"\n      Name: \"matrix_db_id\"\n     Description: \"Entity identifier from MatrixDB database\"\n      Unique Values: \"6\"\n      Name: \"evidence\"\n     Description: \"NCBI PubMed Id (PMID) or DOI (Digital Object Identifier) as evidence for the entry/annotation\"\n      Unique Values: \"79\"\n      Name: \"chebi_id\"\n     Description: \"Entity identifier from ChEBI  database\"\n      Unique Values: \"6\"\n      Name: \"saccharide\"\n     Description: \"Sugar\"\n      Unique Values: \"4\"\n      Name: \"gag_interactor_biological_role\"\n     Description: \"Biological role of the Glycosylaminoglycan from MatrixDB\"\n      Unique Values: \"3\"",
    "downloadurl": "/ln2data/releases/data/v-1.5.30/reviewed/human_protein_matrixdb.csv"
}