{ "bcoid": "GLY_001047", "title": "Rat Glycan Interaction Data (MatrixDB)", "description": "The Rat Glycan Interaction Data (MatrixDB) dataset contains interaction data between Rattus norvegicus ...", "filename_list": "rat_protein_matrixdb.csv", "filename": "rat_protein_matrixdb.csv", "filetype": "csv", "categories": { "species": [ "Rattus norvegicus" ], "molecule": [ "Protein" ], "tag": [ "MatrixDB" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ], "file_category": [ "others" ] }, "minitable": { "content": [ [ "P15127-1...", "GAG_1..." ], [ "P15127-1...", "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" } ], [ "P15127-1", "GAG_1", "matrixdb:Heparin(short label)", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:21454685", "", "Glycosaminoglycan", "MatrixDB", "matrixdb:GAG_1", "glycan_xref_matrixdb", "GAG_1", "glycan_xref_matrixdb", "GAG_1" ], [ "P15127-1", "GAG_1", "matrixdb:Heparin(short label)", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:21454685", "", "Glycosaminoglycan", "MatrixDB", "matrixdb:GAG_1", "protein_xref_pubmed", "21454685", "glycan_xref_matrixdb", "GAG_1" ] ] }, "readme": "Name\n - Rat Glycan Interaction Data (MatrixDB)\n\nVersion\n - v-2.12.1\n\nModified on\n - 2024-05-21T16:19:48.659Z\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 Rat Glycan Interaction Data (MatrixDB) dataset contains interaction data between Rattus norvegicus [taxid:10116] 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_000244).\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-2.12.1/reviewed/glycan_masterlist.csv\n Name: matrix_db_label.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/misc/matrix_db_label.csv\n Name: matrixdb.tsv\n URI: https:/data.glygen.org/ln2downloads/glytoucan/2026_07_27/export/matrixdb.tsv\n Name: matrixdb_CORE.tab\n URI: https:/data.glygen.org/ln2downloads/matrixdb/2026_05_28/matrixdb_CORE.tab\n Output Subdomain\n Name: rat_protein_matrixdb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/rat_protein_matrixdb.csv\n Name: rat_protein_matrixdb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/rat_protein_matrixdb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\"\n Description: \"\"\n Unique Values: \"149\"", "downloadurl": "/ln2data/releases/data/v-2.12.1/reviewed/rat_protein_matrixdb.csv" }