{ "bcoid": "GLY_000333", "title": "Mouse Interaction data (MatrixDB)", "description": "The Mouse Interaction data (MatrixDB) dataset contains interaction data between Mouse [taxid:10090] proteins ...", "filename": "mouse_protein_matrixdb.csv", "filetype": "csv", "categories": { "species": "Mus musculus", "molecule": "Protein", "tags": "MatrixDB", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P01587-1...", "matrixdb:GAG..." ], [ "P01587-1...", "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" } ], [ "P01587-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:16027123" ], [ "P01587-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:16027123" ], [ "P07214-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:19542224" ], [ "P12850-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:15183770" ], [ "P16092-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:12034712" ], [ "P16092-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:12034712" ], [ "P16092-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:12034712" ], [ "P19137-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:10022829" ], [ "P19137-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:10022829" ], [ "P19137-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:10893232" ], [ "P19137-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:10893232" ], [ "P19137-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:11304538" ], [ "P19137-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:11304538" ], [ "P22777-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:9500522" ], [ "P39876-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:10900194" ], [ "P97927-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:10893232" ], [ "P97927-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:10893232" ], [ "Q9Z0E2-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:15381701" ], [ "Q91V88-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:23357641" ], [ "Q91V88-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "imex:IM-20972" ], [ "Q05793-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:9431988" ], [ "Q60675-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:10022829" ], [ "Q60675-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:10022829" ], [ "Q60675-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:11304538" ], [ "Q61001-1", "matrixdb:GAG_1", "CHEBI:28304", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:11304538" ], [ "P16092-1", "matrixdb:GAG_2", "CHEBI:28815", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:12034712" ], [ "Q91V88-1", "matrixdb:GAG_2", "CHEBI:28815", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:23357641" ], [ "Q91V88-1", "matrixdb:GAG_2", "CHEBI:28815", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "imex:IM-20972" ], [ "P07214-1", "matrixdb:GAG_3", "CHEBI:18376", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:19542224" ], [ "P36363-1", "matrixdb:GAG_6", "CHEBI:37397", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:24447999" ], [ "P36363-1", "matrixdb:GAG_6", "CHEBI:37397", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "imex:IM-22964" ], [ "P37237-1", "matrixdb:GAG_6", "CHEBI:37397", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:24447999" ], [ "P37237-1", "matrixdb:GAG_6", "CHEBI:37397", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "imex:IM-22964" ], [ "P61148-1", "matrixdb:GAG_6", "CHEBI:37397", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:24447999" ], [ "P61148-1", "matrixdb:GAG_6", "CHEBI:37397", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "imex:IM-22964" ], [ "Q91V88-1", "matrixdb:GAG_7", "CHEBI:52562", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "pubmed:23357641" ], [ "Q91V88-1", "matrixdb:GAG_7", "CHEBI:52562", "psi-mi:MI:0499(unspecified role)", "psi-mi:MI:0499(unspecified role)", "imex:IM-20972" ] ] }, "readme": "Name\n - Mouse Interaction data (MatrixDB)\n\nVersion\n - 1.5.23\n\nCreated on\n - 2020-02-10T14:02:01.224476\n\nModified on\n - 2020-03-10T11:07:40.035869\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 Mouse Interaction data (MatrixDB) dataset contains interaction data between Mouse [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/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-1.5.23/source/matrixdb_CORE.csv\n Name: mouse_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/mouse_protein_masterlist.csv\n Output Subdomain\n Name: mouse_protein_matrixdb.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/mouse_protein_matrixdb.csv\n Name: mouse_protein_matrixdb.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/mouse_protein_matrixdb.stat.csv\n\nFields\n Name: \"protein_interactor_biological_role\"\n Description: \"Biological role of the protein from MatrixDB\"\n Unique Values: \"1\"\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: \"16\"\n Name: \"matrix_db_id\"\n Description: \"Entity identifier from MatrixDB database\"\n Unique Values: \"5\"\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: \"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\"", "downloadurl": "/ln2data/releases/data/v-1.5.23/reviewed/mouse_protein_matrixdb.csv" }