{ "bcoid": "GLY_000248", "title": "Rat UniProtKB Xref Pfam", "description": "The Rat UniProtKB Xref Pfam contains rat [taxid:10116] UniProtKB canonical accessions cross-referenced ...", "filename": "rat_protein_xref_pfam.csv", "filetype": "csv", "categories": { "species": "Rattus norvegicus", "molecule": "Protein", "tags": "Pfam cross-references", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q5RJK9-1...", "protein_xref..." ], [ "Q5RJK9-1...", "protein_xref..." ] ], "headers": [ "uniprotkb_ca...", "xref_key..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "xref_label" } ], [ "Q5RJK9-1", "protein_xref_pfam", "PF01193", "RNA_pol_L" ], [ "Q5RJK9-1", "protein_xref_pfam", "PF01000", "RNA_pol_A_bac" ], [ "Q5RJK8-1", "protein_xref_pfam", "PF12796", "Ank_2" ], [ "Q5RJK8-1", "protein_xref_pfam", "PF00887", "ACBP" ], [ "D3ZZY8-1", "protein_xref_pfam", "PF13853", "7tm_4" ], [ "D3ZG10-1", "protein_xref_pfam", "PF00017", "SH2" ], [ "D3ZG10-1", "protein_xref_pfam", "PF00018", "SH3_1" ], [ "D3ZB44-1", "protein_xref_pfam", "PF01352", "KRAB" ], [ "D3ZB44-1", "protein_xref_pfam", "PF00096", "zf-C2H2" ], [ "Q5RJK0-1", "protein_xref_pfam", "PF07092", "DUF1356" ], [ "Q5RJK3-1", "protein_xref_pfam", "PF01746", "tRNA_m1G_MT" ], [ "P30349-1", "protein_xref_pfam", "PF01433", "Peptidase_M1" ], [ "P30349-1", "protein_xref_pfam", "PF09127", "Leuk-A4-hydro_C" ], [ "Q5RJK5-1", "protein_xref_pfam", "PF01393", "Chromo_shadow" ], [ "Q5RJK5-1", "protein_xref_pfam", "PF00385", "Chromo" ], [ "D3ZB48-1", "protein_xref_pfam", "PF05622", "HOOK" ], [ "Q5RJK6-1", "protein_xref_pfam", "PF00459", "Inositol_P" ], [ "A0A096MKC6-1", "protein_xref_pfam", "PF00061", "Lipocalin" ], [ "Q6MG55-1", "protein_xref_pfam", "PF00561", "Abhydrolase_1" ], [ "Q6MG56-1", "protein_xref_pfam", "PF07686", "V-set" ], [ "A0A0G2K0H3-1", "protein_xref_pfam", "PF00057", "Ldl_recept_a" ], [ "A0A0G2K0H3-1", "protein_xref_pfam", "PF00058", "Ldl_recept_b" ], [ "Q5XIH0-1", "protein_xref_pfam", "PF09174", "Maf1" ], [ "Q6MG51-1", "protein_xref_pfam", "PF15576", "DUF4661" ], [ "F1M2W7-1", "protein_xref_pfam", "PF00188", "CAP" ], [ "D4AAV0-1", "protein_xref_pfam", "PF10401", "IRF-3" ], [ "D4AAV0-1", "protein_xref_pfam", "PF00605", "IRF" ], [ "P20961-1", "protein_xref_pfam", "PF00079", "Serpin" ], [ "Q6MG59-1", "protein_xref_pfam", "PF15096", "G6B" ], [ "P01805-1", "protein_xref_pfam", "PF07686", "V-set" ], [ "Q4KLP0-1", "protein_xref_pfam", "PF00676", "E1_dh" ], [ "Q4KLP0-1", "protein_xref_pfam", "PF02779", "Transket_pyr" ], [ "Q4KLP0-1", "protein_xref_pfam", "PF16870", "OxoGdeHyase_C" ], [ "M0RAP0-1", "protein_xref_pfam", "PF01157", "Ribosomal_L21e" ], [ "M0RAP6-1", "protein_xref_pfam", "PF12509", "DUF3715" ], [ "A0A0G2JVG5-1", "protein_xref_pfam", "PF14988", "DUF4515" ], [ "A0A0G2JVG6-1", "protein_xref_pfam", "PF00096", "zf-C2H2" ], [ "M0RAP5-1", "protein_xref_pfam", "PF00169", "PH" ], [ "M0RAP5-1", "protein_xref_pfam", "PF12335", "SBF2" ], [ "M0RAP5-1", "protein_xref_pfam", "PF06602", "Myotub-related" ], [ "M0RAP5-1", "protein_xref_pfam", "PF02893", "GRAM" ], [ "M0RAP5-1", "protein_xref_pfam", "PF02141", "DENN" ], [ "M0RAP5-1", "protein_xref_pfam", "PF03456", "uDENN" ], [ "A0A0G2JVG8-1", "protein_xref_pfam", "PF13853", "7tm_4" ], [ "F1M1W4-1", "protein_xref_pfam", "PF10176", "DUF2370" ], [ "P34997-1", "protein_xref_pfam", "PF00001", "7tm_1" ], [ "M0R5G7-1", "protein_xref_pfam", "PF11759", "KRTAP" ], [ "Q9WUD9-1", "protein_xref_pfam", "PF00017", "SH2" ], [ "Q9WUD9-1", "protein_xref_pfam", "PF00018", "SH3_1" ], [ "Q9WUD9-1", "protein_xref_pfam", "PF07714", "Pkinase_Tyr" ], [ "M0R5G5-1", "protein_xref_pfam", "PF01825", "GPS" ], [ "M0R5G5-1", "protein_xref_pfam", "PF02140", "Gal_Lectin" ], [ "M0R5G5-1", "protein_xref_pfam", "PF00059", "Lectin_C" ], [ "M0R5G5-1", "protein_xref_pfam", "PF08016", "PKD_channel" ], [ "M0R5G5-1", "protein_xref_pfam", "PF01477", "PLAT" ], [ "M0R5G5-1", "protein_xref_pfam", "PF02010", "REJ" ], [ "Q8R553-1", "protein_xref_pfam", "PF00028", "Cadherin" ], [ "Q9QX69-1", "protein_xref_pfam", "PF05147", "LANC_like" ], [ "P30348-1", "protein_xref_pfam", "PF00048", "IL8" ], [ "Q9WUD2-1", "protein_xref_pfam", "PF12796", "Ank_2" ], [ "Q9WUD2-1", "protein_xref_pfam", "PF00520", "Ion_trans" ], [ "A0A0G2JUK9-1", "protein_xref_pfam", "PF13853", "7tm_4" ], [ "D3ZLV0-1", "protein_xref_pfam", "PF13853", "7tm_4" ], [ "Q07969-1", "protein_xref_pfam", "PF01130", "CD36" ], [ "D3ZLV5-1", "protein_xref_pfam", "PF12443", "AKNA" ], [ "A0A096MJY8-1", "protein_xref_pfam", "PF00108", "Thiolase_N" ], [ "A0A096MJY8-1", "protein_xref_pfam", "PF02803", "Thiolase_C" ], [ "Q8VHI8-1", "protein_xref_pfam", "PF03908", "Sec20" ], [ "D3ZLV9-1", "protein_xref_pfam", "PF00651", "BTB" ], [ "D3ZLV9-1", "protein_xref_pfam", "PF01344", "Kelch_1" ], [ "D3ZLV9-1", "protein_xref_pfam", "PF07707", "BACK" ], [ "A0A096MJY4-1", "protein_xref_pfam", "PF00319", "SRF-TF" ], [ "A0A096MJY4-1", "protein_xref_pfam", "PF12347", "HJURP_C" ], [ "O88181-1", "protein_xref_pfam", "PF00046", "Homeodomain" ], [ "A0A096MJY1-1", "protein_xref_pfam", "PF01153", "Glypican" ], [ "Q2KMM2-1", "protein_xref_pfam", "PF04099", "Sybindin" ], [ "Q2KN99-1", "protein_xref_pfam", "PF00307", "CH" ], [ "A0A096MJY2-1", "protein_xref_pfam", "PF01145", "Band_7" ], [ "D4A838-1", "protein_xref_pfam", "PF13853", "7tm_4" ], [ "Q5M808-1", "protein_xref_pfam", "PF05603", "DUF775" ], [ "D3ZKU2-1", "protein_xref_pfam", "PF13853", "7tm_4" ], [ "O55043-1", "protein_xref_pfam", "PF00169", "PH" ], [ "O55043-1", "protein_xref_pfam", "PF00621", "RhoGEF" ], [ "O55043-1", "protein_xref_pfam", "PF07653", "SH3_2" ] ] }, "readme": "Name\n - Rat UniProtKB Xref Pfam\n\nVersion\n - 1.5.30\n\nCreated on\n - 2019-09-06T14:06:38.974540\n\nModified on\n - 2020-04-10T11:59:22.752887\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@email.gwu.edu]\n\nAuthors\n - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The Rat UniProtKB Xref Pfam contains rat [taxid:10116] UniProtKB canonical accessions cross-referenced to Pfam database accessions/identifiers. Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The dataset is derived from 2019-05 UniProt release. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen\n\nDescription Domain\n Keywords\n - protein family\n - Pfam\n - cross-reference\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB canonical accessions that are cross-referenced to Pfam database accessions/identifiers from the triplestore containing triples from nt file and extracts the data as a csv dataset\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: uniprot-proteome-rattus-norvegicus.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.30/source/uniprot-proteome-rattus-norvegicus.nt\n Name: rat_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.30/reviewed/rat_protein_masterlist.csv\n Output Subdomain\n Name: rat_protein_xref_pfam.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.30/reviewed/rat_protein_xref_pfam.csv\n Name: rat_protein_xref_pfam.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.30/reviewed/rat_protein_xref_pfam.stat.csv\n\nFields\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: \"19431\"\n Name: \"xref_label\"\n Description: \"\"\n Unique Values: \"6052\"\n Name: \"xref_id\"\n Description: \"\"\n Unique Values: \"6052\"\n Name: \"xref_key\"\n Description: \"\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.5.30/reviewed/rat_protein_xref_pfam.csv" }