{ "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": [ [ "D3ZB44-1...", "protein_xref..." ], [ "D3ZB44-1...", "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" } ], [ "D3ZB44-1", "protein_xref_pfam", "PF01352", "KRAB" ], [ "D3ZB44-1", "protein_xref_pfam", "PF00096", "zf-C2H2" ], [ "D3ZXJ3-1", "protein_xref_pfam", "PF01352", "KRAB" ], [ "D3ZXJ3-1", "protein_xref_pfam", "PF00096", "zf-C2H2" ], [ "D3ZB48-1", "protein_xref_pfam", "PF05622", "HOOK" ], [ "D3ZB48-1", "protein_xref_pfam", "PF19047", "HOOK_N" ], [ "Q5RJZ1-1", "protein_xref_pfam", "PF06733", "DEAD_2" ], [ "Q5RJZ1-1", "protein_xref_pfam", "PF13307", "Helicase_C_2" ], [ "Q04462-1", "protein_xref_pfam", "PF00043", "GST_C" ], [ "Q0HA29-1", "protein_xref_pfam", "PF01467", "CTP_transf_like" ], [ "A0A0G2JVG5-1", "protein_xref_pfam", "PF14988", "DUF4515" ], [ "A0A0G2JVG6-1", "protein_xref_pfam", "PF00096", "zf-C2H2" ], [ "P30938-1", "protein_xref_pfam", "PF00001", "7tm_1" ], [ "A0A0G2JVG8-1", "protein_xref_pfam", "PF13853", "7tm_4" ], [ "Q07969-1", "protein_xref_pfam", "PF01130", "CD36" ], [ "A0A096MJY8-1", "protein_xref_pfam", "PF00108", "Thiolase_N" ], [ "A0A096MJY8-1", "protein_xref_pfam", "PF02803", "Thiolase_C" ], [ "Q9QYG8-1", "protein_xref_pfam", "PF00485", "PRK" ], [ "A0A096MJY4-1", "protein_xref_pfam", "PF00319", "SRF-TF" ], [ "A0A096MJY4-1", "protein_xref_pfam", "PF12347", "HJURP_C" ], [ "A0A096MJY1-1", "protein_xref_pfam", "PF01153", "Glypican" ], [ "A0A0G2KA92-1", "protein_xref_pfam", "PF00176", "SNF2_N" ], [ "A0A0G2KA92-1", "protein_xref_pfam", "PF00271", "Helicase_C" ], [ "A0A0G2KA92-1", "protein_xref_pfam", "PF13907", "DUF4208" ], [ "A0A0G2KA92-1", "protein_xref_pfam", "PF00385", "Chromo" ], [ "A0A0G2KA92-1", "protein_xref_pfam", "PF18375", "CDH1_2_SANT_HL1" ], [ "A0A096MJY2-1", "protein_xref_pfam", "PF01145", "Band_7" ], [ "A0A0G2K4P4-1", "protein_xref_pfam", "PF14988", "DUF4515" ], [ "Q5RJK6-1", "protein_xref_pfam", "PF00459", "Inositol_P" ], [ "Q62949-1", "protein_xref_pfam", "PF03002", "Somatostatin" ], [ "P01946-1", "protein_xref_pfam", "PF00042", "Globin" ], [ "Q63358-1", "protein_xref_pfam", "PF00620", "RhoGAP" ], [ "Q63358-1", "protein_xref_pfam", "PF00788", "RA" ], [ "Q63358-1", "protein_xref_pfam", "PF00612", "IQ" ], [ "Q63358-1", "protein_xref_pfam", "PF00063", "Myosin_head" ], [ "Q5M9G9-1", "protein_xref_pfam", "PF06743", "FAST_1" ], [ "Q5M9G9-1", "protein_xref_pfam", "PF08368", "FAST_2" ], [ "Q5M9G9-1", "protein_xref_pfam", "PF08373", "RAP" ], [ "A0A1W2Q6N1-1", "protein_xref_pfam", "PF09067", "EpoR_lig-bind" ], [ "P30936-1", "protein_xref_pfam", "PF00001", "7tm_1" ], [ "O35158-1", "protein_xref_pfam", "PF07679", "I-set" ], [ "O35158-1", "protein_xref_pfam", "PF00041", "fn3" ], [ "P02761-1", "protein_xref_pfam", "PF00061", "Lipocalin" ], [ "Q9QYH1-1", "protein_xref_pfam", "PF00595", "PDZ" ], [ "Q9QYH1-1", "protein_xref_pfam", "PF00625", "Guanylate_kin" ], [ "P02764-1", "protein_xref_pfam", "PF00061", "Lipocalin" ], [ "P02767-1", "protein_xref_pfam", "PF00576", "Transthyretin" ], [ "D4A4W8-1", "protein_xref_pfam", "PF00907", "T-box" ], [ "D4A4W9-1", "protein_xref_pfam", "PF01199", "Ribosomal_L34e" ], [ "D4A4W0-1", "protein_xref_pfam", "PF13853", "7tm_4" ], [ "D4A4W1-1", "protein_xref_pfam", "PF06679", "DUF1180" ], [ "D4A4W2-1", "protein_xref_pfam", "PF01554", "MatE" ], [ "F7EN52-1", "protein_xref_pfam", "PF00067", "p450" ], [ "D4A4W4-1", "protein_xref_pfam", "PF12697", "Abhydrolase_6" ], [ "D4A4W5-1", "protein_xref_pfam", "PF16209", "PhoLip_ATPase_N" ], [ "D4A4W5-1", "protein_xref_pfam", "PF16212", "PhoLip_ATPase_C" ], [ "D4A4W6-1", "protein_xref_pfam", "PF00076", "RRM_1" ], [ "D4A4W7-1", "protein_xref_pfam", "PF14962", "AIF-MLS" ], [ "G3V6I3-1", "protein_xref_pfam", "PF12542", "CWC25" ], [ "G3V6I3-1", "protein_xref_pfam", "PF10197", "Cir_N" ], [ "P21932-1", "protein_xref_pfam", "PF00211", "Guanylate_cyc" ], [ "P21932-1", "protein_xref_pfam", "PF16214", "AC_N" ], [ "Q8K4K5-1", "protein_xref_pfam", "PF08596", "Lgl_C" ], [ "Q8K4K5-1", "protein_xref_pfam", "PF08366", "LLGL" ], [ "Q4L0E8-1", "protein_xref_pfam", "PF00615", "RGS" ], [ "G3V6I6-1", "protein_xref_pfam", "PF03006", "HlyIII" ], [ "A0A0G2K5E4-1", "protein_xref_pfam", "PF01556", "DnaJ_C" ], [ "A0A0G2K5E4-1", "protein_xref_pfam", "PF00226", "DnaJ" ], [ "G3V6I4-1", "protein_xref_pfam", "PF03473", "MOSC" ], [ "G3V6I4-1", "protein_xref_pfam", "PF03476", "MOSC_N" ], [ "P12749-1", "protein_xref_pfam", "PF00467", "KOW" ], [ "P12749-1", "protein_xref_pfam", "PF16906", "Ribosomal_L26" ], [ "O08812-1", "protein_xref_pfam", "PF13906", "AA_permease_C" ], [ "O08812-1", "protein_xref_pfam", "PF13520", "AA_permease_2" ], [ "P39020-1", "protein_xref_pfam", "PF00046", "Homeodomain" ], [ "P11980-1", "protein_xref_pfam", "PF00224", "PK" ], [ "P11980-1", "protein_xref_pfam", "PF02887", "PK_C" ], [ "A0A0G2K0T8-1", "protein_xref_pfam", "PF15825", "FAM25" ], [ "Q6P6Q9-1", "protein_xref_pfam", "PF13202", "EF-hand_5" ], [ "Q6P6Q9-1", "protein_xref_pfam", "PF13833", "EF-hand_8" ], [ "Q63544-1", "protein_xref_pfam", "PF01387", "Synuclein" ], [ "A0A0G2K0T7-1", "protein_xref_pfam", "PF00096", "zf-C2H2" ], [ "P28648-1", "protein_xref_pfam", "PF00335", "Tetraspanin" ], [ "D3ZVR6-1", "protein_xref_pfam", "PF16770", "RTT107_BRCT_5" ] ] }, "readme": "Name\n - Rat UniProtKB Xref Pfam\n\nVersion\n - 1.11.2\n\nCreated on\n - 2019-09-06T14:06:38.974540\n\nModified on\n - 2022-01-19T13:09:46.126082\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], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@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: rat_protein_masterlist.csv\n URI: https://data.glygen.org//ln2data/releases/data/v-1.11.2/reviewed/rat_protein_masterlist.csv\n Name: uniprot-proteome-rattus-norvegicus.nt\n URI: https://data.glygen.org//ln2downloads/ebi/2021_03/uniprot-proteome-rattus-norvegicus.nt\n Output Subdomain\n Name: rat_protein_xref_pfam.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.12.1/reviewed/rat_protein_xref_pfam.csv\n Name: rat_protein_xref_pfam.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.12.1/reviewed/rat_protein_xref_pfam.stat.csv", "downloadurl": "/ln2data/releases/data/v-1.12.1/reviewed/rat_protein_xref_pfam.csv" }