{ "bcoid": "GLY_000234", "title": "Rat UniProtKB Xref CDD", "description": "The Rat UniProtKB Xref CDD contains rat [taxid:10116] UniProtKB canonical accessions cross-referenced ...", "filename": "rat_protein_xref_cdd.csv", "filetype": "csv", "categories": { "species": [ "Rattus norvegicus" ], "molecule": [ "Protein" ], "tags": [ "Cdd cross-references" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "Q5RJZ1-1...", "protein_xref..." ], [ "Q5RJZ1-1...", "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" } ], [ "Q5RJZ1-1", "protein_xref_cdd", "cd17970", "DEAHc_FancJ" ], [ "Q5RJZ1-1", "protein_xref_cdd", "cd13932", "HN_RTEL1" ], [ "Q0HA29-1", "protein_xref_cdd", "cd09286", "NMNAT_Eukarya" ], [ "Q9WVK3-1", "protein_xref_cdd", "cd05369", "TER_DECR_SDR_a" ], [ "A0A0G2JVG6-1", "protein_xref_cdd", "cd07765", "KRAB_A-box" ], [ "P32301-1", "protein_xref_cdd", "cd15268", "7tmB1_GLP1R" ], [ "A0A8I5ZR95-1", "protein_xref_cdd", "cd13284", "PH_OSBP_ORP4" ], [ "A0A0G2K069-1", "protein_xref_cdd", "cd00110", "LamG" ], [ "A0A8I5Y4X4-1", "protein_xref_cdd", "cd14293", "UBA3_NUB1" ], [ "A0A8I5Y4X4-1", "protein_xref_cdd", "cd14291", "UBA1_NUB1_like" ], [ "P30937-1", "protein_xref_cdd", "cd15973", "7tmA_SSTR4" ], [ "O35152-1", "protein_xref_cdd", "cd15853", "SNARE_Bet1" ], [ "O35158-1", "protein_xref_cdd", "cd00063", "FN3" ], [ "O35158-1", "protein_xref_cdd", "cd00096", "Ig" ], [ "F7FI04-1", "protein_xref_cdd", "cd06898", "PX_SNX10" ], [ "P02761-1", "protein_xref_cdd", "cd19428", "lipocalin_MUP-like" ], [ "Q9QYH1-1", "protein_xref_cdd", "cd12034", "SH3_MPP4" ], [ "Q9QYH1-1", "protein_xref_cdd", "cd00992", "PDZ_signaling" ], [ "Q9QYH1-1", "protein_xref_cdd", "cd00071", "GMPK" ], [ "P02764-1", "protein_xref_cdd", "cd19451", "lipocalin_AGP-like" ], [ "P02767-1", "protein_xref_cdd", "cd05821", "TLP_Transthyretin" ], [ "D4A4W8-1", "protein_xref_cdd", "cd20202", "T-box_TBXT" ], [ "D4A4W0-1", "protein_xref_cdd", "cd15407", "7tmA_OR5B-like" ], [ "D4A4W2-1", "protein_xref_cdd", "cd13132", "MATE_eukaryotic" ], [ "F7EN52-1", "protein_xref_cdd", "cd20613", "CYP46A1-like" ], [ "D4A4W5-1", "protein_xref_cdd", "cd02073", "P-type_ATPase_APLT_Dnf-like" ], [ "D4A4W6-1", "protein_xref_cdd", "cd12242", "RRM_SLIRP" ], [ "P07727-1", "protein_xref_cdd", "cd19009", "LGIC_ECD_GlyR_alpha" ], [ "P07727-1", "protein_xref_cdd", "cd19060", "LGIC_TM_GlyR_alpha" ], [ "D4A6Q6-1", "protein_xref_cdd", "cd18002", "DEXQc_INO80" ], [ "D4A6Q6-1", "protein_xref_cdd", "cd18793", "SF2_C_SNF" ], [ "P01237-1", "protein_xref_cdd", "cd10288", "prolactin_like" ], [ "P01230-1", "protein_xref_cdd", "cd00069", "GHB_like" ], [ "P09006-1", "protein_xref_cdd", "cd19551", "serpinA3_A1AC" ], [ "Q6AYS7-1", "protein_xref_cdd", "cd05646", "M20_AcylaseI_like" ], [ "Q9JHY8-1", "protein_xref_cdd", "cd07900", "Adenylation_DNA_ligase_I_Euk" ], [ "Q9JHY8-1", "protein_xref_cdd", "cd07969", "OBF_DNA_ligase_I" ], [ "Q9JHY7-1", "protein_xref_cdd", "cd00022", "BIR" ], [ "Q9WU49-1", "protein_xref_cdd", "cd04458", "CSP_CDS" ], [ "F1MAA4-1", "protein_xref_cdd", "cd07542", "P-type_ATPase_cation" ], [ "P30277-1", "protein_xref_cdd", "cd20565", "CYCLIN_CCNB1_rpt1" ], [ "Q66HR5-1", "protein_xref_cdd", "cd21967", "Zn-C2H2_CALCOCO1" ], [ "A0A8L2QVZ0-1", "protein_xref_cdd", "cd00904", "Ferritin" ], [ "Q05474-1", "protein_xref_cdd", "cd01793", "Ubl_FUBI" ], [ "Q5XI22-1", "protein_xref_cdd", "cd00751", "thiolase" ], [ "P83748-1", "protein_xref_cdd", "cd00190", "Tryp_SPc" ], [ "P18508-1", "protein_xref_cdd", "cd19000", "LGIC_ECD_GABAAR_G" ], [ "P18508-1", "protein_xref_cdd", "cd19054", "LGIC_TM_GABAAR_gamma" ], [ "P04757-1", "protein_xref_cdd", "cd19016", "LGIC_ECD_nAChR_A3" ], [ "P04757-1", "protein_xref_cdd", "cd19064", "LGIC_TM_nAChR" ], [ "Q8R512-1", "protein_xref_cdd", "cd17077", "UBX_UBXN11" ], [ "E9PTQ3-1", "protein_xref_cdd", "cd04269", "ZnMc_adamalysin_II_like" ], [ "P84083-1", "protein_xref_cdd", "cd04150", "Arf1_5_like" ], [ "P47709-1", "protein_xref_cdd", "cd08384", "C2B_Rabphilin_Doc2" ], [ "B0BMY7-1", "protein_xref_cdd", "cd11284", "ADF_Twf-C_like" ], [ "B0BMY7-1", "protein_xref_cdd", "cd11285", "ADF_Twf-N_like" ], [ "A0A8I5ZRF2-1", "protein_xref_cdd", "cd00063", "FN3" ], [ "D3ZGN2-1", "protein_xref_cdd", "cd01459", "vWA_copine_like" ], [ "D3ZGN2-1", "protein_xref_cdd", "cd04047", "C2B_Copine" ], [ "D3ZGN2-1", "protein_xref_cdd", "cd04048", "C2A_Copine" ], [ "Q9Z0V5-1", "protein_xref_cdd", "cd03015", "PRX_Typ2cys" ], [ "A0A0G2JYZ1-1", "protein_xref_cdd", "cd14129", "STKc_TTBK2" ], [ "A0A8I6AVR1-1", "protein_xref_cdd", "cd02440", "AdoMet_MTases" ], [ "D3ZV60-1", "protein_xref_cdd", "cd01374", "KISc_CENP_E" ], [ "P0CAX5-1", "protein_xref_cdd", "cd01249", "BAR-PH_GRAF_family" ], [ "P0CAX5-1", "protein_xref_cdd", "cd04374", "RhoGAP_Graf" ], [ "P0CAX5-1", "protein_xref_cdd", "cd07633", "BAR_OPHN1" ], [ "D3ZIY3-1", "protein_xref_cdd", "cd21134", "YTH" ], [ "Q62952-1", "protein_xref_cdd", "cd01314", "D-HYD" ], [ "A0A8I6GKG1-1", "protein_xref_cdd", "cd01718", "Sm_E" ], [ "D4A1P8-1", "protein_xref_cdd", "cd08320", "Pyrin_NALPs" ], [ "D3ZSP7-1", "protein_xref_cdd", "cd16481", "RING-H2_TTC3" ], [ "O88553-1", "protein_xref_cdd", "cd07765", "KRAB_A-box" ], [ "D3ZFP4-1", "protein_xref_cdd", "cd17754", "MCM3" ], [ "D3ZFP7-1", "protein_xref_cdd", "cd21966", "INSC_LBD" ], [ "A0A1W2Q641-1", "protein_xref_cdd", "cd01134", "V_A-ATPase_A" ], [ "A0A1W2Q641-1", "protein_xref_cdd", "cd18111", "ATP-synt_V_A-type_alpha_C" ], [ "A0A1W2Q641-1", "protein_xref_cdd", "cd18119", "ATP-synt_V_A-type_alpha_N" ], [ "P09875-1", "protein_xref_cdd", "cd03784", "GT1_Gtf-like" ], [ "Q6AYC4-1", "protein_xref_cdd", "cd11289", "gelsolin_S2_like" ], [ "Q6AYC4-1", "protein_xref_cdd", "cd11290", "gelsolin_S1_like" ], [ "Q6AYC4-1", "protein_xref_cdd", "cd11292", "gelsolin_S3_like" ], [ "Q5PQK4-1", "protein_xref_cdd", "cd20912", "AIR_RAP80-like" ], [ "A0A8I5ZPP3-1", "protein_xref_cdd", "cd07936", "SCAN" ] ] }, "readme": "Name\n - Rat UniProtKB Xref CDD\n\nVersion\n - v-2.1.1\n\nCreated on\n - 2019-09-06T14:06:38.961924\n\nModified on\n - 2022-09-26T09:04:47.933127\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Jingyue Wu [jingyue.wu@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 CDD contains rat [taxid:10116] UniProtKB canonical accessions cross-referenced to CDD database accessions/identifiers. The dataset is derived from 2019-09 UniProtKB release. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen. \n - The Conserved Domain Database is a database of well-annotated multiple sequence alignment models and derived database search models, for ancient domains and full-length proteins. \n\nDescription Domain\n Keywords\n - protein domains\n - CDD\n - cross-reference\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB canonical accessions that are cross-referenced to CDD 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/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: uniprot-proteome-rattus-norvegicus.nt\n URI: /data/shared/glyds/downloads/ebi/2023_02/uniprot-proteome-rattus-norvegicus.nt\n Output Subdomain\n Name: rat_protein_xref_cdd.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/rat_protein_xref_cdd.csv\n Name: rat_protein_xref_cdd.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/rat_protein_xref_cdd.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"11366\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"7595\"\n Name: \"xref_label\"\n Description: \"Label/Name associated with x-ref\"\n Unique Values: \"7591\"", "downloadurl": "/ln2data/releases/data/v-2.1.1/reviewed/rat_protein_xref_cdd.csv" }