{ "bcoid": "GLY_000936", "title": "Pig Gene Locus (Ensembl)", "description": "The Pig Gene Locus (Ensembl) contains Sus scrofa [taxid:9823] UniProtKB canonical accessions mapped to ...", "filename": "pig_protein_genelocus.csv", "filetype": "csv", "categories": { "species": [ "Sus scrofa" ], "molecule": [ "Protein" ], "tag": [ "Gene Coordinates" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "A0A287BN22-1...", "BTBD10..." ], [ "A0A287A8B3-1...", "CALCB..." ] ], "headers": [ "uniprotkb_ca...", "gene_symbol..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "gene_symbol" }, { "type": "string", "label": "ensembl_gene_id" }, { "type": "string", "label": "chromosome_id" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "strand" } ], [ "A0A287BN22-1", "BTBD10", "ENSSSCG00045020439", "LUXT01062900.1", "1428303", "1523625", "0" ], [ "A0A287A8B3-1", "CALCB", "ENSSSCG00015035413", "AORO02048604.1", "199006", "204486", "0" ], [ "A0A287BN27-1", "PABIR2", "ENSSSCG00000012685", "X", "110593937", "110617787", "1" ], [ "A0A287A5F7-1", "PPP2R1B", "ENSSSCG00000029538", "9", "39480331", "39517629", "1" ], [ "D7PF45-1", "INPPL1", "ENSSSCG00060076105", "LUXY01060053.1", "834657", "849844", "0" ], [ "A0A4X1U326-1", "RAB38", "ENSSSCG00000033878", "9", "21577033", "21640115", "1" ], [ "A0A287ANF4-1", "TOGARAM1", "ENSSSCG00005000924", "KQ001821.1", "622930", "699656", "1" ], [ "A0A287ANF5-1", "AVEN", "ENSSSCG00000029474", "7", "80447524", "80640119", "0" ], [ "I3LFU4-1", "CCDC14", "ENSSSCG00005001935", "KQ001911.1", "1717282", "1771685", "1" ], [ "A0A287ANF8-1", "ATPAF1", "ENSSSCG00045016514", "LUXT01071540.1", "480550", "508554", "1" ], [ "A0A287ANF9-1", "PTGS1", "ENSSSCG00000005533", "1", "262456155", "262483035", "0" ], [ "I3LQS2-1", "NT5C", "ENSSSCG00070021591", "12", "5845448", "5846953", "0" ], [ "I3LHI0-1", "KRT23", "ENSSSCG00000024067", "12", "21528155", "21547062", "0" ], [ "Q6RVA9-1", "CAV1", "ENSSSCG00030052856", "LUXR01101794.1", "7907790", "7942235", "0" ], [ "P05383-1", "PRKACB", "ENSSSCG00045035983", "LUXT01090307.1", "435513", "554121", "0" ], [ "F1RTM0-1", "LOC100522569", "ENSSSCG00000009285", "11", "2792193", "2803447", "1" ], [ "F1RTM6-1", "AR", "ENSSSCG00070026766", "X", "54459422", "54651034", "0" ], [ "A0A5G2QM40-1", "CUX1", "ENSSSCG00035012995", "LUXS01018418.1", "1876480", "2229130", "1" ], [ "F1S7I3-1", "DEFB115", "ENSSSCG00000007216", "17", "35028972", "35031088", "0" ], [ "A0A287A8B9-1", "PATE2", "ENSSSCG00070023973", "9", "85741644", "85743012", "1" ], [ "F1SJB9-1", "CEMIP2", "ENSSSCG00055000546", "LUXU01009285.1", "1536004", "1685709", "1" ], [ "A0A8W4FCQ3-1", "ANKRD39", "ENSSSCG00070028657", "3", "55393478", "55433623", "0" ], [ "A0A287ATT8-1", "LOC100514973", "ENSSSCG00000032727", "AEMK02000610.1", "8450", "9400", "0" ], [ "A0A287ATT9-1", "PTTG1IP", "ENSSSCG00070007308", "13", "1512230", "1525982", "0" ], [ "F1SJI8-1", "C1H15orf61", "ENSSSCG00055029975", "LUXU01078208.1", "1193227", "1198149", "1" ], [ "C0JPM4-1", "TIMP2", "ENSSSCG00065067547", "LUXW01080577.1", "366052", "412435", "0" ], [ "A0A287B1P5-1", "GUCD1", "ENSSSCG00025056214", "LUXX01068597.1", "1201964", "1214876", "0" ], [ "F1SJI3-1", "RBM44", "ENSSSCG00000016332", "15", "137444855", "137481025", "0" ], [ "F1RMF0-1", "OR5B21", "ENSSSCG00000013157", "2", "12603912", "12604838", "0" ], [ "A0A4X1V1L8-1", "GSTT4", "ENSSSCG00000010065", "14", "49812019", "49819248", "1" ], [ "F1RMF7-1", "GLYAT", "ENSSSCG00000062244", "2", "12365195", "12395232", "0" ], [ "F1RMF9-1", "FAM111B", "ENSSSCG00030063217", "LUXR01112853.1", "161115", "171985", "1" ], [ "Q8MIS1-1", "KCNE3", "ENSSSCG00045025724", "LUXT01044332.1", "1533484", "1545193", "1" ], [ "Q8MIS4-1", "OPTC", "ENSSSCG00025010044", "LUXX01023885.1", "718104", "727598", "0" ], [ "A0A4X1U6F0-1", "GALR1", "ENSSSCG00000036984", "1", "147443821", "147463542", "1" ], [ "P01232-1", "LHB", "ENSSSCG00000044760", "6", "54263576", "54271086", "1" ], [ "F1RWU4-1", "CAPN6", "ENSSSCG00000012584", "X", "91258688", "91288077", "1" ], [ "A0A5G2QG63-1", "HPSE", "ENSSSCG00055004350", "LUXU01006526.1", "3133041", "3172262", "0" ], [ "F1S899-1", "EBF4", "ENSSSCG00000007171", "17", "32876089", "32944678", "1" ], [ "F1SUD9-1", "IPPK", "ENSSSCG00045007671", "LUXT01027709.1", "63484", "123628", "0" ], [ "A0A287BFE6-1", "RAB35", "ENSSSCG00035034665", "LUXS01048950.1", "310510", "327851", "1" ], [ "A0A5G2R053-1", "GALM", "ENSSSCG00000008486", "3", "101617526", "101753125", "1" ], [ "F1SUD6-1", "FAM120A", "ENSSSCG00000008079", "3", "42861410", "42974866", "0" ], [ "I3LHP2-1", "LYPLA2", "ENSSSCG00035072358", "LUXS01072971.1", "5363533", "5368066", "1" ], [ "I3LHP0-1", "DPH1", "ENSSSCG00000028078", "12", "48146417", "48161770", "0" ], [ "I3LQL4-1", "POU3F3", "ENSSSCG00000022096", "3", "49806161", "49807666", "1" ], [ "I3LHP5-1", "LIMK1", "ENSSSCG00040043885", "LUXQ01057543.1", "1139956", "1166320", "0" ], [ "A0A4X1TF52-1", "LOC100626190", "ENSSSCG00005045674", "KQ004274.1", "23994", "24983", "1" ], [ "I3LHP8-1", "ENHO", "ENSSSCG00005029141", "KQ004018.1", "251731", "253826", "0" ], [ "A0A287BFE7-1", "SLC35D2", "ENSSSCG00065013855", "LUXW01026845.1", "5276188", "5330610", "1" ], [ "F1SEQ5-1", "SH2D4B", "ENSSSCG00000010342", "14", "82379176", "82467221", "0" ], [ "F1SEQ1-1", "LRIT2", "ENSSSCG00055018625", "LUXU01053491.1", "345681", "350407", "0" ], [ "A0A286ZNE1-1", "LOC110258054", "ENSSSCG00000058166", "AEMK02000440.1", "1366", "2304", "0" ], [ "A0A287B7F1-1", "KLHDC9", "ENSSSCG00000038597", "4", "89341652", "89343857", "1" ], [ "A0A286ZNE4-1", "SUSD5", "ENSSSCG00055016816", "LUXU01052497.1", "18261", "63162", "1" ], [ "F1SEQ8-1", "DYDC2", "ENSSSCG00070001005", "14", "58913662", "58926092", "1" ], [ "F1RGT4-1", "MCRIP2", "ENSSSCG00070001057", "NPJO01000029.1", "529665", "534560", "0" ], [ "F1RGT7-1", "CAPN15", "ENSSSCG00000007993", "3", "41190830", "41208653", "1" ], [ "F1RGT2-1", "EGLN1", "ENSSSCG00070015927", "14", "81806394", "81862179", "1" ], [ "I3L6G5-1", "DPF1", "ENSSSCG00000025160", "6", "47142702", "47155346", "1" ], [ "Q8MJS1-1", "IL12RB2", "ENSSSCG00005023942", "KQ004046.1", "84996", "155614", "1" ], [ "A0A4X1VBA4-1", "NAPEPLD", "ENSSSCG00005041033", "KQ004553.1", "3506588", "3560633", "1" ], [ "A0A4X1W748-1", "SVBP", "ENSSSCG00035044521", "LUXS01048203.1", "440640", "445441", "1" ], [ "A0A4X1UGW7-1", "BLNK", "ENSSSCG00000010504", "14", "107625803", "107715364", "1" ], [ "A0A286ZWN9-1", "RDH13", "ENSSSCG00000038287", "6", "59274387", "59292765", "1" ], [ "F1S9N3-1", "OR4D5", "ENSSSCG00000015152", "9", "50758169", "50759113", "0" ], [ "A0A286ZWN1-1", "LOC100515562", "ENSSSCG00000055805", "9", "3653979", "3654941", "1" ], [ "A0A286ZWN0-1", "LOC110258869", "ENSSSCG00000058860", "AEMK02000522.1", "350248", "351186", "0" ], [ "A0A286ZWN7-1", "LOC100623999", "ENSSSCG00005006014", "KQ001994.1", "57640", "58569", "1" ], [ "A0A287AH76-1", "SS18", "ENSSSCG00070025348", "6", "56335553", "56496716", "0" ], [ "F1SRN9-1", "ZNF777", "ENSSSCG00040028573", "LUXQ01063064.1", "85582", "116316", "1" ], [ "A0A8D1DGD3-1", "SGSM2", "ENSSSCG00000017829", "12", "48416790", "48462846", "0" ], [ "F1SRN1-1", "ANKH", "ENSSSCG00000016784", "16", "4105165", "4271170", "1" ], [ "P81693-1", "ACP1", "ENSSSCG00070018094", "3", "130667626", "130682843", "1" ], [ "F1SRN4-1", "TRIO", "ENSSSCG00000016781", "16", "3564171", "3921553", "0" ], [ "C1JEX7-1", "SPAG6", "ENSSSCG00000011080", "10", "52494755", "52571990", "1" ], [ "I3LRZ7-1", "COA7", "ENSSSCG00000027119", "6", "159511860", "159528049", "0" ], [ "A0A5G2RGX7-1", "VWA3A", "ENSSSCG00000025266", "3", "24031331", "24097393", "1" ], [ "A0A287BF76-1", "HOXB9", "ENSSSCG00000061856", "12", "24875723", "24880333", "1" ], [ "I3LGF1-1", "CD72", "ENSSSCG00000005311", "1", "236345903", "236355702", "1" ], [ "A0A287BF73-1", "KCTD16", "ENSSSCG00000032826", "2", "145707261", "145981909", "0" ], [ "A0A287BF71-1", "TJP1", "ENSSSCG00000004854", "1", "144930370", "145195836", "1" ], [ "B1NI70-1", "AK4", "ENSSSCG00040013868", "LUXQ01014049.1", "1584176", "1690369", "1" ], [ "A0A287BF79-1", "PLPPR3", "ENSSSCG00040064865", "LUXQ01124934.1", "366879", "379711", "0" ] ] }, "readme": "Name\n - Pig Gene Locus (Ensembl)\n\nVersion\n - v-2.4.1\n\nCreated on\n - \n\nModified on\n - \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], 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 Pig Gene Locus (Ensembl) contains Sus scrofa [taxid:9823] UniProtKB canonical accessions mapped to the corresponding ensembl Gene ID, chromosome ID along with the gene's start and end position on the chromosome. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen.\n\nDescription Domain\n Keywords\n - gene coordinates\n - chromosome\n - start position\n - end position\n - Ensembl\n - strand\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB canonical accessions that are mapped to ENSEMBL Gene 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: pig_protein_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/pig_protein_masterlist.csv\n Name: uniprot-proteome-sus_scrofa.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2024_02_19/uniprot-proteome-sus_scrofa.nt\n Output Subdomain\n Name: pig_protein_genelocus.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/pig_protein_genelocus.csv\n Name: pig_protein_genelocus.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/pig_protein_genelocus.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"18498\"\n Name: \"gene_symbol\"\n Description: \"\"Official gene name/symbol assigned to the gene. Human gene names/symbols are approved by the HUGO Gene Nomenclature Committee (HGNC)\"\n Unique Values: \"17651\"\n Name: \"ensembl_gene_id\"\n Description: \"Gene Identifier in Ensembl database\"\n Unique Values: \"17651\"\n Name: \"chromosome_id\"\n Description: \"Chromosome number identifier\"\n Unique Values: \"3990\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"17631\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"17634\"\n Name: \"strand\"\n Description: \"The strand of the gene\"\n Unique Values: \"2\"", "downloadurl": "/ln2data/releases/data/v-2.4.1/reviewed/pig_protein_genelocus.csv" }