{"id":24940,"date":"2024-01-17T16:55:22","date_gmt":"2024-01-17T08:55:22","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24940"},"modified":"2024-01-17T16:55:25","modified_gmt":"2024-01-17T08:55:25","slug":"%e9%9d%9e%e6%a8%a1%e5%bc%8f%e7%94%9f%e7%89%a9%e5%9f%ba%e5%9b%a0%e6%b3%a8%e9%87%8a%e4%bf%a1%e6%81%af%e4%b8%8d%e4%bc%9a%e6%89%be%ef%bc%9f%e4%b8%8d%e6%80%95%ef%bc%8c%e5%b0%8f%e6%9e%9c%e6%95%99%e4%bd%a0","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24940","title":{"rendered":"\u975e\u6a21\u5f0f\u751f\u7269\u57fa\u56e0\u6ce8\u91ca\u4fe1\u606f\u4e0d\u4f1a\u627e\uff1f\u4e0d\u6015\uff0c\u5c0f\u679c\u6559\u4f60\u7528AnnotationHub\u5305\u8f7b\u677e\u62ff\u634f"},"content":{"rendered":"

\u975e\u6a21\u5f0f\u751f\u7269\u7684\u6ce8\u91ca\u4fe1\u606f\u68c0\u7d22<\/strong><\/h2>\n

\u81eaRNA\u6d4b\u5e8f\uff08RNA-seq\uff09\u7684\u6280\u672f\u88ab\u53d1\u660e\u4ee5\u6765\uff0c\u5b83\u5728\u5206\u5b50\u751f\u7269\u5b66\u7684\u9886\u57df\u5185\u5f97\u5230\u4e86\u5e7f\u6cdb\u7684\u5e94\u7528\u3002\u4e0e\u4f20\u7edf\u7684\u65b9\u6cd5\u76f8\u6bd4\uff0cRNA-seq\u66f4\u80fd\u591f\u5168\u9762\u548c\u7cbe\u51c6\u5730\u63ed\u793a\u57fa\u56e0\u5728\u4e0d\u540c\u5c42\u9762\u4e0a\u7684\u529f\u80fd\u548c\u4f5c\u7528\u3002\u8fd9\u4e00\u6280\u672f\u7a81\u51fa\u4e86mRNA\u526a\u63a5\u7684\u590d\u6742\u6027\uff0c\u5e76\u9610\u660e\u4e86\u975e\u7f16\u7801RNA\u4ee5\u53ca\u589e\u5f3a\u5b50RNA\u5bf9\u4e8e\u57fa\u56e0\u8868\u8fbe\u7684\u8c03\u63a7\u673a\u5236\uff0c\u589e\u5f3a\u4e86\u6211\u4eec\u5bf9\u4e8e\u751f\u7269\u8fc7\u7a0b\u7684\u4e86\u89e3\uff0c\u63a8\u52a8\u4e86\u751f\u7269\u5b66\u5728\u57fa\u56e0\u7ec4\u3001\u8f6c\u5f55\u7ec4\u4ee5\u53ca\u8868\u89c2\u9057\u4f20\u5b66\u7b49\u65b9\u9762\u7684\u7814\u7a76\u8fdb\u6b65\u3002<\/p>\n

\u7136\u800c\uff0c\u5f53\u6211\u4eec\u901a\u8fc7RNA-seq\u5f97\u5230\u4e86\u4e00\u7cfb\u5217\u5dee\u5f02\u57fa\u56e0\u7684geneid\u540e\uff0c\u4e00\u4e2a\u95ee\u9898\u6446\u5728\u6211\u4eec\u9762\u524d\uff1a\u6211\u4eec\u5e76\u4e0d\u6e05\u695a\u8fd9\u4e9bgeneid\u5b9e\u9645\u4e0a\u5bf9\u5e94\u7684\u662f\u54ea\u4e9b\u57fa\u56e0\u3002\u6b64\u65f6\uff0c\u6211\u4eec\u9700\u8981\u5bf9\u8fd9\u4e9b\u57fa\u56e0\u505a\u8fdb\u4e00\u6b65\u7684\u529f\u80fd\u6ce8\u91ca\uff0c\u4e5f\u5c31\u662f\u627e\u51fa\u8fd9\u4e9b\u57fa\u56e0\u5728\u751f\u7269\u4f53\u4e2d\u5b9e\u9645\u4e0a\u8d77\u4e86\u4ec0\u4e48\u4f5c\u7528\uff0c\u8fd9\u4e9b\u5dee\u5f02\u8868\u8fbe\u7684\u57fa\u56e0\u662f\u5426\u4e0e\u7279\u5b9a\u7684\u8868\u578b\u76f8\u5173\uff1f\u8981\u89e3\u7b54\u8fd9\u4e9b\u95ee\u9898\uff0c\u5c31\u9700\u8981\u6211\u4eec\u628a\u5f97\u5230\u7684geneid\u4e0egene\u6570\u636e\u5e93\u8fdb\u884c\u6bd4\u5bf9\uff0c\u6316\u6398\u51fa\u6bcf\u4e00\u4e2ageneid\u80cc\u540e\u7684\u57fa\u56e0\u4fe1\u606f\u3002\u8fd9\u4e2a\u8fc7\u7a0b\u5c31\u597d\u6bd4\u67e5\u5b57\u5178\u4e00\u6837\uff0c\u6211\u4eec\u6709\u4e86\u9875\u7801\uff0c\u63a5\u4e0b\u6765\u5c31\u9700\u8981\u77e5\u9053\u8fd9\u4e2a\u9875\u7801\u5bf9\u5e94\u7684\u662f\u4ec0\u4e48\u5185\u5bb9\u3002<\/p>\n

\u5bf9\u4e8e\u50cf\u4eba\u7c7b\u3001\u5c0f\u9f20\u3001\u62df\u5357\u82a5\u3001\u5927\u80a0\u6746\u83cc\u7b49\u6a21\u5f0f\u751f\u7269\u6765\u8bf4\uff0c\u8fdb\u884c\u57fa\u56e0\u6ce8\u91ca\u7684\u8fc7\u7a0b\u76f8\u5bf9\u5bb9\u6613\uff0c\u56e0\u4e3a\u5b83\u4eec\u90fd\u6709\u76f8\u5bf9\u5b8c\u5584\u7684\u6570\u636e\u5e93\u53ef\u4ee5\u53c2\u8003\u3002\u4f46\u662f\uff0c\u5bf9\u4e8e\u975e\u6a21\u5f0f\u751f\u7269\uff0c\u7531\u4e8e\u901a\u5e38\u7f3a\u4e4f\u826f\u597d\u7684\u53c2\u8003\u57fa\u56e0\u5e93\uff0c\u8fdb\u884c\u57fa\u56e0\u6ce8\u91ca\u7684\u8fc7\u7a0b\u5c31\u663e\u5f97\u5341\u5206\u56f0\u96be\u3002\u6b64\u65f6\uff0cR\u5305AnnotationHub\u63d0\u4f9b\u4e86\u4e00\u79cd\u975e\u5e38\u6709\u6548\u7684\u89e3\u51b3\u65b9\u6848\u3002\u5b83\u80fd\u591f\u8f7b\u677e\u5730\u68c0\u7d22\u975e\u6a21\u5f0f\u751f\u7269\u7684\u6ce8\u91ca\u4fe1\u606f\uff0c\u5bf9\u8fc7\u53bb\u5728\u6ce8\u91ca\u975e\u6a21\u5f0f\u751f\u7269\u57fa\u56e0\u65f6\u9047\u5230\u7684\u95ee\u9898\u63d0\u4f9b\u4e86\u6709\u6548\u7684\u89e3\u51b3\u65b9\u5f0f\u3002<\/p>\n

\u4e0b\u9762\u5c0f\u679c\u7528\u7389\u7c73\u4f5c\u4e3a\u793a\u8303<\/strong><\/h2>\n

\u4e0b\u8f7dAnnotationHub\u5305\u5e76\u52a0\u8f7d<\/strong><\/h3>\n

BiocManager::install(“AnnotationHub\u201d) #\u5305\u4e0b\u8f7d
\nlibrary(AnnotationHub) #\u52a0\u8f7d<\/p>\n

\u6709\u4e24\u79cd\u65b9\u5f0f\u53ef\u4ee5\u627e\u5230\u60f3\u8981\u7684\u975e\u6a21\u5f0f\u751f\u7269\u6ce8\u91ca\u4fe1\u606f<\/strong><\/h3>\n

\u7b2c\u4e00\u79cd<\/strong><\/h4>\n

ah <- AnnotationHub()<\/p>\n

query(hub, “zea”)
\nAnnotationHub with 12 records
\n# snapshotDate(): 2022-10-31
\n# $dataprovider: ftp:\/\/ftp.ncbi.nlm.nih.gov\/gene\/DATA\/, NCBI,DBCLS, WikiPathways, …
\n# $species: Zea mays, Gibberella zeae, Zea mays_var._japonica, Heliothis zea, Heli…
\n# $rdataclass: OrgDb, SQLiteFile, Tibble, Inparanoid8Db
\n# additional mcols(): taxonomyid, genome, description, coordinate_1_based,
\n# maintainer, rdatadateadded, preparerclass, tags, rdatapath, sourceurl,
\n# sourcetype
\n# retrieve records with, e.g., ‘object[[“AH10514”]]’<\/p>\n

title
\nAH10514 | hom.Gibberella_zeae.inp8.sqlite
\nAH91642 | MeSHDb for Zea mays (Corn, v001)
\nAH91804 | wikipathways_Gibberella_zeae_metabolites.rda
\nAH91817 | wikipathways_Zea_mays_metabolites.rda
\nAH97909 | MeSHDb for Zea mays (Corn, v002)
\n… …
\nAH107469 | org.Zea_mays.eg.sqlite
\nAH107470 | org.Zea_mays_var._japonica.eg.sqlite
\nAH108747 | org.Helicoverpa_zea.eg.sqlite
\nAH108748 | org.Heliothis_zea.eg.sqlite
\nAH109103 | org.Gibberella_zeae_PH-1.eg.sqlite<\/p>\n

\u901a\u8fc7\u68c0\u7d22\uff0corg.Zea_mays.eg.sqlite\u5c31\u662f\u5c0f\u679c\u60f3\u627e\u7684\u7389\u7c73Org\u6570\u636e\u5e93\u3002<\/p>\n

\u7b2c\u4e8c\u79cd<\/strong><\/h4>\n

\u6211\u4eec\u4e5f\u53ef\u4ee5\u8bbf\u95ee\u5b83\u7684\u5b98\u65b9\u63a5\u53e3\u6765\u66f4\u5feb\u5730\u83b7\u53d6<\/p>\n

BiocHub Server API<\/a><\/p>\n

<\/p>\n

\u518d\u7136\u540e\u6211\u4eec\u5c31\u53ef\u4ee5\u70b9\u51fbspecies\u6309\u7167\u7269\u79cd\u6765\u8fdb\u884c\u5feb\u901f\u68c0\u7d22<\/p>\n

\u4ece\u5de6\u4e0b\u89d2\u53ef\u4ee5\u6e05\u695a\u5730\u770b\u5230\u6709\u5c06\u8fd16000\u79cd\u53ef\u7528\u7684\u7269\u79cd\uff0c\u8fd9\u662f\u4e0d\u662f\u6bd4\u4f60\u60f3\u8c61\u5f97\u591a\u5f88\u591a\u5462\uff1f<\/p>\n

<\/p>\n

\u8f93\u5165\u5c0f\u679c\u7684\u597d\u670b\u53cb\u7389\u7c73\u7684\u5b66\u540dzea mays<\/p>\n

<\/p>\n

\u70b9\u51fbzea mays\uff0c\u592a\u597d\u4e86\u5c0f\u679c\u627e\u5230\u4e86\u7389\u7c73\u7684org\u6570\u636e\u5e93~<\/p>\n\n\n\n
<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

\u83b7\u53d6\u7389\u7c73\u6ce8\u91ca\u4fe1\u606f<\/strong><\/h3>\n

\u901a\u8fc7\u5bf9\u5e94\u7684accession number, \u83b7\u53d6\u6587\u4ef6AH107469 \u3002<\/p>\n

\u5e76\u5c06\u6587\u4ef6\u5b58\u5165maize\u5bf9\u8c61\u4e2d\uff0c\u6211\u4eec\u53ef\u4ee5\u770b\u5230\u5b83\u5305\u542b\u4e86\u7389\u7c7349905\u4e2a\u57fa\u56e0\u7684\u6ce8\u91ca\u3002<\/p>\n

> maize <- hub[[‘AH107469’]]
\ndownloading 1 resources
\nretrieving 1 resource
\n|==============================================| 100%
\nloading from cache
\n> length(keys(maize))
\n[1] 49905<\/p>\n

\u8fd9\u4e2aOrg\u6570\u636e\u5e93\uff0c\u5305\u542b\u6709\u4ee5\u4e0b\u4e00\u4e9b\u6ce8\u91ca\u4fe1\u606f\uff08\u597d\u591a\u5c0f\u679c\u90fd\u8fd8\u672a\u63a5\u89e6\u8fc7\uff09\uff1a<\/p>\n

> columns(maize)
\n[1] “ACCNUM” “ALIAS” “CHR”
\n[4] “ENTREZID” “EVIDENCE” “EVIDENCEALL”
\n[7] “GENENAME” “GID” “GO”<\/p>\n

[10] “GOALL” “ONTOLOGY” “ONTOLOGYALL”
\n[13] “PMID” “REFSEQ” “SYMBOL”<\/p>\n

[16] “UNIGENE”<\/p>\n

\u6709\u4e86Org\u6570\u636e\u5e93\u4e4b\u540e\u5c31\u53ef\u4ee5\u8fdb\u884c\u540e\u7eed\u7684\u64cd\u4f5c\u4e86\u3002\u6bd4\u5982\u4e0d\u540c\u6570\u636e\u5e93\u7684ID\u8f6c\u5316\uff0c\u57fa\u56e0\/\u8f6c\u5f55\u672c\/\u86cb\u767d\u7684ID\u8f6c\u5316\uff0cGO\u6ce8\u91ca\u4ee5\u53ca\u5176\u4ed6\u6ce8\u91ca\u3002<\/p>\n

\u600e\u4e48\u6837\u662f\u4e0d\u662f\u5f88\u65b9\u4fbf\u5462\uff0c\u6b22\u8fce\u548c\u5c0f\u679c\u8ba8\u8bba~<\/p>\n

\u5c0f\u679c\u7684\u4e91\u751f\u4fe1\u5e73\u53f0\u8fd8\u6709\u66f4\u591a\u65b9\u4fbf\u5b9e\u7528\u7684\u5de5\u5177\uff0c\u5feb\u6765\u77a7\u77a7\u5427<\/p>\n

\u4e91\u751f\u4fe1\u5e73\u53f0\u94fe\u63a5\uff1ahttp:\/\/www.biocloudservice.com\/home.html<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

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