{"id":598,"date":"2013-02-26T16:27:42","date_gmt":"2013-02-26T08:27:42","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=598"},"modified":"2013-02-27T15:40:03","modified_gmt":"2013-02-27T07:40:03","slug":"go-class%e7%9a%84%e7%9a%84%e5%88%b6%e4%bd%9c","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=598","title":{"rendered":"go.class\u7684\u5236\u4f5c"},"content":{"rendered":"

\u65b9\u6cd5\uff1a<\/h1>\n

1. \u4f7f\u7528OBO-Edit\u6765\u641c\u7d22GO\u4e8c\u7ea7\u6c34\u5e73term\u5305\u542b\u7684terms\uff0c\u5e76\u751f\u6210\u76f8\u5e94\u7684obo\u6587\u4ef6\uff1b
\n2. \u4f7f\u7528\u7f16\u5199\u7684perl\u7a0b\u5e8f\u6765\u63d0\u53d6obo\u6587\u4ef6\u4e2d\u7684\u5185\u5bb9\u3002<\/p>\n

\u8fc7\u7a0b\uff1a<\/h1>\n

1. \u4e0b\u8f7dgene_ontology.1_2.obo\u6587\u4ef6\u3002<\/p>\n

\u4e0b\u8f7d\u7f51\u9875\uff1ahttp:\/\/www.geneontology.org\/GO.downloads.ontology.shtml<\/pre>\n
2. \u5b89\u88c5OBO-Edit\u5e76\u8fd0\u884c\u3002<\/p>\n
\u5728\u5b98\u7f51http:\/\/www.oboedit.org\/\u4e0a\u4e0b\u8f7dOBO-Edit\u5e76\u5b89\u88c5\u3002\r\n\u6587\u7ae0\u5199\u7684\u65f6\u95f4\u5bf9\u5e94\u7684\u7248\u672c\u662foboedit_2_3-b3_unix_install4j.sh (45.0 MB)\r\n# sh oboedit_2_3-b3_unix_install4j.sh\r\n\u6309\u63d0\u793a\u8fdb\u884c\u5b89\u88c5\u3002\r\n$ rm oboedit_config -rf\r\n$ OBO-Edit\r\n\u8fd0\u884c\u8be5\u7a0b\u5e8f\u9700\u8981java\u652f\u6301\u3002<\/pre>\n
3. \u4f7f\u7528gene_ontology.1_2.obo\u6587\u4ef6\u6765search\uff0c\u5f97\u5230\u4e8c\u7ea7\u6c34\u5e73\u7684GO term\u7684\u5b50terms\u3002<\/p>\n
1. File\u83dc\u5355\u4e0bLoad Ontologies\uff0c\u8f7d\u5165gene_ontology.1_2.obo\u6587\u4ef6;\r\n2. File\u83dc\u5355\u4e0bSave as\uff0c\u8fdb\u5165Write ontology\u753b\u9762\uff1b\r\n3. \u70b9\u51fbAdvanced\u2014\u2014\u70b9\u51fbAdd\u2014\u2014\u8f93\u5165\u4fdd\u5b58\u8def\u5f84(biological adhesion\u4e3a\u4f8b)\u2014\u2014\u6253\u52feFilter terms\u2014\u2014\u70b9\u51fb+\u53f7\u2014\u2014Find terms that have a ID that equals the value GO:0022610 in Ancestor that can be reached via any tyep\u2014\u2014\u70b9\u51fbOK\r\n4. \u7b49\u5f85\u4e00\u6bb5\u65f6\u95f4\uff0c\u5219\u4f1a\u751f\u6210\u6587\u4ef6\u540d\u4e3a\u201cbiological ahension\u201d\u7684obo\u6587\u4ef6<\/pre>\n
4. \u5bf9\u6bcf\u4e00\u4e2aGO\u4e8c\u7ea7\u6c34\u5e73\u7684term\u90fd\u8fdb\u884c\u8fd9\u6837\u7684search\u548csave\uff0c\u5f97\u5230\u5f88\u591aobo\u6587\u4ef6\u3002\u4f7f\u7528perl\u7a0b\u5e8fmake_go_class.pl\u6765\u751f\u6210go.class\u6587\u4ef6\u3002<\/p>\n
$ perl make_go_class.pl *    #\u5176\u4e2d*\u4ee3\u8868\u751f\u6210\u7684\u6240\u6709\u7684obo\u6587\u4ef6\r\n\u8be5\u7a0b\u5e8f\u4ee5\u2018>>'\u7684\u65b9\u5f0f\u5199\u5165\u5230\u6587\u4ef6\u53e5\u67c4\u4e2d\uff0c\u6ce8\u610f\u4e0d\u8981\u91cd\u590d\u547d\u4ee4\u3002<\/pre>\n
5. \u8fd8\u6709GO\u4e8c\u7ea7terms\u672c\u8eab\u6ca1\u6709\u52a0\u5165\u5230go.class\u4e2d\u53bb\u3002\u6309\u4ee5\u4e0a\u7684search\u548csave\u65b9\u5f0f\u8fdb\u884c\u5176obo\u6587\u4ef6\u7684\u5236\u4f5c\uff0c\u4e0d\u540c\u7684\u662f\u5c06Ancestor\u6362\u6210Parent\u3002\u5f97\u5230\u7684obo\u6587\u4ef6\u4f7f\u7528make_go_class.pl\u6765\u6210\u624dgo.class\u6587\u4ef6\u3002\u8be5go.class\u6587\u4ef6\u662f\u9519\u8bef\u7684\uff0c\u9700\u8981\u624b\u52a8\u4fee\u6539\u540e\u518d\u6574\u5408\u5230\u603b\u7684go.class\u6587\u4ef6\u4e2d\u53bb\u3002
\n6. \u6700\u540e\u751f\u6210\u4e86go.class\u6587\u4ef6\u4e3a\u6700\u65b0\u7684\u6587\u4ef6\u4e86\u3002\u4f46\u662f\u4f7f\u7528http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=586<\/a>\u4e2d\u7684\u65b9\u6cd5\u505aGO\u5206\u7c7b\u56fe\u7684\u65f6\u5019\uff0c\u4f9d\u65e7\u63d0\u793aerror\u7684GO\u53f7\uff0c\u8fd9\u4e9bGO\u53f7\u90fd\u662f\u5e9f\u5f03\u4e86\u7684GO\u53f7\u3002
\n7. go.class\u6587\u4ef6\u4e0b\u8f7d\uff082013.2.27\uff09<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"
\u65b9\u6cd5\uff1a 1. \u4f7f\u7528OBO-Edit\u6765\u641c\u7d22GO\u4e8c\u7ea7\u6c34\u5e73term\u5305\u542b\u7684terms\uff0c\u5e76 … \u7ee7\u7eed\u9605\u8bfb →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[3],"tags":[25],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/598"}],"collection":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=598"}],"version-history":[{"count":9,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/598\/revisions"}],"predecessor-version":[{"id":618,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/598\/revisions\/618"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=598"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=598"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=598"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}