UCSC Genome Browser Home

id summary reporter owner description type status priority milestone component version resolution keywords cc include_gantt dependencies due_assign due_close 47 検索 WebAPI 機能の仕様 h-morita yy "= 検索 WebAPI 機能の仕様 = == インタフェース == === SOAP === * WSDL * /search/service.wsdl * エントリポイント * /search/api * SOAPAction * /search/api/GetResourceInfoByQueryTerm * パラメータ仕様 || パラメータ名 || パラメータ内容 || 必須/オプション || デフォルト値 || 設定可能な値 || || expression || 検索文字列 || 必須 || ー || !IndriRunQuery が対応可能な式 || || max_results || 最大検索件数 || 必須 || ー || 1 〜 1000 || || order || ソート方法 || 必須 || ー || relevance もしくは date || || enable_hide_unfetched || 404ページの表示/非表示 || 必須 || ー || true もしくは false || || enable_relevance_feedback || 疑似関連フィードバック || 必須|| ー || true もしくは false || * エラー仕様 * できうる限り SOAP エラー仕様に従ってエラーを返す * パラメータが不足している場合内部サーバエラーで処理される場合がある === REST === * URI * /search.xml * パラメータ仕様 * GET パラメータもしくは POST パラメータとして付与 || パラメータ名 || パラメータ内容 || 必須/オプション || デフォルト値 || 設定可能な値 || || query || 検索文字列 || 必須 || ー || !IndriRunQuery が対応可能な式 || || count || 最大検索件数 || オプション || 100 || 1 〜 1000 || || sort_by || ソート方法 || オプション || relevance || relevance もしくは date || || hide_unfetched || 404ページの表示/非表示 || オプション || on || on もしくは off || || feedback || 疑似関連フィードバック || オプション || off || on もしくは off || * エラー仕様 * 基本的には HTTP ステータスをもとにエラーハンドリングを行うこと * ユーザパラメータにエラーがある場合は出来うる限りそのエラー内容を XML で返す * エラー内容の仕様 * errors: エラーリスト * error: エラー * http_status_code: HTTP ステータスコード * code: アプリケーションエラーコード * name: エラー名 * message: エラーメッセージ * エラーサンプル {{{ 400 40003 Orefil::InvalidCountError Set integer of 1 or more to `Max Results` value. }}} == レスポンス仕様 == * Result_Set: 結果セット ( REST の場合は result_set ) * query: デフォルト値反映後の問い合わせ内容 * expression: 検索文字列パラメータ * option: オプション系パラメータ * max_results: 出力最大件数 * order: ソート方法 * enable_hide_unfetched: 404なオンラインリソース結果を表示するかどうか ( true / false ) * enable_relevance_feedback: 疑似フィードバックの有無 ( true / false ) * last_index_date: インデックスの更新日時 * status: 実行結果ステータス ( SOAP のみに存在 ) * code: ステータスコード * name: ステータス名 * message: ステータスメッセージ * results: 検索結果リスト * item: 検索結果単体 ( REST の場合は result ) * id: オンラインリソース ID * rank: 検索一致ランク * title: オンラインリソースタイトル * updated_at: データ更新日 ( XML Schema 形式の日付で記載 ) * average_stars: レーティング平均値 * snippet: スニペット * mesh_term_list: MeSH リスト * item: MeSH 単体 ( REST の場合は mesh_term ) * url: オンラインリソース URL * pages: 参照リンク検索 URL リスト * item: 参照リンク検索 ( REST の場合は page ) * name: 検索エンジン名 * url: 参照リンク検索 URL * papers: 参照文献検索 URI リスト * item: 参照文献検索 ( REST の場合は paper ) * name: 検索エンジン名 * url: 参照文献検索 URL * pmid_list: 参照 !PubMed の PMID リスト * item: 参照 !PubMed の pmid ( REST の場合は pmid ) == リクエスト/レスポンスサンプル == 以下のクエリで Web API を呼び出すリクエストとその結果のレスポンスを SOAP / REST の二つでサンプルとして示す。 * リクエスト内容 * 検索文字列 : #filreq(DNA.majr #combine(genome)) * クエリオプション * 最大結果件数 : 3 件 * ソート方法 : 関連度順 * 404ページの表示/ 非表示 : 表示 * 疑似関連フィードバック : 無効 === SOAP === * リクエスト {{{

#filreq(DNA.majr #combine(genome)) 3 relevance true false

}}} * レスポンス {{{ 4980 Abnormalities, Multiple Carbamoyl-Phosphate Synthase I Deficiency Disease Chickens Chromosome Deletion Chromosome Mapping Chromosomes, Human, Pair 2 Computational Biology DNA Primers Database Management Systems Databases, Genetic Databases, Nucleic Acid Databases, Protein Exons Genome Genome, Human Genomics Information Storage and Retrieval Internet Linkage (Genetics) Microsatellite Repeats Polymorphism, Single Nucleotide Proteins Proteome Proteomics RNA, Messenger Sequence Alignment Software Zebrafish UCSC Genome Browser Home 16888352 16381938 12045153 15216554 17151077 16888348 16372332 11932250 16722777 12519945 16500937 17142222 15554057 15608236 16888346 Comparative Genomic Analysis Using the UCSC Genome Browser. Comparative analysis of DNA sequence from multiple species can provide insights into the function...sequence from multiple species can provide insights into the function and evolutionary processes that shape genomes. The University of California Santa Cruz (UCSC) Genome Bioinformatics group has developed several tools and methodologies in its study of comparative genomics, many... 1 http://www.biomedcentral.com/search/results.asp?txtSearch1=http%3A%2F%2Fgenome.ucsc.edu%2F&chkBMCJournals=true&chkCurrentOpinion=true&drpFromDate=&drpToDate=&chkNSP=true&drpAddedInLast=&drpOrderBy=by+date&drpPerPage=20&drpAbstract=no+abstract&strTempString=&strSearchBoxType=bmc_boolean_results&Search.x=10&jou_id=&Search.x=0&Search.y=0&Search=Search http://www.scirus.com/srsapp/search?q=http%3A%2F%2Fgenome.ucsc.edu%2F&ds=jnl&g=s&t=all http://highwire.org/cgi/searchresults?fulltext=http%3A%2F%2Fgenome.ucsc.edu%2F http://scholar.google.com/scholar?hl=en&lr=&q=http%3A%2F%2Fgenome.ucsc.edu%2F&btnG=Search +3.666666666666667 http://genome.ucsc.edu/ http://www.google.com/search?hl=en&q=link%3ahttp%3A%2F%2Fgenome.ucsc.edu%2F&btnG=Google+Search http://www.altavista.com/web/results?itag=ody&q=link:http%3A%2F%2Fgenome.ucsc.edu%2F&kgs=0&kls=1 2008-02-20T00:00:00+09:00 7142 Chromosome Mapping Databases, Genetic Gene Expression Profiling Genome Oligonucleotide Array Sequence Analysis Sequence Alignment Sequence Analysis, DNA Software User-Computer Interface UCSC Genome Browser Home 14681485 16108715 Finding anchors for genomic sequence comparison . Recent sequencing of the human and other mammalian genomes has brought about the necessity to align them , to identify and characterize their commonalities and...Algorithms Amino Acid Motifs Chromosome Mapping Sequence Analysis, DNA User-Computer Interface Databases, Genetic Mice Genome Information Storage and Retrieval Internet Rats Computational Biology Software Models, Genetic Animals Oligonucleotide Array Sequence Analysis Databases, Genetic Genome Gene Expression Profiling Sequence Alignment Software Chromosome Mapping Oligonucleotide Array Sequence Analysis User-Computer Interface Sequence Analysis, ... Nucleic Acid Hybridization Microarray Analysis Genetic Techniques Information Storage and Retrieval Sequence Analysis Chemistry, Analytical... 2 http://www.biomedcentral.com/search/results.asp?txtSearch1=http%3A%2F%2Fwww.genome.ucsc.edu%2F&chkBMCJournals=true&chkCurrentOpinion=true&drpFromDate=&drpToDate=&chkNSP=true&drpAddedInLast=&drpOrderBy=by+date&drpPerPage=20&drpAbstract=no+abstract&strTempString=&strSearchBoxType=bmc_boolean_results&Search.x=10&jou_id=&Search.x=0&Search.y=0&Search=Search http://www.scirus.com/srsapp/search?q=http%3A%2F%2Fwww.genome.ucsc.edu%2F&ds=jnl&g=s&t=all http://highwire.org/cgi/searchresults?fulltext=http%3A%2F%2Fwww.genome.ucsc.edu%2F http://scholar.google.com/scholar?hl=en&lr=&q=http%3A%2F%2Fwww.genome.ucsc.edu%2F&btnG=Search +3 http://www.genome.ucsc.edu/ http://www.google.com/search?hl=en&q=link%3ahttp%3A%2F%2Fwww.genome.ucsc.edu%2F&btnG=Google+Search http://www.altavista.com/web/results?itag=ody&q=link:http%3A%2F%2Fwww.genome.ucsc.edu%2F&kgs=0&kls=1 2008-02-18T00:00:00+09:00 7515 Computational Biology Genomics Isochores Software UCSC Genome Browser Home 15215396 IsoFinder : computational prediction of isochores in genome sequences . Isochores are long genome segments homogeneous in G+C . Here , we describe an algorithm ( IsoFinder ) running on the web...by each cut . This leads to the decomposition of a chromosome sequence into long homogeneous genome regions ( LHGRs ) with well-defined mean G+C contents , each significantly different from the G... 3 http://www.biomedcentral.com/search/results.asp?txtSearch1=http%3A%2F%2Fgenome.cse.ucsc.edu%2F&chkBMCJournals=true&chkCurrentOpinion=true&drpFromDate=&drpToDate=&chkNSP=true&drpAddedInLast=&drpOrderBy=by+date&drpPerPage=20&drpAbstract=no+abstract&strTempString=&strSearchBoxType=bmc_boolean_results&Search.x=10&jou_id=&Search.x=0&Search.y=0&Search=Search http://www.scirus.com/srsapp/search?q=http%3A%2F%2Fgenome.cse.ucsc.edu%2F&ds=jnl&g=s&t=all http://highwire.org/cgi/searchresults?fulltext=http%3A%2F%2Fgenome.cse.ucsc.edu%2F http://scholar.google.com/scholar?hl=en&lr=&q=http%3A%2F%2Fgenome.cse.ucsc.edu%2F&btnG=Search +3 http://genome.cse.ucsc.edu/ http://www.google.com/search?hl=en&q=link%3ahttp%3A%2F%2Fgenome.cse.ucsc.edu%2F&btnG=Google+Search http://www.altavista.com/web/results?itag=ody&q=link:http%3A%2F%2Fgenome.cse.ucsc.edu%2F&kgs=0&kls=1 2008-02-17T00:00:00+09:00 #filreq(DNA.majr #combine(genome)) 2008-03-17T15:34:23+09:00 Orefil::Success 20000 success. BioMed Central Scirus HighWire Press Google Scholar Google AltaVista }}} === REST === * リクエスト {{{ /search.xml?query=%23filreq%28DNA.majr+%23combine%28genome%29%29&count=3&sort_by=relevance&hide_unfetched=on }}} * レスポンス {{{ #filreq(DNA.majr #combine(genome)) 2008-03-04T17:05:26+09:00 4980 1 UCSC Genome Browser Home 2008-02-20T00:00:00+09:00 3.4 Comparative Genomic Analysis Using the UCSC Genome Browser. Comparative analysis of DNA sequence from multiple species can provide insights into the function...sequence from multiple species can provide insights into the function and evolutionary processes that shape genomes. The University of California Santa Cruz (UCSC) Genome Bioinformatics group has developed several tools and methodologies in its study of comparative genomics, many... Abnormalities, Multiple Carbamoyl-Phosphate Synthase I Deficiency Disease Chickens Chromosome Deletion Chromosome Mapping Chromosomes, Human, Pair 2 Computational Biology DNA Primers Database Management Systems Databases, Genetic Databases, Nucleic Acid Databases, Protein Exons Genome Genome, Human Genomics Information Storage and Retrieval Internet Linkage (Genetics) Microsatellite Repeats Polymorphism, Single Nucleotide Proteins Proteome Proteomics RNA, Messenger Sequence Alignment Software Zebrafish http://genome.ucsc.edu/ Google http://www.google.com/search?hl=en&q=link%3ahttp%3A%2F%2Fgenome.ucsc.edu%2F&btnG=Google+Search AltaVista http://www.altavista.com/web/results?itag=ody&q=link:http%3A%2F%2Fgenome.ucsc.edu%2F&kgs=0&kls=1 BioMed Central http://www.biomedcentral.com/search/results.asp?txtSearch1=http%3A%2F%2Fgenome.ucsc.edu%2F&chkBMCJournals=true&chkCurrentOpinion=true&drpFromDate=&drpToDate=&chkNSP=true&drpAddedInLast=&drpOrderBy=by+date&drpPerPage=20&drpAbstract=no+abstract&strTempString=&strSearchBoxType=bmc_boolean_results&Search.x=10&jou_id=&Search.x=0&Search.y=0&Search=Search Scirus http://www.scirus.com/srsapp/search?q=http%3A%2F%2Fgenome.ucsc.edu%2F&ds=jnl&g=s&t=all HighWire Press http://highwire.org/cgi/searchresults?fulltext=http%3A%2F%2Fgenome.ucsc.edu%2F&andorexactfulltext=and&author1=&pubdate_year=&volume=&firstpage=&src=hw&searchsubmit=redo&resourcetype=1&search=Search&fmonth=Jan&fyear=1844&tmonth=Dec&tyear=2007&fdatedef=1+January+1844&tdatedef=31+Dec+2007 Google Scholar http://scholar.google.com/scholar?hl=en&lr=&q=http%3A%2F%2Fgenome.ucsc.edu%2F&btnG=Search 16888352 16381938 12045153 15216554 17151077 16888348 16372332 11932250 16722777 12519945 16500937 17142222 15554057 15608236 16888346 7142 2 UCSC Genome Browser Home 2008-02-18T00:00:00+09:00 3.0 Finding anchors for genomic sequence comparison . Recent sequencing of the human and other mammalian genomes has brought about the necessity to align them , to identify and characterize their commonalities and...Algorithms Amino Acid Motifs Chromosome Mapping Sequence Analysis, DNA User-Computer Interface Databases, Genetic Mice Genome Information Storage and Retrieval Internet Rats Computational Biology Software Models, Genetic Animals Oligonucleotide Array Sequence Analysis Databases, Genetic Genome Gene Expression Profiling Sequence Alignment Software Chromosome Mapping Oligonucleotide Array Sequence Analysis User-Computer Interface Sequence Analysis, ... Nucleic Acid Hybridization Microarray Analysis Genetic Techniques Information Storage and Retrieval Sequence Analysis Chemistry, Analytical... Chromosome Mapping Databases, Genetic Gene Expression Profiling Genome Oligonucleotide Array Sequence Analysis Sequence Alignment Sequence Analysis, DNA Software User-Computer Interface http://www.genome.ucsc.edu/ Google http://www.google.com/search?hl=en&q=link%3ahttp%3A%2F%2Fwww.genome.ucsc.edu%2F&btnG=Google+Search AltaVista http://www.altavista.com/web/results?itag=ody&q=link:http%3A%2F%2Fwww.genome.ucsc.edu%2F&kgs=0&kls=1 BioMed Central http://www.biomedcentral.com/search/results.asp?txtSearch1=http%3A%2F%2Fwww.genome.ucsc.edu%2F&chkBMCJournals=true&chkCurrentOpinion=true&drpFromDate=&drpToDate=&chkNSP=true&drpAddedInLast=&drpOrderBy=by+date&drpPerPage=20&drpAbstract=no+abstract&strTempString=&strSearchBoxType=bmc_boolean_results&Search.x=10&jou_id=&Search.x=0&Search.y=0&Search=Search Scirus http://www.scirus.com/srsapp/search?q=http%3A%2F%2Fwww.genome.ucsc.edu%2F&ds=jnl&g=s&t=all HighWire Press http://highwire.org/cgi/searchresults?fulltext=http%3A%2F%2Fwww.genome.ucsc.edu%2F&andorexactfulltext=and&author1=&pubdate_year=&volume=&firstpage=&src=hw&searchsubmit=redo&resourcetype=1&search=Search&fmonth=Jan&fyear=1844&tmonth=Dec&tyear=2007&fdatedef=1+January+1844&tdatedef=31+Dec+2007 Google Scholar http://scholar.google.com/scholar?hl=en&lr=&q=http%3A%2F%2Fwww.genome.ucsc.edu%2F&btnG=Search 14681485 16108715 7515 3 UCSC Genome Browser Home 2008-02-17T00:00:00+09:00 3.0 IsoFinder : computational prediction of isochores in genome sequences . Isochores are long genome segments homogeneous in G+C . Here , we describe an algorithm ( IsoFinder ) running on the web...by each cut . This leads to the decomposition of a chromosome sequence into long homogeneous genome regions ( LHGRs ) with well-defined mean G+C contents , each significantly different from the G... Computational Biology Genomics Isochores Software http://genome.cse.ucsc.edu/ Google http://www.google.com/search?hl=en&q=link%3ahttp%3A%2F%2Fgenome.cse.ucsc.edu%2F&btnG=Google+Search AltaVista http://www.altavista.com/web/results?itag=ody&q=link:http%3A%2F%2Fgenome.cse.ucsc.edu%2F&kgs=0&kls=1 BioMed Central http://www.biomedcentral.com/search/results.asp?txtSearch1=http%3A%2F%2Fgenome.cse.ucsc.edu%2F&chkBMCJournals=true&chkCurrentOpinion=true&drpFromDate=&drpToDate=&chkNSP=true&drpAddedInLast=&drpOrderBy=by+date&drpPerPage=20&drpAbstract=no+abstract&strTempString=&strSearchBoxType=bmc_boolean_results&Search.x=10&jou_id=&Search.x=0&Search.y=0&Search=Search Scirus http://www.scirus.com/srsapp/search?q=http%3A%2F%2Fgenome.cse.ucsc.edu%2F&ds=jnl&g=s&t=all HighWire Press http://highwire.org/cgi/searchresults?fulltext=http%3A%2F%2Fgenome.cse.ucsc.edu%2F&andorexactfulltext=and&author1=&pubdate_year=&volume=&firstpage=&src=hw&searchsubmit=redo&resourcetype=1&search=Search&fmonth=Jan&fyear=1844&tmonth=Dec&tyear=2007&fdatedef=1+January+1844&tdatedef=31+Dec+2007 Google Scholar http://scholar.google.com/scholar?hl=en&lr=&q=http%3A%2F%2Fgenome.cse.ucsc.edu%2F&btnG=Search 15215396 }}}" 仕様 closed 各マイルストーンで解決する Iterate5(1/10) OReFiL fixed 0 YYYY/MM/DD YYYY/MM/DD