WABI (REST) GTPSの仕様 (2009)

service_name	GTPS service_desc_en	"GTPS" is acronym of Gene Trek in Procaryote Space. Various complete genomes of eubacteria and archaea have been registered in the International Nucleotide Sequence Databases (INSD) of DDBJ/EMBL/GenBank. The annotation and sequence data are available from GIB (Genome Information Broker; http://gib.genes.nig.ac.jp/). However, annotations for genomic sequence of eubacteria and archaea released from INSD are often carried out by the different protocols such as minimum length of the ORF specified by the prediction program, threshold value of blast search and version number of the reference data used for blast and motif scan. Therefore, some inconsistencies of the ORF data are found in genomic annotations. The purpose of GTPS is to reannotate the ORFs among microorganisms in GIB data by using a common protocol and diffuse the results to every users as a resource for gnomescale analysis on microbes. The results are graded into AAAA (top grade) to X (lowermost grade) categories by curating the result of blastp and InterProScan analysis. We provide you with all the result of reannotated data by the graphical interface and the flat file. service_desc_jp	GTPS は Gene Trek in Procaryote Space の略称です. さまざまな真正細菌や古細菌のゲノムがINSD(国際塩基配列データベース)であるDDBJ/EMBL/GenBank に登録されてきました. それらのゲノムのアノテーションや配列は GIB でご利用可能です. しかしながら、そのゲノム配列のアノテーションは異なる解析手順で実行されています. 例えば、ORF予測プログラムを実行する際のORFの最短長の条件やBLAST検索の閾値、BLAST検索やモチーフ検索を実行する際に使用する参照データベースのバージョンが異なります. したがって、複数のゲノムアノテーションにおけるORFにいくつか矛盾が見つかることがあります. GTPS の目的は、GIBで公開されている微生物データを 共通の条件で各 ORF を再度アノテーション付与しゲノムワイドな解析の情報源として公開することです. それぞれの結果は BLAST や InterProscan 等の結果から最もORFの確からしさが高いグレード AAAA から確からしさが低い X に分類されております. link_en	http://gtps.ddbj.nig.ac.jp/ link_jp	http://gtps.ddbj.nig.ac.jp/ wsdl	http://xml.nig.ac.jp/wsdl/GTPS.wsdl method_name	checkAnnotation method_desc_en	Check annotation of the specified protein ID. If the annotation is unknown 'hypothetical protein' is returned, otherwise the valid annotation of the specified protein ID is returned. This method is based on the ontology. See more detailed information (Hypothetical product ontology in GTPS). method_desc_jp	プロテイン ID から アノテーション を取得します. もしアノテーション付けがされていなければ 'hypothetical protein' が返されます. このメソッドはオントロジーが基盤となっております. 詳しくは Hypothetical product ontology in GTPS を参照ください. param_start	0 param_print_name	proteinId param_inout_name	文字列型 param_desc_en	protein ID param_desc_jp	プロテインID param_example_start param_example	AAB40160.1 param_example_end param_end	0 result_format_en	product name result_format_jp	プロダクト名 result_inout_name	文字列型 result_example_start result_example	hypothetical protein result_example_end method_name	getChIDFromOrganismName method_desc_en	Get chromosome ID of a organism. method_desc_jp	生物種名から chromosome ID を取得します. param_start	0 param_print_name	orgName param_inout_name	文字列型 param_desc_en	organism name param_desc_jp	生物種名 param_example_start param_example	Aeropyrum pernix K1 param_example_end param_end	0 result_format_en	Chromosome ID registered in GTPS database result_format_jp	GTPS に登録されている Chromosome ID が返されます. result_inout_name	文字列型 result_example_start result_example	Aper_K1: result_example_end method_name	getChIDList method_desc_en	Get chromosome ID list registered in GTPS database. method_desc_jp	GTPS データベースに登録されている chromoseme ID の一覧を返します. result_format_en	Chromosome ID list registered in GTPS database result_format_jp	GTPS データベースに登録されている chromoseme ID の一覧 result_inout_name	文字列型 result_example_start result_example	Aaeo_VF5: result_example	Aaeo_VF5:ece1 result_example	Abac_ELLIN345: result_example	Abor_SK2: result_example	Acin_ADP1: result_example	Adeh_2CPC: result_example	Aehr_HLHE1: result_example	Aful_DSM4304: result_example	Amar_MARIES: result_example	Aper_K1: result_example	Apha_HZ: result_example	Atum_C58_CEREON:01C result_example	Atum_C58_CEREON:02L result_example	Atum_C58_CEREON:AT result_example	Atum_C58_CEREON:Ti result_example_end method_name	getFeatureInformation method_desc_en	Get feature information of a chromosome ID and a feature ID. method_desc_jp	Chromosome ID と feature ID からフィーチャーの詳細を取得します. param_start	0 param_print_name	chid param_inout_name	文字列型 param_desc_en	chromosome ID param_desc_jp	chromosome ID param_example_start param_example	Aper_K1: param_example_end param_end	0 param_start	1 param_print_name	ftid param_inout_name	文字列型 param_desc_en	feature ID param_desc_jp	feature ID param_example_start param_example	1 param_example_end param_end	1 result_format_en	Feature information of a chromosome ID and a feature ID. The first column shows feature qualifier name, the second column shows qualifier value. result_format_jp	Chromosome ID と feature ID に対応するフィーチャーの詳細がタブ区切りフォーマットで返されます. 1項目目は フィーチャークオリファイア名、2項目目は クオリファイア値 が返されます. result_inout_name	文字列型 result_example_start result_example	Species ID	Aper_K1 result_example	Chromosome ID	Aper_K1: result_example	Feature ID	1 result_example	Feature key	CDS result_example	ID	Aper_K1:PL1 result_example	location	complement(213..938) result_example	product	hypothetical protein result_example	grade	D1 result_example	flag	N-1-1-3-1-2-4 result_example	Amino acid	MVDILSSLLLSLPFGVIGFLLVLSPGSIWTPVKESIGYVYVSRRVTVKASKLLGSLTLLASLISFVVGAAYGITIQASTLALLLALITVVTVEYSMRLAEIESLNQPVLEGFEPVGSIKLKYLTIILLVYLISIVFSIEGSLKLYSIGAYGTLASHLSIEILAGYTVFLSVKRPEAYVIPGLSRETIELLQFFMPTSLSLIAIGVYMILAGFHMWWIILLAGVTTLFVVTMLIMINKEGKY result_example	Nucleotide	atggtagatatactatcttcactcctgctgtcgcttccatttggtgtaattggatttctcttggtattgtctcctgggtcaatatggacgcctgtaaaggagagcataggctatgtttatgtttctaggcgcgtcacggttaaagcgagcaagctattgggttcgcttactttgttagcgagtttaatatcttttgtggttggtgcagcatatggtattactattcaggcatctacactagccctattacttgcattgataaccgtagttaccgtggaatattctatgaggctcgccgaaatagagtctttaaaccaaccagtccttgaaggattcgagccagtaggttctattaaattaaaatatttgactattatattactagtttatctaatctcgattgtattctcaattgaaggttctcttaaactatatagtattggtgcatacggaacgttagcttcacatttatctattgaaatattagcaggatataccgtttttctatctgtaaaaaggccggaagcatatgtaataccaggactaagtcgggaaacgatcgagctattacaatttttcatgccaacctccttatctctcatagctataggtgtatatatgattttagcaggattccatatgtggtggataatcctgttggcgggagtgaccactctattcgttgtaacaatgttaattatgattaataaagagggtaagtattga result_example_end method_name	getFtIDList method_desc_en	Get feature ID list of a chromosome ID. method_desc_jp	Chromosome ID から feature ID の一覧を返します. param_start	0 param_print_name	chid param_inout_name	文字列型 param_desc_en	chromosome ID param_desc_jp	chromosome ID param_example_start param_example	Aper_K1: param_example_end param_end	0 result_format_en	Feature ID list of a chromosome ID result_format_jp	Chromosome ID に対応する feature ID の一覧 result_inout_name	文字列型 result_example_start result_example	800001 result_example	800002 result_example	800003 result_example	800004 result_example	800005 result_example	800006 result_example	800007 result_example	800008 result_example_end method_name	getOrganismList method_desc_en	Get organism name list registered in GTPS database. method_desc_jp	GTPS に登録されている生物種一覧を取得します. result_format_en	Organism name list registered in GTPS database result_format_jp	GTPS に登録されている生物種名一覧 result_inout_name	文字列型 result_example_start result_example	Acidobacteria bacterium Ellin345 result_example	Acinetobacter sp. ADP1 result_example	Aeropyrum pernix K1 result_example	Agrobacterium tumefaciens C58 (Cereon) circular chromosome result_example	Agrobacterium tumefaciens C58 (U. Washington) circular chromosome result_example	Alcanivorax borkumensis SK2 result_example	Alkalilimnicola ehrlichei MLHE-1 result_example	Anabaena variabilis ATCC 29413 result_example	Anaeromyxobacter dehalogenans 2CP-C result_example	Anaplasma marginale St. Maries result_example	Anaplasma phagocytophilum HZ result_example	Aquifex aeolicus VF5 result_example	Archaeoglobus fulgidus DSM 4304 result_example	Aster yellows witches'-broom phytoplasma AYWB result_example	Azoarcus sp. EbN1 result_example_end method_name	getOrganismNameFromChid method_desc_en	Get organism name of a chromosome ID. method_desc_jp	Chromosome ID に対応する生物種名を返します. param_start	0 param_print_name	chid param_inout_name	入出力型 param_desc_en	chromosome ID param_desc_jp	chromosome ID param_example_start param_example	Aper_K1: param_example_end param_end	0 result_format_en	Organism name of a chromosome ID result_format_jp	Chromosome ID に対応する生物種名 result_inout_name	文字列型 result_example_start result_example	Aeropyrum pernix K1 result_example_end method_name	searchSimple method_desc_en	Search features against GTPS database. method_desc_jp	GTPS に対してキーワード検索を行います. param_start	0 param_print_name	keyword param_inout_name	文字列型 param_desc_en	search keyword param_desc_jp	検索キーワード param_example_start param_example	protein param_example_end param_end	0 param_start	1 param_print_name	offset param_inout_name	文字列型 param_desc_en	offset position param_desc_jp	取得開始位置 param_example_start param_example	1 param_example_end param_end	1 param_start	2 param_print_name	limit param_inout_name	文字列型 param_desc_en	get count of result param_desc_jp	取得件数 param_example_start param_example	100 param_example_end param_end	2 result_format_en	The first line shows the count of hits. Below lines show search result. This format is [spid, chid, ftid, organism, product, start, stop, strand, grade]. result_format_jp	最初の1行目はヒット件数を表します. 2行目からは以下の項目がタブ区切りフォーマットで表示されます. [spid, chid, ftid, organism, product, start, stop, strand, grade] result_inout_name	文字列型 result_example_start result_example	hitcount	906957 result_example	spid	chid	ftid	organism	product	start	stop	strand	grade result_example	Erum_WELGEVONDEN	Erum_WELGEVONDEN:	944	Ehrlichia ruminantium Welgevonden (South Africa)	hypothetical protein	284413	284610	+	AAAA3 result_example	Nost_PCC7120	Nost_PCC7120:	4622	Nostoc sp. PCC 7120	serinethreonine kinase	2893436	2895472	+	AAAA2 result_example	Nost_PCC7120	Nost_PCC7120:	10004	Nostoc sp. PCC 7120	secretory protein	6320845	6321066	+	AAAA1 result_example	Erum_WELGEVONDEN_CIRAD	Erum_WELGEVONDEN_CIRAD:	897	Ehrlichia ruminantium Welgevonden (CIRAD)	hypothetical protein	264658	264855	+	AAAA2 result_example	Erum_GARDEL	Erum_GARDEL:	831	Ehrlichia ruminantium Gardel	hypothetical protein	261779	261976	+	AAAA2 result_example	Pmul_PM70	Pmul_PM70:	2366	Pasteurella multocida subsp. multocida Pm70	SecE	1966796	1967206	-	AAAA1 result_example	Rcon_MALISH7	Rcon_MALISH7:	307	Rickettsia conorii Malish 7	preprotein translocase SecE subunit	174758	175012	+	AAAA1 result_example	Rcon_MALISH7	Rcon_MALISH7:	271	Rickettsia conorii Malish 7	protein-export membrane protein secF	153861	154787	+	AAAA1 result_example	Rcon_MALISH7	Rcon_MALISH7:	1585	Rickettsia conorii Malish 7	protein-export membrane protein secD	840126	841682	+	AAAA1 result_example	Rpro_MADRIDE	Rpro_MADRIDE:	203	Rickettsia prowazekii Madrid E	unknown (secE)	156550	156750	+	AAAA1 result_example_end