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Ensembl API Modules

INPUTs : species, Gene_symbol(should be accurate),Type(orthologues/paralogues),AlignedOUTPUTs : 해당 species의 gene의 paralogues 혹은 orthologues의 정보를 반환한다. ( * 본인의 gene 정보는 같은 형식으로 반환하지 않는다.)SOURCE : GET homology/symbol/:species/:symbolOPTIONAL : callback, cigar_line, compara, external_db, format, sequence,target_species, target_taxon INPUTs : id(An Ensembl stable ID)OUTPUTs : 해당 ID의 개략적인 정보를 반환한다(default format=condensed).SOURCE : GET lookup/id/:idOPTIONAL : callback, db_type, expand, format, phenotypes, species, utr Double-click top left corner to edit. Double-click top left corner to edit. INPUTs : speciesOUTPUTs : 해당 species의 접근가능한 개략적 정보를 반환한다.SOURCE : GET info/assembly/:speciesOPTIONAL : callback, bands, synonyms INPUTs : species, ch#, startbp, endbp(~5MB), (masking), feature,Source_Restriction(e.g. ensembl_havana,blank)OUTPUTs : 해당 species ch#의 startbp부터 endbp사이에 bp가 start하는 feature의 정보를 Source Restiriction해서 반환한다.SOURCE : GET overlap/region/:species/:regionOPTIONAL : biotype, callback, db_type, logic_name, misc_set, so_term,species_set, trim_downstream, trim_upstream, variant_set Essential INPUTs : ch# length(Integer)OUTPUTs : ch# length를 5MB로 fragmentize 시킨 startbp, endbpch# length가 5MB이더라도 가능. RULES1. 내가 만든 variable name의 첫문자는 Capitalize! : JSON의 variable은 모두 소문자로 구성되어 있어서 구분하기 위해 INPUTs : OUTPUTs : 사용가능한 species의 정보를 반환한다.SOURCE : GET info/speciesOPTIONAL : callback, division, hide_strain_info, strain_collection INPUTs : species, Gene_symbol(should be accurate),Type(orthologues/paralogues),AlignedOUTPUTs : 해당 species의 gene의 paralogues 혹은 orthologues의 정보를 반환한다. + 본인의 gene 정보도 일부 반환한다.SOURCE : GET homology/symbol/:species/:symbolOPTIONAL : callback, cigar_line, compara, external_db, format, sequence,target_species, target_taxon INPUTs : id(An Ensembl stable ID)OUTPUTs : 해당 id의 gene tree를 반환한다.SOURCE : GET genetree/member/id:idOPTIONAL : callback, compara,db_type, nh_format, object_type, species//Still working INPUTs : species, region, method, species_set, aligned- methods : Enum(EPO, EPO_LOW_COVERAGE, PECAN, LASTZ_NET,BLASTZ_NET, TRANSLATED_BLAT_NET, CACTUS_HAL)OUTPUTs : 해당 species의 region에 alignment되는 정보를 반환한다.SOURCE : GET alignment/region/:species/:regionOPTIONAL : callback, compact, compara, display_species_set, mask,species_set_group INPUTs : OUTPUTs : 모든 사용가능한 compara analyses를 반환한다.SOURCE : GET info/compara/methodsOPTIONAL : callback, class, compara INPUTs : methodOUTPUTs : 해당 method로 분석된 모든 species를 반환한다.SOURCE : GET info/compara/species_sets/:methodOPTIONAL : callback, compara DELETE THEM IF YOU WANT DELETE THEM IF YOU WANT DELETE THEM IF YOU WANT DELETE THEM IF YOU WANT DELETE THEM IF YOU WANT DELETE THEM IF YOU WANT DELETE THEM IF YOU WANT *Format*In : (Data) length : e_Source_Seq_Region_Name의 bp길이e_Source_Seq_Region_Name : chromosome, scafford, etc(Variables)e_Source_Speciese_Sense : 1, -1 (sense, antisense)e_Feature : gene, transcript, exon, etce_Trim_Upstream : 1(start가 범위 밖에 있으면 제외),0e_Trim_Downstream : 1(end가 범위 밖에 있으면 제외),0e_Source_Restriction : ensembl_havana, etce_Species_Local_Path : 저장위치 Out :(Data) e_Species_Local_Path에 e_Source_Seq_Region_Name을 가지는 폴더 각각 e_Feature 정보를 .csv 파일로 저장한다./String value : Http_url로부터 받은 정보를 String value이름으로반환한다.(Variable)blablabla Features : String value != missingString value != Html Format 기존에 붙은 노드를 사용하지 말고 이것으로 교체해서 써라. 잘못된 metanode Universial Input Directory Specification Only Available Species Available Species + Appending constant column *Format*In : (Data) gene_id : ENSG00000223972 Out :(Data) 각 row 당, gene_id에 해당하는 1) external name + synonyms2) Gene Ontology (GO; Biological Process, Cellularcomponent, Molecular function을 모두 retrieve하여concatenate)3) 위 1), 2)를 만든 source json format data 각 gene synonyms으로 Pubmed에 검색을 했을 때 검색결과의 수가 0, 1, 1 이상일때를 나누어 결과를 다르게 한다. 0 : none 1 : 처음과 마지막 논문의 정보를 같게 함 > 1 : 처음과 마지막 논문의 정보가 다르게 함 *Format*In : (Data) <gene synonyms를 바탕으로 pubmed에 검색하여 검색결과의 수와 첫 논문과 마지막 논문의publish 일자를 반환한다.>>gene synonyms Out :(Data) 1) count2) 마지막 논문 PMID(Pubmed unique id)3) 첫 논문 PMID4) 마지막 논문 출판 날짜5) 첫 논문 출판 날짜 * 아주 최근 논문, 대략 현재로부터 일주일내 정도의 논문은 API로 검색이 안된다.* 아주 오래된 논문의 경우 검색이 잘 안되는경우가 있다. *Format*In : (Data) >gene_id : ENSG00000223972>e_GO_Representative_Cellular_Location : membrane>GO parameter : plasma membrane, etc Out :(Data) 1) e_GO_Representative_Cellular_Location 이 해당하는 지의여부2) GO parameter 중 있을 경우 concatanete 한 string. *Format*In : (Data) external name + descriptions-> Pubmed input terms를 만드는 데 이용.(external name+AND+descriptions) Out :(Data) Pubmed Paper Count & First and last Years gene_id를 이용하여 Open Target Platform에서 정보를 disease와 연결하여 가져온다.raw data는 이미 json 파일로 저장해 놓았다.gene별로 disease와 연관된 정도를 literature, genetciassociation 등의 기준으로 수치화 한 것을 반환한다.주의 : string value가 missing인 경우 수동으로 빼내어 다시 돌려야 한다. 두 파일을 gene의 external_name를 base로 join하는 flow.external_name으로 일치가 안되는 경우, synonyms로 일치시킨다. *Format*In : (Data) >gene_id : ENSG00000223972 Out :(Data) <Open target platform data 기원>gene_id 에 해당하는 disease의 수를 retreive한다.disease는 현재 Genetic Association, RNA expression, SomaticMutation 자료만 counting한다.이때 원하는 disease category는 정해서 넣어 줘야 한다. InputsNode 9994Node 9995Node 10007Node 10013InputsString length<=60?Node 10077Node 10079Node 10082ONLY choromosomeNode 10087Node 10117Node 10118ExclusionsONLY Source_RestrictionNode 10158String==[ ] ?InputsNode 10167Node 10169Node 10173Raw ResultsNode 10177Node 10179Selection for 1st IfException forEmpty DataSelectionRaw ResultsNode 10194Node 10196Exception forEmpty DataNode 10205Node 10214Node 10215* Quotientendbp+5MBLength_Chromosome >= 5MB ?SelectionGet Quotientstartbp+5MBNode 10225Node 10226last startbplast endbpNode 10231Node 10232ResultsAdd startbpAdd endbpNode 10238InputsNode 10242Node 10245Selection MethodException forEmpty DataNode 10257Node 10259Node 10264Node 10267ExcludingPre-Branch = "bottom"CAUTIONExcludingPre-Branch = "bottom"CAUTIONExclusionsExcludingPre-Branch = "bottom"CAUTIONString length<=60?ExclusionsResultsNode 10321Node 10325String length<=60?Selection MethodException forEmpty DataNode 10331Raw ResultsExcludingPre-Branch = "bottom"CAUTIONExclusionsNode 10336Node 10337InputsNode 10360Node 10361Node 10362Node 10363ExclusionsNode 10365String length<=60?Raw ResultsNode 10380ExcludingPre-Branch = "bottom"CAUTIONSelection MethodNode 10385InputsNode 10388Node 10390Node 10394ExclusionsNode 10398Exception forEmpty DataNode 10401Node 10403Selection for 2nd IfNode 10407Node 10409Node 10410Node 10414Node 10415Node 10416Node 10427Node 10428InputsNode 10430Node 10431Selection MethodException forEmpty DataNode 10440Node 10441ExclusionsNode 10443Node 10444ExcludingPre-Branch = "bottom"CAUTIONNode 10447String length<=60?Raw ResultsNode 10450Node 10451Node 10452Node 10453Node 10454Node 10456ExcludingPre-Branch = "bottom"CAUTIONString length<=60?SelectionNode 10461Node 10462ExclusionsNode 10465Exception forEmpty DataNode 10471Raw ResultsONLY choromosomeInputsInputsNode 10494ExclusionsExclusionsSelectionRaw ResultsString length<=60?Exception forEmpty DataNode 10502Node 10508Node 10509InputsExcludingPre-Branch = "bottom"CAUTIONNode 10515Node 10518ResultsInputsInput : Http_urlOutput : String value(e.g. string withJSON Format)Input : Http_urlOutput : String value(e.g. string withJSON Format)Input : Http_urlOutput : String value(e.g. string withJSON Format)Input : Http_urlOutput : String value(e.g. string withJSON Format)Input : Http_urlOutput : String value(e.g. string withJSON Format)Input : Http_urlOutput : String value(e.g. string withJSON Format)Input : Http_urlOutput : String value(e.g. string withJSON Format)Input : Http_urlOutput : String value(e.g. string withJSON Format)Input : Http_urlOutput : String value(e.g. string withJSON Format)Input : Http_urlOutput : String value(e.g. string withJSON Format)Target_FileNamee_TargetSubSubDirectory_Pathe_Chromosome_SubSubDirectory_Pathe_Species_SubDirectory_PathUniversialDirectory InputsStarte_Base_Directory_PathSPECIFY STARTInputsAvailable SpeciesInputsRef To JoinJoin based on Refe_Source_SpeciesSpeciesSelectionFiltering LocationD:\데이터\BioDATA\Ensemble_Source_SpeciesFiltering LocationSpeciesSelectiontable row to variable이하나의 row밖에지정이 안됨.D:\데이터\BioDATA\EnsemblInputsException forEmpty DataSelection MethodString length<=60?Node 11865Node 11869Exception forEmpty DataRaw ResultsSelection MethodNode 12146READhuman gene fileNode 12149Node 12150Node 12151Node 12152Node 12153Node 12155Node 12156Node 12157Node 12158Node 12159Node 12160Node 12161Node 12162Tasks 나누기 위한 filterNode 12164Node 12165Node 12167Node 12169String length<=60?Node 12171Node 12172Node 12173Protein_codingNode 12175Node 12176Node 12191Node 12192Node 12194Node 12195Node 12196FilePreparing URLGO parameterWhat to SelectWhole GeneNode 12229Node 12230membrane OR extracellular regionby Selected Parameterse_GO_Representative_Cellular_LocationShould be Manually TypedFilter 해당 사항 없는경우 그냥 passNode 12236Node 12238Node 12239Node 12240Tasks 나누기 위한 filterPubmed_Count>=2 1st port=1 2nd port=0 3rd portCollect resultsException forEmpty DataString length<=60?Selection MethodString length<=60?Exception forEmpty DataSelection MethodNode 12275Node 12285Node 12286String length<=60?Selection MethodException forEmpty DataRESULTsNode 13006Node 13274Node 13275Node 13277Node 13278Node 13279Node 13282Node 13283Node 13284Node 13285Node 13286Node 13287Node 13288Node 13292Node 13293Node 13312Node 13313Node 13314Node 13315Node 13317Node 13478Node 13479Node 13480Node 13481Node 13483Node 13484Node 13485Node 13487Node 13488Node 13491Node 13493Node 13494Node 13495Node 13496Node 13497Node 13499Node 13500Node 13505Node 13507Node 13509Node 13510Node 13511Node 13512Node 13515Node 13518Node 13519Node 13520Node 13523Node 13524Node 13525Node 13526Node 13527Node 13528Node 13529Node 13531Node 13532Node 13535Node 13538Node 13539Node 13541Node 13542Genetic Association& RNA Expression& Somatic MutationDisease We Wanted to know abouttherapeutic_areas가 없는 경우Node 13619Node 13620Node 13635INPUT FileTable Creator JSON Path String to JSON Ungroup JSON to Table String Manipulation Table Creator String Manipulation Column Resorter Ungroup JSON Path JSON to Table Rule-basedRow Filter Sorter ParallelChunk Start Parallel Chunk End Column Filter Rule-basedRow Filter String to JSON String Manipulation Table Creator Ungroup Column Resorter String Manipulation JSON to Table JSON Path Table Rowto Variable Loop End String Manipulation End IF Rule Engine IF Switch Rule Engine Table Rowto Variable Loop End End IF String to JSON IF Switch String Manipulation Table Creator RecursiveLoop Start Recursive Loop End Math Formula IF Switch Rule Engine Table Rowto Variable Math Formula(Multi Column) Math Formula Double To Int Column Filter Math Formula Math Formula Concatenate End IF Rule-basedRow Filter ConstantValue Column ConstantValue Column Chunk Loop Start Table Creator Chunk Loop Start String Manipulation Column Resorter Rule Engine Table Rowto Variable IF Switch End IF Chunk Loop Start Loop End String Manipulation JSON to Table String to JSON Rule-basedRow Filter Rule-basedRow Filter Column Filter Rule-basedRow Filter String Manipulation Column Filter RowID String Manipulation String Manipulation Chunk Loop Start String Manipulation Rule Engine Table Rowto Variable IF Switch End IF Loop End Rule-basedRow Filter Column Filter Column Resorter Column Rename Table Creator JSON to Table String to JSON JSON Path Ungroup Column Resorter Column Filter RowID String Manipulation Loop End End IF JSON to Table Rule-basedRow Filter Rule Engine String Manipulation Table Creator Chunk Loop Start Column Resorter String Manipulation JSON Path Column Filter Ungroup Table Rowto Variable IF Switch String to JSON IF Switch Rule Engine End IF Row Filter Column Splitter JSON to Table Column Splitter JSON to Table Row Filter Column Filter Concatenate Row Filter ConstantValue Column Joiner Table Creator End IF Chunk Loop Start JSON to Table Rule Engine Table Rowto Variable IF Switch JSON Path Column Resorter Column Filter Column Rename Ungroup String Manipulation Rule-basedRow Filter String to JSON String Manipulation Loop End TreeRecon PairAlign SeqanTcoffee String to JSON String Manipulation Column Resorter Rule-basedRow Filter String Manipulation Rule Engine End IF Chunk Loop Start JSON to Table Column Filter JSON Path String Manipulation IF Switch Table Rowto Variable Ungroup Loop End Rule-basedRow Filter Table Creator JSON to Table Table Creator String to JSON Column Filter Column Filter Rule Engine Loop End String Manipulation IF Switch Ungroup JSON to Table End IF Chunk Loop Start Table Rowto Variable String Manipulation Table Creator Rule-basedRow Filter JSON Path String to JSON Transpose Table Creator Extract_Data_From_Http_url Extract_Data_From_Http_url Extract_Data_From_Http_url Extract_Data_From_Http_url Extract_Data_From_Http_url Extract_Data_From_Http_url Extract_Data_From_Http_url Extract_Data_From_Http_url Extract_Data_From_Http_url Extract_Data_From_Http_url String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) Table Rowto Variable String Manipulation(Variable) Create Directory String Manipulation(Variable) Table Rowto Variable Create Directory Create Directory Table Creator Create Directory String Manipulation(Variable) Table Creator Table Creator ExtractSpecies Info Bring 5Mb FragmentedBase Pair String Manipulation Extract & Save FeaturesData From Coord System Time And RandomNumber Generator Table Creator ConstantValue Column Joiner Column Rename Rule-basedRow Filter Column Filter List Folders Column Rename Column Filter Rule-basedRow Filter Extract MultipleHttp_url Data Make Whole Gene Set FromRaw Fragmented Gene Set Extract Multiple Http_urlData (Size Selectable) Extract & Save FeaturesFrom Coord Systems List Folders Table Creator Extract MultipleHttp_url Data IF Switch Rule Engine String Manipulation String to JSON