{"id":"https://openalex.org/W2159938295","doi":"https://doi.org/10.1093/bioinformatics/bts630","title":"XiP: a computational environment to create, extend and share workflows","display_name":"XiP: a computational environment to create, extend and share workflows","publication_year":2012,"publication_date":"2012-10-25","ids":{"openalex":"https://openalex.org/W2159938295","doi":"https://doi.org/10.1093/bioinformatics/bts630","mag":"2159938295","pmid":"https://pubmed.ncbi.nlm.nih.gov/23104885"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts630","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts630","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/1/137/49060286/bioinformatics_29_1_137.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/1/137/49060286/bioinformatics_29_1_137.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025220924","display_name":"Masao Nagasaki","orcid":"https://orcid.org/0000-0002-4292-8785"},"institutions":[{"id":"https://openalex.org/I201537933","display_name":"Tohoku University","ror":"https://ror.org/01dq60k83","country_code":"JP","type":"education","lineage":["https://openalex.org/I201537933"]},{"id":"https://openalex.org/I4210136366","display_name":"Tohoku Medical Megabank Organization","ror":"https://ror.org/03zzyap02","country_code":"JP","type":"healthcare","lineage":["https://openalex.org/I4210136366"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Masao Nagasaki","raw_affiliation_strings":["1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Japan, 2Department of Computer Science, Institute of Mathematics and Statistics, University of S\u00e3o Paulo, Brazil and 3Human Genome Center, Institute of Medical Science, University of Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Japan, 2Department of Computer Science, Institute of Mathematics and Statistics, University of S\u00e3o Paulo, Brazil and 3Human Genome Center, Institute of Medical Science, University of Tokyo, Japan","institution_ids":["https://openalex.org/I201537933","https://openalex.org/I4210136366","https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067767544","display_name":"Andr\u00e9 Fujita","orcid":"https://orcid.org/0000-0002-7756-7051"},"institutions":[{"id":"https://openalex.org/I201537933","display_name":"Tohoku University","ror":"https://ror.org/01dq60k83","country_code":"JP","type":"education","lineage":["https://openalex.org/I201537933"]},{"id":"https://openalex.org/I4210136366","display_name":"Tohoku Medical Megabank Organization","ror":"https://ror.org/03zzyap02","country_code":"JP","type":"healthcare","lineage":["https://openalex.org/I4210136366"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Andr\u00e9 Fujita","raw_affiliation_strings":["1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Japan, 2Department of Computer Science, Institute of Mathematics and Statistics, University of S\u00e3o Paulo, Brazil and 3Human Genome Center, Institute of Medical Science, University of Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Japan, 2Department of Computer Science, Institute of Mathematics and Statistics, University of S\u00e3o Paulo, Brazil and 3Human Genome Center, Institute of Medical Science, University of Tokyo, Japan","institution_ids":["https://openalex.org/I201537933","https://openalex.org/I4210136366","https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049465469","display_name":"Yayoi Sekiya","orcid":null},"institutions":[{"id":"https://openalex.org/I201537933","display_name":"Tohoku University","ror":"https://ror.org/01dq60k83","country_code":"JP","type":"education","lineage":["https://openalex.org/I201537933"]},{"id":"https://openalex.org/I4210136366","display_name":"Tohoku Medical Megabank Organization","ror":"https://ror.org/03zzyap02","country_code":"JP","type":"healthcare","lineage":["https://openalex.org/I4210136366"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yayoi Sekiya","raw_affiliation_strings":["1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Japan, 2Department of Computer Science, Institute of Mathematics and Statistics, University of S\u00e3o Paulo, Brazil and 3Human Genome Center, Institute of Medical Science, University of Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Japan, 2Department of Computer Science, Institute of Mathematics and Statistics, University of S\u00e3o Paulo, Brazil and 3Human Genome Center, Institute of Medical Science, University of Tokyo, Japan","institution_ids":["https://openalex.org/I201537933","https://openalex.org/I4210136366","https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079013346","display_name":"Ayumu Saito","orcid":null},"institutions":[{"id":"https://openalex.org/I201537933","display_name":"Tohoku University","ror":"https://ror.org/01dq60k83","country_code":"JP","type":"education","lineage":["https://openalex.org/I201537933"]},{"id":"https://openalex.org/I4210136366","display_name":"Tohoku Medical Megabank Organization","ror":"https://ror.org/03zzyap02","country_code":"JP","type":"healthcare","lineage":["https://openalex.org/I4210136366"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ayumu Saito","raw_affiliation_strings":["1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Japan, 2Department of Computer Science, Institute of Mathematics and Statistics, University of S\u00e3o Paulo, Brazil and 3Human Genome Center, Institute of Medical Science, University of Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Japan, 2Department of Computer Science, Institute of Mathematics and Statistics, University of S\u00e3o Paulo, Brazil and 3Human Genome Center, Institute of Medical Science, University of Tokyo, Japan","institution_ids":["https://openalex.org/I201537933","https://openalex.org/I4210136366","https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028000595","display_name":"Emi Ikeda","orcid":null},"institutions":[{"id":"https://openalex.org/I201537933","display_name":"Tohoku University","ror":"https://ror.org/01dq60k83","country_code":"JP","type":"education","lineage":["https://openalex.org/I201537933"]},{"id":"https://openalex.org/I4210136366","display_name":"Tohoku Medical Megabank Organization","ror":"https://ror.org/03zzyap02","country_code":"JP","type":"healthcare","lineage":["https://openalex.org/I4210136366"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Emi Ikeda","raw_affiliation_strings":["1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Japan, 2Department of Computer Science, Institute of Mathematics and Statistics, University of S\u00e3o Paulo, Brazil and 3Human Genome Center, Institute of Medical Science, University of Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Japan, 2Department of Computer Science, Institute of Mathematics and Statistics, University of S\u00e3o Paulo, Brazil and 3Human Genome Center, Institute of Medical Science, University of Tokyo, Japan","institution_ids":["https://openalex.org/I201537933","https://openalex.org/I4210136366","https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100369876","display_name":"Chen Li","orcid":"https://orcid.org/0000-0002-8014-6848"},"institutions":[{"id":"https://openalex.org/I201537933","display_name":"Tohoku University","ror":"https://ror.org/01dq60k83","country_code":"JP","type":"education","lineage":["https://openalex.org/I201537933"]},{"id":"https://openalex.org/I4210136366","display_name":"Tohoku Medical Megabank Organization","ror":"https://ror.org/03zzyap02","country_code":"JP","type":"healthcare","lineage":["https://openalex.org/I4210136366"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Chen Li","raw_affiliation_strings":["1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Japan, 2Department of Computer Science, Institute of Mathematics and Statistics, University of S\u00e3o Paulo, Brazil and 3Human Genome Center, Institute of Medical Science, University of Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Japan, 2Department of Computer Science, Institute of Mathematics and Statistics, University of S\u00e3o Paulo, Brazil and 3Human Genome Center, Institute of Medical Science, University of Tokyo, Japan","institution_ids":["https://openalex.org/I201537933","https://openalex.org/I4210136366","https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088167618","display_name":"Satoru Miyano","orcid":"https://orcid.org/0000-0002-1753-6616"},"institutions":[{"id":"https://openalex.org/I201537933","display_name":"Tohoku University","ror":"https://ror.org/01dq60k83","country_code":"JP","type":"education","lineage":["https://openalex.org/I201537933"]},{"id":"https://openalex.org/I4210136366","display_name":"Tohoku Medical Megabank Organization","ror":"https://ror.org/03zzyap02","country_code":"JP","type":"healthcare","lineage":["https://openalex.org/I4210136366"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Satoru Miyano","raw_affiliation_strings":["1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Japan, 2Department of Computer Science, Institute of Mathematics and Statistics, University of S\u00e3o Paulo, Brazil and 3Human Genome Center, Institute of Medical Science, University of Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Japan, 2Department of Computer Science, Institute of Mathematics and Statistics, University of S\u00e3o Paulo, Brazil and 3Human Genome Center, Institute of Medical Science, University of Tokyo, Japan","institution_ids":["https://openalex.org/I201537933","https://openalex.org/I4210136366","https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5025220924"],"corresponding_institution_ids":["https://openalex.org/I201537933","https://openalex.org/I4210136366","https://openalex.org/I74801974"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":1.4409,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.89050252,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"29","issue":"1","first_page":"137","last_page":"139"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.4325999915599823,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.4325999915599823,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.21960000693798065,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.10409999638795853,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7524615526199341},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7471151947975159},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.6623578667640686},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.641247034072876},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.602938175201416},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.5978245735168457},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.5587215423583984},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.5262545347213745},{"id":"https://openalex.org/keywords/grid","display_name":"Grid","score":0.5106080174446106},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.5060378909111023},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.49536383152008057},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4563617408275604},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.4499536156654358},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.4376451075077057},{"id":"https://openalex.org/keywords/application-programming-interface","display_name":"Application programming interface","score":0.4353472590446472},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.432010293006897},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.28309494256973267}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7524615526199341},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7471151947975159},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.6623578667640686},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.641247034072876},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.602938175201416},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.5978245735168457},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.5587215423583984},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.5262545347213745},{"id":"https://openalex.org/C187691185","wikidata":"https://www.wikidata.org/wiki/Q2020720","display_name":"Grid","level":2,"score":0.5106080174446106},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.5060378909111023},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.49536383152008057},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4563617408275604},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.4499536156654358},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.4376451075077057},{"id":"https://openalex.org/C99613125","wikidata":"https://www.wikidata.org/wiki/Q165194","display_name":"Application programming interface","level":2,"score":0.4353472590446472},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.432010293006897},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.28309494256973267},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bts630","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts630","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/1/137/49060286/bioinformatics_29_1_137.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23104885","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23104885","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:2527664","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3530915","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.903.7989","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.903.7989","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2012/10/25/bioinformatics.bts630.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts630","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts630","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/1/137/49060286/bioinformatics_29_1_137.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5066906062","display_name":"RNA-Seq data analysis for ncRNA function prediction to thousands public RNA-Seq data on super computer","funder_award_id":"23650150","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G6384727432","display_name":"Drug-response pathway analysis methods based on network analysis","funder_award_id":"22300099","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"},{"id":"https://openalex.org/F4320320997","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","ror":"https://ror.org/02ddkpn78"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320336716","display_name":"Institute of Medical Science, University of Tokyo","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2159938295.pdf","grobid_xml":"https://content.openalex.org/works/W2159938295.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W188614979","https://openalex.org/W1621944069","https://openalex.org/W1976746127","https://openalex.org/W2100827887","https://openalex.org/W2103953991","https://openalex.org/W2123663722","https://openalex.org/W2128374023","https://openalex.org/W2136482257","https://openalex.org/W2147546613","https://openalex.org/W2148523353","https://openalex.org/W2155570949","https://openalex.org/W2171594815","https://openalex.org/W2582743722","https://openalex.org/W2972770296","https://openalex.org/W6636766374","https://openalex.org/W6678222360"],"related_works":["https://openalex.org/W2046765700","https://openalex.org/W4384345686","https://openalex.org/W1981780420","https://openalex.org/W2182707996","https://openalex.org/W2357937784","https://openalex.org/W45233828","https://openalex.org/W2964988449","https://openalex.org/W2547618384","https://openalex.org/W4394391052","https://openalex.org/W2390396596"],"abstract_inverted_index":{"UNLABELLED:":[0],"XiP":[1,30,70,91],"(eXtensible":[2],"integrative":[3],"Pipeline)":[4],"is":[5,92],"a":[6,13,66],"flexible,":[7],"editable":[8],"and":[9,27,43,54,68,83,86,104],"modular":[10],"environment":[11],"with":[12,73],"user-friendly":[14],"interface":[15],"that":[16,61],"does":[17],"not":[18],"require":[19],"previous":[20],"advanced":[21],"programming":[22],"skills":[23],"to":[24],"run,":[25],"construct":[26],"edit":[28],"workflows.":[29],"allows":[31],"the":[32,45,56,79,98],"construction":[33],"of":[34,47,58],"workflows":[35],"by":[36],"linking":[37],"components":[38],"written":[39],"in":[40,50,65],"both":[41],"R":[42],"Java,":[44],"analysis":[46,85],"high-throughput":[48],"data":[49],"grid":[51],"engine":[52],"systems":[53],"also":[55],"development":[57],"customized":[59],"pipelines":[60],"can":[62,105],"be":[63,106],"encapsulated":[64],"package":[67],"distributed.":[69],"already":[71],"comes":[72],"several":[74],"ready-to-use":[75],"pipeline":[76],"flows":[77],"for":[78],"most":[80],"common":[81],"genomic":[82],"transcriptomic":[84],"\u223c300":[87],"computational":[88],"components.":[89],"AVAILABILITY:":[90],"open":[93],"source,":[94],"freely":[95],"available":[96],"under":[97],"Lesser":[99],"General":[100],"Public":[101],"License":[102],"(LGPL)":[103],"downloaded":[107],"from":[108],"http://xip.hgc.jp.":[109]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-08-27T14:10:00.468798","created_date":"2025-10-10T00:00:00"}
