{"id":"https://openalex.org/W2946409717","doi":"https://doi.org/10.1186/s12859-019-2805-6","title":"Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration","display_name":"Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration","publication_year":2019,"publication_date":"2019-05-17","ids":{"openalex":"https://openalex.org/W2946409717","doi":"https://doi.org/10.1186/s12859-019-2805-6","mag":"2946409717","pmid":"https://pubmed.ncbi.nlm.nih.gov/31101000"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2805-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2805-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2805-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2805-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102838242","display_name":"Joseph Brown","orcid":"https://orcid.org/0000-0002-7678-6105"},"institutions":[{"id":"https://openalex.org/I142606810","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307","country_code":"US","type":"facility","lineage":["https://openalex.org/I1325736334","https://openalex.org/I1330989302","https://openalex.org/I142606810","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Joseph Brown","raw_affiliation_strings":["Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA","Present address: Department of Human Genetics, University of Utah, Salt Lake City, UT, 84105, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA","institution_ids":["https://openalex.org/I142606810"]},{"raw_affiliation_string":"Present address: Department of Human Genetics, University of Utah, Salt Lake City, UT, 84105, USA","institution_ids":["https://openalex.org/I223532165"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Aaron R. Phillips","orcid":null},"institutions":[{"id":"https://openalex.org/I142606810","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307","country_code":"US","type":"facility","lineage":["https://openalex.org/I1325736334","https://openalex.org/I1330989302","https://openalex.org/I142606810","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aaron R. Phillips","raw_affiliation_strings":["Computing & Analytics Division, Pacific Northwest National Laboratory, Richland, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computing & Analytics Division, Pacific Northwest National Laboratory, Richland, WA, USA","institution_ids":["https://openalex.org/I142606810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084351153","display_name":"David A. Lewis","orcid":"https://orcid.org/0000-0002-3225-6778"},"institutions":[{"id":"https://openalex.org/I142606810","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307","country_code":"US","type":"facility","lineage":["https://openalex.org/I1325736334","https://openalex.org/I1330989302","https://openalex.org/I142606810","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David A. Lewis","raw_affiliation_strings":["Computing & Analytics Division, Pacific Northwest National Laboratory, Richland, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computing & Analytics Division, Pacific Northwest National Laboratory, Richland, WA, USA","institution_ids":["https://openalex.org/I142606810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072221598","display_name":"Michael-Andres Mans","orcid":null},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael-Andres Mans","raw_affiliation_strings":["Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, USA","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075469209","display_name":"Yvonne Chang","orcid":"https://orcid.org/0000-0001-5967-3099"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yvonne Chang","raw_affiliation_strings":["Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, USA","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010885167","display_name":"Robert L. Tanguay","orcid":"https://orcid.org/0000-0001-6190-3682"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert L. Tanguay","raw_affiliation_strings":["Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, USA","Superfund Research Center, Oregon State University, Corvallis, OR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, USA","institution_ids":["https://openalex.org/I131249849"]},{"raw_affiliation_string":"Superfund Research Center, Oregon State University, Corvallis, OR, USA","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040788704","display_name":"Elena Peterson","orcid":null},"institutions":[{"id":"https://openalex.org/I142606810","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307","country_code":"US","type":"facility","lineage":["https://openalex.org/I1325736334","https://openalex.org/I1330989302","https://openalex.org/I142606810","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elena S. Peterson","raw_affiliation_strings":["Computing & Analytics Division, Pacific Northwest National Laboratory, Richland, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computing & Analytics Division, Pacific Northwest National Laboratory, Richland, WA, USA","institution_ids":["https://openalex.org/I142606810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053476989","display_name":"Katrina M. Waters","orcid":"https://orcid.org/0000-0003-4696-5396"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]},{"id":"https://openalex.org/I142606810","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307","country_code":"US","type":"facility","lineage":["https://openalex.org/I1325736334","https://openalex.org/I1330989302","https://openalex.org/I142606810","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Katrina M. Waters","raw_affiliation_strings":["Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. katrina.waters@pnnl.gov","Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, USA. katrina.waters@pnnl.gov","Superfund Research Center, Oregon State University, Corvallis, OR, USA. katrina.waters@pnnl.gov","Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. katrina.waters@pnnl.gov","institution_ids":["https://openalex.org/I142606810"]},{"raw_affiliation_string":"Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, USA. katrina.waters@pnnl.gov","institution_ids":["https://openalex.org/I131249849"]},{"raw_affiliation_string":"Superfund Research Center, Oregon State University, Corvallis, OR, USA. katrina.waters@pnnl.gov","institution_ids":["https://openalex.org/I131249849"]},{"raw_affiliation_string":"Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, USA","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077210745","display_name":"Susan C. Tilton","orcid":"https://orcid.org/0000-0002-5427-6462"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Susan C. Tilton","raw_affiliation_strings":["Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, USA. susan.tilton@oregonstate.edu","Superfund Research Center, Oregon State University, Corvallis, OR, USA. susan.tilton@oregonstate.edu","Superfund Research Center, Oregon State University, Corvallis, OR, USA"],"raw_orcid":"https://orcid.org/0000-0002-5427-6462","affiliations":[{"raw_affiliation_string":"Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, USA. susan.tilton@oregonstate.edu","institution_ids":["https://openalex.org/I131249849"]},{"raw_affiliation_string":"Superfund Research Center, Oregon State University, Corvallis, OR, USA. susan.tilton@oregonstate.edu","institution_ids":["https://openalex.org/I131249849"]},{"raw_affiliation_string":"Superfund Research Center, Oregon State University, Corvallis, OR, USA","institution_ids":["https://openalex.org/I131249849"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5102838242"],"corresponding_institution_ids":["https://openalex.org/I142606810","https://openalex.org/I223532165"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.4637,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.57352509,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"20","issue":"1","first_page":"255","last_page":"255"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.3052000105381012,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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"}},"topics":[{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.3052000105381012,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.25920000672340393,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.030899999663233757,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6521425247192383},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.6306107044219971},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5755987167358398},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5651252865791321},{"id":"https://openalex.org/keywords/microrna","display_name":"microRNA","score":0.5452171564102173},{"id":"https://openalex.org/keywords/zebrafish","display_name":"Zebrafish","score":0.525901734828949},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.4108968675136566},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.35638105869293213},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3237295150756836},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2588319182395935},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2286035418510437},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13773566484451294}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6521425247192383},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.6306107044219971},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5755987167358398},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5651252865791321},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.5452171564102173},{"id":"https://openalex.org/C2776878037","wikidata":"https://www.wikidata.org/wiki/Q169444","display_name":"Zebrafish","level":3,"score":0.525901734828949},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.4108968675136566},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.35638105869293213},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3237295150756836},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2588319182395935},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2286035418510437},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13773566484451294},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008253","descriptor_name":"Macaca mulatta","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008253","descriptor_name":"Macaca mulatta","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008253","descriptor_name":"Macaca mulatta","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","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":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-019-2805-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2805-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2805-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31101000","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31101000","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:44adda79a1c342609972a611f806d27f","is_oa":true,"landing_page_url":"https://doaj.org/article/44adda79a1c342609972a611f806d27f","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss 1, Pp 1-8 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5503576","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6525352","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"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-2805-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2805-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2805-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1899721271","display_name":null,"funder_award_id":"AC05-76RL01830","funder_id":"https://openalex.org/F4320306250","funder_display_name":"Battelle"},{"id":"https://openalex.org/G1967746503","display_name":null,"funder_award_id":"DE-AC05-76RL01830","funder_id":"https://openalex.org/F4320338354","funder_display_name":"Pacific Northwest National Laboratory"},{"id":"https://openalex.org/G2506945562","display_name":null,"funder_award_id":"76RL01830","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G2510423872","display_name":null,"funder_award_id":"AC05-76RL01830","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G3448260292","display_name":null,"funder_award_id":"Contract DE-AC05-76RL01830","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G4702076777","display_name":null,"funder_award_id":"P42 ES016465","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"},{"id":"https://openalex.org/G5090555917","display_name":null,"funder_award_id":"ES016465","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"},{"id":"https://openalex.org/G5200347334","display_name":null,"funder_award_id":"DE-AC05-76RL01830","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G5321382714","display_name":null,"funder_award_id":"76RL01830","funder_id":"https://openalex.org/F4320338354","funder_display_name":"Pacific Northwest National Laboratory"},{"id":"https://openalex.org/G5726405315","display_name":null,"funder_award_id":"DE-AC05","funder_id":"https://openalex.org/F4320306250","funder_display_name":"Battelle"},{"id":"https://openalex.org/G6631213390","display_name":null,"funder_award_id":"P42 ES016465","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6664334341","display_name":null,"funder_award_id":"DE-AC05-76RL01830","funder_id":"https://openalex.org/F4320306250","funder_display_name":"Battelle"},{"id":"https://openalex.org/G7820375068","display_name":null,"funder_award_id":"DE-AC05-76RL01830","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"},{"id":"https://openalex.org/G7995982022","display_name":null,"funder_award_id":"DE-AC05","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G8101016290","display_name":null,"funder_award_id":"T32ES07060","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320306250","display_name":"Battelle","ror":"https://ror.org/01h5tnr73"},{"id":"https://openalex.org/F4320337361","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63"},{"id":"https://openalex.org/F4320338354","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2946409717.pdf","grobid_xml":"https://content.openalex.org/works/W2946409717.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1971204432","https://openalex.org/W1976942746","https://openalex.org/W2012555772","https://openalex.org/W2042203018","https://openalex.org/W2044832480","https://openalex.org/W2070571588","https://openalex.org/W2077327925","https://openalex.org/W2083396498","https://openalex.org/W2096525273","https://openalex.org/W2109488005","https://openalex.org/W2134629862","https://openalex.org/W2151163584","https://openalex.org/W2158217645","https://openalex.org/W2159675211","https://openalex.org/W2176909577","https://openalex.org/W2335866275","https://openalex.org/W2347037915","https://openalex.org/W2541513861","https://openalex.org/W2604652930","https://openalex.org/W2726115670","https://openalex.org/W2766195206","https://openalex.org/W2767546566","https://openalex.org/W2768781242","https://openalex.org/W2917207851","https://openalex.org/W2953282253","https://openalex.org/W4233120011","https://openalex.org/W4243601081","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W3129642199","https://openalex.org/W4256528904","https://openalex.org/W1597543017","https://openalex.org/W4293058866","https://openalex.org/W4245153001","https://openalex.org/W3147492987","https://openalex.org/W4243165149","https://openalex.org/W4237600267","https://openalex.org/W4283069614","https://openalex.org/W2003750019"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,187],"Bioinformatics":[2],"Resource":[3],"Manager":[4],"(BRM)":[5],"is":[6],"a":[7,49,58],"web-based":[8],"tool":[9],"developed":[10,273],"to":[11,47,66,71,84,132,139,153,163,197,211,249],"facilitate":[12],"identifier":[13,53,87,91,102],"conversion":[14],"and":[15,31,107,115,151,175,193,238,258,267,276,280],"data":[16,136,263],"integration":[17,259],"for":[18,202,216],"Homo":[19],"sapiens":[20],"(human),":[21],"Mus":[22],"musculus":[23],"(mouse),":[24],"Rattus":[25],"norvegicus":[26],"(rat),":[27],"Danio":[28],"rerio":[29],"(zebrafish),":[30],"Macaca":[32],"mulatta":[33],"(macaque),":[34],"as":[35,37,170,219],"well":[36],"perform":[38,72,85],"orthologous":[39],"conversions":[40],"among":[41],"the":[42,82,105,117,159,166,177],"supported":[43],"species.":[44],"In":[45],"addition":[46],"providing":[48],"robust":[50],"means":[51],"of":[52,60,143,147,168,172,181,222,240,260],"conversion,":[54],"BRM":[55,80,131,190,245,270],"also":[56],"incorporates":[57],"suite":[59],"microRNA":[61],"(miRNA)-target":[62],"databases":[63,113],"upon":[64],"which":[65],"query":[67],"target":[68,74],"genes":[69],"or":[70,98],"reverse":[73],"lookups":[75,88],"using":[76,284],"gene":[77,119],"identifiers.":[78],"RESULTS:":[79],"has":[81],"capability":[83],"cross-species":[86],"across":[89,96,137],"common":[90,141],"types,":[92],"directly":[93,194],"integrate":[94,116,133],"datasets":[95],"platform":[97],"species":[99,138],"by":[100],"performing":[101],"retrievals":[103],"in":[104,130,184,225,274],"background,":[106],"retrieve":[108],"miRNA":[109,160],"targets":[110,120],"from":[111,189,264],"multiple":[112],"simultaneously":[114],"resulting":[118],"with":[121,230,256],"experimental":[122],"mRNA":[123],"data.":[124],"Here":[125],"we":[126,208],"use":[127,158],"workflows":[128,271],"provided":[129],"RNA":[134],"sequencing":[135],"identify":[140,176,212],"biomarkers":[142],"exposure":[144],"after":[145],"treatment":[146],"human":[148,226],"lung":[149,227],"cells":[150,228],"zebrafish":[152],"benzo[a]pyrene":[154],"(BAP).":[155],"We":[156],"further":[157,203],"Target":[161],"workflow":[162],"experimentally":[164],"determine":[165],"role":[167,215],"miRNAs":[169,218],"regulators":[171,221],"BAP":[173,223],"toxicity":[174,224],"predicted":[178],"functional":[179],"consequences":[180],"miRNA-target":[182],"regulation":[183,239],"our":[185],"system.":[186],"output":[188],"can":[191],"easily":[192],"be":[195],"uploaded":[196],"freely":[198],"available":[199],"visualization":[200],"tools":[201,248],"analysis.":[204],"From":[205],"these":[206],"examples,":[207],"were":[209,272],"able":[210],"an":[213],"important":[214],"several":[217],"potential":[220],"associated":[229],"cell":[231,233,235,241],"migration,":[232],"communication,":[234],"junction":[236],"assembly":[237],"death.":[242],"CONCLUSIONS:":[243],"Overall,":[244],"provides":[246],"bioinformatics":[247],"assist":[250],"biologists":[251],"having":[252],"minimal":[253],"programming":[254],"skills":[255],"analysis":[257],"high-content":[261],"omics'":[262],"various":[265],"transcriptomic":[266],"proteomic":[268],"platforms.":[269],"Java":[275],"other":[277],"open-source":[278],"technologies":[279],"are":[281],"served":[282],"publicly":[283],"Apache":[285],"Tomcat":[286],"at":[287],"https://cbb.pnnl.gov/brm/":[288],".":[289]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
