{"id":"https://openalex.org/W2119178570","doi":"https://doi.org/10.1142/s0219720015500213","title":"Knowledge-based reasoning to annotate noncoding RNA using multi-agent system","display_name":"Knowledge-based reasoning to annotate noncoding RNA using multi-agent system","publication_year":2015,"publication_date":"2015-06-25","ids":{"openalex":"https://openalex.org/W2119178570","doi":"https://doi.org/10.1142/s0219720015500213","mag":"2119178570","pmid":"https://pubmed.ncbi.nlm.nih.gov/26223200"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720015500213","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720015500213","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110216791","display_name":"Wosley C. Arruda","orcid":null},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Wosley C. Arruda","raw_affiliation_strings":["Department of Computer Science, University of Bras\u00edlia, Campus Universit\u00e1rio Darcy Ribeiro Pr\u00e9dio CIC/EST, ASA Norte, Bras\u00edlia-DF,CEP: 70910\u2013900, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Bras\u00edlia, Campus Universit\u00e1rio Darcy Ribeiro Pr\u00e9dio CIC/EST, ASA Norte, Bras\u00edlia-DF,CEP: 70910\u2013900, Brazil","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029596374","display_name":"Daniel da Silva Souza","orcid":"https://orcid.org/0000-0003-3157-013X"},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Daniel S. Souza","raw_affiliation_strings":["Department of Computer Science, University of Bras\u00edlia, Campus Universit\u00e1rio Darcy Ribeiro Pr\u00e9dio CIC/EST, ASA Norte, Bras\u00edlia-DF,CEP: 70910\u2013900, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Bras\u00edlia, Campus Universit\u00e1rio Darcy Ribeiro Pr\u00e9dio CIC/EST, ASA Norte, Bras\u00edlia-DF,CEP: 70910\u2013900, Brazil","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087625675","display_name":"C\u00e9lia Ghedini Ralha","orcid":"https://orcid.org/0000-0002-2983-2180"},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"C\u00e9lia G. Ralha","raw_affiliation_strings":["Department of Computer Science, University of Bras\u00edlia, Campus Universit\u00e1rio Darcy Ribeiro Pr\u00e9dio CIC/EST, ASA Norte, Bras\u00edlia-DF,CEP: 70910\u2013900, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Bras\u00edlia, Campus Universit\u00e1rio Darcy Ribeiro Pr\u00e9dio CIC/EST, ASA Norte, Bras\u00edlia-DF,CEP: 70910\u2013900, Brazil","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071276748","display_name":"Maria Em\u00edlia M. T. Walter","orcid":"https://orcid.org/0000-0001-6822-931X"},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Maria Emilia M. T. Walter","raw_affiliation_strings":["Department of Computer Science, University of Bras\u00edlia, Campus Universit\u00e1rio Darcy Ribeiro Pr\u00e9dio CIC/EST, ASA Norte, Bras\u00edlia-DF,CEP: 70910\u2013900, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Bras\u00edlia, Campus Universit\u00e1rio Darcy Ribeiro Pr\u00e9dio CIC/EST, ASA Norte, Bras\u00edlia-DF,CEP: 70910\u2013900, Brazil","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072259448","display_name":"Tain\u00e1 Raiol","orcid":"https://orcid.org/0000-0001-9948-5164"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tain\u00e1 Raiol","raw_affiliation_strings":["Le\u00f4nidas and Maria Deane Research Center (Fiocruz Amaz\u00f4nia), Rua Teresina, 476 Adrian\u00f3polis, Manaus-AM, CEP: 69027-070, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Le\u00f4nidas and Maria Deane Research Center (Fiocruz Amaz\u00f4nia), Rua Teresina, 476 Adrian\u00f3polis, Manaus-AM, CEP: 69027-070, Brazil","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004764405","display_name":"Marcelo M. Br\u00edgido","orcid":"https://orcid.org/0000-0002-7136-7059"},"institutions":[{"id":"https://openalex.org/I150729083","display_name":"Universidade de Bras\u00edlia","ror":"https://ror.org/02xfp8v59","country_code":"BR","type":"education","lineage":["https://openalex.org/I150729083"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Marcelo M. Brigido","raw_affiliation_strings":["Department of Cellular Biology, Institute of Biology, University of Bras\u00edlia, Campus Universit\u00e1rio Darcy Ribeiro, Pr\u00e9dio do Institute de Biologia, ASA Norte, Bras\u00edlia-DF,CEP: 70910-900, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cellular Biology, Institute of Biology, University of Bras\u00edlia, Campus Universit\u00e1rio Darcy Ribeiro, Pr\u00e9dio do Institute de Biologia, ASA Norte, Bras\u00edlia-DF,CEP: 70910-900, Brazil","institution_ids":["https://openalex.org/I150729083"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016104736","display_name":"Peter F. Stadler","orcid":"https://orcid.org/0000-0002-5016-5191"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Peter F. Stadler","raw_affiliation_strings":["Department of Computer Science and the Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107, Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and the Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstrasse 16-18, D-04107, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.05441515,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"13","issue":"06","first_page":"1550021","last_page":"1550021"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9991999864578247,"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"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9991999864578247,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9797000288963318,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9786999821662903,"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/computer-science","display_name":"Computer science","score":0.5804135799407959},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5056240558624268},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44160833954811096},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.425674706697464},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.362085223197937},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3005636930465698},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2050321400165558},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15081149339675903}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5804135799407959},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5056240558624268},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44160833954811096},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.425674706697464},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.362085223197937},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3005636930465698},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2050321400165558},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15081149339675903}],"mesh":[{"descriptor_ui":"D010228","descriptor_name":"Paracoccidioides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010228","descriptor_name":"Paracoccidioides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010228","descriptor_name":"Paracoccidioides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012568","descriptor_name":"Schizosaccharomyces","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012568","descriptor_name":"Schizosaccharomyces","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012568","descriptor_name":"Schizosaccharomyces","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"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":"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":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720015500213","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720015500213","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:26223200","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26223200","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W143799877","https://openalex.org/W1542426682","https://openalex.org/W1543796220","https://openalex.org/W1903683453","https://openalex.org/W1904065432","https://openalex.org/W1983583458","https://openalex.org/W1984675364","https://openalex.org/W1990937720","https://openalex.org/W2002532798","https://openalex.org/W2009736453","https://openalex.org/W2011368877","https://openalex.org/W2025763720","https://openalex.org/W2043831708","https://openalex.org/W2055043387","https://openalex.org/W2086255487","https://openalex.org/W2096913845","https://openalex.org/W2097862215","https://openalex.org/W2102749300","https://openalex.org/W2105292164","https://openalex.org/W2112192177","https://openalex.org/W2116502002","https://openalex.org/W2122410182","https://openalex.org/W2127861583","https://openalex.org/W2145628933","https://openalex.org/W2149429041","https://openalex.org/W2151804955","https://openalex.org/W2158381555","https://openalex.org/W2159006685","https://openalex.org/W2169271641","https://openalex.org/W4250052351"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W1971568933","https://openalex.org/W3204019825"],"abstract_inverted_index":{"Noncoding":[0],"RNAs":[1],"(ncRNAs)":[2],"have":[3],"been":[4],"focus":[5],"of":[6,18,55,78,96,112],"intense":[7],"research":[8],"over":[9],"the":[10,53,69,76,97,110],"last":[11],"few":[12],"years.":[13],"Since":[14],"characteristics":[15],"and":[16,100],"signals":[17],"ncRNAs":[19,50],"are":[20],"not":[21],"entirely":[22],"known,":[23],"researchers":[24],"use":[25],"different":[26,56],"computational":[27],"tools":[28],"together":[29],"with":[30,66,80],"their":[31],"biological":[32],"knowledge":[33],"to":[34,48,61,74,85],"predict":[35],"putative":[36,106],"ncRNAs.":[37],"In":[38],"this":[39,41],"context,":[40],"work":[42],"presents":[43],"ncRNA-Agents,":[44,79],"a":[45,87],"multi-agent":[46],"system":[47],"annotate":[49],"based":[51],"on":[52],"output":[54],"tools,":[57],"using":[58],"inference":[59],"rules":[60],"simulate":[62],"biologists'":[63],"reasoning.":[64],"Experiments":[65],"data":[67,95],"from":[68],"fungus":[70],"Saccharomyces":[71],"cerevisiae":[72],"allowed":[73],"measure":[75],"performance":[77],"better":[81],"sensibility,":[82],"when":[83],"compared":[84],"Infernal,":[86],"widely":[88],"used":[89],"tool":[90],"for":[91],"annotating":[92],"ncRNA.":[93],"Besides,":[94],"Schizosaccharomyces":[98],"pombe":[99],"Paracoccidioides":[101],"brasiliensis":[102],"fungi":[103],"identified":[104],"novel":[105],"ncRNAs,":[107],"which":[108],"demonstrated":[109],"usefulness":[111],"our":[113],"approach.":[114],"NcRNA-Agents":[115],"can":[116],"be":[117,118],"found":[119],"at:":[120],"http://www.biomol.unb.br/ncrna-agents.":[121]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
