{"id":"https://openalex.org/W2212328387","doi":"https://doi.org/10.1109/bibm.2015.7359907","title":"Reconstructing transcriptional Regulatory Networks using data integration and Text Mining","display_name":"Reconstructing transcriptional Regulatory Networks using data integration and Text Mining","publication_year":2015,"publication_date":"2015-11-01","ids":{"openalex":"https://openalex.org/W2212328387","doi":"https://doi.org/10.1109/bibm.2015.7359907","mag":"2212328387"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2015.7359907","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2015.7359907","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/1822/39418","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103259228","display_name":"Rafael T. Pereira","orcid":"https://orcid.org/0000-0003-4901-1619"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Rafael T. Pereira","raw_affiliation_strings":["Centre of Biological Engineering University of Minho, Braga, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre of Biological Engineering University of Minho, Braga, Portugal","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090172347","display_name":"Hugo Costa","orcid":"https://orcid.org/0000-0002-3155-2110"},"institutions":[{"id":"https://openalex.org/I4210114428","display_name":"SilicoLife (Portugal)","ror":"https://ror.org/029gksr15","country_code":"PT","type":"company","lineage":["https://openalex.org/I4210114428"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Hugo Costa","raw_affiliation_strings":["SilicoLife, Braga, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"SilicoLife, Braga, Portugal","institution_ids":["https://openalex.org/I4210114428"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054642116","display_name":"S\u00f3nia Carneiro","orcid":"https://orcid.org/0000-0001-8037-937X"},"institutions":[{"id":"https://openalex.org/I4210114428","display_name":"SilicoLife (Portugal)","ror":"https://ror.org/029gksr15","country_code":"PT","type":"company","lineage":["https://openalex.org/I4210114428"]},{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Sonia Carneiro","raw_affiliation_strings":["Centre of Biological Engineering University of Minho, Braga, Portugal","SilicoLife, Braga, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre of Biological Engineering University of Minho, Braga, Portugal","institution_ids":["https://openalex.org/I99682543"]},{"raw_affiliation_string":"SilicoLife, Braga, Portugal","institution_ids":["https://openalex.org/I4210114428"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040524717","display_name":"Miguel Rocha","orcid":"https://orcid.org/0000-0001-8439-8172"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Miguel Rocha","raw_affiliation_strings":["Centre of Biological Engineering University of Minho, Braga, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre of Biological Engineering University of Minho, Braga, Portugal","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081140606","display_name":"Rui Mendes","orcid":"https://orcid.org/0000-0002-5321-6863"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Rui Mendes","raw_affiliation_strings":["Centre of Biological Engineering University of Minho, Braga, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre of Biological Engineering University of Minho, Braga, Portugal","institution_ids":["https://openalex.org/I99682543"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.1506,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.57675852,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"1552","last_page":"1558"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9983999729156494,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9907000064849854,"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/identifier","display_name":"Identifier","score":0.7708678245544434},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7265737652778625},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.6885223984718323},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5532061457633972},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.5392943620681763},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5099507570266724},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.5058903098106384},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.49427008628845215},{"id":"https://openalex.org/keywords/biological-database","display_name":"Biological database","score":0.4348650872707367},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4345018267631531},{"id":"https://openalex.org/keywords/unique-identifier","display_name":"Unique identifier","score":0.4332495629787445},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4274940490722656},{"id":"https://openalex.org/keywords/subject","display_name":"Subject (documents)","score":0.4250257611274719},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.42152950167655945},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.3880952000617981},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3605653643608093},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3098618984222412},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2700844705104828},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11845916509628296},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08990588784217834}],"concepts":[{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.7708678245544434},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7265737652778625},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.6885223984718323},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5532061457633972},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.5392943620681763},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5099507570266724},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.5058903098106384},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.49427008628845215},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.4348650872707367},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4345018267631531},{"id":"https://openalex.org/C119839945","wikidata":"https://www.wikidata.org/wiki/Q6545185","display_name":"Unique identifier","level":3,"score":0.4332495629787445},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4274940490722656},{"id":"https://openalex.org/C2777855551","wikidata":"https://www.wikidata.org/wiki/Q12310021","display_name":"Subject (documents)","level":2,"score":0.4250257611274719},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.42152950167655945},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.3880952000617981},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3605653643608093},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3098618984222412},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2700844705104828},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11845916509628296},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08990588784217834},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/bibm.2015.7359907","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2015.7359907","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmh:oai:repositorium.sdum.uminho.pt:1822/39418","is_oa":true,"landing_page_url":"http://hdl.handle.net/1822/39418","pdf_url":null,"source":{"id":"https://openalex.org/S4306400354","display_name":"Reposit\u00f3riUM (Universidade do Minho)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99682543","host_organization_name":"University of Minho","host_organization_lineage":["https://openalex.org/I99682543"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"conference paper"},{"id":"pmh:oai:repositorium.uminho.pt:1822/39418","is_oa":true,"landing_page_url":"https://hdl.handle.net/1822/39418","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"conference paper"}],"best_oa_location":{"id":"pmh:oai:repositorium.sdum.uminho.pt:1822/39418","is_oa":true,"landing_page_url":"http://hdl.handle.net/1822/39418","pdf_url":null,"source":{"id":"https://openalex.org/S4306400354","display_name":"Reposit\u00f3riUM (Universidade do Minho)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99682543","host_organization_name":"University of Minho","host_organization_lineage":["https://openalex.org/I99682543"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"conference paper"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1923384484","https://openalex.org/W1982309495","https://openalex.org/W2023716649","https://openalex.org/W2043748764","https://openalex.org/W2047226970","https://openalex.org/W2100627415","https://openalex.org/W2105440823","https://openalex.org/W2108078368","https://openalex.org/W2108918329","https://openalex.org/W2110699703","https://openalex.org/W2113002560","https://openalex.org/W2120433106","https://openalex.org/W2123179625","https://openalex.org/W2131706188","https://openalex.org/W2146856779","https://openalex.org/W2156206665","https://openalex.org/W2157253968","https://openalex.org/W2157641143","https://openalex.org/W2158505321","https://openalex.org/W2159640576","https://openalex.org/W2168905447","https://openalex.org/W2324870989","https://openalex.org/W2914096745","https://openalex.org/W2993222596","https://openalex.org/W4252024798","https://openalex.org/W4301881503","https://openalex.org/W6676213046","https://openalex.org/W6677096123","https://openalex.org/W6700702580"],"related_works":["https://openalex.org/W3004288456","https://openalex.org/W2017675085","https://openalex.org/W4396918568","https://openalex.org/W2548624545","https://openalex.org/W2987255980","https://openalex.org/W4288094423","https://openalex.org/W2980250610","https://openalex.org/W4378419072","https://openalex.org/W4387606006","https://openalex.org/W2134429551"],"abstract_inverted_index":{"Transcriptional":[0,257],"Regulatory":[1,258],"Networks":[2,259],"(TRNs)":[3],"are":[4,111],"powerful":[5],"tool":[6,252],"for":[7,121,225],"representing":[8],"several":[9,102],"interactions":[10],"that":[11,67,126,177,210],"occur":[12],"within":[13],"a":[14,139,162,194,207],"cell.":[15],"Recent":[16],"studies":[17],"have":[18,68],"provided":[19],"information":[20,39,130],"to":[21,40,48,60,90,154,160,192,212,253],"help":[22],"researchers":[23],"in":[24,85,190],"the":[25,35,49,62,78,91,97,122,128,180,183,217,255],"tasks":[26,202],"of":[27,34,38,53,65,80,93,99,124,164,196,231],"building":[28],"and":[29,106,109,135,166,172,245],"understanding":[30],"these":[31,170,201],"networks.":[32],"One":[33],"major":[36],"sources":[37],"build":[41,155],"TRNs":[42,125],"is":[43,57],"biomedical":[44],"literature.":[45,263],"However,":[46,157],"due":[47],"rapidly":[50],"increasing":[51],"number":[52,98],"scientific":[54,185,262],"papers,":[55],"it":[56,137],"quite":[58],"difficult":[59],"analyse":[61],"large":[63],"amount":[64],"papers":[66,186],"been":[69],"published":[70],"about":[71,198],"this":[72,86,114,151,251],"subject.":[73],"This":[74],"fact":[75],"has":[76],"heightened":[77],"importance":[79],"Biomedical":[81,218],"Text":[82,219],"Mining":[83,220],"approaches":[84],"task.":[87],"Also,":[88,144],"owing":[89],"lack":[92],"adequate":[94],"standards,":[95],"as":[96],"databases":[100,134],"increases,":[101],"inconsistencies":[103],"concerning":[104],"gene":[105],"protein":[107],"names":[108,165],"identifiers":[110],"common.":[112],"In":[113],"work,":[115],"we":[116,145],"developed":[117],"an":[118,175,223],"integrated":[119,152,204],"approach":[120,176],"reconstruction":[123,256],"retrieve":[127],"relevant":[129,233],"from":[131,182,216,235],"important":[132],"biological":[133,241],"insert":[136],"into":[138,205],"unique":[140],"repository,":[141],"named":[142],"KREN.":[143],"applied":[146],"text":[147],"mining":[148],"techniques":[149],"over":[150],"repository":[153],"TRNs.":[156],"was":[158],"necessary":[159],"create":[161,193],"dictionary":[163],"synonyms":[167],"associated":[168],"with":[169],"entities":[171,242],"also":[173],"develop":[174],"retrieves":[178],"all":[179,232],"abstracts":[181],"related":[184],"stored":[187],"on":[188],"PubMed,":[189],"order":[191],"corpora":[195],"data":[197],"genes.":[199],"Furthermore,":[200],"were":[203],"@Note,":[206],"software":[208],"system":[209],"allows":[211],"use":[213],"some":[214],"methods":[215],"field,":[221],"including":[222],"algorithms":[224],"Named":[226],"Entity":[227],"Recognition":[228],"(NER),":[229],"extraction":[230,238],"terms":[234],"publication":[236],"abstracts,":[237],"relationships":[239],"between":[240],"(genes,":[243],"proteins":[244],"transcription":[246],"factors).":[247],"And":[248],"finally,":[249],"extended":[250],"allow":[254],"through":[260],"using":[261]},"counts_by_year":[{"year":2017,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}