{"id":"https://openalex.org/W4396678025","doi":"https://doi.org/10.1007/s13721-024-00458-1","title":"How natural language processing derived techniques are used on biological data: a systematic review","display_name":"How natural language processing derived techniques are used on biological data: a systematic review","publication_year":2024,"publication_date":"2024-05-06","ids":{"openalex":"https://openalex.org/W4396678025","doi":"https://doi.org/10.1007/s13721-024-00458-1"},"language":"en","primary_location":{"id":"doi:10.1007/s13721-024-00458-1","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s13721-024-00458-1","pdf_url":"https://link.springer.com/content/pdf/10.1007/s13721-024-00458-1.pdf","source":{"id":"https://openalex.org/S4210178532","display_name":"Network Modeling Analysis in Health Informatics and Bioinformatics","issn_l":"2192-6662","issn":["2192-6662","2192-6670"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310321666","host_organization_name":"Springer Vienna","host_organization_lineage":["https://openalex.org/P4310321666","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Vienna","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":"Network Modeling Analysis in Health Informatics and Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s13721-024-00458-1.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025599420","display_name":"Emmanouil D. Oikonomou","orcid":"https://orcid.org/0009-0004-9227-1365"},"institutions":[{"id":"https://openalex.org/I194019607","display_name":"University of Ioannina","ror":"https://ror.org/01qg3j183","country_code":"GR","type":"education","lineage":["https://openalex.org/I194019607"]},{"id":"https://openalex.org/I231025917","display_name":"Hellenic Open University","ror":"https://ror.org/02kq26x23","country_code":"GR","type":"education","lineage":["https://openalex.org/I231025917"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Emmanouil D. Oikonomou","raw_affiliation_strings":["Human Computer Interaction Laboratory, Department of Informatics and Telecommunications, University of Ioannina, 47150, Kostakioi Arta, Greece","School of Science & Technology, Hellenic Open University, 26335, Patra, Greece"],"raw_orcid":"https://orcid.org/0009-0004-9227-1365","affiliations":[{"raw_affiliation_string":"Human Computer Interaction Laboratory, Department of Informatics and Telecommunications, University of Ioannina, 47150, Kostakioi Arta, Greece","institution_ids":["https://openalex.org/I194019607"]},{"raw_affiliation_string":"School of Science & Technology, Hellenic Open University, 26335, Patra, Greece","institution_ids":["https://openalex.org/I231025917"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058278718","display_name":"Petros Karvelis","orcid":"https://orcid.org/0000-0002-0483-4868"},"institutions":[{"id":"https://openalex.org/I194019607","display_name":"University of Ioannina","ror":"https://ror.org/01qg3j183","country_code":"GR","type":"education","lineage":["https://openalex.org/I194019607"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Petros Karvelis","raw_affiliation_strings":["Department of Informatics and Telecommunications, University of Ioannina,  47150, Kostakioi Arta, Greece"],"raw_orcid":"https://orcid.org/0000-0002-0483-4868","affiliations":[{"raw_affiliation_string":"Department of Informatics and Telecommunications, University of Ioannina,  47150, Kostakioi Arta, Greece","institution_ids":["https://openalex.org/I194019607"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027454960","display_name":"\u039d\u03b9\u03ba\u03cc\u03bb\u03b1\u03bf\u03c2 \u0393\u03b9\u03b1\u03bd\u03bd\u03b1\u03ba\u03ad\u03b1\u03c2","orcid":"https://orcid.org/0000-0002-0615-783X"},"institutions":[{"id":"https://openalex.org/I194019607","display_name":"University of Ioannina","ror":"https://ror.org/01qg3j183","country_code":"GR","type":"education","lineage":["https://openalex.org/I194019607"]}],"countries":["GR"],"is_corresponding":true,"raw_author_name":"Nikolaos Giannakeas","raw_affiliation_strings":["Human Computer Interaction Laboratory, Department of Informatics and Telecommunications, University of Ioannina, 47150, Kostakioi Arta, Greece"],"raw_orcid":"https://orcid.org/0000-0002-0615-783X","affiliations":[{"raw_affiliation_string":"Human Computer Interaction Laboratory, Department of Informatics and Telecommunications, University of Ioannina, 47150, Kostakioi Arta, Greece","institution_ids":["https://openalex.org/I194019607"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113199291","display_name":"Aristidis Vrachatis","orcid":null},"institutions":[{"id":"https://openalex.org/I187792471","display_name":"Ionian University","ror":"https://ror.org/01xm4n520","country_code":"GR","type":"education","lineage":["https://openalex.org/I187792471"]},{"id":"https://openalex.org/I231025917","display_name":"Hellenic Open University","ror":"https://ror.org/02kq26x23","country_code":"GR","type":"education","lineage":["https://openalex.org/I231025917"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Aristidis Vrachatis","raw_affiliation_strings":["Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, 49100, Corfu, Greece","School of Science & Technology, Hellenic Open University, 26335, Patra, Greece"],"raw_orcid":"https://orcid.org/0000-0003-1892-0000","affiliations":[{"raw_affiliation_string":"Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, 49100, Corfu, Greece","institution_ids":["https://openalex.org/I187792471"]},{"raw_affiliation_string":"School of Science & Technology, Hellenic Open University, 26335, Patra, Greece","institution_ids":["https://openalex.org/I231025917"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031438015","display_name":"Euripidis Glavas","orcid":"https://orcid.org/0000-0002-5604-3507"},"institutions":[{"id":"https://openalex.org/I194019607","display_name":"University of Ioannina","ror":"https://ror.org/01qg3j183","country_code":"GR","type":"education","lineage":["https://openalex.org/I194019607"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Evripidis Glavas","raw_affiliation_strings":["Human Computer Interaction Laboratory, Department of Informatics and Telecommunications, University of Ioannina, 47150, Kostakioi Arta, Greece"],"raw_orcid":"https://orcid.org/0000-0002-5604-3507","affiliations":[{"raw_affiliation_string":"Human Computer Interaction Laboratory, Department of Informatics and Telecommunications, University of Ioannina, 47150, Kostakioi Arta, Greece","institution_ids":["https://openalex.org/I194019607"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000270870","display_name":"Alexandros T. Tzallas","orcid":"https://orcid.org/0000-0001-9043-1290"},"institutions":[{"id":"https://openalex.org/I194019607","display_name":"University of Ioannina","ror":"https://ror.org/01qg3j183","country_code":"GR","type":"education","lineage":["https://openalex.org/I194019607"]},{"id":"https://openalex.org/I231025917","display_name":"Hellenic Open University","ror":"https://ror.org/02kq26x23","country_code":"GR","type":"education","lineage":["https://openalex.org/I231025917"]}],"countries":["GR"],"is_corresponding":true,"raw_author_name":"Alexandros T. Tzallas","raw_affiliation_strings":["Human Computer Interaction Laboratory, Department of Informatics and Telecommunications, University of Ioannina, 47150, Kostakioi Arta, Greece","School of Science & Technology, Hellenic Open University, 26335, Patra, Greece"],"raw_orcid":"https://orcid.org/0000-0001-9043-1290","affiliations":[{"raw_affiliation_string":"Human Computer Interaction Laboratory, Department of Informatics and Telecommunications, University of Ioannina, 47150, Kostakioi Arta, Greece","institution_ids":["https://openalex.org/I194019607"]},{"raw_affiliation_string":"School of Science & Technology, Hellenic Open University, 26335, Patra, Greece","institution_ids":["https://openalex.org/I231025917"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5000270870","https://openalex.org/A5027454960"],"corresponding_institution_ids":["https://openalex.org/I194019607","https://openalex.org/I231025917"],"apc_list":{"value":2390,"currency":"EUR","value_usd":2990},"apc_paid":{"value":2390,"currency":"EUR","value_usd":2990},"fwci":3.2409,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.9250635,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"13","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9980999827384949,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9980999827384949,"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":0.991100013256073,"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/T10028","display_name":"Topic Modeling","score":0.9904000163078308,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/computer-science","display_name":"Computer science","score":0.5798816680908203},{"id":"https://openalex.org/keywords/natural","display_name":"Natural (archaeology)","score":0.4759499728679657},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.40927568078041077},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3776274025440216},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18254020810127258}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5798816680908203},{"id":"https://openalex.org/C2776608160","wikidata":"https://www.wikidata.org/wiki/Q4785462","display_name":"Natural (archaeology)","level":2,"score":0.4759499728679657},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.40927568078041077},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3776274025440216},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18254020810127258},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/s13721-024-00458-1","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s13721-024-00458-1","pdf_url":"https://link.springer.com/content/pdf/10.1007/s13721-024-00458-1.pdf","source":{"id":"https://openalex.org/S4210178532","display_name":"Network Modeling Analysis in Health Informatics and Bioinformatics","issn_l":"2192-6662","issn":["2192-6662","2192-6670"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310321666","host_organization_name":"Springer Vienna","host_organization_lineage":["https://openalex.org/P4310321666","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Vienna","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":"Network Modeling Analysis in Health Informatics and Bioinformatics","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1007/s13721-024-00458-1","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s13721-024-00458-1","pdf_url":"https://link.springer.com/content/pdf/10.1007/s13721-024-00458-1.pdf","source":{"id":"https://openalex.org/S4210178532","display_name":"Network Modeling Analysis in Health Informatics and Bioinformatics","issn_l":"2192-6662","issn":["2192-6662","2192-6670"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310321666","host_organization_name":"Springer Vienna","host_organization_lineage":["https://openalex.org/P4310321666","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Vienna","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":"Network Modeling Analysis in Health Informatics and Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.4099999964237213}],"awards":[],"funders":[{"id":"https://openalex.org/F4320318628","display_name":"Hellenic Academic Libraries Link","ror":null},{"id":"https://openalex.org/F4320331527","display_name":"University of Ioannina","ror":"https://ror.org/01qg3j183"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4396678025.pdf"},"referenced_works_count":104,"referenced_works":["https://openalex.org/W1612034467","https://openalex.org/W1988037271","https://openalex.org/W2004147962","https://openalex.org/W2008056655","https://openalex.org/W2114268578","https://openalex.org/W2295124130","https://openalex.org/W2295598076","https://openalex.org/W2400080550","https://openalex.org/W2550535012","https://openalex.org/W2775102587","https://openalex.org/W2777416523","https://openalex.org/W2786757148","https://openalex.org/W2789876780","https://openalex.org/W2800388620","https://openalex.org/W2800857888","https://openalex.org/W2804025582","https://openalex.org/W2896161497","https://openalex.org/W2896262061","https://openalex.org/W2899325668","https://openalex.org/W2900694973","https://openalex.org/W2911930496","https://openalex.org/W2912802963","https://openalex.org/W2914698725","https://openalex.org/W2949346354","https://openalex.org/W2952253955","https://openalex.org/W2952631022","https://openalex.org/W2954442758","https://openalex.org/W2954820957","https://openalex.org/W2962756421","https://openalex.org/W2963514026","https://openalex.org/W2971248389","https://openalex.org/W2971874382","https://openalex.org/W2987707723","https://openalex.org/W2990063070","https://openalex.org/W2991321419","https://openalex.org/W2998220730","https://openalex.org/W3003053789","https://openalex.org/W3004305487","https://openalex.org/W3004987428","https://openalex.org/W3013230828","https://openalex.org/W3013382035","https://openalex.org/W3026298573","https://openalex.org/W3031691322","https://openalex.org/W3033577323","https://openalex.org/W3036648540","https://openalex.org/W3044326329","https://openalex.org/W3089123840","https://openalex.org/W3089862415","https://openalex.org/W3093585277","https://openalex.org/W3111567820","https://openalex.org/W3118324533","https://openalex.org/W3118615836","https://openalex.org/W3120018424","https://openalex.org/W3126162820","https://openalex.org/W3137414883","https://openalex.org/W3138964863","https://openalex.org/W3163867547","https://openalex.org/W3164597438","https://openalex.org/W3165640073","https://openalex.org/W3186135460","https://openalex.org/W3190763963","https://openalex.org/W3196282583","https://openalex.org/W3198604700","https://openalex.org/W3198971816","https://openalex.org/W3200220209","https://openalex.org/W3205595869","https://openalex.org/W3207774560","https://openalex.org/W4200505767","https://openalex.org/W4205697550","https://openalex.org/W4205820032","https://openalex.org/W4210584212","https://openalex.org/W4211064337","https://openalex.org/W4213041764","https://openalex.org/W4213102919","https://openalex.org/W4220693339","https://openalex.org/W4224992156","https://openalex.org/W4226022817","https://openalex.org/W4226192705","https://openalex.org/W4233520916","https://openalex.org/W4242729757","https://openalex.org/W4282935413","https://openalex.org/W4283391017","https://openalex.org/W4283706978","https://openalex.org/W4283735109","https://openalex.org/W4283816456","https://openalex.org/W4285188807","https://openalex.org/W4287837163","https://openalex.org/W4288384170","https://openalex.org/W4291221220","https://openalex.org/W4291301137","https://openalex.org/W4292676375","https://openalex.org/W4295519908","https://openalex.org/W4296394114","https://openalex.org/W4303520619","https://openalex.org/W4306776210","https://openalex.org/W4308834893","https://openalex.org/W4308992137","https://openalex.org/W4311948367","https://openalex.org/W4312178960","https://openalex.org/W4316465078","https://openalex.org/W4317779194","https://openalex.org/W4321510669","https://openalex.org/W4322504259","https://openalex.org/W4384080511"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W4395014643","https://openalex.org/W4391913857","https://openalex.org/W2350741829"],"abstract_inverted_index":{"Abstract":[0],"The":[1,150,203],"decoding":[2],"of":[3,22,26,64,74,111,133,152,163,205,213,227,240],"the":[4,36,62,72,78,123,131,161,175,189,206,211,214,219,238],"human":[5,98],"genome,":[6],"completed":[7],"two":[8],"decades":[9],"ago,":[10],"marked":[11],"a":[12,19,48,178],"revolutionary":[13],"moment":[14],"in":[15,86,120,236],"biology":[16,112],"by":[17],"introducing":[18],"vast":[20],"amount":[21],"data.":[23,76],"This":[24],"avalanche":[25],"information":[27],"presented":[28],"several":[29],"computational":[30],"challenges.":[31],"Machine":[32,65,81,171],"Learning":[33,66,82,172],"has":[34],"become":[35],"dominant":[37],"method":[38],"to":[39,71,89],"address":[40],"these":[41],"challenges,":[42],"with":[43],"Natural":[44,68,134,153],"Language":[45,69,135,154],"Processing":[46,70,155],"playing":[47],"significant":[49],"role":[50],"and":[51,67,100,103,113,116,147,169,196,218,234],"offering":[52],"promising":[53],"results.":[54],"In":[55,181],"this":[56,182],"systematic":[57,179],"review,":[58],"we":[59,230],"will":[60],"explore":[61],"application":[63],"study":[73],"biological":[75,216],"On":[77,122],"one":[79],"hand,":[80,125],"is":[83,130,156],"widely":[84],"used":[85],"Artificial":[87],"Intelligence":[88],"improve":[90,114],"automation,":[91],"carry":[92],"out":[93],"tasks":[94],"that":[95],"require":[96],"no":[97],"interaction,":[99],"perform":[101],"analytical":[102],"physical":[104],"activities.":[105],"It":[106],"helps":[107],"advance":[108],"our":[109,224],"understanding":[110],"healthcare":[115],"drug":[117],"development":[118],"processes":[119],"bioinformatics.":[121,241],"other":[124],"improved":[126],"machine-human":[127],"language":[128],"interaction":[129],"aim":[132],"Processing.":[136],"Its":[137],"three":[138],"main":[139],"goals":[140],"are":[141],"character":[142],"sequence":[143],"processing,":[144],"pattern":[145],"recognition,":[146],"algorithm":[148],"development.":[149],"use":[151],"becoming":[157],"increasingly":[158],"important":[159],"for":[160,177],"analysis":[162],"omics":[164],"data":[165,217],"using":[166],"both":[167],"modern":[168],"conventional":[170],"models,":[173],"underscoring":[174],"necessity":[176],"review.":[180],"work,":[183],"82":[184],"studies":[185],"were":[186],"included":[187],"following":[188],"PRISMA":[190],"guidelines,":[191],"sourced":[192],"from":[193],"PubMed,":[194],"Scopus":[195],"IEEE":[197],"Xplore":[198],"on":[199,210],"April":[200],"4th,":[201],"2023.":[202],"evaluation":[204],"publications":[207],"was":[208],"based":[209],"type":[212],"studied":[215],"employed":[220],"NLP":[221,228],"techniques.":[222],"Through":[223],"in-depth":[225],"exploration":[226],"approaches,":[229],"highlight":[231],"their":[232],"significance":[233],"potential":[235],"advancing":[237],"field":[239]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-16T09:24:06.705377","created_date":"2025-10-10T00:00:00"}