{"id":"https://openalex.org/W2897782208","doi":"https://doi.org/10.1093/bioinformatics/bty871","title":"Thalia: semantic search engine for biomedical abstracts","display_name":"Thalia: semantic search engine for biomedical abstracts","publication_year":2018,"publication_date":"2018-10-16","ids":{"openalex":"https://openalex.org/W2897782208","doi":"https://doi.org/10.1093/bioinformatics/bty871","mag":"2897782208","pmid":"https://pubmed.ncbi.nlm.nih.gov/30329013"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty871","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty871","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/10/1799/28604744/bty871.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/10/1799/28604744/bty871.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074068834","display_name":"Axel J. Soto","orcid":"https://orcid.org/0000-0002-9021-7566"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Axel J Soto","raw_affiliation_strings":["National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, UK"],"raw_orcid":"https://orcid.org/0000-0002-9021-7566","affiliations":[{"raw_affiliation_string":"National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, UK","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024181945","display_name":"Piotr Przyby\u0142a","orcid":"https://orcid.org/0000-0001-9043-6817"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Piotr Przyby\u0142a","raw_affiliation_strings":["National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, UK"],"raw_orcid":"https://orcid.org/0000-0001-9043-6817","affiliations":[{"raw_affiliation_string":"National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, UK","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077976343","display_name":"Sophia Ananiadou","orcid":"https://orcid.org/0000-0002-4097-9191"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Sophia Ananiadou","raw_affiliation_strings":["National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, UK","institution_ids":["https://openalex.org/I28407311"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5077976343"],"corresponding_institution_ids":["https://openalex.org/I28407311"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":1161,"currency":"EUR","value_usd":1252},"fwci":2.4359,"has_fulltext":true,"cited_by_count":63,"citation_normalized_percentile":{"value":0.90096763,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"35","issue":"10","first_page":"1799","last_page":"1801"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9118000268936157,"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":0.9118000268936157,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.026100000366568565,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.012000000104308128,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.7426880598068237},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.6068841814994812},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6057742238044739},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5961585640907288},{"id":"https://openalex.org/keywords/search-engine","display_name":"Search engine","score":0.47266992926597595},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.4675043523311615},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.46747398376464844},{"id":"https://openalex.org/keywords/semantic-search","display_name":"Semantic search","score":0.4258069097995758},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08264604210853577}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7426880598068237},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.6068841814994812},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6057742238044739},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5961585640907288},{"id":"https://openalex.org/C97854310","wikidata":"https://www.wikidata.org/wiki/Q19541","display_name":"Search engine","level":2,"score":0.47266992926597595},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4675043523311615},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.46747398376464844},{"id":"https://openalex.org/C166423231","wikidata":"https://www.wikidata.org/wiki/Q1891170","display_name":"Semantic search","level":3,"score":0.4258069097995758},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08264604210853577},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","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":true},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/bty871","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty871","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/10/1799/28604744/bty871.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30329013","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30329013","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pure.atira.dk:openaire/ddd954de-a5c3-4c28-83ab-16327887d616","is_oa":true,"landing_page_url":"https://research.manchester.ac.uk/en/publications/ddd954de-a5c3-4c28-83ab-16327887d616","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Soto, A, Przybyla, P & Ananiadou, S 2018, 'Thalia: Semantic search engine for biomedical abstracts', Bioinformatics. https://doi.org/10.1093/bioinformatics/bty871","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:ri.conicet.gov.ar:11336/90965","is_oa":true,"landing_page_url":"http://hdl.handle.net/11336/90965","pdf_url":"http://hdl.handle.net/11336/90965","source":{"id":"https://openalex.org/S4306402455","display_name":"CONICET Digital (CONICET)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210148385","host_organization_name":"Biomedicine Research Institute of Buenos Aires - CONICET - Partner Institute of the Max Planck Society","host_organization_lineage":["https://openalex.org/I4210148385"],"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":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6513154","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6513154","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:publications/ddd954de-a5c3-4c28-83ab-16327887d616","is_oa":true,"landing_page_url":"https://www.research.manchester.ac.uk/portal/en/publications/thalia-semantic-search-engine-for-biomedical-abstracts(ddd954de-a5c3-4c28-83ab-16327887d616).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"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":"Soto, A, Przybyla, P & Ananiadou, S 2018, 'Thalia: Semantic search engine for biomedical abstracts', Bioinformatics. https://doi.org/10.1093/bioinformatics/bty871","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty871","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty871","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/10/1799/28604744/bty871.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4365314885","display_name":null,"funder_award_id":"MR/N00583X/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G4492632425","display_name":"Enriching Metabolic PATHwaY models with evidence from the literature (EMPATHY)","funder_award_id":"BB/M006891/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G473771980","display_name":null,"funder_award_id":"BB/M006891/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G6457786194","display_name":null,"funder_award_id":"BB/P025684/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G7679475066","display_name":"Japan Partnering Award. Text mining and bioinformatics platforms for metabolic pathway modelling.","funder_award_id":"BB/P025684/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2897782208.pdf","grobid_xml":"https://content.openalex.org/works/W2897782208.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1964670939","https://openalex.org/W1977289091","https://openalex.org/W2092489937","https://openalex.org/W2096525273","https://openalex.org/W2097678794","https://openalex.org/W2099701465","https://openalex.org/W2105939244","https://openalex.org/W2109252435","https://openalex.org/W2120754707","https://openalex.org/W2158191506","https://openalex.org/W2162965868","https://openalex.org/W2164394614","https://openalex.org/W2212494754","https://openalex.org/W2402320467","https://openalex.org/W2533611849","https://openalex.org/W2574149054","https://openalex.org/W3099272318","https://openalex.org/W4234797890"],"related_works":["https://openalex.org/W2023370952","https://openalex.org/W2187134628","https://openalex.org/W167737004","https://openalex.org/W1964038241","https://openalex.org/W2185038817","https://openalex.org/W2385957133","https://openalex.org/W2004064649","https://openalex.org/W3590553","https://openalex.org/W1974306718","https://openalex.org/W3141094475"],"abstract_inverted_index":{"SUMMARY:":[0],"Although":[1],"the":[2,6,14,17,85,98,104],"publication":[3],"rate":[4],"of":[5,19,47,67,89,97,101,106],"biomedical":[7,51],"literature":[8],"has":[9],"been":[10],"growing":[11],"steadily":[12],"during":[13],"last":[15],"decades,":[16],"accessibility":[18],"pertinent":[20],"research":[21],"publications":[22],"for":[23],"biologist":[24],"and":[25],"medical":[26],"practitioners":[27],"remains":[28],"a":[29,37,57,61,79,107],"challenge.":[30],"This":[31],"article":[32],"describes":[33],"Thalia,":[34],"which":[35],"is":[36,54,71,74,115],"semantic":[38],"search":[39,69],"engine":[40,70],"that":[41,72],"can":[42],"recognize":[43],"eight":[44],"different":[45],"types":[46],"concepts":[48],"occurring":[49],"in":[50,103],"abstracts.":[52],"Thalia":[53,102,114],"available":[55,116,124],"via":[56],"web-based":[58],"interface":[59],"or":[60],"RESTful":[62],"API.":[63],"A":[64],"key":[65],"aspect":[66],"our":[68,90],"it":[73],"updated":[75],"from":[76],"PubMed":[77],"on":[78],"daily":[80],"basis.":[81],"We":[82],"describe":[83],"here":[84],"main":[86],"building":[87],"blocks":[88],"tool":[91],"as":[92,94],"well":[93],"an":[95],"evaluation":[96],"retrieval":[99],"capabilities":[100],"context":[105],"precision":[108],"medicine":[109],"dataset.":[110],"AVAILABILITY":[111],"AND":[112],"IMPLEMENTATION:":[113],"at":[117,125],"http://nactem.ac.uk/Thalia_BI/.":[118],"SUPPLEMENTARY":[119],"INFORMATION:":[120],"Supplementary":[121],"data":[122],"are":[123],"Bioinformatics":[126],"online.":[127]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":8}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
