{"id":"https://openalex.org/W2119207919","doi":"https://doi.org/10.1186/s13326-015-0033-1","title":"KneeTex: an ontology\u2013driven system for information extraction from MRI reports","display_name":"KneeTex: an ontology\u2013driven system for information extraction from MRI reports","publication_year":2015,"publication_date":"2015-09-07","ids":{"openalex":"https://openalex.org/W2119207919","doi":"https://doi.org/10.1186/s13326-015-0033-1","mag":"2119207919","pmid":"https://pubmed.ncbi.nlm.nih.gov/26347806"},"language":"en","primary_location":{"id":"doi:10.1186/s13326-015-0033-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-015-0033-1","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-015-0033-1","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"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":"Journal of Biomedical Semantics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-015-0033-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016345745","display_name":"\u202aIrena Spasi\u0107","orcid":"https://orcid.org/0000-0002-8132-3885"},"institutions":[{"id":"https://openalex.org/I79510175","display_name":"Cardiff University","ror":"https://ror.org/03kk7td41","country_code":"GB","type":"education","lineage":["https://openalex.org/I79510175"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Irena Spasi\u0107","raw_affiliation_strings":["School of Computer Science & Informatics, Cardiff University, Cardiff, CF24 3AA UK","School of Computer Science and Informatics, Cardiff University Cardiff UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science & Informatics, Cardiff University, Cardiff, CF24 3AA UK","institution_ids":["https://openalex.org/I79510175"]},{"raw_affiliation_string":"School of Computer Science and Informatics, Cardiff University Cardiff UK","institution_ids":["https://openalex.org/I79510175"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055778766","display_name":"Bo Zhao","orcid":"https://orcid.org/0000-0002-3799-9183"},"institutions":[{"id":"https://openalex.org/I79510175","display_name":"Cardiff University","ror":"https://ror.org/03kk7td41","country_code":"GB","type":"education","lineage":["https://openalex.org/I79510175"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Bo Zhao","raw_affiliation_strings":["School of Computer Science & Informatics, Cardiff University, Cardiff, CF24 3AA UK","School of Computer Science and Informatics, Cardiff University Cardiff UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science & Informatics, Cardiff University, Cardiff, CF24 3AA UK","institution_ids":["https://openalex.org/I79510175"]},{"raw_affiliation_string":"School of Computer Science and Informatics, Cardiff University Cardiff UK","institution_ids":["https://openalex.org/I79510175"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061033797","display_name":"Christopher B. Jones","orcid":"https://orcid.org/0000-0001-6847-7575"},"institutions":[{"id":"https://openalex.org/I79510175","display_name":"Cardiff University","ror":"https://ror.org/03kk7td41","country_code":"GB","type":"education","lineage":["https://openalex.org/I79510175"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Christopher B. Jones","raw_affiliation_strings":["School of Computer Science & Informatics, Cardiff University, Cardiff, CF24 3AA UK","School of Computer Science and Informatics, Cardiff University Cardiff UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science & Informatics, Cardiff University, Cardiff, CF24 3AA UK","institution_ids":["https://openalex.org/I79510175"]},{"raw_affiliation_string":"School of Computer Science and Informatics, Cardiff University Cardiff UK","institution_ids":["https://openalex.org/I79510175"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008939552","display_name":"Kate Button","orcid":"https://orcid.org/0000-0003-1073-9901"},"institutions":[{"id":"https://openalex.org/I79510175","display_name":"Cardiff University","ror":"https://ror.org/03kk7td41","country_code":"GB","type":"education","lineage":["https://openalex.org/I79510175"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Kate Button","raw_affiliation_strings":["School of Healthcare Sciences, Cardiff University, Cardiff, CF14 4XN UK","School of Healthcare Sciences, Cardiff University, Cardiff, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Healthcare Sciences, Cardiff University, Cardiff, CF14 4XN UK","institution_ids":["https://openalex.org/I79510175"]},{"raw_affiliation_string":"School of Healthcare Sciences, Cardiff University, Cardiff, UK","institution_ids":["https://openalex.org/I79510175"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5016345745"],"corresponding_institution_ids":["https://openalex.org/I79510175"],"apc_list":{"value":1190,"currency":"GBP","value_usd":1459},"apc_paid":{"value":2132,"currency":"EUR","value_usd":2299},"fwci":1.9579,"has_fulltext":true,"cited_by_count":30,"citation_normalized_percentile":{"value":0.86284962,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"6","issue":"1","first_page":"34","last_page":"34"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.8877999782562256,"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":0.8877999782562256,"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":0.05260000005364418,"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"}},{"id":"https://openalex.org/T10181","display_name":"Natural Language Processing Techniques","score":0.00860000029206276,"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":0.841826319694519},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6790400743484497},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.6110701560974121},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5701656341552734},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5500893592834473},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4745291769504547},{"id":"https://openalex.org/keywords/sublanguage","display_name":"Sublanguage","score":0.4524076581001282},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.44676294922828674}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.841826319694519},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6790400743484497},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.6110701560974121},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5701656341552734},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5500893592834473},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4745291769504547},{"id":"https://openalex.org/C2776411971","wikidata":"https://www.wikidata.org/wiki/Q17141398","display_name":"Sublanguage","level":2,"score":0.4524076581001282},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.44676294922828674},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13326-015-0033-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-015-0033-1","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-015-0033-1","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"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":"Journal of Biomedical Semantics","raw_type":"journal-article"},{"id":"pmid:26347806","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26347806","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 biomedical semantics","raw_type":null},{"id":"pmh:oai:https://orca.cardiff.ac.uk:75959","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306401195","display_name":"ORCA Online Research @Cardiff (Cardiff University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79510175","host_organization_name":"Cardiff University","host_organization_lineage":["https://openalex.org/I79510175"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:europepmc.org:3539179","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4561435","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/s13326-015-0033-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13326-015-0033-1","pdf_url":"https://jbiomedsem.biomedcentral.com/counter/pdf/10.1186/s13326-015-0033-1","source":{"id":"https://openalex.org/S172276550","display_name":"Journal of Biomedical Semantics","issn_l":"2041-1480","issn":["2041-1480"],"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":"Journal of Biomedical Semantics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.8299999833106995}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2119207919.pdf","grobid_xml":"https://content.openalex.org/works/W2119207919.grobid-xml"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W8550301","https://openalex.org/W41404523","https://openalex.org/W159602031","https://openalex.org/W191202953","https://openalex.org/W333927187","https://openalex.org/W1036172382","https://openalex.org/W1485658078","https://openalex.org/W1504212872","https://openalex.org/W1545047802","https://openalex.org/W1550258693","https://openalex.org/W1556946521","https://openalex.org/W1646278814","https://openalex.org/W1745514781","https://openalex.org/W1967565781","https://openalex.org/W1973401962","https://openalex.org/W1975879668","https://openalex.org/W1978394996","https://openalex.org/W1980212706","https://openalex.org/W1990272394","https://openalex.org/W2000042664","https://openalex.org/W2012560661","https://openalex.org/W2034497973","https://openalex.org/W2037471118","https://openalex.org/W2044070623","https://openalex.org/W2044655214","https://openalex.org/W2052601836","https://openalex.org/W2056713699","https://openalex.org/W2056734074","https://openalex.org/W2058490165","https://openalex.org/W2076424959","https://openalex.org/W2091963680","https://openalex.org/W2092419931","https://openalex.org/W2093892101","https://openalex.org/W2096704019","https://openalex.org/W2104655020","https://openalex.org/W2104842437","https://openalex.org/W2104950455","https://openalex.org/W2104990432","https://openalex.org/W2105824687","https://openalex.org/W2109228592","https://openalex.org/W2114063639","https://openalex.org/W2117815774","https://openalex.org/W2123152121","https://openalex.org/W2131598923","https://openalex.org/W2133627190","https://openalex.org/W2141766660","https://openalex.org/W2144949988","https://openalex.org/W2144981148","https://openalex.org/W2146089916","https://openalex.org/W2146763133","https://openalex.org/W2156518033","https://openalex.org/W2159583324","https://openalex.org/W2162506959","https://openalex.org/W2163589808","https://openalex.org/W2163670493","https://openalex.org/W2164777277","https://openalex.org/W2168435845","https://openalex.org/W2331384579","https://openalex.org/W2341078838","https://openalex.org/W2394634366","https://openalex.org/W2608311702","https://openalex.org/W3103362336"],"related_works":["https://openalex.org/W2250416822","https://openalex.org/W256033851","https://openalex.org/W74549753","https://openalex.org/W1513056508","https://openalex.org/W2352298027","https://openalex.org/W4319940250","https://openalex.org/W842810586","https://openalex.org/W2092919065","https://openalex.org/W4236762297","https://openalex.org/W3138801416"],"abstract_inverted_index":{"BACKGROUND:":[0],"In":[1,100,158],"the":[2,12,19,53,81,143,161,166,218,277,303,332,361,369,372,377,399,421],"realm":[3],"of":[4,14,49,55,83,90,126,145,165,182,232,289,297,320,324,329,334,360,379,401,430],"knee":[5,20,76,84,170,402,431],"pathology,":[6,77],"magnetic":[7],"resonance":[8],"imaging":[9],"(MRI)":[10],"has":[11],"advantage":[13],"visualising":[15],"all":[16],"structures":[17],"within":[18,237],"joint,":[21],"which":[22,272,335],"makes":[23,123],"it":[24],"a":[25,87,146,180,266,286,405],"valuable":[26,44],"tool":[27],"for":[28,59,154,230,235,349,398,413],"increasing":[29],"diagnostic":[30,45],"accuracy":[31],"and":[32,86,132,152,203,249,258,312,327,409],"planning":[33],"surgical":[34],"treatments.":[35],"Therefore,":[36],"clinical":[37,63,374],"narratives":[38],"found":[39],"in":[40,73,112,169,337,376],"MRI":[41,71,171,291,358,365,423],"reports":[42,72,172,354],"convey":[43],"information.":[46],"A":[47,293],"range":[48,89],"studies":[50,429],"have":[51],"proven":[52],"feasibility":[54],"natural":[56],"language":[57],"processing":[58,178,192],"information":[60,107,119,317,350,386,411],"extraction":[61,108,120,281,351],"from":[62,244,352],"narratives.":[64],"However,":[65],"no":[66],"study":[67],"focused":[68],"specifically":[69],"on":[70,285],"relation":[74],"to":[75,80,129,141,175,216,253,276,416],"possibly":[78],"due":[79],"complexity":[82],"anatomy":[85,311,313],"wide":[88],"conditions":[91],"that":[92,110,355,393],"may":[93],"be":[94,417],"associated":[95],"with":[96,149,160,186,199,265,302,318,339],"different":[97],"anatomical":[98],"entities.":[99],"this":[101,113],"paper":[102],"we":[103],"describe":[104,356],"KneeTex,":[105],"an":[106,117,127,225,345,357,364,391],"system":[109,370],"operates":[111],"domain.":[114],"METHODS:":[115],"As":[116,404],"ontology-driven":[118],"system,":[121],"KneeTex":[122,264,315,343],"active":[124],"use":[125,236],"ontology":[128,148,242,392],"strongly":[130],"guide":[131],"constrain":[133],"text":[134,155,208],"analysis.":[135,189],"We":[136,223],"used":[137,168,215],"automatic":[138],"term":[139],"recognition":[140,197],"facilitate":[142],"development":[144],"domain-specific":[147],"sufficient":[150],"detail":[151],"coverage":[153],"mining":[156],"applications.":[157],"combination":[159],"ontology,":[162,227],"high":[163],"regularity":[164],"sublanguage":[167],"allowed":[173],"us":[174],"model":[176],"its":[177],"by":[179,207],"set":[181,288],"sophisticated":[183],"lexico-semantic":[184,269],"rules":[185],"minimal":[187],"syntactic":[188],"The":[190,239,384],"main":[191],"steps":[193],"involve":[194],"named":[195],"entity":[196],"combined":[198],"coordination,":[200],"enumeration,":[201],"ambiguity":[202],"co-reference":[204],"resolution,":[205],"followed":[206],"segmentation.":[209],"Ontology-based":[210],"semantic":[211],"typing":[212],"is":[213,273,344,387],"then":[214],"drive":[217],"template":[219,300],"filling":[220],"process.":[221],"RESULTS:":[222],"adopted":[224],"existing":[226],"TRAK":[228,241],"(Taxonomy":[229],"RehAbilitation":[231],"Knee":[233],"conditions),":[234],"KneeTex.":[238],"original":[240,422],"expanded":[243],"1,292":[245],"concepts,":[246,255],"1,720":[247],"synonyms":[248,257],"518":[250],"relationship":[251,260],"instances":[252],"1,621":[254],"2,550":[256],"560":[259],"instances.":[261],"This":[262],"provided":[263],"very":[267],"fine-grained":[268],"knowledge":[270,396],"base,":[271],"highly":[274],"attuned":[275],"given":[278],"sublanguage.":[279],"Information":[280],"results":[282],"were":[283],"evaluated":[284],"test":[287],"100":[290],"reports.":[292],"gold":[294],"standard":[295],"consisted":[296],"1,259":[298],"filled":[299],"records":[301],"following":[304],"slots:":[305],"finding,":[306],"finding":[307],"qualifier,":[308],"negation,":[309],"certainty,":[310],"qualifier.":[314],"extracted":[316,385],"precision":[319],"98.00":[321],"%,":[322,331],"recall":[323],"97.63":[325],"%":[326],"F-measure":[328],"97.81":[330],"values":[333],"are":[336],"line":[338],"human-like":[340],"performance.":[341],"CONCLUSIONS:":[342],"open-source,":[346],"stand-alone":[347],"application":[348],"narrative":[353],"scan":[359],"knee.":[362],"Given":[363],"report":[366],"as":[367],"input,":[368],"outputs":[371],"corresponding":[373],"findings":[375],"form":[378],"JavaScript":[380],"Object":[381],"Notation":[382],"objects.":[383],"mapped":[388],"onto":[389],"TRAK,":[390],"formally":[394,407],"models":[395],"relevant":[397],"rehabilitation":[400],"conditions.":[403,432],"result,":[406],"structured":[408],"coded":[410],"allows":[412],"complex":[414],"searches":[415],"conducted":[418],"efficiently":[419],"over":[420],"reports,":[424],"thereby":[425],"effectively":[426],"supporting":[427],"epidemiologic":[428]},"counts_by_year":[{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":4}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
