{"id":"https://openalex.org/W4403486856","doi":"https://doi.org/10.3233/faia241059","title":"GIF: An Automated Genomic Information Finder to Extract Data from Reports","display_name":"GIF: An Automated Genomic Information Finder to Extract Data from Reports","publication_year":2024,"publication_date":"2024-10-16","ids":{"openalex":"https://openalex.org/W4403486856","doi":"https://doi.org/10.3233/faia241059"},"language":"en","primary_location":{"id":"doi:10.3233/faia241059","is_oa":true,"landing_page_url":"https://doi.org/10.3233/faia241059","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/FAIA241059","source":{"id":"https://openalex.org/S4210201731","display_name":"Frontiers in artificial intelligence and applications","issn_l":"0922-6389","issn":["0922-6389","1879-8314"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Artificial Intelligence and Applications","raw_type":"book-chapter"},"type":"book-chapter","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/FAIA241059","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5108495406","display_name":"Pavithra Rajendran","orcid":null},"institutions":[{"id":"https://openalex.org/I2800349819","display_name":"Great Ormond Street Hospital for Children NHS Foundation Trust","ror":"https://ror.org/03zydm450","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800349819"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Pavithra Rajendran","raw_affiliation_strings":["Great Ormond Street Hospital NHS Foundation Trust"],"affiliations":[{"raw_affiliation_string":"Great Ormond Street Hospital NHS Foundation Trust","institution_ids":["https://openalex.org/I2800349819"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069241667","display_name":"Alexandros Zenonos","orcid":"https://orcid.org/0000-0003-4694-1642"},"institutions":[{"id":"https://openalex.org/I4210153988","display_name":"Roche (Bosnia-Herzegovina)","ror":"https://ror.org/04gbzz966","country_code":"BA","type":"company","lineage":["https://openalex.org/I118019719","https://openalex.org/I4210153988"]}],"countries":["BA"],"is_corresponding":false,"raw_author_name":"Alexandros Zenonos","raw_affiliation_strings":["Roche Products Ltd"],"affiliations":[{"raw_affiliation_string":"Roche Products Ltd","institution_ids":["https://openalex.org/I4210153988"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093676690","display_name":"Sebin Sabu","orcid":null},"institutions":[{"id":"https://openalex.org/I2800349819","display_name":"Great Ormond Street Hospital for Children NHS Foundation Trust","ror":"https://ror.org/03zydm450","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800349819"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sebin Sabu","raw_affiliation_strings":["Great Ormond Street Hospital NHS Foundation Trust"],"affiliations":[{"raw_affiliation_string":"Great Ormond Street Hospital NHS Foundation Trust","institution_ids":["https://openalex.org/I2800349819"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003953097","display_name":"Anastassia Spiridou","orcid":"https://orcid.org/0000-0001-6576-0244"},"institutions":[{"id":"https://openalex.org/I2800349819","display_name":"Great Ormond Street Hospital for Children NHS Foundation Trust","ror":"https://ror.org/03zydm450","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800349819"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Anastasia Spiridou","raw_affiliation_strings":["Great Ormond Street Hospital NHS Foundation Trust"],"affiliations":[{"raw_affiliation_string":"Great Ormond Street Hospital NHS Foundation Trust","institution_ids":["https://openalex.org/I2800349819"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113286567","display_name":"Helena Spiridou Goncalves","orcid":"https://orcid.org/0009-0002-6970-5618"},"institutions":[{"id":"https://openalex.org/I2800349819","display_name":"Great Ormond Street Hospital for Children NHS Foundation Trust","ror":"https://ror.org/03zydm450","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800349819"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Helena Spiridou Goncalves","raw_affiliation_strings":["Great Ormond Street Hospital NHS Foundation Trust"],"affiliations":[{"raw_affiliation_string":"Great Ormond Street Hospital NHS Foundation Trust","institution_ids":["https://openalex.org/I2800349819"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114301698","display_name":"Nastazja Laskowski","orcid":null},"institutions":[{"id":"https://openalex.org/I4210153988","display_name":"Roche (Bosnia-Herzegovina)","ror":"https://ror.org/04gbzz966","country_code":"BA","type":"company","lineage":["https://openalex.org/I118019719","https://openalex.org/I4210153988"]}],"countries":["BA"],"is_corresponding":false,"raw_author_name":"Nastazja Laskowski","raw_affiliation_strings":["Roche Products Ltd"],"affiliations":[{"raw_affiliation_string":"Roche Products Ltd","institution_ids":["https://openalex.org/I4210153988"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025962709","display_name":"Daniel Key","orcid":"https://orcid.org/0000-0002-9559-1784"},"institutions":[{"id":"https://openalex.org/I2800349819","display_name":"Great Ormond Street Hospital for Children NHS Foundation Trust","ror":"https://ror.org/03zydm450","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800349819"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Daniel Key","raw_affiliation_strings":["Great Ormond Street Hospital NHS Foundation Trust"],"affiliations":[{"raw_affiliation_string":"Great Ormond Street Hospital NHS Foundation Trust","institution_ids":["https://openalex.org/I2800349819"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109732497","display_name":"S. Patel","orcid":null},"institutions":[{"id":"https://openalex.org/I2800349819","display_name":"Great Ormond Street Hospital for Children NHS Foundation Trust","ror":"https://ror.org/03zydm450","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800349819"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Shiren Patel","raw_affiliation_strings":["Great Ormond Street Hospital NHS Foundation Trust"],"affiliations":[{"raw_affiliation_string":"Great Ormond Street Hospital NHS Foundation Trust","institution_ids":["https://openalex.org/I2800349819"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008687314","display_name":"Rebecca Pope","orcid":"https://orcid.org/0000-0001-6889-589X"},"institutions":[{"id":"https://openalex.org/I4210153988","display_name":"Roche (Bosnia-Herzegovina)","ror":"https://ror.org/04gbzz966","country_code":"BA","type":"company","lineage":["https://openalex.org/I118019719","https://openalex.org/I4210153988"]}],"countries":["BA"],"is_corresponding":false,"raw_author_name":"Rebecca Pope","raw_affiliation_strings":["Roche Products Ltd"],"affiliations":[{"raw_affiliation_string":"Roche Products Ltd","institution_ids":["https://openalex.org/I4210153988"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037501835","display_name":"Neil J. Sebire","orcid":"https://orcid.org/0000-0001-5348-9063"},"institutions":[{"id":"https://openalex.org/I2800349819","display_name":"Great Ormond Street Hospital for Children NHS Foundation Trust","ror":"https://ror.org/03zydm450","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800349819"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Neil Sebire","raw_affiliation_strings":["Great Ormond Street Hospital NHS Foundation Trust"],"affiliations":[{"raw_affiliation_string":"Great Ormond Street Hospital NHS Foundation Trust","institution_ids":["https://openalex.org/I2800349819"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5108495406"],"corresponding_institution_ids":["https://openalex.org/I2800349819"],"apc_list":null,"apc_paid":null,"fwci":1.5407,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.83294393,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.6823999881744385,"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":0.6823999881744385,"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":0.5335092544555664},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4967213273048401},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.33637744188308716},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2625012695789337}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5335092544555664},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4967213273048401},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.33637744188308716},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2625012695789337}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.3233/faia241059","is_oa":true,"landing_page_url":"https://doi.org/10.3233/faia241059","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/FAIA241059","source":{"id":"https://openalex.org/S4210201731","display_name":"Frontiers in artificial intelligence and applications","issn_l":"0922-6389","issn":["0922-6389","1879-8314"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Artificial Intelligence and Applications","raw_type":"book-chapter"}],"best_oa_location":{"id":"doi:10.3233/faia241059","is_oa":true,"landing_page_url":"https://doi.org/10.3233/faia241059","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/FAIA241059","source":{"id":"https://openalex.org/S4210201731","display_name":"Frontiers in artificial intelligence and applications","issn_l":"0922-6389","issn":["0922-6389","1879-8314"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Artificial Intelligence and Applications","raw_type":"book-chapter"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.46000000834465027,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4403486856.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Genomic":[0],"testing":[1],"is":[2],"becoming":[3],"increasingly":[4],"used":[5],"within":[6,135,184],"the":[7,39,48,60,68,72,102,136,142,145,161,185],"UK":[8],"National":[9],"Health":[10],"Service":[11],"(NHS)":[12],"in":[13,29,41,47,170,175],"an":[14,105],"effort":[15],"to":[16,120],"deliver":[17],"precision":[18],"medicine":[19],"that":[20,108],"can":[21],"directly":[22],"benefit":[23],"patient":[24],"management":[25],"and":[26,37,63,116,129,158,163,174,181],"care.":[27],"Typically,":[28],"hospital":[30,186],"settings":[31],"clinical":[32],"scientists":[33],"interpret":[34],"genomic":[35,137],"results":[36,157],"store":[38],"output":[40],"reports":[42],"(unstructured":[43],"format).":[44],"Recent":[45],"advances":[46],"field":[49],"of":[50,67,78,86,104,113,126,144,165],"Natural":[51],"Language":[52],"Processing":[53],"(NLP)":[54],"techniques":[55],"have":[56],"significant":[57],"advantage":[58],"over":[59],"common":[61],"time-consuming":[62],"laborious":[64],"manual":[65],"extraction":[66],"relevant":[69],"information":[70,125,133],"from":[71],"reports.":[73,139,155],"There":[74],"are":[75,179],"a":[76,110,148,171],"plethora":[77],"open-source":[79],"NLP":[80,118],"models":[81,119,169],"available,":[82],"but":[83],"limited":[84],"evidence":[85],"their":[87],"performance":[88,143],"on":[89],"real-world":[90,172],"healthcare":[91],"tasks,":[92],"specifically":[93],"for":[94],"paediatric":[95],"data.":[96],"In":[97],"this":[98],"paper,":[99],"we":[100],"describe":[101],"development":[103],"automated":[106],"pipeline":[107,146],"uses":[109],"hybrid":[111],"approach":[112],"combining":[114],"rules":[115],"pretrained":[117,168],"extract":[121],"gene":[122,131],"variants,":[123],"related":[124],"these":[127],"variants":[128],"any":[130],"panel":[132],"present":[134],"test":[138],"We":[140],"evaluated":[141],"against":[147],"manually-curated,":[149],"expert-annotated,":[150],"in-house":[151],"data":[152],"containing":[153],"372":[154],"Our":[156],"evaluation":[159],"highlights":[160],"advantages":[162],"limitations":[164],"using":[166],"existing":[167],"setting,":[173],"particular,":[176],"when":[177],"there":[178],"computation":[180],"resource":[182],"constraints":[183],"setting.":[187]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2025-11-06T06:51:31.235846","created_date":"2025-10-10T00:00:00"}
