{"id":"https://openalex.org/W4415147143","doi":"https://doi.org/10.1093/bib/bbaf534","title":"Microllm: a structured information extraction tool using large language models and named entity recognition in microbiology","display_name":"Microllm: a structured information extraction tool using large language models and named entity recognition in microbiology","publication_year":2025,"publication_date":"2025-08-31","ids":{"openalex":"https://openalex.org/W4415147143","doi":"https://doi.org/10.1093/bib/bbaf534","pmid":"https://pubmed.ncbi.nlm.nih.gov/41081727"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf534","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf534","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf534/64659548/bbaf534.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf534/64659548/bbaf534.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5107845542","display_name":"Jing Lu","orcid":"https://orcid.org/0009-0007-7144-1398"},"institutions":[{"id":"https://openalex.org/I37987034","display_name":"Guangzhou University","ror":"https://ror.org/05ar8rn06","country_code":"CN","type":"education","lineage":["https://openalex.org/I37987034"]},{"id":"https://openalex.org/I4210159575","display_name":"Huashan Hospital","ror":"https://ror.org/05201qm87","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jing Lu","raw_affiliation_strings":["Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University , 12 Middle Wulumuqi Road, Shanghai 200040 ,","Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University , 2 Nanjiang Road, Guangzhou 511458 ,","Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University, 12 Middle Wulumuqi Road, Shanghai 200040, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University , 12 Middle Wulumuqi Road, Shanghai 200040 ,","institution_ids":["https://openalex.org/I4210159575"]},{"raw_affiliation_string":"Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University , 2 Nanjiang Road, Guangzhou 511458 ,","institution_ids":["https://openalex.org/I37987034"]},{"raw_affiliation_string":"Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University, 12 Middle Wulumuqi Road, Shanghai 200040, China","institution_ids":["https://openalex.org/I4210159575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102714697","display_name":"Fei Li","orcid":"https://orcid.org/0000-0003-3685-7164"},"institutions":[{"id":"https://openalex.org/I37987034","display_name":"Guangzhou University","ror":"https://ror.org/05ar8rn06","country_code":"CN","type":"education","lineage":["https://openalex.org/I37987034"]},{"id":"https://openalex.org/I4210126203","display_name":"Hubei University of Automotive Technology","ror":"https://ror.org/039m95m06","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210126203"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fei Li","raw_affiliation_strings":["Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University , 2 Nanjiang Road, Guangzhou 511458 ,","School of Intelligent Connected Vehicle, Hubei University of Automotive Technology , 167 Checheng West Road, Shiyan 442002 ,","Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, 2 Nanjiang Road, Guangzhou 511458, China","School of Intelligent Connected Vehicle, Hubei University of Automotive Technology, 167 Checheng West Road, Shiyan 442002, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University , 2 Nanjiang Road, Guangzhou 511458 ,","institution_ids":["https://openalex.org/I37987034"]},{"raw_affiliation_string":"School of Intelligent Connected Vehicle, Hubei University of Automotive Technology , 167 Checheng West Road, Shiyan 442002 ,","institution_ids":["https://openalex.org/I4210126203"]},{"raw_affiliation_string":"Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, 2 Nanjiang Road, Guangzhou 511458, China","institution_ids":["https://openalex.org/I37987034"]},{"raw_affiliation_string":"School of Intelligent Connected Vehicle, Hubei University of Automotive Technology, 167 Checheng West Road, Shiyan 442002, China","institution_ids":["https://openalex.org/I4210126203"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023910969","display_name":"Lei Feng","orcid":"https://orcid.org/0000-0001-6053-8417"},"institutions":[{"id":"https://openalex.org/I37987034","display_name":"Guangzhou University","ror":"https://ror.org/05ar8rn06","country_code":"CN","type":"education","lineage":["https://openalex.org/I37987034"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lei Feng","raw_affiliation_strings":["Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University , 2 Nanjiang Road, Guangzhou 511458 ,","Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, 2 Nanjiang Road, Guangzhou 511458, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University , 2 Nanjiang Road, Guangzhou 511458 ,","institution_ids":["https://openalex.org/I37987034"]},{"raw_affiliation_string":"Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, 2 Nanjiang Road, Guangzhou 511458, China","institution_ids":["https://openalex.org/I37987034"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062035699","display_name":"Zhengyu Yu","orcid":"https://orcid.org/0000-0002-8888-4570"},"institutions":[{"id":"https://openalex.org/I37987034","display_name":"Guangzhou University","ror":"https://ror.org/05ar8rn06","country_code":"CN","type":"education","lineage":["https://openalex.org/I37987034"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhengyu Yu","raw_affiliation_strings":["Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University , 2 Nanjiang Road, Guangzhou 511458 ,","Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, 2 Nanjiang Road, Guangzhou 511458, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University , 2 Nanjiang Road, Guangzhou 511458 ,","institution_ids":["https://openalex.org/I37987034"]},{"raw_affiliation_string":"Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, 2 Nanjiang Road, Guangzhou 511458, China","institution_ids":["https://openalex.org/I37987034"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101482323","display_name":"Jianyu Lu","orcid":"https://orcid.org/0000-0003-2929-0024"},"institutions":[{"id":"https://openalex.org/I37987034","display_name":"Guangzhou University","ror":"https://ror.org/05ar8rn06","country_code":"CN","type":"education","lineage":["https://openalex.org/I37987034"]},{"id":"https://openalex.org/I4210159575","display_name":"Huashan Hospital","ror":"https://ror.org/05201qm87","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianyu Lu","raw_affiliation_strings":["Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University , 12 Middle Wulumuqi Road, Shanghai 200040 ,","Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University , 2 Nanjiang Road, Guangzhou 511458 ,","Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, 2 Nanjiang Road, Guangzhou 511458, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University , 12 Middle Wulumuqi Road, Shanghai 200040 ,","institution_ids":["https://openalex.org/I4210159575"]},{"raw_affiliation_string":"Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University , 2 Nanjiang Road, Guangzhou 511458 ,","institution_ids":["https://openalex.org/I37987034"]},{"raw_affiliation_string":"Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, 2 Nanjiang Road, Guangzhou 511458, China","institution_ids":["https://openalex.org/I37987034"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109693096","display_name":"Mingyuan Qin","orcid":"https://orcid.org/0009-0006-8260-7966"},"institutions":[{"id":"https://openalex.org/I37987034","display_name":"Guangzhou University","ror":"https://ror.org/05ar8rn06","country_code":"CN","type":"education","lineage":["https://openalex.org/I37987034"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mingyuan Qin","raw_affiliation_strings":["Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University , 2 Nanjiang Road, Guangzhou 511458 ,","Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, 2 Nanjiang Road, Guangzhou 511458, China"],"raw_orcid":"https://orcid.org/0009-0006-8260-7966","affiliations":[{"raw_affiliation_string":"Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University , 2 Nanjiang Road, Guangzhou 511458 ,","institution_ids":["https://openalex.org/I37987034"]},{"raw_affiliation_string":"Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, 2 Nanjiang Road, Guangzhou 511458, China","institution_ids":["https://openalex.org/I37987034"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006736352","display_name":"Shengnan She","orcid":null},"institutions":[{"id":"https://openalex.org/I37987034","display_name":"Guangzhou University","ror":"https://ror.org/05ar8rn06","country_code":"CN","type":"education","lineage":["https://openalex.org/I37987034"]},{"id":"https://openalex.org/I4210159575","display_name":"Huashan Hospital","ror":"https://ror.org/05201qm87","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shengnan She","raw_affiliation_strings":["Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University , 12 Middle Wulumuqi Road, Shanghai 200040 ,","Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University , 2 Nanjiang Road, Guangzhou 511458 ,","Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University, 12 Middle Wulumuqi Road, Shanghai 200040, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University , 12 Middle Wulumuqi Road, Shanghai 200040 ,","institution_ids":["https://openalex.org/I4210159575"]},{"raw_affiliation_string":"Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University , 2 Nanjiang Road, Guangzhou 511458 ,","institution_ids":["https://openalex.org/I37987034"]},{"raw_affiliation_string":"Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University, 12 Middle Wulumuqi Road, Shanghai 200040, China","institution_ids":["https://openalex.org/I4210159575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087099602","display_name":"Haoqiang Jiang","orcid":null},"institutions":[{"id":"https://openalex.org/I37987034","display_name":"Guangzhou University","ror":"https://ror.org/05ar8rn06","country_code":"CN","type":"education","lineage":["https://openalex.org/I37987034"]},{"id":"https://openalex.org/I4210159575","display_name":"Huashan Hospital","ror":"https://ror.org/05201qm87","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haoqiang Jiang","raw_affiliation_strings":["Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University , 12 Middle Wulumuqi Road, Shanghai 200040 ,","Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University , 2 Nanjiang Road, Guangzhou 511458 ,","Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University, 12 Middle Wulumuqi Road, Shanghai 200040, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University , 12 Middle Wulumuqi Road, Shanghai 200040 ,","institution_ids":["https://openalex.org/I4210159575"]},{"raw_affiliation_string":"Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University , 2 Nanjiang Road, Guangzhou 511458 ,","institution_ids":["https://openalex.org/I37987034"]},{"raw_affiliation_string":"Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University, 12 Middle Wulumuqi Road, Shanghai 200040, China","institution_ids":["https://openalex.org/I4210159575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008126365","display_name":"Zhiming Guo","orcid":"https://orcid.org/0000-0002-8351-8571"},"institutions":[{"id":"https://openalex.org/I37987034","display_name":"Guangzhou University","ror":"https://ror.org/05ar8rn06","country_code":"CN","type":"education","lineage":["https://openalex.org/I37987034"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhiming Guo","raw_affiliation_strings":["Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University , 2 Nanjiang Road, Guangzhou 511458 ,","Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, 2 Nanjiang Road, Guangzhou 511458, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University , 2 Nanjiang Road, Guangzhou 511458 ,","institution_ids":["https://openalex.org/I37987034"]},{"raw_affiliation_string":"Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, 2 Nanjiang Road, Guangzhou 511458, China","institution_ids":["https://openalex.org/I37987034"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048340322","display_name":"Jingjing Xia","orcid":"https://orcid.org/0000-0002-2892-4032"},"institutions":[{"id":"https://openalex.org/I37987034","display_name":"Guangzhou University","ror":"https://ror.org/05ar8rn06","country_code":"CN","type":"education","lineage":["https://openalex.org/I37987034"]},{"id":"https://openalex.org/I4210159575","display_name":"Huashan Hospital","ror":"https://ror.org/05201qm87","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159575"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jingjing Xia","raw_affiliation_strings":["Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University , 12 Middle Wulumuqi Road, Shanghai 200040 ,","Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University , 2 Nanjiang Road, Guangzhou 511458 ,","Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University, 12 Middle Wulumuqi Road, Shanghai 200040, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University , 12 Middle Wulumuqi Road, Shanghai 200040 ,","institution_ids":["https://openalex.org/I4210159575"]},{"raw_affiliation_string":"Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University , 2 Nanjiang Road, Guangzhou 511458 ,","institution_ids":["https://openalex.org/I37987034"]},{"raw_affiliation_string":"Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University, 12 Middle Wulumuqi Road, Shanghai 200040, China","institution_ids":["https://openalex.org/I4210159575"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040394206","display_name":"Lianyi Han","orcid":"https://orcid.org/0000-0002-6364-7843"},"institutions":[{"id":"https://openalex.org/I4210159575","display_name":"Huashan Hospital","ror":"https://ror.org/05201qm87","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159575"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Lianyi Han","raw_affiliation_strings":["Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University , 12 Middle Wulumuqi Road, Shanghai 200040 ,","Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University, 12 Middle Wulumuqi Road, Shanghai 200040, China"],"raw_orcid":"https://orcid.org/0000-0002-6364-7843","affiliations":[{"raw_affiliation_string":"Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University , 12 Middle Wulumuqi Road, Shanghai 200040 ,","institution_ids":["https://openalex.org/I4210159575"]},{"raw_affiliation_string":"Department of Dermatology, Huashan Hospital, School of Life Sciences, Fudan University, 12 Middle Wulumuqi Road, Shanghai 200040, China","institution_ids":["https://openalex.org/I4210159575"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5040394206","https://openalex.org/A5048340322"],"corresponding_institution_ids":["https://openalex.org/I37987034","https://openalex.org/I4210159575"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.8148,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.73276939,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"26","issue":"5","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":0.9846000075340271,"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":0.9846000075340271,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9502999782562256,"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":0.9463000297546387,"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/named-entity-recognition","display_name":"Named-entity recognition","score":0.7071999907493591},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.5914999842643738},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.43070000410079956},{"id":"https://openalex.org/keywords/natural-language","display_name":"Natural language","score":0.4115000069141388},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.3662000000476837},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.3452000021934509},{"id":"https://openalex.org/keywords/taxonomy","display_name":"Taxonomy (biology)","score":0.3328000009059906},{"id":"https://openalex.org/keywords/json","display_name":"JSON","score":0.3192000091075897}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7820000052452087},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.7071999907493591},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.5914999842643738},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.43700000643730164},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.43070000410079956},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41269999742507935},{"id":"https://openalex.org/C195324797","wikidata":"https://www.wikidata.org/wiki/Q33742","display_name":"Natural language","level":2,"score":0.4115000069141388},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3725999891757965},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.3662000000476837},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.3452000021934509},{"id":"https://openalex.org/C58642233","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Taxonomy (biology)","level":2,"score":0.3328000009059906},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.31929999589920044},{"id":"https://openalex.org/C2780416260","wikidata":"https://www.wikidata.org/wiki/Q2063","display_name":"JSON","level":2,"score":0.3192000091075897},{"id":"https://openalex.org/C44291984","wikidata":"https://www.wikidata.org/wiki/Q1074173","display_name":"Question answering","level":2,"score":0.3181000053882599},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.30720001459121704},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.29409998655319214},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.29179999232292175},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.2782000005245209},{"id":"https://openalex.org/C155092808","wikidata":"https://www.wikidata.org/wiki/Q182557","display_name":"Computational linguistics","level":2,"score":0.2667999863624573},{"id":"https://openalex.org/C2779439875","wikidata":"https://www.wikidata.org/wiki/Q1078276","display_name":"Natural language understanding","level":3,"score":0.266400009393692},{"id":"https://openalex.org/C14919245","wikidata":"https://www.wikidata.org/wiki/Q1976109","display_name":"Language technology","level":4,"score":0.2655999958515167},{"id":"https://openalex.org/C21338462","wikidata":"https://www.wikidata.org/wiki/Q1662581","display_name":"Information model","level":2,"score":0.26080000400543213},{"id":"https://openalex.org/C2777466982","wikidata":"https://www.wikidata.org/wiki/Q5227287","display_name":"Data extraction","level":3,"score":0.25760000944137573}],"mesh":[{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008829","descriptor_name":"Microbiology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008829","descriptor_name":"Microbiology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008829","descriptor_name":"Microbiology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008829","descriptor_name":"Microbiology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf534","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf534","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf534/64659548/bbaf534.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41081727","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41081727","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:11324632","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12516959","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12516959/pdf/bbaf534.pdf","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf534","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf534","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf534/64659548/bbaf534.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G157653555","display_name":null,"funder_award_id":"2025YFC3508403","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G6012653959","display_name":null,"funder_award_id":"shslczdzk01002","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G6099485535","display_name":null,"funder_award_id":"2023ZZ02018","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4415147143.pdf","grobid_xml":"https://content.openalex.org/works/W4415147143.grobid-xml"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W1974754328","https://openalex.org/W2024471867","https://openalex.org/W2037833069","https://openalex.org/W2042411773","https://openalex.org/W2065207967","https://openalex.org/W2111358533","https://openalex.org/W2129767020","https://openalex.org/W2149369282","https://openalex.org/W2152682668","https://openalex.org/W2154142897","https://openalex.org/W2156546195","https://openalex.org/W2169099542","https://openalex.org/W2346452181","https://openalex.org/W2520355709","https://openalex.org/W2560737530","https://openalex.org/W2562274706","https://openalex.org/W2739769226","https://openalex.org/W2754579667","https://openalex.org/W2900678973","https://openalex.org/W2911489562","https://openalex.org/W2954325397","https://openalex.org/W2970771982","https://openalex.org/W2982940135","https://openalex.org/W2983315135","https://openalex.org/W2990074895","https://openalex.org/W2992412259","https://openalex.org/W3012760258","https://openalex.org/W3021868763","https://openalex.org/W3106931025","https://openalex.org/W3167018133","https://openalex.org/W3168867926","https://openalex.org/W3193938401","https://openalex.org/W3195487229","https://openalex.org/W3196182470","https://openalex.org/W3201170423","https://openalex.org/W3205270560","https://openalex.org/W4206826315","https://openalex.org/W4212796599","https://openalex.org/W4233573641","https://openalex.org/W4287265459","https://openalex.org/W4385245566","https://openalex.org/W4388909657","https://openalex.org/W4389725563","https://openalex.org/W4391294068","https://openalex.org/W4391836235","https://openalex.org/W4393094733","https://openalex.org/W4393118716","https://openalex.org/W4393399274","https://openalex.org/W4399837985","https://openalex.org/W4400047099","https://openalex.org/W4403022023","https://openalex.org/W4404534210"],"related_works":[],"abstract_inverted_index":{"Understanding":[0],"the":[1,26,32,41,81,96,104,134],"characteristics":[2],"of":[3,28,37,43,83,106,136,143],"individual":[4],"microorganisms":[5],"is":[6,23],"crucial":[7],"for":[8,127],"deciphering":[9],"microbial":[10,21,84,144],"community":[11],"structures":[12],"and":[13,34,40,72,100,108,118,139,146],"enabling":[14],"effective":[15],"system":[16],"manipulation.":[17],"Large-scale":[18],"analysis":[19],"in":[20,50],"bioinformatics":[22],"hindered":[24],"by":[25],"scarcity":[27],"high-quality":[29],"annotated":[30],"datasets,":[31],"labor-intensive,":[33],"time-consuming":[35],"process":[36],"manual":[38],"review,":[39],"limitations":[42],"current":[44],"natural":[45],"language":[46,69],"processing":[47],"(NLP)":[48],"technologies":[49],"effectively":[51],"capturing":[52],"comprehensive":[53],"information.":[54,86,120],"To":[55],"tackle":[56],"these":[57],"challenges,":[58],"we":[59],"developed":[60],"a":[61,124],"new":[62],"tool":[63],"MicroLLM,":[64],"which":[65],"integrates":[66],"fine-tuned":[67],"large":[68],"models":[70],"(LLMs)":[71],"bidirectional":[73],"encoder":[74],"representations":[75],"from":[76],"Transformers":[77],"(BERT)":[78],"to":[79],"enhance":[80],"extraction":[82],"phenotypic":[85],"MicroLLM":[87],"converts":[88],"unstructured":[89],"text":[90],"into":[91],"structured":[92,130],"JSON":[93],"objects,":[94],"making":[95],"data":[97],"more":[98],"accessible":[99],"organized.":[101],"By":[102],"leveraging":[103],"strengths":[105],"LLMs":[107],"named":[109],"entity":[110],"recognition":[111],"(NER),":[112],"it":[113],"efficiently":[114],"extracts":[115],"complex,":[116],"multirelational,":[117],"multi-entity":[119],"This":[121],"method":[122],"establishes":[123],"strong":[125],"foundation":[126],"constructing":[128],"large-scale":[129],"knowledge":[131],"bases,":[132],"streamlining":[133],"creation":[135],"scientific":[137],"knowledge,":[138],"advancing":[140],"our":[141],"understanding":[142],"ecosystems":[145],"their":[147],"impacts":[148],"on":[149],"health.":[150]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-14T00:00:00"}
