{"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":null,"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":null,"license_id":null,"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://doi.org/10.1093/bib/bbaf534","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":true,"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 ,","School of Intelligent Connected Vehicle, Hubei University of Automotive Technology, 167 Checheng West Road, Shiyan 442002, China","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":"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":"School of Intelligent Connected Vehicle, Hubei University of Automotive Technology, 167 Checheng West Road, Shiyan 442002, China","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"]}]},{"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":false,"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":false,"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":11,"corresponding_author_ids":["https://openalex.org/A5107845542"],"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":0.6255,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.72771401,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"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":null,"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":null,"license_id":null,"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":null,"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":null,"license_id":null,"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"}],"funders":[{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"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":2025,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-14T00:00:00"}
