{"id":"https://openalex.org/W4416196043","doi":"https://doi.org/10.1186/s13040-025-00502-4","title":"From prompt engineering to agent engineering: expanding the AI toolbox with autonomous agentic AI collaborators for biomedical discovery","display_name":"From prompt engineering to agent engineering: expanding the AI toolbox with autonomous agentic AI collaborators for biomedical discovery","publication_year":2025,"publication_date":"2025-11-13","ids":{"openalex":"https://openalex.org/W4416196043","doi":"https://doi.org/10.1186/s13040-025-00502-4","pmid":"https://pubmed.ncbi.nlm.nih.gov/41233899"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-025-00502-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00502-4","pdf_url":null,"source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s13040-025-00502-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032971510","display_name":"Jason H. Moore","orcid":"https://orcid.org/0000-0002-5015-1099"},"institutions":[{"id":"https://openalex.org/I1282927834","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1282927834"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jason H. Moore","raw_affiliation_strings":["Department of Computational Biomedicine, Cedars-Sinai Health Sciences University, Los Angeles, CA, USA. Jason.Moore@csmc.edu","Department of Computational Biomedicine, Cedars-Sinai Health Sciences University, Los Angeles, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational Biomedicine, Cedars-Sinai Health Sciences University, Los Angeles, CA, USA. Jason.Moore@csmc.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Computational Biomedicine, Cedars-Sinai Health Sciences University, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I1282927834"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086753691","display_name":"Nicholas P. Tatonetti","orcid":"https://orcid.org/0000-0002-2700-2597"},"institutions":[{"id":"https://openalex.org/I1282927834","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1282927834"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicholas P. Tatonetti","raw_affiliation_strings":["Department of Computational Biomedicine, Cedars-Sinai Health Sciences University, Los Angeles, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational Biomedicine, Cedars-Sinai Health Sciences University, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I1282927834"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5032971510"],"corresponding_institution_ids":["https://openalex.org/I1282927834"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.6995,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.9276981,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"18","issue":"1","first_page":"78","last_page":"78"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10456","display_name":"Multi-Agent Systems and Negotiation","score":0.2709999978542328,"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"}},"topics":[{"id":"https://openalex.org/T10456","display_name":"Multi-Agent Systems and Negotiation","score":0.2709999978542328,"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/T10906","display_name":"AI-based Problem Solving and Planning","score":0.09510000050067902,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.03830000013113022,"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/toolbox","display_name":"Toolbox","score":0.8705000281333923},{"id":"https://openalex.org/keywords/scientific-discovery","display_name":"Scientific discovery","score":0.2897000014781952},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.2329999953508377}],"concepts":[{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.8705000281333923},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.703000009059906},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4984000027179718},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36980000138282776},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.310699999332428},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.30630001425743103},{"id":"https://openalex.org/C2984917352","wikidata":"https://www.wikidata.org/wiki/Q12772819","display_name":"Scientific discovery","level":2,"score":0.2897000014781952},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2379000037908554},{"id":"https://openalex.org/C56739046","wikidata":"https://www.wikidata.org/wiki/Q192060","display_name":"Knowledge management","level":1,"score":0.23309999704360962},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.2329999953508377}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13040-025-00502-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00502-4","pdf_url":null,"source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:41233899","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41233899","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":"BioData mining","raw_type":null},{"id":"pmh:oai:doaj.org/article:af4f04f8985d4cce94d406d74f92cec3","is_oa":true,"landing_page_url":"https://doaj.org/article/af4f04f8985d4cce94d406d74f92cec3","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Mining, Vol 18, Iss 1, Pp 1-3 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11421942","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12613637","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13040-025-00502-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00502-4","pdf_url":null,"source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-11-13T00:00:00"}
