{"id":"https://openalex.org/W4402567773","doi":"https://doi.org/10.1093/bioinformatics/btae560","title":"Biomedical knowledge graph-optimized prompt generation for large language models","display_name":"Biomedical knowledge graph-optimized prompt generation for large language models","publication_year":2024,"publication_date":"2024-09-01","ids":{"openalex":"https://openalex.org/W4402567773","doi":"https://doi.org/10.1093/bioinformatics/btae560","pmid":"https://pubmed.ncbi.nlm.nih.gov/39288310"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae560","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae560","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/9/btae560/59459865/btae560.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"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/bioinformatics/article-pdf/40/9/btae560/59459865/btae560.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021696721","display_name":"Karthik Soman","orcid":"https://orcid.org/0000-0002-3490-9306"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Karthik Soman","raw_affiliation_strings":["Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco , San Francisco, CA 94158,"],"affiliations":[{"raw_affiliation_string":"Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco , San Francisco, CA 94158,","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070583038","display_name":"Peter W. Rose","orcid":"https://orcid.org/0000-0001-9981-9750"},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter W Rose","raw_affiliation_strings":["San Diego Supercomputer Center, University of California , San Diego, CA 92093,"],"affiliations":[{"raw_affiliation_string":"San Diego Supercomputer Center, University of California , San Diego, CA 92093,","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054399637","display_name":"John H. Morris","orcid":"https://orcid.org/0000-0003-0290-7979"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John H Morris","raw_affiliation_strings":["Department of Pharmaceutical Chemistry, School of Pharmacy, University of California , San Francisco, CA 94158,"],"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, School of Pharmacy, University of California , San Francisco, CA 94158,","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057174073","display_name":"Rabia E Akbas","orcid":"https://orcid.org/0009-0009-0217-9554"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rabia E Akbas","raw_affiliation_strings":["Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco , San Francisco, CA 94158,"],"affiliations":[{"raw_affiliation_string":"Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco , San Francisco, CA 94158,","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101687211","display_name":"Brett Smith","orcid":"https://orcid.org/0000-0002-2586-5014"},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brett Smith","raw_affiliation_strings":["Institute for Systems Biology , Seattle, WA 98109,"],"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology , Seattle, WA 98109,","institution_ids":["https://openalex.org/I3148997608"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093393064","display_name":"Braian Peetoom","orcid":null},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Braian Peetoom","raw_affiliation_strings":["Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco , San Francisco, CA 94158,"],"affiliations":[{"raw_affiliation_string":"Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco , San Francisco, CA 94158,","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093393065","display_name":"Catalina Villouta-Reyes","orcid":null},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Catalina Villouta-Reyes","raw_affiliation_strings":["Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco , San Francisco, CA 94158,"],"affiliations":[{"raw_affiliation_string":"Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco , San Francisco, CA 94158,","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041140760","display_name":"Gabriel Cerono","orcid":"https://orcid.org/0000-0002-9411-2526"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gabriel Cerono","raw_affiliation_strings":["Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco , San Francisco, CA 94158,"],"affiliations":[{"raw_affiliation_string":"Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco , San Francisco, CA 94158,","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031344696","display_name":"Yongmei Shi","orcid":null},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yongmei Shi","raw_affiliation_strings":["Bakar Computational Health Sciences Institute, University of California , San Francisco, CA 94158,"],"affiliations":[{"raw_affiliation_string":"Bakar Computational Health Sciences Institute, University of California , San Francisco, CA 94158,","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047214463","display_name":"Angela Rizk\u2010Jackson","orcid":"https://orcid.org/0000-0002-1732-8550"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Angela Rizk-Jackson","raw_affiliation_strings":["Bakar Computational Health Sciences Institute, University of California , San Francisco, CA 94158,"],"affiliations":[{"raw_affiliation_string":"Bakar Computational Health Sciences Institute, University of California , San Francisco, CA 94158,","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070192310","display_name":"Sharat Israni","orcid":null},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sharat Israni","raw_affiliation_strings":["Bakar Computational Health Sciences Institute, University of California , San Francisco, CA 94158,"],"affiliations":[{"raw_affiliation_string":"Bakar Computational Health Sciences Institute, University of California , San Francisco, CA 94158,","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025355562","display_name":"Charlotte Nelson","orcid":"https://orcid.org/0000-0002-3687-1102"},"institutions":[{"id":"https://openalex.org/I4210140900","display_name":"Fisher Bioservices (United States)","ror":"https://ror.org/041mbwk52","country_code":"US","type":"company","lineage":["https://openalex.org/I4210140900"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Charlotte A Nelson","raw_affiliation_strings":["Mate Bioservices, Inc. Swallowtail Ct. , Brisbane, CA 94005,"],"affiliations":[{"raw_affiliation_string":"Mate Bioservices, Inc. Swallowtail Ct. , Brisbane, CA 94005,","institution_ids":["https://openalex.org/I4210140900"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019206785","display_name":"Sui Huang","orcid":"https://orcid.org/0000-0002-3545-4665"},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sui Huang","raw_affiliation_strings":["Institute for Systems Biology , Seattle, WA 98109,"],"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology , Seattle, WA 98109,","institution_ids":["https://openalex.org/I3148997608"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014721690","display_name":"Sergio E. Baranzini","orcid":"https://orcid.org/0000-0003-0067-194X"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sergio E Baranzini","raw_affiliation_strings":["Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco , San Francisco, CA 94158,"],"affiliations":[{"raw_affiliation_string":"Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco , San Francisco, CA 94158,","institution_ids":["https://openalex.org/I180670191"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":14,"corresponding_author_ids":["https://openalex.org/A5021696721"],"corresponding_institution_ids":["https://openalex.org/I180670191"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":30.2689,"has_fulltext":true,"cited_by_count":90,"citation_normalized_percentile":{"value":0.99782587,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"40","issue":"9","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9983000159263611,"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/T10028","display_name":"Topic Modeling","score":0.9983000159263611,"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/T11636","display_name":"Artificial Intelligence in Healthcare and Education","score":0.979200005531311,"subfield":{"id":"https://openalex.org/subfields/2718","display_name":"Health Informatics"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9294000267982483,"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":0.7397638559341431},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.526139497756958},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.46573179960250854},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4452110528945923},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4425146281719208},{"id":"https://openalex.org/keywords/biomedicine","display_name":"Biomedicine","score":0.4288969337940216},{"id":"https://openalex.org/keywords/domain-knowledge","display_name":"Domain knowledge","score":0.41860708594322205},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4139569103717804},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3481314182281494},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.12451386451721191}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7397638559341431},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.526139497756958},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.46573179960250854},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4452110528945923},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4425146281719208},{"id":"https://openalex.org/C66782513","wikidata":"https://www.wikidata.org/wiki/Q864601","display_name":"Biomedicine","level":2,"score":0.4288969337940216},{"id":"https://openalex.org/C207685749","wikidata":"https://www.wikidata.org/wiki/Q2088941","display_name":"Domain knowledge","level":2,"score":0.41860708594322205},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4139569103717804},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3481314182281494},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.12451386451721191},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btae560","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae560","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/9/btae560/59459865/btae560.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39288310","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39288310","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt1nc6k3m1","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/1nc6k3m1","pdf_url":"https://escholarship.org/content/qt1nc6k3m1/qt1nc6k3m1.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol 40, iss 9","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11441322","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11441322","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11441322/pdf/btae560.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae560","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae560","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/9/btae560/59459865/btae560.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G1440349447","display_name":null,"funder_award_id":"NIH/NCATS","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2789588635","display_name":null,"funder_award_id":"NCATS","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4125610929","display_name":null,"funder_award_id":"OT2TR003450","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G5453956405","display_name":null,"funder_award_id":"2033569","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6932168162","display_name":null,"funder_award_id":"NSF_2033569","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332622","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4402567773.pdf","grobid_xml":"https://content.openalex.org/works/W4402567773.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W2117446654","https://openalex.org/W2187413858","https://openalex.org/W2537679995","https://openalex.org/W2558643140","https://openalex.org/W2911489562","https://openalex.org/W2949311246","https://openalex.org/W2961798429","https://openalex.org/W2990374909","https://openalex.org/W2998374885","https://openalex.org/W3027879771","https://openalex.org/W3046375318","https://openalex.org/W3118305256","https://openalex.org/W4200481829","https://openalex.org/W4221143046","https://openalex.org/W4223944906","https://openalex.org/W4224037213","https://openalex.org/W4229376653","https://openalex.org/W4281557260","https://openalex.org/W4281737056","https://openalex.org/W4297253404","https://openalex.org/W4307003748","https://openalex.org/W4309674289","https://openalex.org/W4309848029","https://openalex.org/W4319813194","https://openalex.org/W4378746334","https://openalex.org/W4392003803","https://openalex.org/W6777615688","https://openalex.org/W6781031682","https://openalex.org/W6788664974","https://openalex.org/W6809646742","https://openalex.org/W6810125524","https://openalex.org/W6810311434","https://openalex.org/W6838865847","https://openalex.org/W6845952779","https://openalex.org/W6847450257"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2000169967","https://openalex.org/W2112883198"],"abstract_inverted_index":{"SPOKE":[0],"KG":[1],"can":[2,8],"be":[3,10],"accessed":[4,11],"at":[5,20],"https://spoke.rbvi.ucsf.edu/neighborhood.html.":[6],"It":[7],"also":[9],"using":[12],"REST-API":[13],"(https://spoke.rbvi.ucsf.edu/swagger/).":[14],"KG-RAG":[15],"code":[16],"is":[17],"made":[18,30],"available":[19,31],"https://github.com/BaranziniLab/KG_RAG.":[21],"Biomedical":[22],"benchmark":[23],"datasets":[24],"used":[25],"in":[26,36],"this":[27],"study":[28],"are":[29],"to":[32],"the":[33,37],"research":[34],"community":[35],"same":[38],"GitHub":[39],"repository.":[40]},"counts_by_year":[{"year":2026,"cited_by_count":20},{"year":2025,"cited_by_count":62},{"year":2024,"cited_by_count":8}],"updated_date":"2026-04-17T18:11:37.981687","created_date":"2025-10-10T00:00:00"}
