{"id":"https://openalex.org/W7163654354","doi":"https://doi.org/10.1093/bioinformatics/btag355","title":"BioMedGraphica: an all-in-one platform for joint textual biomedical prior knowledge and numeric graph generation","display_name":"BioMedGraphica: an all-in-one platform for joint textual biomedical prior knowledge and numeric graph generation","publication_year":2026,"publication_date":"2026-06-01","ids":{"openalex":"https://openalex.org/W7163654354","doi":"https://doi.org/10.1093/bioinformatics/btag355","pmid":"https://pubmed.ncbi.nlm.nih.gov/42246943"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag355","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag355","pdf_url":null,"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://doi.org/10.1093/bioinformatics/btag355","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5137978560","display_name":"Heming Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210163477","display_name":"Institute for Medical Informatics and Biostatistics","ror":"https://ror.org/04e79zk25","country_code":"CH","type":"facility","lineage":["https://openalex.org/I4210163477"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Heming Zhang","raw_affiliation_strings":["The Center for Translational Bioinformatics (CTBI), Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine , St. Louis, MO 63110,"],"raw_orcid":"https://orcid.org/0000-0002-2025-9090","affiliations":[{"raw_affiliation_string":"The Center for Translational Bioinformatics (CTBI), Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I4210163477"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109069227","display_name":"S. Liang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210163477","display_name":"Institute for Medical Informatics and Biostatistics","ror":"https://ror.org/04e79zk25","country_code":"CH","type":"facility","lineage":["https://openalex.org/I4210163477"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Shunning Liang","raw_affiliation_strings":["The Center for Translational Bioinformatics (CTBI), Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine , St. Louis, MO 63110,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Center for Translational Bioinformatics (CTBI), Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I4210163477"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137996727","display_name":"Tim Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210163477","display_name":"Institute for Medical Informatics and Biostatistics","ror":"https://ror.org/04e79zk25","country_code":"CH","type":"facility","lineage":["https://openalex.org/I4210163477"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Tim Xu","raw_affiliation_strings":["The Center for Translational Bioinformatics (CTBI), Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine , St. Louis, MO 63110,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Center for Translational Bioinformatics (CTBI), Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I4210163477"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100371213","display_name":"Weiwei Li","orcid":"https://orcid.org/0000-0002-7329-4236"},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wenyu Li","raw_affiliation_strings":["Department of Computer Science and Engineering, Washington University in St. Louis , St. Louis, MO 63130,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Washington University in St. Louis , St. Louis, MO 63130,","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137976745","display_name":"Di Huang","orcid":null},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]},{"id":"https://openalex.org/I4210163477","display_name":"Institute for Medical Informatics and Biostatistics","ror":"https://ror.org/04e79zk25","country_code":"CH","type":"facility","lineage":["https://openalex.org/I4210163477"]}],"countries":["CH","US"],"is_corresponding":false,"raw_author_name":"Di Huang","raw_affiliation_strings":["Department of Computer Science and Engineering, Washington University in St. Louis , St. Louis, MO 63130,","The Center for Translational Bioinformatics (CTBI), Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine , St. Louis, MO 63110,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Washington University in St. Louis , St. Louis, MO 63130,","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"The Center for Translational Bioinformatics (CTBI), Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I4210163477"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108047157","display_name":"Yuhan Dong","orcid":"https://orcid.org/0000-0001-5275-1787"},"institutions":[{"id":"https://openalex.org/I4210163477","display_name":"Institute for Medical Informatics and Biostatistics","ror":"https://ror.org/04e79zk25","country_code":"CH","type":"facility","lineage":["https://openalex.org/I4210163477"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Yuhan Dong","raw_affiliation_strings":["The Center for Translational Bioinformatics (CTBI), Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine , St. Louis, MO 63110,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Center for Translational Bioinformatics (CTBI), Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I4210163477"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086997032","display_name":"Guangfu Li","orcid":"https://orcid.org/0000-0002-9817-568X"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]},{"id":"https://openalex.org/I75929689","display_name":"UConn Health","ror":"https://ror.org/02kzs4y22","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I75929689"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guangfu Li","raw_affiliation_strings":["Department of Surgery, School of Medicine, University of Connecticut , Farmington, CT 06032,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Surgery, School of Medicine, University of Connecticut , Farmington, CT 06032,","institution_ids":["https://openalex.org/I140172145","https://openalex.org/I75929689"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137992087","display_name":"J Philip Miller","orcid":null},"institutions":[{"id":"https://openalex.org/I4210163477","display_name":"Institute for Medical Informatics and Biostatistics","ror":"https://ror.org/04e79zk25","country_code":"CH","type":"facility","lineage":["https://openalex.org/I4210163477"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Philip Miller","raw_affiliation_strings":["The Center for Translational Bioinformatics (CTBI), Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine , St. Louis, MO 63110,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Center for Translational Bioinformatics (CTBI), Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I4210163477"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137990795","display_name":"S Peter Goedegebuure","orcid":null},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter Goedegebuure","raw_affiliation_strings":["Department of Surgery, Washington University School of Medicine , St. Louis, MO 63110,","Siteman Cancer Center, Washington University School of Medicine , St. Louis, MO 63110,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Surgery, Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Siteman Cancer Center, Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081495214","display_name":"Marco Sardiello","orcid":"https://orcid.org/0000-0001-6484-0250"},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marco Sardiello","raw_affiliation_strings":["Department of Pediatrics, Washington University School of Medicine , St. Louis, MO 63110,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatrics, Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126215145","display_name":"Jonathan Cooper","orcid":null},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan Cooper","raw_affiliation_strings":["Department of Pediatrics, Washington University School of Medicine , St. Louis, MO 63110,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatrics, Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113168452","display_name":"William Buchser","orcid":null},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William Buchser","raw_affiliation_strings":["Department of Genetics, Washington University School of Medicine , St. Louis, MO 63110,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112081854","display_name":"PATRICIA DICKSON","orcid":null},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Patricia Dickson","raw_affiliation_strings":["Department of Pediatrics, Washington University School of Medicine , St. Louis, MO 63110,"],"raw_orcid":"https://orcid.org/0000-0003-3467-8488","affiliations":[{"raw_affiliation_string":"Department of Pediatrics, Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137985583","display_name":"Ryan C Fields","orcid":null},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ryan C Fields","raw_affiliation_strings":["Department of Surgery, Washington University School of Medicine , St. Louis, MO 63110,","Siteman Cancer Center, Washington University School of Medicine , St. Louis, MO 63110,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Surgery, Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Siteman Cancer Center, Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137949168","display_name":"Carlos Cruchaga","orcid":null},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carlos Cruchaga","raw_affiliation_strings":["Department of Psychiatry, Washington University School of Medicine , St. Louis, MO 63110,","NeuroGenomics and Informatics, Washington University School of Medicine , St. Louis, MO 63110,"],"raw_orcid":"https://orcid.org/0000-0002-5261-689X","affiliations":[{"raw_affiliation_string":"Department of Psychiatry, Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"NeuroGenomics and Informatics, Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137964263","display_name":"Yixin Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yixin Chen","raw_affiliation_strings":["Department of Computer Science and Engineering, Washington University in St. Louis , St. Louis, MO 63130,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Washington University in St. Louis , St. Louis, MO 63130,","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032738541","display_name":"M A Province","orcid":null},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Province","raw_affiliation_strings":["Division of Statistical Genomics, Washington University School of Medicine , St. Louis, MO 63110,","NeuroGenomics and Informatics, Washington University School of Medicine , St. Louis, MO 63110,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Statistical Genomics, Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"NeuroGenomics and Informatics, Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071367198","display_name":"Philip Payne","orcid":"https://orcid.org/0000-0002-9532-2998"},"institutions":[{"id":"https://openalex.org/I4210163477","display_name":"Institute for Medical Informatics and Biostatistics","ror":"https://ror.org/04e79zk25","country_code":"CH","type":"facility","lineage":["https://openalex.org/I4210163477"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Philip Payne","raw_affiliation_strings":["The Center for Translational Bioinformatics (CTBI), Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine , St. Louis, MO 63110,"],"raw_orcid":"https://orcid.org/0000-0002-9532-2998","affiliations":[{"raw_affiliation_string":"The Center for Translational Bioinformatics (CTBI), Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I4210163477"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5137949243","display_name":"Fuhai Li","orcid":null},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]},{"id":"https://openalex.org/I4210163477","display_name":"Institute for Medical Informatics and Biostatistics","ror":"https://ror.org/04e79zk25","country_code":"CH","type":"facility","lineage":["https://openalex.org/I4210163477"]}],"countries":["CH","US"],"is_corresponding":true,"raw_author_name":"Fuhai Li","raw_affiliation_strings":["Department of Computer Science and Engineering, Washington University in St. Louis , St. Louis, MO 63130,","Department of Pediatrics, Washington University School of Medicine , St. Louis, MO 63110,","The Center for Translational Bioinformatics (CTBI), Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine , St. Louis, MO 63110,"],"raw_orcid":"https://orcid.org/0000-0002-3773-146X","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Washington University in St. Louis , St. Louis, MO 63130,","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Department of Pediatrics, Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"The Center for Translational Bioinformatics (CTBI), Institute for Informatics, Data Science and Biostatistics (I2DB), Washington University School of Medicine , St. Louis, MO 63110,","institution_ids":["https://openalex.org/I4210163477"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5137949243"],"corresponding_institution_ids":["https://openalex.org/I204465549","https://openalex.org/I4210163477"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.67727504,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.7479000091552734,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.7479000091552734,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.13410000503063202,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.03929999843239784,"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/leverage","display_name":"Leverage (statistics)","score":0.6137999892234802},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5465999841690063},{"id":"https://openalex.org/keywords/knowledge-graph","display_name":"Knowledge graph","score":0.5034000277519226},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.46389999985694885},{"id":"https://openalex.org/keywords/bridging","display_name":"Bridging (networking)","score":0.44690001010894775},{"id":"https://openalex.org/keywords/data-type","display_name":"Data type","score":0.41999998688697815},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.3837999999523163},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.3763999938964844},{"id":"https://openalex.org/keywords/knowledge-extraction","display_name":"Knowledge extraction","score":0.3582000136375427}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8202999830245972},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.6137999892234802},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5465999841690063},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.5034000277519226},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.46389999985694885},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.45570001006126404},{"id":"https://openalex.org/C174348530","wikidata":"https://www.wikidata.org/wiki/Q188635","display_name":"Bridging (networking)","level":2,"score":0.44690001010894775},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.41999998688697815},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3882000148296356},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.3837999999523163},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.3763999938964844},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.3582000136375427},{"id":"https://openalex.org/C176225458","wikidata":"https://www.wikidata.org/wiki/Q595971","display_name":"Graph database","level":3,"score":0.35690000653266907},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.3450999855995178},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.3370000123977661},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3294000029563904},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.3025999963283539},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.29319998621940613},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.29179999232292175},{"id":"https://openalex.org/C191015642","wikidata":"https://www.wikidata.org/wiki/Q1132459","display_name":"Fragmentation (computing)","level":2,"score":0.2800999879837036},{"id":"https://openalex.org/C16311509","wikidata":"https://www.wikidata.org/wiki/Q4148050","display_name":"Dependency graph","level":3,"score":0.266400009393692},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2662999927997589},{"id":"https://openalex.org/C75684735","wikidata":"https://www.wikidata.org/wiki/Q858810","display_name":"Big data","level":2,"score":0.26420000195503235},{"id":"https://openalex.org/C5274069","wikidata":"https://www.wikidata.org/wiki/Q2285707","display_name":"Categorical variable","level":2,"score":0.2612000107765198},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.25459998846054077},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.2500999867916107}],"mesh":[{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","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":"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":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btag355","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag355","pdf_url":null,"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:42246943","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42246943","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:digitalcommons.wustl.edu:oa_4-7837","is_oa":true,"landing_page_url":"https://digitalcommons.wustl.edu/oa_4/6849","pdf_url":null,"source":{"id":"https://openalex.org/S4306400764","display_name":"Digital Commons@Becker (Washington University School of Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I204465549","host_organization_name":"Washington University in St. Louis","host_organization_lineage":["https://openalex.org/I204465549"],"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":"2020-Current year OA Pubs","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:13281933","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13281933/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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/btag355","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag355","pdf_url":null,"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":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4199518859386444}],"awards":[{"id":"https://openalex.org/G5820215617","display_name":null,"funder_award_id":"1U19AI181984","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G8661732570","display_name":null,"funder_award_id":"1RM1NS132962-01","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"},{"id":"https://openalex.org/G8853103523","display_name":null,"funder_award_id":"1R01LM013902-01A1","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"}],"funders":[{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320337359","display_name":"National Institute of Neurological Disorders and Stroke","ror":"https://ror.org/01s5ya894"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":80,"referenced_works":["https://openalex.org/W1988925586","https://openalex.org/W1995576455","https://openalex.org/W2033377040","https://openalex.org/W2034285706","https://openalex.org/W2040676413","https://openalex.org/W2041214225","https://openalex.org/W2043398720","https://openalex.org/W2053039860","https://openalex.org/W2062584010","https://openalex.org/W2096173332","https://openalex.org/W2108068107","https://openalex.org/W2127553917","https://openalex.org/W2142529576","https://openalex.org/W2142572836","https://openalex.org/W2143284241","https://openalex.org/W2148866288","https://openalex.org/W2151350595","https://openalex.org/W2156443053","https://openalex.org/W2159092541","https://openalex.org/W2159583324","https://openalex.org/W2161732286","https://openalex.org/W2163485494","https://openalex.org/W2173732482","https://openalex.org/W2204695023","https://openalex.org/W2537679995","https://openalex.org/W2539985226","https://openalex.org/W2592518050","https://openalex.org/W2754483429","https://openalex.org/W2790974918","https://openalex.org/W2803050835","https://openalex.org/W2807176368","https://openalex.org/W2809330972","https://openalex.org/W2888515069","https://openalex.org/W2889019390","https://openalex.org/W2899798803","https://openalex.org/W2900569176","https://openalex.org/W2903096015","https://openalex.org/W2910430842","https://openalex.org/W2911489562","https://openalex.org/W2912621306","https://openalex.org/W2916749909","https://openalex.org/W2917858269","https://openalex.org/W2918066696","https://openalex.org/W2919720720","https://openalex.org/W2944727022","https://openalex.org/W2949311246","https://openalex.org/W2967338832","https://openalex.org/W3048090444","https://openalex.org/W3093194543","https://openalex.org/W3095049046","https://openalex.org/W3106811464","https://openalex.org/W3176163250","https://openalex.org/W4205247356","https://openalex.org/W4206447491","https://openalex.org/W4211050998","https://openalex.org/W4220825176","https://openalex.org/W4233698560","https://openalex.org/W4247859549","https://openalex.org/W4285031001","https://openalex.org/W4294216483","https://openalex.org/W4295198017","https://openalex.org/W4297183943","https://openalex.org/W4297312281","https://openalex.org/W4318983406","https://openalex.org/W4319813194","https://openalex.org/W4388019990","https://openalex.org/W4388615774","https://openalex.org/W4389004870","https://openalex.org/W4392168151","https://openalex.org/W4400222836","https://openalex.org/W4401814202","https://openalex.org/W4404566604","https://openalex.org/W4404566628","https://openalex.org/W4404793799","https://openalex.org/W4405515957","https://openalex.org/W4409201831","https://openalex.org/W4412906959","https://openalex.org/W4413427262","https://openalex.org/W4416308726","https://openalex.org/W7133224126"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"Multiomics":[1],"data":[2,18,115,170,213],"analysis":[3,14,19,33,219],"is":[4,48,77,208,226],"essential":[5],"for":[6,99,116,215],"scientific":[7,22,117],"discovery":[8],"in":[9,66],"precision":[10],"medicine.":[11],"However,":[12,74],"translating":[13],"results":[15,34],"of":[16,107],"omics":[17],"into":[20,95,144],"novel":[21,124,166,210,217],"hypotheses":[23,38],"remains":[24],"a":[25,96,123,145,165,209],"significant":[26],"challenge.":[27],"Human":[28],"experts":[29],"must":[30],"manually":[31],"review":[32],"and":[35,42,50,69,85,137,156,192,211,230],"generate":[36],"new":[37],"based":[39],"on":[40],"extensive":[41],"interconnected":[43],"biomedical":[44,71,75,114,130,190],"prior":[45,72,148,177,202],"knowledge,":[46],"which":[47],"subjective":[49],"not":[51],"scalable.":[52],"While":[53],"large":[54],"language":[55],"models":[56],"can":[57,196,235],"accelerate":[58],"the":[59,105,193],"discovery,":[60],"their":[61],"reasoning":[62],"improves":[63],"when":[64],"grounded":[65],"structured,":[67],"auditable,":[68],"comprehensive":[70],"knowledge.":[73],"knowledge":[76,149,179,203,232],"scattered":[78],"across":[79],"heterogeneous":[80],"databases":[81,143],"that":[82,127],"use":[83],"diverse":[84],"inconsistent":[86],"nomenclature":[87],"systems,":[88],"making":[89],"it":[90],"difficult":[91],"to":[92,111],"integrate":[93],"resources":[94,131],"unified":[97,146],"format":[98],"scalable":[100],"analysis.":[101],"This":[102],"fragmentation":[103],"limits":[104],"ability":[106],"artificial":[108],"intelligence":[109],"systems":[110],"fully":[112],"leverage":[113],"discovery.":[118],"RESULTS:":[119],"We":[120],"developed":[121],"BioMedGraphica,":[122],"all-in-one":[125],"platform":[126],"harmonizes":[128],"fragmented":[129],"by":[132],"integrating":[133],"11":[134],"entity":[135],"types":[136,140],"30":[138],"relation":[139],"from":[141,238],"43":[142],"textual":[147,174],"graph":[150,168,218,233],"containing":[151],"2":[152],"306":[153],"921":[154],"entities":[155],"27":[157],"232":[158],"091":[159],"relations.":[160],"In":[161],"addition,":[162],"we":[163],"present":[164],"textual-numeric":[167],"(TNG)":[169],"structure":[171,214],"concept,":[172],"where":[173],"information":[175],"captures":[176],"biological":[178],"(e.g.":[180],"transcription":[181],"start":[182],"sites,":[183],"functions,":[184],"mechanisms),":[185],"numeric":[186],"values":[187],"represent":[188],"quantitative":[189],"features,":[191],"integrated":[194],"relations":[195],"help":[197],"uncover":[198],"mechanisms.":[199],"By":[200],"bridging":[201],"with":[204],"user-specific":[205],"data,":[206],"TNG":[207],"ideal":[212],"developing":[216],"models.":[220],"AVAILABILITY":[221],"AND":[222],"IMPLEMENTATION:":[223],"The":[224],"code":[225],"available":[227],"at:":[228],"https://github.com/FuhaiLiAiLab/BioMedGraphica":[229],"BioMedGraphica":[231],"database":[234],"be":[236],"downloaded":[237],"huggingface":[239],"dataset:":[240],"https://huggingface.co/datasets/FuhaiLiAiLab/BioMedGraphica.":[241]},"counts_by_year":[],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2026-06-06T00:00:00"}
