{"doi":"10.1093/bioinformatics/btad440","title":"RDBridge: a knowledge graph of rare diseases based on large-scale text mining","abstract":"<jats:title>Abstract</jats:title>\n               <jats:sec>\n                  <jats:title>Motivation</jats:title>\n                  <jats:p>Despite low prevalence, rare diseases affect 300 million people worldwide. Research on pathogenesis and drug development lags due to limited commercial potential, insufficient epidemiological data, and a dearth of publications. The unique characteristics of rare diseases, including limited annotated data, intricate processes for extracting pertinent entity relationships, and difficulties in standardizing data, represent challenges for text mining.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Results</jats:title>\n                  <jats:p>We developed a rare disease data acquisition framework using text mining and knowledge graphs and constructed the most comprehensive rare disease knowledge graph to date, Rare Disease Bridge (RDBridge). RDBridge offers search functions for genes, potential drugs, pathways, literature, and medical imaging data that will support mechanistic research, drug development, diagnosis, and treatment for rare diseases.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation</jats:title>\n                  <jats:p>RDBridge is freely available at http://rdb.lifesynther.com/.</jats:p>\n               </jats:sec>","journal":"Bioinformatics","year":2023,"id":638998,"datarank":0.31191623125197543,"base_score":2.0794415416798357,"endowment":2.0794415416798357,"self_citation_contribution":0.31191623125197543,"citation_network_contribution":0.0,"self_endowment_contribution":0.31191623125197543,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1407361,"name":"Dachuan Zhang","orcid":"0009-0003-9484-086X","position":1,"is_corresponding":false},{"id":1659952,"name":"Pengli Cai","orcid":null,"position":2,"is_corresponding":false},{"id":604716,"name":"Rui Zhang","orcid":"0000-0003-0310-6030","position":3,"is_corresponding":false},{"id":1659954,"name":"Qian-Nan Hu","orcid":null,"position":4,"is_corresponding":false},{"id":1659950,"name":"Huadong Xing","orcid":"0000-0002-6545-9627","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"RDBridge: a knowledge graph of rare diseases based on large-scale text mining","abstract":"<jats:title>Abstract</jats:title>\n               <jats:sec>\n                  <jats:title>Motivation</jats:title>\n                  <jats:p>Despite low prevalence, rare diseases affect 300 million people worldwide. Research on pathogenesis and drug development lags due to limited commercial potential, insufficient epidemiological data, and a dearth of publications. The unique characteristics of rare diseases, including limited annotated data, intricate processes for extracting pertinent entity relationships, and difficulties in standardizing data, represent challenges for text mining.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Results</jats:title>\n                  <jats:p>We developed a rare disease data acquisition framework using text mining and knowledge graphs and constructed the most comprehensive rare disease knowledge graph to date, Rare Disease Bridge (RDBridge). RDBridge offers search functions for genes, potential drugs, pathways, literature, and medical imaging data that will support mechanistic research, drug development, diagnosis, and treatment for rare diseases.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation</jats:title>\n                  <jats:p>RDBridge is freely available at http://rdb.lifesynther.com/.</jats:p>\n               </jats:sec>","is_dataset_classified":null,"base_score":2.0794415416798357,"endowment":2.0794415416798357,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"37458501","pmcid":null,"openalex_id":"https://openalex.org/W4384625960","authors":[],"funders":[{"funder_name":"National Key Research and Development Program of China","grant_id":"2018YFA0900700","title":null},{"funder_name":"National Key Research and Development Program of China","grant_id":"2019YFA0904300","title":null}],"total_grants":2,"fwci":1.8331,"citation_percentile":0.86538812,"influential_citations":0,"citation_trend":[{"year":2024,"count":2},{"year":2025,"count":1},{"year":2026,"count":4}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad440/50894725/btad440.pdf","host_type":"journal"},{"url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad440/50894725/btad440.pdf","host_type":"publisher"},{"url":"https://academic.oup.com/bioinformatics/article-pdf/39/7/btad440/50962248/btad440.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/bioinformatics/btad440","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/37458501","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10368801","host_type":"repository"},{"url":"http://hdl.handle.net/20.500.11850/625509","host_type":"repository"},{"url":"https://doi.org/10.3929/ethz-b-000625509","host_type":"repository"},{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10368801/pdf/btad440.pdf","host_type":"repository"}],"fields_of_study":["Genomics and Rare Diseases","Biomedical Text Mining and Ontologies","Bioinformatics and Genomic Networks","Humans","Rare Diseases","Pattern Recognition, Automated","Data Mining"],"mesh_terms":["Humans","Pattern Recognition, Automated","Rare Diseases","Data Mining"],"keywords":["Computer science","Rare disease","Data science","Disease","Graph","Knowledge graph","Data mining","Medicine","Information retrieval","Pathology","Theoretical computer science"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Good health and well-being"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-06T22:10:16.057392Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}