{"doi":"10.3791/65084","title":"A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease <em>via</em> Biomedical Reports","abstract":"The rapidly increasing and vast quantities of biomedical reports, each containing numerous entities and rich information, represent a rich resource for biomedical text-mining applications. These tools enable investigators to integrate, conceptualize, and translate these discoveries to uncover new insights into disease pathology and therapeutics. In this protocol, we present CaseOLAP LIFT, a new computational pipeline to investigate cellular components and their disease associations by extracting user-selected information from text datasets (e.g., biomedical literature). The software identifies sub-cellular proteins and their functional partners within disease-relevant documents. Additional disease-relevant documents are identified via the software's label imputation method. To contextualize the resulting protein-disease associations and to integrate information from multiple relevant biomedical resources, a knowledge graph is automatically constructed for further analyses. We present one use case with a corpus of ~34 million text documents downloaded online to provide an example of elucidating the role of mitochondrial proteins in distinct cardiovascular disease phenotypes using this method. Furthermore, a deep learning model was applied to the resulting knowledge graph to predict previously unreported relationships between proteins and disease, resulting in 1,583 associations with predicted probabilities >0.90 and with an area under the receiver operating characteristic curve (AUROC) of 0.91 on the test set. This software features a highly customizable and automated workflow, with a broad scope of raw data available for analysis; therefore, using this method, protein-disease associations can be identified with enhanced reliability within a text corpus.","journal":"Journal of Visualized Experiments","year":2023,"id":385465,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.5439,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":820044,"name":"Dylan Steinecke","orcid":"0000-0002-0469-0868","position":1,"is_corresponding":false},{"id":762308,"name":"Dibakar Sigdel","orcid":"0000-0002-2599-1192","position":2,"is_corresponding":false},{"id":1153914,"name":"Irsyad Adam","orcid":null,"position":3,"is_corresponding":false},{"id":6460,"name":"J. Harry Caufield","orcid":"0000-0001-5705-7831","position":4,"is_corresponding":false},{"id":762812,"name":"Vladimir Guevara-Gonzalez","orcid":null,"position":5,"is_corresponding":false},{"id":1153915,"name":"Joseph Ramirez","orcid":null,"position":6,"is_corresponding":false},{"id":1153491,"name":"Aarushi Verma","orcid":"0000-0002-3985-798X","position":7,"is_corresponding":false},{"id":1153916,"name":"Kaitlyn Bali","orcid":null,"position":8,"is_corresponding":false},{"id":1153917,"name":"Katherine Downs","orcid":null,"position":9,"is_corresponding":false},{"id":311300,"name":"Wei Wang","orcid":"0000-0002-8180-2886","position":10,"is_corresponding":false},{"id":64664,"name":"Alex Bui","orcid":"0000-0002-4702-1373","position":11,"is_corresponding":false},{"id":64665,"name":"Peipei Ping","orcid":"0000-0003-3583-3881","position":12,"is_corresponding":false},{"id":1057080,"name":"Alexander R. Pelletier","orcid":"0000-0002-1945-8420","position":0,"is_corresponding":true}],"reference_count":40,"raw_metadata":null,"created_at":"2026-07-19T01:17:52.636565Z","pmid":"37902366","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":[]}