{"id":"https://openalex.org/W4417095315","doi":"https://doi.org/10.1186/s12859-025-06335-6","title":"GeDi: simplifying gene set distances for enhanced omics interpretation in R/Bioconductor","display_name":"GeDi: simplifying gene set distances for enhanced omics interpretation in R/Bioconductor","publication_year":2025,"publication_date":"2025-12-07","ids":{"openalex":"https://openalex.org/W4417095315","doi":"https://doi.org/10.1186/s12859-025-06335-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/41354776"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06335-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06335-6","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC 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/10.1186/s12859-025-06335-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005408698","display_name":"Annekathrin Silvia Nedwed","orcid":"https://orcid.org/0000-0002-2475-4945"},"institutions":[{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]},{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Annekathrin Silvia Nedwed","raw_affiliation_strings":["Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany. anedwed@uni-mainz.de","Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany. annekathrin.nedwed@gmail.com"],"affiliations":[{"raw_affiliation_string":"Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany. anedwed@uni-mainz.de","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]},{"raw_affiliation_string":"Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany. annekathrin.nedwed@gmail.com","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039591070","display_name":"Arsenij Ustjanzew","orcid":"https://orcid.org/0000-0002-1014-4521"},"institutions":[{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]},{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Arsenij Ustjanzew","raw_affiliation_strings":["Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5094005270","display_name":"Najla Abassi","orcid":"https://orcid.org/0000-0001-8357-0938"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Najla Abassi","raw_affiliation_strings":["Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102822506","display_name":"Leon Dammer","orcid":"https://orcid.org/0009-0008-4132-7639"},"institutions":[{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]},{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Leon Dammer","raw_affiliation_strings":["Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001630716","display_name":"Alicia Schulze","orcid":"https://orcid.org/0000-0003-2527-0763"},"institutions":[{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]},{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Alicia Schulze","raw_affiliation_strings":["Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064264142","display_name":"Sara Salome Helbich","orcid":"https://orcid.org/0000-0003-0479-5448"},"institutions":[{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]},{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sara Salome Helbich","raw_affiliation_strings":["Institute of Immunology, University Medical Center Mainz, Mainz, Germany","Research Center for Immunotherapy (FZI), Mainz, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Immunology, University Medical Center Mainz, Mainz, Germany","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]},{"raw_affiliation_string":"Research Center for Immunotherapy (FZI), Mainz, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072787875","display_name":"Michael Delacher","orcid":"https://orcid.org/0000-0002-6716-9156"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Michael Delacher","raw_affiliation_strings":["Institute of Immunology, University Medical Center Mainz, Mainz, Germany","Research Center for Immunotherapy (FZI), Mainz, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Immunology, University Medical Center Mainz, Mainz, Germany","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]},{"raw_affiliation_string":"Research Center for Immunotherapy (FZI), Mainz, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030831306","display_name":"Konstantin Strauch","orcid":"https://orcid.org/0000-0002-1814-5860"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Konstantin Strauch","raw_affiliation_strings":["Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087884887","display_name":"F\u00e9d\u00e9rico Marini","orcid":"https://orcid.org/0000-0003-3252-7758"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I164387090","display_name":"University of Applied Sciences Mainz","ror":"https://ror.org/02re32a17","country_code":"DE","type":"education","lineage":["https://openalex.org/I164387090"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Federico Marini","raw_affiliation_strings":["Center for Thrombosis and Hemostasis (CTH), Mainz, Germany. marinif@uni-mainz.de","Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany. marinif@uni-mainz.de","Research Center for Immunotherapy (FZI), Mainz, Germany. marinif@uni-mainz.de"],"affiliations":[{"raw_affiliation_string":"Center for Thrombosis and Hemostasis (CTH), Mainz, Germany. marinif@uni-mainz.de","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]},{"raw_affiliation_string":"Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany. marinif@uni-mainz.de","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]},{"raw_affiliation_string":"Research Center for Immunotherapy (FZI), Mainz, Germany. marinif@uni-mainz.de","institution_ids":["https://openalex.org/I164387090"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5005408698"],"corresponding_institution_ids":["https://openalex.org/I197323543","https://openalex.org/I4210094062"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.34367338,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"1","first_page":"14","last_page":"14"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9829000234603882,"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":0.9829000234603882,"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/T10885","display_name":"Gene expression and cancer classification","score":0.006500000134110451,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.0035000001080334187,"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/bioconductor","display_name":"Bioconductor","score":0.7684000134468079},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6643999814987183},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6590999960899353},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5985000133514404},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.5133000016212463},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.5016999840736389},{"id":"https://openalex.org/keywords/interpretation","display_name":"Interpretation (philosophy)","score":0.4964999854564667},{"id":"https://openalex.org/keywords/redundancy","display_name":"Redundancy (engineering)","score":0.45980000495910645},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.44519999623298645}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.7684000134468079},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7041000127792358},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6643999814987183},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6590999960899353},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5985000133514404},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5450000166893005},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5133000016212463},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.5016999840736389},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.4964999854564667},{"id":"https://openalex.org/C152124472","wikidata":"https://www.wikidata.org/wiki/Q1204361","display_name":"Redundancy (engineering)","level":2,"score":0.45980000495910645},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.44519999623298645},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.4219000041484833},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4047999978065491},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.3287999927997589},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.3165999948978424},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3165999948978424},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.31290000677108765},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.30880001187324524},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.30640000104904175},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.2992999851703644},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.2987000048160553},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.296999990940094},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.2946999967098236},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.2842999994754791},{"id":"https://openalex.org/C2781162219","wikidata":"https://www.wikidata.org/wiki/Q26250693","display_name":"Replicate","level":2,"score":0.2816999852657318},{"id":"https://openalex.org/C12590798","wikidata":"https://www.wikidata.org/wiki/Q3933199","display_name":"Replication (statistics)","level":2,"score":0.2808000147342682},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.2720000147819519},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.27079999446868896},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.26840001344680786},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.26429998874664307},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.25780001282691956},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.25429999828338623}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06335-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06335-6","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41354776","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41354776","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:6f79f71100084ec9960090d2cbb29f1b","is_oa":true,"landing_page_url":"https://doaj.org/article/6f79f71100084ec9960090d2cbb29f1b","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":"BMC Bioinformatics, Vol 27, Iss 1, Pp 1-13 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12809992","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12809992/","pdf_url":null,"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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06335-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06335-6","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320336167","display_name":"Universit\u00e4tsmedizin der Johannes Gutenberg-Universit\u00e4t Mainz","ror":"https://ror.org/00q1fsf04"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W1973094248","https://openalex.org/W2033403400","https://openalex.org/W2053154970","https://openalex.org/W2086320398","https://openalex.org/W2097553067","https://openalex.org/W2097795961","https://openalex.org/W2097948046","https://openalex.org/W2100761975","https://openalex.org/W2100980426","https://openalex.org/W2103017472","https://openalex.org/W2120024428","https://openalex.org/W2123402141","https://openalex.org/W2124166542","https://openalex.org/W2130410032","https://openalex.org/W2131681506","https://openalex.org/W2133465414","https://openalex.org/W2158217645","https://openalex.org/W2214074259","https://openalex.org/W2345356016","https://openalex.org/W2898389114","https://openalex.org/W2898598946","https://openalex.org/W2906480617","https://openalex.org/W2947925171","https://openalex.org/W2950595506","https://openalex.org/W2984996233","https://openalex.org/W2989807288","https://openalex.org/W3000221858","https://openalex.org/W3004747635","https://openalex.org/W3025060722","https://openalex.org/W3038655749","https://openalex.org/W3092495933","https://openalex.org/W3153543576","https://openalex.org/W4214879506","https://openalex.org/W4220684489","https://openalex.org/W4224792601","https://openalex.org/W4225463239","https://openalex.org/W4233698560","https://openalex.org/W4306353191","https://openalex.org/W4307425304","https://openalex.org/W4372332501","https://openalex.org/W4387521577","https://openalex.org/W4392168151","https://openalex.org/W4412006463"],"related_works":[],"abstract_inverted_index":{"Functional":[0],"enrichment":[1,84,171],"analysis":[2,11],"is":[3,63,153,196,212],"a":[4,15,95,126,131,157,181,209],"standard":[5],"component":[6],"in":[7,199],"many":[8],"omics":[9],"data":[10],"workflows,":[12],"supported":[13],"by":[14,66,135,173],"variety":[16],"of":[17,40,82,97,117,125,170],"methods":[18,29],"and":[19,25,37,45,78,102,109,141,149,152,160,176,192,208],"algorithms.":[20],"However,":[21],"despite":[22],"their":[23,142],"utility":[24],"wide":[26],"application,":[27],"these":[28],"often":[30,64],"return":[31],"the":[32,80,115,123,200,204,215],"results":[33,172],"as":[34,155],"an":[35,72,161],"extensive":[36],"redundant":[38],"list":[39],"gene":[41,88,98],"sets,":[42],"impeding":[43],"interpretation":[44,81,169],"hypothesis":[46],"generation.":[47],"Moreover,":[48],"network":[49,177],"based":[50],"information":[51],"can":[52],"provide":[53],"additional":[54],"biological":[55,133,187],"context":[56,134],"through":[57,122],"functional":[58,83,137],"interaction":[59,119],"data,":[60,121],"yet":[61],"this":[62],"overlooked":[65],"existing":[67],"tools.":[68],"We":[69],"developed":[70],"GeDi,":[71],"R/Bioconductor":[73],"package":[74,145],"designed":[75],"to":[76,106,180],"streamline":[77],"standardize":[79],"results.":[85],"GeDi":[86,112,165,195],"aggregates":[87],"sets":[89],"into":[90],"biologically":[91],"meaningful":[92],"clusters":[93],"using":[94],"suite":[96],"set":[99],"distance":[100,128],"metrics":[101],"clustering":[103,175],"algorithms,":[104],"aimed":[105],"reduce":[107],"redundancy":[108],"improve":[110],"clarity.":[111],"also":[113],"enables":[114],"integration":[116],"protein\u2013protein":[118],"(PPI)":[120],"implementation":[124],"weighted":[127],"metric,":[129],"providing":[130],"richer":[132],"capturing":[136],"connectivity":[138],"between":[139],"pathways":[140],"components.":[143],"The":[144],"offers":[146],"visualizations,":[147],"aggregation,":[148],"automated":[150],"reporting,":[151],"available":[154,198],"both":[156,190],"stand-alone":[158],"R-package":[159],"interactive":[162],"Shiny":[163,216],"application.":[164],"facilitates":[166],"clearer,":[167],"faster":[168],"combining":[174],"context.":[178],"Application":[179],"public":[182],"RNA-seq":[183],"dataset":[184],"revealed":[185],"coherent":[186],"themes,":[188],"supporting":[189],"experimental":[191],"computational":[193],"research.":[194],"freely":[197],"Bioconductor":[201],"project":[202],"under":[203],"MIT":[205],"license":[206],"(https://bioconductor.org/packages/GeDi),":[207],"demo":[210],"instance":[211],"accessible":[213],"on":[214],"server":[217],"(http://shiny.imbei.uni-mainz.de:3838/GeDi).":[218]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-12-07T00:00:00"}
