{"id":"https://openalex.org/W4388139915","doi":"https://doi.org/10.1186/s12859-023-05539-y","title":"Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models","display_name":"Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models","publication_year":2023,"publication_date":"2023-11-01","ids":{"openalex":"https://openalex.org/W4388139915","doi":"https://doi.org/10.1186/s12859-023-05539-y","pmid":"https://pubmed.ncbi.nlm.nih.gov/37915001"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-023-05539-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05539-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05539-y","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://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05539-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086619052","display_name":"Robert J. Millikin","orcid":"https://orcid.org/0000-0001-7440-3695"},"institutions":[{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert J. Millikin","raw_affiliation_strings":["Morgridge Institute for Research, Madison, WI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI, USA","institution_ids":["https://openalex.org/I29680605"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024997718","display_name":"Kalpana Raja","orcid":"https://orcid.org/0000-0002-3156-4197"},"institutions":[{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]},{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kalpana Raja","raw_affiliation_strings":["Currently at Biomedical Informatics and Data Science, Yale University, New Haven, CT, USA","Morgridge Institute for Research, Madison, WI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Currently at Biomedical Informatics and Data Science, Yale University, New Haven, CT, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI, USA","institution_ids":["https://openalex.org/I29680605"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050910062","display_name":"John Steill","orcid":"https://orcid.org/0000-0003-2994-3400"},"institutions":[{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John Steill","raw_affiliation_strings":["Morgridge Institute for Research, Madison, WI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI, USA","institution_ids":["https://openalex.org/I29680605"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090816556","display_name":"Cannon Lock","orcid":null},"institutions":[{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cannon Lock","raw_affiliation_strings":["Morgridge Institute for Research, Madison, WI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI, USA","institution_ids":["https://openalex.org/I29680605"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113035674","display_name":"Xuancheng Tu","orcid":null},"institutions":[{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xuancheng Tu","raw_affiliation_strings":["Morgridge Institute for Research, Madison, WI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI, USA","institution_ids":["https://openalex.org/I29680605"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108080096","display_name":"I. Ross","orcid":"https://orcid.org/0000-0003-1888-1689"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I4210151837","display_name":"High Throughput Biology (United States)","ror":"https://ror.org/05h1bjp83","country_code":"US","type":"company","lineage":["https://openalex.org/I4210151837"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ian Ross","raw_affiliation_strings":["Center for High Throughput Computing, Computer Sciences Department, University of Wisconsin, Madison, WI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for High Throughput Computing, Computer Sciences Department, University of Wisconsin, Madison, WI, USA","institution_ids":["https://openalex.org/I4210151837","https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057653412","display_name":"Lam C. Tsoi","orcid":"https://orcid.org/0000-0003-1627-5722"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lam C. Tsoi","raw_affiliation_strings":["Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA","Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA","Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037353356","display_name":"Finn Kuusisto","orcid":"https://orcid.org/0000-0001-6487-4397"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Finn Kuusisto","raw_affiliation_strings":["Currently at Data Science Institute, University of Wisconsin, Madison, WI, USA","Morgridge Institute for Research, Madison, WI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Currently at Data Science Institute, University of Wisconsin, Madison, WI, USA","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI, USA","institution_ids":["https://openalex.org/I29680605"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073567755","display_name":"Zijian Ni","orcid":"https://orcid.org/0000-0003-1181-8337"},"institutions":[{"id":"https://openalex.org/I1311688040","display_name":"Amazon (United States)","ror":"https://ror.org/04mv4n011","country_code":"US","type":"company","lineage":["https://openalex.org/I1311688040"]},{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zijian Ni","raw_affiliation_strings":["Currently at Amazon, Seattle, WA, USA","Department of Statistics, University of Wisconsin, Madison, WI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Currently at Amazon, Seattle, WA, USA","institution_ids":["https://openalex.org/I1311688040"]},{"raw_affiliation_string":"Department of Statistics, University of Wisconsin, Madison, WI, USA","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042010270","display_name":"Miron Livny","orcid":"https://orcid.org/0000-0001-5444-7439"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]},{"id":"https://openalex.org/I4210151837","display_name":"High Throughput Biology (United States)","ror":"https://ror.org/05h1bjp83","country_code":"US","type":"company","lineage":["https://openalex.org/I4210151837"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Miron Livny","raw_affiliation_strings":["Center for High Throughput Computing, Computer Sciences Department, University of Wisconsin, Madison, WI, USA","Morgridge Institute for Research, Madison, WI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for High Throughput Computing, Computer Sciences Department, University of Wisconsin, Madison, WI, USA","institution_ids":["https://openalex.org/I4210151837","https://openalex.org/I135310074"]},{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI, USA","institution_ids":["https://openalex.org/I29680605"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101621571","display_name":"Brian Bockelman","orcid":"https://orcid.org/0000-0003-2981-3809"},"institutions":[{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian Bockelman","raw_affiliation_strings":["Morgridge Institute for Research, Madison, WI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI, USA","institution_ids":["https://openalex.org/I29680605"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110433162","display_name":"James Thomson","orcid":null},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Thomson","raw_affiliation_strings":["Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI, USA","Morgridge Institute for Research, Madison, WI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI, USA","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI, USA","institution_ids":["https://openalex.org/I29680605"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083447121","display_name":"Ron Stewart","orcid":"https://orcid.org/0000-0002-9041-1828"},"institutions":[{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ron Stewart","raw_affiliation_strings":["Morgridge Institute for Research, Madison, WI, USA. rstewart@morgridge.org","Morgridge Institute for Research, Madison, WI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI, USA. rstewart@morgridge.org","institution_ids":["https://openalex.org/I29680605"]},{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI, USA","institution_ids":["https://openalex.org/I29680605"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":13,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.1412,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.78928181,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"24","issue":"1","first_page":"412","last_page":"412"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9853000044822693,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9853000044822693,"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/T10028","display_name":"Topic Modeling","score":0.0034000000450760126,"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/T13702","display_name":"Machine Learning in Healthcare","score":0.0010999999940395355,"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/computer-science","display_name":"Computer science","score":0.721194326877594},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.5761288404464722},{"id":"https://openalex.org/keywords/term","display_name":"Term (time)","score":0.4746090769767761},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.39202970266342163},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3656774163246155},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07345515489578247}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.721194326877594},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.5761288404464722},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.4746090769767761},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.39202970266342163},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3656774163246155},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07345515489578247},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019359","descriptor_name":"Knowledge","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019359","descriptor_name":"Knowledge","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019359","descriptor_name":"Knowledge","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019359","descriptor_name":"Knowledge","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019359","descriptor_name":"Knowledge","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063369","descriptor_name":"Knowledge Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063369","descriptor_name":"Knowledge Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063369","descriptor_name":"Knowledge Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063369","descriptor_name":"Knowledge Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063369","descriptor_name":"Knowledge Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-023-05539-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05539-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05539-y","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:37915001","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37915001","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:pubmedcentral.nih.gov:10619245","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10619245","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10619245/pdf/12859_2023_Article_5539.pdf","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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:d8781b15ff3f482f95868b84ad1c6b1a","is_oa":true,"landing_page_url":"https://doaj.org/article/d8781b15ff3f482f95868b84ad1c6b1a","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 24, Iss 1, Pp 1-14 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-023-05539-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05539-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05539-y","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":[{"id":"https://openalex.org/G1551139157","display_name":null,"funder_award_id":"K01AR07212","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4905714862","display_name":null,"funder_award_id":"NIH GM102756","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6382328078","display_name":null,"funder_award_id":"T15 LM007359","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4388139915.pdf"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1965037168","https://openalex.org/W1981276685","https://openalex.org/W2011726136","https://openalex.org/W2024030746","https://openalex.org/W2067096102","https://openalex.org/W2074813714","https://openalex.org/W2089177530","https://openalex.org/W2100822723","https://openalex.org/W2117446654","https://openalex.org/W2118002992","https://openalex.org/W2138548161","https://openalex.org/W2141243410","https://openalex.org/W2411035889","https://openalex.org/W2591078482","https://openalex.org/W2605963676","https://openalex.org/W2786651430","https://openalex.org/W2896730986","https://openalex.org/W2911489562","https://openalex.org/W2921377602","https://openalex.org/W2987066226","https://openalex.org/W3011575855","https://openalex.org/W3026298482","https://openalex.org/W3028004046","https://openalex.org/W3033896008","https://openalex.org/W3043957438","https://openalex.org/W3046324834","https://openalex.org/W3046375318","https://openalex.org/W3139277674","https://openalex.org/W3180882235","https://openalex.org/W4221047109","https://openalex.org/W4226167522","https://openalex.org/W4253608092","https://openalex.org/W4282012582","https://openalex.org/W4283318325","https://openalex.org/W4306696320","https://openalex.org/W6907225408"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W4391913857","https://openalex.org/W2350741829","https://openalex.org/W2530322880"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,44,113],"PubMed":[2],"archive":[3],"contains":[4],"more":[5,105,146],"than":[6],"34":[7],"million":[8],"articles;":[9],"consequently,":[10],"it":[11],"is":[12,50,117,193,322,339],"becoming":[13],"increasingly":[14],"difficult":[15],"for":[16,93,186,196,218,341],"a":[17,80,126,132,154,205,219,271,293,323,364],"biomedical":[18,42,221],"researcher":[19],"to":[20,34,51,169,201,246,264,279,331],"keep":[21],"up-to-date":[22],"with":[23,270,275,303,347],"different":[24],"knowledge":[25,272,375],"domains.":[26],"Computationally":[27],"efficient":[28],"and":[29,38,74,102,136,207,231,260,295,310,354],"interpretable":[30],"tools":[31,129,140],"are":[32,77,124,141,216,368],"needed":[33],"help":[35],"researchers":[36],"find":[37],"understand":[39],"associations":[40,262],"between":[41,98,204,285,334],"concepts.":[43,337],"goal":[45],"of":[46,68,115,147,160,174,189,210,238,306,350,360,363],"literature-based":[47],"discovery":[48],"(LBD)":[49],"connect":[52],"concepts":[53],"in":[54,143,251,281],"isolated":[55],"literature":[56],"domains":[57],"that":[58,122,130,137,234,313,326],"would":[59],"normally":[60],"go":[61],"undiscovered.":[62],"This":[63],"usually":[64],"takes":[65],"the":[66,120,138,148,158,167,198,208,283,357],"form":[67],"an":[69,90,99,228,361],"A-B-C":[70,249],"relationship,":[71,161],"where":[72],"A":[73,100],"C":[75,106,177,190,351],"terms":[76,107,191,286],"linked":[78],"through":[79,108],"B":[81,110,175],"term":[82,101,111,352],"intermediate.":[83],"Here":[84],"we":[85,267,291],"describe":[86],"Serial":[87],"KinderMiner":[88],"(SKiM),":[89],"LBD":[91,128,256,329],"algorithm":[92,325],"finding":[94,261],"statistically":[95],"significant":[96],"links":[97],"one":[103,144],"or":[104,145,176,213],"some":[109],"intermediate(s).":[112],"development":[114],"SKiM":[116,269,318,321,338],"motivated":[118],"by":[119,288],"observation":[121],"there":[123],"only":[125],"few":[127],"provide":[131,170,227,292],"functional":[133],"web":[134,232,298],"interface,":[135],"available":[139,211],"limited":[142],"following":[149],"ways:":[150],"(1)":[151],"they":[152,163,182,215],"identify":[153],"relationship":[155,370],"but":[156],"not":[157,165,184],"type":[159,371],"(2)":[162],"do":[164,183],"allow":[166,185],"user":[168,199],"their":[171],"own":[172],"lists":[173,305],"terms,":[178],"hindering":[179],"flexibility,":[180],"(3)":[181],"querying":[187],"thousands":[188,209,349],"(which":[192],"crucial":[194],"if,":[195],"instance,":[197],"wants":[200],"query":[202],"connections":[203],"disease":[206],"drugs),":[212],"(4)":[214],"specific":[217],"particular":[220],"domain":[222],"(such":[223],"as":[224],"cancer).":[225],"We":[226,242],"open-source":[229,297],"tool":[230],"interface":[233,299],"improves":[235],"on":[236],"all":[237],"these":[239],"issues.":[240],"RESULTS:":[241],"demonstrate":[243],"SKiM's":[244],"ability":[245],"discover":[247,332],"useful":[248],"linkages":[250],"three":[252],"control":[253],"experiments:":[254],"classic":[255],"discoveries,":[257],"drug":[258],"repurposing,":[259],"related":[263],"cancer.":[265],"Furthermore,":[266],"supplement":[268],"graph":[273],"built":[274],"transformer":[276],"machine-learning":[277],"models":[278],"aid":[280],"interpreting":[282],"relationships":[284,333,367],"found":[287],"SKiM.":[289],"Finally,":[290],"simple":[294,324,358],"intuitive":[296],"(":[300],"https://skim.morgridge.org":[301],")":[302],"comprehensive":[304],"drugs,":[307],"diseases,":[308],"phenotypes,":[309],"symptoms":[311],"so":[312],"anyone":[314],"can":[315,327,344],"easily":[316],"perform":[317,328,345],"searches.":[319],"CONCLUSIONS:":[320],"searches":[330,346],"arbitrary":[335],"user-defined":[336],"generalized":[340],"any":[342],"domain,":[343],"many":[348,366],"concepts,":[353],"moves":[355],"beyond":[356],"identification":[359],"existence":[362],"relationship;":[365],"given":[369],"labels":[372],"from":[373],"our":[374],"graph.":[376]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
