{"id":"https://openalex.org/W4410560166","doi":"https://doi.org/10.1186/s13321-025-01017-0","title":"A resource description framework (RDF) model of named entity co-occurrences in biomedical literature and its integration with PubChemRDF","display_name":"A resource description framework (RDF) model of named entity co-occurrences in biomedical literature and its integration with PubChemRDF","publication_year":2025,"publication_date":"2025-05-21","ids":{"openalex":"https://openalex.org/W4410560166","doi":"https://doi.org/10.1186/s13321-025-01017-0","pmid":"https://pubmed.ncbi.nlm.nih.gov/40399973"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-01017-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01017-0","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01017-0","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01017-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100613839","display_name":"Qingliang Li","orcid":"https://orcid.org/0000-0002-6453-236X"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Qingliang Li","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100430147","display_name":"Sunghwan Kim","orcid":"https://orcid.org/0000-0001-9828-2074"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sunghwan Kim","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069076714","display_name":"Leonid Zaslavsky","orcid":"https://orcid.org/0000-0001-5873-4873"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Leonid Zaslavsky","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071322222","display_name":"Tiejun Cheng","orcid":"https://orcid.org/0000-0002-4486-3356"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tiejun Cheng","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090242045","display_name":"Bo Yu","orcid":"https://orcid.org/0000-0003-3952-8921"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bo Yu","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015494748","display_name":"Evan Bolton","orcid":"https://orcid.org/0000-0002-5959-6190"},"institutions":[{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Evan E. Bolton","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA. bolton@ncbi.nlm.nih.gov"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA. bolton@ncbi.nlm.nih.gov","institution_ids":["https://openalex.org/I4210109390"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5100613839"],"corresponding_institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":1.5784,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.82584039,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"17","issue":"1","first_page":"79","last_page":"79"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"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":0.9998999834060669,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9970999956130981,"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/T10028","display_name":"Topic Modeling","score":0.9672999978065491,"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/sparql","display_name":"SPARQL","score":0.8220950365066528},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8117216229438782},{"id":"https://openalex.org/keywords/rdf","display_name":"RDF","score":0.7919210195541382},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.5923230648040771},{"id":"https://openalex.org/keywords/resource","display_name":"Resource (disambiguation)","score":0.5715020298957825},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5688226222991943},{"id":"https://openalex.org/keywords/linked-data","display_name":"Linked data","score":0.5125608444213867},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.5055396556854248},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4602893590927124},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.33118629455566406},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.3286491632461548},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.25425300002098083},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.2262077033519745}],"concepts":[{"id":"https://openalex.org/C41009113","wikidata":"https://www.wikidata.org/wiki/Q54871","display_name":"SPARQL","level":4,"score":0.8220950365066528},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8117216229438782},{"id":"https://openalex.org/C147497476","wikidata":"https://www.wikidata.org/wiki/Q54872","display_name":"RDF","level":3,"score":0.7919210195541382},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.5923230648040771},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.5715020298957825},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5688226222991943},{"id":"https://openalex.org/C69075417","wikidata":"https://www.wikidata.org/wiki/Q515701","display_name":"Linked data","level":3,"score":0.5125608444213867},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.5055396556854248},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4602893590927124},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.33118629455566406},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.3286491632461548},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.25425300002098083},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.2262077033519745},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-025-01017-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01017-0","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01017-0","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:40399973","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40399973","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":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12096534","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12096534","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":"J Cheminform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:02a895456fd24a8498ec65f6610f9fe0","is_oa":true,"landing_page_url":"https://doaj.org/article/02a895456fd24a8498ec65f6610f9fe0","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":"Journal of Cheminformatics, Vol 17, Iss 1, Pp 1-18 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-01017-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01017-0","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01017-0","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.5}],"awards":[],"funders":[{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410560166.pdf","grobid_xml":"https://content.openalex.org/works/W4410560166.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W73222560","https://openalex.org/W1736726159","https://openalex.org/W1852306145","https://openalex.org/W1935434993","https://openalex.org/W2013068027","https://openalex.org/W2024932032","https://openalex.org/W2052250375","https://openalex.org/W2087779040","https://openalex.org/W2101746535","https://openalex.org/W2136794542","https://openalex.org/W2138129943","https://openalex.org/W2141541659","https://openalex.org/W2144427809","https://openalex.org/W2159583324","https://openalex.org/W2169546341","https://openalex.org/W2412696399","https://openalex.org/W2479356696","https://openalex.org/W2547231910","https://openalex.org/W2577502906","https://openalex.org/W2901527454","https://openalex.org/W3038022589","https://openalex.org/W3156288747","https://openalex.org/W3175801695","https://openalex.org/W3181209248","https://openalex.org/W3191852652","https://openalex.org/W3214608846","https://openalex.org/W4213009331","https://openalex.org/W4224037213","https://openalex.org/W4229070142","https://openalex.org/W4285084981","https://openalex.org/W4306353191","https://openalex.org/W4310240482","https://openalex.org/W4319655725","https://openalex.org/W4327712031","https://openalex.org/W4388007339","https://openalex.org/W4388615767","https://openalex.org/W4393184735","https://openalex.org/W4393306739","https://openalex.org/W4393547505","https://openalex.org/W4403284571","https://openalex.org/W4403479110","https://openalex.org/W4404458588","https://openalex.org/W4404511389","https://openalex.org/W4405224584","https://openalex.org/W4405228746","https://openalex.org/W4405231264","https://openalex.org/W4408531428"],"related_works":["https://openalex.org/W199330785","https://openalex.org/W2615202182","https://openalex.org/W2904139343","https://openalex.org/W2767591199","https://openalex.org/W98016204","https://openalex.org/W2101525042","https://openalex.org/W2776293731","https://openalex.org/W4388184885","https://openalex.org/W4322622679","https://openalex.org/W4243630814"],"abstract_inverted_index":{"Named":[0],"entities,":[1],"such":[2],"as":[3],"chemicals/drugs,":[4],"genes/proteins,":[5],"and":[6,8,27,61,72,88,130,146,156],"diseases,":[7],"their":[9,89],"associations":[10,38,90],"are":[11],"not":[12],"only":[13],"important":[14],"components":[15],"of":[16,23,35,95,97,105,119],"biomedical":[17,25,45,98,141,150],"literature,":[18],"but":[19],"also":[20],"the":[21,33,65,106,120,123,126],"foundation":[22],"creating":[24],"knowledgebases":[26],"knowledge":[28,151],"graphs.":[29],"This":[30],"work":[31],"addresses":[32],"challenges":[34],"expressing":[36],"co-occurrence":[37,77],"between":[39],"named":[40,86],"entities":[41,87],"extracted":[42],"from":[43,92],"a":[44,49,54,83],"literature":[46],"corpus":[47],"in":[48,101,152],"machine-readable":[50],"format.":[51],"We":[52],"developed":[53,76],"Resource":[55],"Description":[56],"Framework":[57],"(RDF)":[58],"data":[59,78,107,134],"model":[60,79,108,135],"integrated":[62],"it":[63],"into":[64,82],"PubChemRDF":[66],"resource,":[67],"which":[68],"is":[69],"freely":[70],"accessible":[71],"publicly":[73],"available.":[74],"The":[75,103],"was":[80,109],"populated":[81],"triplestore":[84],"with":[85,116],"derived":[91],"text":[93],"mining":[94],"millions":[96],"references":[99,121],"found":[100],"PubMed.":[102],"utility":[104],"demonstrated":[110],"through":[111,143],"multiple":[112],"use":[113,157],"cases.":[114,158],"Together":[115],"meta-data":[117],"modeling":[118],"including":[122],"information":[124],"about":[125],"author,":[127],"journal,":[128],"grant,":[129],"funding":[131],"agency,":[132],"this":[133],"allows":[136],"researchers":[137],"to":[138,148],"address":[139],"pertinent":[140],"questions":[142],"SPARQL":[144],"queries":[145],"helps":[147],"exploit":[149],"various":[153],"user":[154],"perspectives":[155]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-02T15:55:50.835912","created_date":"2025-10-10T00:00:00"}
