{"id":"https://openalex.org/W7124919016","doi":"https://doi.org/10.1093/bioinformatics/btag031","title":"textToKnowledgeGraph: generation of molecular interaction knowledge graphs using large language models for exploration in Cytoscape","display_name":"textToKnowledgeGraph: generation of molecular interaction knowledge graphs using large language models for exploration in Cytoscape","publication_year":2026,"publication_date":"2026-01-15","ids":{"openalex":"https://openalex.org/W7124919016","doi":"https://doi.org/10.1093/bioinformatics/btag031","pmid":"https://pubmed.ncbi.nlm.nih.gov/41555498"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag031","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag031","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"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/10.1093/bioinformatics/btag031","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5123449874","display_name":"Favour James","orcid":null},"institutions":[{"id":"https://openalex.org/I45711476","display_name":"Obafemi Awolowo University","ror":"https://ror.org/04snhqa82","country_code":"NG","type":"education","lineage":["https://openalex.org/I45711476"]}],"countries":["NG"],"is_corresponding":true,"raw_author_name":"Favour James","raw_affiliation_strings":["Department of Electronic and Electrical Engineering, Obafemi Awolowo University , Ife-Ife, Osun, 220103,"],"affiliations":[{"raw_affiliation_string":"Department of Electronic and Electrical Engineering, Obafemi Awolowo University , Ife-Ife, Osun, 220103,","institution_ids":["https://openalex.org/I45711476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123422975","display_name":"Dexter Pratt","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dexter Pratt","raw_affiliation_strings":["Department of Medicine, University of California, San Diego , La Jolla, CA, 92093,"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California, San Diego , La Jolla, CA, 92093,","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008857083","display_name":"Christopher Churas","orcid":"https://orcid.org/0000-0001-9998-705X"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher Churas","raw_affiliation_strings":["Department of Medicine, University of California, San Diego , La Jolla, CA, 92093,"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California, San Diego , La Jolla, CA, 92093,","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5122978529","display_name":"Augustin Luna","orcid":null},"institutions":[{"id":"https://openalex.org/I2800548410","display_name":"United States National Library of Medicine","ror":"https://ror.org/0060t0j89","country_code":"US","type":"archive","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Augustin Luna","raw_affiliation_strings":["Computational Biology Branch, National Library of Medicine and Developmental Therapeutics Branch, National Cancer Institute , 9000 Rockville Pike , Bethesda, MD, 20892,"],"affiliations":[{"raw_affiliation_string":"Computational Biology Branch, National Library of Medicine and Developmental Therapeutics Branch, National Cancer Institute , 9000 Rockville Pike , Bethesda, MD, 20892,","institution_ids":["https://openalex.org/I4210140884","https://openalex.org/I2800548410"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5123449874"],"corresponding_institution_ids":["https://openalex.org/I45711476"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.11978157,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.8335999846458435,"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":0.8335999846458435,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.06289999932050705,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.03840000182390213,"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/knowledge-graph","display_name":"Knowledge graph","score":0.41780000925064087},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.41530001163482666},{"id":"https://openalex.org/keywords/language-understanding","display_name":"Language understanding","score":0.2888000011444092},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.28439998626708984},{"id":"https://openalex.org/keywords/data-exploration","display_name":"Data exploration","score":0.27790001034736633}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7809000015258789},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.47589999437332153},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.45660001039505005},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.41780000925064087},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.41530001163482666},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3443000018596649},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.30250000953674316},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.30140000581741333},{"id":"https://openalex.org/C2983448237","wikidata":"https://www.wikidata.org/wiki/Q1078276","display_name":"Language understanding","level":2,"score":0.2888000011444092},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.28439998626708984},{"id":"https://openalex.org/C2780977526","wikidata":"https://www.wikidata.org/wiki/Q42417149","display_name":"Data exploration","level":3,"score":0.27790001034736633},{"id":"https://openalex.org/C2984968299","wikidata":"https://www.wikidata.org/wiki/Q1077784","display_name":"Software tool","level":3,"score":0.2639999985694885},{"id":"https://openalex.org/C2984499602","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Computer software","level":2,"score":0.250900000333786}],"mesh":[{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag031","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag031","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41555498","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41555498","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12916169","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12916169/","pdf_url":null,"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag031","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag031","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7872335314750671,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G3714160756","display_name":null,"funder_award_id":"R01HG009979","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8798940694","display_name":null,"funder_award_id":"U19AI135990","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8841462186","display_name":null,"funder_award_id":"U54CA209891","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G919333870","display_name":null,"funder_award_id":"U24CA184427","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W1871096589","https://openalex.org/W2060871034","https://openalex.org/W2069157810","https://openalex.org/W2112651905","https://openalex.org/W2159675211","https://openalex.org/W2167253239","https://openalex.org/W2766482558","https://openalex.org/W4285153328","https://openalex.org/W4319813194","https://openalex.org/W4327900239","https://openalex.org/W4393936594","https://openalex.org/W4406098046","https://openalex.org/W4409986716"],"related_works":[],"abstract_inverted_index":{"https://github.com/ndexbio/llm-text-to-knowledge-graph.":[0]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2026-01-21T00:00:00"}
