{"id":"https://openalex.org/W4392619039","doi":"https://doi.org/10.1093/bioinformatics/btae104","title":"Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning","display_name":"Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning","publication_year":2024,"publication_date":"2024-02-21","ids":{"openalex":"https://openalex.org/W4392619039","doi":"https://doi.org/10.1093/bioinformatics/btae104","pmid":"https://pubmed.ncbi.nlm.nih.gov/38383067"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae104","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae104","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/3/btae104/56912793/btae104.pdf","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://academic.oup.com/bioinformatics/article-pdf/40/3/btae104/56912793/btae104.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035050896","display_name":"J. Harry Caufield","orcid":"https://orcid.org/0000-0001-5705-7831"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"J Harry Caufield","raw_affiliation_strings":["Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, United States"],"affiliations":[{"raw_affiliation_string":"Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, United States","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057750338","display_name":"Harshad Hegde","orcid":"https://orcid.org/0000-0002-2411-565X"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Harshad Hegde","raw_affiliation_strings":["Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, United States"],"affiliations":[{"raw_affiliation_string":"Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, United States","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064028156","display_name":"Vincent Emonet","orcid":"https://orcid.org/0000-0002-1501-1082"},"institutions":[{"id":"https://openalex.org/I34352273","display_name":"Maastricht University","ror":"https://ror.org/02jz4aj89","country_code":"NL","type":"education","lineage":["https://openalex.org/I34352273"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Vincent Emonet","raw_affiliation_strings":["Institute of Data Science, Faculty of Science and Engineering, Maastricht University , 6200 MD Maastricht, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Institute of Data Science, Faculty of Science and Engineering, Maastricht University , 6200 MD Maastricht, The Netherlands","institution_ids":["https://openalex.org/I34352273"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031007073","display_name":"Nomi L. Harris","orcid":"https://orcid.org/0000-0001-6315-3707"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nomi L Harris","raw_affiliation_strings":["Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, United States"],"affiliations":[{"raw_affiliation_string":"Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, United States","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062038813","display_name":"Marcin P. Joachimiak","orcid":"https://orcid.org/0000-0001-8175-045X"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marcin P Joachimiak","raw_affiliation_strings":["Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, United States"],"affiliations":[{"raw_affiliation_string":"Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, United States","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040603724","display_name":"Nicolas Matentzoglu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nicolas Matentzoglu","raw_affiliation_strings":["Semanticly , Athens, Greece"],"affiliations":[{"raw_affiliation_string":"Semanticly , Athens, Greece","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021102273","display_name":"HyeongSik Kim","orcid":"https://orcid.org/0000-0002-3002-9838"},"institutions":[{"id":"https://openalex.org/I4210120115","display_name":"Robert Bosch (United States)","ror":"https://ror.org/02venad53","country_code":"US","type":"company","lineage":["https://openalex.org/I4210120115","https://openalex.org/I889804353"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"HyeongSik Kim","raw_affiliation_strings":["Robert Bosch LLC , Sunnyvale, CA 94085, United States"],"affiliations":[{"raw_affiliation_string":"Robert Bosch LLC , Sunnyvale, CA 94085, United States","institution_ids":["https://openalex.org/I4210120115"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019077587","display_name":"Sierra Moxon","orcid":"https://orcid.org/0000-0002-8719-7760"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sierra Moxon","raw_affiliation_strings":["Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, United States"],"affiliations":[{"raw_affiliation_string":"Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, United States","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073533486","display_name":"Justin Reese","orcid":"https://orcid.org/0000-0002-2170-2250"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Justin T Reese","raw_affiliation_strings":["Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, United States"],"affiliations":[{"raw_affiliation_string":"Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, United States","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064320417","display_name":"Melissa Haendel","orcid":"https://orcid.org/0000-0001-9114-8737"},"institutions":[{"id":"https://openalex.org/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Melissa A Haendel","raw_affiliation_strings":["Department of Biomedical Informatics, University of Colorado, Anschutz Medical Campus , Aurora, CO 80217, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Colorado, Anschutz Medical Campus , Aurora, CO 80217, United States","institution_ids":["https://openalex.org/I51713134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033225381","display_name":"Peter N. Robinson","orcid":"https://orcid.org/0000-0002-0736-9199"},"institutions":[{"id":"https://openalex.org/I4210139777","display_name":"Berlin Institute of Health at Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/0493xsw21","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210139777","https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Peter N Robinson","raw_affiliation_strings":["Berlin Institute of Health at Charit\u00e9 , 10178 Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Berlin Institute of Health at Charit\u00e9 , 10178 Berlin, Germany","institution_ids":["https://openalex.org/I4210139777"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002223413","display_name":"Chris Mungall","orcid":"https://orcid.org/0000-0002-6601-2165"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher J Mungall","raw_affiliation_strings":["Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, United States"],"affiliations":[{"raw_affiliation_string":"Biosystems Data Science, Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, United States","institution_ids":["https://openalex.org/I148283060"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":12,"corresponding_author_ids":["https://openalex.org/A5035050896"],"corresponding_institution_ids":["https://openalex.org/I148283060"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":19.2604,"has_fulltext":true,"cited_by_count":93,"citation_normalized_percentile":{"value":0.99683689,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"40","issue":"3","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":0.9997000098228455,"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":0.9997000098228455,"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":0.9904000163078308,"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":0.9623000025749207,"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":0.8626769781112671},{"id":"https://openalex.org/keywords/schema","display_name":"Schema (genetic algorithms)","score":0.6092340350151062},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.6048544049263},{"id":"https://openalex.org/keywords/question-answering","display_name":"Question answering","score":0.5273552536964417},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.5119470357894897},{"id":"https://openalex.org/keywords/knowledge-base","display_name":"Knowledge base","score":0.5061821341514587},{"id":"https://openalex.org/keywords/interrogation","display_name":"Interrogation","score":0.4944150447845459},{"id":"https://openalex.org/keywords/knowledge-extraction","display_name":"Knowledge extraction","score":0.47814759612083435},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.4652584195137024},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.43751391768455505},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.43071386218070984},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.4150627851486206},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.4111129641532898},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.2882702350616455},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2421075999736786}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8626769781112671},{"id":"https://openalex.org/C52146309","wikidata":"https://www.wikidata.org/wiki/Q7431116","display_name":"Schema (genetic algorithms)","level":2,"score":0.6092340350151062},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.6048544049263},{"id":"https://openalex.org/C44291984","wikidata":"https://www.wikidata.org/wiki/Q1074173","display_name":"Question answering","level":2,"score":0.5273552536964417},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.5119470357894897},{"id":"https://openalex.org/C4554734","wikidata":"https://www.wikidata.org/wiki/Q593744","display_name":"Knowledge base","level":2,"score":0.5061821341514587},{"id":"https://openalex.org/C2776240099","wikidata":"https://www.wikidata.org/wiki/Q327018","display_name":"Interrogation","level":2,"score":0.4944150447845459},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.47814759612083435},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.4652584195137024},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43751391768455505},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.43071386218070984},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.4150627851486206},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4111129641532898},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.2882702350616455},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2421075999736786},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":8,"locations":[{"id":"doi:10.1093/bioinformatics/btae104","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae104","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/3/btae104/56912793/btae104.pdf","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:38383067","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38383067","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:cris.maastrichtuniversity.nl:openaire_cris_publications/462c3a0c-0914-4ef4-bd29-2fb9649d225a","is_oa":true,"landing_page_url":"https://cris.maastrichtuniversity.nl/en/publications/462c3a0c-0914-4ef4-bd29-2fb9649d225a","pdf_url":null,"source":{"id":"https://openalex.org/S4306402616","display_name":"Research Publications (Maastricht University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I34352273","host_organization_name":"Maastricht University","host_organization_lineage":["https://openalex.org/I34352273"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Caufield, J H, Hegde, H, Emonet, V, Harris, N L, Joachimiak, M P, Matentzoglu, N, Kim, H, Moxon, S, Reese, J T, Haendel, M A, Robinson, P N & Mungall, C J 2024, 'Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES) : a method for populating knowledge bases using zero-shot learning', Bioinformatics, vol. 40, no. 3, btae104. https://doi.org/10.1093/bioinformatics/btae104","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt7b51j34r","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/7b51j34r","pdf_url":"https://escholarship.org/content/qt7b51j34r/qt7b51j34r.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"Bioinformatics, vol 40, iss 3","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10924283","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10924283","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10924283/pdf/btae104.pdf","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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:mouseion.jax.org:stfb2024-1056","is_oa":true,"landing_page_url":"https://mouseion.jax.org/stfb2024/76","pdf_url":null,"source":{"id":"https://openalex.org/S4377196421","display_name":"The Mouseion at the JAXlibrary (Jackson Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210115256","host_organization_name":"Jackson Laboratory","host_organization_lineage":["https://openalex.org/I4210115256"],"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":"Faculty Research 2024","raw_type":"text"},{"id":"pmh:oai:osti.gov:2322444","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/2322444","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:osti.gov:2426861","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/2426861","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae104","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae104","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/3/btae104/56912793/btae104.pdf","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":[],"awards":[{"id":"https://openalex.org/G1256250982","display_name":null,"funder_award_id":"RM1 HG010860","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G4508309178","display_name":null,"funder_award_id":"DE-AC0205CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4392619039.pdf"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W90362830","https://openalex.org/W102787101","https://openalex.org/W1853055766","https://openalex.org/W1935434993","https://openalex.org/W1989277387","https://openalex.org/W2044065390","https://openalex.org/W2078336590","https://openalex.org/W2085752173","https://openalex.org/W2123152121","https://openalex.org/W2131420674","https://openalex.org/W2153225416","https://openalex.org/W2346452181","https://openalex.org/W2624086276","https://openalex.org/W2767891136","https://openalex.org/W2772877400","https://openalex.org/W2903298154","https://openalex.org/W2911448018","https://openalex.org/W2950595506","https://openalex.org/W2965518110","https://openalex.org/W3004346089","https://openalex.org/W3094834348","https://openalex.org/W3197984051","https://openalex.org/W3217398853","https://openalex.org/W4233698560","https://openalex.org/W4281481995","https://openalex.org/W4281704579","https://openalex.org/W4285153328","https://openalex.org/W4297253404","https://openalex.org/W4309418205","https://openalex.org/W4381594492","https://openalex.org/W4388144297","https://openalex.org/W4389178822","https://openalex.org/W4391836235","https://openalex.org/W6603694148","https://openalex.org/W6604181502","https://openalex.org/W6639081951","https://openalex.org/W6782087937"],"related_works":["https://openalex.org/W2401316817","https://openalex.org/W1589588912","https://openalex.org/W2382804087","https://openalex.org/W173870552","https://openalex.org/W2167202928","https://openalex.org/W2604144356","https://openalex.org/W4379379356","https://openalex.org/W3095980030","https://openalex.org/W3198510869","https://openalex.org/W3099647347"],"abstract_inverted_index":{"SPIRES":[0],"is":[1],"available":[2],"as":[3],"part":[4],"of":[5],"the":[6],"open":[7],"source":[8],"OntoGPT":[9],"package:":[10],"https://github.com/monarch-initiative/ontogpt.":[11]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":44},{"year":2024,"cited_by_count":31},{"year":2023,"cited_by_count":10}],"updated_date":"2026-04-02T15:55:50.835912","created_date":"2025-10-10T00:00:00"}
