{"id":"https://openalex.org/W4316926564","doi":"https://doi.org/10.1093/bioinformatics/btad035","title":"Discovering research articles containing evolutionary timetrees by machine learning","display_name":"Discovering research articles containing evolutionary timetrees by machine learning","publication_year":2023,"publication_date":"2023-01-01","ids":{"openalex":"https://openalex.org/W4316926564","doi":"https://doi.org/10.1093/bioinformatics/btad035","pmid":"https://pubmed.ncbi.nlm.nih.gov/36648314"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad035","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad035","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btad035/48959142/btad035.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/39/1/btad035/48959142/btad035.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023801090","display_name":"Marija Stanojevi\u0107","orcid":"https://orcid.org/0000-0001-8227-6577"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Marija Stanojevic","raw_affiliation_strings":["Center for Data Analytics and Biomedical Informatics, Computer and Information Science Department, Temple University , Philadelphia, PA 19121, USA"],"raw_orcid":"https://orcid.org/0000-0001-8227-6577","affiliations":[{"raw_affiliation_string":"Center for Data Analytics and Biomedical Informatics, Computer and Information Science Department, Temple University , Philadelphia, PA 19121, USA","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075143293","display_name":"Jovan Andjelkovic","orcid":"https://orcid.org/0009-0009-4319-6051"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jovan Andjelkovic","raw_affiliation_strings":["Center for Data Analytics and Biomedical Informatics, Computer and Information Science Department, Temple University , Philadelphia, PA 19121, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Data Analytics and Biomedical Informatics, Computer and Information Science Department, Temple University , Philadelphia, PA 19121, USA","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028989535","display_name":"Adrienne E Kasprowicz","orcid":"https://orcid.org/0000-0002-8069-2144"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adrienne Kasprowicz","raw_affiliation_strings":["Department of Biology, Temple University , Philadelphia, PA 19121, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University , Philadelphia, PA 19121, USA","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005665859","display_name":"Louise A. Huuki-Myers","orcid":"https://orcid.org/0000-0001-5148-3602"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Louise A Huuki","raw_affiliation_strings":["Department of Biology, Temple University , Philadelphia, PA 19121, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University , Philadelphia, PA 19121, USA","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036159954","display_name":"Jennifer R. Chao","orcid":"https://orcid.org/0000-0002-6859-5552"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jennifer Chao","raw_affiliation_strings":["Center for Data Analytics and Biomedical Informatics, Computer and Information Science Department, Temple University , Philadelphia, PA 19121, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Data Analytics and Biomedical Informatics, Computer and Information Science Department, Temple University , Philadelphia, PA 19121, USA","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056603005","display_name":"S. Blair Hedges","orcid":"https://orcid.org/0000-0002-0652-2411"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S Blair Hedges","raw_affiliation_strings":["Department of Biology, Temple University , Philadelphia, PA 19121, USA","Institute for Genomics and Evolutionary Medicine, Temple University , Philadelphia, PA 19121, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University , Philadelphia, PA 19121, USA","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine, Temple University , Philadelphia, PA 19121, USA","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100680948","display_name":"Sudhir Kumar","orcid":"https://orcid.org/0000-0002-9918-8212"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sudhir Kumar","raw_affiliation_strings":["Department of Biology, Temple University , Philadelphia, PA 19121, USA","Institute for Genomics and Evolutionary Medicine, Temple University , Philadelphia, PA 19121, USA"],"raw_orcid":"https://orcid.org/0000-0002-9918-8212","affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University , Philadelphia, PA 19121, USA","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine, Temple University , Philadelphia, PA 19121, USA","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044038055","display_name":"Zoran Obradovi\u0107","orcid":"https://orcid.org/0000-0002-2051-0142"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zoran Obradovic","raw_affiliation_strings":["Center for Data Analytics and Biomedical Informatics, Computer and Information Science Department, Temple University , Philadelphia, PA 19121, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Data Analytics and Biomedical Informatics, Computer and Information Science Department, Temple University , Philadelphia, PA 19121, USA","institution_ids":["https://openalex.org/I84392919"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5023801090","https://openalex.org/A5044038055","https://openalex.org/A5100680948"],"corresponding_institution_ids":["https://openalex.org/I84392919"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.4044,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.63624905,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"39","issue":"1","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":0.2782999873161316,"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":0.2782999873161316,"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/T12205","display_name":"Time Series Analysis and Forecasting","score":0.19519999623298645,"subfield":{"id":"https://openalex.org/subfields/1711","display_name":"Signal Processing"},"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/T11937","display_name":"Research Data Management Practices","score":0.1509999930858612,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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":0.775980532169342},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5762869715690613},{"id":"https://openalex.org/keywords/inclusion","display_name":"Inclusion (mineral)","score":0.5255593061447144},{"id":"https://openalex.org/keywords/automation","display_name":"Automation","score":0.49412086606025696},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.48818451166152954},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.45962750911712646},{"id":"https://openalex.org/keywords/resource","display_name":"Resource (disambiguation)","score":0.4542357325553894},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.42534250020980835},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.41739484667778015},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.4152202308177948},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4021192491054535},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36501556634902954},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3406582474708557},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.30389702320098877},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.21589446067810059},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09405398368835449}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.775980532169342},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5762869715690613},{"id":"https://openalex.org/C109359841","wikidata":"https://www.wikidata.org/wiki/Q728944","display_name":"Inclusion (mineral)","level":2,"score":0.5255593061447144},{"id":"https://openalex.org/C115901376","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automation","level":2,"score":0.49412086606025696},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.48818451166152954},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.45962750911712646},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.4542357325553894},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.42534250020980835},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.41739484667778015},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.4152202308177948},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4021192491054535},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36501556634902954},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3406582474708557},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.30389702320098877},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.21589446067810059},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09405398368835449},{"id":"https://openalex.org/C107993555","wikidata":"https://www.wikidata.org/wiki/Q1662673","display_name":"Gender studies","level":1,"score":0.0},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"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/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","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":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btad035","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad035","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btad035/48959142/btad035.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:36648314","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36648314","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:9887078","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9887078","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9887078/pdf/btad035.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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:null:20.500.12613/10810","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.12613/10810","pdf_url":null,"source":{"id":"https://openalex.org/S4306402624","display_name":"TUScholarShare (Temple University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I84392919","host_organization_name":"Temple University","host_organization_lineage":["https://openalex.org/I84392919"],"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":null,"raw_type":"Journal article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad035","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad035","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btad035/48959142/btad035.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/G1017287825","display_name":null,"funder_award_id":"W911NF-16-2-0189","funder_id":"https://openalex.org/F4320338295","funder_display_name":"Army Research Laboratory"},{"id":"https://openalex.org/G2762979999","display_name":null,"funder_award_id":"MRI 1625061","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4412420759","display_name":"MRI: Acquisition of a Flexible High-Performance Computing System for Data and Compute Driven Scientific Discovery","funder_award_id":"1625061","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5259331294","display_name":null,"funder_award_id":"W911NF","funder_id":"https://openalex.org/F4320338295","funder_display_name":"Army Research Laboratory"},{"id":"https://openalex.org/G8096768565","display_name":"CIBR:Accelerating the discovery and utility of the timescale of life","funder_award_id":"1932765","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8913858690","display_name":null,"funder_award_id":"DBI 1932765","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320338295","display_name":"Army Research Laboratory","ror":"https://ror.org/011hc8f90"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4316926564.pdf"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1985697096","https://openalex.org/W2135046866","https://openalex.org/W2144211451","https://openalex.org/W2153452535","https://openalex.org/W2911489562","https://openalex.org/W4290075586","https://openalex.org/W4294170691","https://openalex.org/W6682691769"],"related_works":["https://openalex.org/W2887358545","https://openalex.org/W3185553570","https://openalex.org/W2155401483","https://openalex.org/W3045247719","https://openalex.org/W2914463643","https://openalex.org/W2102102835","https://openalex.org/W4241083716","https://openalex.org/W2096951189","https://openalex.org/W3185751515","https://openalex.org/W2757130632"],"abstract_inverted_index":{"MOTIVATION:":[0],"Timetrees":[1],"depict":[2],"evolutionary":[3,109],"relationships":[4],"between":[5],"species":[6],"and":[7,36,71,82,220,228],"the":[8,77,115,143,153,170,187,193,204,218],"geological":[9],"times":[10],"of":[11,15,49,62,79,131,145,161,222],"their":[12],"divergence.":[13],"Hundreds":[14],"research":[16,87,105],"articles":[17,41,64,88,126,162,179,210],"containing":[18,65,89],"timetrees":[19,38,66,90,223],"are":[20,239],"published":[21,209],"in":[22,114,152,186],"scientific":[23],"journals":[24],"every":[25],"year.":[26],"The":[27,59,147],"TimeTree":[28,48],"(TT)":[29],"project":[30],"has":[31],"been":[32],"manually":[33],"locating,":[34],"curating":[35],"synthesizing":[37],"from":[39],"these":[40],"for":[42,112],"almost":[43],"two":[44],"decades":[45],"into":[46],"a":[47,53,104,197],"Life,":[50],"delivered":[51],"through":[52],"unique,":[54],"user-friendly":[55],"web":[56],"interface":[57],"(timetree.org).":[58],"manual":[60],"process":[61],"finding":[63],"is":[67,150,211],"becoming":[68],"increasingly":[69],"expensive":[70],"time-consuming.":[72],"So,":[73],"we":[74,134],"have":[75,94],"explored":[76],"effectiveness":[78],"text-mining":[80,139],"approaches":[81],"developed":[83,95],"optimizations":[84],"to":[85,101,136,163,196],"find":[86],"automatically.":[91],"RESULTS:":[92],"We":[93,118,167],"an":[96,108,128],"optimized":[97],"machine":[98],"learning":[99],"system":[100],"determine":[102],"if":[103],"article":[106,140],"contains":[107],"timetree":[110],"appropriate":[111],"inclusion":[113,185],"TT":[116,188],"resource.":[117],"found":[119],"that":[120,169,203],"BERT":[121],"classification":[122],"fine-tuned":[123],"on":[124,206],"whole-text":[125],"achieved":[127],"F1":[129],"score":[130],"0.67,":[132],"which":[133,157],"increased":[135],"0.88":[137],"by":[138],"excerpts":[141],"surrounding":[142],"mentioning":[144],"figures.":[146],"new":[148],"method":[149],"implemented":[151],"TimeTreeFinder":[154],"(TTF)":[155],"tool,":[156],"automatically":[158],"processes":[159],"millions":[160],"discover":[164],"timetree-containing":[165,178],"articles.":[166],"estimate":[168],"TTF":[171],"tool":[172],"would":[173,190],"produce":[174],"twice":[175],"as":[176,180],"many":[177],"those":[181],"discovered":[182],"manually,":[183],"whose":[184],"database":[189],"potentially":[191],"double":[192],"knowledge":[194],"accessible":[195],"wider":[198],"community.":[199],"Manual":[200],"inspection":[201],"showed":[202],"precision":[205],"out-of-distribution":[207],"recently":[208],"87%.":[212],"This":[213],"automation":[214],"will":[215],"speed":[216],"up":[217],"collection":[219],"curation":[221],"with":[224],"much":[225],"lower":[226],"human":[227],"time":[229],"costs.":[230],"AVAILABILITY":[231],"AND":[232],"IMPLEMENTATION:":[233],"https://github.com/marija-stanojevic/time-tree-classification.":[234],"SUPPLEMENTARY":[235],"INFORMATION:":[236],"Supplementary":[237],"data":[238],"available":[240],"at":[241],"Bioinformatics":[242],"online.":[243]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-07-10T07:45:09.275182","created_date":"2025-10-10T00:00:00"}