{"id":"https://openalex.org/W4408650424","doi":"https://doi.org/10.1186/s13040-025-00438-9","title":"Automatic detection and extraction of key resources from tables in biomedical papers","display_name":"Automatic detection and extraction of key resources from tables in biomedical papers","publication_year":2025,"publication_date":"2025-03-20","ids":{"openalex":"https://openalex.org/W4408650424","doi":"https://doi.org/10.1186/s13040-025-00438-9","pmid":"https://pubmed.ncbi.nlm.nih.gov/40114222"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-025-00438-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00438-9","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00438-9","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00438-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024882547","display_name":"\u0130brahim Burak \u00d6zyurt","orcid":"https://orcid.org/0000-0003-3944-1893"},"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"]},{"id":"https://openalex.org/I4210118524","display_name":"Universit\u00e9 Bourgogne Franche-Comt\u00e9","ror":"https://ror.org/02dn7x778","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210118524"]}],"countries":["FR","US"],"is_corresponding":true,"raw_author_name":"Ibrahim Burak Ozyurt","raw_affiliation_strings":["FDI Lab Dept of Neuroscience, UCSD, 9500 Gilman Drive M/C 0608, La Jolla, CA, 92093-0608, USA. iozyurt@health.ucsd.edu","FDI Lab Dept of Neuroscience, UCSD, 9500 Gilman Drive M/C 0608, La Jolla, CA, 92093-0608, USA"],"affiliations":[{"raw_affiliation_string":"FDI Lab Dept of Neuroscience, UCSD, 9500 Gilman Drive M/C 0608, La Jolla, CA, 92093-0608, USA. iozyurt@health.ucsd.edu","institution_ids":[]},{"raw_affiliation_string":"FDI Lab Dept of Neuroscience, UCSD, 9500 Gilman Drive M/C 0608, La Jolla, CA, 92093-0608, USA","institution_ids":["https://openalex.org/I36258959","https://openalex.org/I4210118524"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058460697","display_name":"Anita Bandrowski","orcid":"https://orcid.org/0000-0002-5497-0243"},"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"]},{"id":"https://openalex.org/I4210118524","display_name":"Universit\u00e9 Bourgogne Franche-Comt\u00e9","ror":"https://ror.org/02dn7x778","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210118524"]}],"countries":["FR","US"],"is_corresponding":false,"raw_author_name":"Anita Bandrowski","raw_affiliation_strings":["FDI Lab Dept of Neuroscience, UCSD, 9500 Gilman Drive M/C 0608, La Jolla, CA, 92093-0608, USA"],"affiliations":[{"raw_affiliation_string":"FDI Lab Dept of Neuroscience, UCSD, 9500 Gilman Drive M/C 0608, La Jolla, CA, 92093-0608, USA","institution_ids":["https://openalex.org/I36258959","https://openalex.org/I4210118524"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5024882547"],"corresponding_institution_ids":["https://openalex.org/I36258959","https://openalex.org/I4210118524"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.04769708,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"18","issue":"1","first_page":"23","last_page":"23"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9994999766349792,"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":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9980999827384949,"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/T13083","display_name":"Advanced Text Analysis Techniques","score":0.9961000084877014,"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":0.8530482649803162},{"id":"https://openalex.org/keywords/table","display_name":"Table (database)","score":0.755598783493042},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.6525100469589233},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5794364213943481},{"id":"https://openalex.org/keywords/table-of-contents","display_name":"Table of contents","score":0.5551193952560425},{"id":"https://openalex.org/keywords/resource","display_name":"Resource (disambiguation)","score":0.5528483390808105},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.46534478664398193},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.44216811656951904},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40990781784057617},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37414443492889404},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.37119096517562866},{"id":"https://openalex.org/keywords/computer-security","display_name":"Computer security","score":0.13279753923416138}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8530482649803162},{"id":"https://openalex.org/C45235069","wikidata":"https://www.wikidata.org/wiki/Q278425","display_name":"Table (database)","level":2,"score":0.755598783493042},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.6525100469589233},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5794364213943481},{"id":"https://openalex.org/C68476402","wikidata":"https://www.wikidata.org/wiki/Q1456936","display_name":"Table of contents","level":2,"score":0.5551193952560425},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.5528483390808105},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.46534478664398193},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.44216811656951904},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40990781784057617},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37414443492889404},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.37119096517562866},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.13279753923416138},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13040-025-00438-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00438-9","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00438-9","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:40114222","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40114222","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":"BioData mining","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt5v6514p4","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/5v6514p4","pdf_url":"https://escholarship.org/content/qt5v6514p4/qt5v6514p4.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":"BioData Mining, vol 18, iss 1","raw_type":"article"},{"id":"pmh:oai:doaj.org/article:b0e9754fde0744d594316810616c639e","is_oa":true,"landing_page_url":"https://doaj.org/article/b0e9754fde0744d594316810616c639e","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":"BioData Mining, Vol 18, Iss 1, Pp 1-18 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11924859","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11924859","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":"BioData Min","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13040-025-00438-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00438-9","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00438-9","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.49000000953674316,"id":"https://metadata.un.org/sdg/8","display_name":"Decent work and economic growth"}],"awards":[{"id":"https://openalex.org/G7912237117","display_name":null,"funder_award_id":"GM144308","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306192","display_name":"Silicon Valley Community Foundation","ror":"https://ror.org/001ader08"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4408650424.pdf"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W28412257","https://openalex.org/W1569639771","https://openalex.org/W1592986776","https://openalex.org/W1597533204","https://openalex.org/W1995296910","https://openalex.org/W2064675550","https://openalex.org/W2074231493","https://openalex.org/W2102189859","https://openalex.org/W2128863362","https://openalex.org/W2137998699","https://openalex.org/W2250539671","https://openalex.org/W2346015361","https://openalex.org/W2786162033","https://openalex.org/W2913991821","https://openalex.org/W2951325952","https://openalex.org/W2963341956","https://openalex.org/W2980011270","https://openalex.org/W3034997246","https://openalex.org/W3094030525","https://openalex.org/W3096609285","https://openalex.org/W3107064625","https://openalex.org/W3217518891","https://openalex.org/W4200474128","https://openalex.org/W4250156895","https://openalex.org/W4385991106","https://openalex.org/W4387213419","https://openalex.org/W4390902490","https://openalex.org/W4402670299","https://openalex.org/W6739901393"],"related_works":["https://openalex.org/W4394360958","https://openalex.org/W2948670949","https://openalex.org/W4288047943","https://openalex.org/W4394193569","https://openalex.org/W2140798747","https://openalex.org/W1797990060","https://openalex.org/W2948169060","https://openalex.org/W4232484699","https://openalex.org/W4256318226","https://openalex.org/W4253980046"],"abstract_inverted_index":{"Our":[0],"pipelines":[1],"allow":[2],"the":[3,17,40],"detection":[4],"and":[5,38,52],"extraction":[6,23],"of":[7,19,42],"key":[8,32],"resources":[9,33],"from":[10],"tables":[11],"with":[12],"much":[13],"higher":[14],"accuracy,":[15],"enabling":[16],"deployment":[18],"automated":[20],"research":[21],"resource":[22],"tools":[24],"on":[25],"BioRxiv":[26],"to":[27],"help":[28],"authors":[29],"correct":[30],"unidentifiable":[31],"detected":[34],"in":[35],"their":[36,43],"articles":[37],"improve":[39],"reproducibility":[41],"findings.":[44],"The":[45],"code,":[46],"table-specific":[47],"language":[48],"model,":[49],"annotated":[50],"training":[51],"evaluation":[53],"data":[54],"are":[55],"publicly":[56],"available.":[57]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
