{"id":"https://openalex.org/W2152274790","doi":"https://doi.org/10.1186/1471-2105-15-s14-s5","title":"EXACT2: the semantics of biomedical protocols","display_name":"EXACT2: the semantics of biomedical protocols","publication_year":2014,"publication_date":"2014-11-27","ids":{"openalex":"https://openalex.org/W2152274790","doi":"https://doi.org/10.1186/1471-2105-15-s14-s5","mag":"2152274790","pmid":"https://pubmed.ncbi.nlm.nih.gov/25472549"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-15-s14-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s14-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S14-S5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S14-S5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022052915","display_name":"Larisa Soldatova","orcid":"https://orcid.org/0000-0001-6489-3029"},"institutions":[{"id":"https://openalex.org/I59433898","display_name":"Brunel University of London","ror":"https://ror.org/00dn4t376","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I59433898"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Larisa N Soldatova","raw_affiliation_strings":["Centre for Systems and Synthetic Biology, Brunel University, Kingston Lane, Uxbridge, London, UB83PH, UK","Department of Computer science, Brunel University, Kingston Lane, Middlesex, London, UB83PH, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Systems and Synthetic Biology, Brunel University, Kingston Lane, Uxbridge, London, UB83PH, UK","institution_ids":["https://openalex.org/I59433898"]},{"raw_affiliation_string":"Department of Computer science, Brunel University, Kingston Lane, Middlesex, London, UB83PH, UK","institution_ids":["https://openalex.org/I59433898"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037876196","display_name":"Daniel Nadis","orcid":null},"institutions":[{"id":"https://openalex.org/I4210086895","display_name":"Community Connections","ror":"https://ror.org/00109m582","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210086895"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel Nadis","raw_affiliation_strings":["Directed Connections Ltd., 59 Elm Street, New Haven, CT, 06510, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Directed Connections Ltd., 59 Elm Street, New Haven, CT, 06510, USA","institution_ids":["https://openalex.org/I4210086895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020822487","display_name":"Ross D. King","orcid":"https://orcid.org/0000-0001-7208-4387"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ross D King","raw_affiliation_strings":["Manchester Institute of Biotechnology, the University of Manchester, 131 Princess Street, Manchester, M13 9PL, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Manchester Institute of Biotechnology, the University of Manchester, 131 Princess Street, Manchester, M13 9PL, UK","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036766667","display_name":"Piyali S. Basu","orcid":null},"institutions":[{"id":"https://openalex.org/I59433898","display_name":"Brunel University of London","ror":"https://ror.org/00dn4t376","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I59433898"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Piyali S Basu","raw_affiliation_strings":["Centre for Systems and Synthetic Biology, Brunel University, Kingston Lane, Uxbridge, London, UB83PH, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Systems and Synthetic Biology, Brunel University, Kingston Lane, Uxbridge, London, UB83PH, UK","institution_ids":["https://openalex.org/I59433898"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070625594","display_name":"E. Haddi","orcid":null},"institutions":[{"id":"https://openalex.org/I59433898","display_name":"Brunel University of London","ror":"https://ror.org/00dn4t376","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I59433898"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Emma Haddi","raw_affiliation_strings":["Department of Computer science, Brunel University, Kingston Lane, Middlesex, London, UB83PH, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer science, Brunel University, Kingston Lane, Middlesex, London, UB83PH, UK","institution_ids":["https://openalex.org/I59433898"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105938982","display_name":"V\u00e9ronique Bauml\u00e9","orcid":null},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Lyon 1 Universit\u00e9","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I113428412","display_name":"\u00c9cole Normale Sup\u00e9rieure de Lyon","ror":"https://ror.org/04zmssz18","country_code":"FR","type":"education","lineage":["https://openalex.org/I113428412","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"V\u00e9ronique Bauml\u00e9","raw_affiliation_strings":["Laboratory of Molecular Biology of the Cell, CNRS, Ecole Normale Sup\u00e9rieure de Lyon, University of Lyon, 1, 46 all\u00e9e d\u00b9Italie, Lyon, 69364, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Molecular Biology of the Cell, CNRS, Ecole Normale Sup\u00e9rieure de Lyon, University of Lyon, 1, 46 all\u00e9e d\u00b9Italie, Lyon, 69364, France","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088371706","display_name":"Nigel J. Saunders","orcid":"https://orcid.org/0000-0002-0160-4573"},"institutions":[{"id":"https://openalex.org/I59433898","display_name":"Brunel University of London","ror":"https://ror.org/00dn4t376","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I59433898"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nigel J Saunders","raw_affiliation_strings":["Centre for Systems and Synthetic Biology, Brunel University, Kingston Lane, Uxbridge, London, UB83PH, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Systems and Synthetic Biology, Brunel University, Kingston Lane, Uxbridge, London, UB83PH, UK","institution_ids":["https://openalex.org/I59433898"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002359152","display_name":"Wolfgang Marwan","orcid":"https://orcid.org/0000-0002-6311-5433"},"institutions":[{"id":"https://openalex.org/I95793202","display_name":"Otto-von-Guericke-Universit\u00e4t Magdeburg","ror":"https://ror.org/00ggpsq73","country_code":"DE","type":"education","lineage":["https://openalex.org/I95793202"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Wolfgang Marwan","raw_affiliation_strings":["Magdeburg Centre for Systems Biology, Otto von Guericke University, MagdeburgPf\u00e4lzerstr. 5, Magdeburg, 39106, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Magdeburg Centre for Systems Biology, Otto von Guericke University, MagdeburgPf\u00e4lzerstr. 5, Magdeburg, 39106, Germany","institution_ids":["https://openalex.org/I95793202"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029698156","display_name":"Brian B. Rudkin","orcid":"https://orcid.org/0000-0003-3700-1982"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Lyon 1 Universit\u00e9","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I113428412","display_name":"\u00c9cole Normale Sup\u00e9rieure de Lyon","ror":"https://ror.org/04zmssz18","country_code":"FR","type":"education","lineage":["https://openalex.org/I113428412","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Brian B Rudkin","raw_affiliation_strings":["Laboratory of Molecular Biology of the Cell, CNRS, Ecole Normale Sup\u00e9rieure de Lyon, University of Lyon, 1, 46 all\u00e9e d\u00b9Italie, Lyon, 69364, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Molecular Biology of the Cell, CNRS, Ecole Normale Sup\u00e9rieure de Lyon, University of Lyon, 1, 46 all\u00e9e d\u00b9Italie, Lyon, 69364, France","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5022052915"],"corresponding_institution_ids":["https://openalex.org/I59433898"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.9501,"has_fulltext":true,"cited_by_count":51,"citation_normalized_percentile":{"value":0.86521242,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"15","issue":"S14","first_page":"S5","last_page":"S5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.7696999907493591,"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":0.7696999907493591,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.041200000792741776,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.026499999687075615,"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":0.8230293989181519},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.6564047336578369},{"id":"https://openalex.org/keywords/biomedicine","display_name":"Biomedicine","score":0.571643054485321},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5481449365615845},{"id":"https://openalex.org/keywords/protocol","display_name":"Protocol (science)","score":0.4963114857673645},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.4857088029384613},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.4727690517902374},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4144291877746582},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.41365134716033936},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.41223713755607605},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2798742651939392},{"id":"https://openalex.org/keywords/ontology-alignment","display_name":"Ontology alignment","score":0.2365114390850067},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.18240588903427124},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.16425129771232605},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.16037511825561523},{"id":"https://openalex.org/keywords/upper-ontology","display_name":"Upper ontology","score":0.14609399437904358},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.11367416381835938}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8230293989181519},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.6564047336578369},{"id":"https://openalex.org/C66782513","wikidata":"https://www.wikidata.org/wiki/Q864601","display_name":"Biomedicine","level":2,"score":0.571643054485321},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5481449365615845},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.4963114857673645},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.4857088029384613},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.4727690517902374},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4144291877746582},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.41365134716033936},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.41223713755607605},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2798742651939392},{"id":"https://openalex.org/C98893333","wikidata":"https://www.wikidata.org/wiki/Q4339878","display_name":"Ontology alignment","level":4,"score":0.2365114390850067},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.18240588903427124},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.16425129771232605},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.16037511825561523},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.14609399437904358},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.11367416381835938},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C204787440","wikidata":"https://www.wikidata.org/wiki/Q188504","display_name":"Alternative medicine","level":2,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001330","descriptor_name":"Electronic Data Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001330","descriptor_name":"Electronic Data Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001330","descriptor_name":"Electronic Data Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-15-s14-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s14-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S14-S5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25472549","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25472549","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4255744","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4255744","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:eprints.gold.ac.uk:23612","is_oa":true,"landing_page_url":null,"pdf_url":"https://research.gold.ac.uk/id/eprint/23612/1/1471-2105-15-S14-S5.pdf","source":{"id":"https://openalex.org/S4306400496","display_name":"Goldsmiths (University of London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I166337079","host_organization_name":"Queen Mary University of London","host_organization_lineage":["https://openalex.org/I166337079"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:bura.brunel.ac.uk:2438/9597","is_oa":true,"landing_page_url":"http://www.biomedcentral.com/1471-2105/15/S14/S5","pdf_url":null,"source":{"id":"https://openalex.org/S4306401473","display_name":"Brunel University Research Archive (BURA) (Brunel University London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I59433898","host_organization_name":"Brunel University of London","host_organization_lineage":["https://openalex.org/I59433898"],"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":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-15-s14-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s14-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S14-S5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2152274790.pdf","grobid_xml":"https://content.openalex.org/works/W2152274790.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W131136971","https://openalex.org/W139644854","https://openalex.org/W1489737525","https://openalex.org/W1544455702","https://openalex.org/W1602659612","https://openalex.org/W1982258868","https://openalex.org/W1986409260","https://openalex.org/W2008415486","https://openalex.org/W2010342709","https://openalex.org/W2013434113","https://openalex.org/W2014664086","https://openalex.org/W2017055915","https://openalex.org/W2022451103","https://openalex.org/W2033377040","https://openalex.org/W2054558802","https://openalex.org/W2062558911","https://openalex.org/W2098057270","https://openalex.org/W2103956502","https://openalex.org/W2114648293","https://openalex.org/W2114804859","https://openalex.org/W2122786045","https://openalex.org/W2134784304","https://openalex.org/W2135561728","https://openalex.org/W2142793248","https://openalex.org/W2144593174","https://openalex.org/W2149378423","https://openalex.org/W2158568548","https://openalex.org/W2178026535","https://openalex.org/W2335400770","https://openalex.org/W2401742761","https://openalex.org/W2405033759","https://openalex.org/W4235408951","https://openalex.org/W4246224631","https://openalex.org/W4255852734","https://openalex.org/W4300022934"],"related_works":["https://openalex.org/W2251332378","https://openalex.org/W2127299687","https://openalex.org/W122651434","https://openalex.org/W1506177826","https://openalex.org/W2532736362","https://openalex.org/W2726617685","https://openalex.org/W1562796463","https://openalex.org/W1530162452","https://openalex.org/W2106349067","https://openalex.org/W2008629522"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,144,161,227],"reliability":[2],"and":[3,66,200,252],"reproducibility":[4],"of":[5,11,24,49,64,73,103,109,117,136,158,163,169,216,249,271],"experimental":[6,50,198,250],"procedures":[7,171],"is":[8,15,52,129,183,224,230],"a":[9,16,77,94,148,175,186,220,235,264,278],"cornerstone":[10],"scientific":[12],"practice.":[13],"There":[14],"pressing":[17],"technological":[18],"need":[19],"for":[20,46,80,114,140,189,213,267,268],"the":[21,47,82,91,101,106,115,123,133,155,167,214,239,269],"better":[22,35],"representation":[23,157],"biomedical":[25,68,137,159,170,204,217,243,272],"protocols":[26,51,69,92,138,205,218,273],"to":[27,34,54,89,131,165,193,197,219,232],"enable":[28],"other":[29],"agents":[30],"(human":[31],"or":[32],"machine)":[33],"reproduce":[36],"results.":[37],"A":[38],"framework":[39,212],"that":[40,42,128,153],"ensures":[41],"all":[43],"information":[44,84,241],"required":[45,83,139],"replication":[48],"essential":[53,240],"achieve":[55],"reproducibility.":[56,142],"To":[57],"construct":[58],"EXACT2":[59,104,125,152,164,182,228,245],"we":[60,85],"manually":[61],"inspected":[62],"hundreds":[63],"published":[65],"commercial":[67],"from":[70],"several":[71],"areas":[72],"biomedicine.":[74],"After":[75],"establishing":[76],"clear":[78],"pattern":[79],"extracting":[81],"utilized":[86],"text-mining":[87],"tools":[88,192],"translate":[90],"into":[93,277],"machine":[95,221,236],"amenable":[96,222],"format.":[97,280],"We":[98,120],"have":[99,121],"verified":[100,173],"utility":[102],"through":[105,174],"successful":[107],"processing":[108],"previously":[110],"'unseen'":[111],"(not":[112],"used":[113,184,255],"construction":[116],"EXACT2)protocols.":[118],"METHODS:":[119],"developed":[122],"ontology":[124,229],"(EXperimental":[126],"ACTions)":[127],"designed":[130],"capture":[132,166],"full":[134],"semantics":[135,168,248],"their":[141,201],"RESULTS:":[143],"paper":[145],"reports":[146],"on":[147],"fundamentally":[149],"new":[150],"version":[151],"supports":[154],"semantically-defined":[156,279],"protocols.":[160,244],"ability":[162],"was":[172],"text":[176,190],"mining":[177,191],"use":[178],"case.":[179],"In":[180],"this":[181],"as":[185,263],"reference":[187,265],"model":[188,266],"identify":[194],"terms":[195],"pertinent":[196],"actions,":[199,251],"properties,":[202],"in":[203,207,234,274],"expressed":[206],"natural":[208,275],"language.":[209],"An":[210],"EXACT2-based":[211],"translation":[215,270],"format":[223],"proposed.":[225],"CONCLUSIONS:":[226],"sufficient":[231],"record,":[233],"processable":[237],"form,":[238],"about":[242],"defines":[246],"explicit":[247],"can":[253,261],"be":[254],"by":[256],"various":[257],"computer":[258],"applications.":[259],"It":[260],"serve":[262],"language":[276]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1}],"updated_date":"2026-08-05T07:39:15.569665","created_date":"2025-10-10T00:00:00"}
