{"id":"https://openalex.org/W2163598668","doi":"https://doi.org/10.1186/1471-2105-12-285","title":"S3QL: A distributed domain specific language for controlled semantic integration of life sciences data","display_name":"S3QL: A distributed domain specific language for controlled semantic integration of life sciences data","publication_year":2011,"publication_date":"2011-07-14","ids":{"openalex":"https://openalex.org/W2163598668","doi":"https://doi.org/10.1186/1471-2105-12-285","mag":"2163598668","pmid":"https://pubmed.ncbi.nlm.nih.gov/21756325"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-12-285","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-285","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-285","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/10.1186/1471-2105-12-285","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086141196","display_name":"Helena Deus","orcid":"https://orcid.org/0000-0003-2995-568X"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]},{"id":"https://openalex.org/I2802623135","display_name":"Enterprise Ireland","ror":"https://ror.org/023z51242","country_code":"IE","type":"government","lineage":["https://openalex.org/I2802623135"]},{"id":"https://openalex.org/I83558840","display_name":"Universidade Nova de Lisboa","ror":"https://ror.org/02xankh89","country_code":"PT","type":"education","lineage":["https://openalex.org/I83558840"]}],"countries":["IE","PT"],"is_corresponding":true,"raw_author_name":"Helena F Deus","raw_affiliation_strings":["Digital Enterprise Research Institute, National University of Ireland at Galway, IDA Business Park, Lower Dangan, Galway, Ireland. helena.deus@deri.org","Biomathematics, Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica, Av. da Rep\u00fablica, Esta\u00e7\u00e3o Agron\u00f3mica Nacional, Universidade Nova de Lisboa, Oeiras, Portugal","Digital Enterprise Research Institute, National University of Ireland at Galway, Lower Dangan, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Digital Enterprise Research Institute, National University of Ireland at Galway, IDA Business Park, Lower Dangan, Galway, Ireland. helena.deus@deri.org","institution_ids":["https://openalex.org/I188760350","https://openalex.org/I2802623135"]},{"raw_affiliation_string":"Biomathematics, Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica, Av. da Rep\u00fablica, Esta\u00e7\u00e3o Agron\u00f3mica Nacional, Universidade Nova de Lisboa, Oeiras, Portugal","institution_ids":["https://openalex.org/I83558840"]},{"raw_affiliation_string":"Digital Enterprise Research Institute, National University of Ireland at Galway, Lower Dangan, Ireland","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082970587","display_name":"Miri\u00e3 C Correa","orcid":null},"institutions":[{"id":"https://openalex.org/I4210142352","display_name":"Laborat\u00f3rio Nacional de Computa\u00e7\u00e3o Cient\u00edfica","ror":"https://ror.org/0498ekt05","country_code":"BR","type":"government","lineage":["https://openalex.org/I4210142352"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Miri\u00e3 C Correa","raw_affiliation_strings":["Laborat\u00f3rio Nacional de Computa\u00e7\u00e3o Ci\u00eantifica, Av. Get\u00falio Vargas, 333,Quitandinha, 25651-075, Petr\u00f3polis, Brasil","Laborat\u00f3rio Nacional de Computa\u00e7\u00e3o Ci\u00eantifica, Av. Get\u00falio Vargas, Petr\u00f3polis, Brasil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laborat\u00f3rio Nacional de Computa\u00e7\u00e3o Ci\u00eantifica, Av. Get\u00falio Vargas, 333,Quitandinha, 25651-075, Petr\u00f3polis, Brasil","institution_ids":["https://openalex.org/I4210142352"]},{"raw_affiliation_string":"Laborat\u00f3rio Nacional de Computa\u00e7\u00e3o Ci\u00eantifica, Av. Get\u00falio Vargas, Petr\u00f3polis, Brasil","institution_ids":["https://openalex.org/I4210142352"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056565633","display_name":"Romesh Stanislaus","orcid":null},"institutions":[{"id":"https://openalex.org/I4210111804","display_name":"Sanofi (United States)","ror":"https://ror.org/027vj4x92","country_code":"US","type":"company","lineage":["https://openalex.org/I3018075036","https://openalex.org/I4210111804"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Romesh Stanislaus","raw_affiliation_strings":["Sanofi Pasteur, 38 Sidney Street, Cambridge, MA, 02139, USA","Sanofi Pasteur, Cambridge, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sanofi Pasteur, 38 Sidney Street, Cambridge, MA, 02139, USA","institution_ids":["https://openalex.org/I4210111804"]},{"raw_affiliation_string":"Sanofi Pasteur, Cambridge, USA","institution_ids":["https://openalex.org/I4210111804"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056518605","display_name":"Maria Miragaia","orcid":"https://orcid.org/0000-0002-1323-7184"},"institutions":[{"id":"https://openalex.org/I83558840","display_name":"Universidade Nova de Lisboa","ror":"https://ror.org/02xankh89","country_code":"PT","type":"education","lineage":["https://openalex.org/I83558840"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Maria Miragaia","raw_affiliation_strings":["Laboratory of Molecular Genetics, Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica, Universidade Nova de Lisboa, Av. da Rep\u00fablica, Esta\u00e7\u00e3o Agron\u00f3mica Nacional, 2780-157, Oeiras, Portugal","Laboratory of Molecular Genetics, Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica, Universidade Nova de Lisboa, Av. da Rep\u00fablica, Esta\u00e7\u00e3o Agron\u00f3mica Nacional, Oeiras, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Molecular Genetics, Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica, Universidade Nova de Lisboa, Av. da Rep\u00fablica, Esta\u00e7\u00e3o Agron\u00f3mica Nacional, 2780-157, Oeiras, Portugal","institution_ids":["https://openalex.org/I83558840"]},{"raw_affiliation_string":"Laboratory of Molecular Genetics, Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica, Universidade Nova de Lisboa, Av. da Rep\u00fablica, Esta\u00e7\u00e3o Agron\u00f3mica Nacional, Oeiras, Portugal","institution_ids":["https://openalex.org/I83558840"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032544239","display_name":"Wolfgang Maa\u00df","orcid":"https://orcid.org/0000-0003-4057-0924"},"institutions":[{"id":"https://openalex.org/I882953328","display_name":"Furtwangen University","ror":"https://ror.org/02m11x738","country_code":"DE","type":"education","lineage":["https://openalex.org/I882953328"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Wolfgang Maass","raw_affiliation_strings":["Research Center for Intelligent Media, Furtwangen University, Furtwangen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Center for Intelligent Media, Furtwangen University, Furtwangen, Germany","institution_ids":["https://openalex.org/I882953328"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076223619","display_name":"Herm\u0131\u0301nia de Lencastre","orcid":null},"institutions":[{"id":"https://openalex.org/I83399316","display_name":"Rockefeller University","ror":"https://ror.org/0420db125","country_code":"US","type":"education","lineage":["https://openalex.org/I83399316"]},{"id":"https://openalex.org/I83558840","display_name":"Universidade Nova de Lisboa","ror":"https://ror.org/02xankh89","country_code":"PT","type":"education","lineage":["https://openalex.org/I83558840"]}],"countries":["PT","US"],"is_corresponding":false,"raw_author_name":"Herm\u00ednia de Lencastre","raw_affiliation_strings":["Laboratory of Microbiology, The Rockefeller University, 10021, New York, USA","Laboratory of Molecular Genetics, Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica, Universidade Nova de Lisboa, Av. da Rep\u00fablica, Esta\u00e7\u00e3o Agron\u00f3mica Nacional, 2780-157, Oeiras, Portugal","Laboratory of Microbiology, The Rockefeller University, New York, USA","Laboratory of Molecular Genetics, Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica, Universidade Nova de Lisboa, Av. da Rep\u00fablica, Esta\u00e7\u00e3o Agron\u00f3mica Nacional, Oeiras, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Microbiology, The Rockefeller University, 10021, New York, USA","institution_ids":["https://openalex.org/I83399316"]},{"raw_affiliation_string":"Laboratory of Molecular Genetics, Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica, Universidade Nova de Lisboa, Av. da Rep\u00fablica, Esta\u00e7\u00e3o Agron\u00f3mica Nacional, 2780-157, Oeiras, Portugal","institution_ids":["https://openalex.org/I83558840"]},{"raw_affiliation_string":"Laboratory of Microbiology, The Rockefeller University, New York, USA","institution_ids":["https://openalex.org/I83399316"]},{"raw_affiliation_string":"Laboratory of Molecular Genetics, Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica, Universidade Nova de Lisboa, Av. da Rep\u00fablica, Esta\u00e7\u00e3o Agron\u00f3mica Nacional, Oeiras, Portugal","institution_ids":["https://openalex.org/I83558840"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040459591","display_name":"Ronan Fox","orcid":null},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]},{"id":"https://openalex.org/I2802623135","display_name":"Enterprise Ireland","ror":"https://ror.org/023z51242","country_code":"IE","type":"government","lineage":["https://openalex.org/I2802623135"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Ronan Fox","raw_affiliation_strings":["Digital Enterprise Research Institute, National University of Ireland at Galway, IDA Business Park, Lower Dangan, Galway, Ireland","Digital Enterprise Research Institute, National University of Ireland at Galway, Lower Dangan, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Digital Enterprise Research Institute, National University of Ireland at Galway, IDA Business Park, Lower Dangan, Galway, Ireland","institution_ids":["https://openalex.org/I188760350","https://openalex.org/I2802623135"]},{"raw_affiliation_string":"Digital Enterprise Research Institute, National University of Ireland at Galway, Lower Dangan, Ireland","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012322429","display_name":"Jonas S. Almeida","orcid":"https://orcid.org/0000-0002-7883-7922"},"institutions":[{"id":"https://openalex.org/I32389192","display_name":"University of Alabama at Birmingham","ror":"https://ror.org/008s83205","country_code":"US","type":"education","lineage":["https://openalex.org/I32389192"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonas S Almeida","raw_affiliation_strings":["Division of Informatics, Department of Pathology, University of Alabama at Birmingham, 619 South 19th Street, Birmingham, Alamaba, USA","Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Informatics, Department of Pathology, University of Alabama at Birmingham, 619 South 19th Street, Birmingham, Alamaba, USA","institution_ids":["https://openalex.org/I32389192"]},{"raw_affiliation_string":"Division of Informatics, Department of Pathology, University of Alabama at Birmingham, Birmingham, USA","institution_ids":["https://openalex.org/I32389192"]}]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5086141196"],"corresponding_institution_ids":["https://openalex.org/I188760350","https://openalex.org/I2802623135","https://openalex.org/I83558840"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.8519,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.72215988,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"12","issue":"1","first_page":"285","last_page":"285"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.7153000235557556,"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":0.7153000235557556,"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":0.2101999968290329,"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/T14427","display_name":"Environmental Monitoring and Data Management","score":0.0210999995470047,"subfield":{"id":"https://openalex.org/subfields/1907","display_name":"Geology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7943570613861084},{"id":"https://openalex.org/keywords/interoperation","display_name":"Interoperation","score":0.44755274057388306},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.43419817090034485},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.42365944385528564},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.414632648229599},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.41299015283584595},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.34711965918540955},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2752649784088135},{"id":"https://openalex.org/keywords/ontology-based-data-integration","display_name":"Ontology-based data integration","score":0.2572231888771057},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.16556909680366516},{"id":"https://openalex.org/keywords/ontology-alignment","display_name":"Ontology alignment","score":0.14302369952201843}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7943570613861084},{"id":"https://openalex.org/C139458680","wikidata":"https://www.wikidata.org/wiki/Q12184942","display_name":"Interoperation","level":3,"score":0.44755274057388306},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.43419817090034485},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.42365944385528564},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.414632648229599},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.41299015283584595},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.34711965918540955},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2752649784088135},{"id":"https://openalex.org/C22550185","wikidata":"https://www.wikidata.org/wiki/Q7095047","display_name":"Ontology-based data integration","level":3,"score":0.2572231888771057},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.16556909680366516},{"id":"https://openalex.org/C98893333","wikidata":"https://www.wikidata.org/wiki/Q4339878","display_name":"Ontology alignment","level":4,"score":0.14302369952201843},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001695","descriptor_name":"Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001695","descriptor_name":"Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001695","descriptor_name":"Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","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":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1186/1471-2105-12-285","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-285","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-285","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:21756325","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21756325","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:http://www.rian.ie/116597/","is_oa":false,"landing_page_url":"http://hdl.handle.net/10379/2710","pdf_url":null,"source":{"id":"https://openalex.org/S4306400033","display_name":"Arrow@dit (Dublin Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I115570527","host_organization_name":"Dublin Institute of Technology","host_organization_lineage":["https://openalex.org/I115570527"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Journal article"},{"id":"pmh:oai:www.alexandria.unisg.ch:173033","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400650","display_name":"Alexandria (UniSG) (University of St.Gallen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210158813","host_organization_name":"St.Gallen University of Teacher Education","host_organization_lineage":["https://openalex.org/I4210158813"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Journal paper"},{"id":"pmh:http://www.rian.ie/160998/","is_oa":false,"landing_page_url":"http://hdl.handle.net/10379/11167","pdf_url":null,"source":{"id":"https://openalex.org/S4306400033","display_name":"Arrow@dit (Dublin Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I115570527","host_organization_name":"Dublin Institute of Technology","host_organization_lineage":["https://openalex.org/I115570527"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal article"},{"id":"pmh:oai:doaj.org/article:45873f0f360b4066abbe12877bfcb8cc","is_oa":false,"landing_page_url":"https://doaj.org/article/45873f0f360b4066abbe12877bfcb8cc","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 12, Iss 1, p 285 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2161493","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3155508","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-12-285","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-285","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-285","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":[{"id":"https://openalex.org/G2458437736","display_name":null,"funder_award_id":"5UL1 RR025777","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G2744372981","display_name":null,"funder_award_id":"RR025777","funder_id":"https://openalex.org/F4320310431","funder_display_name":"University of Alabama at Birmingham"},{"id":"https://openalex.org/G3144121387","display_name":null,"funder_award_id":"5UL1 RR025777-03","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G5060993504","display_name":null,"funder_award_id":"SFI/02/CE1/I131","funder_id":"https://openalex.org/F4320320847","funder_display_name":"Science Foundation Ireland"},{"id":"https://openalex.org/G5910938572","display_name":null,"funder_award_id":"RR025777","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7560307215","display_name":null,"funder_award_id":"1U24CA143883-01","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G7705996978","display_name":null,"funder_award_id":"5UL1 RR025777","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320310431","display_name":"University of Alabama at Birmingham","ror":"https://ror.org/008s83205"},{"id":"https://openalex.org/F4320312852","display_name":"University of Alabama","ror":"https://ror.org/03xrrjk67"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320847","display_name":"Science Foundation Ireland","ror":"https://ror.org/0271asj38"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320333360","display_name":"Center for Clinical and Translational Sciences, University of Texas Health Science Center at Houston","ror":null},{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2163598668.pdf","grobid_xml":"https://content.openalex.org/works/W2163598668.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W51161195","https://openalex.org/W812314648","https://openalex.org/W1485293642","https://openalex.org/W1527578413","https://openalex.org/W1595410789","https://openalex.org/W1597754213","https://openalex.org/W1967115261","https://openalex.org/W1971676632","https://openalex.org/W1977069051","https://openalex.org/W1979916898","https://openalex.org/W1980030331","https://openalex.org/W1990505073","https://openalex.org/W1998543083","https://openalex.org/W1999417916","https://openalex.org/W2003798170","https://openalex.org/W2015191210","https://openalex.org/W2050554833","https://openalex.org/W2054176838","https://openalex.org/W2056519407","https://openalex.org/W2061476066","https://openalex.org/W2062926086","https://openalex.org/W2063007776","https://openalex.org/W2097390075","https://openalex.org/W2103017472","https://openalex.org/W2106980948","https://openalex.org/W2107580398","https://openalex.org/W2113142309","https://openalex.org/W2114833437","https://openalex.org/W2116200341","https://openalex.org/W2116753120","https://openalex.org/W2131581981","https://openalex.org/W2131660156","https://openalex.org/W2137698872","https://openalex.org/W2146506075","https://openalex.org/W2152577585","https://openalex.org/W2158351585","https://openalex.org/W2158441613","https://openalex.org/W2165428180","https://openalex.org/W2168482920","https://openalex.org/W2168783124","https://openalex.org/W2169569887","https://openalex.org/W2414558272","https://openalex.org/W2498603544","https://openalex.org/W2608145068","https://openalex.org/W3015465063","https://openalex.org/W4213060373","https://openalex.org/W4252207876","https://openalex.org/W4360975506","https://openalex.org/W4406406874"],"related_works":["https://openalex.org/W2359057422","https://openalex.org/W2355894329","https://openalex.org/W2999699891","https://openalex.org/W2380556669","https://openalex.org/W2157836056","https://openalex.org/W2144347024","https://openalex.org/W2373434917","https://openalex.org/W2105576003","https://openalex.org/W2383759688","https://openalex.org/W2538079489"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,220,233],"value":[2],"and":[3,51,55,66,92,123,125,159,189,238,260,268],"usefulness":[4],"of":[5,21,31,162,171,207,230,241],"data":[6,168,270],"increases":[7],"when":[8],"it":[9],"is":[10,17,38,202],"explicitly":[11],"interlinked":[12],"with":[13,47,60,86,118,204],"related":[14],"data.":[15],"This":[16,200],"the":[18,29,61,98,136,147,167,196,205,215],"core":[19,157,198],"principle":[20],"Linked":[22,32,81,114,163],"Data.":[23,164],"For":[24],"life":[25],"sciences":[26],"researchers,":[27],"harnessing":[28],"power":[30],"Data":[33,82,115],"to":[34,44,152,211,248,253],"improve":[35],"biological":[36,78],"discovery":[37],"still":[39],"challenged":[40],"by":[41,232],"a":[42,128,143,250],"need":[43],"keep":[45],"pace":[46],"rapidly":[48],"evolving":[49],"domains":[50],"requirements":[52],"for":[53,76,108,127,183,256],"collaboration":[54],"control":[56,130],"as":[57,59,80,90,104,178],"well":[58],"reference":[62],"semantic":[63],"web":[64],"ontologies":[65],"standards.":[67],"Knowledge":[68,217],"organization":[69,111],"systems":[70,112,185],"(KOSs)":[71],"can":[72],"provide":[73,249],"an":[74,105,179,208],"abstraction":[75],"publishing":[77],"discoveries":[79],"without":[83],"complicating":[84],"transactions":[85],"contextual":[87],"minutia":[88],"such":[89],"provenance":[91],"access":[93],"control.We":[94],"have":[95],"previously":[96],"described":[97],"Simple":[99,216],"Sloppy":[100],"Semantic":[101],"Database":[102],"(S3DB)":[103],"efficient":[106],"model":[107,158],"creating":[109],"knowledge":[110],"using":[113],"best":[116],"practices":[117],"explicit":[119],"distinction":[120],"between":[121,135,258],"domain":[122,144],"instantiation":[124],"support":[126],"permission":[129],"mechanism":[131,252],"that":[132],"automatically":[133],"migrates":[134],"two.":[137],"In":[138],"this":[139],"report":[140],"we":[141],"present":[142],"specific":[145],"language,":[146],"S3DB":[148,184,197],"query":[149,210],"language":[150],"(S3QL),":[151],"operate":[153],"on":[154],"its":[155,190],"underlying":[156],"facilitate":[160],"management":[161],"RESULTS:":[165],"Reflecting":[166],"driven":[169],"nature":[170],"our":[172],"approach,":[173],"S3QL":[174,209,245],"has":[175],"been":[176],"implemented":[177],"application":[180],"programming":[181],"interface":[182],"hosting":[186],"biomedical":[187,265],"data,":[188],"syntax":[191],"was":[192,246],"subsequently":[193],"generalized":[194],"beyond":[195],"model.":[199],"achievement":[201],"illustrated":[203],"assembly":[206],"manage":[212],"entities":[213],"from":[214],"Organization":[218],"System.":[219],"illustrative":[221],"use":[222],"cases":[223],"include":[224],"gastrointestinal":[225],"clinical":[226],"trials,":[227],"genomic":[228],"characterization":[229],"cancer":[231],"Cancer":[234],"Genome":[235],"Atlas":[236],"(TCGA)":[237],"molecular":[239],"epidemiology":[240],"infectious":[242],"diseases.":[243],"CONCLUSIONS:":[244],"found":[247],"convenient":[251],"represent":[254],"context":[255],"interoperation":[257],"public":[259],"private":[261],"datasets":[262],"hosted":[263],"at":[264],"research":[266],"institutions":[267],"linked":[269],"formalisms.":[271]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}