{"id":"https://openalex.org/W1977069051","doi":"https://doi.org/10.1186/1471-2105-11-387","title":"S3DB core: a framework for RDF generation and management in bioinformatics infrastructures","display_name":"S3DB core: a framework for RDF generation and management in bioinformatics infrastructures","publication_year":2010,"publication_date":"2010-07-20","ids":{"openalex":"https://openalex.org/W1977069051","doi":"https://doi.org/10.1186/1471-2105-11-387","mag":"1977069051","pmid":"https://pubmed.ncbi.nlm.nih.gov/20646315"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-387","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-387","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-387","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/10.1186/1471-2105-11-387","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012322429","display_name":"Jonas S. Almeida","orcid":"https://orcid.org/0000-0002-7883-7922"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jonas S Almeida","raw_affiliation_strings":["Department of Bioinformatics and Computational Biology, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd Houston, TX 77030, USA. jalmeida@mathbiol.org","Department of Bioinformatics and Computational Biology, The University of Texas M D Anderson Cancer Center, , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Computational Biology, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd Houston, TX 77030, USA. jalmeida@mathbiol.org","institution_ids":["https://openalex.org/I1343551460"]},{"raw_affiliation_string":"Department of Bioinformatics and Computational Biology, The University of Texas M D Anderson Cancer Center, , USA","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086141196","display_name":"Helena Deus","orcid":"https://orcid.org/0000-0003-2995-568X"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]},{"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":"Helena F Deus","raw_affiliation_strings":["Department of Bioinformatics and Computational Biology, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd Houston, TX, 77030, USA","Institute of Chemical and Biological Technology, Universidade Nova de Lisboa, Oeiras, Portugal","Department of Bioinformatics and Computational Biology, The University of Texas M D Anderson Cancer Center, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Computational Biology, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd Houston, TX, 77030, USA","institution_ids":["https://openalex.org/I1343551460"]},{"raw_affiliation_string":"Institute of Chemical and Biological Technology, Universidade Nova de Lisboa, Oeiras, Portugal","institution_ids":["https://openalex.org/I83558840"]},{"raw_affiliation_string":"Department of Bioinformatics and Computational Biology, The University of Texas M D Anderson Cancer Center, USA","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"last","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"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5012322429"],"corresponding_institution_ids":["https://openalex.org/I1343551460"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":7.2485,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.96439427,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"11","issue":"1","first_page":"387","last_page":"387"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.7135999798774719,"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"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.7135999798774719,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.11289999634027481,"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":0.026900000870227814,"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":0.7973324060440063},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.6259123086929321},{"id":"https://openalex.org/keywords/rdf","display_name":"RDF","score":0.5189142227172852},{"id":"https://openalex.org/keywords/personalization","display_name":"Personalization","score":0.4686300754547119},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.46361643075942993},{"id":"https://openalex.org/keywords/linked-data","display_name":"Linked data","score":0.4483012557029724},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.38546299934387207},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3299219608306885}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7973324060440063},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.6259123086929321},{"id":"https://openalex.org/C147497476","wikidata":"https://www.wikidata.org/wiki/Q54872","display_name":"RDF","level":3,"score":0.5189142227172852},{"id":"https://openalex.org/C183003079","wikidata":"https://www.wikidata.org/wiki/Q1000371","display_name":"Personalization","level":2,"score":0.4686300754547119},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.46361643075942993},{"id":"https://openalex.org/C69075417","wikidata":"https://www.wikidata.org/wiki/Q515701","display_name":"Linked data","level":3,"score":0.4483012557029724},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.38546299934387207},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3299219608306885}],"mesh":[{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-11-387","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-387","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-387","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:20646315","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20646315","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:www.alexandria.unisg.ch:68304","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:oai:doaj.org/article:9a50ebc1f2e8496ab26d559e64587fbe","is_oa":true,"landing_page_url":"https://doaj.org/article/9a50ebc1f2e8496ab26d559e64587fbe","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 11, Iss 1, p 387 (2010)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:1999646","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2918582","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:10.1186/1471-2105-11-387","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-387","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-387","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":[{"id":"https://metadata.un.org/sdg/9","score":0.6399999856948853,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G2223084270","display_name":null,"funder_award_id":"1UL1RR024148","funder_id":"https://openalex.org/F4320333360","funder_display_name":"Center for Clinical and Translational Sciences, University of Texas Health Science Center at Houston"},{"id":"https://openalex.org/G4481661528","display_name":null,"funder_award_id":"1UL1RR024148","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"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"}],"funders":[{"id":"https://openalex.org/F4320316438","display_name":"Georgia Clinical and Translational Science Alliance","ror":null},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"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/W1977069051.pdf","grobid_xml":"https://content.openalex.org/works/W1977069051.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W1485293642","https://openalex.org/W1548849615","https://openalex.org/W1967841763","https://openalex.org/W2001143464","https://openalex.org/W2005494948","https://openalex.org/W2007239153","https://openalex.org/W2020112523","https://openalex.org/W2054176838","https://openalex.org/W2120337732","https://openalex.org/W2127451705","https://openalex.org/W2146144840","https://openalex.org/W2154687603","https://openalex.org/W2155149969","https://openalex.org/W2158441613","https://openalex.org/W2169049983","https://openalex.org/W2169569887","https://openalex.org/W2171999860","https://openalex.org/W2172307690","https://openalex.org/W2414558272","https://openalex.org/W2914428814","https://openalex.org/W3207397737"],"related_works":["https://openalex.org/W2283287182","https://openalex.org/W82112649","https://openalex.org/W1485690712","https://openalex.org/W2058923328","https://openalex.org/W2897957211","https://openalex.org/W2776293731","https://openalex.org/W2610919777","https://openalex.org/W2965230088","https://openalex.org/W4293389049","https://openalex.org/W1534806717"],"abstract_inverted_index":{"BACKGROUND:":[0],"Biomedical":[1],"research":[2,25],"is":[3],"set":[4],"to":[5,55,105,119,125,177,186],"greatly":[6],"benefit":[7],"from":[8,113],"the":[9,16,39,42,58,63,73,134,138,149,159,169,188],"use":[10],"of":[11,18,29,44,66,79,109,152,158,191],"semantic":[12,85],"web":[13,86],"technologies":[14],"in":[15,38,173],"design":[17,189],"computational":[19,48,193],"infrastructure.":[20],"However,":[21],"beyond":[22,148],"well":[23],"defined":[24],"initiatives,":[26],"substantial":[27],"issues":[28],"data":[30,60,70,116,120,129],"heterogeneity,":[31],"source":[32,101],"distribution,":[33],"and":[34,62,68,142,144,175,205],"privacy":[35],"currently":[36],"stand":[37],"way":[40],"towards":[41],"personalization":[43],"Medicine.":[45],"RESULTS:":[46],"A":[47],"framework":[49,77],"for":[50,168],"bioinformatic":[51],"infrastructure":[52],"was":[53,103,184],"designed":[54],"deal":[56],"with":[57,84,89],"heterogeneous":[59],"sources":[61],"sensitive":[64],"mixture":[65],"public":[67],"private":[69],"that":[71,93,111,123],"characterizes":[72],"biomedical":[74,192],"domain.":[75],"This":[76,131],"consists":[78],"a":[80,90,107,162,165],"logical":[81,141],"model":[82,167,182],"build":[83],"tools,":[87],"coupled":[88],"Markov":[91],"process":[92],"propagates":[94],"user":[95],"operator":[96],"states.":[97],"An":[98],"accompanying":[99],"open":[100],"prototype":[102],"developed":[104],"meet":[106],"series":[108],"applications":[110,122],"range":[112],"collaborative":[114],"multi-institution":[115],"acquisition":[117],"efforts":[118],"analysis":[121],"need":[124],"quickly":[126],"traverse":[127],"complex":[128],"structures.":[130],"report":[132],"describes":[133],"two":[135],"abstractions":[136],"underlying":[137],"S3DB-based":[139],"infrastructure,":[140,194],"numerical,":[143],"discusses":[145],"its":[146],"generality":[147],"immediate":[150],"confines":[151],"existing":[153],"implementations.":[154],"CONCLUSIONS:":[155],"The":[156,179],"emergence":[157],"\"web":[160],"as":[161,196],"computer\"":[163],"requires":[164],"formal":[166],"different":[170],"functionalities":[171],"involved":[172],"reading":[174],"writing":[176],"it.":[178],"S3DB":[180],"core":[181],"proposed":[183],"found":[185],"address":[187],"criteria":[190],"such":[195],"those":[197],"supporting":[198],"large":[199],"scale":[200],"multi-investigator":[201],"research,":[202],"clinical":[203],"trials,":[204],"molecular":[206],"epidemiology.":[207]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
