{"id":"https://openalex.org/W1999853092","doi":"https://doi.org/10.1186/2047-2501-1-7","title":"Dynamic integration of biological data sources using the data concierge","display_name":"Dynamic integration of biological data sources using the data concierge","publication_year":2013,"publication_date":"2013-02-04","ids":{"openalex":"https://openalex.org/W1999853092","doi":"https://doi.org/10.1186/2047-2501-1-7","mag":"1999853092","pmid":"https://pubmed.ncbi.nlm.nih.gov/25825659"},"language":"en","primary_location":{"id":"doi:10.1186/2047-2501-1-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2047-2501-1-7","pdf_url":"https://link.springer.com/content/pdf/10.1186%2F2047-2501-1-7.pdf","source":{"id":"https://openalex.org/S4210178793","display_name":"Health Information Science and Systems","issn_l":"2047-2501","issn":["2047-2501"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319965","host_organization_name":"Springer Nature","host_organization_lineage":["https://openalex.org/P4310319965"],"host_organization_lineage_names":["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":"Health Information Science and Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1186%2F2047-2501-1-7.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102147815","display_name":"Peng Gong","orcid":null},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]},{"id":"https://openalex.org/I2799732068","display_name":"Royal Prince Alfred Hospital","ror":"https://ror.org/05gpvde20","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I2799732068"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Peng Gong","raw_affiliation_strings":["Biomedical and Multimedia Information Technology (BMIT) Research Group, School of Information Technologies, the University of Sydney, Sydney, NSW 2006 Australia ; Department of PET and Nuclear Medicine, RPA Hospital, Camperdown, NSW 2050 Australia","Biomedical and Multimedia Information Technology (BMIT) Research Group, School of Information Technologies, the University of Sydney, Sydney, Australia","Department of PET and Nuclear Medicine, RPA Hospital, Camperdown, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical and Multimedia Information Technology (BMIT) Research Group, School of Information Technologies, the University of Sydney, Sydney, NSW 2006 Australia ; Department of PET and Nuclear Medicine, RPA Hospital, Camperdown, NSW 2050 Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Biomedical and Multimedia Information Technology (BMIT) Research Group, School of Information Technologies, the University of Sydney, Sydney, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Department of PET and Nuclear Medicine, RPA Hospital, Camperdown, Australia","institution_ids":["https://openalex.org/I2799732068"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5102147815"],"corresponding_institution_ids":["https://openalex.org/I129604602","https://openalex.org/I2799732068"],"apc_list":{"value":3590,"currency":"USD","value_usd":3590},"apc_paid":{"value":3590,"currency":"USD","value_usd":3590},"fwci":0.8151,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.82884411,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"1","issue":"1","first_page":"7","last_page":"7"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.8693000078201294,"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":0.8693000078201294,"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":0.02410000003874302,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.010300000198185444,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8180161118507385},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.6073629856109619},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.6008737683296204},{"id":"https://openalex.org/keywords/middleware","display_name":"Middleware (distributed applications)","score":0.5664923787117004},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.549471378326416},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.5226119160652161},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.5200733542442322},{"id":"https://openalex.org/keywords/evolvability","display_name":"Evolvability","score":0.5126811265945435},{"id":"https://openalex.org/keywords/dynamic-data","display_name":"Dynamic data","score":0.5015695095062256},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.4817409813404083},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.43809887766838074},{"id":"https://openalex.org/keywords/data-type","display_name":"Data type","score":0.4355573058128357},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.4111418128013611},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2729916572570801},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2543584406375885},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.19163107872009277},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.12288430333137512},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.12174275517463684}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8180161118507385},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.6073629856109619},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.6008737683296204},{"id":"https://openalex.org/C169468491","wikidata":"https://www.wikidata.org/wiki/Q146923","display_name":"Middleware (distributed applications)","level":2,"score":0.5664923787117004},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.549471378326416},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.5226119160652161},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.5200733542442322},{"id":"https://openalex.org/C176147130","wikidata":"https://www.wikidata.org/wiki/Q909622","display_name":"Evolvability","level":2,"score":0.5126811265945435},{"id":"https://openalex.org/C197298091","wikidata":"https://www.wikidata.org/wiki/Q5318963","display_name":"Dynamic data","level":2,"score":0.5015695095062256},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.4817409813404083},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.43809887766838074},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.4355573058128357},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.4111418128013611},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2729916572570801},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2543584406375885},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.19163107872009277},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.12288430333137512},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.12174275517463684},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/2047-2501-1-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2047-2501-1-7","pdf_url":"https://link.springer.com/content/pdf/10.1186%2F2047-2501-1-7.pdf","source":{"id":"https://openalex.org/S4210178793","display_name":"Health Information Science and Systems","issn_l":"2047-2501","issn":["2047-2501"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319965","host_organization_name":"Springer Nature","host_organization_lineage":["https://openalex.org/P4310319965"],"host_organization_lineage_names":["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":"Health Information Science and Systems","raw_type":"journal-article"},{"id":"pmid:25825659","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25825659","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":"Health information science and systems","raw_type":null},{"id":"pmh:oai:europepmc.org:3339434","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4340781","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:10.1186/2047-2501-1-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/2047-2501-1-7","pdf_url":"https://link.springer.com/content/pdf/10.1186%2F2047-2501-1-7.pdf","source":{"id":"https://openalex.org/S4210178793","display_name":"Health Information Science and Systems","issn_l":"2047-2501","issn":["2047-2501"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319965","host_organization_name":"Springer Nature","host_organization_lineage":["https://openalex.org/P4310319965"],"host_organization_lineage_names":["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":"Health Information Science and Systems","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Decent work and economic growth","score":0.4300000071525574,"id":"https://metadata.un.org/sdg/8"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1999853092.pdf","grobid_xml":"https://content.openalex.org/works/W1999853092.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W11383479","https://openalex.org/W119851965","https://openalex.org/W123447907","https://openalex.org/W172445582","https://openalex.org/W1509396824","https://openalex.org/W1515884279","https://openalex.org/W1569952392","https://openalex.org/W1756130223","https://openalex.org/W1961884151","https://openalex.org/W1971676632","https://openalex.org/W1983594585","https://openalex.org/W1991427566","https://openalex.org/W2007206683","https://openalex.org/W2020808776","https://openalex.org/W2028496064","https://openalex.org/W2040572073","https://openalex.org/W2051231851","https://openalex.org/W2081213386","https://openalex.org/W2093410900","https://openalex.org/W2094258495","https://openalex.org/W2098035424","https://openalex.org/W2100357759","https://openalex.org/W2103129584","https://openalex.org/W2103487267","https://openalex.org/W2103538877","https://openalex.org/W2114478923","https://openalex.org/W2120615294","https://openalex.org/W2126471648","https://openalex.org/W2128860178","https://openalex.org/W2134298747","https://openalex.org/W2155592392","https://openalex.org/W2156620408","https://openalex.org/W2157938327","https://openalex.org/W2160948978","https://openalex.org/W2161666572","https://openalex.org/W2164649389","https://openalex.org/W2165428180","https://openalex.org/W2166548438","https://openalex.org/W2169465962","https://openalex.org/W2170526892","https://openalex.org/W2916406266","https://openalex.org/W2993222596","https://openalex.org/W4253490510"],"related_works":["https://openalex.org/W2307569040","https://openalex.org/W2366067673","https://openalex.org/W2060096282","https://openalex.org/W2131941936","https://openalex.org/W2541393756","https://openalex.org/W2385643360","https://openalex.org/W4285502407","https://openalex.org/W4375944314","https://openalex.org/W1906884313","https://openalex.org/W3120201329"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,167,185],"ever-changing":[2],"landscape":[3],"of":[4,192],"large-scale":[5],"network":[6],"environments":[7],"and":[8,44,53,109,136,160,206],"innovative":[9],"biology":[10],"technologies":[11,27],"require":[12],"dynamic":[13,97,148],"mechanisms":[14],"to":[15,31,33,46,78,95,104,128,132,170,215],"rapidly":[16],"integrate":[17,80,171],"previously":[18],"unknown":[19],"bioinformatics":[20,50],"sources":[21,84,175,196],"at":[22],"runtime.":[23],"However,":[24],"existing":[25,198],"integration":[26,41,191],"lack":[28],"sufficient":[29],"flexibility":[30],"adapt":[32],"these":[34],"changes,":[35],"because":[36],"the":[37,72,86,92,119,150,181,189,216],"techniques":[38],"used":[39],"for":[40,88,146],"are":[42,126,176],"static,":[43],"sensitive":[45],"new":[47,68,172,193],"or":[48],"changing":[49],"source":[51,115,164],"implementations":[52],"evolutionary":[54],"biologist":[55],"requirements.":[56],"METHODS:":[57],"To":[58],"address":[59],"this":[60,63,208],"challenge,":[61],"in":[62,197],"paper":[64],"we":[65],"propose":[66],"a":[67,212],"semantics-based":[69],"adaptive":[70],"middleware,":[71],"Data":[73,151,182,186],"Concierge,":[74],"which":[75],"is":[76,102],"able":[77,127],"dynamically":[79,105,161],"heterogeneous":[81],"biological":[82,113,173,194],"data":[83,114,163,174,195],"without":[85],"need":[87],"wrappers.":[89],"Along":[90],"with":[91,200],"architecture":[93],"necessary":[94],"facilitate":[96],"integration,":[98],"API":[99,165],"description":[100],"mechanism":[101,209],"proposed":[103],"classify,":[106],"recognize,":[107],"locate,":[108],"invoke":[110],"newly":[111],"added":[112],"functionalities.":[116],"Based":[117],"on":[118,156],"unified":[120],"semantic":[121],"metadata,":[122],"XML-based":[123],"state":[124],"machines":[125],"provide":[129,211],"flexible":[130],"configurations":[131],"execute":[133],"biologist's":[134],"abstract":[135],"complex":[137],"operations.":[138],"RESULTS":[139],"AND":[140],"DISCUSSION:":[141],"Experimental":[142],"results":[143],"demonstrate":[144],"that":[145],"obtaining":[147],"features,":[149],"Concierge":[152,187],"sacrifices":[153],"reasonable":[154],"performance":[155],"reasoning":[157],"knowledge":[158],"models":[159],"doing":[162],"invocations.":[166],"overall":[168],"costs":[169],"significantly":[177],"lower":[178],"when":[179],"using":[180],"Concierge.":[183],"CONCLUSIONS:":[184],"facilitates":[188],"rapid":[190],"applications":[199],"no":[201],"repetitive":[202],"software":[203,218],"development":[204],"required,":[205],"hence,":[207],"would":[210],"cost-effective":[213],"solution":[214],"labor-intensive":[217],"engineering":[219],"tasks.":[220]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":6},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
