{"id":"https://openalex.org/W2161230830","doi":"https://doi.org/10.1093/bib/bbp007","title":"Scaling the walls of discovery: using semantic metadata for integrative problem solving","display_name":"Scaling the walls of discovery: using semantic metadata for integrative problem solving","publication_year":2009,"publication_date":"2009-03-01","ids":{"openalex":"https://openalex.org/W2161230830","doi":"https://doi.org/10.1093/bib/bbp007","mag":"2161230830","pmid":"https://pubmed.ncbi.nlm.nih.gov/19304872"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbp007","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbp007","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101148413","display_name":"Maurice Manning","orcid":null},"institutions":[{"id":"https://openalex.org/I4210128633","display_name":"Experimental Drug Development Centre","ror":"https://ror.org/03kx02w94","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210128633"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"M. Manning","raw_affiliation_strings":["Lilly Singapore Centre for Drug Discovery, 8A Biomedical Grove #02-05, Immunos, Biopolis, 138648, Singapore"],"affiliations":[{"raw_affiliation_string":"Lilly Singapore Centre for Drug Discovery, 8A Biomedical Grove #02-05, Immunos, Biopolis, 138648, Singapore","institution_ids":["https://openalex.org/I4210128633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108098728","display_name":"Amit Aggarwal","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. Aggarwal","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102410810","display_name":"Kevin Gao","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"K. Gao","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5064577241","display_name":"Greg Tucker\u2010Kellogg","orcid":"https://orcid.org/0000-0001-8407-9251"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"G. Tucker-Kellogg","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5101148413"],"corresponding_institution_ids":["https://openalex.org/I4210128633"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.9186,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.74295346,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"10","issue":"2","first_page":"164","last_page":"176"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9970999956130981,"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":0.9970999956130981,"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":0.9941999912261963,"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":0.9898999929428101,"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":0.8444566130638123},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.7520186305046082},{"id":"https://openalex.org/keywords/rdf","display_name":"RDF","score":0.5962737798690796},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5520548820495605},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5372509956359863},{"id":"https://openalex.org/keywords/semantic-integration","display_name":"Semantic integration","score":0.48440390825271606},{"id":"https://openalex.org/keywords/data-mapping","display_name":"Data mapping","score":0.4701262414455414},{"id":"https://openalex.org/keywords/metadata-repository","display_name":"Metadata repository","score":0.4658285975456238},{"id":"https://openalex.org/keywords/semantic-grid","display_name":"Semantic grid","score":0.4636930227279663},{"id":"https://openalex.org/keywords/data-discovery","display_name":"Data discovery","score":0.44269368052482605},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.43539154529571533},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.4351179897785187},{"id":"https://openalex.org/keywords/linked-data","display_name":"Linked data","score":0.4223329424858093},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3631761074066162},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.33034271001815796},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3056831657886505},{"id":"https://openalex.org/keywords/semantic-web-stack","display_name":"Semantic Web Stack","score":0.2280285358428955}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8444566130638123},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.7520186305046082},{"id":"https://openalex.org/C147497476","wikidata":"https://www.wikidata.org/wiki/Q54872","display_name":"RDF","level":3,"score":0.5962737798690796},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5520548820495605},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5372509956359863},{"id":"https://openalex.org/C110903229","wikidata":"https://www.wikidata.org/wiki/Q7449064","display_name":"Semantic integration","level":4,"score":0.48440390825271606},{"id":"https://openalex.org/C137314826","wikidata":"https://www.wikidata.org/wiki/Q2330408","display_name":"Data mapping","level":2,"score":0.4701262414455414},{"id":"https://openalex.org/C153048206","wikidata":"https://www.wikidata.org/wiki/Q3454922","display_name":"Metadata repository","level":3,"score":0.4658285975456238},{"id":"https://openalex.org/C103692084","wikidata":"https://www.wikidata.org/wiki/Q1765824","display_name":"Semantic grid","level":3,"score":0.4636930227279663},{"id":"https://openalex.org/C2777516300","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data discovery","level":3,"score":0.44269368052482605},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.43539154529571533},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.4351179897785187},{"id":"https://openalex.org/C69075417","wikidata":"https://www.wikidata.org/wiki/Q515701","display_name":"Linked data","level":3,"score":0.4223329424858093},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3631761074066162},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.33034271001815796},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3056831657886505},{"id":"https://openalex.org/C167379230","wikidata":"https://www.wikidata.org/wiki/Q1026884","display_name":"Semantic Web Stack","level":3,"score":0.2280285358428955},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","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":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003661","descriptor_name":"Decision Support Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003661","descriptor_name":"Decision Support Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003661","descriptor_name":"Decision Support Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","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":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","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":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"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":"D033181","descriptor_name":"Information Dissemination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D033181","descriptor_name":"Information Dissemination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D033181","descriptor_name":"Information Dissemination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbp007","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbp007","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19304872","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19304872","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:scholarbank.nus.edu.sg:10635/102533","is_oa":false,"landing_page_url":"http://scholarbank.nus.edu.sg/handle/10635/102533","pdf_url":null,"source":{"id":"https://openalex.org/S7407052290","display_name":"National University of Singapore","issn_l":null,"issn":[],"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":"Scopus","raw_type":"Review"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.4099999964237213}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":56,"referenced_works":["https://openalex.org/W1482515444","https://openalex.org/W1500288590","https://openalex.org/W1509844421","https://openalex.org/W1577783107","https://openalex.org/W1730348256","https://openalex.org/W1971676632","https://openalex.org/W1972954383","https://openalex.org/W1989025739","https://openalex.org/W2013617281","https://openalex.org/W2016758618","https://openalex.org/W2018023891","https://openalex.org/W2020245432","https://openalex.org/W2036197703","https://openalex.org/W2046166587","https://openalex.org/W2050638275","https://openalex.org/W2054800386","https://openalex.org/W2061742318","https://openalex.org/W2072437897","https://openalex.org/W2075343129","https://openalex.org/W2077396040","https://openalex.org/W2082668371","https://openalex.org/W2093410900","https://openalex.org/W2103538877","https://openalex.org/W2106036365","https://openalex.org/W2106791611","https://openalex.org/W2109872885","https://openalex.org/W2111908385","https://openalex.org/W2114649195","https://openalex.org/W2127552463","https://openalex.org/W2129501942","https://openalex.org/W2130479394","https://openalex.org/W2132992030","https://openalex.org/W2136465047","https://openalex.org/W2137028370","https://openalex.org/W2137999759","https://openalex.org/W2140004302","https://openalex.org/W2141009231","https://openalex.org/W2142739240","https://openalex.org/W2145825942","https://openalex.org/W2146453000","https://openalex.org/W2147809382","https://openalex.org/W2148101811","https://openalex.org/W2150852650","https://openalex.org/W2153091158","https://openalex.org/W2156892696","https://openalex.org/W2165428180","https://openalex.org/W2166458835","https://openalex.org/W2169569887","https://openalex.org/W2169896733","https://openalex.org/W2170309361","https://openalex.org/W2415041686","https://openalex.org/W2419641731","https://openalex.org/W2537020829","https://openalex.org/W3192290435","https://openalex.org/W4242161096","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2055917462","https://openalex.org/W1495764866","https://openalex.org/W2376817012","https://openalex.org/W2183628870","https://openalex.org/W2360379972","https://openalex.org/W4293519456","https://openalex.org/W2131092261","https://openalex.org/W2112203342","https://openalex.org/W2032718400","https://openalex.org/W1566552157"],"abstract_inverted_index":{"Current":[0],"data":[1,9,18,31,59,61,82,90,101,140,163,197,217,220],"integration":[2,80],"approaches":[3],"by":[4,158],"bioinformaticians":[5],"frequently":[6],"involve":[7],"extracting":[8],"from":[10,161,198],"a":[11,22,51,84,100,225],"wide":[12],"variety":[13],"of":[14,43,77,81,107,115,123,229],"public":[15],"and":[16,25,40,47,69,92,136,188,201,214,222],"private":[17],"repositories,":[19],"each":[20],"with":[21,119],"unique":[23],"vocabulary":[24],"schema,":[26],"via":[27],"scripts.":[28],"These":[29],"separate":[30],"sets":[32],"must":[33],"then":[34,156],"be":[35],"normalized":[36],"through":[37],"the":[38,112,120,173,179],"tedious":[39],"lengthy":[41],"process":[42],"resolving":[44],"naming":[45],"differences":[46],"collecting":[48],"information":[49],"into":[50,165],"single":[52],"view.":[53],"Attempts":[54],"to":[55,110,132,147,171,178,212],"consolidate":[56],"such":[57],"diverse":[58,219],"using":[60],"warehouses":[62],"or":[63],"federated":[64],"queries":[65],"add":[66],"significant":[67],"complexity":[68,126],"have":[70],"shown":[71],"limitations":[72],"in":[73,88],"flexibility.":[74],"The":[75],"alternative":[76],"complete":[78],"semantic":[79,105,130],"requires":[83],"massive,":[85],"sustained":[86],"effort":[87],"mapping":[89,106,159],"types":[91],"maintaining":[93],"ontologies.":[94],"We":[95,204],"focused":[96],"instead":[97],"on":[98],"creating":[99],"architecture":[102],"that":[103,195],"leverages":[104],"experimental":[108],"metadata,":[109],"support":[111],"rapid":[113],"prototyping":[114],"scientific":[116],"discovery":[117,150],"applications":[118],"twin":[121],"goals":[122],"reducing":[124],"architectural":[125],"while":[127],"still":[128],"leveraging":[129],"technologies":[131],"provide":[133],"flexibility,":[134],"efficiency":[135],"more":[137],"fully":[138],"characterized":[139],"relationships.":[141],"A":[142,152],"metadata":[143,153,160],"ontology":[144],"was":[145,155,181],"developed":[146],"describe":[148,172,205],"our":[149],"process.":[151],"repository":[154,180],"created":[157],"existing":[162],"sources":[164,221],"this":[166,207],"ontology,":[167],"generating":[168],"RDF":[169,200],"triples":[170],"entities.":[174],"Finally":[175],"an":[176],"interface":[177],"designed":[182],"which":[183],"provided":[184],"not":[185],"only":[186],"search":[187],"browse":[189],"capabilities":[190],"but":[191],"complex":[192],"query":[193],"templates":[194],"aggregate":[196],"both":[199],"RDBMS":[202],"sources.":[203],"how":[206],"approach":[208],"(i)":[209],"allows":[210],"scientists":[211],"discover":[213],"link":[215],"relevant":[216],"across":[218],"(ii)":[223],"provides":[224],"platform":[226],"for":[227],"development":[228],"integrative":[230],"informatics":[231],"applications.":[232]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-02-24T19:35:01.260952","created_date":"2025-10-10T00:00:00"}
