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Volumn 12, Issue , 2011, Pages

S3QL: A distributed domain specific language for controlled semantic integration of life sciences data

Author keywords

BLinked Data; knowledge organization system; KOS; Policy; RDF; S3D; SPARQL

Indexed keywords

BLINKED DATA; KNOWLEDGE ORGANIZATION SYSTEMS; KOS; RDF; S3D; SPARQL;

EID: 79960563809     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-285     Document Type: Article
Times cited : (14)

References (58)
  • 1
    • 62149144693 scopus 로고    scopus 로고
    • Computer science. Beyond the data deluge
    • Bell G, Hey T, Szalay A. Computer science. Beyond the data deluge. Science (New York, NY) 2009, 323:1297-8.
    • (2009) Science (New York, NY) , vol.323 , pp. 1297-1298
    • Bell, G.1    Hey, T.2    Szalay, A.3
  • 2
    • 60349110472 scopus 로고    scopus 로고
    • Data-driven methods to discover molecular determinants of serious adverse drug events
    • 10.1038/clpt.2008.274, 2726746, 19177064
    • Chiang AP, Butte AJ. Data-driven methods to discover molecular determinants of serious adverse drug events. Clinical pharmacology and therapeutics 2009, 85:259-68. 10.1038/clpt.2008.274, 2726746, 19177064.
    • (2009) Clinical pharmacology and therapeutics , vol.85 , pp. 259-268
    • Chiang, A.P.1    Butte, A.J.2
  • 3
    • 50649096979 scopus 로고    scopus 로고
    • The end of theory: the data deluge makes the scientific method obsolete
    • The end of theory: the data deluge makes the scientific method obsolete. , http://www.wired.com/science/discoveries/magazine/16-07/pb_theory
  • 4
    • 18444402182 scopus 로고    scopus 로고
    • The Ensembl genome database project
    • 10.1093/nar/30.1.38, 99161, 11752248
    • Hubbard T. The Ensembl genome database project. Nucleic Acids Research 2002, 30:38-41. 10.1093/nar/30.1.38, 99161, 11752248.
    • (2002) Nucleic Acids Research , vol.30 , pp. 38-41
    • Hubbard, T.1
  • 5
    • 0037250168 scopus 로고    scopus 로고
    • The UCSC Genome Browser Database
    • 10.1093/nar/gkg129, 165576, 12519945
    • Karolchik D. The UCSC Genome Browser Database. Nucleic Acids Research 2003, 31:51-54. 10.1093/nar/gkg129, 165576, 12519945.
    • (2003) Nucleic Acids Research , vol.31 , pp. 51-54
    • Karolchik, D.1
  • 6
    • 13444272087 scopus 로고    scopus 로고
    • Entrez Gene: gene-centered information at NCBI
    • 10.1093/nar/gni052, 539985, 15608257
    • Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic acids research 2005, 33:D54-8. 10.1093/nar/gni052, 539985, 15608257.
    • (2005) Nucleic acids research , vol.33
    • Maglott, D.1    Ostell, J.2    Pruitt, K.D.3    Tatusova, T.4
  • 7
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • 10.1038/75556, 3037419, 10802651
    • Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics 2000, 25:25-9. 10.1038/75556, 3037419, 10802651.
    • (2000) Nature genetics , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3
  • 9
    • 84874016872 scopus 로고    scopus 로고
    • Linked Data | Linked Data - Connect Distributed Data across the Web
    • Linked Data | Linked Data - Connect Distributed Data across the Web. , http://linkeddata.org/
  • 10
    • 70450163544 scopus 로고    scopus 로고
    • Linked data - Design issues
    • Linked data - Design issues. , http://www.w3.org/DesignIssues/LinkedData.html
  • 12
    • 84888285772 scopus 로고    scopus 로고
    • Where the semantic web stumbled, linked data will succeed - O'Reilly Radar
    • Where the semantic web stumbled, linked data will succeed - O'Reilly Radar. , http://radar.oreilly.com/2010/11/semantic-web-linked-data.html
  • 14
    • 73949141660 scopus 로고    scopus 로고
    • From the Semantic Web to social machines: A research challenge for AI on the World Wide Web
    • Hendler J, Berners-Lee T. From the Semantic Web to social machines: A research challenge for AI on the World Wide Web. Artificial Intelligence 2010, 174:156-161.
    • (2010) Artificial Intelligence , vol.174 , pp. 156-161
    • Hendler, J.1    Berners-Lee, T.2
  • 15
    • 33748487619 scopus 로고    scopus 로고
    • Data integration gets "Sloppy"
    • 10.1038/nbt0906-1070, 16964209
    • Almeida JS, Chen C, Gorlitsky R, et al. Data integration gets "Sloppy". Nature biotechnology 2006, 24:1070-1. 10.1038/nbt0906-1070, 16964209.
    • (2006) Nature biotechnology , vol.24 , pp. 1070-1071
    • Almeida, J.S.1    Chen, C.2    Gorlitsky, R.3
  • 16
    • 51449093281 scopus 로고    scopus 로고
    • A Semantic Web management model for integrative biomedical informatics
    • 10.1371/journal.pone.0002946, 2491554, 18698353
    • Deus HF, Stanislaus R, Veiga DF, et al. A Semantic Web management model for integrative biomedical informatics. PloS one 2008, 3:e2946. 10.1371/journal.pone.0002946, 2491554, 18698353.
    • (2008) PloS one , vol.3
    • Deus, H.F.1    Stanislaus, R.2    Veiga, D.F.3
  • 17
    • 34548117171 scopus 로고    scopus 로고
    • Putting the Web back in Semantic Web
    • Putting the Web back in Semantic Web. , http://www.w3.org/2005/Talks/1110-iswc-tbl/#(1)
  • 18
    • 84873387744 scopus 로고    scopus 로고
    • SPARQL Query Language for RDF
    • SPARQL Query Language for RDF. , http://www.w3.org/TR/rdf-sparql-query
  • 20
    • 70449457508 scopus 로고    scopus 로고
    • A journey to Semantic Web query federation in the life sciences
    • 10.1186/1471-2105-10-S1-S10, 2788350, 19958509
    • Cheung KH, Frost HR, Marshall MS, et al. A journey to Semantic Web query federation in the life sciences. BMC bioinformatics 2009, 10(Suppl 1):S10. 10.1186/1471-2105-10-S1-S10, 2788350, 19958509.
    • (2009) BMC bioinformatics , vol.10 , Issue.SUPPL. 1
    • Cheung, K.H.1    Frost, H.R.2    Marshall, M.S.3
  • 21
    • 84888275822 scopus 로고    scopus 로고
    • A Prototype Knowledge Base for the Life Sciences
    • A Prototype Knowledge Base for the Life Sciences. , http://www.w3.org/TR/hcls-kb/
  • 23
    • 35948989284 scopus 로고    scopus 로고
    • The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
    • 10.1038/nbt1346, 2814061, 17989687
    • Smith B, Ashburner M, Rosse C, et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature biotechnology 2007, 25:1251-5. 10.1038/nbt1346, 2814061, 17989687.
    • (2007) Nature biotechnology , vol.25 , pp. 1251-1255
    • Smith, B.1    Ashburner, M.2    Rosse, C.3
  • 24
    • 45749118607 scopus 로고    scopus 로고
    • Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
    • 10.1038/nbt.1411, 2771753, 18688244
    • Taylor CF, Field D, Sansone SA, et al. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature biotechnology 2008, 26:889-96. 10.1038/nbt.1411, 2771753, 18688244.
    • (2008) Nature biotechnology , vol.26 , pp. 889-896
    • Taylor, C.F.1    Field, D.2    Sansone, S.A.3
  • 25
    • 67849128700 scopus 로고    scopus 로고
    • BioPortal: ontologies and integrated data resources at the click of a mouse
    • 10.1093/nar/gkp440, 2703982, 19483092
    • Noy NF, Shah NH, Whetzel PL, et al. BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic acids research 2009, 37:W170-3. 10.1093/nar/gkp440, 2703982, 19483092.
    • (2009) Nucleic acids research , vol.37
    • Noy, N.F.1    Shah, N.H.2    Whetzel, P.L.3
  • 26
    • 84888275112 scopus 로고    scopus 로고
    • Provenance of Microarray Experiments for a Better Understanding of Experiment Results
    • Deus HF, Prud E, Zhao J, Marshall MS, Samwald M. Provenance of Microarray Experiments for a Better Understanding of Experiment Results. ISWC 2010 SWPM 2010,
    • (2010) ISWC 2010 SWPM
    • Deus, H.F.1    Prud, E.2    Zhao, J.3    Marshall, M.S.4    Samwald, M.5
  • 27
    • 0038745614 scopus 로고    scopus 로고
    • Integrating biological databases
    • Stein LD. Integrating biological databases. Nature reviews Genetics 2003, 4:337-45.
    • (2003) Nature reviews Genetics , vol.4 , pp. 337-345
    • Stein, L.D.1
  • 28
    • 52949085815 scopus 로고    scopus 로고
    • State of the nation in data integration for bioinformatics
    • 10.1016/j.jbi.2008.01.008, 18358788
    • Goble C, Stevens R. State of the nation in data integration for bioinformatics. Journal of Biomedical Informatics 2008, 41:687-693. 10.1016/j.jbi.2008.01.008, 18358788.
    • (2008) Journal of Biomedical Informatics , vol.41 , pp. 687-693
    • Goble, C.1    Stevens, R.2
  • 29
    • 85015240841 scopus 로고    scopus 로고
    • Scientific Process Automation and Workflow Management
    • Chapman & Hall, Shoshani A, Rotem D
    • Ludäscher B, Altintas I, Bowers S, et al. Scientific Process Automation and Workflow Management. Scientific Data Management 2009, Chapman & Hall, Shoshani A, Rotem D.
    • (2009) Scientific Data Management
    • Ludäscher, B.1    Altintas, I.2    Bowers, S.3
  • 30
    • 70249130850 scopus 로고    scopus 로고
    • Data sharing: Empty archives
    • 10.1038/461160a, 19741679
    • Nelson B. Data sharing: Empty archives. Nature 2009, 461:160-3. 10.1038/461160a, 19741679.
    • (2009) Nature , vol.461 , pp. 160-163
    • Nelson, B.1
  • 32
    • 2942737306 scopus 로고    scopus 로고
    • EURISWEB--Web-based epidemiological surveillance of antibiotic-resistant pneumococci in day care centers
    • 10.1186/1472-6947-3-9, 169165, 12846930
    • Silva S, Gouveia-Oliveira R, Maretzek A, et al. EURISWEB--Web-based epidemiological surveillance of antibiotic-resistant pneumococci in day care centers. BMC medical informatics and decision making 2003, 3:9. 10.1186/1472-6947-3-9, 169165, 12846930.
    • (2003) BMC medical informatics and decision making , vol.3 , pp. 9
    • Silva, S.1    Gouveia-Oliveira, R.2    Maretzek, A.3
  • 33
    • 84862009865 scopus 로고    scopus 로고
    • Describing Linked Datasets with the VoiD Vocabulary
    • Describing Linked Datasets with the VoiD Vocabulary. , http://www.w3.org/TR/2011/NOTE-void-20110303/
  • 34
    • 84874759579 scopus 로고    scopus 로고
    • HIPAA Administrative Simplification Statute and Rules
    • HIPAA Administrative Simplification Statute and Rules. , http://www.hhs.gov/ocr/privacy/hipaa/administrative/index.html
  • 35
    • 84888279101 scopus 로고    scopus 로고
    • Socially Aware Cloud Storage
    • Socially Aware Cloud Storage. , http://www.w3.org/DesignIssues/CloudStorage.html
  • 36
    • 0036546074 scopus 로고    scopus 로고
    • Opinion: Sharing primary data: a threat or asset to discovery?
    • Koslow SH. Opinion: Sharing primary data: a threat or asset to discovery?. Nature reviews Neuroscience 2002, 3:311-3.
    • (2002) Nature reviews Neuroscience , vol.3 , pp. 311-313
    • Koslow, S.H.1
  • 37
    • 77951163222 scopus 로고    scopus 로고
    • Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology
    • Baggerly KA, Coombes KR. Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology. The Annals of Applied Statistics 2009, 3:1309-1334.
    • (2009) The Annals of Applied Statistics , vol.3 , pp. 1309-1334
    • Baggerly, K.A.1    Coombes, K.R.2
  • 39
    • 84872759150 scopus 로고    scopus 로고
    • SKOS Simple Knowledge Organization System Reference
    • SKOS Simple Knowledge Organization System Reference. , http://www.w3.org/TR/skos-reference/
  • 40
    • 77954668353 scopus 로고    scopus 로고
    • S3DB core: a framework for RDF generation and management in bioinformatics infrastructures
    • 10.1186/1471-2105-11-387, 2918582, 20646315
    • Almeida JS, Deus HF, Maass W. S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. BMC bioinformatics 2010, 11:387. 10.1186/1471-2105-11-387, 2918582, 20646315.
    • (2010) BMC bioinformatics , vol.11 , pp. 387
    • Almeida, J.S.1    Deus, H.F.2    Maass, W.3
  • 41
    • 78649318168 scopus 로고    scopus 로고
    • Exposing The Cancer Genome Atlas as a SPARQL endpoint
    • 10.1016/j.jbi.2010.09.004, 3071752, 20851208
    • Deus HF, Veiga DF, Freire PR, et al. Exposing The Cancer Genome Atlas as a SPARQL endpoint. Journal of Biomedical Informatics 2010, 43:998-1008. 10.1016/j.jbi.2010.09.004, 3071752, 20851208.
    • (2010) Journal of Biomedical Informatics , vol.43 , pp. 998-1008
    • Deus, H.F.1    Veiga, D.F.2    Freire, P.R.3
  • 43
    • 58149204044 scopus 로고    scopus 로고
    • Exploratory analysis of the copy number alterations in glioblastoma multiforme
    • 10.1371/journal.pone.0004076, 2605252, 19115005
    • Freire P, Vilela M, Deus H, et al. Exploratory analysis of the copy number alterations in glioblastoma multiforme. PloS one 2008, 3:e4076. 10.1371/journal.pone.0004076, 2605252, 19115005.
    • (2008) PloS one , vol.3
    • Freire, P.1    Vilela, M.2    Deus, H.3
  • 44
    • 84888282840 scopus 로고    scopus 로고
    • NCBO Ontology Widgets
    • NCBO Ontology Widgets. , http://www.bioontology.org/wiki/index.php/NCBO_Widgets
  • 45
    • 39549119389 scopus 로고    scopus 로고
    • Is Semantic Web Technology Taking the Wrong Turn?
    • Bussler C. Is Semantic Web Technology Taking the Wrong Turn?. Ieee Internet Computing 2008, 12:75-79.
    • (2008) Ieee Internet Computing , vol.12 , pp. 75-79
    • Bussler, C.1
  • 46
    • 84888282034 scopus 로고    scopus 로고
    • What people find hard about linked data
    • What people find hard about linked data. , http://dynamicorange.com/2010/11/15/what-people-find-hard-about-linked-data/
  • 48
    • 85034256161 scopus 로고    scopus 로고
    • SPARQL Update
    • SPARQL Update. , http://www.w3.org/TR/sparql11-update/
  • 50
    • 84888282606 scopus 로고    scopus 로고
    • S3DB operator function states
    • S3DB operator function states. , http://code.google.com/p/s3db-operator/
  • 51
    • 84888280988 scopus 로고    scopus 로고
    • S3DB Operators
    • S3DB Operators. , http://s3db-operator.googlecode.com/hg/propagation.html
  • 53
    • 77954595043 scopus 로고    scopus 로고
    • The OAuth 1.0 Protocol
    • The OAuth 1.0 Protocol. , http://tools.ietf.org/html/rfc5849
  • 54
    • 67650093575 scopus 로고    scopus 로고
    • Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach
    • 10.1186/1471-2105-10-152, 2705362, 19450271
    • Francisco AP, Bugalho M, Ramirez M, Carriço JA. Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach. BMC bioinformatics 2009, 10:152. 10.1186/1471-2105-10-152, 2705362, 19450271.
    • (2009) BMC bioinformatics , vol.10 , pp. 152
    • Francisco, A.P.1    Bugalho, M.2    Ramirez, M.3    Carriço, J.A.4
  • 55
    • 84888276373 scopus 로고    scopus 로고
    • S3QL serialization engine
    • S3QL serialization engine. , http://js.s3db.googlecode.com/hg/translate/quickTranslate.html
  • 57
    • 75649084906 scopus 로고    scopus 로고
    • Evolution of MRSA during hospital transmission and intercontinental spread
    • Harris SR, Feil EJ, Holden MTG, et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science (New York, NY) 2010, 327:469-74.
    • (2010) Science (New York, NY) , vol.327 , pp. 469-474
    • Harris, S.R.1    Feil, E.J.2    Holden, M.T.G.3
  • 58
    • 84888277712 scopus 로고    scopus 로고
    • Linked Data API
    • Linked Data API. , http://code.google.com/p/linked-data-api/


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.