Publishing Chinese medicine knowledge as Linked Data on the Web

BackgroundChinese medicine (CM) draws growing attention from Western healthcare practitioners and patients. However, the integration of CM knowledge and Western medicine (WM) has been hindered by a barrier of languages and cultures as well as a lack of scientific evidence for CM's efficacy and safety. In addition, most of CM knowledge published with relational database technology makes the integration of databases even more challenging.MethodsLinked Data approach was used in publishing CM knowledge. This approach was applied to publishing a CM linked dataset, namely RDF-TCM http://www.open-biomed.org.uk/rdf-tcm/ based on TCMGeneDIT, which provided association information about CM in English.ResultsThe Linked Data approach made CM knowledge accessible through standards-compliant interfaces to facilitate the bridging of CM and WM. The open and programmatically-accessible RDF-TCM facilitated the creation of new data mash-up and novel federated query applications.ConclusionPublishing CM knowledge in Linked Data provides a point of departure for integration of CM databases.

[1]  Christian von Mering,et al.  STITCH: interaction networks of chemicals and proteins , 2007, Nucleic Acids Res..

[2]  Tim Berners-Lee,et al.  Linked data on the web (LDOW2008) , 2008, WWW.

[3]  David S. Wishart,et al.  DrugBank: a knowledgebase for drugs, drug actions and drug targets , 2007, Nucleic Acids Res..

[4]  T. Tatusova,et al.  Entrez Gene: gene-centered information at NCBI , 2006, Nucleic Acids Res..

[5]  Kei-Hoi Cheung,et al.  Advancing translational research with the Semantic Web , 2007, BMC Bioinformatics.

[6]  Leo Sauermann,et al.  Cool URIs for the semantic web , 2007 .

[7]  Lydia B. Chilton,et al.  Tabulator: Exploring and Analyzing linked data on the Semantic Web , 2006 .

[8]  Y. Z. Chen,et al.  Database of traditional Chinese medicine and its application to studies of mechanism and to prescription validation , 2006, British journal of pharmacology.

[9]  Tim Berners-Lee,et al.  Linked Data - The Story So Far , 2009, Int. J. Semantic Web Inf. Syst..

[10]  Olaf Hartig,et al.  Using Web Data Provenance for Quality Assessment , 2009, SWPM.

[11]  P. Bork,et al.  Drug Target Identification Using Side-Effect Similarity , 2008, Science.

[12]  Tim Berners-Lee,et al.  Linked data , 2020, Semantic Web for the Working Ontologist.

[13]  Timothy W. Finin,et al.  Swoogle: a search and metadata engine for the semantic web , 2004, CIKM '04.

[14]  Kei-Hoi Cheung,et al.  YeastHub: a semantic web use case for integrating data in the life sciences domain , 2005, ISMB.

[15]  Olivier Bodenreider,et al.  Bio-ontologies: current trends and future directions , 2006, Briefings Bioinform..

[16]  Hsin-Hsi Chen,et al.  TCMGeneDIT: a database for associated traditional Chinese medicine, gene and disease information using text mining , 2008, BMC complementary and alternative medicine.

[17]  David M. Shotton,et al.  OpenFlyData: An exemplar data web integrating gene expression data on the fruit fly Drosophila melanogaster , 2010, J. Biomed. Informatics.

[18]  Roy T. Fielding,et al.  Principled design of the modern Web architecture , 2000, Proceedings of the 2000 International Conference on Software Engineering. ICSE 2000 the New Millennium.

[19]  Christian Bizer,et al.  D2R Server - Publishing Relational Databases on the Semantic Web , 2004 .

[20]  Jens Lehmann,et al.  DBpedia: A Nucleus for a Web of Open Data , 2007, ISWC/ASWC.

[21]  Jens Lehmann,et al.  Triplify: light-weight linked data publication from relational databases , 2009, WWW '09.

[22]  Jun Zhao,et al.  Describing Linked Datasets On the Design and Usage of voiD, the "Vocabulary Of Interlinked Datasets" , 2009 .

[23]  Nicole Tourigny,et al.  Bio2RDF: Towards a mashup to build bioinformatics knowledge systems , 2008, J. Biomed. Informatics.

[24]  Roy T. Fielding,et al.  Hypertext Transfer Protocol - HTTP/1.1 , 1997, RFC.

[25]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[26]  Christian Bizer,et al.  Executing SPARQL Queries over the Web of Linked Data , 2009, SEMWEB.

[27]  A. Barabasi,et al.  The human disease network , 2007, Proceedings of the National Academy of Sciences.

[28]  Eyal Oren,et al.  Sindice.com: a document-oriented lookup index for open linked data , 2008, Int. J. Metadata Semant. Ontologies.

[29]  Yanli Wang,et al.  PubChem: a public information system for analyzing bioactivities of small molecules , 2009, Nucleic Acids Res..

[30]  Kei-Hoi Cheung,et al.  Linking Open Drug Data , 2009, I-SEMANTICS.

[31]  Roy T. Fielding,et al.  Uniform Resource Identifiers (URI): Generic Syntax , 1998, RFC.

[32]  Martin Gaedke,et al.  Discovering and Maintaining Links on the Web of Data , 2009, SEMWEB.

[33]  Joshua M. Stuart,et al.  Integrating genotype and phenotype information: an overview of the PharmGKB project , 2001, The Pharmacogenomics Journal.

[34]  Russ B. Altman,et al.  PharmGKB: the Pharmacogenetics Knowledge Base , 2002, Nucleic Acids Res..

[35]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[36]  E. Prud hommeaux,et al.  SPARQL query language for RDF , 2011 .

[37]  Jeremy J. Carroll,et al.  Resource description framework (rdf) concepts and abstract syntax , 2003 .

[38]  Carole A. Goble,et al.  State of the nation in data integration for bioinformatics , 2008, J. Biomed. Informatics.

[39]  H. Pearson.  Biology's name game , 2001, Nature.