Semantic Web Atlas: Putting Gene Expression Data into Biological Context

We present an RDF representation of the Gene Expression Atlas (GXA) at the European Bioinformatics Institute. The RDF representation provides new opportunities for data integration, querying, error detection and curation. The GXA RDF connects to other EBI resources including Ensembl, UniProt and Reactome following linked data principles. These links enable queries across resources such as querying differential gene expression in the context of pathway and gene product functions. We show how the RDF representation of the GXA adds value to the existing data through a series of novel biological questions which interrogate the different resources and which were not previously possible through the existing GXA.

[1]  Ibrahim Emam,et al.  ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments , 2010, Nucleic Acids Res..

[2]  Robert Stevens,et al.  Ontologies Come of Age with the {iKUP} Browser , 2011 .

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

[4]  Robert Stevens,et al.  The KUPKB: a novel Web application to access multiomics data on kidney disease , 2012, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[5]  James A. Hendler,et al.  The Semantic Web — ISWC 2002 , 2002, Lecture Notes in Computer Science.

[6]  James A. Hendler,et al.  The Semantic Web" in Scientific American , 2001 .

[7]  Anna Zhukova,et al.  Modeling sample variables with an Experimental Factor Ontology , 2010, Bioinform..

[8]  Robert Stevens,et al.  Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL , 2012, Journal of Biomedical Semantics.

[9]  John P. Overington,et al.  ChEMBL: a large-scale bioactivity database for drug discovery , 2011, Nucleic Acids Res..

[10]  Mark D. Wilkinson,et al.  SADI Semantic Web Services - ‚cause you can't always GET what you want! , 2009, 2009 IEEE Asia-Pacific Services Computing Conference (APSCC).

[11]  M. Scott Marshall,et al.  Translating standards into practice - One Semantic Web API for Gene Expression , 2012, J. Biomed. Informatics.

[12]  Jessica A. Turner,et al.  Modeling biomedical experimental processes with OBI , 2010, J. Biomed. Semant..

[13]  Csongor Nyulas,et al.  BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications , 2011, Nucleic Acids Res..

[14]  Egon L. Willighagen,et al.  Emerging practices for mapping and linking life sciences data using RDF - A case series , 2012, J. Web Semant..

[15]  Barry Bishop,et al.  OWLIM: A family of scalable semantic repositories , 2011, Semantic Web.

[16]  R J Bailey,et al.  Pharmacological characterization of rat amylin receptors: implications for the identification of amylin receptor subtypes , 2012, British journal of pharmacology.

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

[18]  Michel Dumontier,et al.  Building an HIV data mashup using Bio2RDF , 2012, Briefings Bioinform..

[19]  Lee Harland,et al.  Open PHACTS: A Semantic Knowledge Infrastructure for Public and Commercial Drug Discovery Research , 2012, EKAW.

[20]  Seon-Young Kim,et al.  Gene-set approach for expression pattern analysis , 2008, Briefings Bioinform..

[21]  Bart De Moor,et al.  Endeavour update: a web resource for gene prioritization in multiple species , 2008, Nucleic Acids Res..

[22]  M. Ashburner,et al.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration , 2007, Nature Biotechnology.

[23]  Aedín C. Culhane,et al.  Gene Expression Atlas update—a value-added database of microarray and sequencing-based functional genomics experiments , 2011, Nucleic Acids Res..

[24]  A. Rector,et al.  Relations in biomedical ontologies , 2005, Genome Biology.

[25]  Daniel R. Thedens,et al.  Neuronal Receptor Activity–Modifying Protein 1 Promotes Energy Expenditure in Mice , 2011, Diabetes.

[26]  Chris F. Taylor,et al.  The MGED Ontology: a resource for semantics-based description of microarray experiments , 2006, Bioinform..

[27]  Robert Stevens,et al.  Developing a kidney and urinary pathway knowledge base , 2011, J. Biomed. Semant..

[28]  Lincoln Stein,et al.  Reactome: a database of reactions, pathways and biological processes , 2010, Nucleic Acids Res..

[29]  Nicolas Le Novère,et al.  Identifiers.org and MIRIAM Registry: community resources to provide persistent identification , 2011, Nucleic Acids Res..

[30]  陈奕欣.  Ongoing and future developments at the Universal Protein Resource , 2011 .

[31]  Sean Bechhofer,et al.  The OWL API: A Java API for OWL ontologies , 2011, Semantic Web.

[32]  Gautier Koscielny,et al.  Ensembl 2012 , 2011, Nucleic Acids Res..

[33]  Yudong D. He,et al.  Gene expression profiling predicts clinical outcome of breast cancer , 2002, Nature.

[34]  Vipul Kashyap,et al.  The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside , 2011, J. Biomed. Semant..

[35]  Ibrahim Emam,et al.  Gene Expression Atlas at the European Bioinformatics Institute , 2009, Nucleic Acids Res..

[36]  Frank van Harmelen,et al.  Sesame: A Generic Architecture for Storing and Querying RDF and RDF Schema , 2002, SEMWEB.

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

[38]  Robert Stevens,et al.  Adding a Little Reality to Building Ontologies for Biology , 2010, PloS one.

[39]  Martin Kuiper,et al.  Biological knowledge management: the emerging role of the Semantic Web technologies , 2009, Briefings Bioinform..