Achard F, Vaysseix G, Barillot E. (2001). XML, bioinformatics and data integration. Bioinformatics (Oxford, England). 17 [PubMed]
Adams MD et al. (1991). Complementary DNA sequencing: expressed sequence tags and human genome project. Science (New York, N.Y.). 252 [PubMed]
Adomavicius G, Tuzhilin A. (2005). Toward the next generation of recommender systems: a survey of the state-of-the-art and possible extensions IEEE Trans Knowl Data Eng . 17(6)
Andrade L, Silva MJ. (2006). Relevance ranking for geographic IR Workshop on geographic information retrieval SIGIR'06.
Ashburner M et al. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics. 25 [PubMed]
Avraham S et al. (2008). The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic acids research. 36 [PubMed]
Baeza Yates RA, Neto BR. (1999). Modern information retrieval.
Bairoch A et al. (2005). The Universal Protein Resource (UniProt). Nucleic acids research. 33 [PubMed]
Bard JB, Rhee SY. (2004). Ontologies in biology: design, applications and future challenges. Nature reviews. Genetics. 5 [PubMed]
Bentley DR et al. (2008). Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 456 [PubMed]
Bodenreider O, Stevens R. (2006). Bio-ontologies: current trends and future directions. Briefings in bioinformatics. 7 [PubMed]
Botstein D, White RL, Skolnick M, Davis RW. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American journal of human genetics. 32 [PubMed]
Brazma A, Krestyaninova M, Sarkans U. (2006). Standards for systems biology. Nature reviews. Genetics. 7 [PubMed]
Brin S, Page L. (1998). The anatomy of a large-scale hypertextual Web search engine Proceedings of the seventh international conference on world wide web 7, Brisbane. 30
Brockschmidt K. (1995). Inside OLE, 2nd edn.
Bry F, Kroger P. (2003). A computational biology database digest: data, data analysis, and data management Distrib Parallel Databases. 13(1)
Codd EF. (1998). A relational model of data for large shared data banks. 1970. M.D. computing : computers in medical practice. 15 [PubMed]
Cohen-Boulakia S, Leser U. (2011). Next generation data integration for life sciences Proceedings of the 2011 IEEE 27th international conference on data engineering (ICDE'11).
Cuellar A et al. (2015). The CellML 1.1 Specification. Journal of integrative bioinformatics. 12 [PubMed]
Davidson SB, Overton C, Buneman P. (1995). Challenges in integrating biological data sources. Journal of computational biology : a journal of computational molecular cell biology. 2 [PubMed]
Day J. (2001). The quest for information: a guide to searching the Internet. The journal of contemporary dental practice. 2 [PubMed]
Devlin B, Murphy P. (1988). An architecture for a business and information system IBM Syst J. 27(1)
Divoli A, Hearst MA, Wooldridge MA. (2008). Evidence for showing gene/protein name suggestions in bioscience literature search interfaces. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. [PubMed]
Doms A, Schroeder M. (2005). GoPubMed: exploring PubMed with the Gene Ontology. Nucleic acids research. 33 [PubMed]
Dowell RD, Jokerst RM, Day A, Eddy SR, Stein L. (2001). The distributed annotation system. BMC bioinformatics. 2 [PubMed]
Dumais S, Agichtein E, Brill E. (2006). Improving web search ranking by incorporating user behavior information SIGIR'06: proceedings of the 29th annual international ACMSIGIR conference on research and development in information retrieval.
Dumontier M et al. (2008). Bio2RDF network of linked data Semantic web challenge; international semantic web conference (ISWC 2008), Karlsruhe.
Eckerson WW. (2002). Data quality and the bottom line: achieving business success through a commitment to high quality data TDWI report series.
Efthimiadis EN. (2000). Interactive query expansion: a user-based evaluation in a relevance feedback environment. J Am Soc Inf Sci. 51(11)
Elmasri R, Navathe SB. (2000). Fundamentals of database systems 3rd edn.
Etzold T, Harris H, Beaulah S. (). SRS: an integration platform for databanks and analysis tools in bioinformatics Bioinformatics: managing scientific data.
Fenyö D. (1999). The Biopolymer Markup Language. Bioinformatics (Oxford, England). 15 [PubMed]
Fernández-Suárez XM, Galperin MY. (2013). The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection. Nucleic acids research. 41 [PubMed]
Geiger K. (1995). Inside ODBC: [Der Entwicklerleitfaden zum Industriestandard fur Datenbank-Schnittstellen].
Gilmour R. (2000). Taxonomic markup language: applying XML to systematic data. Bioinformatics (Oxford, England). 16 [PubMed]
Gleeson P et al. (2010). NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS computational biology. 6 [PubMed]
Goble C, Stevens R. (2008). State of the nation in data integration for bioinformatics. Journal of biomedical informatics. 41 [PubMed]
Gray J. (2007). Jim gray on eScience: a transformed scientific method. Retrieved from http://research.microsoft.com/en-us/collaboration/fourthparadigm/4th paradigm book jim gray transcript.pdf.
Greifeneder H. (2010). Erfolgreiches SuchmaschinenMarketing: Wie Sie bei Google, Yahoo, MSN & Co. ganz nach oben kommen, 2nd edn.
Gruber TR. (1993). A translation approach to portable ontology specifications Knowl Acquis. 5(2)
Hanisch D, Fundel K, Mevissen HT, Zimmer R, Fluck J. (2005). ProMiner: rule-based protein and gene entity recognition. BMC bioinformatics. 6 Suppl 1 [PubMed]
Hearst M. (2006). Design recommendations for hierarchical faceted search interfaces ACM SIGIR workshop on faceted search, Seattle.
Hearst M. (2009). Search user interfaces.
Henkel R, Endler L, Peters A, Le Novère N, Waltemath D. (2010). Ranked retrieval of Computational Biology models. BMC bioinformatics. 11 [PubMed]
Hines ML, Morse T, Migliore M, Carnevale NT, Shepherd GM. (2004). ModelDB: A Database to Support Computational Neuroscience. Journal of computational neuroscience. 17 [PubMed]
Hoehndorf R et al. (2011). Integrating systems biology models and biomedical ontologies. BMC systems biology. 5 [PubMed]
Hucka M et al. (2015). The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. Journal of integrative bioinformatics. 12 [PubMed]
Ide NC, Loane RF, Demner-Fushman D. (2007). Essie: a concept-based search engine for structured biomedical text. Journal of the American Medical Informatics Association : JAMIA. 14 [PubMed]
Inmon W. (). Building the data warehouse, 4th edn.
Jaiswal P et al. (2002). Gramene: development and integration of trait and gene ontologies for rice. Comparative and functional genomics. 3 [PubMed]
Juty N, Le Novère N, Laibe C. (2012). Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic acids research. 40 [PubMed]
Kasprzyk A. (2011). BioMart: driving a paradigm change in biological data management. Database : the journal of biological databases and curation. 2011 [PubMed]
Kimball K. (1998). Bringing up supermarts - a step-by-step approach to building a data warehouse from granular data DBMS and Internet Syst. 11(1)
Kitano H. (2002). Systems biology: a brief overview. Science (New York, N.Y.). 295 [PubMed]
Krallinger M, Valencia A, Hirschman L. (2008). Linking genes to literature: text mining, information extraction, and retrieval applications for biology. Genome biology. 9 Suppl 2 [PubMed]
Krause F et al. (2010). Annotation and merging of SBML models with semanticSBML. Bioinformatics (Oxford, England). 26 [PubMed]
Lacroix Z, Critchlow T. (2003). Bioinformatics: managing scientific data.
Laibe C, Courtot M, Le Novere M. (2006). Adding semantics in kinetics models of biochemical pathways Proceedings of the 2nd international symposium on experimental standard conditions of enzyme characterizations, Ruedesheim.
Lange M et al. (2010). The LAILAPS search engine: relevance ranking in life science databases. Journal of integrative bioinformatics. 7 [PubMed]
Lassila O, Swick RR, Consortium WWW. (1998). resource description framework (RDF) model and syntax specification. http://www.w3.org/1998/10/WD-rdf-syntax-19981008.
Le Novère N et al. (2005). Minimum information requested in the annotation of biochemical models (MIRIAM). Nature biotechnology. 23 [PubMed]
Lee TJ et al. (2006). BioWarehouse: a bioinformatics database warehouse toolkit. BMC bioinformatics. 7 [PubMed]
Li C et al. (2010). BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC systems biology. 4 [PubMed]
Lloyd CM, Lawson JR, Hunter PJ, Nielsen PF. (2008). The CellML Model Repository. Bioinformatics (Oxford, England). 24 [PubMed]
Lu Z. (2011). PubMed and beyond: a survey of web tools for searching biomedical literature. Database : the journal of biological databases and curation. 2011 [PubMed]
Magrane M, UniProt Consortium. (2011). UniProt Knowledgebase: a hub of integrated protein data. Database : the journal of biological databases and curation. 2011 [PubMed]
Marenco L et al. (2003). Achieving evolvable Web-database bioscience applications using the EAV/CR framework: recent advances. Journal of the American Medical Informatics Association : JAMIA. 10 [PubMed]
Margulies M et al. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature. 437 [PubMed]
Maxam AM, Gilbert W. (1977). A new method for sequencing DNA. Proceedings of the National Academy of Sciences of the United States of America. 74 [PubMed]
McWilliam H et al. (2009). Web services at the European Bioinformatics Institute-2009. Nucleic acids research. 37 [PubMed]
Mehlhorn H, Lange M, Scholz U, Schreiber F. (2012). IDPredictor: predict database links in biomedical database. Journal of integrative bioinformatics. 9 [PubMed]
Meyer CD, Langville AN. (2006). Google's PageRank and beyond: the science of search engine rankings.
Murray-Rust P, Rzepa H. (1999). Chemical markup, XML, and the World Wide Web. 1. Basic principles J Chem Inf Comput Sci http://www.xml-cml.org. 39(6)
NLM US. (2011). United States National Library of Medicine celebrates its 10th anniversary. http://www.nlm.nih.gov/pubs/techbull/so06/so06 pm 10.html.
O'Connor BD et al. (2008). GMODWeb: a web framework for the Generic Model Organism Database. Genome biology. 9 [PubMed]
O'Donnell J, Pietrzak RH, Ellis KC, Snyder PJ, Maruff P. (2011). Understanding failure of visual paired associate learning in amnestic mild cognitive impairment. Journal of clinical and experimental neuropsychology. 33 [PubMed]
Odgers CL, Caspi A, Bates CJ, Sampson RJ, Moffitt TE. (2012). Systematic social observation of children's neighborhoods using Google Street View: a reliable and cost-effective method. Journal of child psychology and psychiatry, and allied disciplines. 53 [PubMed]
Olivier BG, Snoep JL. (2004). Web-based kinetic modelling using JWS Online. Bioinformatics (Oxford, England). 20 [PubMed]
Pearson WR, Lipman DJ. (1988). Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences of the United States of America. 85 [PubMed]
Prud'hommeaux E, Seaborne A. (2008). SPARQL query language for RDF. http://www.w3. org/TR/rdf-sparql-query/.
Richardson M, Prakash A, Brill E. (2006). Beyond pagerank: machine learning for static ranking. WWW'06: proceedings of the 15th international conference onWorldWideWeb, Edinburgh.
Roos DS. (2001). Computational biology. Bioinformatics--trying to swim in a sea of data. Science (New York, N.Y.). 291 [PubMed]
Saake G, Heuer A. (1999). Datenbanken: Implementierungstechniken, 1st edn.
Sanger F, Nicklen S, Coulson AR. (1977). DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences of the United States of America. 74 [PubMed]
Schadt EE, Linderman MD, Sorenson J, Lee L, Nolan GP. (2010). Computational solutions to large-scale data management and analysis. Nature reviews. Genetics. 11 [PubMed]
Schena M, Shalon D, Davis RW, Brown PO. (1995). Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science (New York, N.Y.). 270 [PubMed]
Schmitt I. (1998). Schemaintegration fur den Entwurf Foderierter Datenbanken.
Schonsleben P. (2001). Integrales Informationsmanagement: Informationssysteme fur Geschaftsprozesse - Management, Modellierung, Lebenszyklus und Technologie, 2nd edn.
Schuler GD, Epstein JA, Ohkawa H, Kans JA. (1996). Entrez: molecular biology database and retrieval system. Methods in enzymology. 266 [PubMed]
Schulz M, Krause F, Le Novère N, Klipp E, Liebermeister W. (2011). Retrieval, alignment, and clustering of computational models based on semantic annotations. Molecular systems biology. 7 [PubMed]
Shah SP et al. (2005). Atlas - a data warehouse for integrative bioinformatics. BMC bioinformatics. 6 [PubMed]
Siegel J. (1996). CORBA fundamentals and programming.
Siple MD. (1998). The complete guide to Java database programming with JDBC.
Smedley D et al. (2009). BioMart--biological queries made easy. BMC genomics. 10 [PubMed]
Smith B et al. (2007). The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature biotechnology. 25 [PubMed]
Stein LD. (2010). The case for cloud computing in genome informatics. Genome biology. 11 [PubMed]
Stephens SM, Chen JY, Davidson MG, Thomas S, Trute BM. (2005). Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences. Nucleic acids research. 33 [PubMed]
Taylor CF et al. (2008). Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature biotechnology. 26 [PubMed]
Valencia A. (2002). Search and retrieve. Large-scale data generation is becoming increasingly important in biological research. But how good are the tools to make sense of the data? EMBO reports. 3 [PubMed]
Waltemath D, Henkel R, Wolkenhauer O, Winter F. (2013). Reproducibility of model-based results in systems biology Systems biology: integrative biology and simulation tools.
Weiner MP, Hudson TJ. (2002). Introduction to SNPs: discovery of markers for disease. BioTechniques. Suppl [PubMed]
Weise S et al. (2006). Meta-All: a system for managing metabolic pathway information. BMC bioinformatics. 7 [PubMed]
Whetzel PL et al. (2011). BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic acids research. 39 [PubMed]
Whetzel PL et al. (2006). The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics (Oxford, England). 22 [PubMed]
Wiederhold G. (1996). Intelligent integration of information - foreword J Intell Inf Syst. 6(2/3)
Wiederhold G. (1997). Mediators in the architecture of future information systems Readings in agents.
Wu D et al. (2005). The EMBL nucleotide sequence database Nucl Acids Res. 33(supp1)
Yu T et al. (2011). The Physiome Model Repository 2. Bioinformatics (Oxford, England). 27 [PubMed]