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DiscoveryLink: A system for integrated access to life sciences data sources

L. M. Haas, P. M. Schwarz, P. Kodali, E. Kotlar, J. E. Rice, W. C. Swope
2001 IBM Systems Journal  
We describe the DiscoveryLink offering, focusing on two key elements, the wrapper architecture and the query optimizer, and illustrate how it can be used to integrate the access to life sciences data from  ...  IBM's DiscoveryLink is one such system, targeted to applications from the life sciences industry.  ...  Discussion From the preceding pages, we hope it is clear that DiscoveryLink can play a useful role in integrating access to life science data.  ... 
doi:10.1147/sj.402.0489 fatcat:qx3a5lh5ebeornmns3viy2y3bu

BioDWH: A Data Warehouse Kit for Life Science Data Integration

Thoralf Töpel, Benjamin Kormeier, Andreas Klassen, Ralf Hofestädt
2008 Journal of Integrative Bioinformatics  
SummaryThis paper presents a novel bioinformatics data warehouse software kit that integrates biological information from multiple public life science data sources into a local database management system  ...  This open source software can be used as a general infrastructure for integrative bioinformatics research and development.  ...  Acknowledgements This work is supported by Sixth Framework Programme Priority 1 Life Sciences, Genomics and Biotechnology for Health: "CardioWorkBench -Drug Design for Cardiovascular Diseases: Integration  ... 
doi:10.1515/jib-2008-93 fatcat:f7pd2hs37jbj7d2yg6fsaj5jpq

Technologies for integrating biological data

L. Wong
2002 Briefings in Bioinformatics  
We use the Kleisli system to illustrate the properties found in such a general data integration system.  ...  The process of building a new database relevant to some field of study in biomedicine involves transforming, integrating, and cleansing multiple data sources, as well as adding new material and annotations  ...  SRS and DiscoveryLink were claimed by their inventors as general data integration systems for biomedicine.  ... 
doi:10.1093/bib/3.4.389 pmid:12511067 fatcat:dwjbtbyytvc53oxhe5qn5rqolq

BioDWH: a data warehouse kit for life science data integration

Thoralf Töpel, Benjamin Kormeier, Andreas Klassen, Ralf Hofestädt
2008 Journal of Integrative Bioinformatics  
This paper presents a novel bioinformatics data warehouse software kit that integrates biological information from multiple public life science data sources into a local database management system.  ...  This open source software can be used as a general infrastructure for integrative bioinformatics research and development.  ...  Acknowledgements This work is supported by Sixth Framework Programme Priority 1 Life Sciences, Genomics and Biotechnology for Health: "CardioWorkBench -Drug Design for Cardiovascular Diseases: Integration  ... 
doi:10.2390/biecoll-jib-2008-93 pmid:20134070 fatcat:6znf76ylf5ht7pbo3dxjpysz4u

VINEdb: a data warehouse for integration and interactive exploration of life science data

Sridhar Hariharaputran, Thoralf Töpel, Björn Brockschmidt, Ralf Hofestädt
2007 Journal of Integrative Bioinformatics  
with and to explore integrated life science data.  ...  Furthermore, the system is supported by a visualization component to allow interactive graphical exploration of the integrated data.  ...  In this paper we introduce VINEdb, a data warehouse for integration and interactive exploration of life science data.  ... 
doi:10.1515/jib-2007-63 fatcat:kjjxvkl3ofb6hkcyae5izxrdjy

Recent trends in knowledge and data integration for the life sciences

Ken McGarry, Sheila Garfield, Nick Morris
2006 Expert systems  
The challenge for bioinformatics is to tackle the problem of fragmentation of knowledge by integrating the many sources of heterogeneous information into a coherent entity.  ...  Such technologies are of critical importance to biology, medical science and in drug discovery.  ...  Acknowledgements This work was supported by a Research Development Fellowship funded by HEFCE.  ... 
doi:10.1111/j.1468-0394.2006.00414.x fatcat:qb5qruvuk5a2zngwnc5i6wq6tm

VINEdb: a data warehouse for integration and interactive exploration of life science data

Sridhar Hariharaputran, Thoralf Töpel, Björn Brockschmidt, Ralf Hofestädt, Bioinformatics, Medical Informatics Department, Bielefeld University Library, Publikationsdienste.Ub@Uni-Bielefeld.De, BieColl, Bielefeld University
2008 Journal of Integrative Bioinformatics  
Here we present VINEdb, a data warehouse developed to interact with and to explore integrated life science data.  ...  Furthermore, the system is supported by a visualization component to allow interactive graphical exploration of the integrated data.  ...  In this paper we introduce VINEdb, a data warehouse for integration and interactive exploration of life science data.  ... 
doi:10.2390/biecoll-jib-2007-63 dblp:journals/jib/HariharaputranTBH07 fatcat:lhysmhjc75hydeituotepr57aa

TECHNOLOGIES FOR BIOLOGICAL DATA INTEGRATION [chapter]

Limsoon Wong
2004 The Practical Bioinformatician  
arguably the most widely used database query and navigation system for the Life Science community.  ...  DiscoveryLink DiscoveryLink ¿½½ is an IBM product and, in principle, it goes one step beyond SRS as a general data integration system for biomedical data.  ... 
doi:10.1142/9789812562340_0017 fatcat:24zwwoahhfffzd2dbyovjzzeqi

Biodiversity information retrieval across networked data sets

K.K.S. Sarinder, L.H.S. Lim, A.F. Merican, K. Dimyati, Vanda Broughton
2010 ASLIB Proceedings  
The approach presented in this paper is important for scientists as findings in science are useful should be shared among the scientists for a better living.  ...  To solve this, we present an approach to integrate data through wrapping of various datasets stored in relational databases located on networked platforms.  ...  We also would like to thank Prof Mashkuri Yaacob, Dr Lai Weng Kin and Mr Jingyuan Luke of MIMOS Sdn Bhd, Malaysia for allowing us to use their facilities to test the system.  ... 
doi:10.1108/00012531011074744 fatcat:t4vet5kmhzenfmyeon5y7jguui

Combining applications and remote databases view in a common SQL distributed genomic database

Pierre-Emmanuel Gros, Joan Hérisson, Nicolas Ferey, Rachid Gherbi
2005 Data Science Journal  
High-throughput experimental methods produce masses of data, so that the whole of biology has changed from a data-light science into a data-driven science.  ...  Our framework, GenoMEDIA provides two main middleware to help for this integration, Lydia and Antje.  ...  In such system, the language used is SQL and a wrapper is used in order to access database. The general schema of using DiscoveryLink is as foolowing: 1.  ... 
doi:10.2481/dsj.4.244 fatcat:r2jetsz7ofgszf3bmga33cams4

Information Management for Genome Level Bioinformatics

Norman W. Paton, Carole A. Goble
2001 Very Large Data Bases Conference  
., K2/Kleisli and GUS: Experiments in integrated access to genomic data sources, IBM Systems Journal, 40(2), 512-531, 2001. Not much to see: SQL query ranges over tables from different databases.  ...  OMG Life Sciences. I3C.  ... 
dblp:conf/vldb/PatonG01 fatcat:yh7mzvvc4zefrmzxiu55nuj6t4

Federating data with Information Integrator

A. D. Arenson
2003 Briefings in Bioinformatics  
in combining data from disparate sources, and SQL access to non-SQL data, easing the task of automating data analysis.  ...  Information Integrator is an extension to IBM's relational database DB2, which uses data federation to provide benefits to molecular biology researchers through two unique capabilities: increased flexibility  ...  The third data federation extension to DB2 provided by Information Integrator is called 'Life Sciences Data Connect'.  ... 
doi:10.1093/bib/4.4.375 pmid:14725350 fatcat:23jgz3zojfalpjykhobhlk2yk4

Information technology to the rescue!

Jeffrey Augen
2001 Nature Biotechnology  
Other data-integration solutions allow users to connect to and view data sources through a single interface.  ...  Life sciences researchers will also have to grapple with the problem of data arising from highly heterogeneous sources.  ... 
doi:10.1038/89420 pmid:11433250 fatcat:yhzrgwqjirhzrevjtsoxgibwlm

A system for knowledge management in bioinformatics

Sudeshna Adak, Vishal S. Batra, Deo N. Bhardwaj, P. V. Kamesam, Pankaj Kankar, Manish P. Kurhekar, Biplav Srivastava
2002 Proceedings of the eleventh international conference on Information and knowledge management - CIKM '02  
We address this problem in a comprehensive system for knowledge management in bioinformatics called e2e.  ...  it can use any data integration solution to retrieve data and return results corresponding to the semantic view.  ...  A variety of approaches have been developed for integrated access to heterogeneous data sources in genomics.  ... 
doi:10.1145/584792.584905 dblp:conf/cikm/AdakBBKKKS02 fatcat:ueh36lhoeng6zpsvzqbayn56sq

Transparent mediation-based access to multiple yeast data sources using an ontology driven interface

Abdelaali Briache, Kamar Marrakchi, Amine Kerzazi, Ismael Navas-Delgado, Badr D Rossi Hassani, Khalid Lairini, José F Aldana-Montes
2011 BMC Bioinformatics  
Conclusions: YeastMed is the first mediation-based system specific for integrating yeast data sources.  ...  In this paper, we present our approach in developing this system which takes advantage of SB-KOM to perform the query transformation needed and a set of Data Services to reach the integrated data sources  ...  This article has been published as part of BMC Bioinformatics Volume 13 Supplement 1, 2012: Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 2010.  ... 
doi:10.1186/1471-2105-13-s1-s7 pmid:22372975 pmcid:PMC3471333 fatcat:k4s5yu2ivzabnikb3n6yzv3zr4
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