Addressing the problems with life-science databases for traditional uses and systems biology

Philippi, Stephan; Köhler, Jacob

doi:10.1038/nrg1872

Cited by 81 publications

(62 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Unison is a practical solution to a significant problem and it addresses many common shortcomings of integrative databases [2] [3]. Unison data models are concise and readily understood.…”

Section: Discussionmentioning

confidence: 99%

“…There are technical, practical, and legal reasons that current databases do not meet the needs of computational biologists [2] [3]. A few of these reasons are: limited content/project specificity, inaccurate or outof-date data, limited access methods, necessity for local deployment, and licensing restrictions.…”

Section: Introductionmentioning

confidence: 99%

“…There are many techniques for data integration (for review, see [2][3]). Link integration, such as that provided by web pages, enables users to follow prescribed links between data sources.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Unison: An Integrated Platform for Computational Biology Discovery

Hart¹,

Mukhyala

2008

Biocomputing 2009

View full text Add to dashboard Cite

This paper describes the design and applications of Unison, a comprehensive and integrated warehouse of protein sequences, diverse precomputed predictions, and other biological data. Unison provides a practical solution to the burden of preparing data for computational discovery projects, enables holistic feature-based mining queries regarding protein composition and functions, and provides a foundation for the development of new tools. Unison is available for immediate use online via direct database connections and a web interface. In addition, the database schema, command line tools, web interface, and non-proprietary precomputed predictions are released under the Academic Free License and available for download at http://unison-db.org/. This project has resulted in a system that significantly reduces several practical impediments to the initiation of computational biology discovery projects.

show abstract

“…Unison is a practical solution to a significant problem and it addresses many common shortcomings of integrative databases [2] [3]. Unison data models are concise and readily understood.…”

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Unison: An Integrated Platform for Computational Biology Discovery

Hart¹,

Mukhyala

2008

Biocomputing 2009

View full text Add to dashboard Cite

show abstract

“…Traditionally, databases were distributed using proprietary flatfile formats or tab delimited database dumps. It is a popular myth that the appearance of XML has made these formats obsolete, however our experience shows that still only about 5% of all databases provide an XML based format [6]. Several databases are still exclusively distributed in proprietary flatfile formats or as database dumps.…”

Section: Introductionmentioning

confidence: 99%

The OXL format for the exchange of integrated datasets

Taubert

Sieren

Hindle

et al. 2007

Journal of Integrative Bioinformatics

Self Cite

View full text Add to dashboard Cite

A prerequisite for systems biology is the integration and analysis of heterogeneous experimental data stored in hundreds of life-science databases and millions of scientific publications. Several standardised formats for the exchange of specific kinds of biological information exist. Such exchange languages facilitate the integration process; however they are not designed to transport integrated datasets. A format for exchanging integrated datasets needs to i) cover data from a broad range of application domains, ii) be flexible and extensible to combine many different complex data structures, iii) include metadata and semantic definitions, iv) include inferred information, v) identify the original data source for integrated entities and vi) transport large integrated datasets. Unfortunately, none of the exchange formats from the biological domain (e.g. BioPAX, MAGE-ML, PSI-MI, SBML) or the generic approaches (RDF, OWL) fulfil these requirements in a systematic way. We present OXL, a format for the exchange of integrated data sets, and detail how the aforementioned requirements are met within the OXL format. OXL is the native format within the data integration and text mining system ONDEX. Although OXL was developed with the ONDEX system in mind, it also has the potential to be used in several other biological and non-biological applications described in this paper. Availability: The OXL format is an integral part of the ONDEX system which is freely available under the GPL at http://ondex.sourceforge.net/. Sample files can be found at http://prdownloads.sourceforge.net/ondex/ and the XML Schema at http://ondex.svn.sf.net/viewvc/*checkout*/ondex/trunk/backend/data/xml/ondex.xsd. IntroductionThe importance of database integration for all Life Sciences is generally recognised. Especially in the Pharmaceutical Industry [1; 2] data integration is a crucial technology for the drug discovery process [3; 4]. Although many different approaches to data integration exist, and have been reviewed by [5], there are no standard formats, specifically designed for the exchange of integrated datasets. Thus, users of database integration systems have to rely on the proprietary interfaces and exchange formats from the different data integration platforms. Although the use of XML, RDF and OWL simplifies the exchange of integrated datasets, none of the existing XML, RDF and OWL based formats is suitable as a generic format for the exchange of integrated datasets.Data integration has to deal with a broad range of heterogeneous data sources. Traditionally, databases were distributed using proprietary flatfile formats or tab delimited database dumps. It is a popular myth that the appearance of XML has made these formats obsolete, however our experience shows that still only about 5% of all databases provide an XML based format * To whom correspondence should be addressed. [6]. Several databases are still exclusively distributed in proprietary flatfile formats or as database dumps. A high percentage of these databases provide no ...

show abstract

“…In fact, recent work suggests that integrative approaches can be highly useful for molecular target discovery [9,11,12], but there are still significant hurdles at the level of dataflow and data analysis workflow architecture, and deficiencies in software infrastructure, that retard progress in this research area. A very recent Nature Reviews in Genetics Perspectives report [8] discusses disparities between standard approaches to databasing genomic data and metadata and requirements of systems biology. Among the issues identified are deficiencies in meta-information necessary for resource discovery (by humans or by software), impoverishment of search predicate formulation options, unavailability of scalable/programmatic query resolution for queries with large payloads, non-robustness of client applications to alterations in central server data management patterns, resistance to adoption of XML markups (necessitating detailed nongeneric parser development e orts), inappropriate conceptualizations (e.g., functions should be predicated of gene products, not genes, owing to splice variation) and a variety of difficulties related to communication, education, and licensing shortfalls.…”

Section: Introductionmentioning

confidence: 99%

Sgdi: System for Genomic Data Integration

et al. 2007

View full text Add to dashboard Cite

This paper describes a framework for collecting, annotating, and archiving high-throughput assays from multiple experiments conducted on one or more series of samples. Specific applications include support for large-scale surveys of related transcriptional profiling studies, for investigations of the genetics of gene expression and for joint analysis of copy number variation and mRNA abundance. Our approach consists of data capture and modeling processes rooted in R/Bioconductor, sample annotation and sequence constituent ontology management based in R, secure data archiving in PostgreSQL, and browser-based workspace creation and management rooted in Zope. This e ort has generated a completely transparent, extensible, and customizable interface to large archives of highthroughput assays. Sources and prototype interfaces are accessible at www.sgdi.org/software.

show abstract

Addressing the problems with life-science databases for traditional uses and systems biology

Cited by 81 publications

References 55 publications

Unison: An Integrated Platform for Computational Biology Discovery

Unison: An Integrated Platform for Computational Biology Discovery

The OXL format for the exchange of integrated datasets

Sgdi: System for Genomic Data Integration

Contact Info

Product

Resources

About