ArticleBMC bioinformatics2006
XML schemas for common bioinformatic data types and their application in workflow systems.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community).F1000Research · 2020Article
- Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data.F1000Research · 2017Article
- Experiences with workflows for automating data-intensive bioinformatics.Biology direct · 2015Article
- Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package.BMC bioinformatics · 2012Article
- BioXSD: the common data-exchange format for everyday bioinformatics web services.Bioinformatics (Oxford, England) · 2010Article
- Towards interoperable and reproducible QSAR analyses: Exchange of datasets.Journal of cheminformatics · 2010Article
- Trends in modeling Biomedical Complex Systems.BMC bioinformatics · 2009Article
- Techniques for integrating -omics data.Bioinformation · 2009Article
- GeneFisher-P: variations of GeneFisher as processes in Bio-jETI.BMC bioinformatics · 2008Article
- Integrating sequence and structural biology with DAS.BMC bioinformatics · 2007Article
- RNA Movies 2: sequential animation of RNA secondary structures.Nucleic acids research · 2007Article
- 4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing.BMC bioinformatics · 2006Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundToday, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data--therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats.
resultsAcknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at http://bioschemas.sourceforge.net, the BioDOM library can be obtained at http://biodom.sourceforge.net.
conclusionThe HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios.
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