TY  - JOUR
AU  - Seibel, P. N.
AU  - Krüger, J.
AU  - Hartmeier, S.
AU  - Schwarzer, K.
AU  - Löwenthal, K.
AU  - Mersch, H.
AU  - Dandekar, Th.
AU  - Giegerich, R.
TI  - XML schemas for common bioinformatic data types and their application in workflow systems
JO  - BMC bioinformatics
VL  - 7
SN  - 1471-2105
CY  - London
PB  - BioMed Central
M1  - PreJuSER-57085
SP  - 490
PY  - 2006
N1  - Record converted from VDB: 12.11.2012
AB  - Today, 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.Acknowledging 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.The 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.
KW  - Algorithms
KW  - Computational Biology: methods
KW  - Computer Graphics
KW  - Database Management Systems
KW  - Information Storage and Retrieval
KW  - Programming Languages
KW  - Sequence Alignment
KW  - Software
KW  - Systems Integration
KW  - User-Computer Interface
KW  - J (WoSType)
LB  - PUB:(DE-HGF)16
C6  - pmid:17087823
C2  - pmc:PMC2001303
UR  - <Go to ISI:>//WOS:000242316200001
DO  - DOI:10.1186/1471-2105-7-490
UR  - https://juser.fz-juelich.de/record/57085
ER  -