TY - JOUR
T1 - BioXSD: the common data-exchange format for everyday bioinformatics web services
AU - Kalas, M.
AU - Puntervoll, P.
AU - Joseph, A.
AU - Bartaseviciute, Edita
AU - Topfer, A.
AU - Venkataraman, P.
AU - Pettifer, S.
AU - Bryne, J.C.
AU - Ison, J.
AU - Blanchet, C.
AU - Rapacki, Kristoffer
AU - Jonassen, I.
PY - 2010
Y1 - 2010
N2 - Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of the resources offer programmatic web-service interface. However, efficient use of the resources is hampered by the lack of widely used, standard data-exchange formats for the basic, everyday bioinformatics data types. Results: BioXSD has been developed as a candidate for standard, canonical exchange format for basic bioinformatics data. BioXSD is represented by a dedicated XML Schema and defines syntax for biological sequences, sequence annotations, alignments and references to resources. We have adapted a set of web services to use BioXSD as the input and output format, and implemented a test-case workflow. This demonstrates that the approach is feasible and provides smooth interoperability. Semantics for BioXSD is provided by annotation with the EDAM ontology. We discuss in a separate section how BioXSD relates to other initiatives and approaches, including existing standards and the Semantic Web.
AB - Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of the resources offer programmatic web-service interface. However, efficient use of the resources is hampered by the lack of widely used, standard data-exchange formats for the basic, everyday bioinformatics data types. Results: BioXSD has been developed as a candidate for standard, canonical exchange format for basic bioinformatics data. BioXSD is represented by a dedicated XML Schema and defines syntax for biological sequences, sequence annotations, alignments and references to resources. We have adapted a set of web services to use BioXSD as the input and output format, and implemented a test-case workflow. This demonstrates that the approach is feasible and provides smooth interoperability. Semantics for BioXSD is provided by annotation with the EDAM ontology. We discuss in a separate section how BioXSD relates to other initiatives and approaches, including existing standards and the Semantic Web.
U2 - 10.1093/bioinformatics/btq391
DO - 10.1093/bioinformatics/btq391
M3 - Journal article
C2 - 20823319
SN - 1367-4803
VL - 26
SP - i540-i546
JO - Bioinformatics
JF - Bioinformatics
IS - 18
ER -