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Generating Data Converters to Help Compose Services in Bioinformatics Workflows

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Abstract

Heterogeneity of data and data formats in bioinformatics often entail a mismatch between inputs and outputs of different services, making it difficult to compose them into workflows. To reduce those mismatches bioinformatics platforms propose ad'hoc converters written by hand. This article proposes to systematically detect convertibility from output types to input types. Convertibility detection relies on abstract types, close to XML Schema, allowing to abstract data while precisely accounting for its composite structure. Detection is accompanied by an automatic generation of converters between input and output XML data. Our experiment on bioinformatics services and datatypes, performed with an implementation of our approach, shows that the detected convertibilities and produced converters are relevant from a biological point of view. Furthermore they automatically produce a graph of potentially compatible services with a connectivity higher than with the ad'hoc approaches.
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Dates and versions

hal-01122399 , version 1 (03-03-2015)

Identifiers

  • HAL Id : hal-01122399 , version 1

Cite

Mouhamadou Ba, Sébastien Ferré, Mireille Ducassé. Generating Data Converters to Help Compose Services in Bioinformatics Workflows. Int. Conf. Database and Expert Systems Applications (DEXA), 2014, Munich, Germany. pp.15. ⟨hal-01122399⟩
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