Skip to Main content Skip to Navigation
Conference papers

Generating Data Converters to Help Compose Services in Bioinformatics Workflows

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.
Complete list of metadatas

https://hal.inria.fr/hal-01122399
Contributor : Mireille Ducassé <>
Submitted on : Tuesday, March 3, 2015 - 5:42:55 PM
Last modification on : Tuesday, March 10, 2020 - 10:10:03 AM

Identifiers

  • HAL Id : hal-01122399, version 1

Citation

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⟩

Share

Metrics

Record views

311