2017
DOI: 10.1093/gigascience/gix022
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ReGaTE: Registration of Galaxy Tools in Elixir

Abstract: Background: Bioinformaticians routinely use multiple software tools and data sources in their day-to-day work and have been guided in their choices by a number of cataloguing initiatives. The ELIXIR Tools and Data Services Registry (bio.tools) aims to provide a central information point, independent of any specific scientific scope within bioinformatics or technological implementation. Meanwhile, efforts to integrate bioinformatics software in workbench and workflow environments have accelerated to enable the … Show more

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Cited by 13 publications
(7 citation statements)
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References 19 publications
(15 reference statements)
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“…EDAM annotations allow to classify tools according the type of data they consume or produce and provides a controlled vocabulary to define their precise functionality. This information has been used to derive tools’ annotation for CWL, or Galaxy 44,45 automatically. Unfortunately, ontology terms for structural bioinformatics, in general, and biomolecular simulation specifically, were scarce in EDAM.…”
Section: Resultsmentioning
confidence: 99%
“…EDAM annotations allow to classify tools according the type of data they consume or produce and provides a controlled vocabulary to define their precise functionality. This information has been used to derive tools’ annotation for CWL, or Galaxy 44,45 automatically. Unfortunately, ontology terms for structural bioinformatics, in general, and biomolecular simulation specifically, were scarce in EDAM.…”
Section: Resultsmentioning
confidence: 99%
“…The Dockerized Galaxy embedding examples of Dockerized tools (Docker in Docker), the ReGaTE [ 37 ] traceability metadata creation system, configuration files, and code, and the AnalysisManager module (see Fig. 3 ) connecting a sequencer to the services of the Galaxy platform directly can be found online [ 38 ].…”
Section: Resultsmentioning
confidence: 99%
“…A metadata file is generated along with the result detailing the input parameters and the version of the tool. We leverage the ReGaTE metadata system [ 37 ], which itself uses EDAM [ 44 ] ontology for bioinformatics processes. Reproducibility.…”
Section: Discussionmentioning
confidence: 99%
See 1 more Smart Citation
“…A significant part of the metadata stored in the descriptions is, however, common to registries and workbench environments systems 19 , and strategies relying on a mapping between these different description formats can help avoid redundancy and mislabeling of tools Figure 1 ). The ReGaTE utility 20 illustrates this by using tool descriptions from Galaxy to publish available services on bio.tools. Another application is to facilitate workbench environment integration, by reusing tool descriptions from registries.…”
Section: Introductionmentioning
confidence: 99%