Automatic OpenAPI to Bio.tools Conversion

Willighagen, Egon; Mélius, Jonathan

doi:10.1101/170274

Cited by 3 publications

(1 citation statement)

References 22 publications

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“…The popularity of OpenAPI is also highlighted by its use in other domains. For example [30] describes a case where OpenAPI 2.0 is used in combination of other tools from the life sciences community and points out that the specification extension mechanism of OpenAPI 3.0 (that we use in this article) might be an interesting opportunity of improvement. Another example in the telecommunication domain is presented in [14] which provides a section to emphasizes the trade-offs of Model-Driven Engineering and argues that they can be overcomed "with increased investment in the tools that support the development process"; we share the same vision in the present proposal.…”

Section: Related Workmentioning

confidence: 99%

A Model-Driven Method for Fast Building Consistent Web Services from OpenAPI-Compatible Models

Sferruzza

Rocheteau

Attiogbé

et al. 2019

Communications in Computer and Information Science

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Lots of software companies rely on web technologies to test market hypotheses in order to develop viable businesses. They often need to quickly build web services that are at the core of their Minimum Viable Products (MVPs). MVPs must be reliable whereas they are based on specifications and hypotheses that are likely to change. Web services need to be well documented, to make it easy to develop applications that consume them. Model Driven Engineering approaches have been proposed and used to develop and evolve web services on one hand, and document them on the other hand. However, these approaches lack the ability to be suitable for both (i) rapid prototyping, (ii) model verification, (iii) compatibility with common programming languages and (iv) alignment between documentation and implementation. Here we propose a meta-model to express web services, the related tool to verify models consistency and an integration of this approach into the OpenAPI Specification. We adopt a shallow verification process to allow rapid prototyping by developers who are not formal methods experts, while still offering design-time guarantees that improve product quality and development efficiency. Web services are defined using parametric components which enable to express and formally verify web service patterns and to safely reuse them in other contexts. We built a tool to check consistency of extended OpenAPI 3.0 models and associated components implementations in order to generate corresponding web services. This allows us to give flexibility and verification support to developers, even in the context of an incremental development, as illustrated by a case study.

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Section: Related Workmentioning

confidence: 99%

A Model-Driven Method for Fast Building Consistent Web Services from OpenAPI-Compatible Models

Sferruzza

Rocheteau

Attiogbé

et al. 2019

Communications in Computer and Information Science

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biotoolsSchema: a formalized schema for bioinformatics software description

et al. 2021

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Background Life scientists routinely face massive and heterogeneous data analysis tasks and must find and access the most suitable databases or software in a jungle of web-accessible resources. The diversity of information used to describe life-scientific digital resources presents an obstacle to their utilization. Although several standardization efforts are emerging, no information schema has been sufficiently detailed to enable uniform semantic and syntactic description—and cataloguing—of bioinformatics resources. Findings Here we describe biotoolsSchema, a formalized information model that balances the needs of conciseness for rapid adoption against the provision of rich technical information and scientific context. biotoolsSchema results from a series of community-driven workshops and is deployed in the bio.tools registry, providing the scientific community with >17,000 machine-readable and human-understandable descriptions of software and other digital life-science resources. We compare our approach to related initiatives and provide alignments to foster interoperability and reusability. Conclusions biotoolsSchema supports the formalized, rigorous, and consistent specification of the syntax and semantics of bioinformatics resources, and enables cataloguing efforts such as bio.tools that help scientists to find, comprehend, and compare resources. The use of biotoolsSchema in bio.tools promotes the FAIRness of research software, a key element of open and reproducible developments for data-intensive sciences.

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The bio.tools registry of software tools and data resources for the life sciences

et al. 2019

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Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue ( https://bio.tools ) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information. Electronic supplementary material The online version of this article (10.1186/s13059-019-1772-6) contains supplementary material, which is available to authorized users.

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Automatic OpenAPI to Bio.tools Conversion

Abstract: 2

Cited by 3 publications

References 22 publications

A Model-Driven Method for Fast Building Consistent Web Services from OpenAPI-Compatible Models

A Model-Driven Method for Fast Building Consistent Web Services from OpenAPI-Compatible Models

biotoolsSchema: a formalized schema for bioinformatics software description

The bio.tools registry of software tools and data resources for the life sciences

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