## 2 FAIRification of ROs with OpenBio.eu
\begin{table}
\begin{tabular}{l c} \hline \hline
**FAIR Principle [21]** & **How It Is Addressed in OpenBio.eu** \\ \hline F1. (Meta)data are assigned a globally unique and & All ROs have a unique and permanent URL. \\ persistent identifier. & \\ F2. Data are described with rich metadata (defined by & Data/Tools/WFs can be downloaded in JSON including all metadata (i.e., description, dependencies). \\ F3. Metadata clearly and explicitly include the identifier of the & Metadata reference other ROs in the format of a persistent identifier with a common pattern. For example: t/Neji/2.0.2/2 (tool, name, version, edit). \\ F4. (Meta)data are registered or indexed in a searchable & All ROs are indexed and searched in a common UI. \\ A1. (Meta)data are retrievable by their identifier using a & OpenBio.eu includes a documented REST-API with a standard gateway for accessing ROs + metadata. \\ A1.1 The protocol is open, free, and universally implementable. & Yes. Even unregistered users have access. The implementation is open source. \\ A1.2 The protocol allows for an authentication and & Not needed. All ROs are open and accessible for all users. \\ Authorization procedure, where necessary. & True. ROs cannot be deleted. Even if the tools/data are deleted from their source, the metadata remain. \\ I1. (Meta)data use a formal, accessible, shared, and broadly & Data from the API are available in JSON format. The data model is available on the projects’ documentation page. \\ I2. (Meta)data use vocabularies that follow FAIR principles. & Currently, there is no predefined ontology or vocabulary used for tagging or describing Ros. \\ I3. (Meta)data include qualified references to other (meta)data. & Yes. All qualified references are OpenBio.eu IDs. \\ R1. Meta(data) are richly described with a plurality of accurate & Yes. Metadata include all information required to reproduce and run an RO. \\ R1.1. (Meta)data are released with a clear and accessible data & Yes. Both the Terms and Conditions and the Privacy Statement are listed. Terms include that all ROs also follow the \\ usage license. & BSD license. \\ R1.2. (Meta)data are associated with detailed provenance. & Yes. Metadata include edit number and are linked with \\  & previous edits for complete history tracking. \\ R1.3. (Meta)data meet domain-relevant community standards. & Yes, considering community standards for open-source \\ \hline \hline \end{tabular}
\end{table} 
Table 1: List of all official FAIR principles and how they are addressed in OpenBio.eu. (www.nextflow.io, accessed on 11 October 2021) [29], Airflow, and Argo. Some of these WfMSs (i.e., CWL, Airflow, Nextflow) support execution in a virtualized environment (through Docker). This enhances reproducibility and alleviates potential problems such as system upgrades that might break compatibility between the system's libraries and an installed RO. _Reusability._ All the above features also contribute to the reusability guideline of FAIR. In OpenBio.eu, reusability is achieved with two mechanisms. The first, also common in other WfMSs, is by allowing the rich annotation of research objects. The second is by encouraging the community to provide reliable and accurate instructions to reproduce and reuse a RO in a real programming language. Reusability is measured objectively as the number of succesful uses of this RO from other users, as well as from the positive/negative criticism that it received from the community. In this context, an RO in OpenBio.eu is linked with a users' profile and respective published material. This acts as a multi-directional connection between reproducible ROs, scientific publications, and user profiles. Users are awarded credit every time an RO that they \"own\" is reused, thus providing a previously missing incentive for RO sharing in academia. It is stressed here that ROs are not simple descriptions or annotations of \"real-life\" tools, data, or workflows; they are software components, directly downloadable and executable in any modern computation environment.