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| # Crosswalk with FAIR4RS Principles | ||
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| We summarize below how sPARcRNA_Viz aligns with the FAIR4RS Principles. A description of the compliance is provided to help users understand how the software aligns with the principles. The compliance is scored on a scale of 0 to 2, where 0 indicates no compliance, 1 indicates partial compliance, and 2 indicates full compliance. An N/A indicates that the principle is not applicable to the software. The compliance is based on the information provided in the software repository and the Zenodo record. | ||
| This document summarizes how sPARcRNA_Viz aligns with the FAIR4RS Principles. We provide a brief explanation of compliance for each principle to help users understand how the software meets these standards. Compliance is scored on a scale of 0 to 2: | ||
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| | [FAIR4RS Principles](https://doi.org/10.1038/s41597-022-01710-x) | Score | Explanation | | ||
| | ------------------------------------------------------------------------------------------------------ | ----- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | ||
| | F1. Software is assigned a globally unique and persistent identifier. | 2 | Our software application has been assigned a DOI (Digital Object Identifier) that is unique and persistent. We are using Zenodo to assign a DOI to our software. | | ||
| | F1.1. Components of the software representing levels of granularity are assigned distinct identifiers. | 2 | The software components are assigned distinct identifiers. SoftWare Heritage persistent IDentifier (SWHID) is a unique identifier that will assign a distinct identifier to each component of the software (eg. source code, releases, files, commits, code fragments, etc.). | | ||
| | F1.2. Different versions of the software are assigned distinct identifiers. | 2 | Different versions of the software are assigned distinct identifiers. The software is versioned using the Semantic Versioning (SemVer) scheme. Each version of the software is assigned a unique identifier via the Zenodo release process. | | ||
| | F2. Software is described with rich metadata. | 2 | The software is described with rich metadata. The metadata includes information about the software, such as the title, authors, description, keywords, license, and funding information. The metadata is provided in the Zenodo record for the software. We also have included codemeta.json and CITATION.cff files within the repository. | | ||
| | F3. Metadata clearly and explicitly include the identifier of the software they describe. | 2 | The metadata clearly and explicitly include the identifier of the software they describe. The metadata includes the DOI of the software. | | ||
| | F4. Metadata are FAIR, searchable and indexable. | 2 | The metadata are FAIR, searchable, and indexable. The metadata are provided in a machine-readable format (JSON) and are indexed by Zenodo. | | ||
| | A1. Software is retrievable by its identifier using a standardised communications protocol. | 2 | The http protocol is used to retrieve the software by its identifier. The software is hosted on Zenodo, which provides a standardised communications protocol for accessing the software. | | ||
| | A1.1. The protocol is open, free, and universally implementable. | 2 | The protocol is open, free, and universally implementable. The software is hosted on Zenodo, which is an open-access repository. Everything on Software Heritage is open access. | | ||
| | A1.2. The protocol allows for an authentication and authorization procedure, where necessary. | N/A | Zenodo has a process in place to handle closed or embargoed access, but this application is publicly available and does not require authentication or authorization. | | ||
| | A2. Metadata are accessible, even when the software is no longer available. | 2 | The metadata are accessible, even when the software is no longer available. The metadata are stored in Zenodo, and the DOI can be used to access the metadata even if the software is no longer available. | | ||
| | I1. Software reads, writes and exchanges data in a way that meets domain-relevant community standards. | 2 | The software uses JSON and CSV file formats to read, write, and exchange data. These file formats are commonly used in the bioinformatics community. | | ||
| | I2. Software includes qualified references to other objects. | 0 | The software does not include qualified references to other objects. | | ||
| | R1. Software is described with a plurality of accurate and relevant attributes. | 2 | The software is described with a plurality of accurate and relevant attributes. The metadata includes information about the software, such as the title, authors, description, keywords, license, and funding information. | | ||
| | R1.1. Software is given a clear and accessible license. | 2 | The software is given a clear and accessible license. The software is licensed under the MIT License, which is a permissive open-source license. | | ||
| | R1.2. Software is associated with detailed provenance. | 2 | The software is associated with detailed provenance. The metadata includes information about the authors, contributors, and funding information. Details about the origin and history of the software are provided in the README file. | | ||
| | R2. Software includes qualified references to other software. | 0 | The software does not include qualified references to other software. | | ||
| | R3. Software meets domain-relevant community standards. | 0 | The software does not meet domain-relevant community standards. | | ||
| - 0: No compliance | ||
| - 1: Partial compliance | ||
| - 2: Full compliance | ||
| - N/A: Not applicable to the software | ||
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| Our assessment is based on information from the software repository and the Zenodo record. | ||
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| | FAIR4RS Principle | Score | Explanation | | ||
| | ------------------------------------------------------------------------------------------------------ | ----- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | ||
| | F1. Software is assigned a globally unique and persistent identifier. | 2 | Our software has been assigned a Digital Object Identifier (DOI) through Zenodo, ensuring a unique and persistent identifier. Additionally, our software is archived in Software Heritage, providing another layer of identification and preservation. | | ||
| | F1.1. Components of the software representing levels of granularity are assigned distinct identifiers. | 2 | Software components are assigned distinct identifiers using SoftWare Heritage persistent IDentifier (SWHID). This system provides unique identifiers for various elements such as source code, releases, files, commits, and even code fragments, ensuring fine-grained identification. | | ||
| | F1.2. Different versions of the software are assigned distinct identifiers. | 2 | We use Semantic Versioning (SemVer) for version control. Each software version receives a unique identifier through the Zenodo release process. Software Heritage also preserves each version of our software, assigning distinct SWHIDs to different releases and commits. | | ||
| | F2. Software is described with rich metadata. | 2 | Comprehensive metadata is provided in the Zenodo record, including title, authors, description, keywords, license, and funding information. We've also included codemeta.json and CITATION.cff files in the repository. | | ||
| | F3. Metadata clearly and explicitly include the identifier of the software they describe. | 2 | The software's DOI is clearly included in the metadata. The SWHID is also available through Software Heritage. | | ||
| | F4. Metadata are FAIR, searchable and indexable. | 2 | Metadata is provided in machine-readable JSON format and is indexed by Zenodo, ensuring it is FAIR, searchable, and indexable. Software Heritage also indexes our software and its metadata, enhancing discoverability. | | ||
| | A1. Software is retrievable by its identifier using a standardised communications protocol. | 2 | The software can be retrieved via HTTP protocol using its identifier. Zenodo provides a standardized method for accessing the software. | | ||
| | A1.1. The protocol is open, free, and universally implementable. | 2 | Zenodo is an open-access repository, ensuring the protocol is open, free, and universally implementable. Software Heritage also provides open access to archived software. | | ||
| | A1.2. The protocol allows for an authentication and authorization procedure, where necessary. | N/A | Our application is publicly available and does not require authentication or authorization. | | ||
| | A2. Metadata are accessible, even when the software is no longer available. | 2 | Metadata is stored in Zenodo and remains accessible via DOI even if the software becomes unavailable. | | ||
| | I1. Software reads, writes and exchanges data in a way that meets domain-relevant community standards. | 2 | We use JSON and CSV file formats, which are widely accepted in the bioinformatics community. | | ||
| | I2. Software includes qualified references to other objects. | 0 | Currently, the software does not include qualified references to other objects. | | ||
| | R1. Software is described with a plurality of accurate and relevant attributes. | 2 | The metadata provides comprehensive information about the software, including title, authors, description, keywords, license, and funding details. | | ||
| | R1.1. Software is given a clear and accessible license. | 2 | The software is licensed under the MIT License, a permissive open-source license. This license information is preserved in both Zenodo and Software Heritage. | | ||
| | R1.2. Software is associated with detailed provenance. | 2 | Detailed provenance information, including authors, contributors, and funding, is provided in the metadata and README file. Software Heritage preserves the entire development history, enhancing provenance tracking. | | ||
| | R2. Software includes qualified references to other software. | 0 | At present, the software does not include qualified references to other software. | | ||
| | R3. Software meets domain-relevant community standards. | 0 | The software does not currently meet all domain-relevant community standards. | | ||
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| This assessment highlights areas where sPARcRNA_Viz excels in FAIR principles and identifies opportunities for improvement. We welcome feedback and suggestions for enhancing our alignment with these principles. |