FAIR Compliance

PHASTEST is FAIR. Specifically, it is:

F1. (meta)data are assigned a globally unique and eternally persistent identifier.
All data and metadata in the PHASTEST are well annotated using our automated pipelines This data is searchable within the webserver and associated with all the metadata in the online database. Furthermore, the results are downloadable, viewable from the PHASTEST webpage.
F2. data are described with rich metadata.
All data in the PHASTEST are described with rich metadata. Every phage , bacterial component is annotated and described in detail. These annotated sections can be easily viewed in a tabular format and also in a graphical genome viewer. This genome viewer supports an interactive view and it lets the users view the information on Phage and bacterial genes.
F3. (meta)data are registered or indexed in a searchable resource.
All the genomes (~78K, confirm the number) and their annotation results as generated by an automated PHASTEST pipeline are provided as a viewable searchable resource.
F4. metadata specify the data identifier.
All metadata in the PHASTEST are directly linked to the phage and bacterial genes.

A1 (meta)data are retrievable by their identifier using a standardized communications protocol.
All data and metadata in the PHASTEST are retrievable from their GenBank Accession Number or Submission identifier through the PHASTEST website. Similarly, all data in the PHASTEST may be downloaded in JSON, CSV, TXT, DB, and/or PNG format via the PHASTEST's download section through a standard internet communications protocol.
A1.1 the protocol is open, free, and universally implementable.
The HMDB website is open and free and its data download operation is compatible with all modern web browsers. The HMDB’s downloadable data is in multiple formats (JSON, CSV, TXT, PNG, XML, and/or DB) that are universally readable.
A1.2 the protocol allows for an authentication and authorization procedure, where necessary.
No authentication or authorization is required to access or download the PHASTEST's data.
A2 metadata are accessible, even when the data are no longer available.
All of the PHASTEST's metadata are linked or linkable to more permanent data sources (PubMed, PubChem, ChEBI, MetaboLights, NP-MRD, MarkerDB, etc). The availability of freely downloadable data (and metadata) for the HMDB ensures that its metadata will exist and be accessible for beyond the lifetime of the database.

I1. (meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation.
All textual data and metadata in the PHASTEST are written in English, provided as both tabular and graphical format. All the annotated genomes are available as summarized into different regions (phage and bacterial) Annotations are viewable in an interactive genome viewer. The summary of results are downloadable and easily accessible. All annotations are stored in text/tabular format and images are stored in PNG format.
I2. (meta)data use vocabularies that follow FAIR principles.
All data and metadata in the PHASTEST annotations use standard nomenclature and vocabularies that are open, findable, accessible, interoperable and re-usable.
I3. (meta)data include qualified references to other (meta)data.
All data and metadata in the PHASTEST are fully referenced and are associated with their provenance and sources.

R1. meta(data) have a plurality of accurate and relevant attributes.
All data and metadata in the PHASTEST annotations are carefully checked its team have been vetted for its accuracy by multiple skilled team members. All generated results and metadata in the PHASTEST have attributes that are relevant, up-to-date and accurate to the best of the PHASTEST team's knowledge.
R1.1. (meta)data are released with a clear and accessible data usage license.
All data and metadata in the PHASTEST are released under the Creative Commons (CC) Attribution-NonCommercial (NC) 4.0 International Licensing condition.
R1.2. (meta)data are associated with their provenance.
All data and metadata and its annotations in the PHASTEST are associated and referenced with their provenance and sources.
R1.3. (meta)data meet domain-relevant community standards.
The data and metadata nd the annotations generated in the PHASTEST have undergone extensive peer review by the members of Phage and bacterial community and by the previous users of PHAST and PHASTER.

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