PlantGenIE and GenIE Systems dedicated to following FAIR guiding principles as detailed below. It is one of the long-term goals for the PlantGenIE project.
Findable – Find data and data sources: organise and label data, so the researchers can easily identify by using gene names, transcript ids or standard representations. Searchable metadata provides information to the users to make persistent links between other resources or publications.
F1. (meta)Data are assigned a globally unique and eternally persistent identifier.
Work in progress, once all dependencies have been identified, Restful web services can be uniquely identified by the URL.
F2. Data are described with rich metadata.
Restful web service provides necessary metadata within the JSON object.
F3. (meta)Data are registered or indexed in a searchable resource.
Work in progress, some of the metadata is already searchable. However, we will make more metadata searchable in the future.
F4. Metadata specify the data identifier.
Data identifiers uses standard representation and constructed from meta-data standard principle terms.
Accessible – Access data and data sources: anyone with a computer and an internet connection can be able to access, edit and share data. To accomplish that, PlantGenIE and GenIE-Sys provide long term availability of data for users around the world. However, accessible in FAIR does not mean open without constraint.
A1. (meta)Data are retrievable by their identifier using a standardized communications protocol.
Yes, via Hypertext Transfer Protocol Secure protocol.
A2. The protocol is open, free, and universally implementable.
A3. The protocol allows for an authentication and authorization procedure, where necessary.
A4. Metadata are accessible, even when the data are no longer available.
When PlantGenIE FTP server is not available, necessary meta-data is still available through restful web-service.
Interoperable – Interoperate between data providers: user can be able to apply the additional annotation to enhance the functionality of data and use community standard metadata. Cross-site communication can be achieved using a list of gene identifiers.
I1. (meta)Data use a formal, accessible, shared, and broadly applicable language for knowledge representation.
meta-data has not been fully formalized yet, we are working progress for optimisation using ontologies.
I2. (meta)Data use vocabulary that follows FAIR principles.
PlantGenIE uses standard representations and ontologies
I3. (meta)Data include qualified references to other (meta)data.
Work in progress.
Reusable – Reuse data: allow for new scientific discoveries to be made with existing data with a non-redundant and consistent set of tools. Tools and the analysis can be reused over and over again to reproduce the results. Metadata such as ontologies can also be reused with other frameworks or platforms (ex: Pythzome, Galaxy).
R1. (meta)Data have a plurality of accurate and relevant attributes.
Relevant consistent metadata included as additional information in tools, documentation and FTP.
R2. (meta)Data are released with a clear and accessible data usage license.
yes, PlantGenIE uses Free and Open source BSD licence.
R3. (meta)Data are associated with their provenance.
PlantGenIE keeps a separate database for different versions and species. Furthermore, PlantGenIE assures the consistency between source data and PlantGenIE.
R4. (meta)Data meet domain-relevant community standards.
yes, Standard file formats such as FASTA, GFF TAB-delimited were used in PlatGenIE. Restful Meta-data can be accessed as a JSON object.
PlantGenIE as knowledgebases allows users to search, analyse, visualise data using various analysis tools.