FAIR Data
The Pathogen Portal Node Costa Rica encourages researchers to share their data in alignment with the FAIR Data Principles, which promote the Findability, Accessibility, Interoperability, and Reusability of data. Researchers are expected to make their data publicly accessible in digital repositories. For researchers working with biomolecular data, the ELIXIR Deposition Databases for Biomolecular Data provide a valuable resource. This platform helps you identify recommended databases for depositing your data, ensuring compliance with best practices in data sharing. You can explore these resources here (https://elixir-europe.org/platforms/data/elixir-deposition-databases).
Below, you will find a list of databases where you can submit your data.
Molecular sequence data from pathogens
This class includes molecular sequence data from any organism considered a pathogen. All sequencing library types, all platforms, all library methods and all levels of processing (from raw data to assembled sequences) are included in this class.
Deposition actions:
- Users should submit data to the European Nucleotide Archive (ENA).
- A dedicated Pathogens Submissions Guide is available which provides some tips for pathogen data submissions.
- Users may contact ENA for submissions support at ena-path-collabs@ebi.ac.uk.
PRIDE PRoteomics IDEntifications (PRIDE)
The PRIDE PRoteomics IDEntifications (PRIDE) Archive database is a core member in the ProteomeXchange (PX) consortium, which provides a standardised way for submitting mass spectrometry based proteomics data to public-domain repositories. Datasets are submitted to ProteomeXchange via PRIDE and are handled by expert bio-curators. All PRIDE public datasets can also be searched in ProteomeCentral, the portal for all ProteomeXchange datasets.
All public datasets available in PRIDE Archive in the repository can be accessed via the:
- Website, for users to explore through a web browser. https://www.ebi.ac.uk/pride/archive
- If you have further queries please consult our Help FAQ or please contact pride-support@ebi.ac.uk.
Human host data including sequences or phenotypic/clinical information
This class covers all sequences and all other molecular biology data types of human source as well as clinical, epidemiological or phenotypic data. Such data are potentially identifying the research subject and must therefore be managed under controlled access.
Deposition actions:
- Users should submit data to European Genome-phenome Archive (EGA)
- Some users may want to contact their national nodes of EGA or other national infrastructure for the management of these data.
Biological sample metadata
Please register your data as ENA Samples or alternatively into the BioSamples Database
Contact ena-path-collabs@ebi.ac.uk to discuss linking data types.
To enquire on how to collaborate on the Pathogens Platform: ena-path-collabs@ebi.ac.uk