FISH-EU-TrustBase
About us
Duccio Cavalieri
Massimiliano Marvasi
Giovanni Bacci
Alessandro Russo (Dottorando)
Aldo d'Alessandro (Assegnista)
The project
To achieve the scope of developing biomarkers for fish origin and fish freshness we have developed Fish-EU-TrustBase, the database is an in-house relational database that links public identifiers to sample accessions that will be used to upload metadata into other dedicated databases, such as Dryad or Zenodo.
Final goal
Our ultimate goal is to consolidate fragmented Fish microbiome and isotopedata from various sources, including that produced within the Fish Eu trust project, into a seamless workflow, ultimately improving our understanding of the interaction between fish origin, freshness, diet and the microbiome.
Data and storage
Raw data generated during the project has been and will be stored in dedicated, public databases to completely fulfill FAIR principles. In particular, nucleotide sequences will be converted into fastq files and uploaded to the european nucleotide archive (ENA) with all technical and experimental data associated with them. This way, our data will be findable (a public identifier will be univocally associated to our data), accessible (fastq files represent the standard used in genomic and metagenomic analyses), interoperable (technical and experimental data will be linked to raw data), and reusable (researcher can use our data by simply downloading then from the database).
At present
Currently the first set of 60 metagenomic experiments has been uploaded on ENA- with the accession number of PRJEB67338. Another dataset of 180 microbiomes is currently being uploaded on ENA. The dataset will be updated with the results of the microbiome sequencing from the samples from the CLLs. The same samples will be genetically characterized.
The database will also store stable isotope and elemental composition data for seafood that currently include the literature data and is part of isofoodtrack.ijs.si.
The isotope data will be upgraded with the real samples from CLLs and combined with microbiome and genetic markers.
What to expect from the Database
The database will also store stable isotope and elemental composition data for seafood that currently include the literature data and is part of isofoodtrack.ijs.si. The isotope data will be upgraded with the real samples from CLLs and combined with microbiome and genetic markers.
The database includes a detailed description of the metadata of every sample and the outcome of the stable isotopes measurements for the samples. Our open-source online tools enable researchers to easily find and merge Fish EU Trust data with microbiome-related datasets stored in public repositories, linking to all the public datasets related to fish metagenomics and stable isotopes data, including those of the Elixir-EU community on marine metagenomics (https://elixir-europe.org/communities/marine-metagenomics)
The database includes also the results of the analyses describing the first sets of metagenomic markers associated to the fish origin and freshness. These are in the form of a set of ASV, metagenomic DNA sequences, associated to stable isotopes measurements that can be used to link a sample to a sampling site.
Currently the access to the database is restricted to the partners of FISH-EU Trust but the database will be made public by the end of the project. The database structure will be continuously updated during the project and kept updated for at least 12 months after the conclusion of the project.
The protocols implemented will guarantee the full interoperability and findability of all data produced in the project without the need to rely on external services. The developer database will be stored in the server of the HPC of the Department of Biology-University of Florence for at least 36 months after the duration of the project. The database will be mirrored with the database developed in the FNS-Cloud project, Fairspace (https://fnscloud.eu/catalogues/tools/95) and integrated into a powerful platform to streamline and enhance the analysis of microbiomes in relation to fish origin and shelf life.
Overall through our resources users will be provided with the access to a wealth of valuable information, empowering them to conduct comprehensive analyses and download relevant data.
Link utili:
link al progetto europeo associato: https://fisheutrust.org/
Ultimo aggiornamento
17.04.2024