All HoloFood samples are registered in BioSamples, which has its own documentation.

Most analyses of the samples are stored in further appropriate supporting databases, with a small number hosted directly in the HoloFood data portal.

ENA Samples / BioSamples

BioSamples are the “source of truth” for animals and derived samples created by the project. Some samples are also present in ENA (with the same primary accession / identifier), if those samples pertain to nucleotide read data.

An ENA Sample is part of the ENA Metadata Model.

A sample contains information about the sequenced source material. Samples are associated with checklists, which define the fields used to annotate the samples.

ENA has extensive documentation.

ENA Checklist Metadata

An ENA Checklist is a set of metadata (some mandatory) for a given sample type.

The HoloFood checklist is ERC000052.

BioSamples Metadata

BioSamples is an EBI service hosting annotations keyed against an existing sample hosted elsewhere (in HoloFood’s case, ENA). For HoloFood biosamples, these are registered against a specific ontology.

The majority of HoloFood samples’ metadata are hosted in BioSamples.

HoloFood data for samples that don’t have a particular repository are also stored as structured data in BioSamples. For example, histology measurements, inflammatory markers, and fatty acid measurements are stored in the structured data of those samples. This contrasts to e.g. nucleotide read, metagenome sequencing, and metabolomic mass spectromoetry data which are available through specific repositories.

There is a BioSamples online training course to learn more.

MGnify: Metagenomics

Metagenomic-derived analyses are available for some HoloFood samples.

These datasets and analysis features are hosted by MGnify, which also has extensive documentation.

MGnify is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data.

Metagenome Assembled Genome (MAG) Catalogues

MAG Catalogues are available for selected biomes. MAGs are draft genomes created by binning assembled metagenomic reads. These MAGs are created using the MGnify Genomes Pipeline. MAGs are annotated using various functional and taxonomic characterisation tools.

HoloFood MAGs are those created using only reads from HoloFood samples. However, there are other non-HoloFood public data available for the same biomes sampled by this project.

Each HoloFood MAG Catalogue therefore referenced a public MAG Catalogue in MGnify, which is a superset of the HoloFood data and other public data.

Each MAG in the HoloFood catalogue references a MAG in the MGnify catalogue which represents the same species. In some cases, the HoloFood MAG is the best available sequence for that species level cluster, so the HoloFood MAG points to itself on the MGnify website. In other cases, a more complete, less contaminated, or isolate genome exists representing the same species, so the HoloFood MAG points to this better representative on MGnify.

Viral (fragment) Catalogues

Viral catalogues are lists of the unique (at species-level) viruses found in HoloFood samples. Viral sequences are detected using VIRify. Viruses are shown as fragments (regions) of the parent contigs in which they were found. The contigs are those stored in MGnify, from the HoloFood Sample sequencing. Annotations are available on the contigs from the MGnify analysis pipeline.

MetaboLights: Metabolomics

Metabolomics-derived analyses are available for some HoloFood samples.

These datasets are hosted by MetaboLights.

Summary analyses

Summary analyses are higher level analyses of a Sample or collection of Samples; written documents serving as short analysis summaries.

These summaries are hosted directly by the HoloFood data portal.

The documents are written by HoloFood partners and moderated by the HoloFood consortium, but are not peer-reviewed research articles.

Each analysis summary is linked to one or more Samples that were included in the analysis or are relevant to it.