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Update src/docs/multiomics_submission.md
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Co-authored-by: Sandy Rogers <sandyr@ebi.ac.uk>
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Ales-ibt and SandyRogers authored Mar 5, 2024
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Expand Up @@ -39,7 +39,7 @@ The HoloFood project adopts a 'hologenomic' approach to enhance the efficiency o

Multi-omics data generated from both animal host and microbiome, along with physiochemical and physiological data, have been deposited into the BioSamples database and other relevant repositories. To avoid multiple levels of nested relationships, the authors opt for assigning a BioSamples ID to each animal and linking it to the corresponding biological samples through ‘DERIVED FROM’ relationships. For instance, animal [`SAMEA112905287`](https://www.ebi.ac.uk/biosamples/samples/SAMEA112905287) has 8 derived samples with external links to other repositories when relevant (see (@SAMEA112905287_example)). Examples of samples with “derived from” relationships to animal `SAMEA112905287` are host genomics (linked to the ENA), metagenomic assembly (linked to the ENA), and metabolomic (linked to MetaboLights). Other animal samples can also have associated transcriptomics (ENA), metatranscriptomics (ENA), inflammatory markers (stored in BioSamples), or histological data (stored in BioSamples).

[Figure 2. Example of an animal sample having multiple derived samples associated with it](images/multiomics/SAMEA112905287_example.png){#SAMEA112905287_example .tall-figure fig-align="left"}
![Example of an animal sample having multiple derived samples associated with it](images/multiomics/SAMEA112905287_example.png){#SAMEA112905287_example .tall-figure fig-align="left"}

The ENA and BioSamples databases are connected by the `SAME` (or interchangeably `SAMN`/`SAMD` depending on the original deposition resource) sample accession IDs, as BioSamples accessions can be used as primary or secondary identifiers in ENA. Microbiome annotation data in MGnify inherits ENA metadata, connecting the BioSamples ID automatically under the ‘sample_biosample’ field in the metadata table. For the rest of the databases (MetaboLights in this particular example), `SAME` IDs per sample and animal were used to populate the metadata tables under the ‘Comment[BioSamples accession]’ and ‘Factor Value[Animal ID]’ fields respectively during the data submission.

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