Here we outline the steps of the integrative processing of sample metadata, sample character data and their taxon assignment, as it has been developed and is being implemented in the EDIT Platform.
Finally, all heatmaps can be exported as portable network graphics (PNG) images labeled with metadata, sample IDs and color keys by using the 'Download' function from the top toolbar.
Such data must be accompanied by enough contextual information (i.e. metadata; sample characteristics, technology and measurement types; instrument parameters and sample-to-data relationships) to make datasets comprehensible and reusable if they are to underpin future investigations.
The metadata for samples used in RNA-Seq studies are deposited in the NCBI Biosample database.
Yet the metadata describing sampling location, habitat quality and interacting taxa are often excluded from the published supplementary datasets.
To compare microbiome structures based on categorical metadata, samples were pooled into binds (healthy/patient, male/female, VTM/aspirate/sputum, smoking/non-smoking, ages, causal viruses, etc).
A recent data exploration tool is GEOmetadb (15), a GEO microarray search tool that leverages the metadata associated with samples, platforms and data sets.
Furthermore, a monodimensional H NMR spectrum could become part of the metadata associated with each sample stored in biobanks.
This allows users to easily visualize the relationship between the sample metadata and the structure of the microbial communities present in the samples.
Originating tissue types were assigned for each GEO sample using the metadata in the database, allowing validation of the matched samples and the construction of precision-recall curves for each tissue.
