I'm looking at better database/storage solutions for NCBI virus data, with all attributes particularly year and country of isolation, together with structural data, possible antibody data, T-cell data and bioinformatics data such as %GC etc... The amount of data is comparatively small, with a maximum size of
3 x ([6000 < no. viruses < 20000] for 10 genes) and each entry will contain nucleotide, amino acid and one or more pieces of alignment data (i.e. with indels).
The data will be used for numerous different calculations from structural biology, phylogenetics, and deep learning. Some of the calculations will require parallel processing. A typical calculation would be to identify a clade/similarity/difference then screen the database to look at the isolates information.
Previously I've used lots of flat files which are loaded at initiation and are held within a data pipeline either as an object (Python) or especially a multi-dimensional hash (Perl, preferred).
The two solutions that I think look suitable are:
- BioSQL - The official Genbank solution, however my SQL commands are very basic and the documentation appears minimal (for BioSQL)
- HDF5 (hierarchical data format) - this looks good because it uses complex hashes (dictionaries), and allows layering of multiple information onto a single Genbank sequence code (key). It has strong documentation. However, I understand this isn't a "database" (long term storage), but thats how I intend to use it.
JSON/Pickling I had a look at JSON, which to me looks okay, because I'm fond of complex hashes / dictionaries, but it appears to be more of a Web solution. Finally, "pickling" (Python) is cool, very cool, but I understand this not a database solution, because it risk compatibility issues, e.g. with future Python releases.
I am interested in knowing what archival systems board members are using, and a critique whether my assessment is ok for moving forward.