I have a list of about 900 E.coli genome ids (Genbank plus NCTC ids), e.g.:
NCTC8196_1 NCTC11105_1 CP027464.1 CP027459.1 CP027363.1 CP027388.1 CP027355.1 CP027675.1 CP027445.1 CP027325.1 CP027219.1
and I would like to find pathogenicity metadata for them so that I can classify the molecular data I found with the metadata.
Is there a way to get a table of metadata from these genomes that I can use to associate with my molecular data?
After some searching online, I found Enterobase (http://enterobase.warwick.ac.uk), but it seems the site is mostly dedicated to MLST typing, thus they use different naming conventions than the Genbank id. Maybe there is a way to link the info in Enterobase with Genbank ids somehow?
It seems like Enterobase contains project ids, e.g. PRJNA218110. These project ids can also be found on the other side in the GenBank entries, for which we could associate the GenBank chromosomal ids.
Searching for PRJNA218110 in Enterobase gives a very long list of entries that seem to be from Illumina sequencing data, but in this list, the 'Path/Nonpath' column is always empty.
Enterobase seems to contain lots of entries with useful information, such as: the strain is pathogenic, and produced diarrhea in humans. So a table with entries like the one below would be very useful:
Genbank_id: CPXXXXXXX.1 Path/Nonpath: Pathogenic Disease: Diarrhea Genbank_id: CPYYYYYYY.1 Path/Nonpath: Nonpathogenic Disease: NA