This will likely be a 'meta issue', since multiple changes may be required for this.
The NCBI is in the process of phasing out GI numbers as identifiers for sequences. This only effects the sequence database nuccore, gss, est, protein and popset.
This means flat files (like fasta) and BLAST output will no longer have the GI numbers included
New sequences will not be assigned GIs (old ones will still work)
As far as I know, none of the rentrez code, documentations or tests rely on parsing out GI numbers, so this should not break anything.
However, there will be new behaviors that rentrez should take advantage of
argument idtype=acc will be able to be used to pass versioned accessions to search, fetch and (eventually) summary.
some GI-less sequences like WGS and transcriptome contigs will be accessible for the first time
To keep up to date with these changes we should at least
[ ] Ensure that these changes won't break existing code, tests or documentation
[x] Document and test idtype=acc for
[x] search
[x] summary
[x] fetch
[ ] Write a blogpost introducing these changes and how they might be useful to users
This will likely be a 'meta issue', since multiple changes may be required for this.
The NCBI is in the process of phasing out GI numbers as identifiers for sequences. This only effects the sequence database
nuccore,gss,est,proteinandpopset.As far as I know, none of the rentrez code, documentations or tests rely on parsing out GI numbers, so this should not break anything.
However, there will be new behaviors that rentrez should take advantage of
idtype=accwill be able to be used to pass versioned accessions to search, fetch and (eventually) summary.To keep up to date with these changes we should at least
idtype=accfor