BioJava
Working with BioJava-live SVN version 4721.
Fasta Format
Major Issues
None
Minor Issues
Sequence case is not preserved. Line length varies (default is 80 cpl). ===Read-Write-Read=== Succeeds!
Genbank format
Major Issues
None.
Minor Issues
Feature qualifier order is not preserved. Because NCBI Taxonomy is referenced from memory or database if the version used doesn't match the version that was used to construct the record then minor differences appear. For example the common name of Arabidopsis changed from thale cress to mouse ear cress. ===Read-Write-Read===
GenbankXML format
Major Issues
Not supported (INSD is).
INSD Format
Major Issues
None.
Minor Issues
* BioJava inlcudes the Reference_position tag. NCBI doesn't unless it is not 1..1
<INSDReference_position>1..1</INSDReference_position>
* There are other examples of this redundancy. I think if this doesn't break the dtd then it doesn't matter. * Qualifiers order is not preserved. I don't think this matters. ===Read-Write-Read===
EMBL Format
Major Issues
No major issues
Minor Issues
- Version in date is not correct on output.
- Two XX lines after references.
- Feature qualifiers out of order.
===Read-Write-Read=== Succeeds!
SwissProt/ Uniprot
Major Issues
Minor Issues
- BioSQL cannot store more than one database reference for a single publication,
eg Pubmed and medline Id and DOI.
- We are putting 'and' before the last author.
- We loose the copyright statement.
===Read-Write-Read===
UniprotXML
Major Issues
- Missing the namespace and the version from entry tag
- Don't write editor list if there are no editors
- Reference tag not correctly constructed.
- When writing Uniprot XML it would be illegal to use anything other than
Swiss-Prot or TrEMBL as the Namespace
Minor Issues
===Read-Write-Read===
EMBLxml
Major Issues
Can read but produced XML doesn't validate against the xsd
Minor Issues
===Read-Write-Read===
