| | 1 | = BioJava = |
| | 2 | Working with BioJava-live SVN version 4721. |
| | 3 | == Fasta Format == |
| | 4 | === Major Issues === |
| | 5 | None |
| | 6 | === Minor Issues === |
| | 7 | Sequence case is not preserved. Line length varies (default is 80 cpl). |
| | 8 | ===Read-Write-Read=== |
| | 9 | Succeeds! |
| | 10 | |
| | 11 | |
| | 12 | == Genbank format == |
| | 13 | === Major Issues === |
| | 14 | None. |
| | 15 | === Minor Issues === |
| | 16 | Feature qualifier order is not preserved. |
| | 17 | Because NCBI Taxonomy is referenced from memory or database if the version used |
| | 18 | doesn't match the version that was used to construct the record then minor |
| | 19 | differences appear. For example the common name of Arabidopsis changed from thale cress |
| | 20 | to mouse ear cress. |
| | 21 | ===Read-Write-Read=== |
| | 22 | |
| | 23 | == GenbankXML format == |
| | 24 | == Major Issues == |
| | 25 | Not supported (INSD is). |
| | 26 | |
| | 27 | == INSD Format == |
| | 28 | == Major Issues == |
| | 29 | None. |
| | 30 | == Minor Issues == |
| | 31 | * BioJava inlcudes the Reference_position tag. NCBI doesn't unless it is not 1..1 |
| | 32 | {{{ |
| | 33 | <INSDReference_position>1..1</INSDReference_position> |
| | 34 | }}} |
| | 35 | * There are other examples of this redundancy. I think if this doesn't break the |
| | 36 | dtd then it doesn't matter. |
| | 37 | * Qualifiers order is not preserved. I don't think this matters. |
| | 38 | ===Read-Write-Read=== |
| | 39 | |
| | 40 | == EMBL Format == |
| | 41 | === Major Issues === |
| | 42 | No major issues |
| | 43 | === Minor Issues === |
| | 44 | * Version in date is not correct on output. |
| | 45 | * Two XX lines after references. |
| | 46 | * Feature qualifiers out of order. |
| | 47 | ===Read-Write-Read=== |
| | 48 | Succeeds! |
| | 49 | |
| | 50 | == SwissProt/ Uniprot == |
| | 51 | === Major Issues === |
| | 52 | === Minor Issues === |
| | 53 | * BioSQL cannot store more than one database reference for a single publication, |
| | 54 | eg Pubmed and medline Id and DOI. |
| | 55 | * We are putting 'and' before the last author. |
| | 56 | * We loose the copyright statement. |
| | 57 | ===Read-Write-Read=== |
| | 58 | |
| | 59 | == UniprotXML == |
| | 60 | === Major Issues === |
| | 61 | * Missing the namespace and the version from entry tag |
| | 62 | * Don't write editor list if there are no editors |
| | 63 | * Reference tag not correctly constructed. |
| | 64 | * When writing Uniprot XML it would be illegal to use anything other than |
| | 65 | Swiss-Prot or TrEMBL as the Namespace |
| | 66 | === Minor Issues === |
| | 67 | ===Read-Write-Read=== |
| | 68 | |
| | 69 | == EMBLxml == |
| | 70 | === Major Issues === |
| | 71 | Can read but produced XML doesn't validate against the xsd |
| | 72 | === Minor Issues === |
| | 73 | ===Read-Write-Read=== |
