Changes between Initial Version and Version 1 of BioJavaRoundTripSecondPass

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Timestamp:
2008/02/13 17:55:25 (12 years ago)
Author:
markjschreiber
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  • BioJavaRoundTripSecondPass

    v1 v1  
     1= BioJava = 
     2Working with BioJava-live SVN version 4721. 
     3== Fasta Format == 
     4=== Major Issues === 
     5None 
     6=== Minor Issues === 
     7Sequence case is not preserved. Line length varies (default is 80 cpl). 
     8===Read-Write-Read=== 
     9Succeeds! 
     10 
     11 
     12== Genbank format == 
     13=== Major Issues === 
     14None. 
     15=== Minor Issues === 
     16Feature qualifier order is not preserved. 
     17Because NCBI Taxonomy is referenced from memory or database if the version used 
     18doesn't match the version that was used to construct the record then minor  
     19differences appear. For example the common name of Arabidopsis changed from thale cress 
     20to mouse ear cress. 
     21===Read-Write-Read=== 
     22 
     23== GenbankXML format == 
     24== Major Issues == 
     25Not supported (INSD is). 
     26 
     27== INSD Format == 
     28== Major Issues == 
     29None. 
     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 
     36dtd 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 === 
     42No 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=== 
     48Succeeds! 
     49 
     50== SwissProt/ Uniprot == 
     51=== Major Issues === 
     52=== Minor Issues === 
     53 * BioSQL cannot store more than one database reference for a single publication, 
     54eg 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 === 
     71Can read but produced XML doesn't validate against the xsd 
     72=== Minor Issues === 
     73===Read-Write-Read===