[Psidev-pi-dev] Issue 42 in psi-pi: Issues with the CV

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Comment #81 on issue 42 by dcreasy: Issues with the CV
http://code.google.com/p/psi-pi/issues/detail?id=42

We seem to have two different ways of specifying taxonomy:
   <SequenceCollection>
     <DBSequence id="DBSeq_HSP7D_MANSE" length="652"
SearchDatabase_ref="SDB_SwissProt" accession="HSP7D_MANSE" >
        
<seq>MAKAPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTDRLIGDAAKNQVAMNP...</seq>
       <cvParam accession="MS:1001088" name="protein description"  
cvRef="PSI-MS"
value="Heat shock 70 kDa protein cognate... - Manduca sexta ..." />
       <cvParam accession="MS:1001469" name="taxonomy: scientific name"  
cvRef="PSI-MS"
value="Manduca sexta"/>
       <cvParam accession="MS:1001467" name="taxonomy: NCBI TaxID"  
cvRef="PSI-MS"
value="7130"/>
     </DBSequence>

and
     <cv id="NCBI-TAXONOMY" fullName="NCBI-TAXONOMY"
URI="ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz"></cv>
  . . .
       <DatabaseFilters>
         <Filter>
           <FilterType>
             <cvParam accession="MS:1001020" name="DB filter taxonomy"  
cvRef="PSI-MS" />
           </FilterType>
           <Include>
             <cvParam accession="NCBI:33208" name="Metazoa"  
cvRef="NCBI-TAXONOMY" />
           </Include>
         </Filter>
       </DatabaseFilters>

Obviously we should be consistent and get rid of one of the methods.

The other CV that could be used in the first example is:

id: MS:1001470
name: taxonomy: Swiss-Prot ID

id: MS:1001468
name: taxonomy: common name


I suggest that we ditch the second method and allow:

MS:1001467 - taxonomy: NCBI TaxID
MS:1001468 - taxonomy: common name
MS:1001469 - taxonomy: scientific name
MS:1001470 - taxonomy: Swiss-Prot ID

to be included in DatabaseFilters/Filter/Include
For MS:1001468, MS:1001469, MS:1001470, I would like to see something like  
this added
to the def:
  Recommend using MS:1001467 where possible

For MS:1001467, the type should be an unsigned 32 bit integer


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