mged

Hi,

we have come across a problem adding id's for papers to eg Medline and PubMed.
Accession is not an attribute of Bibliographic reference and it's hard to 
explicitly link to an accession if the uri has already been used for the journal.

We have been providing medline and pubmed id's via the DatabaseEntry_assn to 
OntologyEntry, but this is actually a subversion of the intended use, as 
DatabaseEntry should refer to the Ontologyentry and not the accession of the 
BibliographicReference in an external DB (example below).

Ugis and I discussed a few solutions:
1. add an attribute accession and database to Bibiliographic reference
  2. Code two ontology entries for each BQS, one that is used correctly to 
specificy the type of BQS , and create a second, where the value is the id of 
the medline record and the DatabaseEntry is the same id of the medline record.
3. Create each 1 Description per BibliographicRef and use the 
DatabaseReferences_assn from Decription to DatabaseEntry to code the Medline 
information.


my preference would be to add the attributes needed, would this be possible?

cheers

Helen

Example of how we do it now, i.e. wrong.

  <Experiment identifier="test">
     <Descriptions_assnlist>
       <Description>
         <BibliographicReferences_assnlist>
           <BibliographicReference>
         <Parameters_assnlist>
           <OntologyEntry category="PublicationType" value="journal article">
             <OntologyReference_assn>
               <DatabaseEntry accession="12345">
             <Database_assnref>
               <Database_ref identifier="medline"/>
             </Database_assnref>
               </DatabaseEntry>
             </OntologyReference_assn>
           </OntologyEntry>
         </Parameters_assnlist>
           </BibliographicReference>
         </BibliographicReferences_assnlist>
       </Description>
     </Descriptions_assnlist>