[MOBY-l] Hmmm... ID objects or SpecificID objects??

[Suzanna Lewis]

>
>
>
>They really are two separate issues, what the datatype is, and who
>named the data. That way a service could be agnostic who named the
>data if it wanted to be, so if two naming authorities named the same
>sequence by two different identifiers:
>
>        <ComplexSeq  namespace="GenbankGI" id="1223647">
>          AACGTCCAAA...
>        </ComplexSeq>
>
>        <ComplexSeq  namespace="EMBL" id="7463221"/>
>          AACGTCCAAA...
>        </ComplexSeq>
>
>Some applications could accept either because the actual nucleotide
>sequence is present (that would mean defining the service on the
>'ComplexSeq' type and not the subclass 'Seq' type which only has the
>identifier). 
>

I really shouldn't be getting sucked into this, but here goes.

just two comments:
1. The LSID thing of a triple (authority, namespace, uniqueid) is a Good 
Thing (JS
     has the tm on that). It helps a lot when one authority (say TIGR) 
has multiple
     databases (say Arabidopsis or Methanococcus).

2. Within the document the id must be unique and all the above 
discussion is useful.
    But that can be independent of what some external naming authority 
calls it and
    it would be useful to have both available.
     e.g.
     <ComplexSeq auth="blah" namespace="diblah" id="whatever">
         <external_ref>
            <authority>TIGR</authority>
            <for-db>arabidopsis</for-db>
            <id>11111</id>
        </external_ref>
          <external_ref>
            <authority>EMBL</authority>
            <for-db>NA</for-db>
            <id>P12345</id>
        </external_ref>
          <external_ref>
            <authority>TAIR</authority>
            <for-db>NA</for-db>
            <id>A99999</id>
        </external_ref>
   </ComplexSeq>

Bear in mind that I'm only basing this on what has been discussed over 
e-mail
and a quick reading and so if this is already in the repository and is 
covered
then egg-on-my-face and sorry and all that.