[DAS2] alteration to /type response

[Allen Day]

Hi,

I'd like to have the <TYPE/> element contain 0..N <PARENT/> subelements.
Consider the following subgraph of SOFA, described as das2xml:

<TYPE
    id="SO:mRNA"
    ontology="sofa.ontology"
    name="mRNA"
    definition="The intermediate molecule between DNA and protein.">
  <PARENT id="SO:located_sequence_feature" relationship="OBO_REL:is_a">
  <PARENT id="SO:gene_part" relationship="OBO_REL:is_a">
</TYPE>

<TYPE
    id="SO:CDS"
    ontology="sofa.ontology"
    name="CDS"
    definition="A contiguous RNA sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.">
  <PARENT id="SO:mRNA" relationship="OBO_REL:part_of">
  <PARENT id="SO:gene_part" relationship="OBO_REL:is_a">
</TYPE>

<TYPE
    id="SO:located_sequence_feature"
    ontology="sofa.ontology" 
    name="located_sequence_feature"
    definition="A biological feature that can be attributed to a region of biological sequence."
/>

<TYPE
    id="SO:gene_part"
    ontology="sofa.ontology"
    name="gene_part" 
    definition="A part of a gene."
/>

Showing the types/supertypes available in this way allows the client to
infer that a request for "feature?type=SO:mRNA" is going to return both
"SO:mRNA" and "SO:CDS" records -- even if the "SO:CDS" are not directly
attached to a "SO:mRNA" parent (review "type" vs. "exacttype" feature
filters to understand why).  This information would also be useful for
rendering a tree widget in a client for selecting types of interest.

Also, for the "type" feature filter, we may only want to traverse
"OBO_REL:is_a" edges and not "OBO_REL:part_of" edges, or other edge types
such as "OBO_REL:adjacent_to"... this would prevent the server from
returning "SO:CDS" features when "SO:mRNA" is requested, but not prevent
the return of "SO:polycistronic_mRNA" features, because
"SO:polycistronic_mRNA" "OBO_REL:is_a" "SO:mRNA".

-Allen