[Psidev-pi-dev] Issue 44 in psi-pi: Issues with all instance docs

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Comment #13 on issue 44 by andrewrobertjones: Issues with all instance docs
http://code.google.com/p/psi-pi/issues/detail?id=44

Re-opening this issue:

We don't currently have an example for MS:1001089 and MS:1001090 and they
are not well defined.

[Term]
id: MS:1001089
name: protein taxonomy
def: "The taxonomy of the resultant protein from the search." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001085 ! protein result details

[Term]
id: MS:1001090
name: taxonomy nomenclature
def: "The system used to indicate taxonomy. There should be an enumerated
list of options: latin name, NCBI TaxID, common name, Swiss-Prot species ID
(ex. RABIT from the full protein ID ALBU_RABIT)." [PSI:PI]
is_a: MS:1001089 ! protein taxonomy

This seems a little unwieldy to me. How about just having different CV for
each type of ID. For example


<DBSequence id="x" length="449" SearchDatabase_ref="y" accession="z" >
   <seq>MGKEKFHINIVVIGHVDSGKSTTTGHLIY...</seq>
   <pf:cvParam accession="MS:1001088" name="protein description"
cvRef="PSI-MS" value="Elongation factor..." />
   <pf:cvParam accession="MS:xxxxxx1" name="taxonomy: NCBI TaxID"
cvRef="PSI-MS" value="9606" />
   <pf:cvParam accession="MS:xxxxxx2" name="taxonomy: common name"
cvRef="PSI-MS" value="human" />
   <pf:cvParam accession="MS:xxxxxx3" name="taxonomy: scientific name"
cvRef="PSI-MS" value="Homo sapiens" />
   <pf:cvParam accession="MS:xxxxxx4" name="taxonomy: Swiss-Prot ID"
cvRef="PSI-MS" value="HUMAN" />
</DBSequence>


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