Hello,
Thanks Andy for the examples about the use of the URI, now is much clear
for me. I haven't implemented the small code to built the URI from the
URI and base parameters but I will soon.
Following the idea of use the PROP tag to put the attributes missed for
DAS/2 that are required in DAS/1.53 I have modify my XML example as follows:
<WRITEBACK xmlns="http://biodas.org/documents/das2";
xml:base="http://das.sanger.ac.uk:80/das/interpro/features";>
<MESSAGE>phosphoinositide 3-kinase in leukocytes</MESSAGE>
<FEATURES>
<FEATURE uri="G3DSA:1.10.1070.11" title="PI3/4_kinase_cat"
type="inferred from sequence similarity (ECO:0000044)" >
<LOC segment="O00329" range="1:1044" />
<PROP start="830" />
<PROP stop="1031" />
<PROP typeId="SO:0001069" />
<PROP typeCategory="inferred from sequence similarity
(ECO:0000044)" />
<PROP typeLabel="polypeptide_structural_domain" />
<PROP methodId="GENE3D" />
<PROP methodLabel="GENE3D" />
<PROP phase="-" />
<PROP score="0.0" />
<PROP commit_msg="added a new feature G3DSA:1.10.1070.11" />
<PROP user="http://user.myopenid.com/"; />
</FEATURE>
</FEATURES>
</WRITEBACK>
As you can notice i've also add the properties start and stop for the
position of the feature since i noticed that the range in LOC is for the
location of the segment and a segment can have several features in
different positions.
In my first tests with a document like this I can built the next answer
with MyDas that looks correct for DAS/1.53
<DASGFF>
<GFF version="1.0"
href="http://localhost:8080/MyDas/das/writeback/features?segment=O00329";>
<SEGMENT id="O00329" start="1" stop="1044" version="writeback"
label="O00329">
<FEATURE id="G3DSA:1.10.1070.11" label="PI3/4_kinase_cat">
<TYPE id="SO:0001069" category="inferred from sequence
similarity (ECO:0000044)">polypeptide_structural_domain</TYPE>
<METHOD id="GENE3D">GENE3D</METHOD>
<START>830</START>
<END>1031</END>
<SCORE>0.0</SCORE>
<ORIENTATION>0</ORIENTATION>
<PHASE>-</PHASE>
</FEATURE>
</SEGMENT>
</GFF>
</DASGFF>
Cheers,
Gustavo.
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