[DAS] [DAS2] [Fwd: Re: Writeback implementation]

[Gustavo Salazar]

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.