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

[Gregg Helt]

Forwarding more messages that didn't get cross-posted to das2 list:

---------- Forwarded message ----------
From: Gustavo Salazar <gustavo at nbn.ac.za>
Date: Tue, Nov 4, 2008 at 9:27 AM
Subject: Re: [DAS] [DAS2] [Fwd: Re: Writeback implementation]
To: Andy Jenkinson <andy.jenkinson at ebi.ac.uk>
Cc: das at lists.open-bio.org

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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