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

[Andy Jenkinson]

As I understand, the DAS/2 "type" attribute is a URI, to match the 
"types" schema. This is really the equivalent of the type ID. Also, 
<PROP> elements cannot have arbitrary attributes, instead they need two 
attributes, one called "key" and the other "value":

  so it would look more like:
<FEATURE uri="..." title="..." type="SO:0001069" >
   <PROP name="typeLabel"    value="polypeptide_structural_domain" />
   <PROP name="typeCategory" value="inferred ..." />

With regards to the <LOC> element, this refers to the location of the 
feature within a segment. In DAS/2 there can be more than one (i.e. the 
same feature in multiple locations), but for DAS just send one LOC 
element. The range attribute should be the start/end/strand positions of 
the _feature_, so you do not need to send separate start and end properties:
<FEATURE ... >
   <LOC segment="O00329" range="830:1031" />

However I would be careful with the numbers as I believe DAS/2 uses 
zero-indexed start positions.

Gustavo Salazar wrote:
> 
> 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.