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

[Gustavo Salazar]

Hello,

Thanks Andy for the comments about the XML example .
I notice that in your message said that the attribute in PROP should be 
"key" but in the example you used "name". I look into the schema and the 
right one is "key".
About the LOC I'm still confused because if you see the answer(DAS/1.53) 
the element SEGMENT has its own start and stop attribute, independently 
of the start and stop attributes for each feature. And even the class in 
MyDas indicates that the start and stop attributes are mandatory for 
both segment and feature element. And thats why I though that the range 
in LOC belongs to the segment and then the start and stop should be 
extra properties. And so, if those values are about just the feature i 
dont have any information about the segment position, and therefore I 
won't be able to create an instance of Segment which is the type of the 
return parameter for the function getFeatures of MyDas.

Cheers,

Gustavo.


Andy Jenkinson wrote:
> 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.