Christoph,

Here is the example

<?xml version="1.0" ?><rdf:RDF xmlns:ot="http://www.opentox.org/api/1.1#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:owl="
http://www.w3.org/2002/07/owl#"
xmlns:dc="http://purl.org/dc/elements/1.1/"><owl:Class
rdf:about="http://www.opentox.org/api/1.1#Dataset"></owl:Class><owl:Class
rdf:about="http://www.opentox.org/api/1.1#DataEntry"></owl:Class><owl:Class
rdf:about="http://www.opentox.org/api/1.1#Feature"></owl:Class><owl:Class
rdf:about="http://www.opentox.org/api/1.1#FeatureValue"></owl:Class><owl:Class
rdf:about="http://www.opentox.org/api/1.1#Compound"></owl:Class><owl:ObjectProperty
rdf:about="http://www.opentox.org/api/1.1#compound"></owl:ObjectProperty><owl:ObjectProperty
rdf:about="http://www.opentox.org/api/1.1#dataEntry"></owl:ObjectProperty><owl:ObjectProperty
rdf:about="http://www.opentox.org/api/1.1#values"></owl:ObjectProperty><owl:ObjectProperty
rdf:about="http://www.opentox.org/api/1.1#feature"></owl:ObjectProperty><owl:ObjectProperty
rdf:about="http://www.opentox.org/api/1.1#hasSource"></owl:ObjectProperty><owl:ObjectProperty
rdf:about="http://www.opentox.org/api/1.1#acceptValue"></owl:ObjectProperty><owl:DatatypeProperty
rdf:about="http://www.opentox.org/api/1.1#units"></owl:DatatypeProperty><owl:DatatypeProperty
rdf:about="http://www.opentox.org/api/1.1#value"></owl:DatatypeProperty><owl:AnnotationProperty
rdf:about="http://purl.org/dc/elements/1.1/description"></owl:AnnotationProperty><owl:AnnotationProperty
rdf:about="http://purl.org/dc/elements/1.1/creator"></owl:AnnotationProperty><owl:AnnotationProperty
rdf:about="http://purl.org/dc/elements/1.1/type"></owl:AnnotationProperty><owl:AnnotationProperty
rdf:about="http://purl.org/dc/elements/1.1/title"></owl:AnnotationProperty><ot:Dataset
rdf:about="https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/36400"><ot:dataEntry><ot:DataEntry><ot:compound><ot:Compound
rdf:about="
https://ambit.uni-plovdiv.bg:8443/ambit2/compound/163134/conformer/506294"></ot:Compound></ot:compound><ot:values><ot:FeatureValue><ot:feature
rdf:resource="https://ambit.uni-plovdiv.bg:8443/ambit2/feature/178539"></ot:feature><ot:value
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HC
HO
CHHHN
CHHCC
CHCC
CHCN
CCCC
CCCN
NCCC
NCO
OHN
C(C(CCC)C(CC-H)N(CC-C))
C(C(CCC)C(CC-H)-H(C))
C(C(CCC)C(CN-H)-C(C-C-N))
C(C(CCN)C(CC-H)C(CC-C))
C(C(CCN)C(CC-H)-H(C))
C(C(CC-H)C(CC-H)-H(C))
C(C(CC-H)C(CC-H)-C(C-H-H-C))
C(C(CC-H)C(CC-C)-H(C))
C(C(CC-C)N(CC-C)-H(C))
N(C(CCN)C(CN-H)-C(N-H-H-H))
-H(C(CC-H))
-H(C(CN-H))
-H(-C(C-H-H-C))
-H(-C(N-H-H-H))
-H(-O(-H-N))
-C(C(CC-C)-H(-C)-H(-C)-C(C-C-N))
-C(C(CC-C)-C(C-H-H-C)-N(-C-O))
-C(N(CC-C)-H(-C)-H(-C)-H(-C))
-N(-C(C-C-N)-O(-H-N))
-O(-H(-O)-N(-C-O))

</ot:value></ot:FeatureValue></ot:values></ot:DataEntry></ot:dataEntry></ot:Dataset><ot:Feature
rdf:about="https://ambit.uni-plovdiv.bg:8443/ambit2/feature/178539
"><dc:creator>Default</dc:creator><ot:hasSource>
http://195.178.207.160/OpenTox/MNAGet</ot:hasSource><owl:sameAs
rdf:resource="http://www.opentox.org/api/1.1#MNA
"></owl:sameAs><ot:units></ot:units><dc:title>MNA</dc:title></ot:Feature></rdf:RDF>


Nina

On 13 December 2010 10:28, Nina Jeliazkova <jeliazkova.nina at gmail.com>wrote:

> Dear Dmitry,
>
> On 3 December 2010 16:08, Druzhilovsky <dmitry.druzhilovsky at ibmc.msk.ru>wrote:
>
>> Dear Nina, All,
>>
>> We finished MakeMNA/MakeQNA service, and presented it:
>>
>> http://195.178.207.160/OpenTox/MakeMNA
>> http://195.178.207.160/OpenTox/MakeQNA
>>
>> Could you check and give comments? And how could we integrate our service
>> into ToxCreate?
>>
>> Example POST:
>>
>> curl -X POST -d
>> dataset_uri=https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/2765 -d
>> dataset_service=https://ambit.uni-plovdiv.bg:8443/ambit2/dataset
>> http://195.178.207.160/OpenTox/MakeMNA
>>
>
> curl -X POST -d \
> > dataset_uri=https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/2765 -d \
> > dataset_service=https://ambit.uni-plovdiv.bg:8443/ambit2/dataset \
> > http://195.178.207.160/OpenTox/MakeMNA
> <?xml version="1.0" encoding="UTF-8"?>
> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>   xmlns:ns0="http://www.opentox.org/api/1.1#"
>   xmlns:ns1="http://purl.org/dc/elements/1.1/">
>
>   <rdf:Description rdf:about="http://www.opentox.org/api/1.1#DataSet">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
>   </rdf:Description>
>
>   <rdf:Description rdf:about="
> http://apps.ideaconsult.net:8080/ambit2/dataset/">
>     <ns0:dataEntry rdf:nodeID="arc056fb1"/>
>   </rdf:Description>
>
>   <rdf:Description rdf:nodeID="arc056fb1">
>     <rdf:type rdf:resource="http://www.opentox.org/api/1.1#DataEntry"/>
>     <ns0:compound rdf:resource="
> https://ambit.uni-plovdiv.bg:8443/ambit2/compound/163134/conformer/506294
> "/>
>     <ns0:values rdf:nodeID="MNA1"/>
>   </rdf:Description>
>
>   <rdf:Description rdf:nodeID="MNA1">
>     <rdf:type rdf:resource="http://www.opentox.org/api/1.1#FeatureValue"/>
>     <ns0:feature rdf:nodeID="Feature11"/>
>     <ns0:value rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HC
> HO
> CHHHN
> CHHCC
> CHCC
> CHCN
> CCCC
> CCCN
> NCCC
> NCO
> OHN
> C(C(CCC)C(CC-H)N(CC-C))
> C(C(CCC)C(CC-H)-H(C))
> C(C(CCC)C(CN-H)-C(C-C-N))
> C(C(CCN)C(CC-H)C(CC-C))
> C(C(CCN)C(CC-H)-H(C))
> C(C(CC-H)C(CC-H)-H(C))
> C(C(CC-H)C(CC-H)-C(C-H-H-C))
> C(C(CC-H)C(CC-C)-H(C))
> C(C(CC-C)N(CC-C)-H(C))
> N(C(CCN)C(CN-H)-C(N-H-H-H))
> -H(C(CC-H))
> -H(C(CN-H))
> -H(-C(C-H-H-C))
> -H(-C(N-H-H-H))
> -H(-O(-H-N))
> -C(C(CC-C)-H(-C)-H(-C)-C(C-C-N))
> -C(C(CC-C)-C(C-H-H-C)-N(-C-O))
> -C(N(CC-C)-H(-C)-H(-C)-H(-C))
> -N(-C(C-C-N)-O(-H-N))
> -O(-H(-O)-N(-C-O))
>
> </ns0:value>
>   </rdf:Description>
>
>   <rdf:Description rdf:nodeID="Feature11">
>     <rdf:type rdf:resource="http://www.opentox.org/api/1.1#Feature"/>
>     <ns0:hasSource rdf:datatype="http://www.w3.org/2001/XMLSchema#string">
> http://195.178.207.160/OpenTox/MNAGet</ns0:hasSource>
>     <ns1:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string
> ">MNA</ns1:title>
>   </rdf:Description>
>
> </rdf:RDF><rdf:RDF
>     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>     xmlns:ot="http://www.opentox.org/api/1.1#"
>     xmlns:bx="http://purl.org/net/nknouf/ns/bibtex#"
>     xmlns:owl="http://www.w3.org/2002/07/owl#"
>     xmlns:otee="http://www.opentox.org/echaEndpoints.owl#"
>     xmlns:dc="http://purl.org/dc/elements/1.1/"
>     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
>     xmlns:ota="http://www.opentox.org/algorithmTypes.owl#"
>     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
>   <owl:Class rdf:about="http://www.opentox.org/api/1.1#Task"/>
>   <owl:DatatypeProperty rdf:about="
> http://www.opentox.org/api/1.1#percentageCompleted"/>
>   <owl:DatatypeProperty rdf:about="
> http://www.opentox.org/api/1.1#hasStatus"/>
>   <ot:Task rdf:about="
> https://ambit.uni-plovdiv.bg:8443/ambit2/task/80a6cf85-a807-4347-8c94-9abc220bf039
> ">
>     <ot:percentageCompleted rdf:datatype="
> http://www.w3.org/2001/XMLSchema#float"
>     >0.0</ot:percentageCompleted>
>     <ot:hasStatus rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>     >Running</ot:hasStatus>
>     <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime"
>     >1292228310135</dc:date>
>     <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>     >File import application/rdf+xml [1938]</dc:title>
>   </ot:Task>
>   <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/date
> "/>
>   <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/title
> "/>
> </rdf:RDF>
>
> curl -L -k -H "Accept:text/uri-list" "
> https://ambit.uni-plovdiv.bg:8443/ambit2/task/80a6cf85-a807-4347-8c94-9abc220bf039
> "
> https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/36400
>
> As it could be seen, finally the URI of the dataset with MNA descriptors is
> returned, so it works fine. However, the dataset representation, SMILES
> string and anything, which is not ot:Task  representation and is returned
> from the first POST call, should not be there.
>
> Another comment is the MNA/QNA descriptor calculation is returning Task URI
> only after all the processing is completed and results sent to the dataset
> service. This means , the HTTP POST call may not complete for long time, if
> the dataset to be processed  contains more than few compounds.  OpenTox API
> recommends to return task URI immediately after accepting the processing,
> and then the client polls the task URI to find if it is completed.
>
> I have not tested how well the services work if sending multiple requests
> in parallel, would be better if you agree to setup smokeping testing for
> this purpose.
>
>
>> But as you asked me,  if the MNA are still described as one string
>> feature,
>> nobody else will be able to make sense of them ... We are suggesting such
>> structure: representation line contains only 1 or 0, which means presents
>> or
>> absence MNA descriptor. For each structure we'll generate fixed number of
>> MNA descriptors for example 500. So each partners could be used this
>> string
>> us independent variables (which the number 500) for regression analysis.
>> For
>> QNA representation Chebyshev polynomials will be used. So each string will
>> be include 100 independent variables. Variable means  Chebyshev polynomial
>> value obtained QNA descriptor.
>>
>>
> I guess the best way to handle custom formats for feature values content
> (in addition to standard string and number types ) is to propose specific
> MIME format and document them at OpenTox site. There might be better ways,
> would be good to discuss during today meeting.
>
>
>
>> And more, how kind date format do you use for uploading data for lasar
>> regression?
>>
>
> I hope Christoph could answer ToxCreate and lazar related questions.
>
> Best regards,
> Nina
>
>
>>
>> Best regards
>> Dmitry
>>
>> _______________________________________________
>> Development mailing list
>> Development at opentox.org
>> http://www.opentox.org/mailman/listinfo/development
>>
>
>