GET Requests on DAS/2 Assay URLs

The primary way to retrieve information from a DAS/2 server is to perform a GET request on a DAS/2 URL.

Fetching Information about Experiments

text/x-das-experiments+xml

REQUEST:

GET http://das.biopackages.net/das/assay/human/17/experiment

RESPONSE:

Content-Type: text/x-das-experiments+xml

<Experiment_assnlist>
<Experiment identifier="787"
            name="491 - HCC Hep">
  <Providers_assnreflist>
    <Contact_ref identifier="../contact/150"/>
  </Providers_assnreflist>
  <BioAssays_assnreflist>
    <BioAssay_ref identifier="../assay/4839"/>
    <BioAssay_ref identifier="../assay/4840"/>
  </BioAssays_assnreflist>
</Experiment>
<Experiment identifier="788"
            name="473 - Glycerolkinase chips 4">
  <Providers_assnreflist>
    <Contact_ref identifier="../contact/200"/>
  </Providers_assnreflist>
  <BioAssays_assnreflist>
    <BioAssay_ref identifier="../assay/4841"/>
    <BioAssay_ref identifier="../assay/4842"/>
    <BioAssay_ref identifier="../assay/4843"/>
    <BioAssay_ref identifier="../assay/4844"/>
  </BioAssays_assnreflist>
</Experiment>
</Experiment_assnlist>

Fetching Information about Experimental Factors

text/x-das-factors+xml

REQUEST:

GET http://das.biopackages.net/das/assay/human/17/factor

RESPONSE:

Content-Type: text/x-das-factors+xml

Fetching Information about Contacts

text/x-das-contacts+xml

REQUEST:

GET http://das.biopackages.net/das/assay/human/17/contact

RESPONSE:

Content-Type: text/x-das-contacts+xml

<Contact_assnlist>
<Organization identifier="1"
              name="Affymetrix">
</Organization>
<Organization identifier="2"
              name="Helt, Gregg">
  <Parent_assnref>
    <Organization_ref identifier="1"/>
  </Parent_assnref>
</Organization>
</Contact_assnlist>

Fetching Information about Biological Materials

text/x-das-materials+xml

REQUEST:

GET http://das.biopackages.net/das/assay/human/17/material

RESPONSE:

Content-Type: text/x-das-materials+xml

<BioMaterial_assnlist>
<BioSource identifier="source_4610"
           name="1388 - Ctrl Pt 1 - Timestep 2( )">
  <Characteristics_assnlist>
    <OntologyEntry category="MGED:Anatomy">
      <OntologyReference_assn>
        <DatabaseEntry URI="../type/MA:body">
        </DatabaseEntry>
      </OntologyReference_assn>
    </OntologyEntry>
  </Characteristics_assnlist>
  <SourceContact_assnreflist>
    <Organization_ref identifier="../contact/150"/>
  </SourceContact_assnreflist>
</BioSource>
<LabeledExtract identifier="4610">
  <Treatments_assnlist>
    <Treatment identifier="treatment_4610">
      <SourceBioMaterialMeasurements_assnlist>
        <BioMaterialMeasurement>
          <BioMaterial_assnref>
            <BioSource_ref identifier="source_4610"/>
          </BioMaterial_assnref>
        </BioMaterialMeasurement>
      </SourceBioMaterialMeasurements_assnlist>
    </Treatment>
  </Treatments_assnlist>
</LabeledExtract>
<BioSource identifier="source_4611"
           name="1389 - Exp Pt 1 - Timestep 2( )">
  <Characteristics_assnlist>
    <OntologyEntry category="MGED:Anatomy">
      <OntologyReference_assn>
        <DatabaseEntry URI="../type/MA:body">
        </DatabaseEntry>
      </OntologyReference_assn>
    </OntologyEntry>
  </Characteristics_assnlist>
  <SourceContact_assnreflist>
    <Organization_ref identifier="../contact/150"/>
  </SourceContact_assnreflist>
</BioSource>
<LabeledExtract identifier="4611">
  <Treatments_assnlist>
    <Treatment identifier="treatment_4611">
      <SourceBioMaterialMeasurements_assnlist>
        <BioMaterialMeasurement>
          <BioMaterial_assnref>
            <BioSource_ref identifier="source_4611"/>
          </BioMaterial_assnref>
        </BioMaterialMeasurement>
      </SourceBioMaterialMeasurements_assnlist>
    </Treatment>
  </Treatments_assnlist>
</LabeledExtract>
</BioMaterial_assnlist>

Fetching Information about Biological Material Properties

there is some instability related to whether the material annotations are under /property or /type. this section of the spec is unstable.

text/x-das-properties+xml

REQUEST:

GET http://das.biopackages.net/das/assay/human/17/property

RESPONSE:

Content-Type: text/x-das-properties+xml

Fetching Information about Biological Material Types

there is some instability related to whether the material annotations are under /property or /type. this section of the spec is unstable.

text/x-das-types+xml

REQUEST:

GET http://das.biopackages.net/das/assay/human/17/type

RESPONSE:

Content-Type: text/x-das-types+xml

Fetching Information about Treatments on Biological Materials

i haven't added feature treatments to any records on the prototype server, so this aspect of the spec is not yet written

text/x-das-treatments+xml

REQUEST:

GET http://das.biopackages.net/das/assay/human/17/treatment

RESPONSE:

Content-Type: text/x-das-treatments+xml

Fetching Information about Protocols

text/x-das-protocols+xml

REQUEST:

GET http://das.biopackages.net/das/assay/human/17/protocol

RESPONSE:

Content-Type: text/x-das-protocols+xml

<Protocol_assnlist>
<Protocol identifier="dabg"
          title="dabg">
</Protocol>
<Protocol identifier="dchip"
          title="dchip">
</Protocol>
</Protocol_assnlist>

Fetching Information about Assays on Biological Materials

text/x-das-assays+xml

REQUEST:

GET http://das.biopackages.net/das/assay/human/17/assay

RESPONSE:

Content-Type: text/x-das-materials+xml

<BioAssay_assnlist>
<PhysicalBioAssay identifier="4851">
  <PhysicalBioAssayData_assnlist>
    <Image URI="../image/4851">
    </Image>
  </PhysicalBioAssayData_assnlist>
  <BioAssayCreation_assn>
    <Hybridization>
      <SourceBioMaterialMeasurements_assnlist>
        <BioMaterialMeasurement>
          <BioMaterial_assnref>
            <BioMaterial_ref identifier="../material/4618"/>
          </BioMaterial_assnref>
          <Measurement_assn>
            <Measurement>
            </Measurement>
          </Measurement_assn>
        </BioMaterialMeasurement>
      </SourceBioMaterialMeasurements_assnlist>
      <Array_assnref>
        <Array_ref identifier="../platform/Affymetrix_MG-U74Av2"/>
      </Array_assnref>
    </Hybridization>
  </BioAssayCreation_assn>
</PhysicalBioAssay>
<PhysicalBioAssay identifier="4852">
  <PhysicalBioAssayData_assnlist>
    <Image URI="../image/4852">
    </Image>
  </PhysicalBioAssayData_assnlist>
  <BioAssayCreation_assn>
    <Hybridization>
      <SourceBioMaterialMeasurements_assnlist>
        <BioMaterialMeasurement>
          <BioMaterial_assnref>
            <BioMaterial_ref identifier="../material/4619"/>
          </BioMaterial_assnref>
          <Measurement_assn>
            <Measurement>
            </Measurement>
          </Measurement_assn>
        </BioMaterialMeasurement>
      </SourceBioMaterialMeasurements_assnlist>
      <Array_assnref>
        <Array_ref identifier="../platform/Affymetrix_MG-U74Av2"/>
      </Array_assnref>
    </Hybridization>
  </BioAssayCreation_assn>
</PhysicalBioAssay>
</BioAssay_assnlist>

Fetching Information about Images Acquired from Assays

text/x-das-images+xml

REQUEST:

GET http://das.biopackages.net/das/assay/human/17/image

RESPONSE:

Content-Type: text/x-das-assays+xml

Fetching Information about Transformed Results from Acquired Images

text/x-das-results+xml

REQUEST:

GET http://das.biopackages.net/das/assay/human/17/image

RESPONSE:

Content-Type: text/x-das-images+xml

<RESULTS>
  <RESULT id="3862" assay="../assay/4033" image="../image/4033" protocol="../protocol/4"/>
  <RESULT id="3863" assay="../assay/3990" image="../image/3990" protocol="../protocol/4"/>
  <RESULT id="3864" assay="../assay/3991" image="../image/3991" protocol="../protocol/4"/>
  <RESULT id="3865" assay="../assay/3992" image="../image/3992" protocol="../protocol/4"/>
</RESULTS>

Fetching Information about Assay Platforms

text/x-das-platforms+xml

REQUEST:

GET http://das.biopackages.net/das/assay/human/17/platform

RESPONSE:

Content-Type: text/x-das-platforms+xml

<ArrayDesign_assnlist>
<ArrayDesign identifier="Affymetrix_ATH1-121501">
  <DesignProviders_assnreflist>
    <Contact_ref identifier="../contact/1"/>
  </DesignProviders_assnreflist>
</ArrayDesign>
<ArrayDesign identifier="Affymetrix_Mouse430A_2">
  <DesignProviders_assnreflist>
    <Contact_ref identifier="../contact/1"/>
  </DesignProviders_assnreflist>
</ArrayDesign>
<ArrayDesign identifier="Affymetrix_Mouse430_2">
  <DesignProviders_assnreflist>
    <Contact_ref identifier="../contact/1"/>
  </DesignProviders_assnreflist>
</ArrayDesign>
<ArrayDesign identifier="Affymetrix_MOE430B">
  <DesignProviders_assnreflist>
    <Contact_ref identifier="../contact/1"/>
  </DesignProviders_assnreflist>
</ArrayDesign>
</ArrayDesign_assnlist>

Notes and Discussion Points