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Bio4j Go Tools

Bio4j Go Tools consists of several GO-related Web Services using Bio4j platform as back-end. Besides, some AIR apps are provided for both user-friendly requests to these services and visualization of the results.

Services

All services are XML-based HTTP POST requests. Their implementations can be found at Bio4jTestServer github project. Every service uses the same communication schema sending <request/> elements and getting <response/> elements. All these XML wrappers used for client-server communication are described and implemented by the github open source project Era7XmlApi.

Bio4jGoTools github project includes the AIR apps for both user-friendly services data retrieving and visualization.

In the case you want to perform the request yourself, the temporal base address for the services is: http://gotools.bio4j.com:8080/Bio4jTestServer

Don't forget assigning the request xml to a POST variable called 'request'.

Go Annotation

This service expects a list of Uniprot protein accessions and returns their respective GO annotations as result. There are two different versions depending on the format of the result, (an XML file or just text representing this XML).

Use one these two url patterns for this service:

/GoAnnotation –> XML text response
/DownloadGoAnnotation –> XML file response

Example (protein with accession = P05552):

Request XML:

<request method="go_annotation">
  <parameters>
    <proteins>
      <protein>
        <id>P05552</id>
      </protein>
    </proteins>
  </parameters>
</request>

Change the method attribute to 'download_go_annotation' in case you want an XML file as response

Response XML:

<response status="ok" id="100000" method="go_annotation">
  <go_annotation>
    <protein_annotations>
      <protein>
        <id>P05552</id>
        <go_terms>
          <biological_process>
            <go_term>
              <id>GO:0006350</id>
              <aspect>biological_process</aspect>
              <name>transcription</name>
              <evidence>IEA:UniProtKB-KW</evidence>
            </go_term>
            <go_term>
              <id>GO:0007416</id>
              <aspect>biological_process</aspect>
              <name>synapse assembly</name>
              <evidence>IMP:FlyBase</evidence>
            </go_term>
            <go_term>
              <id>GO:0045941</id>
              <aspect>biological_process</aspect>
              <name>positive regulation of transcription</name>
              <evidence>TAS:FlyBase</evidence>
            </go_term>
            <go_term>
              <id>GO:0008355</id>
              <aspect>biological_process</aspect>
              <name>olfactory learning</name>
              <evidence>NAS:FlyBase</evidence>
            </go_term>
            <go_term>
              <id>GO:0007616</id>
              <aspect>biological_process</aspect>
              <name>long-term memory</name>
              <evidence>TAS:FlyBase</evidence>
            </go_term>
            <go_term>
              <id>GO:0040011</id>
              <aspect>biological_process</aspect>
              <name>locomotion</name>
              <evidence>IMP:FlyBase</evidence>
            </go_term>
            <go_term>
              <id>GO:0008345</id>
              <aspect>biological_process</aspect>
              <name>larval locomotory behavior</name>
              <evidence>NAS:FlyBase</evidence>
            </go_term>
            <go_term>
              <id>GO:0048813</id>
              <aspect>biological_process</aspect>
              <name>dendrite morphogenesis</name>
              <evidence>IMP:FlyBase</evidence>
            </go_term>
          </biological_process>
          <molecular_function>
            <go_term>
              <id>GO:0042802</id>
              <aspect>molecular_function</aspect>
              <name>identical protein binding</name>
              <evidence>IPI:IntAct</evidence>
            </go_term>
            <go_term>
              <id>GO:0003677</id>
              <aspect>molecular_function</aspect>
              <name>DNA binding</name>
              <evidence>IEA:UniProtKB-KW</evidence>
            </go_term>
          </molecular_function>
          <cellular_component>
            <go_term>
              <id>GO:0005634</id>
              <aspect>cellular_component</aspect>
              <name>nucleus</name>
              <evidence>IDA:FlyBase</evidence>
            </go_term>
          </cellular_component>
        </go_terms>
      </protein>
    </protein_annotations>
    <annotator_go_terms>
      <go_term>
        <id>GO:0040011</id>
        <aspect>biological_process</aspect>
        <name>locomotion</name>
        <evidence>IMP:FlyBase</evidence>
        <annotations_count>1</annotations_count>
      </go_term>
      <go_term>
        <id>GO:0048813</id>
        <aspect>biological_process</aspect>
        <name>dendrite morphogenesis</name>
        <evidence>IMP:FlyBase</evidence>
        <annotations_count>1</annotations_count>
      </go_term>
      <go_term>
        <id>GO:0008345</id>
        <aspect>biological_process</aspect>
        <name>larval locomotory behavior</name>
        <evidence>NAS:FlyBase</evidence>
        <annotations_count>1</annotations_count>
      </go_term>
      <go_term>
        <id>GO:0008355</id>
        <aspect>biological_process</aspect>
        <name>olfactory learning</name>
        <evidence>NAS:FlyBase</evidence>
        <annotations_count>1</annotations_count>
      </go_term>
      <go_term>
        <id>GO:0045941</id>
        <aspect>biological_process</aspect>
        <name>positive regulation of transcription</name>
        <evidence>TAS:FlyBase</evidence>
        <annotations_count>1</annotations_count>
      </go_term>
      <go_term>
        <id>GO:0007616</id>
        <aspect>biological_process</aspect>
        <name>long-term memory</name>
        <evidence>TAS:FlyBase</evidence>
        <annotations_count>1</annotations_count>
      </go_term>
      <go_term>
        <id>GO:0005634</id>
        <aspect>cellular_component</aspect>
        <name>nucleus</name>
        <evidence>IDA:FlyBase</evidence>
        <annotations_count>1</annotations_count>
      </go_term>
      <go_term>
        <id>GO:0003677</id>
        <aspect>molecular_function</aspect>
        <name>DNA binding</name>
        <evidence>IEA:UniProtKB-KW</evidence>
        <annotations_count>1</annotations_count>
      </go_term>
      <go_term>
        <id>GO:0007416</id>
        <aspect>biological_process</aspect>
        <name>synapse assembly</name>
        <evidence>IMP:FlyBase</evidence>
        <annotations_count>1</annotations_count>
      </go_term>
      <go_term>
        <id>GO:0042802</id>
        <aspect>molecular_function</aspect>
        <name>identical protein binding</name>
        <evidence>IPI:IntAct</evidence>
        <annotations_count>1</annotations_count>
      </go_term>
      <go_term>
        <id>GO:0006350</id>
        <aspect>biological_process</aspect>
        <name>transcription</name>
        <evidence>IEA:UniProtKB-KW</evidence>
        <annotations_count>1</annotations_count>
      </go_term>
    </annotator_go_terms>
  </go_annotation>
</response>

Go Slim

This service maps a set of protein annotations up to their parent GO slim terms, returning which proteins are consequently annotated by which (if any) terms of the SlimSet. (If you don't know what is a Slim set or a Go Slim you can find more information in the Gene Ontology website).

Use one these two url patterns for this service:

/GoSlim –> XML text response
/DownloadGoSlim –> XML file response

Example:

Protein set: D5ADG8, P12345, Q9ZS97, Q9ZSA2

GoSlim set: GO:0000003, GO:0000166, GO:0003674, GO:0008152, GO:0005829

Request XML:

<request method="go_slim">
  <parameters>
    <proteins>
      <protein>
        <id>D5ADG8</id>
      </protein>
      <protein>
        <id>P12345</id>
      </protein>
      <protein>
        <id>Q9ZS97</id>
      </protein>
      <protein>
        <id>Q9ZSA2</id>
      </protein>
    </proteins>
    <slim_set>
      <go_term>
        <id>GO:0000003</id>
      </go_term>
      <go_term>
        <id>GO:0000166</id>
      </go_term>
      <go_term>
        <id>GO:0003674</id>
      </go_term>
      <go_term>
        <id>GO:0008152</id>
      </go_term>
      <go_term>
        <id>GO:0005829</id>
      </go_term>
    </slim_set>
  </parameters>
</request>

Change the method attribute to 'download_go_slim' in case you want an XML file as response

Response XML:

<go_slim>
  <proteins>
    <protein>
      <id>D5ADG8</id>
      <go_terms>
        <molecular_function>
          <go_term>
            <id><![CDATA[GO:0003674]]></id>
            <aspect>molecular_function</aspect>
            <name>molecular_function</name>
            <protein_annotation_leading_to_slim_term>
              <go_term>
                <id>GO:0019787</id>
                <aspect>molecular_function</aspect>
                <name>small conjugating protein ligase activity</name>
                <evidence>IEA:InterPro</evidence>
              </go_term>
            </protein_annotation_leading_to_slim_term>
          </go_term>
        </molecular_function>
        <biological_process>
          <go_term>
            <id><![CDATA[GO:0008152]]></id>
            <aspect>biological_process</aspect>
            <name>metabolic process</name>
            <protein_annotation_leading_to_slim_term>
              <go_term>
                <id>GO:0043687</id>
                <aspect>biological_process</aspect>
                <name>post-translational protein modification</name>
                <evidence>IEA:InterPro</evidence>
              </go_term>
            </protein_annotation_leading_to_slim_term>
          </go_term>
        </biological_process>
      </go_terms>
    </protein>
    <protein>
      <id>P12345</id>
      <go_terms>
        <molecular_function>
          <go_term>
            <id><![CDATA[GO:0003674]]></id>
            <aspect>molecular_function</aspect>
            <name>molecular_function</name>
            <protein_annotation_leading_to_slim_term>
              <go_term>
                <id>GO:0004069</id>
                <aspect>molecular_function</aspect>
                <name>L-aspartate:2-oxoglutarate aminotransferase activity</name>
                <evidence>ISS:UniProtKB</evidence>
              </go_term>
            </protein_annotation_leading_to_slim_term>
          </go_term>
        </molecular_function>
        <biological_process>
          <go_term>
            <id><![CDATA[GO:0008152]]></id>
            <aspect>biological_process</aspect>
            <name>metabolic process</name>
            <protein_annotation_leading_to_slim_term>
              <go_term>
                <id>GO:0006457</id>
                <aspect>biological_process</aspect>
                <name>protein folding</name>
                <evidence>TAS:HGNC</evidence>
              </go_term>
            </protein_annotation_leading_to_slim_term>
          </go_term>
        </biological_process>
      </go_terms>
    </protein>
    <protein>
      <id>Q9ZS97</id>
      <go_terms>
        <molecular_function>
          <go_term>
            <id><![CDATA[GO:0003674]]></id>
            <aspect>molecular_function</aspect>
            <name>molecular_function</name>
            <protein_annotation_leading_to_slim_term>
              <go_term>
                <id>GO:0042626</id>
                <aspect>molecular_function</aspect>
                <name>ATPase activity, coupled to transmembrane movement of substances</name>
                <evidence>IDA:TAIR</evidence>
              </go_term>
            </protein_annotation_leading_to_slim_term>
          </go_term>
        </molecular_function>
        <biological_process>
          <go_term>
            <id><![CDATA[GO:0008152]]></id>
            <aspect>biological_process</aspect>
            <name>metabolic process</name>
            <protein_annotation_leading_to_slim_term>
              <go_term>
                <id>GO:0016226</id>
                <aspect>biological_process</aspect>
                <name>iron-sulfur cluster assembly</name>
                <evidence>IGI:TAIR</evidence>
              </go_term>
            </protein_annotation_leading_to_slim_term>
          </go_term>
        </biological_process>
      </go_terms>
    </protein>
    <protein>
      <id>Q9ZSA2</id>
      <go_terms>
        <molecular_function>
          <go_term>
            <id><![CDATA[GO:0003674]]></id>
            <aspect>molecular_function</aspect>
            <name>molecular_function</name>
            <protein_annotation_leading_to_slim_term>
              <go_term>
                <id>GO:0005524</id>
                <aspect>molecular_function</aspect>
                <name>ATP binding</name>
                <evidence>IEA:UniProtKB-KW</evidence>
              </go_term>
            </protein_annotation_leading_to_slim_term>
          </go_term>
          <go_term>
            <id><![CDATA[GO:0000166]]></id>
            <aspect>molecular_function</aspect>
            <name>nucleotide binding</name>
            <protein_annotation_leading_to_slim_term>
              <go_term>
                <id>GO:0005524</id>
                <aspect>molecular_function</aspect>
                <name>ATP binding</name>
                <evidence>IEA:UniProtKB-KW</evidence>
              </go_term>
            </protein_annotation_leading_to_slim_term>
          </go_term>
        </molecular_function>
        <biological_process>
          <go_term>
            <id><![CDATA[GO:0008152]]></id>
            <aspect>biological_process</aspect>
            <name>metabolic process</name>
            <protein_annotation_leading_to_slim_term>
              <go_term>
                <id>GO:0006468</id>
                <aspect>biological_process</aspect>
                <name>protein phosphorylation</name>
                <evidence>IEA:InterPro</evidence>
              </go_term>
            </protein_annotation_leading_to_slim_term>
          </go_term>
        </biological_process>
      </go_terms>
    </protein>
  </proteins>
  <slim_set>
    <go_term>
      <id><![CDATA[GO:0000003]]></id>
      <aspect>biological_process</aspect>
      <name>reproduction</name>
      <annotations_count>0</annotations_count>
    </go_term>
    <go_term>
      <id><![CDATA[GO:0000166]]></id>
      <aspect>molecular_function</aspect>
      <name>nucleotide binding</name>
      <annotations_count>1</annotations_count>
    </go_term>
    <go_term>
      <id><![CDATA[GO:0003674]]></id>
      <aspect>molecular_function</aspect>
      <name>molecular_function</name>
      <annotations_count>4</annotations_count>
    </go_term>
    <go_term>
      <id><![CDATA[GO:0008152]]></id>
      <aspect>biological_process</aspect>
      <name>metabolic process</name>
      <annotations_count>4</annotations_count>
    </go_term>
    <go_term>
      <id><![CDATA[GO:0005829]]></id>
      <aspect>cellular_component</aspect>
      <name>cytosol</name>
      <annotations_count>0</annotations_count>
    </go_term>
  </slim_set>
  <sample_gene_number>4</sample_gene_number>
  <sample_annotated_gene_number>4</sample_annotated_gene_number>
</go_slim>

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bio4jgotools.txt · Last modified: 2011/03/29 11:39 by Pablo Pareja Tobes

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