The Reasoner Agent makes request to Database Agents as following message.
(request
	:sender		ReasonerAgent
	:receiver	DBAgent
	:ontology	UDBIO
	:content	(
		<SERVICE>		service-id		</SERVICE>
		<QUERY>			query-id		</QUERY>
		<PROTEIN-SEQUENCE>	protein-sequence	</PROTEIN-SEQUENCE> ))	
		

The Database Agents reply the request as the following format:
(inform
	:sender	DBAgent
	:receiver ReasonerAgent
	:ontology UDBIO
	:content (
	  <BLAST-RESULT> 
	    <QUERY>   query-id	 </QUERY>
	    <BLAST-MATCH> *
	      <BLAST-SCORE> blast-score </BLAST-SCORE>
	      <DATABASE> DBName </DATABASE>	   
	      <GENE>
		<GENE-NAME> gene-name </GENE-NAME>
		<GO-ANNOTATION>
			<BIOLOGICAL-PROCESS> *
			    <GOID>	ProcessGOID	</GOID>
			    <EVIDENCE>	
				<EC>		evidence-code		</EC>
				<EC-URL>	url-of-the-evidence	</EC-URL>
			    </EVIDENCE>
			</BIOLOGICAL-PROCESS>

			<MOLECULAR-FUNCTION> *
			    <GOID>	FunctionGOID	</GOID>
			    <EVIDENCE>
				<EC>		evidence-code		</EC>
				<EC-URL>	url-of-the-evidence	</EC-URL>
			    </EVIDENCE>
			</MOLECULAR-FUNCTION>

			<CELLULAR-COMPONENT> 
			    <GOID>	ComponentGOID	</GOID>
			    <EVIDENCE>
				<EC>		evidence-code		</EC>
				<EC-URL>	url-of-the-evidence	</EC-URL>
			    </EVIDENCE>
			</CELLULAR-COMPONENT> 
		</GO-ANNOTATION>
		<TRANSLATION> translation </TRANSLATION>
		<ACCESSION-NUMBER> accession-number </ACCESSION-NUMBER>		
	      </GENE>
	    </BLAST-MATCH>
	  </BLAST-RESULT>))
		

Next is the conversation between OntologyAgent and DBAgent. DBAgent request OntologyAgent
about translation from Database1, such as terms of SwissProt, to GOID.

(request
	:sender		DBAgent
	:receiver	OntologyAgent
	:ontology	UDBIO
	:content	(
	    <CONVERSION> *
		<FROM>		SwissProt	</FROM>
		<TO>		GO		</TO>
		<CONVERSION-PAIR> *
		    <ORIGIN>	Nuclear protein		</ORIGIN>
		    <GOID>	corresponding-GOID	</GOID>
		</CONVERSION-PAIR>
	    </CONVERSION> ))

(inform
	:sender		OntologyAgent
	:receiver	DBAgent
	:ontology	UDBIO
	:content	(
	    <CONVERSION> *
		<FROM>		SwissProt	</FROM>	
		<TO>		GO		</TO>
		<CONVERSION-PAIR> *
		    <ORIGIN>	Nuclear protein		</ORIGIN>
		    <GOID>	corresponding-GOID	</GOID>
		    <BELONGTO>  belong-to-which areas	</BELONGTO>
		<CONVERSION-PAIR>
	    </CONVERSION> ))