Concepts representing either consumed or created information products and ideas from the reference ontology for connector C was not as direct as for connector C. There have been RN-1734 site instances exactly where no direct association between a notion representing a consumed data item in addition to a idea representing a produced data item had been identified. So, two equivalence relations had to be developed for all those cases. The first equivalence relation was straightforward and was developed to associate an instance of your notion experimentspecific gene identifier having a achievable instance of the concept KEGG identifier. Though each ideas were associated to the reference ontology notion of gene, not all 
instances of experimentspecific gene 
identifier have corresponding situations of KEGG identifier. The Tubacin site second equivalence relation was made to associate the instances in the ideas of experimental situation, ratio intensitybased value and gene expression threshold with an instance of the concept of ratio intensitybased worth. Even though pretty basic in principle, the definition of this equivalence relation was really elaborated. It involved the definition of a mappingover instances of ratio intensitybased worth from the real numbers domain for the up, down and undefined regulation range in accordance with a (userprovided) instance of gene expression threshold. Connector C was also implemented as a separate Java application. This connector provided only manual transfer of control to KEGG Mapper Search Colour Pathway. After the equivalence relations had been defined, the specification and implementation on the grounding operations was simple. Additiolly, the transformation of instances with the concept experimentspecific gene identifier to situations of the concept KEGG identifier was carried out using a platform mapping file (SOFT format), also provided as input to connector C. This mapping is normally carried out in two actions: ) from experimentspecific gene identifier to official gene identifier; and ) from official gene identifier to KEGG identifier. Nevertheless, inside the particular case of Plasmodium vivax, each and every KEGG identifier corresponds straight to its official gene identifier. Within the implementation with the Lowering functiol block instances from the idea ratio intensitybased worth, viz upregulated, downregulated and undefined, have been mapped respectively to the red, green and yellow KEGG Mapper Search Colour Pathway color schema. Detailed facts concerning connector C implementation may also be PubMed ID:http://jpet.aspetjournals.org/content/117/4/451 obtained within a supplementary material (see Additiol File : Connectors C and C Implementation). The second scerio consisted of the integration of tools DMV and TMev so as to clusterize Sulfolobus solfataricus RSeq data. This scerio was inspired by the growing recognition of nextgeneration sequencing platforms for gene expression. Despite the rewards of storing the actual reads in RSeq databases, these raw data files deliver little help for highlevel gene expression alysis. So, they were transformed into a numeric representation to become filtered utilizing DMV based on some user defined criteria. Next, DMV output was utilized as input information for clustering utilizing TMev. Having said that, DMV output information should be normalized to account for various library sizes (total of sequenced reads) just before clusterization by TMev. Figure illustrates the architecture of our second integration scerio with focus on the flow of information. Two connectors have been developed to integrate RSeq data to DMV and TMev. Connector C transforms R.Concepts representing either consumed or made information products and ideas from the reference ontology for connector C was not as direct as for connector C. There were instances where no direct association in between a concept representing a consumed information item plus a notion representing a made data item were identified. So, two equivalence relations had to be made for all those circumstances. The initial equivalence relation was simple and was developed to associate an instance of your concept experimentspecific gene identifier having a doable instance in the concept KEGG identifier. Despite the fact that both concepts have been related towards the reference ontology idea of gene, not all instances of experimentspecific gene identifier have corresponding situations of KEGG identifier. The second equivalence relation was developed to associate the situations on the ideas of experimental situation, ratio intensitybased value and gene expression threshold with an instance with the concept of ratio intensitybased value. While fairly basic in principle, the definition of this equivalence relation was rather elaborated. It involved the definition of a mappingover instances of ratio intensitybased worth from the actual numbers domain towards the up, down and undefined regulation range according to a (userprovided) instance of gene expression threshold. Connector C was also implemented as a separate Java application. This connector offered only manual transfer of control to KEGG Mapper Search Color Pathway. As soon as the equivalence relations were defined, the specification and implementation with the grounding operations was simple. Additiolly, the transformation of situations of your concept experimentspecific gene identifier to instances on the notion KEGG identifier was carried out making use of a platform mapping file (SOFT format), also supplied as input to connector C. This mapping is generally carried out in two methods: ) from experimentspecific gene identifier to official gene identifier; and ) from official gene identifier to KEGG identifier. Having said that, in the precise case of Plasmodium vivax, every KEGG identifier corresponds straight to its official gene identifier. Within the implementation from the Lowering functiol block situations of your concept ratio intensitybased worth, viz upregulated, downregulated and undefined, have been mapped respectively to the red, green and yellow KEGG Mapper Search Color Pathway colour schema. Detailed information relating to connector C implementation may also be PubMed ID:http://jpet.aspetjournals.org/content/117/4/451 obtained in a supplementary material (see Additiol File : Connectors C and C Implementation). The second scerio consisted from the integration of tools DMV and TMev as a way to clusterize Sulfolobus solfataricus RSeq information. This scerio was inspired by the growing reputation of nextgeneration sequencing platforms for gene expression. Regardless of the positive aspects of storing the actual reads in RSeq databases, these raw data files present little help for highlevel gene expression alysis. So, they were transformed into a numeric representation to become filtered making use of DMV according to some user defined criteria. Next, DMV output was employed as input data for clustering employing TMev. Having said that, DMV output data should be normalized to account for various library sizes (total of sequenced reads) prior to clusterization by TMev. Figure illustrates the architecture of our second integration scerio with concentrate around the flow of data. Two connectors had been developed to integrate RSeq data to DMV and TMev. Connector C transforms R.