The concepts based on the equivalence relations specified within the Grounding and semantic transformation definition activity. The Information Output Processing functiol block can also be responsible for accessing the target tool or data supply becoming integrated and realizing the transfer of data andor manage as specified within the Access policy identification activity. The requirements for the implementation of each functiol block may be identified based on the info made by the Interest information detailed description, Grounding and semantic transformation definition and Access policy identification activities. The execution of the functiol blocks must be carried out serially as outlined by the order in which they’ve been defined. Figure illustrates the timeline execution of a connector’s implementation functiol blocks. The connector can be implemented totally independent from tool TA or as an integral component of this tool. The 
independent connector implementation is simpler to become implemented considering the fact that no adjustments are necessary to tool TA. However, this implementation choice relies around the user to explicitly execute the connector. The integral part connector implementation ebles the connector to be automatically executed from tool TA integrated interface. Nonetheless, this implementation option relies on the availability from the supply code of this tool.Methodology applicationWe applied the proposed methodology inside the development of three integration scerios for the alysis of unique kinds of gene expression information. In the 1st scerio, twocolor Plasmodium vivax microarray data had been normalized using RGUI. To be able to facilitate multiple condition normalization by RGUI, different twocolor microarray information ought to be combined into a single multicolumn dataset. Normalized microarray data was then utilised by RGUI PSI-697 itself for the identification of differentially expressed genes. Within the sequel, KEGG Plasmodium vivax pathways have been alysed using KEGG Mapper Search Color Pathway. This tool was utilised to determine which components of pathways were associatedMiyazaki et al. BMC Genomics, (Suppl ):S biomedcentral.comSSPage ofFigure Connector implementation functiol blocks. An arrow represents an implementation functiol block. The left to right serial disposition on the arrows indicates the order in which each and every functiol block ought to be executed, starting in the Information Input Processing block.with all the differential gene expression alysis supplied by RGUI, highlighting up and down regulation based on a color scheme. Figure illustrates the architecture of our initial integration scerio with focus on the flow of data. Two connectors were created to integrate twocolor microarray data to RGUI and KEGG Mapper. Connector C groups MedChemExpress DFMTI separate twocolor microarray data into a single twocolor microarray dataset to facilitate normalization by RGUI, although connector C processes RGUI output data, so they are able to be used by KEGG Mapper. Diverse files were applied to retailer PubMed ID:http://jpet.aspetjournals.org/content/117/4/488 twocolor microarray data (SOFT format), each representing a separate experimental situation. So essentially, connector C was responsible for reading these files and for creating a single (multicolumn) file containing all information to facilitate further alysis activities. From a semantic point of view, the construction of the equivalence table was straightforward because the very same set of concepts was utilised to represent information products each consumed and created by the 
connector. These ideas had been also directly mapped to the ideas in the reference o.The concepts as outlined by the equivalence relations specified within the Grounding and semantic transformation definition activity. The Data Output Processing functiol block can also be accountable for accessing the target tool or data supply getting integrated and realizing the transfer of information andor handle as specified inside the Access policy identification activity. The specifications for the implementation of each and every functiol block could be identified based on the data produced by the Interest data detailed description, Grounding and semantic transformation definition and Access policy identification activities. The execution on the functiol blocks ought to be carried out serially in accordance with the order in which they have been defined. Figure illustrates the timeline execution of a connector’s implementation functiol blocks. The connector could be implemented absolutely independent from tool TA or as an integral portion of this tool. The independent connector implementation is easier to be implemented considering the fact that no alterations are needed to tool TA. Even so, this implementation choice relies on the user to explicitly execute the connector. The integral part connector implementation ebles the connector to be automatically executed from tool TA integrated interface. Nonetheless, this implementation selection relies on the availability from the source code of this tool.Methodology applicationWe applied the proposed methodology within the development of three integration scerios for the alysis of various forms of gene expression data. Within the initial scerio, twocolor Plasmodium vivax microarray data have been normalized applying RGUI. So that you can facilitate various situation normalization by RGUI, unique twocolor microarray information really should be combined into a single multicolumn dataset. Normalized microarray data was then utilised by RGUI itself for the identification of differentially expressed genes. Within the sequel, KEGG Plasmodium vivax pathways have been alysed applying KEGG Mapper Search Colour Pathway. This tool was applied to identify which components of pathways had been associatedMiyazaki et al. BMC Genomics, (Suppl ):S biomedcentral.comSSPage ofFigure Connector implementation functiol blocks. An arrow represents an implementation functiol block. The left to right serial disposition with the arrows indicates the order in which every single functiol block ought to be executed, beginning in the Data Input Processing block.using the differential gene expression alysis offered by RGUI, highlighting up and down regulation as outlined by a colour scheme. Figure illustrates the architecture of our very first integration scerio with concentrate on the flow of data. Two connectors have been created to integrate twocolor microarray information to RGUI and KEGG Mapper. Connector C groups separate twocolor microarray information into a single twocolor microarray dataset to facilitate normalization by RGUI, when connector C processes RGUI output data, so they could be made use of by KEGG Mapper. Unique files were used to shop PubMed ID:http://jpet.aspetjournals.org/content/117/4/488 twocolor microarray information (SOFT format), every representing a separate experimental condition. So basically, connector C was responsible for reading these files and for making a single (multicolumn) file containing all data to facilitate further alysis activities. From a semantic point of view, the construction in the equivalence table was simple because the exact same set of concepts was made use of to represent data products each consumed and created by the connector. These concepts were also directly mapped to the concepts with the reference o.