All research papers produced by researchers worldwide now are based on previous academic publication written by other researchers. There are currently exist many research papers published in electronic media and new media. Recently, the improved technology makes Internet becomes the most widely used media. The research papers are published in many forms, such as in the for of a journal. Relation among journals can be traced though their citations. The number of citation to a journal paper can also be calculated to show the contribution of that particular paper. In order to know the relation among journals published on the Internet, we need a system which can automatically produce a relationship betwen articles from different journal, located in different websites. Therefore, in this work we created a mashup in order to extract website pages and then pick required files automatically. This system produced a database to save the extracted files and then find the relations. The data which has already processed could be seen in user interfaces. The interface has search functionalities by using key words inputted by users. As a result, the whole system forms a Mashup. We created an automatic extraction for Indonesian electronic journal system, using data from four (4) universities e-journal's site. We built the system using PHP language and MySQL database, after carefully study the algorithm in Openkapow Robomaker. The system can successfully extract information from journal provider's web pages, which include special type of PDF pages, then save them in database. The system generated finally shows the connection and the relation among the journals. The test result shows the processing time and memory usage evaluation for a random number of files. The evaluation results show that the execution time is dependent on the number of journal series, volumes, and number of articles on related e-journal sites.