Assessing students has sometimes been problematic for teachers and researchers [1]. The instrument of assessment should be reliable and valid for the exercise and easily used for students, teachers and researchers. Nowadays more attention is paid for students' cognitive development and meaningful learning, but we need researching instruments for examining these parameters. Concept mapping is one of the methods, which is developed, for practise and examining students' meaningful learning and cognitive development; it is based on Ausubel assimilation theory [2]. A concept map links learned concepts, with prior knowledge concepts, forming the base and the new conceptual acquisition building on this. It is easy to make concept maps with computer programs. But there are some questions about the validity of using computer based concept maps as researching and assessing instruments [3]. How much does the concept mapping creating frequency influence the level of concept maps? Does the computer using frequency influence the level of students' made concept maps? The aim of this article is to examine concept map using opportunities as a researching instrument. We observed: a) the validity of using concept mapping method as a research and assessment instrument b) whether concept mapping is adequate method for assessing scientific literacy. Concept mapping method was used as an assessing instrument in Estonian large scale longitudinal study Lotegumn in 2011. 1614 students, aged sixteen to seventeen, from different Estonian high schools were examined with focus question biased and given concept mapping and PISA like three dimensional scenario-based exercises. Students solve four different science exercises. In this study we focus on 343 students, who solved exercise about instant cold pack. Based on our recent researches [4] 30 concepts about the theme were given to students and they had to construct a concept map in allotted time. This study is unique, because it is large scale and carried out with computers- used programme is CmapTools. Before there has not been large scale research, where results of scientific literacy have been compared between concept maps and PISA like test. We have first results of students' concept maps general data, which are also analysed by computer, and answers to question list (we wanted to know concept maps creating frequency and problems, which occurred while the study). These pointed out, that the results of the concept maps (taxonomy score and proposition count) do not depend deeply on concept maps creating frequency nor computer handling skills [5]. For comparing results of ordinary PISA like test Lotegumn and concept maps we marked the answers to the scenario based exercise and propositions (sentences) of the concept maps. Some of the results point out, that students answers to multiple choice exercise and same concept based marked propositions of concept maps are in correlation. We could establish, that computer based concept maps should be used more at schools and in researches, but before using the method, instructors should compose relevant and valid instruction, where the purpose of the work is considered.