The characterisation of biomedical knowledge taking into account the degree of confidence expressed in texts, is an important issue in the biomedical domain. The authors of scientific texts use grammatical and lexical devices to qualify their assertions. We named these markers of qualification "confidence markers". We present here the results of our efforts to collect confidence markers from full texts and abstracts, to classify them on the basis of semantics, and their use within our knowledge extraction system. We propose in this study, an implementation of these confidence markers for functional annotation of the human gene Apolipoprotein (APOE) thought to be involved in Alzheimer's disease. As a result, we obtain, through the extraction system, triplets: (G, F, PMID), in which G is the gene APOE, F is its function found in texts and the PMID of the article from which this knowledge was extracted. Moreover, a spatial 3D of the triplets, relative to each other, is proposed depending on their respective confidence degree.