With the increasing number of publications about COVID-19, it is a challenge to extract personalized knowledge suitable for each researcher. This work aims to build a new semantic-based pipeline for recommending biomedical entities to scientific researchers. To this end, we developed a pipeline that creates an implicit feedback matrix based on Named Entity Recognition (NER) on a corpus of documents, using multidisciplinary ontologies for recognizing and linking the entities. Our hypothesis is that by using ontologies from different fields in the NER phase, we can improve the results for state-of-the-art collaborative-filtering recommender systems applied to the dataset created. The tests performed using the COVID-19 Open Research Dataset (CORD-19) dataset show that when using four ontologies, the results for precision@k, for example, reach the 80%, whereas when using only one ontology, the results for precision@k drops to 20%, for the same users. Furthermore, the use of multi-fields entities may help in the discovery of new items, even if the researchers do not have items from that field in their set of preferences.