Pathogens and Genome Normalization for Literature-based Knowledge Discovery

TitlePathogens and Genome Normalization for Literature-based Knowledge Discovery
Publication TypeConference Proceedings
Year of Publication2011
AuthorsVishnyakova, D, Pasche, E, Teodoro, D, Ruch, P, Lovis, C
Conference Name23 rd International Conference of the European Federation for Medical Informatics
PublisherMIE 2011 / CD / Posters
Conference LocationOslo, Norway
Keywordsgene normalization, Pathogen normalization

We present a new approach of pathogens and genome normalization in the biomedical literature. It was motivated by needs such as literature curation, in particular applied to infectious diseases. Our approach is based on use of an
Ontology Look-up Service, a Gene Ontology Categorizer and Gene Normalization methods. Gene normalization precision is – 0.43%. Pathogen normalization results showed 95% of precision and 93% of recall. The results showed that a correct identification of the species can improve significantly normalization effectiveness
of gene products.