ProMiner System

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A ProMiner System is a dictionary-based protein NER system.



    • ProMiner can handle voluminous dictionaries, complex thesauri and large controlled vocabularies derived from ontologies
    • Regularly updated dictionaries through automatic curation followed by a manualevaluation process
    • Mapping of synonyms to reference names and data sources
    • Context dependent disambiguation of biomedical termini and resolution of acronyms
    • Specific handling of common English word synonyms
    • Spelling variants of expressions in the source dictionary can be recognized
    • High speed tagging and parallel workflow for multiple dictionaries
    • Incorporation of regular expressions (e.g. for the recognition of SNP rs numbers)
    • Full text annotation in XML, HTML or PDF format
    • Patent annotation


  • (Fluck et al., 2007) ⇒ Juliane Fluck, and H. T. Mevissen, H. Dach, M. Oster. and M. Hoffmann-Apitius. (2007). “ProMiner: recognition of human gene and protein names using regularly updated dictionaries.” In: Second BioCreAtIvE Challenge Workshop: Critical Assessment of Information Extraction in Molecular Biology.





  • Daniel Hanisch, Katrin Fundel, H. T. Mevissen, Ralf Zimmer, and Juliane Fluck. (2004). “Prominer: Organism-specific protein name detection using approximate string matching.” In: Proceedings of the BioCreative Challenge Evaluation Workshop 2004.


  • Daniel Hanisch, Juliane Fluck, H. T. Mevissen, and Ralf Zimmer. (2003). “Playing Biology's Name Game: Identifying protein names in scientific text.” In: Pacific Symposium on Biocomputing, 8.