ProMiner System

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

• Context:
  • It was ranked first on two of three BioCreAtIvE Tasks.
• See: PPLRE Project, LingPipe NER System.

---

---

References

2009

• http://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/products/prominer.html?L=1
  • 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

2007

• (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.

2006

• (Fundel & Zimmer, 2006) ⇒ Katrin Fundel, and Ralf Zimmer. (2006). “Gene and Protein Nomenclature in Public Databases.” BMC Bioinformatics, 7(372). doi:10.1186/1471-2105-7-372.

2005

• (Hanisch et al., 2005) ⇒ Daniel Hanisch, Katrin Fundel, Heinz-Theodor Mevissen, Ralf Zimmer, and Juliane Fluck. (2005). “Prominer: Rule-based protein and gene entity recognition." BMC Bioinformatics, 6 (Suppl 1), S14.
  • NOTES: higher cited.
• (Funder et al., 2005) ⇒ Katrin Fundel, Daniel Güttler, Ralf Zimmer, and Joannis Apostolakis. (2005). “A Simple Approach for Protein Name Identification: prospects and limits.” In: BMC Bioinformatics, 6(Suppl 1): 15.

2004

• (Fundel et al., 2004) ⇒ Katrin Fundel, Daniel Guttler, Ralf Zimmer, and Joannis Apostolakis. (2004). “Exact versus approximate string matching for protein name identification.” In: Proceedings of BioCreative 2004 Workshop.

2004

• 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.

2003

• 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.

---