Protein NER System

A Protein NER System is an NER system that can solve a protein NER task.

• Context:
  • It can implement a Protein NER Algorithm.
• Example(s):
  • an UIUC NER System http://cogcomp.cs.illinois.edu/page/demo_view/8
  • an AbGene System (Tanabe & Wilbur, 2002)
  • an Abner System http://pages.cs.wisc.edu/~bsettles/abner/
  • a ProMiner System (Fundel, 2006).
  • a Reflect System.
  • a GAPSCORE System (Chang et al., 2004).
  • a KeX System (Fukuda et al., 1998). http://www.hgc.jp/service/tooldoc/KeX/intro.html
  • an AIIAGMT.
  • a Lingpipe System, trained on a Protein NER Corpus.

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References

• http://alias-i.com/lingpipe/web/competition.html

2006

• (Fundel, 2006) ⇒ Katrin Fundel, and Ralf Zimmer. (2006) Gene and Protein Nomenclature in Public Databases. BMC Bioinformatics, 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.
• (Leser & Hakenberg, 2005) ⇒ Ulf Leser, and Jörg Hakenberg. (2005). “What Makes a Gene Name? Named entity recognition in the biomedical literature." Briefings in Bioinformatics, 6(4).

2004

• (Chang et al., 2004) ⇒ Chang JT, Schütze H, Altman RB. (2004). “GAPSCORE: finding gene and protein names one word at a time.” In: Bioinformatics, 20(2).

2002

• (Tanabe & Wilbur) ⇒ Lorraine Tanabe, and W. John Wilbur. (2002). “Tagging Gene and Protein Names in Biomedical Text.” In: Bioinformatics, 18.

1998

• (Fukuda et al., 1998) ⇒ K Fukuda, T Tsunoda, A Tamura, and T Takagi. (1998). “Toward Information Extraction: identifying protein names from biological papers.” In: Proceedings of Pacific Symposium on Biocomputing 1998.

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