2005 WhatMakesAGeneName

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Subject Headings: Protein NER Task, Protein NER System.

Notes

  • Contains a nice list of publicly available NER - Protein Taggers.
  • Suggest that performance has plateaued, and the future progress may require specialization into subDomains.

Cited By

Quotes

Abstract

The recognition of biomedical concepts in natural text (named entity recognition, NER) is a key technology for automatic or semi-automatic analysis of textual resources. Precise NER tools are a prerequisite for many applications working on text, such as information retrieval, information extraction or document classification. Over the past years, the problem has achieved considerable attention in the bioinformatics community and experience has shown that NER in the life sciences is a rather difficult problem. Several systems and algorithms have been devised and implemented. In this paper, the problems and resources in NER research are described, the principal algorithms underlying most systems sketched, and the current state-of-the-art in the field surveyed.

| Tool | Recognised entities | Available as | Web page || GAPSCORE | Genes and proteins | Online form and web service | http://bionlp.stanford.edu/gapscore || ABNER | Protein, DNA, RNA, cell line, cell type | Java application and API |ttp://www.cs.wisc.edu/~bsettles/abner/ || KeX | Proteins | Shell and Perl scripts | ttp://www.hgc.jp/service/tooldoc/KeX/intro.html || AbGene | Genes | Binaries | ftp://ftp.ncbi.nlm.nih.gov/pub/tanabe/AbGene || LingPipe | Genes | Online form and Java API | http://www.alias-i.com/lingpipe/ |

...

Conclusion

As discussed in the section ‘Evaluation of NER systems’, it is unlikely that much further improvement is possible on the NER problem on general classes, but progress is likely in specialised areas. In particular, species-specific NER is a promising direction, but currently still hindered by the lack of sufficiently large, species-specific corpora.

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 AuthorvolumeDate ValuetitletypejournaltitleUrldoinoteyear
2005 WhatMakesAGeneNameUlf Leser
Jörg Hakenberg
What Makes a Gene Name? Named entity recognition in the biomedical literatureBriefings in Bioinformaticshttp://bib.oxfordjournals.org/cgi/reprint/6/4/357.pdf2005