BioCreative II - Gene Mention Tagging Task

The BioCreative II - Gene Mention Tagging Task is a BioCreative Benchmark Task to evaluate Entity Mention Recognition Systems on their ability to Tag Human Protein Mentions in a MEDLINE Abstract.

• Context:
  • Is a BioCreAtIvE Benchmark Task.
• See: BioCreAtIvE I Evaluation Series, BioCreAtIvE II - Gene Normalization Task, BioCreAtIvE II - Protein-Protein Interaction Task.

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References

• http://biocreative.sourceforge.net/biocreative_2_gn.html
  • Gene Mention Tagging task is concerned with the named entity extraction of gene and gene product mentions in text.
  • Premise: Systems will be required to return the start and end indices corresponding to all the genes and gene products mentioned in a given MEDLINE sentence. This named entity task is a crucial first step for information extraction of relationships between genes and gene products.
  • System Input: The input file will consist of ascii sentences, one per line. Each sentence will be preceded on the same line by a sentence identifier.
  • System Output: Each system must output an ascii list of reported gene name mentions, one per line, and formatted as:

sentence-identifier-1|start-offset-1 end-offset-1|optional text... sentence-identifier-1|start-offset-2 end-offset-2|optional text... sentence-identifier-1|start-offset-3 end-offset-3|optional text... sentence-identifier-2|start-offset-1 end-offset-1|optional text... sentence-identifier-3|start-offset-1 end-offset-1|optional text... . . .

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