2004 ReportOnBioCreative2004Workshop

• (Hirschman et al., 2004) ⇒ Lynette Hirschman, Marc E. Colosimo, Alexander Yeh, Alexander Morgan, Christian Blaschke, Alfonso Valencia. (2004). “Report on the 2004 BioCreAtIvE Workshop.” Presentation.

Subject Headings: BioCreAtIvE Benchmark Task

Quotes

Abstract

• Focus on tasks relevant to biologists:
• Task 1: Gene name extraction and normalization
  • Identification of gene names in PubMed abstracts & normalization to unique gene IDs
  • 1A
    • Identify all mentions of genes, proteins, etc in sentences from PubMed abstracts
  • 1B
    • For yeast, fly, and mouse.
    • For each abstract, return unique gene IDs mentioned in the abstract
• Task 2: Functional annotation
  • Identification of textual evidence and GO codes, for a given protein, in full text articles
  • Return a supporting passage for Protein/GO codes
  • Task 2.1: Given protein, GO code and paper
    • 1076 Protein/GO code combinations in test set
  • Task 2.2: Similar but had to generate GO code as well
  • 145 Protein/Paper pairs with 1211 GO terms

References

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	Author	volume	Date Value	title	type	journal	titleUrl	doi	note	year
2004 ReportOnBioCreative2004Workshop	Alfonso Valencia Lynette Hirschman Marc E. Colosimo Alexander Yeh Alexander Morgan Christian Blaschke			Report on the 2004 BioCreAtIvE Workshop			http://biocurator.org/meetings/eugene/15 BioCreative Colosimo.ppt			2004