2004 ReportOnBioCreative2004Workshop

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Subject Headings: BioCreAtIvE Benchmark Task


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  • 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



 AuthorvolumeDate ValuetitletypejournaltitleUrldoinoteyear
2004 ReportOnBioCreative2004WorkshopLynette Hirschman
Marc E. Colosimo
Alexander Yeh
Alexander Morgan
Christian Blaschke
Alfonso Valencia
Report on the 2004 BioCreAtIvE Workshophttp://biocurator.org/meetings/eugene/15 BioCreative Colosimo.ppt2004