LLL'05 Challenge: Genic Interaction Extraction with Alignments and Finite State Automata

Supplementary information

Data sources

• Learning Logic in Language 2005 - workshop website
• Challenge task website, with training and evaluation data
  
  
• List of nouns indicating interactions (INouns)
• List of verbs indicating interactions (IVerbs)
• final dictionary with modifications
• Evaluation corpus from BioCreAtIvE, 1000 sentences (available on request)
  Mapping from corpus sentences to PubMeds-IDs
  
  
• Part-of-speech tags: Penn Tree Bank tag set,
  for a list see e.g. http://www.comp.leeds.ac.uk/amalgam/tagsets/upenn.html
• Substitution matrix for the PTB (full tag set, we used 19 tags in the challenge)

Software

• POS-Tagging: TnT, Thorsten Brandts, see http://www.coli.uni-sb.de/~thorsten/tnt/
• Stemming: Porter-Stemmer, Martin F. Porter, see http://www.tartarus.org/~martin/PorterStemmer/