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Documentation section

Datasets

• IDP4 (so far using alex's annotations; ideallz combining)
• tmVar
• TODO remember, 10 full text

Goals:

1. Study significance of NL mentions in mutation mention recognition

• ratio of standard vs NL in abstracts & full text
• % of novel mutations not present in SwissProt (would require manual annotation of protein relations)
• dataset of NLs (size depends on significance of NLs)

2. Method for mutation mention extraction grounded to their genes/proteins

• Mutation mention recognizer better than tmVar for standard mentions
• If NLs are relevant, prove good F1 performance (> 70-80)
• Simple or optionally advanced normalization method
• Easy to use program:
  • Good documentation:
    • code
    • end-user (biology researcher level, how to call from the command line, ...)
  • Accept inputs: programmatical call (string), text file, corpora' formats**
  • Accept outputs: ann.json (tagtog suitable)

3. Paper

• Full draft (1 or 2 papers?) by end of August submittable to Burkhard Rost
• Submit by September-October