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Table 2 Examples of how performance evaluation metrics were calculated

From: Microbial phenomics information extractor (MicroPIE): a natural language processing tool for the automated acquisition of prokaryotic phenotypic characters from text sources

Example # Character GSM value # GSM values Extracted value # extracted values Rigid hit score Relaxed hit score
1 %G + C 55.2 │ mol% 1 55.2 │ mol% 1 1 1
2 Organic Compounds NOT Used or NOT Hydrolyzed esculin 1 Neither lactate nor pyruvate 1 0 0
3 Cell Shape short plump │ rods 1 plump │ rods # short 2 0.5 1
4 Motility not │ motile by gliding 1 not │ motile 1 0.5 0.5
5 Fermentation Substrates Used arbutin # salicin # D-raffinose # D-mannose # sucrose # melibiose 6 melibiose # sucrose # D-mannose # D-raffinose # salicin # Most strains ferment arbutin 6 5.5 6
Total    10   11 7.5 8.5
  1. Rigid and relaxed hit scores measuring the match between extracted values and gold standard matrix (GSM) values, illustrated with examples