Table 4

Performance of PPI extraction on the Spies corpus

Corpus

Short description of the submitted run

Precision

Recall

F measure


Spies

Initial pattern set

85.8

15.2

25.8

Spies

CP, single layer (POS tag including entity)

76.6

47.1

58.3

Spies

CP, multilayer (token, POS tag, stem, entity)

78.7

51.9

62.6

Spies

CP, optimized for precision

+1

-4

60.1

Spies

CP, optimized for recall

-5

+5

63.9


Performance of our approach to protein-protein interaction (PPI) extraction on other external corpora. We also show the influence of using part-of-speech (POS) tags only compared with multilayer alignments, and results for optimization towards a single metric (precision or recall). Note that these evaluations do not require the identification of proteins, as in BioCreative II, so figures are higher in general. CP, consensus patterns resulting from clustering and multiple sentence alignment.

Hakenberg et al. Genome Biology 2008 9(Suppl 2):S14   doi:10.1186/gb-2008-9-s2-s14

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