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Table 1 Evaluation results in the CRAFT-ChEBI dataset (top), BC5CDR-Diseases (middle) and BC5CDR-Chemicals (bottom)

From: Linking chemical and disease entities to ontologies by integrating PageRank with extracted relations from literature

Model

CRAFT-ChEBI

P

R

F1

         

String matching

77.8

78.0

77.9

         

PPR-IC

87.1

79.9

83.3

         

REEL(Corpus)

91.3

80.9

85.8

         

REEL(KB+Corpus)

91.3

80.9

85.8

         

BC5CDR-Diseases

Model

All

Train

Dev

Test

P

R

F1

P

R

F1

P

R

F1

P

R

F1

String matching

82.7

74.7

78.5

81.7

74.1

77.7

82.7

72.3

77.2

83.6

77.5

80.4

PPR-IC

83.4

74.9

78.9

84.1

74.6

79.1

86.2

73.0

79.1

87.2

78.2

82.5

REEL(Corpus)

86.9

75.6

80.9

87.8

75.4

81.1

87.9

73.5

80.1

89.0

78.6

83.5

REEL(KB+Corpus)

86.6

75.5

80.7

88.2

75.5

81.4

88.0

73.5

80.1

88.8

78.5

83.3

BC5CDR-Chemicals

Model

All

Train

Dev

Test

P

R

F1

P

R

F1

P

R

F1

P

R

F1

String matching

94.9

84.1

89.2

93.7

84.4

88.8

95.3

85.2

90.0

95.3

82.6

88.5

PPR-IC

96.7

84.4

90.1

97.6

84.9

90.8

97.6

85.5

91.2

98.0

83.0

89.9

REEL(Corpus)

97.0

84.4

90.3

98.0

85.0

91.0

98.3

85.6

91.5

98.4

83.0

90.0

REEL(KB+Corpus)

97.0

84.4

90.3

98.0

85.0

91.0

98.2

85.6

91.5

98.4

83.0

90.0

  1. For the datasets BC5CDR-Diseases and BC5CDR-Chemicals the results for each subset are shown. “All” refer to the entire corpus and “Train”, “Dev” and “Test” refer to the train, development and test sets, respectively