Table 1 Summary of 14 semantic similarity scores for protein pairs.
From: Revealing and avoiding bias in semantic similarity scores for protein pairs
Measure | Description | Range |
|---|---|---|
Similarity scores for term pairs | ||
Resnik [6] | Information content of the most informative common ancestor of two terms | ≥ 0 |
Lin [5] | Normalized Resnik similarity score by assessing how close two terms are to their most informative common ancestor | [0, 1) |
RS [4] | Weighted Lin similarity score by using the probability of annotations of the most informative common ancestor | [0,1) |
Jiang [7] | Based on the difference between two terms and their most informative common ancestor in information content | (0,1] |
Similarity scores for protein pairs based on pairwise similarity scores between term groups | ||
AVG [2] | The average of the similarity scores for all pairs of terms between two groups of protein annotations | Same with those for the corresponding similarity scores for term pairs |
BMA [3] | The score of the best-matching pairs between two groups of protein annotations | Â |
Similarity scores for protein pairs based on groupwise similarity scores between term groups | ||
TO [9] | The number of terms shared by the annotations for two proteins | ≥ 1 |
NTO [9] | Dividing TO by the minimum of the annotation lengths of two proteins | (0,1] |
Dice [12] | Dividing TO by the average of annotation lengths of two proteins | (0,1] |
Kappa [11] | A chance-corrected measure of co-occurrence between two groups of protein annotations | [0, 1] |
GIC [8] | Jaccard index weighted by the information content of each GO term | [0, 1] |
VSM [10] | Cosine similarity weighted by the information content of each GO term | [0, 1] |