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Table 2 Pairwise ontology-based semantic similarity measures implemented by the three main publicly available software libraries for the biomedical domain

From: HESML: a real-time semantic measures library for the biomedical domain with a reproducible survey

 

UMLS::

Similarity

SML

HESML

Gloss-based measures

Banerjee and Pedersen [69]

x

  

Patwardhan and Pedersen [70],

context vector

x

  

Path-based and taxonomy-based measures

Rada et al. [71]

x

x

x*

Wu and Palmer [72]

 

x

x

Wu and Palmer [72] fast

(depth-based approximation)

x

 

x

Leacock and Chodorow [73]

x

x

x*

Stojanovic et al. [74]

 

x

x*

Maedche and Staab [75]

x

  

Zhong et al. [76]

x

  

Pekar and Staab [77]

x

x

x*

Li et al. [78], strategy 3

  

x*

Li et al. [78], strategy 4

  

x*

Liu et al. [79], strategy 1

  

x*

Liu et al. [79], strategy 2

  

x*

Pedersen et al. [44],

reciprocal Rada

x

 

x*

Al-Mubaid and Nguyen [80]

x

 

x*

Kyogoku et al. [81]

 

x

 

Batet et al. [45]

x

  

Hao et al. [82]

  

x*

Hadj Taieb et al. [83], sim1

 

x

Hadj Taieb et al. [83], sim2

 

x

McInnes et al. [84], U-path

x

  

IC-based measures

Resnik [85]

x

x

x

Jiang and Conrath [86]

x

x

x

Lin [87]

x

x

x

Schlicker et al. [88]

 

x

x

Pirró and Seco [89]

  

x

FaITH [90]

x

 

x

Garla and Brandt [91]

  

x

Meng and Gu [92]

  

x

Gao et al. [93], strategy 3

  

x

Lastra&García [35], cosJ&C

 

x

Cai et al. [94], strategy 2

  

x

Hybrid IC-based measures

Li et al. [ [78] strategy 9

  

x*

Zhou et al. [95]

  

x*

Meng et al. [96]

  

x*

Gao et al. [93], strategy 3

  

x*

Lastra and García [35], coswJ&C

 

x*

Lastra and García [35], weigthedJ&C

 

x*

Cai et al. [94], strategy 1

  

x*

Feature-based measures

Sánchez et al. [97]

x

 

x

  1. (*) Real-time reformulation of all path-based measures based on the AncSPL algorithm