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Table 2 Topological parameters for HCM models obtained with Network Analyzer

From: Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation

 

Manual HCM model

Tabular manual HCM model

INDRA-assembled PubMed HCM model

INDRA-assembled PubMed+PathwayCommons HCM model

Truncated INDRA DB HCM model

INDRA DB HCM model

Average number of neighbors

2.309a

2.789

1.917

3.582

1.455

2.059

Network diameter

1a

12

6

8

3

9

Network radius

1a

1

1

1

1

1

Characteristic path length

1.000a

4.334

2.541

2.395

1.299

3.900

Clustering coefficient

0.000a

0.054

0.007

0.006

0.014

0.028

Network density

0.003a

0.009

0.002

0.001

0.010

0.002

Connected components

26a

11

58

51

23

101

Multi-edge node pairs

1a

24

21

213

3

48

Number of self-loops

0a

4

7

14

0

6

  1. a Due to the CellDesigner XML file incompatibility, we suggest that some or all topological measures for the Manual HCM model are calculated falsely by Cytoscape