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Table 1 Mapping between the leaves of the hierarchical task tree and the analyzed papers

From: Modelling the bioinformatics tertiary analysis research process

 

Tree Leaf

[46]

[47]

[48]

[49]

[50]

[40]

[39]

[51]

[52]

[53]

[54]

[55]

[56]

[57]

[58]

1

Research Question Definition

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

2

State of the Art Analysis

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

3

Deliverable Definition

               

4

Public Available Data Research

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

5

Dataset Selection

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

6

Literature Research on the Data

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

7

Data Assessment

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

8

Data Format Check

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

9

Quality Assessment

X

 

X

X

  

X

       

X

10

Bad Data Discard

X

 

X

X

X

 

X

X

 

X

  

X

  

11

Missing Data Imputation

  

X

   

X

        

12

Trimming

X

 

X

X

X

  

X

   

X

X

  

13

Metrics and Normalization Methods Identification

X

  

X

   

X

 

X

     

14

Values Normalization

X

  

X

   

X

 

X

     

15

Visualization Method Identification

X

  

X

 

X

 

X

  

X

X

   

16

Visualization Creation

X

  

X

 

X

 

X

  

X

X

   

17

Literature Research on Integration Methods

 

X

     

X

X

      

18

Integration Method Identification

 

X

     

X

X

      

19

Integration Method Application

 

X

     

X

X

      

20

Literature Research on the Algorithms

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

21

Preliminary Analysis on Data and Algorithms

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

22

Algorithm Implementation

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

23

Data Adaptation to the Algorithm

X

X

X

X

X

X

X

X

   

X

X

X

X

24

Data Split in Training and Testing Set

X

 

X

  

X

    

X

X

X

X

X

25

Hyperparameter and Parameter Tuning

X

 

X

  

X

X

  

X

X

 

X

X

 

26

Algorithm Parameters Check

X

 

X

 

X

X

X

  

X

X

 

X

X

 

27

Optimization

 

X

X

 

X

          

28

Visualization Method Identification

X

  

X

X

 

X

X

 

X

 

X

X

X

X

29

Visualization Creation

X

  

X

X

 

X

X

 

X

 

X

X

X

X

30

Performance Evaluation

X

X

X

X

X

X

  

X

X

X

X

X

X

X

31

Robustness Evaluation

   

X

  

X

        

32

Comparative Analysis

 

X

X

  

X

X

X

X

X

     

33

Testing

     

X

    

X

X

   

34

Enrichment Analysis

  

X

X

X

  

X

       

35

Literature Research on Biological Domain

X

X

X

X

  

X

X

       

36

Relevant Feature Extraction

X

       

X

X

     
  1. Crossed boxes indicate the tasks described explicitly in the paper