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Table 2 Mapping between the leaves of the hierarchical task tree and the analyzed papers

From: Modelling the bioinformatics tertiary analysis research process

 

Tree Leaf

[59]

[60]

[61]

[62]

[63]

[64]

[65]

[37]

[66]

[67]

[68]

[69]

[38]

[70]

[71]

1

Reseach 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

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

 

10

Bad Data Discard

      

X

  

X

    

X

11

Missing Data Imputation

               

12

Trimming

   

X

     

X

X

   

X

13

Metrics and Normalization Methods Identification

X

      

X

  

X

 

X

X

X

14

Values Normalization

X

      

X

  

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

X

 

18

Integration Method Identification

X

    

X

   

X

  

X

X

 

19

Integration Method Application

X

    

X

   

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

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

 

26

Algorithm Parameters Check

 

X

     

X

     

X

 

27

Optimization

   

X

    

X

X

 

X

  

X

28

Visualization Method Identification

X

 

X

X

X

X

X

X

X

X

X

X

X

X

X

29

Visualization Creation

X

 

X

X

X

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

33

Testing

               

34

Enrichment Analysis

X

      

X

    

X

 

X

35

Literature Research on Biological Domain

X

      

X

X

X

  

X

  

36

Relevant Feature Extraction

       

X

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