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Table 3 Biological event and its frequency used in macrophage models and the number of warnings.

From: Ontology-based instance data validation for high-quality curated biological pathways

 

Biological event

Freq.

Warnings

Reasons (freq.)

1

ME_Autocleavage

2

2

# of input (2)

 

ME Binding

1898

253

TYPE (169), # of inputprocess (4), no inputprocess (80)

 

ME_DNABinding

29

0

(0)

 

ME_DNAReplication

6

0

(0)

 

ME_Dissociation

37

3

TYPE (3)

 

ME_GDP-GTPExchange

4

0

(0)

 

ME_Isomerization

1

0

(0)

 

ME_MetabolicReaction

40

7

TYPE (7)

 

ME_ProteasomeDegradation

34

0

(0)

 

ME_ProteinCleavage

5

0

(0)

 

ME_UnknownDegradation

45

1

TYPE (1)

2

ME_Acetylation

3

7

(0)

 

ME ADPRibosylation

2

7

# of input (1)

 

ME_Amidation

1

1

no output (1)

 

ME_Glycosylation

1

3

(0)

 

ME_Nitrosylation

2

6

# of inputprocess (1)

 

ME Oxidation

12

28

(0)

 

ME Phosphorylation

448

967

no inputprocess(1), no output (1)

 

ME_Reduction

1

3

(0)

 

ME_Sumoylation

2

4

(0)

 

ME_Ubiquitination

67

166

(0)

 

ME UnknownActivation

793

1415

# of inputprocess (11), no inputprocess (3)

 

ME_UnknownInactivation

6

16

(0)

 

ME_Autophosphorylation

12

36

# of input (2)

 

ME_Dephosphorylation

9

19

(0)

 

ME_Deubiquitination

4

11

(0)

3

ME_Dimerization

49

50

STOICHIOMETRY (49),

    

# of inputprocess (1)

 

ME_Oligomerization

7

7

STOICHIOMETRY (7)

 

ME Polymerization

5

5

STOICHIOMETRY (5)

4

ME Internalization

9

22

CELLCOMPONENT (10)

 

ME_NuclearExport

4

3

CELLCOMPONENT (3)

 

ME Translocation

136

275

# of output (6), no inputprocess (2)

    

CELLCOMPONENT (87)

5

ME_GeneExpression

721

262

CELLCOMPONENT (259), TYPE (3)

 

ME_IonTransportThroughIonChannel

2

4

TYPE (2)

 

ME Transcription

13

7

CELLCOMPONENT (4), TYPE (3)

 

ME Translation

364

393

# of input (1), TYPE (7),CELLCOMPONENT(385)

n/a

no rules for 8 biological events

136

-

-

 

Total

4910

3983

1121

  1. The biological events are grouped together along with the rules for criteria 2 in Methods. The biological events in the last group have no rules and are notified with n/a in the first column.