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Example 1: a(CHEBI:mifepristone) decreases tscript(p(MGI:Pgr))

Evidence SentenceTreatment with RU486, a progesterone receptor antagonist, blocked progesterone-induced galectin-1 mRNA level in uterine tissues of ovariectomized mouse.





 

Gold Standard
BEL Statement
a(CHEBI:mifepristone) decreases tscript(p(MGI:Pgr))

 

 
  

DETAILED EVALUATION:

---

T = Term-Level: Abundance and Process Functions and namespace + entity id arguments

Ts = Secondary Term-Level: Abundance and Process Functions only

 ---

F = Function-Level: Function and arguments

Fs = Secondary Function-Level: Function only

---

R = Relation-Level: Complete Relationship

Rs = Secondary Relation-Level: Partial Relationship

---

S = Full BEL Statement

-------


TP : True Positives

FP : False Positives

FN : False Negatives

 
 POSSIBLE SUBMISSIONSTTsFFsRRsSEVALUATION EXPLANATION
Correct Submission of Full Statement
a(CHEBI:mifepristone) decreases act(p(MGI:Pgr))

 

Comment: Please use the act() function instead of tscript() and other activity functions

2TP

0FP

0FN

2TP

0FP

0FN

1TP

0FP

0FN

1TP

0FP

0FN

1TP

0FP

0FN

1TP

0FP

0FN

1TP

0FP

0FN

Full score on all levels:

  • T (2 correct terms)

  • F (Function and arguments are correct)
    • Fs (the function is correct regardless of its arguments)
  • R (Relationship and both arguments are correct)
    • Rs (Relationship and at least one argument are correct)

  • S (Full statement is correct)

 

Submission with Placeholders for BEL Terms

 
p(PH:placeholder) decreases act(p(PH:placeholder))
 

Comment: Placeholders are not counted as FP (false positives) but only as FN (false negatives)

0TP

0FP

2FN

1TP

1FP

1FN

0TP

0FP

1FN

1TP

0FP

0FN

0TP

0FP

1FN

0TP

0FP

1FN

0TP

0FP

1FN

Full score on the following levels:

    • Fs (the function is correct regardless of its arguments)

Partial score on the following levels:

  • T (Two placeholders for BEL Terms)
    • Ts (One of two process/abundance functions is correct)

  • F (The argument of the function is a placeholder)

  • R (The relationship is correct and its arguments are placeholders = not counted as false positives)

  • S (Placeholders are used in whole statement)

Submission with Incorrect BEL Terms


 
a(CHEBI:cholesterol)decreases act(p(HGNC:CTNNB1))

0TP

2FP

2FN

2TP

1FP

1FN

0TP

1FP

1FN

1TP

0FP

0FN

0TP

1FP

1FN

0TP

1FP

1FN

0TP

1FP

1FN

 Full score on the following levels:
    • Fs (The function is correct but the argument is incorrect)
    • Ts (Two of two process/abundance functions are correct)

No score on the following levels:

  • T (Both terms are incorrect)
  • F (The argument of the function is incorrect)
  • R (The relationship is correct but both arguments are incorrect)
Submission without Functions
a(CHEBI:mifepristone) decreases p(MGI:Pgr)

2TP

0FP

0FN

2TP

0FP

0FN

0TP

0FP

1FN

0TP

0FP

1FN

1TP

0FP

0FN

1TP

0FP

0FN

0TP

1FP

1FN

Full score on the following levels:

  • T + Ts (All terms are correct)
  • R + Rs(The relationship and its term-arguments are correct)

No score on the following levels:

  • F + Fs  
  • S
Submission with wrong Functions
a(CHEBI:mifepristone) decreases deg(p(MGI:Pgr))

2TP

0FP

0FN

2TP

0FP

0FN

0TP

1FP

1FN

0TP

1FP

1FN

1TP

0FP

0FN

1TP

0FP

0FN

0TP

1FP

1FN

Full score on the following levels:

  • T + Ts (All terms are correct)
  • R + Rs (The relationship and its term-arguments are correct)

No score on the following levels:

  • F + Fs  (the function is incorrect)
  • S (the incorrect function makes the full statement incorrect)

Partially Correct Submission:

One BEL term placeholder

a(CHEBI:mifepristone) decreases act(a(PH:placeholder))

1TP

0FP

1FN

1TP

1FP

1FN

0TP

0FP

1FN

1TP

0FP

0FN

0TP

0FP

1FN

1TP

0FP

0FN

0TP

0FP

1FN

Full score on the following levels:

  • Fs (The function is correct but the argument is incorrect)
  • Rs (The relationship and one term-argument are correct)

Partial score on the following levels:

  • T (One term is correct, One term is a placeholder)
  • R (The relationship and one term-argument are correct, the other term-argument is a placeholder)
  • F (The argument of the function is a placeholder)
  • S (Apart from a correct term, a placeholder is used)

Partially Correct Submission:

One association placeholder

a(CHEBI:mifepristone) association act(p(MGI:Pgr))

 

Comment: Placeholders are not counted as FP (false positives) but only as FN (false negatives)

2TP

0FP

0FN

2TP

0FP

0FN

1TP

0FP

0FN

1TP

0FP

0FN

0TP

0FP

1FN

1TP

0FP

0FN

0TP

0FP

1FN

Full score on the following levels:

  • T+Ts(2 correct terms)
  • F+Fs (Function and arguments are correct)
  • Rs ('association' placeholder is used but both arguments are correct)


Partial score on the following levels:

  • R ('association' placeholder is used)
  • S (Full statement is correct apart from use of 'association' placeholder)

Partially Correct Submission:

Submission without Functions;

One incorrect BEL term

a(CHEBI:mifepristone) decreases p(HGNC:CTNNB1)

1TP

1FP

1FN

2TP

0FP

0FN

0TP

0FP

1FN

0TP

0FP

1FN

0TP

1FP

1FN

1TP

0FP

0FN

0TP

1FP

1FN

Full score on the following levels:

  • Rs (The relationship and one term-argument are correct)
  • Ts (Both process/abundance functions are correct)

Partial score on the following levels:

  • T (One term is correct)

No score on the following levels:

  • F + Fs (The function has not been found)
  • R (Only one term-argument is correct)
  • S

Partially Correct Submission:

Relationship incorrect

a(CHEBI:mifepristone) increases act(p(MGI:Pgr))

2TP

0FP

0FN

2TP

0FP

0FN

1TP

0FP

0FN

1TP

0FP

0FN

0TP

1FP

1FN

1TP

0FP

0FN

0TP

1FP

1FN

Full score on the following levels:

  • T + Ts (All terms are correct)
  • F + Fs
  • Rs (The relationship is incorrect but both term-arguments are correct)

No score on the following levels:

  • R (The relationship is incorrect)
  • S
Partial Submission with Placeholders
p(PH:placeholder) decreases p(PH:placeholder)

0TP

0FP

2FN

1TP

1FP

1FN

0TP

0FP

1FN

0TP

0FP

1FN

0TP

0FP

1FN

0TP

0FP

1FN

0TP

1FP

1FN

Partial score on the following levels:

  • T (both terms are placeholders)
    • Ts (One of two process/abundance functions is correct)

  • R + Rs (The relationship is correct but both term-arguments are placeholders)

No score on the following levels:

  • F + Fs (act() function has not been found)
  • S
Relationship incorrect with Placeholders
p(PH:placeholder) increases p(PH:placeholder)

0TP

0FP

2FN

1TP

1FP

1FN

0TP

0FP

1FN

0TP

0FP

1FN

0TP

1FP

1FN

0TP

0FP

1FN

0TP

1FP

1FN

Partial score on the following levels:

  • T (both terms are placeholders)
    • Ts (One of two process/abundance functions is correct)
  • Rs (Placeholders are used)

No score on the following levels:

  • F + Fs (act() function has not been found)
  • R  (The relationship is incorrect)
  • S


Example 2: a(CHEBI:galangin) decreases complex(a(CHEBI:"2,3,7,8-tetrachlorodibenzodioxine"),p(MGI:Ahr))

 

Evidence Sentence

The ability of galangin to inhibit binding of TCDD, a high-affinity AhR ligand, to the AhR demonstrates that galangin is able to bind to the AhR.







 

Gold Standard
BEL Statement

a(CHEBI:galangin) decreases complex(a(CHEBI:"2,3,7,8-tetrachlorodibenzodioxine"),p(MGI:Ahr))

 

 
  

DETAILED EVALUATION:

---

T = Term-Level: Abundance and Process Functions and namespace + entity id arguments

Ts = Secondary Term-Level: Abundance and Process Functions only

 ---

F = Function-Level: Function and arguments

Fs = Secondary Function-Level: Function only

---

R = Relation-Level: Complete Relationship

Rs = Secondary Relation-Level: Partial Relationship

---

S = Full BEL Statement

-------


TP : True Positives

FP : False Positives

FN : False Negatives

 
 POSSIBLE SUBMISSIONSTTsFFsRRsSEVALUATION EXPLANATION
Correct Submission of Full Statement
a(CHEBI:galangin) 
 decreases 
 complex(a(CHEBI:"2,3,7,8-tetrachlorodibenzodioxine"),p(MGI:Ahr))

 

Comment: The complex() function is counted as a true positive (TP) on the function level (F) if at least one argument-term is correct

3TP

0FP

0FN

3TP

0FP

0FN

1TP

0FP

0FN

1TP

0FP

0FN

1TP

0FP

0FN

1TP

0FP

0FN

1TP

0FP

0FN

Full score on all levels:

  • T (2 correct terms)

  • F (Function and arguments are correct)
    • Fs (the function is correct regardless of its arguments)
  • R (Relationship and both arguments are correct)
    • Rs (Relationship and at least one argument are correct)

  • S (Full statement is correct)

Submission with Placeholders for BEL Terms

 
a(PH:placeholder) decreases complex(a(PH:placeholder),p(PH:placeholder))
 

Comment: Placeholders are not counted as FP (false positives) but only as FN (false negatives)

0TP

0FP

3FN

3TP

0FP

0FN

0TP

0FP

1FN

1TP

0FP

0FN

0TP

0FP

1FN

0TP

0FP

1FN

0TP

0FP

1FN

Full score on the following levels:

    • Fs (the function is correct regardless of its arguments)
    • Ts (All process/abundance functions are correct)

Partial score on the following levels:

  • T (Three placeholders for BEL Terms)

  • F (The argument of the function is a placeholder)

  • R+Rs (The relationship is correct and its arguments are placeholders = not counted as false positives)

  • S (Placeholders are used in whole statement)

Submission with two correct BEL-Terms and one Placeholder as argument to complex()

a(CHEBI:galangin) decreases complex(p(MGI:Ahr),p(PH:Placeholder))

2TP

0FP

1FN

2TP

1FP

1FN

1TP

0FP

0FN

1TP

0FP

0FN

1TP

0FP

0FN

1TP

0FP

0FN

0TP

1FP

1FN

Full score on the following levels:

  • F+Fs (At least one argument of the complex() function is correct)

  • R+Rs  (The relationship is correct and its arguments are both correct =  complex() has at least one correct argument)

Partial score on the following levels:

  • T (One BEL term is a placeholder)
    • Ts (Only two of three process/abundance functions are correct)

No score on the following levels:

  • S (Full statement is incorrect)

Submission with one Incorrect BEL-Term

(duplicate of a correct BEL-Term)

as part of a complex


 
a(CHEBI:galangin) decreases complex(p(MGI:Ahr),a(CHEBI:galangin))

2TP

0FP

1FN

3TP

0FP

0FN

1TP

0FP

0FN

1TP

0FP

0FN

1TP

0FP

0FN

1TP

0FP

0FN

0TP

1FP

1FN

 Full score on the following levels:
    • Ts (All process/abundance functions are correct)
  • F+Fs (At least one argument of the complex() function is correct)
  • R+Rs  (The relationship is correct and its arguments are both correct =  complex() has at least one correct argument)

Partial score on the following levels:

  • T (Two of three BEL terms are correct, One is a duplicate of a correct one)

No score on the following levels:

  • S (Full statement is incorrect)
Fragment submission of complex and arguments
complex(p(MGI:Ahr),a(CHEBI:galangin))

2TP

0FP

1FN

2TP

0FP

1FN

1TP

0FP

0FN

1TP

0FP

0FN

 Full score on the following levels:
  • F+Fs (At least one argument of the complex() function is correct)

Partial score on the following levels:

  • T+Ts (Two of three BEL terms are correct)

The following levels do not apply:

  • R+Rs 
  • S
  • No labels