13

13: What role does the Ligase play in DNA-Ligation

Shaken formulation:

What role(s) does a Ligase play in a DNA-Ligation as the DNA-Ligation ?

Answer

The Ligase is the instrument in the DNA-Ligation

Question in KM

Template

What role(s) does <instance> play in <event>?

Parameters

INSTANCE _Ligase1114

EVENT _DNA-Ligation1112

INSTANCE	_Ligase1114
EVENT	_DNA-Ligation1112

Code

	 
("p31: What role(s) does <instance> play in <event>?"
 (defun answer-p31-data0 (instance event)
  `(answer
      (question-type p31)
      (instance ,instance)
      (event ,event)
      (roles-in-event-tree ,(collect-roles-in-event-tree instance event)))))

(defun collect-roles-in-event-tree (instance event &key (depth-limit 3))
  (cond 
   ((< depth-limit 0) 
    (km-format t "ERROR! Depth-limit reached for ~a in roles-of-instance-in-event! (loop in subevent tree?)~%" instance)
    (km-format t "ERROR! Continuing without descending further..."))
   (t (let ( (roles-in-event (remove nil
			      (mapcar #'(lambda (slot)
					  (let ( (vals (km `#$(the ,SLOT of ,EVENT) :fail-mode 'fail)) )
					    (cond (vals (km-format t "DEBUG: ~a:: ~a: ~a~%" event slot vals)))
					    (cond ((member instance vals) slot))))
; OLD OUTPUT VERSION				   (list (pretty-instance instance :htmlify t) "is the" (pretty-slot slot)
;							 "when" (pretty-event event :htmlify t))))))
				      *case-roles*))) )
	(cons event 
	      (cons roles-in-event
		    (mapcar #'(lambda (subevent)
				(collect-roles-in-event-tree instance subevent :depth-limit (1- depth-limit)))
			    (subevents event))) )))))

Raw Answer

((question-type p31) (instance _ligase1114)
 (event _dna-ligation1112)
 (roles-in-event-tree (_dna-ligation1112 (instrument)))
 (explanations
  ((_dna-ligation1112 instrument _ligase1114
    ((a chemical-object) (a enzyme)
     (a ligase (@ dna-ligation instrument)))))))

Explanation

The Ligase is instrument of the DNA-Ligation

KB rule (English):

The following rule was asserted for Concept

The instrument of a is: a Chemical-Object

Concept DNA-Ligation is a subconcept of concept

KB rule (KM):
```
( (a chemical-object))
```
KB rule (English):

The following rule was asserted for Concept

The instrument of a is: a Enzyme

Concept DNA-Ligation is a subconcept of concept

KB rule (KM):
```
( (a enzyme))
```
KB rule (English):

The following rule was asserted for Concept DNA-Ligation

The instrument of a DNA-Ligation is: a Ligase

KB rule (KM):
```
(every dna-ligation has (instrument ((a ligase))))
```

Terms

Terms		Definitions
the DNA-Ligation		An instance of DNA-Ligation
the Ligase		An instance of Ligase
Chemical-Object		Any object which is typically described in terms of its chemical properties. Includes atoms, molecules, and chemical groups like methyl group. Souther.
DNA-Ligation		The joining of the 3\' end of one nucleic acid strand with the 5\' end of another, forming a continuous strand. see Lodish:MCB:G-10. definition for ligase.
Enzyme		A protein that catalyzes a specific chemical reaction. Alberts:ECB:G-7.
Ligase		Enzyme that joins two segments of DNA or RNA together end to end. Alberts:ECB:G-10.
instrument		the entity that is used (by the agent if there is one) to perform an event.