1

1: What is a DNA-Molecule

Shaken formulation:

What is the DNA-Molecule ?

Answer

Object: a DNA-Molecule

Object Overview:

Definition:

Double-stranded polynucleotide formed from two separate chains of deoxyribonucleotide units; serves as the carrier of genetic information.
Alberts:ECB:G-6

It is a kind of:

Container
Nucleic-Acid-Complex

Object Details:

It is composed of:

structural basic unit Base-Pair
part

DNA-Strand
DNA-Strand
Base-Pair

Specializations:

Eucaryotic-DNA
Procaryotic-DNA
Viral-DNA

Object Significance:

Functions:

in-event Be-Contained
purpose Container

Question in KM

Template

What is <instance>?

Parameters

INSTANCE

INSTANCE

Code

	 
("p6: What is <instance>?

The answer is computed from the EXPLAIN function, which is the general
explanation function used in Shaken for objects and processes. It is
based on the use of Explanation Design Plans (EDPs). EDP structure the
way the infomation (based on slot values) is displayed to the
user. The leaves of this structure are VIEWS of the concept.

A view is a partial and specialized set of slot values of a particular
concept. These slot values are organized by accessors. Each
slot in the base KB is linked to a particular accessor, e.g. the slot
destination is linked to the accessor location.

The result of the explanation is displayed as a list. The
structure of the list follows the hierarchical structure of the
EDP."
 (defun answer-p6-data (instance expanded)
  (setq instance (intern instance :user))
  (let* ((explanation (rkf::list-explain 
		       `(("concept" . ,instance)
			 ("query-type" . ":explain-qn")
			 ("expanded" . ,expanded)
			 ))))
    `(,@explanation
      ("concept" . ,instance)
      ("query-type" . :explain-qn)
      (user::question-type user::p6)
      ("expanded" . ,expanded)))))


(defun list-explain (alist)
  (let* ((user::*show-comments* nil)
	 (*dictionary* nil)
	 (concept-name (util::alist-value alist "concept"))
	 (query-type-string (util::alist-value alist "query-type"))
	 (concept (coerce-concept (intern concept-name :user)))
	 (query-type (and query-type-string
			  (intern (read-from-string query-type-string) :keyword))))
    (if concept
	(let ((query-type (if (equal query-type :explain-qn)
			      (get-concept-query-type concept)
			    (or query-type
				(get-concept-query-type concept)))))
	  (list (cons "explanation" 
		      (list-edp (explain query-type concept alist) alist))
		(cons "question" (user::question-string query-type concept alist))
		(cons "dictionary" *dictionary*))))))

(defun explain (query-type concept alist)
  (when query-type
    (let* ((edp (select-edp query-type))
	   (explanation-plan (construct-node edp concept alist)))
      (apply-edp (get-node-type edp) edp explanation-plan)
      explanation-plan)))

Raw Answer

((values
  (<EDP>Object:  a DNA-Molecule
   (<EDP>Object Overview:
    (<EDP>Definition:
     (( Double-stranded polynucleotide formed from two separate chains of deoxyribonucleotide units; serves as the carrier of genetic information.)
      (Alberts:ECB:G-6 )))
    (<EDP>It is a kind of:
     (Container Nucleic-Acid-Complex)))
   (<EDP>Object Details:
    (<EDP>It is composed of:
     (<SLOT>structural basic unit _Base-Pair976)
     (<SLOT>part _DNA-Strand981 _DNA-Strand980
      _Base-Pair976))
    (<EDP>Specializations:
     (Eucaryotic-DNA Procaryotic-DNA Viral-DNA)))
   (<EDP>Object Significance:
    (<EDP>Functions: (<SLOT>in-event _Be-Contained975)
     (<SLOT>purpose _Container979)))))
 (concept . _dna-molecule971) (query-type . explain-qn)
 (question-type p6) (expanded)
 (explanations
  ((_dna-molecule971 has-part _dna-strand981
    ((a dna-strand called DNA-Strand-2)))
   (_dna-molecule971 has-part _dna-strand980
    ((a nucleotide-sequence)
     (a dna-strand called DNA-Strand-1 with
      (complement
       (((the dna-strand has-part of _dna-molecule971)
         called DNA-Strand-2)))
      (object-of
       ((a be-attached-to with
         (object
          (((the has-part of _dna-molecule971) called
            DNA-Strand-2)))
         (instrument
          ((a chemical-sequence with
            (element-type (hydrogen-bond)))))))))))
   (_dna-molecule971 has-part _base-pair976
    ((the has-basic-structural-unit of _dna-molecule971)))
   (_dna-molecule971 has-basic-structural-unit
    _base-pair976
    ((a base-pair
      (@ dna-molecule has-basic-structural-unit))))
   (_dna-molecule971 purpose _container979
    ((a container with
      (in-event
       ((a genetic-information-storage with
         (object
          ((a genome
            (@ dna-molecule purpose container in-event
             genetic-information-storage object))))
         (@ dna-molecule purpose container in-event))))
      (@ dna-molecule purpose))))
   (_dna-molecule971 in-event _be-contained975
    ((a be-contained with
      (object
       ((the content of _dna-molecule971
         (@ container in-event be-contained object))))
      (@ container in-event)))))))

Explanation

The DNA-Strand is part of the DNA-Molecule

KB rule (English):

The following rule was asserted for Concept

The has-part of a is: a DNA-Strand with the following-properties:
- It is called DNA-Strand-2
Concept DNA-Molecule is a subconcept of concept

KB rule (KM):
```
( (a dna-strand called DNA-Strand-2))
```

The DNA-Strand is part of the DNA-Molecule

KB rule (English):

The following rule was asserted for Concept

The has-part of a is: a Nucleotide-Sequence

Concept DNA-Molecule is a subconcept of concept

KB rule (KM):
```
( (a nucleotide-sequence))
```
KB rule (English):

The following rule was asserted for Concept

The has-part of a is: a DNA-Strand with the following-properties:
- It is called DNA-Strand-1
- Its complement is the DNA-Strand part of the DNA-Molecule called dna-strand-2
- Its object-of is a Be-Attached-To with the following-properties:
  - Its object is the part of the DNA-Molecule called dna-strand-2
  - Its instrument is a Chemical-Sequence with the following-properties:
    - Its element-type is Hydrogen-Bond
Concept DNA-Molecule is a subconcept of concept

KB rule (KM):
```
(
 (a dna-strand called DNA-Strand-1 with
  (complement
   (((the dna-strand has-part of _dna-molecule971) called
     DNA-Strand-2)))
  (object-of
   ((a be-attached-to with
     (object
      (((the has-part of _dna-molecule971) called
        DNA-Strand-2)))
     (instrument
      ((a chemical-sequence with
        (element-type (hydrogen-bond))))))))))
```

The Base-Pair is part of the DNA-Molecule

KB rule (English):

The following rule was asserted for Concept

The has-part of a is: the structural basic unit of the DNA-Molecule

Concept DNA-Molecule is a subconcept of concept

KB rule (KM):
```
(
 (the has-basic-structural-unit of _dna-molecule971))
```

The Base-Pair is structural basic unit of the DNA-Molecule

KB rule (English):

The following rule was asserted for Concept DNA-Molecule

The has-basic-structural-unit of a DNA-Molecule is: a Base-Pair

KB rule (KM):
```
(every dna-molecule has
 (has-basic-structural-unit ((a base-pair))))
```

The Container is purpose of the DNA-Molecule

KB rule (English):

The following rule was asserted for Concept DNA-Molecule

The purpose of a DNA-Molecule is: a Container with the following-properties:
- Its in-event is a Genetic-Information-Storage with the following-properties:
  - Its object is a Genome
KB rule (KM):
```
(every dna-molecule has
 (purpose
  ((a container with
    (in-event
     ((a genetic-information-storage with
       (object ((a genome))))))))))
```

The Be-Contained is in-event of the DNA-Molecule

KB rule (English):

The following rule was asserted for Concept Container

The in-event of a Container is: a Be-Contained with the following-properties:
- Its object is the content of the DNA-Molecule
Concept DNA-Molecule is a subconcept of concept Container

KB rule (KM):
```
(every container has
 (in-event
  ((a be-contained with
    (object ((the content of _dna-molecule971)))))))
```

Terms

Terms		Definitions
the Base-Pair		An instance of Base-Pair
the Be-Contained		An instance of Be-Contained
the Container		An instance of Container
the DNA-Molecule		An instance of DNA-Molecule
the DNA-Strand		An instance of DNA-Strand
the DNA-Strand		An instance of DNA-Strand
the Place		An instance of Place
Base-Pair		Two nucleotides in an RNA or a DNA molecule that are paired by hydrogen bonds - for example, G with C, and A with T or U. Alberts:ECB:G-3.
Be-Attached-To		one object attached to another
Be-Contained		an object is contained in a container
Chemical-Sequence		A sequence of monomers that form a chain, e.g. polymers. Souther:2001
Container		Things that have contents. A container is the Instrument in a Be-Contained state.
DNA-Molecule		Double-stranded polynucleotide formed from two separate chains of deoxyribonucleotide units; serves as the carrier of genetic information. Alberts:ECB:G-6
DNA-Strand		One of two complementary anti-parallel chains that make up the DNA double helical molecule. Souther.
Eucaryotic-DNA		Double-stranded polynucleotide formed from two separate chains of deoxyribonucleotide units; serves as the carrier of genetic information in eucaryotes. Alberts:ECB:G-6.
Genetic-Information-Storage
Genome		The total genetic information carried by a cell or an organism (or the DNA molecules that carry this information. Alberts:ECB:G-8.
Hydrogen-Bond		A weak chemical bond between an electronegative atom such as nitrogen or oxygen and a hydrogen atom bound to another electronegative atom. Alberts:ECB:G-9.
Nucleic-Acid-Complex		A group of nucleic acids which act together to provide structure or perform some function. They are often held together by weak bonds such as hydrogen bonds. Examples: DNA double helix and base pairs. Souther.
Nucleotide-Sequence		A sequence of nucleotides which forms a nucleotide polymer. Souther:2001
Place		No Textual Definition
Procaryotic-DNA		Double-stranded polynucleotide formed from two separate chains of deoxyribonucleotide units; serves as the carrier of genetic information in procaryotes. Alberts:ECB:G-6.
Viral-DNA		The DNA of a virus. Souther.
called		No Textual Definition
complement		an Entity has a complement another Entity.
content		an Entity contains another Entity.
element-type		No Textual Definition
has-basic-structural-unit		the many identical physical things that make up a whole structurally (as opposed to functionally).
has-part		the parts that comprise a whole.
in-event		the entity that plays this Role participates in Event
instrument		the entity that is used (by the agent if there is one) to perform an event.
object		the entity that is acted upon by an Event. The main passive participant in the Event.
object-of		No Textual Definition
purpose		The default purpose of an entity.