Commonly Used GFP Functions
Commonly Used GFP Functions
GFP (Generic Frame Protocol) is the API used to access Pathway Tools
databases (also known as knowledge bases, kbs, and PGDBs) that are stored in the Ocelot object-oriented database
system. Many additional GFP operations are described in the full GFP
specification.
For all functions that have a kb argument, that argument defaults to the currently selected KB, and
allows the programmer to operate on a KB other than the currently
selected KB. Function
select-organism
can be used to change the currently selected KB to the KB for a
different organism.
The frame argument to most GFP functions can be either a symbol frame name,
a string frame name, or a frame object.
Retrieval Functions
Functions described in this section retrieve data from a KB, but do not
modify a KB.
| Function: |
get-slot-values(frame slot kb) |
| Returns: |
A list of all values of Slot of Frame in KB.
|
| Arguments: |
Frame: A frame id or object.
Slot: A slot name (symbol).
|
| Example: |
(get-slot-values 'trp 'synonyms)
|
| Function: |
get-slot-value(frame slot kb) |
| Returns: |
The first value of Slot of Frame.
|
| Arguments: |
Frame: A frame id or object.
Slot: A slot name (symbol).
|
| Example: |
(get-slot-value 'trp 'common-name)
|
| Function: |
get-class-all-instances(class kb) |
| Returns: |
A list of all frames that are direct or indirect instances
of Class.
|
| Arguments: |
Class: A class frame.
|
| Example: |
(get-class-all-instances '|Reactions|)
|
| Function: |
instance-all-instance-of-p(instance class kb) |
| Returns: |
T if Instance is a direct or an indirect child of Class.
|
| Arguments: |
Class: A class frame.
Instance: An instance frame.
|
| Example: |
(instance-all-instance-of-p 'PM338 '|Promoters|)
|
| Function: |
member-slot-value-p(frame slot value kb) |
| Returns: |
T if Value is one of the values of Slot of Frame.
|
| Arguments: |
Frame: A frame id or object.
Slot: A slot name (symbol).
Value: A slot value such as an integer, symbol, or string.
|
| Example: |
(member-slot-value-p 'trp 'common-name "L-tryptophan")
|
| Function: |
fequal(frame1 frame2) |
| Returns: |
T if Frame1 and Frame2 are the same frame. Must be used as
the test function for operations that compare frames.
|
| Arguments: |
Frame1: A frame id or object.
Frame2: A frame id or object.
|
| Example: |
(loop for x in (get-class-all-instances '|Reactions|)
when (member-slot-value-p x 'left 'trp :test #'fequal)
collect x)
|
| Function: |
get-frame-labeled(label kb) |
| Returns: |
A list of frames whose name or synonym matches label
|
| Arguments: |
Label: a string
|
| Example: |
(get-frame-labeled "tryptophan")
|
Update Functions
Functions described in this section modify the data within a KB. To save those modifications,
a call to save-kb must be performed.
| Function: |
put-slot-values(frame slot values kb) |
| Actions: |
Discards the current value(s) of Slot of Frame; the new value(s) of Slot of Frame become the list Values.
|
| Arguments: |
Frame: A frame id or object.
Slot: A slot name (symbol).
Values: A list of values of the appropriate datatype (e.g., a list of integers or a list of strings).
|
| Example: |
(put-slot-values 'trp 'synonyms '("L-trp" "tryptophan"))
|
| Function: |
put-slot-value(frame slot value kb) |
| Actions: |
Discards the current value(s) of Slot of Frame; the new value of Slot of Frame becomes the single value, Value.
|
| Arguments: |
Frame: A frame id or object.
Slot: A slot name (symbol).
Value: A value of the appropriate datatype (e.g., an integer or a string).
|
| Example: |
(put-slot-value 'trp 'synonyms "L-trp")
|
| Function: |
replace-slot-value(frame slot old new kb test) |
| Actions: |
Removes Old as a value of Slot of Frame, replacing it with the value New. Function Test is used to compare Old to the existing slot value(s).
|
| Arguments: |
Frame: A frame id or object.
Slot: A slot name (symbol).
|
| Example: |
(put-slot-values 'trp 'synonyms '("L-trp" "tryptophan"))
|
| Function: |
add-slot-value(frame slot new kb test) |
| Actions: |
Adds the value New as a new value of Slot of Frame.
|
| Arguments: |
Frame: A frame id or object.
Slot: A slot name (symbol).
Old: A value of the appropriate datatype (e.g., an integer or a string).
New: A value of the appropriate datatype (e.g., an integer or a string).
|
| Function: |
remove-slot-value(frame slot value kb test) |
| Actions: |
Removes the value Value as a value of Slot of Frame.
|
| Arguments: |
Frame: A frame id or object.
Slot: A slot name (symbol).
Value: A value of the appropriate datatype (e.g., an integer or a string).
|
| Function: |
remove-local-slot-values(frame slot kb) |
| Actions: |
Removes all values of Slot of Frame, leaving the slot devoid of values.
|
| Arguments: |
Frame: A frame id or object.
Slot: A slot name (symbol).
|
Miscellaneous Functions
| Function: |
current-kb () |
| Returns: |
The currently selected KB.
|
| Arguments: |
None.
|
| Function: |
print-frame (frame kb) |
| Side Effects: |
Prints a description of Frame to standard output.
|
| Arguments: |
Frame: A frame id or object.
|
|