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I'm wondering if there is a way to read out the metacyc pathway hierarchy?
More precisely, I want to get e.g. all pathways from class Detoxification->Acid Resistance. Could this be done via the API or somehow else?
The answer is yes, but the how depends on what you mean by "get" all the pathways. We don't provide a complete expanded tree showing all pathway classes and their instances, but you can browse the pathway hierarchy interactively at https://biocyc.org/META/class-tree?ob.... If you create a SmartTable containing the class(es) you are interested in, there is a transform operation to show the children of each class (this includes both subclasses and pathway instances, however many levels deep). If you're looking to extract this information via our web services, you can construct a biovelo query to do this. For example:
https://websvc.biocyc.org/xmlquery?%5...
retrieves info about all 3 pathways in the Acid-Resistance class, and
https://websvc.biocyc.org/xmlquery?qu...
retrieves info about all 57 pathways in the Detoxification class and its subclasses (other available detail levels are "none" or "full").
Alternatively, if you download the MetaCyc flat files, there is a file that lists all the classes in MetaCyc (not just pathway classes) and their sub- and super-classes, and another file that lists all the pathway instances and their parent classes, so with a little effort you could reconstruct the pathway hierarchy from that.
I hope this helps.
In addition to this, I tried the API to get informations about the hierarchy. Using PythonCyc in the following:
import pythoncyc
meta = pythoncyc.select_organism('meta')
test = meta.get_class_data("Acid-Resistance")
test.get_frame_data
for i in test.instances:
print i.common_name
To get all classes:
meta.get_class_all_subs("|Pathways|")
The first classes are the major classes (biosynthesis, energy metabolism). Using the classes you can get the subclases
bio = meta.get_class_all_subs("|Biosynthesis|")
And for the subclasses all the instances can be retrieved:
meta.get_class_data(bio[0]).instances # instances for the first subclass in biosynthesis pathways
Asked: 2017-07-14 08:01:28 -0500
Seen: 6,133 times
Last updated: Aug 15 '17
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