I am really new to xml and I am trying to read an sbml file using the xml2 package in R.
The demo sbml file is taken from the sbml main page.
I am confused as to how to search for a node using the xpath.
E.g., I tried
test <- read_xml("./scratch.xml")
xml_children(test)[1]
xml_attr(xml_children(test)[1], "name")
works and gives me "EnzymaticReaction" as answer. But, I don't want to access nodes by indices, but by name - so I tried
xml_find_one(test, ".//model")
which gives me error
Error: No matches
Can anyone help me as to what I am doing wrong in calling by xpath? The sbml file is pasted below also.
Thanks!
<?xml version="1.0" encoding="UTF-8"?>
<sbml level="2" version="3" xmlns="http://www.sbml.org/sbml/level2/version3">
<model name="EnzymaticReaction">
<listOfUnitDefinitions>
<unitDefinition id="per_second">
<listOfUnits>
<unit kind="second" exponent="-1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="litre_per_mole_per_second">
<listOfUnits>
<unit kind="mole" exponent="-1"/>
<unit kind="litre" exponent="1"/>
<unit kind="second" exponent="-1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment id="cytosol" size="1e-14"/>
</listOfCompartments>
<listOfSpecies>
<species compartment="cytosol" id="ES" initialAmount="0" name="ES"/>
<species compartment="cytosol" id="P" initialAmount="0" name="P"/>
<species compartment="cytosol" id="S" initialAmount="1e-20" name="S"/>
<species compartment="cytosol" id="E" initialAmount="5e-21" name="E"/>
</listOfSpecies>
<listOfReactions>
<reaction id="veq">
<listOfReactants>
<speciesReference species="E"/>
<speciesReference species="S"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="ES"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci>cytosol</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>kon</ci>
<ci>E</ci>
<ci>S</ci>
</apply>
<apply>
<times/>
<ci>koff</ci>
<ci>ES</ci>
</apply>
</apply>
</apply>
</math>
<listOfParameters>
<parameter id="kon" value="1000000" units="litre_per_mole_per_second"/>
<parameter id="koff" value="0.2" units="per_second"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction id="vcat" reversible="false">
<listOfReactants>
<speciesReference species="ES"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="E"/>
<speciesReference species="P"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci>cytosol</ci>
<ci>kcat</ci>
<ci>ES</ci>
</apply>
</math>
<listOfParameters>
<parameter id="kcat" value="0.1" units="per_second"/>
</listOfParameters>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
In your input document, there is a default namespace:
<sbml xmlns="http://www.sbml.org/sbml/level2/version3">
that applies to all elements by default. An XPath expression like
//model
means looking for an element in no namespace - but in your document, there are no model nodes that are in no namespace.
I am not familiar with R, so I can only suggest something that is more of a workaround than an answer. The workaround is to not directly mention the name of the element, but use an XPath expression like
//*[local-name() = 'model']
But ignoring namespaces is not as good as explicitly mentioning them in your code.
Meanwhile, I've read about this here...
The real solution would be to use a method to declare the namespace URI from your input document in your R code, and use a prefix in the XPath expression. I think that the right way to do it would be
ns <- xml_ns_rename(xml_ns(test), d1 = "sbml")
xml_find_one(test, "/sbml:sbml/sbml:model", ns)
Renaming is not strictly necessary, but it is helpful. The default namespaces in an XML document are named d1, d2 and so on by this XML library.