Source Code for Module TEES.ExampleBuilders.FeatureBuilders.BioInferOntologyFeatureBuilder

 1  """ 
 2  BioInfer ontology based features 
 3  """ 
 4  __version__ = "$Revision: 1.2 $" 
 5   
 6  import sys, os 
 7  try: 
 8      import xml.etree.cElementTree as ET 
 9  except ImportError: 
10      import cElementTree as ET 
11  import Utils.ElementTreeUtils as ETUtils 
12  from FeatureBuilder import FeatureBuilder 
13   
14  g_bioInferFileName = "../../../BioInfer/data/bioinfer.xml" 
15   
16 -def parseNodes(node, ontology): 
17      for child in node: 
18          assert(not ontology.has_key(child.attrib["name"])) 
19          ontology[child.attrib["name"]] = node.attrib["name"] 
20          parseNodes(child, ontology) 
21   
22 -def loadOntologies(bioInferFileName): 
23      bioInferTree = ET.parse(bioInferFileName) 
24      bioInferRoot = bioInferTree.getroot() 
25      ontologyElements = bioInferRoot.findall("ontology") 
26      ontologies = {} 
27      for ontologyElement in ontologyElements: 
28          ontologies[ontologyElement.attrib["type"]] = {} 
29          for node in ontologyElement: 
30              parseNodes(node, ontologies[ontologyElement.attrib["type"]]) 
31      return ontologies 
32   
33 -def printNode(node, indent=""): 
34      print indent + node.attrib["name"] 
35      for child in node: 
36          printNode(child, indent + " ") 
37   
38 -def getParents(term, ontology): 
39      parents = [] 
40      parent = ontology[node] 
41      while parent != None: 
42          parents.append(parent) 
43          parent = ontology[parent] 
44      return parent 
45   
46 -class BioInferOntologyFeatureBuilder(FeatureBuilder): 
47 -    def __init__(self, featureSet): 
48          global g_bioInferFileName 
49          FeatureBuilder.__init__(self, featureSet) 
50          self.ontologies = loadOntologies(g_bioInferFileName) 
51       
52 -    def getTokenAnnotatedType(self, token, sentenceGraph):     
53          if sentenceGraph.tokenIsEntityHead[token] != None: 
54              return sentenceGraph.tokenIsEntityHead[token].attrib["type"] 
55          else: 
56              return None 
57   
58 -    def buildOntologyFeaturesForPath(self, sentenceGraph, pathTokens, pathEdges=None): 
59          for token in pathTokens: 
60              tokenType = self.getTokenAnnotatedType(token, sentenceGraph) 
61              if tokenType != None: 
62                  self.buildOntologyFeatures(tokenType, "ont_") 
63       
64 -    def buildOntologyFeatures(self, term, tag=""): 
65          features = self.getParents(term) 
66          for feature in features: 
67              self.features[tag+feature] = 1 
68       
69 -    def getParents(self, term): 
70          returnValues = [] 
71          for k, ontology in self.ontologies.iteritems(): 
72              if ontology.has_key(term): 
73                  parents = [] 
74                  parent = term 
75                  while ontology.has_key(parent): 
76                      parent = ontology[parent] 
77                      parents.append(parent) 
78                  for parent in parents: 
79                      returnValues.append(k+"_"+parent) 
80          return returnValues 
81   
82  if __name__=="__main__": 
83      ontologies = loadOntologies(g_bioInferFileName) 
84      for k, v in ontologies.iteritems(): 
85          print k + ":" 
86          print v 
87