Fixed the XREF formulation

amr-core.txt

@@ -46,7 +46,7 @@ more
 too
 most
 subset, subset-of
-wiki, xref
+wiki
 product-of, sum-of
 statistical-test
 date-entity, date-interval

amr_to_rdf.py

@@ -64,6 +64,13 @@ def run_main_on_file(args):
  if( not(args.pbankRoles == u'1') ):
  pBankRoles = False
 
+ xref_namespace_lookup = {}
+ with open('xref_namespaces.txt') as f:
+ xref_lines = f.readlines()
+ for l in xref_lines:
+ line = re.split("\t", l)
+ xref_namespace_lookup[line[0]] = line[1].rstrip('\r\n')
+
  # create the basic RDF data structure
  g = rdflib.Graph()
 
@@ -83,7 +90,12 @@ def run_main_on_file(args):
  g.namespace_manager.bind('amr-terms', amr_terms_ns, replace=True)
  g.namespace_manager.bind('entity-types', amr_ne_ns, replace=True) 
  g.namespace_manager.bind('amr-data', amr_data, replace=True) 
-
+
+ for k in xref_namespace_lookup.keys():
+ temp_ns = rdflib.Namespace(xref_namespace_lookup[k])
+ g.namespace_manager.bind(k, temp_ns, replace=True) 
+ xref_namespace_lookup[k] = temp_ns
+
  # Basic AMR Ontology consisting of 
  # 1. concepts
  # 2. roles 
@@ -149,8 +161,7 @@ def run_main_on_file(args):
  for c in corelist:
  ns_lookup[c] = amr_ns 
  class_lookup[c] = conceptClass
-
-
+
  pattfile = codecs.open("amr-core-patterns.txt", encoding='utf8')
  for l in pattfile:
  pattlist.append( w )
@@ -161,7 +172,10 @@ def run_main_on_file(args):
  while True:
  (amr_line, comments) = amr_metadata.get_amr_line(infile)
  cur_amr = None
+
+ vb_lookup = {}
  label_lookup_table = {}
+ xref_variables = {}
 
  if amr_line:
  cur_amr = amr_metadata.AmrMeta.from_parse(amr_line, comments)
@@ -252,9 +266,12 @@ def run_main_on_file(args):
  #o_resolved = pb_ns[str + ".html#" +o ]
  o_resolved = pb_ns[ o ]
  g.add( (o_resolved, rdflib.RDF.type, frameClass) ) 
- elif( not(o == 'name') ): # ignore 'name' objects but add all others
+ elif( o == 'xref' and args.fixXref): 
+ continue
+ elif( not(o == 'name') ): # ignore 'name' objects but add all others.
  o_resolved = amr_terms_ns[o]
  g.add( (o_resolved, rdflib.RDF.type, conceptClass) )
+ # identify xref variables in AMR, don't retain it as a part of the graph.
  else: 
  continue
 
@@ -275,6 +292,11 @@ def run_main_on_file(args):
  # remember which objects have name objects 
  if( p == 'name' ):
  label_lookup_table[o] = s 
+
+ # objects with value objects should also be in 
+ elif( p == 'xref' and args.fixXref):
+ xref_variables[o] = s 
+
  elif( re.search('^ARG\d+$', p) is not None ):
 
  frameRole = frames[s] + "." + p
@@ -283,6 +305,9 @@ def run_main_on_file(args):
 
  g.add( (pb_ns[frameRole], rdflib.RDF.type, frameRoleClass) )
  g.add( (temp_ns[s], pb_ns[frameRole], temp_ns[o] ) ) 
+ vb_lookup[s] = temp_ns[s]
+ vb_lookup[frameRole] = pb_ns[frameRole]
+ vb_lookup[o] = temp_ns[o]
 
  elif( re.search('^ARG\d+\-of$', p) is not None ):
 
@@ -291,10 +316,19 @@ def run_main_on_file(args):
  frameRole = p
 
  g.add( (pb_ns[frameRole], rdflib.RDF.type, frameRoleClass) )
- g.add( (temp_ns[s], pb_ns[frameRole], temp_ns[o] ) ) 
+ g.add( (temp_ns[s], pb_ns[frameRole], temp_ns[o] ) ) 
+ vb_lookup[s] = temp_ns[s]
+ vb_lookup[frameRole] = pb_ns[frameRole]
+ vb_lookup[o] = temp_ns[o]
+
  else:
+
  g.add( (amr_terms_ns[p], rdflib.RDF.type, roleClass) )
  g.add( (temp_ns[s], amr_terms_ns[p], temp_ns[o]) )
+ vb_lookup[s] = temp_ns[s]
+ vb_lookup[p] = amr_terms_ns[p]
+ vb_lookup[o] = temp_ns[o]
+
 
  # Add data properties in the current AMR
  labels = {}
@@ -316,6 +350,18 @@ def run_main_on_file(args):
 
  labels[ss].append( (opN, l) )
 
+ elif( xref_variables.get(s,None) is not None 
+ and p == 'value'
+ and args.fixXref):
+ for k in xref_namespace_lookup.keys():
+ if( l.startswith(k) ):
+ l2 = l[-len(l)+len(k):]
+ xref_vb = xref_variables.get(s,None)
+ resolved_xref_vb = vb_lookup.get(xref_vb,None)
+ g.add( (resolved_xref_vb, 
+ amr_ns['xref'], 
+ xref_namespace_lookup[k][l2]) )
+
  # Special treatment for propbank roles. 
  elif( re.search('ARG\d+$', p) is not None ):
 
@@ -375,6 +421,7 @@ def run_main_on_file(args):
  parser.add_argument('-o', '--outPath', help='RDF output file or directory')
 
  parser.add_argument('-pbr', '--pbankRoles', default='1', help='Do we include PropBank Roles?')
+ parser.add_argument('-kx', '--fixXref', default='1', help='Keep existing Xref formalism?')
  parser.add_argument('-v', '--verbose', action='store_true')
  parser.add_argument('-f', '--format', nargs='?', default='nt',
  help="RDF Format: xml, n3, nt, trix, rdfa")

xref_namespaces.txt

@@ -0,0 +1,3 @@
+UNIPROT http://www.uniprot.org/uniprot/
+PUBCHEM https://pubchem.ncbi.nlm.nih.gov/compound/ 
+GO http://amigo.geneontology.org/amigo/term/GO: