Source Code for Module biana.BianaParser.psimioboParser

  1  """ 
  2      BIANA: Biologic Interactions and Network Analysis 
  3      Copyright (C) 2009  Javier Garcia-Garcia, Emre Guney, Baldo Oliva 
  4   
  5      This program is free software: you can redistribute it and/or modify 
  6      it under the terms of the GNU General Public License as published by 
  7      the Free Software Foundation, either version 3 of the License, or 
  8      (at your option) any later version. 
  9   
 10      This program is distributed in the hope that it will be useful, 
 11      but WITHOUT ANY WARRANTY; without even the implied warranty of 
 12      MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the 
 13      GNU General Public License for more details. 
 14   
 15      You should have received a copy of the GNU General Public License 
 16      along with this program.  If not, see <http://www.gnu.org/licenses/>. 
 17   
 18  """ 
 19   
 20  import sys 
 21   
 22  import re 
 23   
 24  from bianaParser import * 
 25   
 26   
 27 -class PSIMIOBOParser(BianaParser): 
 28      """ 
 29      PSI MI OBO Parser Class 
 30      """ 
 31   
 32      name = "psi_mi_obo" 
 33      description = "This program fills up tables in database biana related with protein interaction ontology" 
 34      external_entity_definition = "A external entity represents an ontology element" 
 35      external_entity_relations = "" 
 36   
 37   
 38 -    def __init__(self): 
 39           
 40          BianaParser.__init__(self, default_db_description = "PSI MI obo", 
 41                               default_script_name = "psimioboParser.py", 
 42                               default_script_description = "This program fills up tables in database piana related to PSI-MI formatted Ontologies") 
 43           
 44   
 45 -    def parse_database(self): 
 46          """ 
 47          Method that implements the specific operations of psi-mi-obo parser 
 48          """ 
 49   
 50          # Add the possibility to transfer taxonomy name and taxonomy category using taxID as a key 
 51          self.biana_access._add_transfer_attribute( externalDatabaseID = self.database.get_id(),  
 52                                                     key_attribute = "Method_id", 
 53                                                     transfer_attribute="psimi_name" ) 
 54          self.default_eE_attribute = "psimi_name" 
 55   
 56          ontology = Ontology( source_database = self.database, linkedAttribute="Method_id", name="psimiobo", descriptionAttribute="psimi_name" ) 
 57   
 58          specific_identifiers_and_parent = {} 
 59   
 60          # Start variables 
 61          term_id = None 
 62          term_name = None 
 63          term_def = None 
 64   
 65          # PSI-MI OMO specific 
 66          term_is_a = [] 
 67          term_part_of = [] 
 68          term_exact_synonyms = [] 
 69          term_related_synonyms = [] 
 70   
 71          self.initialize_input_file_descriptor() 
 72   
 73          # Adding a dummy relation to let the database know that psimi_name attribute is also a possible relation attribute 
 74          externalEntityRelation = ExternalEntityRelation( source_database = self.database, relation_type = "interaction" ) 
 75          externalEntityRelation.add_attribute( ExternalEntityRelationAttribute( attribute_identifier = "psimi_name", value = None) ) 
 76   
 77          for line in self.input_file_fd: 
 78   
 79              if re.search("\[Term\]",line): 
 80                  # New term 
 81                  if term_id is not None: 
 82                      # insert previous 
 83                      externalEntity = ExternalEntity( source_database = self.database, type = "PsiMiOboOntologyElement" ) 
 84                       
 85                      externalEntity.add_attribute( ExternalEntityAttribute( attribute_identifier = "Method_id", value = term_id) ) 
 86   
 87                      externalEntity.add_attribute( ExternalEntityAttribute( attribute_identifier = "psimi_name", value = term_name) ) 
 88   
 89                      externalEntity.add_attribute( ExternalEntityAttribute( attribute_identifier = "description", value = term_def) ) 
 90                       
 91                      for current_synonym in term_exact_synonyms: 
 92                          externalEntity.add_attribute( ExternalEntityAttribute( attribute_identifier = "psimi_name", 
 93                                                                                                 value = current_synonym, 
 94                                                                                                 type = "exact_synonym" ) ) 
 95                       
 96                      for current_synonym in term_related_synonyms: 
 97                          externalEntity.add_attribute( ExternalEntityAttribute( attribute_identifier = "psimi_name", 
 98                                                                                                 value = current_synonym, 
 99                                                                                                 type = "related_synonym" ) ) 
100                           
101                      self.biana_access.insert_new_external_entity( externalEntity ) 
102   
103                      specific_identifiers_and_parent[term_id] = (externalEntity.get_id(),term_is_a,term_part_of) 
104   
105   
106                  # Restart variables 
107                  term_id = None 
108                  term_name = None 
109                  term_def = None 
110                  # PSI-MI OMO specific 
111                  term_is_a = [] 
112                  term_part_of = [] 
113                  term_exact_synonyms = [] 
114                  term_related_synonyms = [] 
115   
116              elif re.search("^id\:",line): 
117                  temp = re.search("MI\:(\d+)",line) 
118                   
119                  if temp: 
120                      term_id = temp.group(1) 
121   
122              elif re.search("^name\:",line): 
123                  temp = re.search("name:\s+(.+)",line) 
124                  term_name = temp.group(1) 
125   
126              elif re.search("^def\:",line): 
127                  temp = re.search("\"(.+)\"",line) 
128                  term_def = temp.group(1) 
129   
130              # PSI-MI OBO synonyms 
131              elif re.search("exact_synonym\:",line): 
132                  temp = re.search("\"(.+)\"",line) 
133                  term_exact_synonyms.append(temp.group(1)) 
134   
135              elif re.search("related_synonym\:",line): 
136                  temp = re.search("\"(.+)\"",line) 
137                  term_related_synonyms.append(temp.group(1)) 
138   
139              elif re.search("is_a\:",line): 
140                  temp = re.search("MI\:(\d+)",line) 
141                  if temp is not None: 
142                      #print "??:", line # malformation --> is_a: regulates ! regulates 
143                      term_is_a.append(temp.group(1)) 
144   
145              elif re.search("relationship\:",line): 
146                  if( re.search("part_of",line) ): 
147                      temp = re.search("part_of\s+MI\:(\d+)",line) 
148                      if temp is not None: 
149                          term_part_of.append(temp.group(1)) 
150   
151              elif re.search("\[Typedef\]", line): 
152                  # insert last 
153                  externalEntity = ExternalEntity( source_database = self.database, type = "PsiMiOboOntologyElement" ) 
154                  externalEntity.add_attribute( ExternalEntityAttribute( attribute_identifier = "Method_id", value = term_id) ) 
155                  externalEntity.add_attribute( ExternalEntityAttribute( attribute_identifier = "psimi_name", value = term_name) ) 
156                  externalEntity.add_attribute( ExternalEntityAttribute( attribute_identifier = "description", value = term_def) ) 
157                  for current_synonym in term_exact_synonyms: 
158                      externalEntity.add_attribute( ExternalEntityAttribute( attribute_identifier = "psimi_name", 
159                                                                                             value = current_synonym, 
160                                                                                             type = "exact_synonym" ) ) 
161                  for current_synonym in term_related_synonyms: 
162                      externalEntity.add_attribute( ExternalEntityAttribute( attribute_identifier = "psimi_name", 
163                                                                                             value = current_synonym, 
164                                                                                             type = "related_synonym" ) ) 
165                  self.biana_access.insert_new_external_entity( externalEntity ) 
166                  specific_identifiers_and_parent[term_id] = (externalEntity.get_id(),term_is_a,term_part_of) 
167   
168   
169          # Set the ontology hierarch and insert elements to ontology 
170          #print  specific_identifiers_and_parent 
171          for current_method_id in specific_identifiers_and_parent: 
172              #print current_method_id 
173              is_a_list = [ specific_identifiers_and_parent[x][0] for x in specific_identifiers_and_parent[current_method_id][1] ] 
174              is_part_of_list = [ specific_identifiers_and_parent[x][0] for x in specific_identifiers_and_parent[current_method_id][2]  ] 
175              ontology.add_element( ontologyElementID = specific_identifiers_and_parent[current_method_id][0], 
176                                    isA = is_a_list, 
177                                    isPartOf = is_part_of_list ) 
178   
179          self.biana_access.insert_new_external_entity(ontology) 
180