New modification statements

indra/resources/statements_schema.json

@@ -302,7 +302,7 @@
                     "properties": {
                         "type": {
                             "type": "string",
-                            "pattern": "^((Phosphorylation)|(Dephosphorylation)|(Ubiquitination)|(Deubiquitination)|(Sumoylation)|(Desumoylation)|(Hydroxylation)|(Dehydroxylation)|(Acetylation)|(Deacetylation)|(Glycosylation)|(Deglycosylation)|(Farnesylation)|(Defarnesylation)|(Geranylgeranylation)|(Degeranylgeranylation)|(Palmitoylation)|(Depalmitoylation)|(Myristoylation)|(Demyristoylation)|(Ribosylation)|(Deribosylation)|(Methylation)|(Demethylation))$",
+                            "pattern": "^((Phosphorylation)|(Dephosphorylation)|(Ubiquitination)|(Deubiquitination)|(Sumoylation)|(Desumoylation)|(Hydroxylation)|(Dehydroxylation)|(Acetylation)|(Deacetylation)|(Glycosylation)|(Deglycosylation)|(Farnesylation)|(Defarnesylation)|(Geranylgeranylation)|(Degeranylgeranylation)|(Palmitoylation)|(Depalmitoylation)|(Myristoylation)|(Demyristoylation)|(Ribosylation)|(Deribosylation)|(Methylation)|(Demethylation)|(Carboxylation)|(Decarboxylation)|(Amidation)|(Deamidation)|(Sulfation)|(Desulfation)|(Neddylation)|(Deneddylation)|(Alkylation)|(Dealkylation)|(Prenylation)|(Deprenylation'))$",
                             "description": "The type of the statement"
                         },
                         "enz": {

indra/statements/statements.py

@@ -52,6 +52,18 @@
 - :py:class:`Deribosylation`
 - :py:class:`Methylation`
 - :py:class:`Demethylation`
+- :py:class:`Carboxylation`
+- :py:class:`Decarboxylation`
+- :py:class:`Amidation`
+- :py:class:`Deamidation`
+- :py:class:`Sulfation`
+- :py:class:`Desulfation`
+- :py:class:`Neddylation`
+- :py:class:`Deneddylation`
+- :py:class:`Alkylation`
+- :py:class:`Dealkylation`
+- :py:class:`Prenylation`
+- :py:class:`Deprenylation`
 
 There are additional subtypes of :py:class:`SelfModification`:
 
@@ -195,6 +207,9 @@
     'Complex', 'Translocation', 'RegulateAmount', 'DecreaseAmount',
     'IncreaseAmount', 'Influence', 'Conversion', 'Unresolved',
     'Association', 'Event', 'Migration',
+    'Carboxylation', 'Decarboxylation', 'Amidation', 'Deamidation', 'Sulfation',
+    'Desulfation', 'Neddylation', 'Deneddylation', 'Alkylation', 'Dealkylation',
+    'Prenylation', 'Deprenylation',
 
     # Error classes
     'InputError', 'UnresolvedUuidError', 'InvalidLocationError',
@@ -1005,6 +1020,54 @@ class Demethylation(RemoveModification):
     """Demethylation modification."""
 
 
+class Carboxylation(AddModification):
+    """Carboxylation modification."""
+
+
+class Decarboxylation(RemoveModification):
+    """Decarboxylation modification."""
+
+
+class Amidation(AddModification):
+    """Amidation modification."""
+
+
+class Deamidation(RemoveModification):
+    """Deamidation modification."""
+
+
+class Sulfation(AddModification):
+    """Sulfation modification."""
+
+
+class Desulfation(RemoveModification):
+    """Desulfation modification."""
+
+
+class Neddylation(AddModification):
+    """Neddylation modification."""
+
+
+class Deneddylation(RemoveModification):
+    """Deneddylation modification."""
+
+
+class Alkylation(AddModification):
+    """Alkylation modification."""
+
+
+class Dealkylation(RemoveModification):
+    """Dealkylation modification."""
+
+
+class Prenylation(AddModification):
+    """Prenylation modification."""
+
+
+class Deprenylation(RemoveModification):
+    """Deprenylation modification."""
+
+
 @python_2_unicode_compatible
 class RegulateActivity(Statement):
     """Regulation of activity.

indra/tests/test_json_schema.py

@@ -61,7 +61,10 @@ def test_valid_modification():
                  'Myristoylation', 'Demyristoylation', 'Ribosylation',
                  'Deribosylation', 'Methylation', 'Demethylation',
                  'Activation', 'Inhibition', 'IncreaseAmount',
-                 'DecreaseAmount']
+                 'DecreaseAmount', 'Carboxylation', 'Decarboxylation',
+                 'Amidation', 'Deamidation', 'Sulfation', 'Desulfation',
+                 'Neddylation', 'Deneddylation', 'Alkylation',
+                 'Dealkylation', 'Prenylation', 'Deprenylation']
 
     for mod_type in mod_types:
         s = {'enz': valid_agent1, 'sub': valid_agent2,