biointerchange 0.2.2 → 1.0.0

data/supplemental/python/biointerchange/gff3o.py

@@ -8,348 +8,348 @@ class GFF3O:
     @classmethod
     def seqid(cls):
         """Establishes the landmark (cls, e.g. a chromosome) on which a feature is located.
-        (GFF3_0004)
+        (http://www.biointerchange.org/gff3o#GFF3_0004)
         """
-        return _namespace_GFF3O('GFF3_0004')
+        return cls._namespace_GFF3O('GFF3_0004')
 
     @classmethod
     def strand(cls):
         """Either:
             Strand of the feature.
-            (cls, GFF3_0010)
+            (cls, http://www.biointerchange.org/gff3o#GFF3_0010)
         Or:
             Strand of a target -- if applicable.
-            (GFF3_0045)
+            (http://www.biointerchange.org/gff3o#GFF3_0045)
         """
-        return [ _namespace_GFF3O('GFF3_0010'), _namespace_GFF3O('GFF3_0045') ]
+        return [ cls._namespace_GFF3O('GFF3_0010'), cls._namespace_GFF3O('GFF3_0045') ]
 
     @classmethod
     def attributes(cls):
         """Tag name/value pair attributes of a feature that are not covered by object-/data-properties of the ontology. Tags that are represented as object-/data-properties are: ID, Name, Alias, Parent, Target, Gap, Derives_from, Dbxref, Ontology_term, Ontology_term, or Is_circular
-        (cls, GFF3_0012)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0012)
         """
-        return _namespace_GFF3O('GFF3_0012')
+        return cls._namespace_GFF3O('GFF3_0012')
 
     @classmethod
     def parent(cls):
         """Link out to the parent feature.
-        (cls, GFF3_0014)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0014)
         """
-        return _namespace_GFF3O('GFF3_0014')
+        return cls._namespace_GFF3O('GFF3_0014')
 
     @classmethod
     def contains(cls):
         """Relationship that describes which features belong to a feature set.
-        (cls, GFF3_0015)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0015)
         """
-        return _namespace_GFF3O('GFF3_0015')
+        return cls._namespace_GFF3O('GFF3_0015')
 
     @classmethod
     def region(cls):
         """Either:
             FALDO "Region" instance replacement for a feature's start, stop, strand properties.
-            (cls, GFF3_0021)
+            (cls, http://www.biointerchange.org/gff3o#GFF3_0021)
         Or:
             FALDO "Region" instance replacement for a target's start, stop, strand  properties.
-            (GFF3_0050)
+            (http://www.biointerchange.org/gff3o#GFF3_0050)
         """
-        return [ _namespace_GFF3O('GFF3_0021'), _namespace_GFF3O('GFF3_0050') ]
+        return [ cls._namespace_GFF3O('GFF3_0021'), cls._namespace_GFF3O('GFF3_0050') ]
 
     @classmethod
     def species(cls):
         """NCBI Taxonomy Ontology "NCBITaxon_1" (cls, or sub-classes) instance that denotes the species for a feature set.
-        (GFF3_0023)
+        (http://www.biointerchange.org/gff3o#GFF3_0023)
         """
-        return _namespace_GFF3O('GFF3_0023')
+        return cls._namespace_GFF3O('GFF3_0023')
 
     @classmethod
     def set_properties(cls):
         """Either:
             Properties that are directly associated with Set class instances.
-            (cls, GFF3_0025)
+            (cls, http://www.biointerchange.org/gff3o#GFF3_0025)
         Or:
             Properties that are directly associated with Set class instances.
-            (GFF3_0027)
+            (http://www.biointerchange.org/gff3o#GFF3_0027)
         """
-        return [ _namespace_GFF3O('GFF3_0025'), _namespace_GFF3O('GFF3_0027') ]
+        return [ cls._namespace_GFF3O('GFF3_0025'), cls._namespace_GFF3O('GFF3_0027') ]
 
     @classmethod
     def feature_properties(cls):
         """Either:
             Properties that are directly associated with Feature class instances.
-            (cls, GFF3_0026)
+            (cls, http://www.biointerchange.org/gff3o#GFF3_0026)
         Or:
             Properties that are directly associated with Feature class instances.
-            (GFF3_0028)
+            (http://www.biointerchange.org/gff3o#GFF3_0028)
         """
-        return [ _namespace_GFF3O('GFF3_0026'), _namespace_GFF3O('GFF3_0028') ]
+        return [ cls._namespace_GFF3O('GFF3_0026'), cls._namespace_GFF3O('GFF3_0028') ]
 
     @classmethod
     def target(cls):
         """Identifies the target that the features aligns to.
-        (cls, GFF3_0039)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0039)
         """
-        return _namespace_GFF3O('GFF3_0039')
+        return cls._namespace_GFF3O('GFF3_0039')
 
     @classmethod
     def target_properties(cls):
         """Either:
             Properties that are directly associated with Target class instances.
-            (cls, GFF3_0044)
+            (cls, http://www.biointerchange.org/gff3o#GFF3_0044)
         Or:
             Properties that are directly associated with Target class instances.
-            (GFF3_0040)
+            (http://www.biointerchange.org/gff3o#GFF3_0040)
         """
-        return [ _namespace_GFF3O('GFF3_0044'), _namespace_GFF3O('GFF3_0040') ]
+        return [ cls._namespace_GFF3O('GFF3_0044'), cls._namespace_GFF3O('GFF3_0040') ]
 
     @classmethod
     def derives_from(cls):
         """Describes a temporal relationship between two features, where the object denotes the subjects origin.
-        (cls, GFF3_0047)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0047)
         """
-        return _namespace_GFF3O('GFF3_0047')
+        return cls._namespace_GFF3O('GFF3_0047')
 
     @classmethod
     def feature_ontology(cls):
         """Explicit link-out to one or more ontologies that have been used for describing features. This is a meta comment about the URIs that link out to SO/SOFA or other ontologies.
-        (cls, GFF3_0056)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0056)
         """
-        return _namespace_GFF3O('GFF3_0056')
+        return cls._namespace_GFF3O('GFF3_0056')
 
     @classmethod
     def source(cls):
         """A free text qualifier that describes the algorithm or operating procedure that generated this feature.  For example, the name of the software that generated this feature or a database name.
-        (cls, GFF3_0005)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0005)
         """
-        return _namespace_GFF3O('GFF3_0005')
+        return cls._namespace_GFF3O('GFF3_0005')
 
     @classmethod
     def type(cls):
         """Type of the feature, which is either an entry the "lite" version of the Sequence Ontology (cls, SOFA) or a child entry of sequence_feature (SO:0000110) of the full Sequence Ontology (SO).
-        (GFF3_0006)
+        (http://www.biointerchange.org/gff3o#GFF3_0006)
         """
-        return _namespace_GFF3O('GFF3_0006')
+        return cls._namespace_GFF3O('GFF3_0006')
 
     @classmethod
     def start(cls):
         """Either:
             Start coordinate of the feature on the seqid landmark.
-            (cls, GFF3_0007)
+            (cls, http://www.biointerchange.org/gff3o#GFF3_0007)
         Or:
             Start coordinate of the target.
-            (GFF3_0042)
+            (http://www.biointerchange.org/gff3o#GFF3_0042)
         Or:
             Genomic start coordinate of the landmark.
-            (GFF3_0054)
+            (http://www.biointerchange.org/gff3o#GFF3_0054)
         """
-        return [ _namespace_GFF3O('GFF3_0007'), _namespace_GFF3O('GFF3_0042'), _namespace_GFF3O('GFF3_0054') ]
+        return [ cls._namespace_GFF3O('GFF3_0007'), cls._namespace_GFF3O('GFF3_0042'), cls._namespace_GFF3O('GFF3_0054') ]
 
     @classmethod
     def end(cls):
         """Either:
             End coordinate of the feature on the seqid landmark.
-            (cls, GFF3_0008)
+            (cls, http://www.biointerchange.org/gff3o#GFF3_0008)
         Or:
             End coordinate of the target.
-            (GFF3_0043)
+            (http://www.biointerchange.org/gff3o#GFF3_0043)
         Or:
             Genomic end coordinate of the landmark.
-            (GFF3_0055)
+            (http://www.biointerchange.org/gff3o#GFF3_0055)
         """
-        return [ _namespace_GFF3O('GFF3_0008'), _namespace_GFF3O('GFF3_0043'), _namespace_GFF3O('GFF3_0055') ]
+        return [ cls._namespace_GFF3O('GFF3_0008'), cls._namespace_GFF3O('GFF3_0043'), cls._namespace_GFF3O('GFF3_0055') ]
 
     @classmethod
     def score(cls):
         """Score of the feature. For example, an E-value for sequence similarity features or a P-value for ab initio gene prediction features.
-        (cls, GFF3_0009)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0009)
         """
-        return _namespace_GFF3O('GFF3_0009')
+        return cls._namespace_GFF3O('GFF3_0009')
 
     @classmethod
     def phase(cls):
         """Phase for "CDS" features. It indicates where the feature begins with reference to the reading frame. For forward strand features, phase is counted from the start field, whilst for reverse strand features, phase is counted from the end field.
-        (cls, GFF3_0011)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0011)
         """
-        return _namespace_GFF3O('GFF3_0011')
+        return cls._namespace_GFF3O('GFF3_0011')
 
     @classmethod
     def tag(cls):
         """Tag name of a feature attribute.
-        (cls, GFF3_0013)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0013)
         """
-        return _namespace_GFF3O('GFF3_0013')
+        return cls._namespace_GFF3O('GFF3_0013')
 
     @classmethod
     def version(cls):
         """Version of the GFF3 specification that defines the feature set contents.
-        (cls, GFF3_0022)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0022)
         """
-        return _namespace_GFF3O('GFF3_0022')
+        return cls._namespace_GFF3O('GFF3_0022')
 
     @classmethod
     def build(cls):
         """Name of a genome assembly build that denotes the provenance of features in a feature set. For example, 'NCBI 36' or 'FlyBase r4.1'.
-        (cls, GFF3_0024)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0024)
         """
-        return _namespace_GFF3O('GFF3_0024')
+        return cls._namespace_GFF3O('GFF3_0024')
 
     @classmethod
     def attribute_properties(cls):
         """Properties that are directly associated with Attribute class instances.
-        (cls, GFF3_0029)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0029)
         """
-        return _namespace_GFF3O('GFF3_0029')
+        return cls._namespace_GFF3O('GFF3_0029')
 
     @classmethod
     def dbxref(cls):
         """A database cross-reference to associate a sequence alteration to its representation in another database.
-        (cls, GFF3_0034)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0034)
         """
-        return _namespace_GFF3O('GFF3_0034')
+        return cls._namespace_GFF3O('GFF3_0034')
 
     @classmethod
     def ontology_term(cls):
         """A cross-reference to an ontology term that is associated with a feature.
-        (cls, GFF3_0035)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0035)
         """
-        return _namespace_GFF3O('GFF3_0035')
+        return cls._namespace_GFF3O('GFF3_0035')
 
     @classmethod
     def name(cls):
         """Name of a feature, which can be used for display purposes. The name is not a unique property among features.
-        (cls, GFF3_0036)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0036)
         """
-        return _namespace_GFF3O('GFF3_0036')
+        return cls._namespace_GFF3O('GFF3_0036')
 
     @classmethod
     def alias(cls):
         """An alternative name for a feature. This can be another descriptive name of a feature, such as a locus name or accession number.
-        (cls, GFF3_0037)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0037)
         """
-        return _namespace_GFF3O('GFF3_0037')
+        return cls._namespace_GFF3O('GFF3_0037')
 
     @classmethod
     def target_id(cls):
         """ID or accession of the target alignment.
-        (cls, GFF3_0041)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0041)
         """
-        return _namespace_GFF3O('GFF3_0041')
+        return cls._namespace_GFF3O('GFF3_0041')
 
     @classmethod
     def gap(cls):
         """Gap describing the feature/target alignment if the sequences are not collinear. The formal description of this property has been lost due to a dead link in the GFF3 specification.
-        (cls, GFF3_0046)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0046)
         """
-        return _namespace_GFF3O('GFF3_0046')
+        return cls._namespace_GFF3O('GFF3_0046')
 
     @classmethod
     def note(cls):
         """A free text note.
-        (cls, GFF3_0048)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0048)
         """
-        return _namespace_GFF3O('GFF3_0048')
+        return cls._namespace_GFF3O('GFF3_0048')
 
     @classmethod
     def is_circular(cls):
         """Describes whether a feature is circular or not.
-        (cls, GFF3_0049)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0049)
         """
-        return _namespace_GFF3O('GFF3_0049')
+        return cls._namespace_GFF3O('GFF3_0049')
 
     @classmethod
     def landmark_properties(cls):
         """Properties that are directly associated with Landmark class instances.
-        (cls, GFF3_0052)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0052)
         """
-        return _namespace_GFF3O('GFF3_0052')
+        return cls._namespace_GFF3O('GFF3_0052')
 
     @classmethod
     def id(cls):
         """ID that uniquely establishes the Landmark's identity within a Set.
-        (cls, GFF3_0053)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0053)
         """
-        return _namespace_GFF3O('GFF3_0053')
+        return cls._namespace_GFF3O('GFF3_0053')
 
     @classmethod
     def sequence(cls):
         """Either:
             Sequence associated with this feature, if it has been specified using a FASTA string.
-            (cls, GFF3_0057)
+            (cls, http://www.biointerchange.org/gff3o#GFF3_0057)
         Or:
             Sequence associated with this feature, if it has been specified using a FASTA string.
-            (GFF3_0058)
+            (http://www.biointerchange.org/gff3o#GFF3_0058)
         """
-        return [ _namespace_GFF3O('GFF3_0057'), _namespace_GFF3O('GFF3_0058') ]
+        return [ cls._namespace_GFF3O('GFF3_0057'), cls._namespace_GFF3O('GFF3_0058') ]
 
     @classmethod
     def Set(cls):
         """Set of genomic sequence features, whose identifiers are unique within the set.
-        (cls, GFF3_0001)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0001)
         """
-        return _namespace_GFF3O('GFF3_0001')
+        return cls._namespace_GFF3O('GFF3_0001')
 
     @classmethod
     def Feature(cls):
         """A genomic sequence feature.
-        (cls, GFF3_0002)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0002)
         """
-        return _namespace_GFF3O('GFF3_0002')
+        return cls._namespace_GFF3O('GFF3_0002')
 
     @classmethod
     def Attribute(cls):
         """Describes additional feature attributes besides ID, Name, Alias, Parent, Target, Gap, Derives_from, Dbxref, Ontology_term, Ontology_term, or Is_circular.
-        (cls, GFF3_0003)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0003)
         """
-        return _namespace_GFF3O('GFF3_0003')
+        return cls._namespace_GFF3O('GFF3_0003')
 
     @classmethod
     def Strand(cls):
         """Class describing a genomic strand. Instances of the class (cls, individuals) are used to denote forward-/reverse-strands, etc.
-        (GFF3_0016)
+        (http://www.biointerchange.org/gff3o#GFF3_0016)
         """
-        return _namespace_GFF3O('GFF3_0016')
+        return cls._namespace_GFF3O('GFF3_0016')
 
     @classmethod
     def Target(cls):
         """Indicates a feature's "target" of a nucleotide-to-nucleotide or protein-to-nucleotide alignment.
-        (cls, GFF3_0038)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0038)
         """
-        return _namespace_GFF3O('GFF3_0038')
+        return cls._namespace_GFF3O('GFF3_0038')
 
     @classmethod
     def Landmark(cls):
         """A landmark that establishes the coordinate system for features.
-        (cls, GFF3_0051)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0051)
         """
-        return _namespace_GFF3O('GFF3_0051')
+        return cls._namespace_GFF3O('GFF3_0051')
 
     @classmethod
     def Positive(cls):
         """Location on the positive (cls, forward) strand.
-        (GFF3_0017)
+        (http://www.biointerchange.org/gff3o#GFF3_0017)
         """
-        return _namespace_GFF3O('GFF3_0017')
+        return cls._namespace_GFF3O('GFF3_0017')
 
     @classmethod
     def Negative(cls):
         """Location on the negative (cls, reverse) strand.
-        (GFF3_0018)
+        (http://www.biointerchange.org/gff3o#GFF3_0018)
         """
-        return _namespace_GFF3O('GFF3_0018')
+        return cls._namespace_GFF3O('GFF3_0018')
 
     @classmethod
     def UnknownStrand(cls):
         """Strand was not determined, which leaves it open whether the location is on the positive (cls, forward) or negative (reverse) strand.
-        (GFF3_0019)
+        (http://www.biointerchange.org/gff3o#GFF3_0019)
         """
-        return _namespace_GFF3O('GFF3_0019')
+        return cls._namespace_GFF3O('GFF3_0019')
 
     @classmethod
     def NotStranded(cls):
         """Strand is not applicable.
-        (cls, GFF3_0020)
+        (cls, http://www.biointerchange.org/gff3o#GFF3_0020)
         """
-        return _namespace_GFF3O('GFF3_0020')
+        return cls._namespace_GFF3O('GFF3_0020')
 
     @classmethod
     def is_object_property(cls, uri):
@@ -357,35 +357,35 @@ class GFF3O:
         
         uri -- URI that is tested for being an object property
         """
-        if uri == _namespace_GFF3O('GFF3_0004'):
+        if uri == cls._namespace_GFF3O('GFF3_0004'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0010'):
+        if uri == cls._namespace_GFF3O('GFF3_0010'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0012'):
+        if uri == cls._namespace_GFF3O('GFF3_0012'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0014'):
+        if uri == cls._namespace_GFF3O('GFF3_0014'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0015'):
+        if uri == cls._namespace_GFF3O('GFF3_0015'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0021'):
+        if uri == cls._namespace_GFF3O('GFF3_0021'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0023'):
+        if uri == cls._namespace_GFF3O('GFF3_0023'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0025'):
+        if uri == cls._namespace_GFF3O('GFF3_0025'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0026'):
+        if uri == cls._namespace_GFF3O('GFF3_0026'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0039'):
+        if uri == cls._namespace_GFF3O('GFF3_0039'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0044'):
+        if uri == cls._namespace_GFF3O('GFF3_0044'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0045'):
+        if uri == cls._namespace_GFF3O('GFF3_0045'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0047'):
+        if uri == cls._namespace_GFF3O('GFF3_0047'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0050'):
+        if uri == cls._namespace_GFF3O('GFF3_0050'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0056'):
+        if uri == cls._namespace_GFF3O('GFF3_0056'):
             return True
         return False
 
@@ -395,63 +395,63 @@ class GFF3O:
         
         uri -- URI that is tested for being a datatype property
         """
-        if uri == _namespace_GFF3O('GFF3_0005'):
+        if uri == cls._namespace_GFF3O('GFF3_0005'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0006'):
+        if uri == cls._namespace_GFF3O('GFF3_0006'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0007'):
+        if uri == cls._namespace_GFF3O('GFF3_0007'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0008'):
+        if uri == cls._namespace_GFF3O('GFF3_0008'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0009'):
+        if uri == cls._namespace_GFF3O('GFF3_0009'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0011'):
+        if uri == cls._namespace_GFF3O('GFF3_0011'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0013'):
+        if uri == cls._namespace_GFF3O('GFF3_0013'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0022'):
+        if uri == cls._namespace_GFF3O('GFF3_0022'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0024'):
+        if uri == cls._namespace_GFF3O('GFF3_0024'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0027'):
+        if uri == cls._namespace_GFF3O('GFF3_0027'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0028'):
+        if uri == cls._namespace_GFF3O('GFF3_0028'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0029'):
+        if uri == cls._namespace_GFF3O('GFF3_0029'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0034'):
+        if uri == cls._namespace_GFF3O('GFF3_0034'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0035'):
+        if uri == cls._namespace_GFF3O('GFF3_0035'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0036'):
+        if uri == cls._namespace_GFF3O('GFF3_0036'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0037'):
+        if uri == cls._namespace_GFF3O('GFF3_0037'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0040'):
+        if uri == cls._namespace_GFF3O('GFF3_0040'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0041'):
+        if uri == cls._namespace_GFF3O('GFF3_0041'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0042'):
+        if uri == cls._namespace_GFF3O('GFF3_0042'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0043'):
+        if uri == cls._namespace_GFF3O('GFF3_0043'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0046'):
+        if uri == cls._namespace_GFF3O('GFF3_0046'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0048'):
+        if uri == cls._namespace_GFF3O('GFF3_0048'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0049'):
+        if uri == cls._namespace_GFF3O('GFF3_0049'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0052'):
+        if uri == cls._namespace_GFF3O('GFF3_0052'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0053'):
+        if uri == cls._namespace_GFF3O('GFF3_0053'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0054'):
+        if uri == cls._namespace_GFF3O('GFF3_0054'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0055'):
+        if uri == cls._namespace_GFF3O('GFF3_0055'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0057'):
+        if uri == cls._namespace_GFF3O('GFF3_0057'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0058'):
+        if uri == cls._namespace_GFF3O('GFF3_0058'):
             return True
         return False
 
@@ -461,17 +461,17 @@ class GFF3O:
         
         uri -- URI that is tested for being a class
         """
-        if uri == _namespace_GFF3O('GFF3_0001'):
+        if uri == cls._namespace_GFF3O('GFF3_0001'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0002'):
+        if uri == cls._namespace_GFF3O('GFF3_0002'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0003'):
+        if uri == cls._namespace_GFF3O('GFF3_0003'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0016'):
+        if uri == cls._namespace_GFF3O('GFF3_0016'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0038'):
+        if uri == cls._namespace_GFF3O('GFF3_0038'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0051'):
+        if uri == cls._namespace_GFF3O('GFF3_0051'):
             return True
         return False
 
@@ -481,13 +481,13 @@ class GFF3O:
         
         uri -- URI that is tested for being a named individual
         """
-        if uri == _namespace_GFF3O('GFF3_0017'):
+        if uri == cls._namespace_GFF3O('GFF3_0017'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0018'):
+        if uri == cls._namespace_GFF3O('GFF3_0018'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0019'):
+        if uri == cls._namespace_GFF3O('GFF3_0019'):
             return True
-        if uri == _namespace_GFF3O('GFF3_0020'):
+        if uri == cls._namespace_GFF3O('GFF3_0020'):
             return True
         return False
 
@@ -513,11 +513,10 @@ class GFF3O:
             return cls.has_parent(cls.__parent_properties[uri], parent)
         return False
 
-__namespace_GFF3O = Namespace('http://www.biointerchange.org/gff3o#')
-
-def _namespace_GFF3O(accession):
-    return __namespace_GFF3O[accession]
+    @classmethod
+    def _namespace_GFF3O(cls, accession):
+        return Namespace('http://www.biointerchange.org/gff3o#')[accession]
 
-    __parent_properties = { _namespace_GFF3O('GFF3_0004') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0010') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0012') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0014') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0015') : _namespace_GFF3O('GFF3_0025') , _namespace_GFF3O('GFF3_0021') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0023') : _namespace_GFF3O('GFF3_0025') , _namespace_GFF3O('GFF3_0039') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0045') : _namespace_GFF3O('GFF3_0044') , _namespace_GFF3O('GFF3_0047') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0050') : _namespace_GFF3O('GFF3_0044') , _namespace_GFF3O('GFF3_0056') : _namespace_GFF3O('GFF3_0025') , _namespace_GFF3O('GFF3_0005') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0006') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0007') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0008') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0009') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0011') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0013') : _namespace_GFF3O('GFF3_0029') , _namespace_GFF3O('GFF3_0022') : _namespace_GFF3O('GFF3_0027') , _namespace_GFF3O('GFF3_0024') : _namespace_GFF3O('GFF3_0027') , _namespace_GFF3O('GFF3_0034') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0035') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0036') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0037') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0041') : _namespace_GFF3O('GFF3_0040') , _namespace_GFF3O('GFF3_0042') : _namespace_GFF3O('GFF3_0040') , _namespace_GFF3O('GFF3_0043') : _namespace_GFF3O('GFF3_0040') , _namespace_GFF3O('GFF3_0046') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0048') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0049') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0053') : _namespace_GFF3O('GFF3_0052') , _namespace_GFF3O('GFF3_0054') : _namespace_GFF3O('GFF3_0052') , _namespace_GFF3O('GFF3_0055') : _namespace_GFF3O('GFF3_0052') , _namespace_GFF3O('GFF3_0057') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0058') : _namespace_GFF3O('GFF3_0052') }
+    __parent_properties = { Namespace('http://www.biointerchange.org/gff3o#GFF3_0004') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0026') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0010') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0026') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0012') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0026') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0014') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0026') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0015') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0025') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0021') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0026') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0023') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0025') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0039') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0026') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0045') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0044') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0047') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0026') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0050') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0044') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0056') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0025') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0005') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0028') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0006') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0028') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0007') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0028') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0008') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0028') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0009') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0028') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0011') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0028') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0013') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0029') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0022') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0027') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0024') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0027') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0034') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0028') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0035') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0028') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0036') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0028') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0037') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0028') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0041') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0040') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0042') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0040') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0043') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0040') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0046') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0028') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0048') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0028') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0049') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0028') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0053') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0052') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0054') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0052') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0055') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0052') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0057') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0028') , Namespace('http://www.biointerchange.org/gff3o#GFF3_0058') : Namespace('http://www.biointerchange.org/gff3o#GFF3_0052') }