biointerchange 0.2.0 → 0.2.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
@@ -9,6 +9,13 @@ def _namespace_GFF3O(accession):
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  class GFF3O:
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+ @classmethod
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+ def seqid(cls):
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+ """Establishes the landmark (cls, e.g. a chromosome) on which a feature is located.
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+ (GFF3_0004)
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+ """
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+ return _namespace_GFF3O('GFF3_0004')
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+
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  @classmethod
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  def strand(cls):
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  """Either:
@@ -81,20 +88,6 @@ class GFF3O:
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  """
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  return [ _namespace_GFF3O('GFF3_0026'), _namespace_GFF3O('GFF3_0028') ]
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- @classmethod
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- def dbxref(cls):
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- """A database cross-reference to associate a sequence alteration to its representation in another database.
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- (cls, GFF3_0034)
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- """
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- return _namespace_GFF3O('GFF3_0034')
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-
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- @classmethod
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- def ontology_term(cls):
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- """A cross-reference to an ontology term that is associated with a feature.
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- (cls, GFF3_0035)
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- """
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- return _namespace_GFF3O('GFF3_0035')
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-
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  @classmethod
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  def target(cls):
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  """Identifies the target that the features aligns to.
@@ -121,11 +114,11 @@ class GFF3O:
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  return _namespace_GFF3O('GFF3_0047')
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115
 
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  @classmethod
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- def seqid(cls):
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- """ID of the landmark that establishes the coordinate system for the current feature.
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- (cls, GFF3_0004)
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+ def feature_ontology(cls):
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+ """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.
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+ (cls, GFF3_0056)
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  """
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- return _namespace_GFF3O('GFF3_0004')
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+ return _namespace_GFF3O('GFF3_0056')
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122
 
130
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  @classmethod
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  def source(cls):
@@ -136,7 +129,7 @@ class GFF3O:
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129
 
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  @classmethod
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  def type(cls):
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- """Type of the feature, which is either a term from the "lite" version of the Sequence Ontology (cls, SOFA), a term from the full Sequence Ontology (SO) that is a child of sequence_feature (SO:0000110), or a SOFA or SO accession number.
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+ """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).
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  (GFF3_0006)
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  """
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  return _namespace_GFF3O('GFF3_0006')
@@ -149,8 +142,11 @@ class GFF3O:
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  Or:
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  Start coordinate of the target.
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  (GFF3_0042)
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+ Or:
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+ Genomic start coordinate of the landmark.
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+ (GFF3_0054)
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  """
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- return [ _namespace_GFF3O('GFF3_0007'), _namespace_GFF3O('GFF3_0042') ]
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+ return [ _namespace_GFF3O('GFF3_0007'), _namespace_GFF3O('GFF3_0042'), _namespace_GFF3O('GFF3_0054') ]
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150
 
155
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  @classmethod
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  def end(cls):
@@ -160,8 +156,11 @@ class GFF3O:
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  Or:
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  End coordinate of the target.
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  (GFF3_0043)
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+ Or:
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+ Genomic end coordinate of the landmark.
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+ (GFF3_0055)
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  """
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- return [ _namespace_GFF3O('GFF3_0008'), _namespace_GFF3O('GFF3_0043') ]
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+ return [ _namespace_GFF3O('GFF3_0008'), _namespace_GFF3O('GFF3_0043'), _namespace_GFF3O('GFF3_0055') ]
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164
 
166
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  @classmethod
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  def score(cls):
@@ -206,29 +205,25 @@ class GFF3O:
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  return _namespace_GFF3O('GFF3_0029')
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206
 
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  @classmethod
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- def dbxref_properties(cls):
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- """Properties that are directly associated with DBXRef class instances.
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- (cls, GFF3_0031)
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+ def dbxref(cls):
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+ """A database cross-reference to associate a sequence alteration to its representation in another database.
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+ (cls, GFF3_0034)
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  """
213
- return _namespace_GFF3O('GFF3_0031')
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+ return _namespace_GFF3O('GFF3_0034')
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213
 
215
214
  @classmethod
216
- def name(cls):
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- """Either:
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- Name of an external database. For example, "dbSNP" or "OMIM".
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- (cls, GFF3_0032)
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- Or:
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- Name of a feature, which can be used for display purposes. The name is not a unique property among features.
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- (GFF3_0036)
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+ def ontology_term(cls):
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+ """A cross-reference to an ontology term that is associated with a feature.
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+ (cls, GFF3_0035)
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  """
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- return [ _namespace_GFF3O('GFF3_0032'), _namespace_GFF3O('GFF3_0036') ]
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+ return _namespace_GFF3O('GFF3_0035')
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220
 
226
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  @classmethod
227
- def xref(cls):
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- """External database identifier. For example, for dbSNP, this identifier could be "rs3131969".
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- (cls, GFF3_0033)
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+ def name(cls):
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+ """Name of a feature, which can be used for display purposes. The name is not a unique property among features.
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+ (cls, GFF3_0036)
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  """
231
- return _namespace_GFF3O('GFF3_0033')
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+ return _namespace_GFF3O('GFF3_0036')
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227
 
233
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  @classmethod
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  def alias(cls):
@@ -265,6 +260,31 @@ class GFF3O:
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  """
266
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  return _namespace_GFF3O('GFF3_0049')
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262
 
263
+ @classmethod
264
+ def landmark_properties(cls):
265
+ """Properties that are directly associated with Landmark class instances.
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+ (cls, GFF3_0052)
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+ """
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+ return _namespace_GFF3O('GFF3_0052')
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+
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+ @classmethod
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+ def id(cls):
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+ """ID that uniquely establishes the Landmark's identity within a Set.
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+ (cls, GFF3_0053)
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+ """
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+ return _namespace_GFF3O('GFF3_0053')
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+
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+ @classmethod
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+ def sequence(cls):
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+ """Either:
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+ Sequence associated with this feature, if it has been specified using a FASTA string.
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+ (cls, GFF3_0057)
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+ Or:
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+ Sequence associated with this feature, if it has been specified using a FASTA string.
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+ (GFF3_0058)
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+ """
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+ return [ _namespace_GFF3O('GFF3_0057'), _namespace_GFF3O('GFF3_0058') ]
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+
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  @classmethod
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  def Set(cls):
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  """Set of genomic sequence features, whose identifiers are unique within the set.
@@ -293,13 +313,6 @@ class GFF3O:
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  """
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  return _namespace_GFF3O('GFF3_0016')
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315
 
296
- @classmethod
297
- def DBXRef(cls):
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- """A class describing relationships between features and external databases.
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- (cls, GFF3_0030)
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- """
301
- return _namespace_GFF3O('GFF3_0030')
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-
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316
  @classmethod
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  def Target(cls):
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  """Indicates a feature's "target" of a nucleotide-to-nucleotide or protein-to-nucleotide alignment.
@@ -307,6 +320,13 @@ class GFF3O:
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  """
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  return _namespace_GFF3O('GFF3_0038')
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322
 
323
+ @classmethod
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+ def Landmark(cls):
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+ """A landmark that establishes the coordinate system for features.
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+ (cls, GFF3_0051)
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+ """
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+ return _namespace_GFF3O('GFF3_0051')
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+
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  @classmethod
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  def Positive(cls):
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  """Location on the positive (cls, forward) strand.
@@ -341,6 +361,8 @@ class GFF3O:
341
361
 
342
362
  uri -- URI that is tested for being an object property
343
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  """
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+ if uri == _namespace_GFF3O('GFF3_0004'):
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+ return True
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366
  if uri == _namespace_GFF3O('GFF3_0010'):
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  return True
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  if uri == _namespace_GFF3O('GFF3_0012'):
@@ -357,10 +379,6 @@ class GFF3O:
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  return True
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380
  if uri == _namespace_GFF3O('GFF3_0026'):
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  return True
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- if uri == _namespace_GFF3O('GFF3_0034'):
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- return True
362
- if uri == _namespace_GFF3O('GFF3_0035'):
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- return True
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382
  if uri == _namespace_GFF3O('GFF3_0039'):
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  return True
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384
  if uri == _namespace_GFF3O('GFF3_0044'):
@@ -371,6 +389,8 @@ class GFF3O:
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  return True
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390
  if uri == _namespace_GFF3O('GFF3_0050'):
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  return True
392
+ if uri == _namespace_GFF3O('GFF3_0056'):
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+ return True
374
394
  return False
375
395
 
376
396
  @classmethod
@@ -379,8 +399,6 @@ class GFF3O:
379
399
 
380
400
  uri -- URI that is tested for being a datatype property
381
401
  """
382
- if uri == _namespace_GFF3O('GFF3_0004'):
383
- return True
384
402
  if uri == _namespace_GFF3O('GFF3_0005'):
385
403
  return True
386
404
  if uri == _namespace_GFF3O('GFF3_0006'):
@@ -405,11 +423,9 @@ class GFF3O:
405
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  return True
406
424
  if uri == _namespace_GFF3O('GFF3_0029'):
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  return True
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- if uri == _namespace_GFF3O('GFF3_0031'):
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- return True
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- if uri == _namespace_GFF3O('GFF3_0032'):
426
+ if uri == _namespace_GFF3O('GFF3_0034'):
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427
  return True
412
- if uri == _namespace_GFF3O('GFF3_0033'):
428
+ if uri == _namespace_GFF3O('GFF3_0035'):
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429
  return True
414
430
  if uri == _namespace_GFF3O('GFF3_0036'):
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431
  return True
@@ -429,6 +445,18 @@ class GFF3O:
429
445
  return True
430
446
  if uri == _namespace_GFF3O('GFF3_0049'):
431
447
  return True
448
+ if uri == _namespace_GFF3O('GFF3_0052'):
449
+ return True
450
+ if uri == _namespace_GFF3O('GFF3_0053'):
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+ return True
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+ if uri == _namespace_GFF3O('GFF3_0054'):
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+ return True
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+ if uri == _namespace_GFF3O('GFF3_0055'):
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+ return True
456
+ if uri == _namespace_GFF3O('GFF3_0057'):
457
+ return True
458
+ if uri == _namespace_GFF3O('GFF3_0058'):
459
+ return True
432
460
  return False
433
461
 
434
462
  @classmethod
@@ -445,10 +473,10 @@ class GFF3O:
445
473
  return True
446
474
  if uri == _namespace_GFF3O('GFF3_0016'):
447
475
  return True
448
- if uri == _namespace_GFF3O('GFF3_0030'):
449
- return True
450
476
  if uri == _namespace_GFF3O('GFF3_0038'):
451
477
  return True
478
+ if uri == _namespace_GFF3O('GFF3_0051'):
479
+ return True
452
480
  return False
453
481
 
454
482
  @classmethod
@@ -489,5 +517,5 @@ class GFF3O:
489
517
  return cls.has_parent(cls.__parent_properties[uri], parent)
490
518
  return False
491
519
 
492
- __parent_properties = { _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_0034') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0035') : _namespace_GFF3O('GFF3_0026') , _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_0004') : _namespace_GFF3O('GFF3_0028') , _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_0032') : _namespace_GFF3O('GFF3_0031') , _namespace_GFF3O('GFF3_0033') : _namespace_GFF3O('GFF3_0031') , _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') }
520
+ __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') }
493
521
 
@@ -9,6 +9,17 @@ def _namespace_GVF1O(accession):
9
9
 
10
10
  class GVF1O:
11
11
 
12
+ @classmethod
13
+ def seqid(cls):
14
+ """Either:
15
+ Establishes the landmark (cls, e.g. a chromosome) on which a feature is located.
16
+ (GVF1_0004)
17
+ Or:
18
+ Link to the landmark that establishes the coordinate system for the breakpoint.
19
+ (GVF1_0072)
20
+ """
21
+ return [ _namespace_GVF1O('GVF1_0004'), _namespace_GVF1O('GVF1_0072') ]
22
+
12
23
  @classmethod
13
24
  def strand(cls):
14
25
  """Either:
@@ -25,10 +36,14 @@ class GVF1O:
25
36
 
26
37
  @classmethod
27
38
  def attributes(cls):
28
- """Tag name/value pair attributes of a feature.
29
- (cls, GVF1_0012)
39
+ """Either:
40
+ Tag name/value pair attributes of a feature.
41
+ (cls, GVF1_0012)
42
+ Or:
43
+ Tag name/value pair attributes that are not captured by the GVF specification.
44
+ (GVF1_0152)
30
45
  """
31
- return _namespace_GVF1O('GVF1_0012')
46
+ return [ _namespace_GVF1O('GVF1_0012'), _namespace_GVF1O('GVF1_0152') ]
32
47
 
33
48
  @classmethod
34
49
  def parent(cls):
@@ -107,13 +122,6 @@ class GVF1O:
107
122
  """
108
123
  return _namespace_GVF1O('GVF1_0043')
109
124
 
110
- @classmethod
111
- def feature_id(cls):
112
- """Features that are affected by this sequence alteration effect.
113
- (cls, GVF1_0044)
114
- """
115
- return _namespace_GVF1O('GVF1_0044')
116
-
117
125
  @classmethod
118
126
  def start_range(cls):
119
127
  """A coordinate range for ambiguous start coordinates.
@@ -188,10 +196,14 @@ class GVF1O:
188
196
 
189
197
  @classmethod
190
198
  def effect_properties(cls):
191
- """Properties that are directly associated with Effect class instances.
192
- (cls, GVF1_0070)
199
+ """Either:
200
+ Properties that are directly associated with Effect class instances.
201
+ (cls, GVF1_0070)
202
+ Or:
203
+ Properties that are directly associated with Effect class instances.
204
+ (GVF1_0158)
193
205
  """
194
- return _namespace_GVF1O('GVF1_0070')
206
+ return [ _namespace_GVF1O('GVF1_0070'), _namespace_GVF1O('GVF1_0158') ]
195
207
 
196
208
  @classmethod
197
209
  def breakpoint_properties(cls):
@@ -206,10 +218,14 @@ class GVF1O:
206
218
 
207
219
  @classmethod
208
220
  def dbxref(cls):
209
- """A database cross-reference to associate a sequence alteration to its representation in another database.
210
- (cls, GVF1_0078)
221
+ """Either:
222
+ A database cross-reference to associate a sequence alteration to its representation in another database.
223
+ (cls, GVF1_0078)
224
+ Or:
225
+ A database cross-reference to associate a structured pragma to a representation in another database.
226
+ (GVF1_0104)
211
227
  """
212
- return _namespace_GVF1O('GVF1_0078')
228
+ return [ _namespace_GVF1O('GVF1_0078'), _namespace_GVF1O('GVF1_0104') ]
213
229
 
214
230
  @classmethod
215
231
  def breakpoint(cls):
@@ -230,15 +246,141 @@ class GVF1O:
230
246
  return [ _namespace_GVF1O('GVF1_0089'), _namespace_GVF1O('GVF1_0092') ]
231
247
 
232
248
  @classmethod
233
- def seqid(cls):
249
+ def technologyplatform_properties(cls):
234
250
  """Either:
235
- ID of the landmark that establishes the coordinate system for a feature.
236
- (cls, GVF1_0004)
251
+ Properties that are directly associated with TechnologyPlatform class instances.
252
+ (cls, GVF1_0102)
237
253
  Or:
238
- ID of the landmark that establishes the coordinate system for a breakpoint.
239
- (GVF1_0072)
254
+ Properties that are directly associated with TechnologyPlatform class instances.
255
+ (GVF1_0107)
240
256
  """
241
- return [ _namespace_GVF1O('GVF1_0004'), _namespace_GVF1O('GVF1_0072') ]
257
+ return [ _namespace_GVF1O('GVF1_0102'), _namespace_GVF1O('GVF1_0107') ]
258
+
259
+ @classmethod
260
+ def datasource_properties(cls):
261
+ """Properties that are directly associated with DataSource class instances.
262
+ (cls, GVF1_0103)
263
+ """
264
+ return _namespace_GVF1O('GVF1_0103')
265
+
266
+ @classmethod
267
+ def structuredpragma_properties(cls):
268
+ """Either:
269
+ Properties describing structured pragma properties.
270
+ (cls, GVF1_0112)
271
+ Or:
272
+ Properties describing structured pragma properties.
273
+ (GVF1_0113)
274
+ """
275
+ return [ _namespace_GVF1O('GVF1_0112'), _namespace_GVF1O('GVF1_0113') ]
276
+
277
+ @classmethod
278
+ def read_type(cls):
279
+ """Types of reads produced by the platform.
280
+ (cls, GVF1_0119)
281
+ """
282
+ return _namespace_GVF1O('GVF1_0119')
283
+
284
+ @classmethod
285
+ def data_type(cls):
286
+ """Datatype of this data source.
287
+ (cls, GVF1_0120)
288
+ """
289
+ return _namespace_GVF1O('GVF1_0120')
290
+
291
+ @classmethod
292
+ def technology_platform(cls):
293
+ """Technology platform that was used to derive the feature.
294
+ (cls, GVF1_0121)
295
+ """
296
+ return _namespace_GVF1O('GVF1_0121')
297
+
298
+ @classmethod
299
+ def data_source(cls):
300
+ """Data source origin of the feature.
301
+ (cls, GVF1_0122)
302
+ """
303
+ return _namespace_GVF1O('GVF1_0122')
304
+
305
+ @classmethod
306
+ def score_method(cls):
307
+ """Used scoring method.
308
+ (cls, GVF1_0123)
309
+ """
310
+ return _namespace_GVF1O('GVF1_0123')
311
+
312
+ @classmethod
313
+ def source_method(cls):
314
+ """Further information about the algorithm/methodologies used.
315
+ (cls, GVF1_0124)
316
+ """
317
+ return _namespace_GVF1O('GVF1_0124')
318
+
319
+ @classmethod
320
+ def phenotype_description(cls):
321
+ """Further information about an individual's phenotype. Applies only to single individual sets.
322
+ (cls, GVF1_0125)
323
+ """
324
+ return _namespace_GVF1O('GVF1_0125')
325
+
326
+ @classmethod
327
+ def attribute_method(cls):
328
+ """Either:
329
+ Further information about the associated attribute(cls, s).
330
+ (GVF1_0126)
331
+ Or:
332
+ Further information about the associated attribute(s).
333
+ (GVF1_0127)
334
+ Or:
335
+ Further information about the associated attribute(s).
336
+ (GVF1_0129)
337
+ Or:
338
+ Further information about the associated attribute(s).
339
+ (GVF1_0130)
340
+ Or:
341
+ Further information about the associated attribute(s).
342
+ (GVF1_0131)
343
+ """
344
+ return [ _namespace_GVF1O('GVF1_0126'), _namespace_GVF1O('GVF1_0127'), _namespace_GVF1O('GVF1_0129'), _namespace_GVF1O('GVF1_0130'), _namespace_GVF1O('GVF1_0131') ]
345
+
346
+ @classmethod
347
+ def attribute_properties(cls):
348
+ """Either:
349
+ Properties about Attribute instances.
350
+ (cls, GVF1_0128)
351
+ Or:
352
+ Properties that are directly associated with Attribute class instances.
353
+ (GVF1_0064)
354
+ """
355
+ return [ _namespace_GVF1O('GVF1_0128'), _namespace_GVF1O('GVF1_0064') ]
356
+
357
+ @classmethod
358
+ def sex(cls):
359
+ """Denotes the sex of the sequenced individual for single-individual sets.
360
+ (cls, GVF1_0147)
361
+ """
362
+ return _namespace_GVF1O('GVF1_0147')
363
+
364
+ @classmethod
365
+ def genomic_source(cls):
366
+ """Denotes the source of genomic data (cls, on a cell-type level).
367
+ (GVF1_0148)
368
+ """
369
+ return _namespace_GVF1O('GVF1_0148')
370
+
371
+ @classmethod
372
+ def feature_ontology(cls):
373
+ """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.
374
+ (cls, GVF1_0150)
375
+ """
376
+ return _namespace_GVF1O('GVF1_0150')
377
+
378
+ @classmethod
379
+ def target(cls):
380
+ """Identifies the target that the features aligns to.
381
+ (cls, GVF1_0155)
382
+ """
383
+ return _namespace_GVF1O('GVF1_0155')
242
384
 
243
385
  @classmethod
244
386
  def source(cls):
@@ -249,7 +391,7 @@ class GVF1O:
249
391
 
250
392
  @classmethod
251
393
  def type(cls):
252
- """Type of the feature, which is either a term from the "lite" version of the Sequence Ontology (cls, SOFA), a term from the full Sequence Ontology (SO) that is a child of sequence_feature (SO:0000110), or a SOFA or SO accession number.
394
+ """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).
253
395
  (GVF1_0006)
254
396
  """
255
397
  return _namespace_GVF1O('GVF1_0006')
@@ -268,8 +410,11 @@ class GVF1O:
268
410
  Or:
269
411
  Start coordinate of the target.
270
412
  (GVF1_0094)
413
+ Or:
414
+ Genomic start coordinate of the landmark.
415
+ (GVF1_0138)
271
416
  """
272
- return [ _namespace_GVF1O('GVF1_0007'), _namespace_GVF1O('GVF1_0048'), _namespace_GVF1O('GVF1_0073'), _namespace_GVF1O('GVF1_0094') ]
417
+ return [ _namespace_GVF1O('GVF1_0007'), _namespace_GVF1O('GVF1_0048'), _namespace_GVF1O('GVF1_0073'), _namespace_GVF1O('GVF1_0094'), _namespace_GVF1O('GVF1_0138') ]
273
418
 
274
419
  @classmethod
275
420
  def end(cls):
@@ -285,8 +430,11 @@ class GVF1O:
285
430
  Or:
286
431
  End coordinate of the target.
287
432
  (GVF1_0095)
433
+ Or:
434
+ Genomic end coordinate of the landmark.
435
+ (GVF1_0139)
288
436
  """
289
- return [ _namespace_GVF1O('GVF1_0008'), _namespace_GVF1O('GVF1_0049'), _namespace_GVF1O('GVF1_0074'), _namespace_GVF1O('GVF1_0095') ]
437
+ return [ _namespace_GVF1O('GVF1_0008'), _namespace_GVF1O('GVF1_0049'), _namespace_GVF1O('GVF1_0074'), _namespace_GVF1O('GVF1_0095'), _namespace_GVF1O('GVF1_0139') ]
290
438
 
291
439
  @classmethod
292
440
  def score(cls):
@@ -297,10 +445,14 @@ class GVF1O:
297
445
 
298
446
  @classmethod
299
447
  def tag(cls):
300
- """Tag name of a feature attribute.
301
- (cls, GVF1_0013)
448
+ """Either:
449
+ Tag name of a feature attribute.
450
+ (cls, GVF1_0013)
451
+ Or:
452
+ Tag name of an user defined structured attribute.
453
+ (GVF1_0154)
302
454
  """
303
- return _namespace_GVF1O('GVF1_0013')
455
+ return [ _namespace_GVF1O('GVF1_0013'), _namespace_GVF1O('GVF1_0154') ]
304
456
 
305
457
  @classmethod
306
458
  def gvf_version(cls):
@@ -325,10 +477,14 @@ class GVF1O:
325
477
 
326
478
  @classmethod
327
479
  def id(cls):
328
- """A unique identifier for the feature within the feature set.
329
- (cls, GVF1_0026)
480
+ """Either:
481
+ A unique identifier for the feature within the feature set.
482
+ (cls, GVF1_0026)
483
+ Or:
484
+ ID that uniquely establishes the Landmark's identity within a Set.
485
+ (GVF1_0137)
330
486
  """
331
- return _namespace_GVF1O('GVF1_0026')
487
+ return [ _namespace_GVF1O('GVF1_0026'), _namespace_GVF1O('GVF1_0137') ]
332
488
 
333
489
  @classmethod
334
490
  def alias(cls):
@@ -337,20 +493,6 @@ class GVF1O:
337
493
  """
338
494
  return _namespace_GVF1O('GVF1_0027')
339
495
 
340
- @classmethod
341
- def name(cls):
342
- """Name of an external database. For example, "dbSNP" or "OMIM".
343
- (cls, GVF1_0029)
344
- """
345
- return _namespace_GVF1O('GVF1_0029')
346
-
347
- @classmethod
348
- def xref(cls):
349
- """External database identifier. For example, for dbSNP, this identifier could be "rs3131969".
350
- (cls, GVF1_0030)
351
- """
352
- return _namespace_GVF1O('GVF1_0030')
353
-
354
496
  @classmethod
355
497
  def reference_seq(cls):
356
498
  """Sequence from the reference genome.
@@ -379,12 +521,23 @@ class GVF1O:
379
521
  """
380
522
  return _namespace_GVF1O('GVF1_0039')
381
523
 
524
+ @classmethod
525
+ def feature(cls):
526
+ """Features that are affected by this sequence alteration effect. This can be an external feature identifier, such as an Ensembl gene/transcript identifier.
527
+ (cls, GVF1_0044)
528
+ """
529
+ return _namespace_GVF1O('GVF1_0044')
530
+
382
531
  @classmethod
383
532
  def phased(cls):
384
- """Unclear from GVF specification.
385
- (cls, GVF1_0050)
533
+ """Either:
534
+ Unclear from GVF specification.
535
+ (cls, GVF1_0050)
536
+ Or:
537
+ Indicates whether this particular is phased. Used to encode ##phased-genotypes statements.
538
+ (GVF1_0101)
386
539
  """
387
- return _namespace_GVF1O('GVF1_0050')
540
+ return [ _namespace_GVF1O('GVF1_0050'), _namespace_GVF1O('GVF1_0101') ]
388
541
 
389
542
  @classmethod
390
543
  def variant_codon(cls):
@@ -421,20 +574,6 @@ class GVF1O:
421
574
  """
422
575
  return _namespace_GVF1O('GVF1_0061')
423
576
 
424
- @classmethod
425
- def dbxref_properties(cls):
426
- """Properties that are directly associated with DBXRef class instances.
427
- (cls, GVF1_0062)
428
- """
429
- return _namespace_GVF1O('GVF1_0062')
430
-
431
- @classmethod
432
- def attribute_properties(cls):
433
- """Properties that are directly associated with Attribute class instances.
434
- (cls, GVF1_0064)
435
- """
436
- return _namespace_GVF1O('GVF1_0064')
437
-
438
577
  @classmethod
439
578
  def a_context(cls):
440
579
  """Sequence context (cls, positive strand) of a feature on the 5' end.
@@ -463,6 +602,87 @@ class GVF1O:
463
602
  """
464
603
  return _namespace_GVF1O('GVF1_0093')
465
604
 
605
+ @classmethod
606
+ def ontology_term(cls):
607
+ """A cross-reference to an ontology term that is associated with a feature.
608
+ (cls, GVF1_0096)
609
+ """
610
+ return _namespace_GVF1O('GVF1_0096')
611
+
612
+ @classmethod
613
+ def comment(cls):
614
+ """An arbitrary comment. Free text.
615
+ (cls, GVF1_0105)
616
+ """
617
+ return _namespace_GVF1O('GVF1_0105')
618
+
619
+ @classmethod
620
+ def platform_class(cls):
621
+ """Type of technology used to gather the variant data. Unrestricted range due to open specification.
622
+ (cls, GVF1_0106)
623
+ """
624
+ return _namespace_GVF1O('GVF1_0106')
625
+
626
+ @classmethod
627
+ def platform_name(cls):
628
+ """Sequencer or other machine used to collect the variant data. Unrestricted range due to open specification.
629
+ (cls, GVF1_0108)
630
+ """
631
+ return _namespace_GVF1O('GVF1_0108')
632
+
633
+ @classmethod
634
+ def read_length(cls):
635
+ """Undocumented in GVF specification.
636
+ (cls, GVF1_0132)
637
+ """
638
+ return _namespace_GVF1O('GVF1_0132')
639
+
640
+ @classmethod
641
+ def read_pair_span(cls):
642
+ """Undocumented in GVF specification.
643
+ (cls, GVF1_0133)
644
+ """
645
+ return _namespace_GVF1O('GVF1_0133')
646
+
647
+ @classmethod
648
+ def average_coverage(cls):
649
+ """Undocumented in GVF specification.
650
+ (cls, GVF1_0134)
651
+ """
652
+ return _namespace_GVF1O('GVF1_0134')
653
+
654
+ @classmethod
655
+ def landmark_properties(cls):
656
+ """Properties that are directly associated with Landmark class instances.
657
+ (cls, GVF1_0136)
658
+ """
659
+ return _namespace_GVF1O('GVF1_0136')
660
+
661
+ @classmethod
662
+ def file_version(cls):
663
+ """Version of the GVF file that this set stems from.
664
+ (cls, GVF1_0149)
665
+ """
666
+ return _namespace_GVF1O('GVF1_0149')
667
+
668
+ @classmethod
669
+ def structuredattribute_properties(cls):
670
+ """Properties that are directly associated with StructuredAttribute class instances.
671
+ (cls, GVF1_0153)
672
+ """
673
+ return _namespace_GVF1O('GVF1_0153')
674
+
675
+ @classmethod
676
+ def sequence(cls):
677
+ """Either:
678
+ Sequence associated with this feature, if it has been specified using a FASTA string.
679
+ (cls, GVF1_0156)
680
+ Or:
681
+ Sequence associated with this feature, if it has been specified using a FASTA string.
682
+ (GVF1_0157)
683
+ """
684
+ return [ _namespace_GVF1O('GVF1_0156'), _namespace_GVF1O('GVF1_0157') ]
685
+
466
686
  @classmethod
467
687
  def Set(cls):
468
688
  """Set of genomic sequence features, whose identifiers are unique within the set.
@@ -479,6 +699,9 @@ class GVF1O:
479
699
 
480
700
  @classmethod
481
701
  def Attribute(cls):
702
+ """Representation of attribute tag/value pairs that are not covered by specific classes such as Effect or Variant.
703
+ (cls, GVF1_0003)
704
+ """
482
705
  return _namespace_GVF1O('GVF1_0003')
483
706
 
484
707
  @classmethod
@@ -488,13 +711,6 @@ class GVF1O:
488
711
  """
489
712
  return _namespace_GVF1O('GVF1_0016')
490
713
 
491
- @classmethod
492
- def DBXRef(cls):
493
- """A class describing relationships between features and external databases.
494
- (cls, GVF1_0028)
495
- """
496
- return _namespace_GVF1O('GVF1_0028')
497
-
498
714
  @classmethod
499
715
  def Variant(cls):
500
716
  """Describing specific alterations of a feature.
@@ -551,6 +767,76 @@ class GVF1O:
551
767
  """
552
768
  return _namespace_GVF1O('GVF1_0088')
553
769
 
770
+ @classmethod
771
+ def TechnologyPlatform(cls):
772
+ """Details about the sequencing/microarray technology used to gather the data in a set.
773
+ (cls, GVF1_0097)
774
+ """
775
+ return _namespace_GVF1O('GVF1_0097')
776
+
777
+ @classmethod
778
+ def DataSource(cls):
779
+ """Provides information about the source of the data. For example, it can link out to actual sequences associated with the Feature individuals in a Set.
780
+ (cls, GVF1_0098)
781
+ """
782
+ return _namespace_GVF1O('GVF1_0098')
783
+
784
+ @classmethod
785
+ def Method(cls):
786
+ """Information about the used scoring algorithm or method.
787
+ (cls, GVF1_0099)
788
+ """
789
+ return _namespace_GVF1O('GVF1_0099')
790
+
791
+ @classmethod
792
+ def PhenotypeDescription(cls):
793
+ """Additional information about an individual's phenotype.
794
+ (cls, GVF1_0100)
795
+ """
796
+ return _namespace_GVF1O('GVF1_0100')
797
+
798
+ @classmethod
799
+ def ReadType(cls):
800
+ """Type of reads obtained for a given technology platform.
801
+ (cls, GVF1_0109)
802
+ """
803
+ return _namespace_GVF1O('GVF1_0109')
804
+
805
+ @classmethod
806
+ def DataType(cls):
807
+ """Determines the datatype of a variant sequence.
808
+ (cls, GVF1_0114)
809
+ """
810
+ return _namespace_GVF1O('GVF1_0114')
811
+
812
+ @classmethod
813
+ def Landmark(cls):
814
+ """A landmark that establishes the coordinate system for features.
815
+ (cls, GVF1_0135)
816
+ """
817
+ return _namespace_GVF1O('GVF1_0135')
818
+
819
+ @classmethod
820
+ def Sex(cls):
821
+ """For single individual sets, the Sex class' OWL-individuals can be used to specify the sex of the sequenced (cls, real-life) individuals.
822
+ (GVF1_0140)
823
+ """
824
+ return _namespace_GVF1O('GVF1_0140')
825
+
826
+ @classmethod
827
+ def GenomicSource(cls):
828
+ """An enumerated class for determining the genomic source (cls, cell type) of sequenced data.
829
+ (GVF1_0141)
830
+ """
831
+ return _namespace_GVF1O('GVF1_0141')
832
+
833
+ @classmethod
834
+ def StructuredAttribute(cls):
835
+ """Representation of attribute tag/value pairs that are specific to particular structured attributes, but which are not covered by the GVF specification.
836
+ (cls, GVF1_0151)
837
+ """
838
+ return _namespace_GVF1O('GVF1_0151')
839
+
554
840
  @classmethod
555
841
  def Positive(cls):
556
842
  """Location on the positive (cls, forward) strand.
@@ -600,12 +886,91 @@ class GVF1O:
600
886
  """
601
887
  return _namespace_GVF1O('GVF1_0087')
602
888
 
889
+ @classmethod
890
+ def Fragment(cls):
891
+ """Denotes reads that are fragments.
892
+ (cls, GVF1_0110)
893
+ """
894
+ return _namespace_GVF1O('GVF1_0110')
895
+
896
+ @classmethod
897
+ def Pair(cls):
898
+ """Denotes reads that are pairs.
899
+ (cls, GVF1_0111)
900
+ """
901
+ return _namespace_GVF1O('GVF1_0111')
902
+
903
+ @classmethod
904
+ def DNASequence(cls):
905
+ """Denotes a DNA sequence.
906
+ (cls, GVF1_0115)
907
+ """
908
+ return _namespace_GVF1O('GVF1_0115')
909
+
910
+ @classmethod
911
+ def RNASequence(cls):
912
+ """Denotes an RNA sequence.
913
+ (cls, GVF1_0116)
914
+ """
915
+ return _namespace_GVF1O('GVF1_0116')
916
+
917
+ @classmethod
918
+ def DNAMicroarray(cls):
919
+ """Denotes a DNA microarray probe.
920
+ (cls, GVF1_0117)
921
+ """
922
+ return _namespace_GVF1O('GVF1_0117')
923
+
924
+ @classmethod
925
+ def ArrayComparativeGenomicHybridization(cls):
926
+ """Denotes an array-comparative genomic hybridization.
927
+ (cls, GVF1_0118)
928
+ """
929
+ return _namespace_GVF1O('GVF1_0118')
930
+
931
+ @classmethod
932
+ def Female(cls):
933
+ """Denotes that a Set contains features of a female.
934
+ (cls, GVF1_0142)
935
+ """
936
+ return _namespace_GVF1O('GVF1_0142')
937
+
938
+ @classmethod
939
+ def Male(cls):
940
+ """Denotes that a Set contains features of a male.
941
+ (cls, GVF1_0143)
942
+ """
943
+ return _namespace_GVF1O('GVF1_0143')
944
+
945
+ @classmethod
946
+ def Prenatal(cls):
947
+ """Denotes that a set contains features of prenatal cells.
948
+ (cls, GVF1_0144)
949
+ """
950
+ return _namespace_GVF1O('GVF1_0144')
951
+
952
+ @classmethod
953
+ def Germline(cls):
954
+ """Denotes that a set contains features of germline cells.
955
+ (cls, GVF1_0145)
956
+ """
957
+ return _namespace_GVF1O('GVF1_0145')
958
+
959
+ @classmethod
960
+ def Somatic(cls):
961
+ """Denotes that a set contains features of somatic cells.
962
+ (cls, GVF1_0146)
963
+ """
964
+ return _namespace_GVF1O('GVF1_0146')
965
+
603
966
  @classmethod
604
967
  def is_object_property(cls, uri):
605
968
  """Determines whether the given URI is an object property.
606
969
 
607
970
  uri -- URI that is tested for being an object property
608
971
  """
972
+ if uri == _namespace_GVF1O('GVF1_0004'):
973
+ return True
609
974
  if uri == _namespace_GVF1O('GVF1_0010'):
610
975
  return True
611
976
  if uri == _namespace_GVF1O('GVF1_0012'):
@@ -630,8 +995,6 @@ class GVF1O:
630
995
  return True
631
996
  if uri == _namespace_GVF1O('GVF1_0043'):
632
997
  return True
633
- if uri == _namespace_GVF1O('GVF1_0044'):
634
- return True
635
998
  if uri == _namespace_GVF1O('GVF1_0046'):
636
999
  return True
637
1000
  if uri == _namespace_GVF1O('GVF1_0047'):
@@ -650,6 +1013,8 @@ class GVF1O:
650
1013
  return True
651
1014
  if uri == _namespace_GVF1O('GVF1_0070'):
652
1015
  return True
1016
+ if uri == _namespace_GVF1O('GVF1_0072'):
1017
+ return True
653
1018
  if uri == _namespace_GVF1O('GVF1_0075'):
654
1019
  return True
655
1020
  if uri == _namespace_GVF1O('GVF1_0078'):
@@ -666,6 +1031,50 @@ class GVF1O:
666
1031
  return True
667
1032
  if uri == _namespace_GVF1O('GVF1_0091'):
668
1033
  return True
1034
+ if uri == _namespace_GVF1O('GVF1_0102'):
1035
+ return True
1036
+ if uri == _namespace_GVF1O('GVF1_0103'):
1037
+ return True
1038
+ if uri == _namespace_GVF1O('GVF1_0104'):
1039
+ return True
1040
+ if uri == _namespace_GVF1O('GVF1_0112'):
1041
+ return True
1042
+ if uri == _namespace_GVF1O('GVF1_0119'):
1043
+ return True
1044
+ if uri == _namespace_GVF1O('GVF1_0120'):
1045
+ return True
1046
+ if uri == _namespace_GVF1O('GVF1_0121'):
1047
+ return True
1048
+ if uri == _namespace_GVF1O('GVF1_0122'):
1049
+ return True
1050
+ if uri == _namespace_GVF1O('GVF1_0123'):
1051
+ return True
1052
+ if uri == _namespace_GVF1O('GVF1_0124'):
1053
+ return True
1054
+ if uri == _namespace_GVF1O('GVF1_0125'):
1055
+ return True
1056
+ if uri == _namespace_GVF1O('GVF1_0126'):
1057
+ return True
1058
+ if uri == _namespace_GVF1O('GVF1_0127'):
1059
+ return True
1060
+ if uri == _namespace_GVF1O('GVF1_0128'):
1061
+ return True
1062
+ if uri == _namespace_GVF1O('GVF1_0129'):
1063
+ return True
1064
+ if uri == _namespace_GVF1O('GVF1_0130'):
1065
+ return True
1066
+ if uri == _namespace_GVF1O('GVF1_0131'):
1067
+ return True
1068
+ if uri == _namespace_GVF1O('GVF1_0147'):
1069
+ return True
1070
+ if uri == _namespace_GVF1O('GVF1_0148'):
1071
+ return True
1072
+ if uri == _namespace_GVF1O('GVF1_0150'):
1073
+ return True
1074
+ if uri == _namespace_GVF1O('GVF1_0152'):
1075
+ return True
1076
+ if uri == _namespace_GVF1O('GVF1_0155'):
1077
+ return True
669
1078
  return False
670
1079
 
671
1080
  @classmethod
@@ -674,8 +1083,6 @@ class GVF1O:
674
1083
 
675
1084
  uri -- URI that is tested for being a datatype property
676
1085
  """
677
- if uri == _namespace_GVF1O('GVF1_0004'):
678
- return True
679
1086
  if uri == _namespace_GVF1O('GVF1_0005'):
680
1087
  return True
681
1088
  if uri == _namespace_GVF1O('GVF1_0006'):
@@ -698,10 +1105,6 @@ class GVF1O:
698
1105
  return True
699
1106
  if uri == _namespace_GVF1O('GVF1_0027'):
700
1107
  return True
701
- if uri == _namespace_GVF1O('GVF1_0029'):
702
- return True
703
- if uri == _namespace_GVF1O('GVF1_0030'):
704
- return True
705
1108
  if uri == _namespace_GVF1O('GVF1_0031'):
706
1109
  return True
707
1110
  if uri == _namespace_GVF1O('GVF1_0032'):
@@ -710,6 +1113,8 @@ class GVF1O:
710
1113
  return True
711
1114
  if uri == _namespace_GVF1O('GVF1_0039'):
712
1115
  return True
1116
+ if uri == _namespace_GVF1O('GVF1_0044'):
1117
+ return True
713
1118
  if uri == _namespace_GVF1O('GVF1_0048'):
714
1119
  return True
715
1120
  if uri == _namespace_GVF1O('GVF1_0049'):
@@ -730,8 +1135,6 @@ class GVF1O:
730
1135
  return True
731
1136
  if uri == _namespace_GVF1O('GVF1_0061'):
732
1137
  return True
733
- if uri == _namespace_GVF1O('GVF1_0062'):
734
- return True
735
1138
  if uri == _namespace_GVF1O('GVF1_0063'):
736
1139
  return True
737
1140
  if uri == _namespace_GVF1O('GVF1_0064'):
@@ -740,8 +1143,6 @@ class GVF1O:
740
1143
  return True
741
1144
  if uri == _namespace_GVF1O('GVF1_0071'):
742
1145
  return True
743
- if uri == _namespace_GVF1O('GVF1_0072'):
744
- return True
745
1146
  if uri == _namespace_GVF1O('GVF1_0073'):
746
1147
  return True
747
1148
  if uri == _namespace_GVF1O('GVF1_0074'):
@@ -762,6 +1163,46 @@ class GVF1O:
762
1163
  return True
763
1164
  if uri == _namespace_GVF1O('GVF1_0095'):
764
1165
  return True
1166
+ if uri == _namespace_GVF1O('GVF1_0096'):
1167
+ return True
1168
+ if uri == _namespace_GVF1O('GVF1_0101'):
1169
+ return True
1170
+ if uri == _namespace_GVF1O('GVF1_0105'):
1171
+ return True
1172
+ if uri == _namespace_GVF1O('GVF1_0106'):
1173
+ return True
1174
+ if uri == _namespace_GVF1O('GVF1_0107'):
1175
+ return True
1176
+ if uri == _namespace_GVF1O('GVF1_0108'):
1177
+ return True
1178
+ if uri == _namespace_GVF1O('GVF1_0113'):
1179
+ return True
1180
+ if uri == _namespace_GVF1O('GVF1_0132'):
1181
+ return True
1182
+ if uri == _namespace_GVF1O('GVF1_0133'):
1183
+ return True
1184
+ if uri == _namespace_GVF1O('GVF1_0134'):
1185
+ return True
1186
+ if uri == _namespace_GVF1O('GVF1_0136'):
1187
+ return True
1188
+ if uri == _namespace_GVF1O('GVF1_0137'):
1189
+ return True
1190
+ if uri == _namespace_GVF1O('GVF1_0138'):
1191
+ return True
1192
+ if uri == _namespace_GVF1O('GVF1_0139'):
1193
+ return True
1194
+ if uri == _namespace_GVF1O('GVF1_0149'):
1195
+ return True
1196
+ if uri == _namespace_GVF1O('GVF1_0153'):
1197
+ return True
1198
+ if uri == _namespace_GVF1O('GVF1_0154'):
1199
+ return True
1200
+ if uri == _namespace_GVF1O('GVF1_0156'):
1201
+ return True
1202
+ if uri == _namespace_GVF1O('GVF1_0157'):
1203
+ return True
1204
+ if uri == _namespace_GVF1O('GVF1_0158'):
1205
+ return True
765
1206
  return False
766
1207
 
767
1208
  @classmethod
@@ -778,8 +1219,6 @@ class GVF1O:
778
1219
  return True
779
1220
  if uri == _namespace_GVF1O('GVF1_0016'):
780
1221
  return True
781
- if uri == _namespace_GVF1O('GVF1_0028'):
782
- return True
783
1222
  if uri == _namespace_GVF1O('GVF1_0033'):
784
1223
  return True
785
1224
  if uri == _namespace_GVF1O('GVF1_0035'):
@@ -796,6 +1235,26 @@ class GVF1O:
796
1235
  return True
797
1236
  if uri == _namespace_GVF1O('GVF1_0088'):
798
1237
  return True
1238
+ if uri == _namespace_GVF1O('GVF1_0097'):
1239
+ return True
1240
+ if uri == _namespace_GVF1O('GVF1_0098'):
1241
+ return True
1242
+ if uri == _namespace_GVF1O('GVF1_0099'):
1243
+ return True
1244
+ if uri == _namespace_GVF1O('GVF1_0100'):
1245
+ return True
1246
+ if uri == _namespace_GVF1O('GVF1_0109'):
1247
+ return True
1248
+ if uri == _namespace_GVF1O('GVF1_0114'):
1249
+ return True
1250
+ if uri == _namespace_GVF1O('GVF1_0135'):
1251
+ return True
1252
+ if uri == _namespace_GVF1O('GVF1_0140'):
1253
+ return True
1254
+ if uri == _namespace_GVF1O('GVF1_0141'):
1255
+ return True
1256
+ if uri == _namespace_GVF1O('GVF1_0151'):
1257
+ return True
799
1258
  return False
800
1259
 
801
1260
  @classmethod
@@ -818,6 +1277,28 @@ class GVF1O:
818
1277
  return True
819
1278
  if uri == _namespace_GVF1O('GVF1_0087'):
820
1279
  return True
1280
+ if uri == _namespace_GVF1O('GVF1_0110'):
1281
+ return True
1282
+ if uri == _namespace_GVF1O('GVF1_0111'):
1283
+ return True
1284
+ if uri == _namespace_GVF1O('GVF1_0115'):
1285
+ return True
1286
+ if uri == _namespace_GVF1O('GVF1_0116'):
1287
+ return True
1288
+ if uri == _namespace_GVF1O('GVF1_0117'):
1289
+ return True
1290
+ if uri == _namespace_GVF1O('GVF1_0118'):
1291
+ return True
1292
+ if uri == _namespace_GVF1O('GVF1_0142'):
1293
+ return True
1294
+ if uri == _namespace_GVF1O('GVF1_0143'):
1295
+ return True
1296
+ if uri == _namespace_GVF1O('GVF1_0144'):
1297
+ return True
1298
+ if uri == _namespace_GVF1O('GVF1_0145'):
1299
+ return True
1300
+ if uri == _namespace_GVF1O('GVF1_0146'):
1301
+ return True
821
1302
  return False
822
1303
 
823
1304
  @classmethod
@@ -842,5 +1323,5 @@ class GVF1O:
842
1323
  return cls.has_parent(cls.__parent_properties[uri], parent)
843
1324
  return False
844
1325
 
845
- __parent_properties = { _namespace_GVF1O('GVF1_0010') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0012') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0014') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0015') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0021') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0023') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0034') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0036') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0038') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0041') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0042') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0043') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0044') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0046') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0047') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0051') : _namespace_GVF1O('GVF1_0067') , _namespace_GVF1O('GVF1_0053') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0078') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0079') : _namespace_GVF1O('GVF1_0075') , _namespace_GVF1O('GVF1_0080') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0083') : _namespace_GVF1O('GVF1_0075') , _namespace_GVF1O('GVF1_0090') : _namespace_GVF1O('GVF1_0089') , _namespace_GVF1O('GVF1_0091') : _namespace_GVF1O('GVF1_0089') , _namespace_GVF1O('GVF1_0004') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0005') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0006') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0007') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0008') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0009') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0013') : _namespace_GVF1O('GVF1_0064') , _namespace_GVF1O('GVF1_0022') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0024') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0025') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0026') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0027') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0029') : _namespace_GVF1O('GVF1_0062') , _namespace_GVF1O('GVF1_0030') : _namespace_GVF1O('GVF1_0062') , _namespace_GVF1O('GVF1_0031') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0032') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0037') : _namespace_GVF1O('GVF1_0065') , _namespace_GVF1O('GVF1_0039') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0048') : _namespace_GVF1O('GVF1_0061') , _namespace_GVF1O('GVF1_0049') : _namespace_GVF1O('GVF1_0061') , _namespace_GVF1O('GVF1_0050') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0054') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0055') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0056') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0057') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0072') : _namespace_GVF1O('GVF1_0071') , _namespace_GVF1O('GVF1_0073') : _namespace_GVF1O('GVF1_0071') , _namespace_GVF1O('GVF1_0074') : _namespace_GVF1O('GVF1_0071') , _namespace_GVF1O('GVF1_0076') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0077') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0081') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0082') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0093') : _namespace_GVF1O('GVF1_0092') , _namespace_GVF1O('GVF1_0094') : _namespace_GVF1O('GVF1_0092') , _namespace_GVF1O('GVF1_0095') : _namespace_GVF1O('GVF1_0092') , _namespace_GVF1O('GVF1_0088') : _namespace_GVF1O('http://www.w3.org/2002/07/owl#Thing') }
1326
+ __parent_properties = { _namespace_GVF1O('GVF1_0004') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0010') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0012') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0014') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0015') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0021') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0023') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0034') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0036') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0038') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0041') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0042') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0043') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0046') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0047') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0051') : _namespace_GVF1O('GVF1_0067') , _namespace_GVF1O('GVF1_0053') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0072') : _namespace_GVF1O('GVF1_0075') , _namespace_GVF1O('GVF1_0078') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0079') : _namespace_GVF1O('GVF1_0075') , _namespace_GVF1O('GVF1_0080') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0083') : _namespace_GVF1O('GVF1_0075') , _namespace_GVF1O('GVF1_0090') : _namespace_GVF1O('GVF1_0089') , _namespace_GVF1O('GVF1_0091') : _namespace_GVF1O('GVF1_0089') , _namespace_GVF1O('GVF1_0102') : _namespace_GVF1O('GVF1_0112') , _namespace_GVF1O('GVF1_0103') : _namespace_GVF1O('GVF1_0112') , _namespace_GVF1O('GVF1_0104') : _namespace_GVF1O('GVF1_0112') , _namespace_GVF1O('GVF1_0119') : _namespace_GVF1O('GVF1_0102') , _namespace_GVF1O('GVF1_0120') : _namespace_GVF1O('GVF1_0103') , _namespace_GVF1O('GVF1_0121') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0122') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0123') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0124') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0125') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0126') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0127') : _namespace_GVF1O('GVF1_0075') , _namespace_GVF1O('GVF1_0129') : _namespace_GVF1O('GVF1_0128') , _namespace_GVF1O('GVF1_0130') : _namespace_GVF1O('GVF1_0089') , _namespace_GVF1O('GVF1_0131') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0147') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0148') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0150') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0152') : _namespace_GVF1O('GVF1_0112') , _namespace_GVF1O('GVF1_0155') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0005') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0006') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0007') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0008') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0009') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0013') : _namespace_GVF1O('GVF1_0064') , _namespace_GVF1O('GVF1_0022') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0024') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0025') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0026') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0027') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0031') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0032') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0037') : _namespace_GVF1O('GVF1_0065') , _namespace_GVF1O('GVF1_0039') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0044') : _namespace_GVF1O('GVF1_0158') , _namespace_GVF1O('GVF1_0048') : _namespace_GVF1O('GVF1_0061') , _namespace_GVF1O('GVF1_0049') : _namespace_GVF1O('GVF1_0061') , _namespace_GVF1O('GVF1_0050') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0054') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0055') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0056') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0057') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0073') : _namespace_GVF1O('GVF1_0071') , _namespace_GVF1O('GVF1_0074') : _namespace_GVF1O('GVF1_0071') , _namespace_GVF1O('GVF1_0076') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0077') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0081') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0082') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0093') : _namespace_GVF1O('GVF1_0092') , _namespace_GVF1O('GVF1_0094') : _namespace_GVF1O('GVF1_0092') , _namespace_GVF1O('GVF1_0095') : _namespace_GVF1O('GVF1_0092') , _namespace_GVF1O('GVF1_0096') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0101') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0105') : _namespace_GVF1O('GVF1_0113') , _namespace_GVF1O('GVF1_0106') : _namespace_GVF1O('GVF1_0107') , _namespace_GVF1O('GVF1_0107') : _namespace_GVF1O('GVF1_0113') , _namespace_GVF1O('GVF1_0108') : _namespace_GVF1O('GVF1_0107') , _namespace_GVF1O('GVF1_0132') : _namespace_GVF1O('GVF1_0107') , _namespace_GVF1O('GVF1_0133') : _namespace_GVF1O('GVF1_0107') , _namespace_GVF1O('GVF1_0134') : _namespace_GVF1O('GVF1_0107') , _namespace_GVF1O('GVF1_0137') : _namespace_GVF1O('GVF1_0136') , _namespace_GVF1O('GVF1_0138') : _namespace_GVF1O('GVF1_0136') , _namespace_GVF1O('GVF1_0139') : _namespace_GVF1O('GVF1_0136') , _namespace_GVF1O('GVF1_0149') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0154') : _namespace_GVF1O('GVF1_0153') , _namespace_GVF1O('GVF1_0156') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0157') : _namespace_GVF1O('GVF1_0136') , _namespace_GVF1O('GVF1_0088') : _namespace_GVF1O('http://www.w3.org/2002/07/owl#Thing') , _namespace_GVF1O('GVF1_0151') : _namespace_GVF1O('http://www.w3.org/2002/07/owl#Thing') }
846
1327