biointerchange 0.1.0 → 0.1.2

data/supplemental/python/biointerchange/gvf1o.py

@@ -0,0 +1,864 @@
+import rdflib
+
+from rdflib import Namespace
+
+__namespace_GVF1O = Namespace('http://www.biointerchange.org/gvf1o#')
+
+def _namespace_GVF1O(accession):
+    return __namespace_GVF1O[accession]
+
+class GVF1O:
+
+    @classmethod
+    def strand(cls):
+        """Strand of the feature.
+        (cls, GVF1_0010)
+        """
+        return _namespace_GVF1O('GVF1_0010')
+
+    @classmethod
+    def attributes(cls):
+        """Tag name/value pair attributes of a feature.
+        (cls, GVF1_0012)
+        """
+        return _namespace_GVF1O('GVF1_0012')
+
+    @classmethod
+    def parent(cls):
+        """Link out to the parent feature.
+        (cls, GVF1_0014)
+        """
+        return _namespace_GVF1O('GVF1_0014')
+
+    @classmethod
+    def contains(cls):
+        """Relationship that describes which features belong to a feature set.
+        (cls, GVF1_0015)
+        """
+        return _namespace_GVF1O('GVF1_0015')
+
+    @classmethod
+    def region(cls):
+        """Either:
+            FALDO "Region" instance replacement for a feature's start, stop, strand properties.
+            (cls, GVF1_0021)
+        Or:
+            FALDO "Region" instance replacement for a breakpoint's start, stop, strand properties.
+            (GVF1_0079)
+        """
+        return [ _namespace_GVF1O('GVF1_0021'), _namespace_GVF1O('GVF1_0079') ]
+
+    @classmethod
+    def species(cls):
+        """NCBI Taxonomy Ontology "NCBITaxon_1" (cls, or sub-classes) instance that denotes the species for a feature set.
+        (GVF1_0023)
+        """
+        return _namespace_GVF1O('GVF1_0023')
+
+    @classmethod
+    def variant(cls):
+        """Specific information about the variant(cls, s) of a feature.
+        (GVF1_0034)
+        """
+        return _namespace_GVF1O('GVF1_0034')
+
+    @classmethod
+    def individual(cls):
+        """Links to information about an individual.
+        (cls, GVF1_0036)
+        """
+        return _namespace_GVF1O('GVF1_0036')
+
+    @classmethod
+    def effect(cls):
+        """An effect of a particular feature variant.
+        (cls, GVF1_0041)
+        """
+        return _namespace_GVF1O('GVF1_0041')
+
+    @classmethod
+    def sequence_variant(cls):
+        """Effect of a sequence alteration on a sequence feature.
+        (cls, GVF1_0042)
+        """
+        return _namespace_GVF1O('GVF1_0042')
+
+    @classmethod
+    def feature_type(cls):
+        """A term that is describing the sequence feature that is being affected.
+        (cls, GVF1_0043)
+        """
+        return _namespace_GVF1O('GVF1_0043')
+
+    @classmethod
+    def feature_id(cls):
+        """Features that are affected by this sequence alteration effect.
+        (cls, GVF1_0044)
+        """
+        return _namespace_GVF1O('GVF1_0044')
+
+    @classmethod
+    def start_range(cls):
+        """A coordinate range for ambiguous start coordinates.
+        (cls, GVF1_0046)
+        """
+        return _namespace_GVF1O('GVF1_0046')
+
+    @classmethod
+    def end_range(cls):
+        """A coordinate range for ambiguous start coordinates.
+        (cls, GVF1_0047)
+        """
+        return _namespace_GVF1O('GVF1_0047')
+
+    @classmethod
+    def chromosome(cls):
+        """Denotes abstract chromosome representations for capturing variants that appear on the same chromosome of a polyploid organism.
+        (cls, GVF1_0051)
+        """
+        return _namespace_GVF1O('GVF1_0051')
+
+    @classmethod
+    def genotype(cls):
+        """Determines the genotype as observed in an individual.
+        (cls, GVF1_0053)
+        """
+        return _namespace_GVF1O('GVF1_0053')
+
+    @classmethod
+    def feature_properties(cls):
+        """Either:
+            Properties that are directly associated with Feature class instances.
+            (cls, GVF1_0066)
+        Or:
+            Properties that are directly associated with Feature class instances.
+            (GVF1_0059)
+        """
+        return [ _namespace_GVF1O('GVF1_0066'), _namespace_GVF1O('GVF1_0059') ]
+
+    @classmethod
+    def sequencedindividual_properties(cls):
+        """Either:
+            Properties that are directly associated with SequencedIndividual class instances.
+            (cls, GVF1_0067)
+        Or:
+            Properties that are directly associated with SequencedIndividual class instances.
+            (GVF1_0065)
+        """
+        return [ _namespace_GVF1O('GVF1_0067'), _namespace_GVF1O('GVF1_0065') ]
+
+    @classmethod
+    def set_properties(cls):
+        """Either:
+            Properties that are directly associated with Set class instances.
+            (cls, GVF1_0068)
+        Or:
+            Properties that are directly associated with Set class instances.
+            (GVF1_0063)
+        """
+        return [ _namespace_GVF1O('GVF1_0068'), _namespace_GVF1O('GVF1_0063') ]
+
+    @classmethod
+    def variant_properties(cls):
+        """Either:
+            Properties that are directly associated with Variant class instances.
+            (cls, GVF1_0069)
+        Or:
+            Properties that are directly associated with Variant class instances.
+            (GVF1_0060)
+        """
+        return [ _namespace_GVF1O('GVF1_0069'), _namespace_GVF1O('GVF1_0060') ]
+
+    @classmethod
+    def effect_properties(cls):
+        """Properties that are directly associated with Effect class instances.
+        (cls, GVF1_0070)
+        """
+        return _namespace_GVF1O('GVF1_0070')
+
+    @classmethod
+    def breakpoint_properties(cls):
+        """Either:
+            Properties that are directly associated with Breakpoint class instances.
+            (cls, GVF1_0075)
+        Or:
+            Properties that are directly associated with Breakpoint class instances.
+            (GVF1_0071)
+        """
+        return [ _namespace_GVF1O('GVF1_0075'), _namespace_GVF1O('GVF1_0071') ]
+
+    @classmethod
+    def dbxref(cls):
+        """A database cross-reference to associate a sequence alteration to its  representation in another database.
+        (cls, GVF1_0078)
+        """
+        return _namespace_GVF1O('GVF1_0078')
+
+    @classmethod
+    def region(cls):
+        """Either:
+            FALDO "Region" instance replacement for a feature's start, stop, strand properties.
+            (cls, GVF1_0021)
+        Or:
+            FALDO "Region" instance replacement for a breakpoint's start, stop, strand properties.
+            (GVF1_0079)
+        """
+        return [ _namespace_GVF1O('GVF1_0021'), _namespace_GVF1O('GVF1_0079') ]
+
+    @classmethod
+    def seqid(cls):
+        """Either:
+            ID of the landmark that establishes the coordinate system for a feature.
+            (cls, GVF1_0004)
+        Or:
+            ID of the landmark that establishes the coordinate system for a breakpoint.
+            (GVF1_0072)
+        """
+        return [ _namespace_GVF1O('GVF1_0004'), _namespace_GVF1O('GVF1_0072') ]
+
+    @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, GVF1_0005)
+        """
+        return _namespace_GVF1O('GVF1_0005')
+
+    @classmethod
+    def type(cls):
+        """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.
+        (GVF1_0006)
+        """
+        return _namespace_GVF1O('GVF1_0006')
+
+    @classmethod
+    def start(cls):
+        """Either:
+            Start coordinate of the feature on the seqid landmark.
+            (cls, GVF1_0007)
+        Or:
+            A coordinate that defines the start of an ambiguous coordinate range.
+            (GVF1_0048)
+        Or:
+            Start coordinate of the feature on the seqid landmark.
+            (GVF1_0073)
+        """
+        return [ _namespace_GVF1O('GVF1_0007'), _namespace_GVF1O('GVF1_0048'), _namespace_GVF1O('GVF1_0073') ]
+
+    @classmethod
+    def end(cls):
+        """Either:
+            End coordinate of the feature on the seqid landmark.
+            (cls, GVF1_0008)
+        Or:
+            A coordinate that defines the end of an ambiguous coordinate range.
+            (GVF1_0049)
+        Or:
+            End coordinate of the feature on the seqid landmark.
+            (GVF1_0074)
+        """
+        return [ _namespace_GVF1O('GVF1_0008'), _namespace_GVF1O('GVF1_0049'), _namespace_GVF1O('GVF1_0074') ]
+
+    @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, GVF1_0009)
+        """
+        return _namespace_GVF1O('GVF1_0009')
+
+    @classmethod
+    def tag(cls):
+        """Tag name of a feature attribute.
+        (cls, GVF1_0013)
+        """
+        return _namespace_GVF1O('GVF1_0013')
+
+    @classmethod
+    def version(cls):
+        """Version of the GVF specification that defines the feature set contents.
+        (cls, GVF1_0022)
+        """
+        return _namespace_GVF1O('GVF1_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, GVF1_0024)
+        """
+        return _namespace_GVF1O('GVF1_0024')
+
+    @classmethod
+    def variant_seq(cls):
+        """All sequence variations at a locus -- including the reference sequence when appropriate (cls, for example, when the locus is heterozygous). If the feature is on the minus strand, then the sequence is the reverse-compliment of the reference genome for these coordinates.
+        (GVF1_0025)
+        """
+        return _namespace_GVF1O('GVF1_0025')
+
+    @classmethod
+    def id(cls):
+        """A unique identifier for the feature within the feature set.
+        (cls, GVF1_0026)
+        """
+        return _namespace_GVF1O('GVF1_0026')
+
+    @classmethod
+    def alias(cls):
+        """Secondary name of a feature, which can be HGVS/ISCN nomenclature names, but not cross-references to databases (cls, e.g. dbSNP, OMIM) which should use the dbxref property.
+        (GVF1_0027)
+        """
+        return _namespace_GVF1O('GVF1_0027')
+
+    @classmethod
+    def name(cls):
+        """Name of an external database. For example, "dbSNP" or "OMIM".
+        (cls, GVF1_0029)
+        """
+        return _namespace_GVF1O('GVF1_0029')
+
+    @classmethod
+    def xref(cls):
+        """External database identifier. For example, for dbSNP, this identifier could be "rs3131969".
+        (cls, GVF1_0030)
+        """
+        return _namespace_GVF1O('GVF1_0030')
+
+    @classmethod
+    def reference_seq(cls):
+        """Sequence from the reference genome.
+        (cls, GVF1_0031)
+        """
+        return _namespace_GVF1O('GVF1_0031')
+
+    @classmethod
+    def variant_reads(cls):
+        """Number of reads that are supporting this variant.
+        (cls, GVF1_0032)
+        """
+        return _namespace_GVF1O('GVF1_0032')
+
+    @classmethod
+    def total_reads(cls):
+        """Total number of reads.
+        (cls, GVF1_0037)
+        """
+        return _namespace_GVF1O('GVF1_0037')
+
+    @classmethod
+    def zygosity(cls):
+        """Zygosity of a feature locus.
+        (cls, GVF1_0038)
+        """
+        return _namespace_GVF1O('GVF1_0038')
+
+    @classmethod
+    def variant_freq(cls):
+        """Frequency of a variant in a population.
+        (cls, GVF1_0039)
+        """
+        return _namespace_GVF1O('GVF1_0039')
+
+    @classmethod
+    def start(cls):
+        """Either:
+            Start coordinate of the feature on the seqid landmark.
+            (cls, GVF1_0007)
+        Or:
+            A coordinate that defines the start of an ambiguous coordinate range.
+            (GVF1_0048)
+        Or:
+            Start coordinate of the feature on the seqid landmark.
+            (GVF1_0073)
+        """
+        return [ _namespace_GVF1O('GVF1_0007'), _namespace_GVF1O('GVF1_0048'), _namespace_GVF1O('GVF1_0073') ]
+
+    @classmethod
+    def end(cls):
+        """Either:
+            End coordinate of the feature on the seqid landmark.
+            (cls, GVF1_0008)
+        Or:
+            A coordinate that defines the end of an ambiguous coordinate range.
+            (GVF1_0049)
+        Or:
+            End coordinate of the feature on the seqid landmark.
+            (GVF1_0074)
+        """
+        return [ _namespace_GVF1O('GVF1_0008'), _namespace_GVF1O('GVF1_0049'), _namespace_GVF1O('GVF1_0074') ]
+
+    @classmethod
+    def phased(cls):
+        """Unclear from GVF specification.
+        (cls, GVF1_0050)
+        """
+        return _namespace_GVF1O('GVF1_0050')
+
+    @classmethod
+    def variant_codon(cls):
+        """Describes the codon that overlaps this variant.
+        (cls, GVF1_0054)
+        """
+        return _namespace_GVF1O('GVF1_0054')
+
+    @classmethod
+    def reference_codon(cls):
+        """Describes the codon from the reference sequence whose coordinates overlap with this variant.
+        (cls, GVF1_0055)
+        """
+        return _namespace_GVF1O('GVF1_0055')
+
+    @classmethod
+    def variant_aa(cls):
+        """Amino acid that overlaps with the variant.
+        (cls, GVF1_0056)
+        """
+        return _namespace_GVF1O('GVF1_0056')
+
+    @classmethod
+    def reference_aa(cls):
+        """Amino acid in the reference genome that overlaps with a variant's genome coordinates.
+        (cls, GVF1_0057)
+        """
+        return _namespace_GVF1O('GVF1_0057')
+
+    @classmethod
+    def feature_properties(cls):
+        """Either:
+            Properties that are directly associated with Feature class instances.
+            (cls, GVF1_0066)
+        Or:
+            Properties that are directly associated with Feature class instances.
+            (GVF1_0059)
+        """
+        return [ _namespace_GVF1O('GVF1_0066'), _namespace_GVF1O('GVF1_0059') ]
+
+    @classmethod
+    def variant_properties(cls):
+        """Either:
+            Properties that are directly associated with Variant class instances.
+            (cls, GVF1_0069)
+        Or:
+            Properties that are directly associated with Variant class instances.
+            (GVF1_0060)
+        """
+        return [ _namespace_GVF1O('GVF1_0069'), _namespace_GVF1O('GVF1_0060') ]
+
+    @classmethod
+    def range_properties(cls):
+        """Properties that are directly associated with Range class instances.
+        (cls, GVF1_0061)
+        """
+        return _namespace_GVF1O('GVF1_0061')
+
+    @classmethod
+    def dbxref_properties(cls):
+        """Properties that are directly associated with DBXRef class instances.
+        (cls, GVF1_0062)
+        """
+        return _namespace_GVF1O('GVF1_0062')
+
+    @classmethod
+    def set_properties(cls):
+        """Either:
+            Properties that are directly associated with Set class instances.
+            (cls, GVF1_0068)
+        Or:
+            Properties that are directly associated with Set class instances.
+            (GVF1_0063)
+        """
+        return [ _namespace_GVF1O('GVF1_0068'), _namespace_GVF1O('GVF1_0063') ]
+
+    @classmethod
+    def attribute_properties(cls):
+        """Properties that are directly associated with Attribute class instances.
+        (cls, GVF1_0064)
+        """
+        return _namespace_GVF1O('GVF1_0064')
+
+    @classmethod
+    def sequencedindividual_properties(cls):
+        """Either:
+            Properties that are directly associated with SequencedIndividual class instances.
+            (cls, GVF1_0067)
+        Or:
+            Properties that are directly associated with SequencedIndividual class instances.
+            (GVF1_0065)
+        """
+        return [ _namespace_GVF1O('GVF1_0067'), _namespace_GVF1O('GVF1_0065') ]
+
+    @classmethod
+    def breakpoint_properties(cls):
+        """Either:
+            Properties that are directly associated with Breakpoint class instances.
+            (cls, GVF1_0075)
+        Or:
+            Properties that are directly associated with Breakpoint class instances.
+            (GVF1_0071)
+        """
+        return [ _namespace_GVF1O('GVF1_0075'), _namespace_GVF1O('GVF1_0071') ]
+
+    @classmethod
+    def seqid(cls):
+        """Either:
+            ID of the landmark that establishes the coordinate system for a feature.
+            (cls, GVF1_0004)
+        Or:
+            ID of the landmark that establishes the coordinate system for a breakpoint.
+            (GVF1_0072)
+        """
+        return [ _namespace_GVF1O('GVF1_0004'), _namespace_GVF1O('GVF1_0072') ]
+
+    @classmethod
+    def start(cls):
+        """Either:
+            Start coordinate of the feature on the seqid landmark.
+            (cls, GVF1_0007)
+        Or:
+            A coordinate that defines the start of an ambiguous coordinate range.
+            (GVF1_0048)
+        Or:
+            Start coordinate of the feature on the seqid landmark.
+            (GVF1_0073)
+        """
+        return [ _namespace_GVF1O('GVF1_0007'), _namespace_GVF1O('GVF1_0048'), _namespace_GVF1O('GVF1_0073') ]
+
+    @classmethod
+    def end(cls):
+        """Either:
+            End coordinate of the feature on the seqid landmark.
+            (cls, GVF1_0008)
+        Or:
+            A coordinate that defines the end of an ambiguous coordinate range.
+            (GVF1_0049)
+        Or:
+            End coordinate of the feature on the seqid landmark.
+            (GVF1_0074)
+        """
+        return [ _namespace_GVF1O('GVF1_0008'), _namespace_GVF1O('GVF1_0049'), _namespace_GVF1O('GVF1_0074') ]
+
+    @classmethod
+    def a_context(cls):
+        """Sequence context (cls, positive strand) of a feature on the 5' end.
+        (GVF1_0076)
+        """
+        return _namespace_GVF1O('GVF1_0076')
+
+    @classmethod
+    def a_context(cls):
+        """Sequence context (cls, positive strand) of a feature on the 3' end.
+        (GVF1_0077)
+        """
+        return _namespace_GVF1O('GVF1_0077')
+
+    @classmethod
+    def Set(cls):
+        """Set of genomic sequence features, whose identifiers are unique within the set.
+        (cls, GVF1_0001)
+        """
+        return _namespace_GVF1O('GVF1_0001')
+
+    @classmethod
+    def Feature(cls):
+        """A genomic sequence feature.
+        (cls, GVF1_0002)
+        """
+        return _namespace_GVF1O('GVF1_0002')
+
+    @classmethod
+    def Attribute(cls):
+        return _namespace_GVF1O('GVF1_0003')
+
+    @classmethod
+    def Strand(cls):
+        """Class describing a genomic strand. Instances of the class (cls, individuals) are used to denote forward-/reverse-strands, etc.
+        (GVF1_0016)
+        """
+        return _namespace_GVF1O('GVF1_0016')
+
+    @classmethod
+    def DBXRef(cls):
+        """A class describing relationships between features and external databases.
+        (cls, GVF1_0028)
+        """
+        return _namespace_GVF1O('GVF1_0028')
+
+    @classmethod
+    def Variant(cls):
+        """Describing specific alterations of a feature.
+        (cls, GVF1_0033)
+        """
+        return _namespace_GVF1O('GVF1_0033')
+
+    @classmethod
+    def SequencedIndividual(cls):
+        """Aggregated sequencing information for a particular individual.
+        (cls, GVF1_0035)
+        """
+        return _namespace_GVF1O('GVF1_0035')
+
+    @classmethod
+    def Effect(cls):
+        """Describing the effect of a feature variant.
+        (cls, GVF1_0040)
+        """
+        return _namespace_GVF1O('GVF1_0040')
+
+    @classmethod
+    def Range(cls):
+        """Describe ambiguity in either start or end coordinates.
+        (cls, GVF1_0045)
+        """
+        return _namespace_GVF1O('GVF1_0045')
+
+    @classmethod
+    def Chromosome(cls):
+        """An abstract representation of a chromosome to represent ploidy.
+        (cls, GVF1_0052)
+        """
+        return _namespace_GVF1O('GVF1_0052')
+
+    @classmethod
+    def Breakpoint(cls):
+        """Describes the source or destination of a zero-length sequence alteration.
+        (cls, GVF1_0058)
+        """
+        return _namespace_GVF1O('GVF1_0058')
+
+    @classmethod
+    def Positive(cls):
+        """Location on the positive (cls, forward) strand.
+        (GVF1_0017)
+        """
+        return _namespace_GVF1O('GVF1_0017')
+
+    @classmethod
+    def Negative(cls):
+        """Location on the negative (cls, reverse) strand.
+        (GVF1_0018)
+        """
+        return _namespace_GVF1O('GVF1_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.
+        (GVF1_0019)
+        """
+        return _namespace_GVF1O('GVF1_0019')
+
+    @classmethod
+    def NotStranded(cls):
+        """Strand is not applicable.
+        (cls, GVF1_0020)
+        """
+        return _namespace_GVF1O('GVF1_0020')
+
+    @classmethod
+    def is_object_property(cls, uri):
+        """Determines whether the given URI is an object property.
+        
+        uri -- URI that is tested for being an object property
+        """
+        if uri == _namespace_GVF1O('GVF1_0010'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0012'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0014'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0015'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0021'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0023'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0034'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0036'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0041'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0042'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0043'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0044'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0046'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0047'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0051'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0053'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0066'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0067'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0068'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0069'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0070'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0075'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0078'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0079'):
+            return True
+        return False
+
+    @classmethod
+    def is_datatype_property(cls, uri):
+        """Determines whether the given URI is a datatype property.
+        
+        uri -- URI that is tested for being a datatype property
+        """
+        if uri == _namespace_GVF1O('GVF1_0004'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0005'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0006'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0007'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0008'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0009'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0013'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0022'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0024'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0025'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0026'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0027'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0029'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0030'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0031'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0032'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0037'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0038'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0039'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0048'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0049'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0050'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0054'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0055'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0056'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0057'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0059'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0060'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0061'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0062'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0063'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0064'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0065'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0071'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0072'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0073'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0074'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0076'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0077'):
+            return True
+        return False
+
+    @classmethod
+    def is_class(cls, uri):
+        """Determines whether the given URI is a class.
+        
+        uri -- URI that is tested for being a class
+        """
+        if uri == _namespace_GVF1O('GVF1_0001'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0002'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0003'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0016'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0028'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0033'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0035'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0040'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0045'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0052'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0058'):
+            return True
+        return False
+
+    @classmethod
+    def is_named_individual(cls, uri):
+        """Determines whether the given URI is a named individual.
+        
+        uri -- URI that is tested for being a named individual
+        """
+        if uri == _namespace_GVF1O('GVF1_0017'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0018'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0019'):
+            return True
+        if uri == _namespace_GVF1O('GVF1_0020'):
+            return True
+        return False
+
+    @classmethod
+    def with_parent(cls, uris, parent):
+        """Returns only those URIs that fall under a designated parent URI.
+        
+        uris -- Set of URIs that are tested whether they have the given parent URI.
+        parent -- Parent URI.
+        """
+        return filter(lambda uri: cls.has_parent(uri, parent), uris)
+
+    @classmethod
+    def has_parent(cls, uri, parent):
+        """Recursively tries to determine the parent for a given URI.
+        
+        uri -- URI that is tested for whether it has the given parent URI.
+        parent -- Parent URI.
+        """
+        if cls.__parent_properties.has_key(uri):
+            if cls.__parent_properties[uri] == parent:
+                return True
+            return cls.has_parent(cls.__parent_properties[uri], parent)
+        return False
+
+    __parent_properties = { _namespace_GVF1O('GVF1_0010') : _namespace_GVF1O('GVF1_0075') , _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_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_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_0038') : _namespace_GVF1O('GVF1_0059') , _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_0060') , _namespace_GVF1O('GVF1_0056') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0057') : _namespace_GVF1O('GVF1_0060') , _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') }
+