import rdflib from rdflib import Namespace class GVF1O: @classmethod def seqid(cls): """Either: Establishes the landmark (cls, e.g. a chromosome) on which a feature is located. (http://www.biointerchange.org/gvf1o#GVF1_0004) Or: Link to the landmark that establishes the coordinate system for the breakpoint. (http://www.biointerchange.org/gvf1o#GVF1_0072) """ return [ cls._namespace_GVF1O('GVF1_0004'), cls._namespace_GVF1O('GVF1_0072') ] @classmethod def strand(cls): """Either: Strand of the feature. (cls, http://www.biointerchange.org/gvf1o#GVF1_0010) Or: Strand of the breakpoint. (http://www.biointerchange.org/gvf1o#GVF1_0083) Or: Strand of a target -- if applicable. (http://www.biointerchange.org/gvf1o#GVF1_0091) """ return [ cls._namespace_GVF1O('GVF1_0010'), cls._namespace_GVF1O('GVF1_0083'), cls._namespace_GVF1O('GVF1_0091') ] @classmethod def attributes(cls): """Either: Tag name/value pair attributes of a feature. (cls, http://www.biointerchange.org/gvf1o#GVF1_0012) Or: Tag name/value pair attributes that are not captured by the GVF specification. (http://www.biointerchange.org/gvf1o#GVF1_0152) """ return [ cls._namespace_GVF1O('GVF1_0012'), cls._namespace_GVF1O('GVF1_0152') ] @classmethod def parent(cls): """Link out to the parent feature. (cls, http://www.biointerchange.org/gvf1o#GVF1_0014) """ return cls._namespace_GVF1O('GVF1_0014') @classmethod def contains(cls): """Relationship that describes which features belong to a feature set. (cls, http://www.biointerchange.org/gvf1o#GVF1_0015) """ return cls._namespace_GVF1O('GVF1_0015') @classmethod def region(cls): """Either: FALDO "Region" instance replacement for a feature's start, stop, strand properties. (cls, http://www.biointerchange.org/gvf1o#GVF1_0021) Or: FALDO "Region" instance replacement for a breakpoint's start, stop, strand properties. (http://www.biointerchange.org/gvf1o#GVF1_0079) Or: FALDO "Region" instance replacement for a target's start, stop, strand properties. (http://www.biointerchange.org/gvf1o#GVF1_0090) """ return [ cls._namespace_GVF1O('GVF1_0021'), cls._namespace_GVF1O('GVF1_0079'), cls._namespace_GVF1O('GVF1_0090') ] @classmethod def species(cls): """NCBI Taxonomy Ontology "NCBITaxon_1" (cls, or sub-classes) instance that denotes the species for a feature set. (http://www.biointerchange.org/gvf1o#GVF1_0023) """ return cls._namespace_GVF1O('GVF1_0023') @classmethod def variant(cls): """Specific information about the variant(cls, s) of a feature. (http://www.biointerchange.org/gvf1o#GVF1_0034) """ return cls._namespace_GVF1O('GVF1_0034') @classmethod def individual(cls): """Links to information about an individual. (cls, http://www.biointerchange.org/gvf1o#GVF1_0036) """ return cls._namespace_GVF1O('GVF1_0036') @classmethod def zygosity(cls): """Zygosity of a variant. (cls, http://www.biointerchange.org/gvf1o#GVF1_0038) """ return cls._namespace_GVF1O('GVF1_0038') @classmethod def effect(cls): """An effect of a particular feature variant. (cls, http://www.biointerchange.org/gvf1o#GVF1_0041) """ return cls._namespace_GVF1O('GVF1_0041') @classmethod def sequence_variant(cls): """Effect of a sequence alteration on a sequence feature. (cls, http://www.biointerchange.org/gvf1o#GVF1_0042) """ return cls._namespace_GVF1O('GVF1_0042') @classmethod def feature_type(cls): """A term that is describing the sequence feature that is being affected. (cls, http://www.biointerchange.org/gvf1o#GVF1_0043) """ return cls._namespace_GVF1O('GVF1_0043') @classmethod def start_range(cls): """A coordinate range for ambiguous start coordinates. (cls, http://www.biointerchange.org/gvf1o#GVF1_0046) """ return cls._namespace_GVF1O('GVF1_0046') @classmethod def end_range(cls): """A coordinate range for ambiguous start coordinates. (cls, http://www.biointerchange.org/gvf1o#GVF1_0047) """ return cls._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, http://www.biointerchange.org/gvf1o#GVF1_0051) """ return cls._namespace_GVF1O('GVF1_0051') @classmethod def genotype(cls): """Determines the genotype as observed in an individual. (cls, http://www.biointerchange.org/gvf1o#GVF1_0053) """ return cls._namespace_GVF1O('GVF1_0053') @classmethod def feature_properties(cls): """Either: Properties that are directly associated with Feature class instances. (cls, http://www.biointerchange.org/gvf1o#GVF1_0066) Or: Properties that are directly associated with Feature class instances. (http://www.biointerchange.org/gvf1o#GVF1_0059) """ return [ cls._namespace_GVF1O('GVF1_0066'), cls._namespace_GVF1O('GVF1_0059') ] @classmethod def sequencedindividual_properties(cls): """Either: Properties that are directly associated with SequencedIndividual class instances. (cls, http://www.biointerchange.org/gvf1o#GVF1_0067) Or: Properties that are directly associated with SequencedIndividual class instances. (http://www.biointerchange.org/gvf1o#GVF1_0065) """ return [ cls._namespace_GVF1O('GVF1_0067'), cls._namespace_GVF1O('GVF1_0065') ] @classmethod def set_properties(cls): """Either: Properties that are directly associated with Set class instances. (cls, http://www.biointerchange.org/gvf1o#GVF1_0068) Or: Properties that are directly associated with Set class instances. (http://www.biointerchange.org/gvf1o#GVF1_0063) """ return [ cls._namespace_GVF1O('GVF1_0068'), cls._namespace_GVF1O('GVF1_0063') ] @classmethod def variant_properties(cls): """Either: Properties that are directly associated with Variant class instances. (cls, http://www.biointerchange.org/gvf1o#GVF1_0069) Or: Properties that are directly associated with Variant class instances. (http://www.biointerchange.org/gvf1o#GVF1_0060) """ return [ cls._namespace_GVF1O('GVF1_0069'), cls._namespace_GVF1O('GVF1_0060') ] @classmethod def effect_properties(cls): """Either: Properties that are directly associated with Effect class instances. (cls, http://www.biointerchange.org/gvf1o#GVF1_0070) Or: Properties that are directly associated with Effect class instances. (http://www.biointerchange.org/gvf1o#GVF1_0158) """ return [ cls._namespace_GVF1O('GVF1_0070'), cls._namespace_GVF1O('GVF1_0158') ] @classmethod def breakpoint_properties(cls): """Either: Properties that are directly associated with Breakpoint class instances. (cls, http://www.biointerchange.org/gvf1o#GVF1_0075) Or: Properties that are directly associated with Breakpoint class instances. (http://www.biointerchange.org/gvf1o#GVF1_0071) """ return [ cls._namespace_GVF1O('GVF1_0075'), cls._namespace_GVF1O('GVF1_0071') ] @classmethod def dbxref(cls): """Either: A database cross-reference to associate a sequence alteration to its representation in another database. (cls, http://www.biointerchange.org/gvf1o#GVF1_0078) Or: A database cross-reference to associate a structured pragma to a representation in another database. (http://www.biointerchange.org/gvf1o#GVF1_0104) """ return [ cls._namespace_GVF1O('GVF1_0078'), cls._namespace_GVF1O('GVF1_0104') ] @classmethod def breakpoint(cls): """Potential source or destination of zero-length sequence alterations. (cls, http://www.biointerchange.org/gvf1o#GVF1_0080) """ return cls._namespace_GVF1O('GVF1_0080') @classmethod def target_properties(cls): """Either: Properties that are directly associated with Target class instances. (cls, http://www.biointerchange.org/gvf1o#GVF1_0089) Or: Properties that are directly associated with Target class instances. (http://www.biointerchange.org/gvf1o#GVF1_0092) """ return [ cls._namespace_GVF1O('GVF1_0089'), cls._namespace_GVF1O('GVF1_0092') ] @classmethod def technologyplatform_properties(cls): """Either: Properties that are directly associated with TechnologyPlatform class instances. (cls, http://www.biointerchange.org/gvf1o#GVF1_0102) Or: Properties that are directly associated with TechnologyPlatform class instances. (http://www.biointerchange.org/gvf1o#GVF1_0107) """ return [ cls._namespace_GVF1O('GVF1_0102'), cls._namespace_GVF1O('GVF1_0107') ] @classmethod def datasource_properties(cls): """Properties that are directly associated with DataSource class instances. (cls, http://www.biointerchange.org/gvf1o#GVF1_0103) """ return cls._namespace_GVF1O('GVF1_0103') @classmethod def structuredpragma_properties(cls): """Either: Properties describing structured pragma properties. (cls, http://www.biointerchange.org/gvf1o#GVF1_0112) Or: Properties describing structured pragma properties. (http://www.biointerchange.org/gvf1o#GVF1_0113) """ return [ cls._namespace_GVF1O('GVF1_0112'), cls._namespace_GVF1O('GVF1_0113') ] @classmethod def read_type(cls): """Types of reads produced by the platform. (cls, http://www.biointerchange.org/gvf1o#GVF1_0119) """ return cls._namespace_GVF1O('GVF1_0119') @classmethod def data_type(cls): """Datatype of this data source. (cls, http://www.biointerchange.org/gvf1o#GVF1_0120) """ return cls._namespace_GVF1O('GVF1_0120') @classmethod def technology_platform(cls): """Technology platform that was used to derive the feature. (cls, http://www.biointerchange.org/gvf1o#GVF1_0121) """ return cls._namespace_GVF1O('GVF1_0121') @classmethod def data_source(cls): """Data source origin of the feature. (cls, http://www.biointerchange.org/gvf1o#GVF1_0122) """ return cls._namespace_GVF1O('GVF1_0122') @classmethod def score_method(cls): """Used scoring method. (cls, http://www.biointerchange.org/gvf1o#GVF1_0123) """ return cls._namespace_GVF1O('GVF1_0123') @classmethod def source_method(cls): """Further information about the algorithm/methodologies used. (cls, http://www.biointerchange.org/gvf1o#GVF1_0124) """ return cls._namespace_GVF1O('GVF1_0124') @classmethod def phenotype_description(cls): """Further information about an individual's phenotype. Applies only to single individual sets. (cls, http://www.biointerchange.org/gvf1o#GVF1_0125) """ return cls._namespace_GVF1O('GVF1_0125') @classmethod def attribute_method(cls): """Either: Further information about the associated attribute(cls, s). (http://www.biointerchange.org/gvf1o#GVF1_0126) Or: Further information about the associated attribute(s). (http://www.biointerchange.org/gvf1o#GVF1_0127) Or: Further information about the associated attribute(s). (http://www.biointerchange.org/gvf1o#GVF1_0129) Or: Further information about the associated attribute(s). (http://www.biointerchange.org/gvf1o#GVF1_0130) Or: Further information about the associated attribute(s). (http://www.biointerchange.org/gvf1o#GVF1_0131) """ return [ cls._namespace_GVF1O('GVF1_0126'), cls._namespace_GVF1O('GVF1_0127'), cls._namespace_GVF1O('GVF1_0129'), cls._namespace_GVF1O('GVF1_0130'), cls._namespace_GVF1O('GVF1_0131') ] @classmethod def attribute_properties(cls): """Either: Properties about Attribute instances. (cls, http://www.biointerchange.org/gvf1o#GVF1_0128) Or: Properties that are directly associated with Attribute class instances. (http://www.biointerchange.org/gvf1o#GVF1_0064) """ return [ cls._namespace_GVF1O('GVF1_0128'), cls._namespace_GVF1O('GVF1_0064') ] @classmethod def sex(cls): """Denotes the sex of the sequenced individual for single-individual sets. (cls, http://www.biointerchange.org/gvf1o#GVF1_0147) """ return cls._namespace_GVF1O('GVF1_0147') @classmethod def genomic_source(cls): """Denotes the source of genomic data (cls, on a cell-type level). (http://www.biointerchange.org/gvf1o#GVF1_0148) """ return cls._namespace_GVF1O('GVF1_0148') @classmethod def feature_ontology(cls): """Explicit link-out to one or more ontologies that have been used for describing features. This is a meta comment about the URIs that link out to SO/SOFA or other ontologies. (cls, http://www.biointerchange.org/gvf1o#GVF1_0150) """ return cls._namespace_GVF1O('GVF1_0150') @classmethod def target(cls): """Identifies the target that the features aligns to. (cls, http://www.biointerchange.org/gvf1o#GVF1_0155) """ return cls._namespace_GVF1O('GVF1_0155') @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, http://www.biointerchange.org/gvf1o#GVF1_0005) """ return cls._namespace_GVF1O('GVF1_0005') @classmethod def type(cls): """Type of the feature, which is either an entry the "lite" version of the Sequence Ontology (cls, SOFA) or a child entry of sequence_feature (SO:0000110) of the full Sequence Ontology (SO). (http://www.biointerchange.org/gvf1o#GVF1_0006) """ return cls._namespace_GVF1O('GVF1_0006') @classmethod def start(cls): """Either: Start coordinate of the feature on the seqid landmark. (cls, http://www.biointerchange.org/gvf1o#GVF1_0007) Or: A coordinate that defines the start of an ambiguous coordinate range. (http://www.biointerchange.org/gvf1o#GVF1_0048) Or: Start coordinate of the feature on the seqid landmark. (http://www.biointerchange.org/gvf1o#GVF1_0073) Or: Start coordinate of the target. (http://www.biointerchange.org/gvf1o#GVF1_0094) Or: Genomic start coordinate of the landmark. (http://www.biointerchange.org/gvf1o#GVF1_0138) """ return [ cls._namespace_GVF1O('GVF1_0007'), cls._namespace_GVF1O('GVF1_0048'), cls._namespace_GVF1O('GVF1_0073'), cls._namespace_GVF1O('GVF1_0094'), cls._namespace_GVF1O('GVF1_0138') ] @classmethod def end(cls): """Either: End coordinate of the feature on the seqid landmark. (cls, http://www.biointerchange.org/gvf1o#GVF1_0008) Or: A coordinate that defines the end of an ambiguous coordinate range. (http://www.biointerchange.org/gvf1o#GVF1_0049) Or: End coordinate of the feature on the seqid landmark. (http://www.biointerchange.org/gvf1o#GVF1_0074) Or: End coordinate of the target. (http://www.biointerchange.org/gvf1o#GVF1_0095) Or: Genomic end coordinate of the landmark. (http://www.biointerchange.org/gvf1o#GVF1_0139) """ return [ cls._namespace_GVF1O('GVF1_0008'), cls._namespace_GVF1O('GVF1_0049'), cls._namespace_GVF1O('GVF1_0074'), cls._namespace_GVF1O('GVF1_0095'), cls._namespace_GVF1O('GVF1_0139') ] @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, http://www.biointerchange.org/gvf1o#GVF1_0009) """ return cls._namespace_GVF1O('GVF1_0009') @classmethod def tag(cls): """Either: Tag name of a feature attribute. (cls, http://www.biointerchange.org/gvf1o#GVF1_0013) Or: Tag name of an user defined structured attribute. (http://www.biointerchange.org/gvf1o#GVF1_0154) """ return [ cls._namespace_GVF1O('GVF1_0013'), cls._namespace_GVF1O('GVF1_0154') ] @classmethod def gvf_version(cls): """Version of the GVF specification that defines the feature set contents. (cls, http://www.biointerchange.org/gvf1o#GVF1_0022) """ return cls._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, http://www.biointerchange.org/gvf1o#GVF1_0024) """ return cls._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. (http://www.biointerchange.org/gvf1o#GVF1_0025) """ return cls._namespace_GVF1O('GVF1_0025') @classmethod def id(cls): """Either: A unique identifier for the feature within the feature set. (cls, http://www.biointerchange.org/gvf1o#GVF1_0026) Or: ID that uniquely establishes the Landmark's identity within a Set. (http://www.biointerchange.org/gvf1o#GVF1_0137) """ return [ cls._namespace_GVF1O('GVF1_0026'), cls._namespace_GVF1O('GVF1_0137') ] @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. (http://www.biointerchange.org/gvf1o#GVF1_0027) """ return cls._namespace_GVF1O('GVF1_0027') @classmethod def reference_seq(cls): """Sequence from the reference genome. (cls, http://www.biointerchange.org/gvf1o#GVF1_0031) """ return cls._namespace_GVF1O('GVF1_0031') @classmethod def variant_reads(cls): """Number of reads that are supporting this variant. (cls, http://www.biointerchange.org/gvf1o#GVF1_0032) """ return cls._namespace_GVF1O('GVF1_0032') @classmethod def total_reads(cls): """Total number of reads. (cls, http://www.biointerchange.org/gvf1o#GVF1_0037) """ return cls._namespace_GVF1O('GVF1_0037') @classmethod def variant_freq(cls): """Frequency of a variant in a population. (cls, http://www.biointerchange.org/gvf1o#GVF1_0039) """ return cls._namespace_GVF1O('GVF1_0039') @classmethod def feature(cls): """Features that are affected by this sequence alteration effect. This can be an external feature identifier, such as an Ensembl gene/transcript identifier. (cls, http://www.biointerchange.org/gvf1o#GVF1_0044) """ return cls._namespace_GVF1O('GVF1_0044') @classmethod def phased(cls): """Either: Unclear from GVF specification. (cls, http://www.biointerchange.org/gvf1o#GVF1_0050) Or: Indicates whether this particular is phased. Used to encode ##phased-genotypes statements. (http://www.biointerchange.org/gvf1o#GVF1_0101) """ return [ cls._namespace_GVF1O('GVF1_0050'), cls._namespace_GVF1O('GVF1_0101') ] @classmethod def variant_codon(cls): """Describes the codon that overlaps this variant. (cls, http://www.biointerchange.org/gvf1o#GVF1_0054) """ return cls._namespace_GVF1O('GVF1_0054') @classmethod def reference_codon(cls): """Describes the codon from the reference sequence whose coordinates overlap with this variant. (cls, http://www.biointerchange.org/gvf1o#GVF1_0055) """ return cls._namespace_GVF1O('GVF1_0055') @classmethod def variant_aa(cls): """Amino acid that overlaps with the variant. (cls, http://www.biointerchange.org/gvf1o#GVF1_0056) """ return cls._namespace_GVF1O('GVF1_0056') @classmethod def reference_aa(cls): """Amino acid in the reference genome that overlaps with a variant's genome coordinates. (cls, http://www.biointerchange.org/gvf1o#GVF1_0057) """ return cls._namespace_GVF1O('GVF1_0057') @classmethod def range_properties(cls): """Properties that are directly associated with Range class instances. (cls, http://www.biointerchange.org/gvf1o#GVF1_0061) """ return cls._namespace_GVF1O('GVF1_0061') @classmethod def a_context(cls): """Sequence context (cls, positive strand) of a feature on the 5' end. (http://www.biointerchange.org/gvf1o#GVF1_0076) """ return cls._namespace_GVF1O('GVF1_0076') @classmethod def gff_version(cls): """Version of the GFF specification that defines the feature set contents apart from GVF related definitions. (cls, http://www.biointerchange.org/gvf1o#GVF1_0081) """ return cls._namespace_GVF1O('GVF1_0081') @classmethod def file_date(cls): """Creation date of the GVF file that this set stems from. (cls, http://www.biointerchange.org/gvf1o#GVF1_0082) """ return cls._namespace_GVF1O('GVF1_0082') @classmethod def target_id(cls): """ID or accession of the target alignment. (cls, http://www.biointerchange.org/gvf1o#GVF1_0093) """ return cls._namespace_GVF1O('GVF1_0093') @classmethod def ontology_term(cls): """A cross-reference to an ontology term that is associated with a feature. (cls, http://www.biointerchange.org/gvf1o#GVF1_0096) """ return cls._namespace_GVF1O('GVF1_0096') @classmethod def comment(cls): """An arbitrary comment. Free text. (cls, http://www.biointerchange.org/gvf1o#GVF1_0105) """ return cls._namespace_GVF1O('GVF1_0105') @classmethod def platform_class(cls): """Type of technology used to gather the variant data. Unrestricted range due to open specification. (cls, http://www.biointerchange.org/gvf1o#GVF1_0106) """ return cls._namespace_GVF1O('GVF1_0106') @classmethod def platform_name(cls): """Sequencer or other machine used to collect the variant data. Unrestricted range due to open specification. (cls, http://www.biointerchange.org/gvf1o#GVF1_0108) """ return cls._namespace_GVF1O('GVF1_0108') @classmethod def read_length(cls): """Undocumented in GVF specification. (cls, http://www.biointerchange.org/gvf1o#GVF1_0132) """ return cls._namespace_GVF1O('GVF1_0132') @classmethod def read_pair_span(cls): """Undocumented in GVF specification. (cls, http://www.biointerchange.org/gvf1o#GVF1_0133) """ return cls._namespace_GVF1O('GVF1_0133') @classmethod def average_coverage(cls): """Undocumented in GVF specification. (cls, http://www.biointerchange.org/gvf1o#GVF1_0134) """ return cls._namespace_GVF1O('GVF1_0134') @classmethod def landmark_properties(cls): """Properties that are directly associated with Landmark class instances. (cls, http://www.biointerchange.org/gvf1o#GVF1_0136) """ return cls._namespace_GVF1O('GVF1_0136') @classmethod def file_version(cls): """Version of the GVF file that this set stems from. (cls, http://www.biointerchange.org/gvf1o#GVF1_0149) """ return cls._namespace_GVF1O('GVF1_0149') @classmethod def structuredattribute_properties(cls): """Properties that are directly associated with StructuredAttribute class instances. (cls, http://www.biointerchange.org/gvf1o#GVF1_0153) """ return cls._namespace_GVF1O('GVF1_0153') @classmethod def sequence(cls): """Either: Sequence associated with this feature, if it has been specified using a FASTA string. (cls, http://www.biointerchange.org/gvf1o#GVF1_0156) Or: Sequence associated with this feature, if it has been specified using a FASTA string. (http://www.biointerchange.org/gvf1o#GVF1_0157) """ return [ cls._namespace_GVF1O('GVF1_0156'), cls._namespace_GVF1O('GVF1_0157') ] @classmethod def Set(cls): """Set of genomic sequence features, whose identifiers are unique within the set. (cls, http://www.biointerchange.org/gvf1o#GVF1_0001) """ return cls._namespace_GVF1O('GVF1_0001') @classmethod def Feature(cls): """A genomic sequence feature. (cls, http://www.biointerchange.org/gvf1o#GVF1_0002) """ return cls._namespace_GVF1O('GVF1_0002') @classmethod def Attribute(cls): """Representation of attribute tag/value pairs that are not covered by specific classes such as Effect or Variant. (cls, http://www.biointerchange.org/gvf1o#GVF1_0003) """ return cls._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. (http://www.biointerchange.org/gvf1o#GVF1_0016) """ return cls._namespace_GVF1O('GVF1_0016') @classmethod def Variant(cls): """Describing specific alterations of a feature. (cls, http://www.biointerchange.org/gvf1o#GVF1_0033) """ return cls._namespace_GVF1O('GVF1_0033') @classmethod def SequencedIndividual(cls): """Aggregated sequencing information for a particular individual. (cls, http://www.biointerchange.org/gvf1o#GVF1_0035) """ return cls._namespace_GVF1O('GVF1_0035') @classmethod def Effect(cls): """Describing the effect of a feature variant. (cls, http://www.biointerchange.org/gvf1o#GVF1_0040) """ return cls._namespace_GVF1O('GVF1_0040') @classmethod def Range(cls): """Describe ambiguity in either start or end coordinates. (cls, http://www.biointerchange.org/gvf1o#GVF1_0045) """ return cls._namespace_GVF1O('GVF1_0045') @classmethod def Chromosome(cls): """An abstract representation of a chromosome to represent ploidy. (cls, http://www.biointerchange.org/gvf1o#GVF1_0052) """ return cls._namespace_GVF1O('GVF1_0052') @classmethod def Breakpoint(cls): """Describes the source or destination of a zero-length sequence alteration. (cls, http://www.biointerchange.org/gvf1o#GVF1_0058) """ return cls._namespace_GVF1O('GVF1_0058') @classmethod def Zygosity(cls): """Denotes the zygosity of alleles. (cls, http://www.biointerchange.org/gvf1o#GVF1_0084) """ return cls._namespace_GVF1O('GVF1_0084') @classmethod def Target(cls): """Indicates a feature's "target" of a nucleotide-to-nucleotide or protein-to-nucleotide alignment. (cls, http://www.biointerchange.org/gvf1o#GVF1_0088) """ return cls._namespace_GVF1O('GVF1_0088') @classmethod def TechnologyPlatform(cls): """Details about the sequencing/microarray technology used to gather the data in a set. (cls, http://www.biointerchange.org/gvf1o#GVF1_0097) """ return cls._namespace_GVF1O('GVF1_0097') @classmethod def DataSource(cls): """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. (cls, http://www.biointerchange.org/gvf1o#GVF1_0098) """ return cls._namespace_GVF1O('GVF1_0098') @classmethod def Method(cls): """Information about the used scoring algorithm or method. (cls, http://www.biointerchange.org/gvf1o#GVF1_0099) """ return cls._namespace_GVF1O('GVF1_0099') @classmethod def PhenotypeDescription(cls): """Additional information about an individual's phenotype. (cls, http://www.biointerchange.org/gvf1o#GVF1_0100) """ return cls._namespace_GVF1O('GVF1_0100') @classmethod def ReadType(cls): """Type of reads obtained for a given technology platform. (cls, http://www.biointerchange.org/gvf1o#GVF1_0109) """ return cls._namespace_GVF1O('GVF1_0109') @classmethod def DataType(cls): """Determines the datatype of a variant sequence. (cls, http://www.biointerchange.org/gvf1o#GVF1_0114) """ return cls._namespace_GVF1O('GVF1_0114') @classmethod def Landmark(cls): """A landmark that establishes the coordinate system for features. (cls, http://www.biointerchange.org/gvf1o#GVF1_0135) """ return cls._namespace_GVF1O('GVF1_0135') @classmethod def Sex(cls): """For single individual sets, the Sex class' OWL-individuals can be used to specify the sex of the sequenced (cls, real-life) individuals. (http://www.biointerchange.org/gvf1o#GVF1_0140) """ return cls._namespace_GVF1O('GVF1_0140') @classmethod def GenomicSource(cls): """An enumerated class for determining the genomic source (cls, cell type) of sequenced data. (http://www.biointerchange.org/gvf1o#GVF1_0141) """ return cls._namespace_GVF1O('GVF1_0141') @classmethod def StructuredAttribute(cls): """Representation of attribute tag/value pairs that are specific to particular structured attributes, but which are not covered by the GVF specification. (cls, http://www.biointerchange.org/gvf1o#GVF1_0151) """ return cls._namespace_GVF1O('GVF1_0151') @classmethod def Positive(cls): """Location on the positive (cls, forward) strand. (http://www.biointerchange.org/gvf1o#GVF1_0017) """ return cls._namespace_GVF1O('GVF1_0017') @classmethod def Negative(cls): """Location on the negative (cls, reverse) strand. (http://www.biointerchange.org/gvf1o#GVF1_0018) """ return cls._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. (http://www.biointerchange.org/gvf1o#GVF1_0019) """ return cls._namespace_GVF1O('GVF1_0019') @classmethod def NotStranded(cls): """Strand is not applicable. (cls, http://www.biointerchange.org/gvf1o#GVF1_0020) """ return cls._namespace_GVF1O('GVF1_0020') @classmethod def Heterozygous(cls): """Denotes heterozygous alleles. (cls, http://www.biointerchange.org/gvf1o#GVF1_0085) """ return cls._namespace_GVF1O('GVF1_0085') @classmethod def Homozygous(cls): """Denotes homozygous alleles. (cls, http://www.biointerchange.org/gvf1o#GVF1_0086) """ return cls._namespace_GVF1O('GVF1_0086') @classmethod def Hemizygous(cls): """Denotes hemizygous alleles. (cls, http://www.biointerchange.org/gvf1o#GVF1_0087) """ return cls._namespace_GVF1O('GVF1_0087') @classmethod def Fragment(cls): """Denotes reads that are fragments. (cls, http://www.biointerchange.org/gvf1o#GVF1_0110) """ return cls._namespace_GVF1O('GVF1_0110') @classmethod def Pair(cls): """Denotes reads that are pairs. (cls, http://www.biointerchange.org/gvf1o#GVF1_0111) """ return cls._namespace_GVF1O('GVF1_0111') @classmethod def DNASequence(cls): """Denotes a DNA sequence. (cls, http://www.biointerchange.org/gvf1o#GVF1_0115) """ return cls._namespace_GVF1O('GVF1_0115') @classmethod def RNASequence(cls): """Denotes an RNA sequence. (cls, http://www.biointerchange.org/gvf1o#GVF1_0116) """ return cls._namespace_GVF1O('GVF1_0116') @classmethod def DNAMicroarray(cls): """Denotes a DNA microarray probe. (cls, http://www.biointerchange.org/gvf1o#GVF1_0117) """ return cls._namespace_GVF1O('GVF1_0117') @classmethod def ArrayComparativeGenomicHybridization(cls): """Denotes an array-comparative genomic hybridization. (cls, http://www.biointerchange.org/gvf1o#GVF1_0118) """ return cls._namespace_GVF1O('GVF1_0118') @classmethod def Female(cls): """Denotes that a Set contains features of a female. (cls, http://www.biointerchange.org/gvf1o#GVF1_0142) """ return cls._namespace_GVF1O('GVF1_0142') @classmethod def Male(cls): """Denotes that a Set contains features of a male. (cls, http://www.biointerchange.org/gvf1o#GVF1_0143) """ return cls._namespace_GVF1O('GVF1_0143') @classmethod def Prenatal(cls): """Denotes that a set contains features of prenatal cells. (cls, http://www.biointerchange.org/gvf1o#GVF1_0144) """ return cls._namespace_GVF1O('GVF1_0144') @classmethod def Germline(cls): """Denotes that a set contains features of germline cells. (cls, http://www.biointerchange.org/gvf1o#GVF1_0145) """ return cls._namespace_GVF1O('GVF1_0145') @classmethod def Somatic(cls): """Denotes that a set contains features of somatic cells. (cls, http://www.biointerchange.org/gvf1o#GVF1_0146) """ return cls._namespace_GVF1O('GVF1_0146') @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 == cls._namespace_GVF1O('GVF1_0004'): return True if uri == cls._namespace_GVF1O('GVF1_0010'): return True if uri == cls._namespace_GVF1O('GVF1_0012'): return True if uri == cls._namespace_GVF1O('GVF1_0014'): return True if uri == cls._namespace_GVF1O('GVF1_0015'): return True if uri == cls._namespace_GVF1O('GVF1_0021'): return True if uri == cls._namespace_GVF1O('GVF1_0023'): return True if uri == cls._namespace_GVF1O('GVF1_0034'): return True if uri == cls._namespace_GVF1O('GVF1_0036'): return True if uri == cls._namespace_GVF1O('GVF1_0038'): return True if uri == cls._namespace_GVF1O('GVF1_0041'): return True if uri == cls._namespace_GVF1O('GVF1_0042'): return True if uri == cls._namespace_GVF1O('GVF1_0043'): return True if uri == cls._namespace_GVF1O('GVF1_0046'): return True if uri == cls._namespace_GVF1O('GVF1_0047'): return True if uri == cls._namespace_GVF1O('GVF1_0051'): return True if uri == cls._namespace_GVF1O('GVF1_0053'): return True if uri == cls._namespace_GVF1O('GVF1_0066'): return True if uri == cls._namespace_GVF1O('GVF1_0067'): return True if uri == cls._namespace_GVF1O('GVF1_0068'): return True if uri == cls._namespace_GVF1O('GVF1_0069'): return True if uri == cls._namespace_GVF1O('GVF1_0070'): return True if uri == cls._namespace_GVF1O('GVF1_0072'): return True if uri == cls._namespace_GVF1O('GVF1_0075'): return True if uri == cls._namespace_GVF1O('GVF1_0078'): return True if uri == cls._namespace_GVF1O('GVF1_0079'): return True if uri == cls._namespace_GVF1O('GVF1_0080'): return True if uri == cls._namespace_GVF1O('GVF1_0083'): return True if uri == cls._namespace_GVF1O('GVF1_0089'): return True if uri == cls._namespace_GVF1O('GVF1_0090'): return True if uri == cls._namespace_GVF1O('GVF1_0091'): return True if uri == cls._namespace_GVF1O('GVF1_0102'): return True if uri == cls._namespace_GVF1O('GVF1_0103'): return True if uri == cls._namespace_GVF1O('GVF1_0104'): return True if uri == cls._namespace_GVF1O('GVF1_0112'): return True if uri == cls._namespace_GVF1O('GVF1_0119'): return True if uri == cls._namespace_GVF1O('GVF1_0120'): return True if uri == cls._namespace_GVF1O('GVF1_0121'): return True if uri == cls._namespace_GVF1O('GVF1_0122'): return True if uri == cls._namespace_GVF1O('GVF1_0123'): return True if uri == cls._namespace_GVF1O('GVF1_0124'): return True if uri == cls._namespace_GVF1O('GVF1_0125'): return True if uri == cls._namespace_GVF1O('GVF1_0126'): return True if uri == cls._namespace_GVF1O('GVF1_0127'): return True if uri == cls._namespace_GVF1O('GVF1_0128'): return True if uri == cls._namespace_GVF1O('GVF1_0129'): return True if uri == cls._namespace_GVF1O('GVF1_0130'): return True if uri == cls._namespace_GVF1O('GVF1_0131'): return True if uri == cls._namespace_GVF1O('GVF1_0147'): return True if uri == cls._namespace_GVF1O('GVF1_0148'): return True if uri == cls._namespace_GVF1O('GVF1_0150'): return True if uri == cls._namespace_GVF1O('GVF1_0152'): return True if uri == cls._namespace_GVF1O('GVF1_0155'): 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 == cls._namespace_GVF1O('GVF1_0005'): return True if uri == cls._namespace_GVF1O('GVF1_0006'): return True if uri == cls._namespace_GVF1O('GVF1_0007'): return True if uri == cls._namespace_GVF1O('GVF1_0008'): return True if uri == cls._namespace_GVF1O('GVF1_0009'): return True if uri == cls._namespace_GVF1O('GVF1_0013'): return True if uri == cls._namespace_GVF1O('GVF1_0022'): return True if uri == cls._namespace_GVF1O('GVF1_0024'): return True if uri == cls._namespace_GVF1O('GVF1_0025'): return True if uri == cls._namespace_GVF1O('GVF1_0026'): return True if uri == cls._namespace_GVF1O('GVF1_0027'): return True if uri == cls._namespace_GVF1O('GVF1_0031'): return True if uri == cls._namespace_GVF1O('GVF1_0032'): return True if uri == cls._namespace_GVF1O('GVF1_0037'): return True if uri == cls._namespace_GVF1O('GVF1_0039'): return True if uri == cls._namespace_GVF1O('GVF1_0044'): return True if uri == cls._namespace_GVF1O('GVF1_0048'): return True if uri == cls._namespace_GVF1O('GVF1_0049'): return True if uri == cls._namespace_GVF1O('GVF1_0050'): return True if uri == cls._namespace_GVF1O('GVF1_0054'): return True if uri == cls._namespace_GVF1O('GVF1_0055'): return True if uri == cls._namespace_GVF1O('GVF1_0056'): return True if uri == cls._namespace_GVF1O('GVF1_0057'): return True if uri == cls._namespace_GVF1O('GVF1_0059'): return True if uri == cls._namespace_GVF1O('GVF1_0060'): return True if uri == cls._namespace_GVF1O('GVF1_0061'): return True if uri == cls._namespace_GVF1O('GVF1_0063'): return True if uri == cls._namespace_GVF1O('GVF1_0064'): return True if uri == cls._namespace_GVF1O('GVF1_0065'): return True if uri == cls._namespace_GVF1O('GVF1_0071'): return True if uri == cls._namespace_GVF1O('GVF1_0073'): return True if uri == cls._namespace_GVF1O('GVF1_0074'): return True if uri == cls._namespace_GVF1O('GVF1_0076'): return True if uri == cls._namespace_GVF1O('GVF1_0077'): return True if uri == cls._namespace_GVF1O('GVF1_0081'): return True if uri == cls._namespace_GVF1O('GVF1_0082'): return True if uri == cls._namespace_GVF1O('GVF1_0092'): return True if uri == cls._namespace_GVF1O('GVF1_0093'): return True if uri == cls._namespace_GVF1O('GVF1_0094'): return True if uri == cls._namespace_GVF1O('GVF1_0095'): return True if uri == cls._namespace_GVF1O('GVF1_0096'): return True if uri == cls._namespace_GVF1O('GVF1_0101'): return True if uri == cls._namespace_GVF1O('GVF1_0105'): return True if uri == cls._namespace_GVF1O('GVF1_0106'): return True if uri == cls._namespace_GVF1O('GVF1_0107'): return True if uri == cls._namespace_GVF1O('GVF1_0108'): return True if uri == cls._namespace_GVF1O('GVF1_0113'): return True if uri == cls._namespace_GVF1O('GVF1_0132'): return True if uri == cls._namespace_GVF1O('GVF1_0133'): return True if uri == cls._namespace_GVF1O('GVF1_0134'): return True if uri == cls._namespace_GVF1O('GVF1_0136'): return True if uri == cls._namespace_GVF1O('GVF1_0137'): return True if uri == cls._namespace_GVF1O('GVF1_0138'): return True if uri == cls._namespace_GVF1O('GVF1_0139'): return True if uri == cls._namespace_GVF1O('GVF1_0149'): return True if uri == cls._namespace_GVF1O('GVF1_0153'): return True if uri == cls._namespace_GVF1O('GVF1_0154'): return True if uri == cls._namespace_GVF1O('GVF1_0156'): return True if uri == cls._namespace_GVF1O('GVF1_0157'): return True if uri == cls._namespace_GVF1O('GVF1_0158'): 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 == cls._namespace_GVF1O('GVF1_0001'): return True if uri == cls._namespace_GVF1O('GVF1_0002'): return True if uri == cls._namespace_GVF1O('GVF1_0003'): return True if uri == cls._namespace_GVF1O('GVF1_0016'): return True if uri == cls._namespace_GVF1O('GVF1_0033'): return True if uri == cls._namespace_GVF1O('GVF1_0035'): return True if uri == cls._namespace_GVF1O('GVF1_0040'): return True if uri == cls._namespace_GVF1O('GVF1_0045'): return True if uri == cls._namespace_GVF1O('GVF1_0052'): return True if uri == cls._namespace_GVF1O('GVF1_0058'): return True if uri == cls._namespace_GVF1O('GVF1_0084'): return True if uri == cls._namespace_GVF1O('GVF1_0088'): return True if uri == cls._namespace_GVF1O('GVF1_0097'): return True if uri == cls._namespace_GVF1O('GVF1_0098'): return True if uri == cls._namespace_GVF1O('GVF1_0099'): return True if uri == cls._namespace_GVF1O('GVF1_0100'): return True if uri == cls._namespace_GVF1O('GVF1_0109'): return True if uri == cls._namespace_GVF1O('GVF1_0114'): return True if uri == cls._namespace_GVF1O('GVF1_0135'): return True if uri == cls._namespace_GVF1O('GVF1_0140'): return True if uri == cls._namespace_GVF1O('GVF1_0141'): return True if uri == cls._namespace_GVF1O('GVF1_0151'): 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 == cls._namespace_GVF1O('GVF1_0017'): return True if uri == cls._namespace_GVF1O('GVF1_0018'): return True if uri == cls._namespace_GVF1O('GVF1_0019'): return True if uri == cls._namespace_GVF1O('GVF1_0020'): return True if uri == cls._namespace_GVF1O('GVF1_0085'): return True if uri == cls._namespace_GVF1O('GVF1_0086'): return True if uri == cls._namespace_GVF1O('GVF1_0087'): return True if uri == cls._namespace_GVF1O('GVF1_0110'): return True if uri == cls._namespace_GVF1O('GVF1_0111'): return True if uri == cls._namespace_GVF1O('GVF1_0115'): return True if uri == cls._namespace_GVF1O('GVF1_0116'): return True if uri == cls._namespace_GVF1O('GVF1_0117'): return True if uri == cls._namespace_GVF1O('GVF1_0118'): return True if uri == cls._namespace_GVF1O('GVF1_0142'): return True if uri == cls._namespace_GVF1O('GVF1_0143'): return True if uri == cls._namespace_GVF1O('GVF1_0144'): return True if uri == cls._namespace_GVF1O('GVF1_0145'): return True if uri == cls._namespace_GVF1O('GVF1_0146'): 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 @classmethod def _namespace_GVF1O(cls, accession): return Namespace('http://www.biointerchange.org/gvf1o#')[accession] __parent_properties = { Namespace('http://www.biointerchange.org/gvf1o#GVF1_0004') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0010') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0012') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0014') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0015') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0068') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0021') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0023') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0068') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0034') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0036') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0038') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0069') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0041') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0069') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0042') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0070') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0043') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0070') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0046') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0070') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0047') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0070') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0051') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0067') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0053') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0069') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0072') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0075') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0078') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0079') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0075') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0080') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0083') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0075') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0090') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0089') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0091') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0089') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0102') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0112') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0103') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0112') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0104') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0112') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0119') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0102') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0120') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0103') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0121') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0122') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0123') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0124') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0125') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0068') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0126') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0070') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0127') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0075') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0129') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0128') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0130') : 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