biointerchange 0.1.0 → 0.1.2

data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java

@@ -0,0 +1,946 @@
+package org.biointerchange.vocabulary;
+
+import java.util.Arrays;
+import java.util.Map;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Set;
+import com.hp.hpl.jena.rdf.model.Property;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.ResourceFactory;
+import org.apache.commons.collections.CollectionUtils;
+import org.apache.commons.collections.Predicate;
+
+public class GVF1O {
+
+  /**
+   * Strand of the feature.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0010)
+   */
+  public static Resource strand() {
+    return _namespace_GVF1O("GVF1_0010");
+  }
+
+  /**
+   * Tag name/value pair attributes of a feature.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0012)
+   */
+  public static Resource attributes() {
+    return _namespace_GVF1O("GVF1_0012");
+  }
+
+  /**
+   * Link out to the parent feature.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0014)
+   */
+  public static Resource parent() {
+    return _namespace_GVF1O("GVF1_0014");
+  }
+
+  /**
+   * Relationship that describes which features belong to a feature set.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0015)
+   */
+  public static Resource contains() {
+    return _namespace_GVF1O("GVF1_0015");
+  }
+
+  /**
+   * Either:
+   *   FALDO "Region" instance replacement for a feature"s start, stop, strand properties.
+   *   (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)
+   */
+  public static Set<Resource> region() {
+    return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0021"), _namespace_GVF1O("GVF1_0079") }));
+  }
+
+  /**
+   * NCBI Taxonomy Ontology "NCBITaxon_1" (or sub-classes) instance that denotes the species for a feature set.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0023)
+   */
+  public static Resource species() {
+    return _namespace_GVF1O("GVF1_0023");
+  }
+
+  /**
+   * Specific information about the variant(s) of a feature.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0034)
+   */
+  public static Resource variant() {
+    return _namespace_GVF1O("GVF1_0034");
+  }
+
+  /**
+   * Links to information about an individual.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0036)
+   */
+  public static Resource individual() {
+    return _namespace_GVF1O("GVF1_0036");
+  }
+
+  /**
+   * An effect of a particular feature variant.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0041)
+   */
+  public static Resource effect() {
+    return _namespace_GVF1O("GVF1_0041");
+  }
+
+  /**
+   * Effect of a sequence alteration on a sequence feature.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0042)
+   */
+  public static Resource sequence_variant() {
+    return _namespace_GVF1O("GVF1_0042");
+  }
+
+  /**
+   * A term that is describing the sequence feature that is being affected.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0043)
+   */
+  public static Resource feature_type() {
+    return _namespace_GVF1O("GVF1_0043");
+  }
+
+  /**
+   * Features that are affected by this sequence alteration effect.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0044)
+   */
+  public static Resource feature_id() {
+    return _namespace_GVF1O("GVF1_0044");
+  }
+
+  /**
+   * A coordinate range for ambiguous start coordinates.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0046)
+   */
+  public static Resource start_range() {
+    return _namespace_GVF1O("GVF1_0046");
+  }
+
+  /**
+   * A coordinate range for ambiguous start coordinates.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0047)
+   */
+  public static Resource end_range() {
+    return _namespace_GVF1O("GVF1_0047");
+  }
+
+  /**
+   * Denotes abstract chromosome representations for capturing variants that appear on the same chromosome of a polyploid organism.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0051)
+   */
+  public static Resource chromosome() {
+    return _namespace_GVF1O("GVF1_0051");
+  }
+
+  /**
+   * Determines the genotype as observed in an individual.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0053)
+   */
+  public static Resource genotype() {
+    return _namespace_GVF1O("GVF1_0053");
+  }
+
+  /**
+   * Either:
+   *   Properties that are directly associated with Feature class instances.
+   *   (http://www.biointerchange.org/gvf1o#GVF1_0066)
+   * Or:
+   *   Properties that are directly associated with Feature class instances.
+   *   (http://www.biointerchange.org/gvf1o#GVF1_0059)
+   */
+  public static Set<Resource> feature_properties() {
+    return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0066"), _namespace_GVF1O("GVF1_0059") }));
+  }
+
+  /**
+   * Either:
+   *   Properties that are directly associated with SequencedIndividual class instances.
+   *   (http://www.biointerchange.org/gvf1o#GVF1_0067)
+   * Or:
+   *   Properties that are directly associated with SequencedIndividual class instances.
+   *   (http://www.biointerchange.org/gvf1o#GVF1_0065)
+   */
+  public static Set<Resource> sequencedindividual_properties() {
+    return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0067"), _namespace_GVF1O("GVF1_0065") }));
+  }
+
+  /**
+   * Either:
+   *   Properties that are directly associated with Set class instances.
+   *   (http://www.biointerchange.org/gvf1o#GVF1_0068)
+   * Or:
+   *   Properties that are directly associated with Set class instances.
+   *   (http://www.biointerchange.org/gvf1o#GVF1_0063)
+   */
+  public static Set<Resource> set_properties() {
+    return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0068"), _namespace_GVF1O("GVF1_0063") }));
+  }
+
+  /**
+   * Either:
+   *   Properties that are directly associated with Variant class instances.
+   *   (http://www.biointerchange.org/gvf1o#GVF1_0069)
+   * Or:
+   *   Properties that are directly associated with Variant class instances.
+   *   (http://www.biointerchange.org/gvf1o#GVF1_0060)
+   */
+  public static Set<Resource> variant_properties() {
+    return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0069"), _namespace_GVF1O("GVF1_0060") }));
+  }
+
+  /**
+   * Properties that are directly associated with Effect class instances.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0070)
+   */
+  public static Resource effect_properties() {
+    return _namespace_GVF1O("GVF1_0070");
+  }
+
+  /**
+   * Either:
+   *   Properties that are directly associated with Breakpoint class instances.
+   *   (http://www.biointerchange.org/gvf1o#GVF1_0075)
+   * Or:
+   *   Properties that are directly associated with Breakpoint class instances.
+   *   (http://www.biointerchange.org/gvf1o#GVF1_0071)
+   */
+  public static Set<Resource> breakpoint_properties() {
+    return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0075"), _namespace_GVF1O("GVF1_0071") }));
+  }
+
+  /**
+   * A database cross-reference to associate a sequence alteration to its  representation in another database.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0078)
+   */
+  public static Resource dbxref() {
+    return _namespace_GVF1O("GVF1_0078");
+  }
+
+  /**
+   * Either:
+   *   ID of the landmark that establishes the coordinate system for a feature.
+   *   (http://www.biointerchange.org/gvf1o#GVF1_0004)
+   * Or:
+   *   ID of the landmark that establishes the coordinate system for a breakpoint.
+   *   (http://www.biointerchange.org/gvf1o#GVF1_0072)
+   */
+  public static Set<Resource> seqid() {
+    return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0004"), _namespace_GVF1O("GVF1_0072") }));
+  }
+
+  /**
+   * 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.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0005)
+   */
+  public static Resource source() {
+    return _namespace_GVF1O("GVF1_0005");
+  }
+
+  /**
+   * Type of the feature, which is either a term from the "lite" version of the Sequence Ontology (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.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0006)
+   */
+  public static Resource type() {
+    return _namespace_GVF1O("GVF1_0006");
+  }
+
+  /**
+   * Either:
+   *   Start coordinate of the feature on the seqid landmark.
+   *   (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)
+   */
+  public static Set<Resource> start() {
+    return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0007"), _namespace_GVF1O("GVF1_0048"), _namespace_GVF1O("GVF1_0073") }));
+  }
+
+  /**
+   * Either:
+   *   End coordinate of the feature on the seqid landmark.
+   *   (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)
+   */
+  public static Set<Resource> end() {
+    return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0008"), _namespace_GVF1O("GVF1_0049"), _namespace_GVF1O("GVF1_0074") }));
+  }
+
+  /**
+   * Score of the feature. For example, an E-value for sequence similarity features or a P-value for ab initio gene prediction features.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0009)
+   */
+  public static Resource score() {
+    return _namespace_GVF1O("GVF1_0009");
+  }
+
+  /**
+   * Tag name of a feature attribute.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0013)
+   */
+  public static Resource tag() {
+    return _namespace_GVF1O("GVF1_0013");
+  }
+
+  /**
+   * Version of the GVF specification that defines the feature set contents.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0022)
+   */
+  public static Resource version() {
+    return _namespace_GVF1O("GVF1_0022");
+  }
+
+  /**
+   * Name of a genome assembly build that denotes the provenance of features in a feature set. For example, "NCBI 36" or "FlyBase r4.1".
+   * (http://www.biointerchange.org/gvf1o#GVF1_0024)
+   */
+  public static Resource build() {
+    return _namespace_GVF1O("GVF1_0024");
+  }
+
+  /**
+   * All sequence variations at a locus -- including the reference sequence when appropriate (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)
+   */
+  public static Resource variant_seq() {
+    return _namespace_GVF1O("GVF1_0025");
+  }
+
+  /**
+   * A unique identifier for the feature within the feature set.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0026)
+   */
+  public static Resource id() {
+    return _namespace_GVF1O("GVF1_0026");
+  }
+
+  /**
+   * Secondary name of a feature, which can be HGVS/ISCN nomenclature names, but not cross-references to databases (e.g. dbSNP, OMIM) which should use the dbxref property.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0027)
+   */
+  public static Resource alias() {
+    return _namespace_GVF1O("GVF1_0027");
+  }
+
+  /**
+   * Name of an external database. For example, "dbSNP" or "OMIM".
+   * (http://www.biointerchange.org/gvf1o#GVF1_0029)
+   */
+  public static Resource name() {
+    return _namespace_GVF1O("GVF1_0029");
+  }
+
+  /**
+   * External database identifier. For example, for dbSNP, this identifier could be "rs3131969".
+   * (http://www.biointerchange.org/gvf1o#GVF1_0030)
+   */
+  public static Resource xref() {
+    return _namespace_GVF1O("GVF1_0030");
+  }
+
+  /**
+   * Sequence from the reference genome.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0031)
+   */
+  public static Resource reference_seq() {
+    return _namespace_GVF1O("GVF1_0031");
+  }
+
+  /**
+   * Number of reads that are supporting this variant.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0032)
+   */
+  public static Resource variant_reads() {
+    return _namespace_GVF1O("GVF1_0032");
+  }
+
+  /**
+   * Total number of reads.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0037)
+   */
+  public static Resource total_reads() {
+    return _namespace_GVF1O("GVF1_0037");
+  }
+
+  /**
+   * Zygosity of a feature locus.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0038)
+   */
+  public static Resource zygosity() {
+    return _namespace_GVF1O("GVF1_0038");
+  }
+
+  /**
+   * Frequency of a variant in a population.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0039)
+   */
+  public static Resource variant_freq() {
+    return _namespace_GVF1O("GVF1_0039");
+  }
+
+  /**
+   * Unclear from GVF specification.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0050)
+   */
+  public static Resource phased() {
+    return _namespace_GVF1O("GVF1_0050");
+  }
+
+  /**
+   * Describes the codon that overlaps this variant.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0054)
+   */
+  public static Resource variant_codon() {
+    return _namespace_GVF1O("GVF1_0054");
+  }
+
+  /**
+   * Describes the codon from the reference sequence whose coordinates overlap with this variant.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0055)
+   */
+  public static Resource reference_codon() {
+    return _namespace_GVF1O("GVF1_0055");
+  }
+
+  /**
+   * Amino acid that overlaps with the variant.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0056)
+   */
+  public static Resource variant_aa() {
+    return _namespace_GVF1O("GVF1_0056");
+  }
+
+  /**
+   * Amino acid in the reference genome that overlaps with a variant"s genome coordinates.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0057)
+   */
+  public static Resource reference_aa() {
+    return _namespace_GVF1O("GVF1_0057");
+  }
+
+  /**
+   * Properties that are directly associated with Range class instances.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0061)
+   */
+  public static Resource range_properties() {
+    return _namespace_GVF1O("GVF1_0061");
+  }
+
+  /**
+   * Properties that are directly associated with DBXRef class instances.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0062)
+   */
+  public static Resource dbxref_properties() {
+    return _namespace_GVF1O("GVF1_0062");
+  }
+
+  /**
+   * Properties that are directly associated with Attribute class instances.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0064)
+   */
+  public static Resource attribute_properties() {
+    return _namespace_GVF1O("GVF1_0064");
+  }
+
+  /**
+   * Sequence context (positive strand) of a feature on the 5" end.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0076)
+   */
+  public static Resource a_context() {
+    return _namespace_GVF1O("GVF1_0076");
+  }
+
+  /**
+   * Set of genomic sequence features, whose identifiers are unique within the set.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0001)
+   */
+  public static Resource Set() {
+    return _namespace_GVF1O("GVF1_0001");
+  }
+
+  /**
+   * A genomic sequence feature.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0002)
+   */
+  public static Resource Feature() {
+    return _namespace_GVF1O("GVF1_0002");
+  }
+
+  public static Resource Attribute() {
+    return _namespace_GVF1O("GVF1_0003");
+  }
+
+  /**
+   * Class describing a genomic strand. Instances of the class (individuals) are used to denote forward-/reverse-strands, etc.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0016)
+   */
+  public static Resource Strand() {
+    return _namespace_GVF1O("GVF1_0016");
+  }
+
+  /**
+   * A class describing relationships between features and external databases.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0028)
+   */
+  public static Resource DBXRef() {
+    return _namespace_GVF1O("GVF1_0028");
+  }
+
+  /**
+   * Describing specific alterations of a feature.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0033)
+   */
+  public static Resource Variant() {
+    return _namespace_GVF1O("GVF1_0033");
+  }
+
+  /**
+   * Aggregated sequencing information for a particular individual.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0035)
+   */
+  public static Resource SequencedIndividual() {
+    return _namespace_GVF1O("GVF1_0035");
+  }
+
+  /**
+   * Describing the effect of a feature variant.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0040)
+   */
+  public static Resource Effect() {
+    return _namespace_GVF1O("GVF1_0040");
+  }
+
+  /**
+   * Describe ambiguity in either start or end coordinates.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0045)
+   */
+  public static Resource Range() {
+    return _namespace_GVF1O("GVF1_0045");
+  }
+
+  /**
+   * An abstract representation of a chromosome to represent ploidy.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0052)
+   */
+  public static Resource Chromosome() {
+    return _namespace_GVF1O("GVF1_0052");
+  }
+
+  /**
+   * Describes the source or destination of a zero-length sequence alteration.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0058)
+   */
+  public static Resource Breakpoint() {
+    return _namespace_GVF1O("GVF1_0058");
+  }
+
+  /**
+   * Location on the positive (forward) strand.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0017)
+   */
+  public static Resource Positive() {
+    return _namespace_GVF1O("GVF1_0017");
+  }
+
+  /**
+   * Location on the negative (reverse) strand.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0018)
+   */
+  public static Resource Negative() {
+    return _namespace_GVF1O("GVF1_0018");
+  }
+
+  /**
+   * Strand was not determined, which leaves it open whether the location is on the positive (forward) or negative (reverse) strand.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0019)
+   */
+  public static Resource UnknownStrand() {
+    return _namespace_GVF1O("GVF1_0019");
+  }
+
+  /**
+   * Strand is not applicable.
+   * (http://www.biointerchange.org/gvf1o#GVF1_0020)
+   */
+  public static Resource NotStranded() {
+    return _namespace_GVF1O("GVF1_0020");
+  }
+
+  /**
+   * Determines whether the given URI is an object property.
+   * 
+   * @param uri URI that is tested for being an object property
+   */
+  public static boolean isObjectProperty(Resource uri) {
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0010"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0012"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0014"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0015"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0021"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0023"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0034"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0036"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0041"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0042"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0043"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0044"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0046"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0047"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0051"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0053"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0067"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0068"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0069"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0070"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0075"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0078"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0079"))) {
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * Determines whether the given URI is a datatype property.
+   * 
+   * @param uri URI that is tested for being a datatype property
+   */
+  public static boolean isDatatypeProperty(Resource uri) {
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0004"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0005"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0006"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0007"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0008"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0009"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0013"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0022"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0024"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0025"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0026"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0027"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0029"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0030"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0031"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0032"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0037"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0038"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0039"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0048"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0049"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0050"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0054"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0055"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0056"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0057"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0060"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0061"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0062"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0063"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0064"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0065"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0071"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0072"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0073"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0074"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0076"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0077"))) {
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * Determines whether the given URI is a class.
+   * 
+   * @param uri URI that is tested for being a class
+   */
+  public static boolean isClass(Resource uri) {
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0001"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0002"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0003"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0016"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0028"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0033"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0035"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0040"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0045"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0052"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0058"))) {
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * Determines whether the given URI is a named individual.
+   * 
+   * @param uri URI that is tested for being a named individual
+   */
+  public static boolean isNamedIndividual(Resource uri) {
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0017"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0018"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0019"))) {
+      return true;
+    }
+    if (uri.equals(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0020"))) {
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * Returns only those URIs that fall under a designated parent URI.
+   * 
+   * @param uris Set of URIs that are tested whether they have the given parent URI.
+   * @param parent Parent URI.
+   */
+  public static Set<Resource> withParent(Set<Resource> uris, final Resource parent) {
+    return new HashSet<Resource>(CollectionUtils.select(uris, new Predicate() { public boolean evaluate(Object uri) { return hasParent((Resource)uri, parent); } }));
+  }
+
+  /**
+   * Recursively tries to determine the parent for a given URI.
+   * 
+   * @param uri URI that is tested for whether it has the given parent URI.
+   * @param parent Parent URI.
+   */
+  public static boolean hasParent(Resource uri, Resource parent) {
+    if (__parent_properties.containsKey(uri)) {
+      if (__parent_properties.get(uri).equals(parent)) {
+        return true;
+      }
+      return hasParent((Resource)__parent_properties.get(uri), parent);
+    }
+    return false;
+  }
+
+  private static Resource _namespace_GVF1O(String accession) {
+    if (isClass(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#" + accession))) {
+      return ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#" + accession);
+    } else {
+      return ResourceFactory.createProperty("http://www.biointerchange.org/gvf1o#" + accession);
+    }
+  }
+
+
+  private static Map<Resource, Resource> __parent_properties = _init___parent_properties();
+
+  private static Map<Resource, Resource> _init___parent_properties() {
+    Map<Resource, Resource> map = new HashMap<Resource, Resource>();
+
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0031"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0009"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0053"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0069"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0042"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0070"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0076"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0054"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0060"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0032"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0060"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0043"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0070"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0021"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0010"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0075"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0077"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0055"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0060"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0022"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0063"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0044"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0070"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0056"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0060"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0078"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0034"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0023"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0068"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0012"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0057"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0060"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0024"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0063"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0013"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0064"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0079"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0075"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0046"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0070"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0025"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0060"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0047"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0070"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0036"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0014"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0048"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0061"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0037"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0065"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0026"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0004"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0015"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0068"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0049"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0061"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0038"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0027"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0005"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0072"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0071"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0050"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0060"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0039"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0060"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0006"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0073"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0071"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0029"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0062"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0007"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0051"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0067"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0074"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0071"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0030"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0062"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0008"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059"));
+    map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0041"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0069"));
+
+    return map;
+  }
+
+
+}