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 { /** * Either: * Establishes the landmark (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) */ public static Set seqid() { return new HashSet(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0004"), _namespace_GVF1O("GVF1_0072") })); } /** * Either: * Strand of the feature. * (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) */ public static Set strand() { return new HashSet(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0010"), _namespace_GVF1O("GVF1_0083"), _namespace_GVF1O("GVF1_0091") })); } /** * Either: * Tag name/value pair attributes of a feature. * (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) */ public static Set attributes() { return new HashSet(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0012"), _namespace_GVF1O("GVF1_0152") })); } /** * 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) * Or: * FALDO "Region" instance replacement for a target"s start, stop, strand properties. * (http://www.biointerchange.org/gvf1o#GVF1_0090) */ public static Set region() { return new HashSet(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0021"), _namespace_GVF1O("GVF1_0079"), _namespace_GVF1O("GVF1_0090") })); } /** * 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"); } /** * Zygosity of a variant. * (http://www.biointerchange.org/gvf1o#GVF1_0038) */ public static Resource zygosity() { return _namespace_GVF1O("GVF1_0038"); } /** * 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"); } /** * 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 feature_properties() { return new HashSet(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 sequencedindividual_properties() { return new HashSet(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 set_properties() { return new HashSet(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 variant_properties() { return new HashSet(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0069"), _namespace_GVF1O("GVF1_0060") })); } /** * Either: * Properties that are directly associated with Effect class instances. * (http://www.biointerchange.org/gvf1o#GVF1_0070) * Or: * Properties that are directly associated with Effect class instances. * (http://www.biointerchange.org/gvf1o#GVF1_0158) */ public static Set effect_properties() { return new HashSet(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0070"), _namespace_GVF1O("GVF1_0158") })); } /** * 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 breakpoint_properties() { return new HashSet(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0075"), _namespace_GVF1O("GVF1_0071") })); } /** * Either: * A database cross-reference to associate a sequence alteration to its representation in another database. * (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) */ public static Set dbxref() { return new HashSet(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0078"), _namespace_GVF1O("GVF1_0104") })); } /** * Potential source or destination of zero-length sequence alterations. * (http://www.biointerchange.org/gvf1o#GVF1_0080) */ public static Resource breakpoint() { return _namespace_GVF1O("GVF1_0080"); } /** * Either: * Properties that are directly associated with Target class instances. * (http://www.biointerchange.org/gvf1o#GVF1_0089) * Or: * Properties that are directly associated with Target class instances. * (http://www.biointerchange.org/gvf1o#GVF1_0092) */ public static Set target_properties() { return new HashSet(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0089"), _namespace_GVF1O("GVF1_0092") })); } /** * Either: * Properties that are directly associated with TechnologyPlatform class instances. * (http://www.biointerchange.org/gvf1o#GVF1_0102) * Or: * Properties that are directly associated with TechnologyPlatform class instances. * (http://www.biointerchange.org/gvf1o#GVF1_0107) */ public static Set technologyplatform_properties() { return new HashSet(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0102"), _namespace_GVF1O("GVF1_0107") })); } /** * Properties that are directly associated with DataSource class instances. * (http://www.biointerchange.org/gvf1o#GVF1_0103) */ public static Resource datasource_properties() { return _namespace_GVF1O("GVF1_0103"); } /** * Either: * Properties describing structured pragma properties. * (http://www.biointerchange.org/gvf1o#GVF1_0112) * Or: * Properties describing structured pragma properties. * (http://www.biointerchange.org/gvf1o#GVF1_0113) */ public static Set structuredpragma_properties() { return new HashSet(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0112"), _namespace_GVF1O("GVF1_0113") })); } /** * Types of reads produced by the platform. * (http://www.biointerchange.org/gvf1o#GVF1_0119) */ public static Resource read_type() { return _namespace_GVF1O("GVF1_0119"); } /** * Datatype of this data source. * (http://www.biointerchange.org/gvf1o#GVF1_0120) */ public static Resource data_type() { return _namespace_GVF1O("GVF1_0120"); } /** * Technology platform that was used to derive the feature. * (http://www.biointerchange.org/gvf1o#GVF1_0121) */ public static Resource technology_platform() { return _namespace_GVF1O("GVF1_0121"); } /** * Data source origin of the feature. * (http://www.biointerchange.org/gvf1o#GVF1_0122) */ public static Resource data_source() { return _namespace_GVF1O("GVF1_0122"); } /** * Used scoring method. * (http://www.biointerchange.org/gvf1o#GVF1_0123) */ public static Resource score_method() { return _namespace_GVF1O("GVF1_0123"); } /** * Further information about the algorithm/methodologies used. * (http://www.biointerchange.org/gvf1o#GVF1_0124) */ public static Resource source_method() { return _namespace_GVF1O("GVF1_0124"); } /** * Further information about an individual"s phenotype. Applies only to single individual sets. * (http://www.biointerchange.org/gvf1o#GVF1_0125) */ public static Resource phenotype_description() { return _namespace_GVF1O("GVF1_0125"); } /** * Either: * Further information about the associated attribute(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) */ public static Set attribute_method() { return new HashSet(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0126"), _namespace_GVF1O("GVF1_0127"), _namespace_GVF1O("GVF1_0129"), _namespace_GVF1O("GVF1_0130"), _namespace_GVF1O("GVF1_0131") })); } /** * Either: * Properties about Attribute instances. * (http://www.biointerchange.org/gvf1o#GVF1_0128) * Or: * Properties that are directly associated with Attribute class instances. * (http://www.biointerchange.org/gvf1o#GVF1_0064) */ public static Set attribute_properties() { return new HashSet(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0128"), _namespace_GVF1O("GVF1_0064") })); } /** * Denotes the sex of the sequenced individual for single-individual sets. * (http://www.biointerchange.org/gvf1o#GVF1_0147) */ public static Resource sex() { return _namespace_GVF1O("GVF1_0147"); } /** * Denotes the source of genomic data (on a cell-type level). * (http://www.biointerchange.org/gvf1o#GVF1_0148) */ public static Resource genomic_source() { return _namespace_GVF1O("GVF1_0148"); } /** * 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. * (http://www.biointerchange.org/gvf1o#GVF1_0150) */ public static Resource feature_ontology() { return _namespace_GVF1O("GVF1_0150"); } /** * Identifies the target that the features aligns to. * (http://www.biointerchange.org/gvf1o#GVF1_0155) */ public static Resource target() { return _namespace_GVF1O("GVF1_0155"); } /** * 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 an entry the "lite" version of the Sequence Ontology (SOFA) or a child entry of sequence_feature (SO:0000110) of the full Sequence Ontology (SO). * (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) * 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) */ public static Set start() { return new HashSet(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0007"), _namespace_GVF1O("GVF1_0048"), _namespace_GVF1O("GVF1_0073"), _namespace_GVF1O("GVF1_0094"), _namespace_GVF1O("GVF1_0138") })); } /** * 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) * 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) */ public static Set end() { return new HashSet(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0008"), _namespace_GVF1O("GVF1_0049"), _namespace_GVF1O("GVF1_0074"), _namespace_GVF1O("GVF1_0095"), _namespace_GVF1O("GVF1_0139") })); } /** * 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"); } /** * Either: * Tag name of a feature attribute. * (http://www.biointerchange.org/gvf1o#GVF1_0013) * Or: * Tag name of an user defined structured attribute. * (http://www.biointerchange.org/gvf1o#GVF1_0154) */ public static Set tag() { return new HashSet(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0013"), _namespace_GVF1O("GVF1_0154") })); } /** * Version of the GVF specification that defines the feature set contents. * (http://www.biointerchange.org/gvf1o#GVF1_0022) */ public static Resource gvf_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"); } /** * Either: * A unique identifier for the feature within the feature set. * (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) */ public static Set id() { return new HashSet(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0026"), _namespace_GVF1O("GVF1_0137") })); } /** * 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"); } /** * 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"); } /** * Frequency of a variant in a population. * (http://www.biointerchange.org/gvf1o#GVF1_0039) */ public static Resource variant_freq() { return _namespace_GVF1O("GVF1_0039"); } /** * Features that are affected by this sequence alteration effect. This can be an external feature identifier, such as an Ensembl gene/transcript identifier. * (http://www.biointerchange.org/gvf1o#GVF1_0044) */ public static Resource feature() { return _namespace_GVF1O("GVF1_0044"); } /** * Either: * Unclear from GVF specification. * (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) */ public static Set phased() { return new HashSet(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0050"), _namespace_GVF1O("GVF1_0101") })); } /** * 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"); } /** * 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"); } /** * Version of the GFF specification that defines the feature set contents apart from GVF related definitions. * (http://www.biointerchange.org/gvf1o#GVF1_0081) */ public static Resource gff_version() { return _namespace_GVF1O("GVF1_0081"); } /** * Creation date of the GVF file that this set stems from. * (http://www.biointerchange.org/gvf1o#GVF1_0082) */ public static Resource file_date() { return _namespace_GVF1O("GVF1_0082"); } /** * ID or accession of the target alignment. * (http://www.biointerchange.org/gvf1o#GVF1_0093) */ public static Resource target_id() { return _namespace_GVF1O("GVF1_0093"); } /** * A cross-reference to an ontology term that is associated with a feature. * (http://www.biointerchange.org/gvf1o#GVF1_0096) */ public static Resource ontology_term() { return _namespace_GVF1O("GVF1_0096"); } /** * An arbitrary comment. Free text. * (http://www.biointerchange.org/gvf1o#GVF1_0105) */ public static Resource comment() { return _namespace_GVF1O("GVF1_0105"); } /** * Type of technology used to gather the variant data. Unrestricted range due to open specification. * (http://www.biointerchange.org/gvf1o#GVF1_0106) */ public static Resource platform_class() { return _namespace_GVF1O("GVF1_0106"); } /** * Sequencer or other machine used to collect the variant data. Unrestricted range due to open specification. * (http://www.biointerchange.org/gvf1o#GVF1_0108) */ public static Resource platform_name() { return _namespace_GVF1O("GVF1_0108"); } /** * Undocumented in GVF specification. * (http://www.biointerchange.org/gvf1o#GVF1_0132) */ public static Resource read_length() { return _namespace_GVF1O("GVF1_0132"); } /** * Undocumented in GVF specification. * (http://www.biointerchange.org/gvf1o#GVF1_0133) */ public static Resource read_pair_span() { return _namespace_GVF1O("GVF1_0133"); } /** * Undocumented in GVF specification. * (http://www.biointerchange.org/gvf1o#GVF1_0134) */ public static Resource average_coverage() { return _namespace_GVF1O("GVF1_0134"); } /** * Properties that are directly associated with Landmark class instances. * (http://www.biointerchange.org/gvf1o#GVF1_0136) */ public static Resource landmark_properties() { return _namespace_GVF1O("GVF1_0136"); } /** * Version of the GVF file that this set stems from. * (http://www.biointerchange.org/gvf1o#GVF1_0149) */ public static Resource file_version() { return _namespace_GVF1O("GVF1_0149"); } /** * Properties that are directly associated with StructuredAttribute class instances. * (http://www.biointerchange.org/gvf1o#GVF1_0153) */ public static Resource structuredattribute_properties() { return _namespace_GVF1O("GVF1_0153"); } /** * Either: * Sequence associated with this feature, if it has been specified using a FASTA string. * (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) */ public static Set sequence() { return new HashSet(Arrays.asList(new Resource[] { _namespace_GVF1O("GVF1_0156"), _namespace_GVF1O("GVF1_0157") })); } /** * 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"); } /** * Representation of attribute tag/value pairs that are not covered by specific classes such as Effect or Variant. * (http://www.biointerchange.org/gvf1o#GVF1_0003) */ 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"); } /** * 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"); } /** * Denotes the zygosity of alleles. * (http://www.biointerchange.org/gvf1o#GVF1_0084) */ public static Resource Zygosity() { return _namespace_GVF1O("GVF1_0084"); } /** * Indicates a feature"s "target" of a nucleotide-to-nucleotide or protein-to-nucleotide alignment. * (http://www.biointerchange.org/gvf1o#GVF1_0088) */ public static Resource Target() { return _namespace_GVF1O("GVF1_0088"); } /** * Details about the sequencing/microarray technology used to gather the data in a set. * (http://www.biointerchange.org/gvf1o#GVF1_0097) */ public static Resource TechnologyPlatform() { return _namespace_GVF1O("GVF1_0097"); } /** * 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. * (http://www.biointerchange.org/gvf1o#GVF1_0098) */ public static Resource DataSource() { return _namespace_GVF1O("GVF1_0098"); } /** * Information about the used scoring algorithm or method. * (http://www.biointerchange.org/gvf1o#GVF1_0099) */ public static Resource Method() { return _namespace_GVF1O("GVF1_0099"); } /** * Additional information about an individual"s phenotype. * (http://www.biointerchange.org/gvf1o#GVF1_0100) */ public static Resource PhenotypeDescription() { return _namespace_GVF1O("GVF1_0100"); } /** * Type of reads obtained for a given technology platform. * (http://www.biointerchange.org/gvf1o#GVF1_0109) */ public static Resource ReadType() { return _namespace_GVF1O("GVF1_0109"); } /** * Determines the datatype of a variant sequence. * (http://www.biointerchange.org/gvf1o#GVF1_0114) */ public static Resource DataType() { return _namespace_GVF1O("GVF1_0114"); } /** * A landmark that establishes the coordinate system for features. * (http://www.biointerchange.org/gvf1o#GVF1_0135) */ public static Resource Landmark() { return _namespace_GVF1O("GVF1_0135"); } /** * For single individual sets, the Sex class" OWL-individuals can be used to specify the sex of the sequenced (real-life) individuals. * (http://www.biointerchange.org/gvf1o#GVF1_0140) */ public static Resource Sex() { return _namespace_GVF1O("GVF1_0140"); } /** * An enumerated class for determining the genomic source (cell type) of sequenced data. * (http://www.biointerchange.org/gvf1o#GVF1_0141) */ public static Resource GenomicSource() { return _namespace_GVF1O("GVF1_0141"); } /** * Representation of attribute tag/value pairs that are specific to particular structured attributes, but which are not covered by the GVF specification. * (http://www.biointerchange.org/gvf1o#GVF1_0151) */ public static Resource StructuredAttribute() { return _namespace_GVF1O("GVF1_0151"); } /** * 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"); } /** * Denotes heterozygous alleles. * (http://www.biointerchange.org/gvf1o#GVF1_0085) */ public static Resource Heterozygous() { return _namespace_GVF1O("GVF1_0085"); } /** * Denotes homozygous alleles. * (http://www.biointerchange.org/gvf1o#GVF1_0086) */ public static Resource Homozygous() { return _namespace_GVF1O("GVF1_0086"); } /** * Denotes hemizygous alleles. * (http://www.biointerchange.org/gvf1o#GVF1_0087) */ public static Resource Hemizygous() { return _namespace_GVF1O("GVF1_0087"); } /** * Denotes reads that are fragments. * (http://www.biointerchange.org/gvf1o#GVF1_0110) */ public static Resource Fragment() { return _namespace_GVF1O("GVF1_0110"); } /** * Denotes reads that are pairs. * (http://www.biointerchange.org/gvf1o#GVF1_0111) */ public static Resource Pair() { return _namespace_GVF1O("GVF1_0111"); } /** * Denotes a DNA sequence. * (http://www.biointerchange.org/gvf1o#GVF1_0115) */ public static Resource DNASequence() { return _namespace_GVF1O("GVF1_0115"); } /** * Denotes an RNA sequence. * (http://www.biointerchange.org/gvf1o#GVF1_0116) */ public static Resource RNASequence() { return _namespace_GVF1O("GVF1_0116"); } /** * Denotes a DNA microarray probe. * (http://www.biointerchange.org/gvf1o#GVF1_0117) */ public static Resource DNAMicroarray() { return _namespace_GVF1O("GVF1_0117"); } /** * Denotes an array-comparative genomic hybridization. * (http://www.biointerchange.org/gvf1o#GVF1_0118) */ public static Resource ArrayComparativeGenomicHybridization() { return _namespace_GVF1O("GVF1_0118"); } /** * Denotes that a Set contains features of a female. * (http://www.biointerchange.org/gvf1o#GVF1_0142) */ public static Resource Female() { return _namespace_GVF1O("GVF1_0142"); } /** * Denotes that a Set contains features of a male. * (http://www.biointerchange.org/gvf1o#GVF1_0143) */ public static Resource Male() { return _namespace_GVF1O("GVF1_0143"); } /** * Denotes that a set contains features of prenatal cells. * (http://www.biointerchange.org/gvf1o#GVF1_0144) */ public static Resource Prenatal() { return _namespace_GVF1O("GVF1_0144"); } /** * Denotes that a set contains features of germline cells. * (http://www.biointerchange.org/gvf1o#GVF1_0145) */ public static Resource Germline() { return _namespace_GVF1O("GVF1_0145"); } /** * Denotes that a set contains features of somatic cells. * (http://www.biointerchange.org/gvf1o#GVF1_0146) */ public static Resource Somatic() { return _namespace_GVF1O("GVF1_0146"); } /** * 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(_namespace_GVF1O("GVF1_0004"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0010"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0012"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0014"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0015"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0021"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0023"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0034"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0036"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0038"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0041"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0042"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0043"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0046"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0047"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0051"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0053"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0066"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0067"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0068"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0069"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0070"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0072"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0075"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0078"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0079"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0080"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0083"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0089"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0090"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0091"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0102"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0103"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0104"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0112"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0119"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0120"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0121"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0122"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0123"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0124"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0125"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0126"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0127"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0128"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0129"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0130"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0131"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0147"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0148"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0150"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0152"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0155"))) { 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(_namespace_GVF1O("GVF1_0005"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0006"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0007"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0008"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0009"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0013"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0022"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0024"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0025"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0026"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0027"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0031"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0032"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0037"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0039"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0044"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0048"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0049"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0050"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0054"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0055"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0056"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0057"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0059"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0060"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0061"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0063"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0064"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0065"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0071"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0073"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0074"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0076"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0077"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0081"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0082"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0092"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0093"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0094"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0095"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0096"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0101"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0105"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0106"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0107"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0108"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0113"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0132"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0133"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0134"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0136"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0137"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0138"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0139"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0149"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0153"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0154"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0156"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0157"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0158"))) { 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(_namespace_GVF1O("GVF1_0001"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0002"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0003"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0016"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0033"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0035"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0040"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0045"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0052"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0058"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0084"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0088"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0097"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0098"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0099"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0100"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0109"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0114"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0135"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0140"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0141"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0151"))) { 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(_namespace_GVF1O("GVF1_0017"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0018"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0019"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0020"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0085"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0086"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0087"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0110"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0111"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0115"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0116"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0117"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0118"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0142"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0143"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0144"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0145"))) { return true; } if (uri.equals(_namespace_GVF1O("GVF1_0146"))) { 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 withParent(Set uris, final Resource parent) { return new HashSet(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) { return ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#" + accession); } private static Map __parent_properties = _init___parent_properties(); private static Map _init___parent_properties() { Map map = new HashMap(); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0004"), 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_0066")); 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_0014"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066")); 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_0021"), 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_0034"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066")); 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_0038"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0069")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0041"), 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_0043"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0070")); 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_0047"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0070")); 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_0053"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0069")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0072"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0075")); 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_0079"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0075")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0080"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0083"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0075")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0090"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0089")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0091"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0089")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0102"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0112")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0103"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0112")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0104"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0112")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0119"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0102")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0120"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0103")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0121"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0122"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0123"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0124"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0125"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0068")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0126"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0070")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0127"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0075")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0129"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0128")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0130"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0089")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0131"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0069")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0147"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0068")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0148"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0068")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0150"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0068")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0152"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0112")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0155"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0066")); 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_0006"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059")); 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_0008"), 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_0013"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0064")); 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_0024"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0063")); 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_0026"), 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_0031"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059")); 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_0037"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0065")); 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_0044"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0158")); 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_0049"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0061")); 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_0054"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0060")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0055"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059")); 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_0057"), 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_0074"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0071")); 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_0077"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0081"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0063")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0082"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0063")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0093"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0092")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0094"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0092")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0095"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0092")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0096"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0101"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0105"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0113")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0106"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0107")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0107"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0113")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0108"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0107")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0132"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0107")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0133"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0107")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0134"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0107")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0137"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0136")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0138"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0136")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0139"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0136")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0149"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0063")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0154"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0153")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0156"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0059")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0157"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0136")); map.put(ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0088"), ResourceFactory.createResource("http://www.biointerchange.org/gvf1o#GVF1_0151")); return map; } }