biointerchange 0.2.1 → 0.2.2

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

@@ -1,5 +1,4 @@
 package org.biointerchange.vocabulary;
-
 import java.util.Arrays;
 import java.util.Map;
 import java.util.HashMap;
@@ -11,6 +10,7 @@ import com.hp.hpl.jena.rdf.model.ResourceFactory;
 import org.apache.commons.collections.CollectionUtils;
 import org.apache.commons.collections.Predicate;
 
+
 public class SO {
 
   /**
@@ -23998,3 +23998,4 @@ public class SO {
 
 
 }
+

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

@@ -1,5 +1,4 @@
 package org.biointerchange.vocabulary;
-
 import java.util.Arrays;
 import java.util.Map;
 import java.util.HashMap;
@@ -11,6 +10,7 @@ import com.hp.hpl.jena.rdf.model.ResourceFactory;
 import org.apache.commons.collections.CollectionUtils;
 import org.apache.commons.collections.Predicate;
 
+
 public class SOFA {
 
   public static Resource adjacent_to() {
@@ -2947,10 +2947,10 @@ public class SOFA {
   }
 
   private static Resource _namespace_SOFA(String accession) {
-    if (isClass(ResourceFactory.createResource("http://purl.obolibrary.org/obo/http_//purl.org/obo/" + accession))) {
-      return ResourceFactory.createResource("http://purl.obolibrary.org/obo/http_//purl.org/obo/" + accession);
+    if (isClass(ResourceFactory.createResource("http://purl.obolibrary.org/obo/" + accession))) {
+      return ResourceFactory.createResource("http://purl.obolibrary.org/obo/" + accession);
     } else {
-      return ResourceFactory.createProperty("http://purl.obolibrary.org/obo/http_//purl.org/obo/" + accession);
+      return ResourceFactory.createProperty("http://purl.obolibrary.org/obo/" + accession);
     }
   }
 
@@ -2966,3 +2966,4 @@ public class SOFA {
 
 
 }
+

data/supplemental/python/biointerchange/faldo.py

@@ -0,0 +1,168 @@
+import rdflib
+
+from rdflib import Namespace
+
+
+class FALDO:
+
+    @classmethod
+    def In_between_positions(cls):
+        """This denotes that a feature is in between two other positions that are both known exactly and next to eaxh other. An example is an restriction enzyme cutting site. The cut is after one nucleotide and before the next i.e. in between
+        (cls, InBetweenPosition)
+        """
+        return _namespace_FALDO('InBetweenPosition')
+
+    @classmethod
+    def Position(cls):
+        """Superclass to group the general concept of a position on a sequence. The sequence is designated via the reference predicate.
+        (cls, Position)
+        """
+        return _namespace_FALDO('Position')
+
+    @classmethod
+    def Exact_position(cls):
+        """Use when you exactly know the position.
+        (cls, ExactPosition)
+        """
+        return _namespace_FALDO('ExactPosition')
+
+    @classmethod
+    def One_of_positions(cls):
+        """The position must be one of the more detailed Positions listed by the location predicate.
+        (cls, OneOfPosition)
+        """
+        return _namespace_FALDO('OneOfPosition')
+
+    @classmethod
+    def Indeterminate_position_within_a_range(cls):
+        """Use when you have an idea of the range in which you can find the position but can not be sure.
+        (cls, InRangePosition)
+        """
+        return _namespace_FALDO('InRangePosition')
+
+    @classmethod
+    def Stranded_position(cls):
+        """Part of the coordinate system is on which strand the feature can be found. If you do not yet know which stand the feature is on you should tag the position with just this class. If you know more you should use one of the subclasses. This means a region descibred with a '.' in GFF3. An GFF3 Unstranded position does not have this type in FALDO those are just a Position.
+        (cls, StrandedPosition)
+        """
+        return _namespace_FALDO('StrandedPosition')
+
+    @classmethod
+    def Fuzzy_position(cls):
+        """Use this class to indicate that you lack exact position data.
+        (cls, FuzzyPosition)
+        """
+        return _namespace_FALDO('FuzzyPosition')
+
+    @classmethod
+    def Positive_strand(cls):
+        """The position is on the forward (cls, positive) strand. Shown as a '+' in GFF3 and GTF
+        (ForwardStrandPosition)
+        """
+        return _namespace_FALDO('ForwardStrandPosition')
+
+    @classmethod
+    def Both_strands(cls):
+        """The both strands position mean that the region spans both strands instead of one. In GGF3 displayed as 0. This does not mean that the position is one or the other strand but is best described as being on both.
+        (cls, BothStrandsPosition)
+        """
+        return _namespace_FALDO('BothStrandsPosition')
+
+    @classmethod
+    def Negative_strand(cls):
+        """The position is on the reverse (cls, complement) strand of the sequence. Shown as '-' in GTF and GFF3
+        (ReverseStrandPosition)
+        """
+        return _namespace_FALDO('ReverseStrandPosition')
+
+    @classmethod
+    def Region(cls):
+        """A region describes an length of sequence with a start and end position that represents a feature on a Sequence. i.e. a gene
+        (cls, Region)
+        """
+        return _namespace_FALDO('Region')
+
+    @classmethod
+    def is_object_property(cls, uri):
+        """Determines whether the given URI is an object property.
+        
+        uri -- URI that is tested for being an object property
+        """
+        return False
+
+    @classmethod
+    def is_datatype_property(cls, uri):
+        """Determines whether the given URI is a datatype property.
+        
+        uri -- URI that is tested for being a datatype property
+        """
+        return False
+
+    @classmethod
+    def is_class(cls, uri):
+        """Determines whether the given URI is a class.
+        
+        uri -- URI that is tested for being a class
+        """
+        if uri == _namespace_FALDO('InBetweenPosition'):
+            return True
+        if uri == _namespace_FALDO('Position'):
+            return True
+        if uri == _namespace_FALDO('ExactPosition'):
+            return True
+        if uri == _namespace_FALDO('OneOfPosition'):
+            return True
+        if uri == _namespace_FALDO('InRangePosition'):
+            return True
+        if uri == _namespace_FALDO('StrandedPosition'):
+            return True
+        if uri == _namespace_FALDO('FuzzyPosition'):
+            return True
+        if uri == _namespace_FALDO('ForwardStrandPosition'):
+            return True
+        if uri == _namespace_FALDO('BothStrandsPosition'):
+            return True
+        if uri == _namespace_FALDO('ReverseStrandPosition'):
+            return True
+        if uri == _namespace_FALDO('Region'):
+            return True
+        return False
+
+    @classmethod
+    def is_named_individual(cls, uri):
+        """Determines whether the given URI is a named individual.
+        
+        uri -- URI that is tested for being a named individual
+        """
+        return False
+
+    @classmethod
+    def with_parent(cls, uris, parent):
+        """Returns only those URIs that fall under a designated parent URI.
+        
+        uris -- Set of URIs that are tested whether they have the given parent URI.
+        parent -- Parent URI.
+        """
+        return filter(lambda uri: cls.has_parent(uri, parent), uris)
+
+    @classmethod
+    def has_parent(cls, uri, parent):
+        """Recursively tries to determine the parent for a given URI.
+        
+        uri -- URI that is tested for whether it has the given parent URI.
+        parent -- Parent URI.
+        """
+        if cls.__parent_properties.has_key(uri):
+            if cls.__parent_properties[uri] == parent:
+                return True
+            return cls.has_parent(cls.__parent_properties[uri], parent)
+        return False
+
+__namespace_FALDO = Namespace('http://biohackathon.org/resource/faldo#')
+
+def _namespace_FALDO(accession):
+    return __namespace_FALDO[accession]
+
+    __parent_properties = { _namespace_FALDO('OneOfPosition') : _namespace_FALDO('FuzzyPosition') , _namespace_FALDO('StrandedPosition') : _namespace_FALDO('Position') , _namespace_FALDO('FuzzyPosition') : _namespace_FALDO('Position') , _namespace_FALDO('ForwardStrandPosition') : _namespace_FALDO('StrandedPosition') , _namespace_FALDO('BothStrandsPosition') : _namespace_FALDO('StrandedPosition') , _namespace_FALDO('ReverseStrandPosition') : _namespace_FALDO('StrandedPosition') }
+
+

data/supplemental/python/biointerchange/gff3o.py

@@ -2,10 +2,6 @@ import rdflib
 
 from rdflib import Namespace
 
-__namespace_GFF3O = Namespace('http://www.biointerchange.org/gff3o#')
-
-def _namespace_GFF3O(accession):
-    return __namespace_GFF3O[accession]
 
 class GFF3O:
 
@@ -517,5 +513,11 @@ class GFF3O:
             return cls.has_parent(cls.__parent_properties[uri], parent)
         return False
 
+__namespace_GFF3O = Namespace('http://www.biointerchange.org/gff3o#')
+
+def _namespace_GFF3O(accession):
+    return __namespace_GFF3O[accession]
+
     __parent_properties = { _namespace_GFF3O('GFF3_0004') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0010') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0012') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0014') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0015') : _namespace_GFF3O('GFF3_0025') , _namespace_GFF3O('GFF3_0021') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0023') : _namespace_GFF3O('GFF3_0025') , _namespace_GFF3O('GFF3_0039') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0045') : _namespace_GFF3O('GFF3_0044') , _namespace_GFF3O('GFF3_0047') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0050') : _namespace_GFF3O('GFF3_0044') , _namespace_GFF3O('GFF3_0056') : _namespace_GFF3O('GFF3_0025') , _namespace_GFF3O('GFF3_0005') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0006') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0007') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0008') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0009') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0011') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0013') : _namespace_GFF3O('GFF3_0029') , _namespace_GFF3O('GFF3_0022') : _namespace_GFF3O('GFF3_0027') , _namespace_GFF3O('GFF3_0024') : _namespace_GFF3O('GFF3_0027') , _namespace_GFF3O('GFF3_0034') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0035') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0036') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0037') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0041') : _namespace_GFF3O('GFF3_0040') , _namespace_GFF3O('GFF3_0042') : _namespace_GFF3O('GFF3_0040') , _namespace_GFF3O('GFF3_0043') : _namespace_GFF3O('GFF3_0040') , _namespace_GFF3O('GFF3_0046') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0048') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0049') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0053') : _namespace_GFF3O('GFF3_0052') , _namespace_GFF3O('GFF3_0054') : _namespace_GFF3O('GFF3_0052') , _namespace_GFF3O('GFF3_0055') : _namespace_GFF3O('GFF3_0052') , _namespace_GFF3O('GFF3_0057') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0058') : _namespace_GFF3O('GFF3_0052') }
 
+

data/supplemental/python/biointerchange/goxref.py

@@ -0,0 +1,1040 @@
+import rdflib
+
+from rdflib import Namespace
+
+
+class GOXRef:
+
+    @classmethod
+    def AGI_LocusCode(cls):
+        """Returns the link-out URI for objects of "Arabidopsis Genome Initiative".
+        """
+        RDF::URI.new("http://arabidopsis.org/servlets/TairObject?type=locus&name=")
+
+    @classmethod
+    def ApiDB_PlasmoDB(cls):
+        """Returns the link-out URI for objects of "PlasmoDB Plasmodium Genome Resource".
+        """
+        RDF::URI.new("http://www.plasmodb.org/gene/")
+
+    @classmethod
+    def AraCyc(cls):
+        """Returns the link-out URI for objects of "AraCyc metabolic pathway database for Arabidopsis thaliana".
+        """
+        RDF::URI.new("http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=NIL&object=")
+
+    @classmethod
+    def ASAP(cls):
+        """Returns the link-out URI for objects of "A Systematic Annotation Package for Community Analysis of Genomes".
+        """
+        RDF::URI.new("https://asap.ahabs.wisc.edu/annotation/php/feature_info.php?FeatureID=")
+
+    @classmethod
+    def AspGD(cls):
+        """Returns the link-out URI for objects of "Aspergillus Genome Database".
+        """
+        RDF::URI.new("http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=")
+
+    @classmethod
+    def AspGD_LOCUS(cls):
+        """Returns the link-out URI for objects of "Aspergillus Genome Database".
+        """
+        RDF::URI.new("http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=")
+
+    @classmethod
+    def AspGD_REF(cls):
+        """Returns the link-out URI for objects of "Aspergillus Genome Database".
+        """
+        RDF::URI.new("http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=")
+
+    @classmethod
+    def BFO(cls):
+        """Returns the link-out URI for objects of "Basic Formal Ontology".
+        """
+        RDF::URI.new("http://purl.obolibrary.org/obo/BFO_")
+
+    @classmethod
+    def BioCyc(cls):
+        """Returns the link-out URI for objects of "BioCyc collection of metabolic pathway databases".
+        """
+        RDF::URI.new("http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=")
+
+    @classmethod
+    def BIOMD(cls):
+        """Returns the link-out URI for objects of "BioModels Database".
+        """
+        RDF::URI.new("http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=")
+
+    @classmethod
+    def BRENDA(cls):
+        """Returns the link-out URI for objects of "BRENDA, The Comprehensive Enzyme Information System".
+        """
+        RDF::URI.new("http://www.brenda-enzymes.info/php/result_flat.php4?ecno=")
+
+    @classmethod
+    def Broad_MGG(cls):
+        """Returns the link-out URI for objects of "Magnaporthe grisea Database".
+        """
+        RDF::URI.new("http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html?sp=S")
+
+    @classmethod
+    def CASGEN(cls):
+        """Returns the link-out URI for objects of "Catalog of Fishes genus database".
+        """
+        RDF::URI.new("http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Genus&id=")
+
+    @classmethod
+    def CASREF(cls):
+        """Returns the link-out URI for objects of "Catalog of Fishes publications database".
+        """
+        RDF::URI.new("http://research.calacademy.org/research/ichthyology/catalog/getref.asp?id=")
+
+    @classmethod
+    def CASSPC(cls):
+        """Returns the link-out URI for objects of "Catalog of Fishes species database".
+        """
+        RDF::URI.new("http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Species&id=1979")
+
+    @classmethod
+    def CDD(cls):
+        """Returns the link-out URI for objects of "Conserved Domain Database at NCBI".
+        """
+        RDF::URI.new("http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=")
+
+    @classmethod
+    def CGD(cls):
+        """Returns the link-out URI for objects of "Candida Genome Database".
+        """
+        RDF::URI.new("http://www.candidagenome.org/cgi-bin/locus.pl?dbid=")
+
+    @classmethod
+    def CGD_LOCUS(cls):
+        """Returns the link-out URI for objects of "Candida Genome Database".
+        """
+        RDF::URI.new("http://www.candidagenome.org/cgi-bin/locus.pl?locus=")
+
+    @classmethod
+    def CGD_REF(cls):
+        """Returns the link-out URI for objects of "Candida Genome Database".
+        """
+        RDF::URI.new("http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=")
+
+    @classmethod
+    def CHEBI(cls):
+        """Returns the link-out URI for objects of "Chemical Entities of Biological Interest".
+        """
+        RDF::URI.new("http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:")
+
+    @classmethod
+    def CL(cls):
+        """Returns the link-out URI for objects of "Cell Type Ontology".
+        """
+        RDF::URI.new("http://purl.obolibrary.org/obo/CL_")
+
+    @classmethod
+    def COG_Cluster(cls):
+        """Returns the link-out URI for objects of "NCBI COG cluster".
+        """
+        RDF::URI.new("http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=")
+
+    @classmethod
+    def COG_Function(cls):
+        """Returns the link-out URI for objects of "NCBI COG function".
+        """
+        RDF::URI.new("http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=")
+
+    @classmethod
+    def COG_Pathway(cls):
+        """Returns the link-out URI for objects of "NCBI COG pathway".
+        """
+        RDF::URI.new("http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=")
+
+    @classmethod
+    def CORUM(cls):
+        """Returns the link-out URI for objects of "CORUM - the Comprehensive Resource of Mammalian protein complexes".
+        """
+        RDF::URI.new("http://mips.gsf.de/genre/proj/corum/complexdetails.html?id=")
+
+    @classmethod
+    def dbSNP(cls):
+        """Returns the link-out URI for objects of "NCBI dbSNP".
+        """
+        RDF::URI.new("http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=")
+
+    @classmethod
+    def DDBJ(cls):
+        """Returns the link-out URI for objects of "DNA Databank of Japan".
+        """
+        RDF::URI.new("http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord=")
+
+    @classmethod
+    def dictyBase(cls):
+        """Returns the link-out URI for objects of "dictyBase".
+        """
+        RDF::URI.new("http://dictybase.org/gene/")
+
+    @classmethod
+    def dictyBase_gene_name(cls):
+        """Returns the link-out URI for objects of "dictyBase".
+        """
+        RDF::URI.new("http://dictybase.org/gene/")
+
+    @classmethod
+    def dictyBase_REF(cls):
+        """Returns the link-out URI for objects of "dictyBase literature references".
+        """
+        RDF::URI.new("http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=")
+
+    @classmethod
+    def DOI(cls):
+        """Returns the link-out URI for objects of "Digital Object Identifier".
+        """
+        RDF::URI.new("http://dx.doi.org/DOI:")
+
+    @classmethod
+    def EC(cls):
+        """Returns the link-out URI for objects of "Enzyme Commission".
+        """
+        RDF::URI.new("http://www.expasy.org/enzyme/")
+
+    @classmethod
+    def EchoBASE(cls):
+        """Returns the link-out URI for objects of "EchoBASE post-genomic database for Escherichia coli".
+        """
+        RDF::URI.new("http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=")
+
+    @classmethod
+    def ECK(cls):
+        """Returns the link-out URI for objects of "EcoGene Database of Escherichia coli Sequence and Function".
+        """
+        RDF::URI.new("http://www.ecogene.org/geneInfo.php?eck_id=")
+
+    @classmethod
+    def EcoCyc(cls):
+        """Returns the link-out URI for objects of "Encyclopedia of E. coli metabolism".
+        """
+        RDF::URI.new("http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=")
+
+    @classmethod
+    def EcoCyc_REF(cls):
+        """Returns the link-out URI for objects of "Encyclopedia of E. coli metabolism".
+        """
+        RDF::URI.new("http://biocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=")
+
+    @classmethod
+    def ECOGENE(cls):
+        """Returns the link-out URI for objects of "EcoGene Database of Escherichia coli Sequence and Function".
+        """
+        RDF::URI.new("http://www.ecogene.org/geneInfo.php?eg_id=")
+
+    @classmethod
+    def EMBL(cls):
+        """Returns the link-out URI for objects of "EMBL Nucleotide Sequence Database".
+        """
+        RDF::URI.new("http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=")
+
+    @classmethod
+    def ENA(cls):
+        """Returns the link-out URI for objects of "European Nucleotide Archive".
+        """
+        RDF::URI.new("http://www.ebi.ac.uk/ena/data/view/")
+
+    @classmethod
+    def ENSEMBL(cls):
+        """Returns the link-out URI for objects of "Ensembl database of automatically annotated genomic data".
+        """
+        RDF::URI.new("http://www.ensembl.org/id/")
+
+    @classmethod
+    def ENSEMBL_GeneID(cls):
+        """Returns the link-out URI for objects of "Ensembl database of automatically annotated genomic data".
+        """
+        RDF::URI.new("http://www.ensembl.org/id/")
+
+    @classmethod
+    def ENSEMBL_ProteinID(cls):
+        """Returns the link-out URI for objects of "Ensembl database of automatically annotated genomic data".
+        """
+        RDF::URI.new("http://www.ensembl.org/id/")
+
+    @classmethod
+    def ENSEMBL_TranscriptID(cls):
+        """Returns the link-out URI for objects of "Ensembl database of automatically annotated genomic data".
+        """
+        RDF::URI.new("http://www.ensembl.org/id/")
+
+    @classmethod
+    def ENZYME(cls):
+        """Returns the link-out URI for objects of "Swiss Institute of Bioinformatics enzyme database".
+        """
+        RDF::URI.new("http://www.expasy.ch/cgi-bin/nicezyme.pl?")
+
+    @classmethod
+    def FBbt(cls):
+        """Returns the link-out URI for objects of "Drosophila gross anatomy".
+        """
+        RDF::URI.new("http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:")
+
+    @classmethod
+    def GDB(cls):
+        """Returns the link-out URI for objects of "Human Genome Database".
+        """
+        RDF::URI.new("http://www.gdb.org/gdb-bin/genera/accno?accessionNum=GDB:")
+
+    @classmethod
+    def GenBank(cls):
+        """Returns the link-out URI for objects of "GenBank".
+        """
+        RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=")
+
+    @classmethod
+    def Gene3D(cls):
+        """Returns the link-out URI for objects of "Domain Architecture Classification".
+        """
+        RDF::URI.new("http://gene3d.biochem.ucl.ac.uk/superfamily/?accession=")
+
+    @classmethod
+    def GeneDB_Gmorsitans(cls):
+        """Returns the link-out URI for objects of "Glossina morsitans GeneDB".
+        """
+        RDF::URI.new("http://www.genedb.org/genedb/Search?organism=glossina&name=")
+
+    @classmethod
+    def GeneDB_Lmajor(cls):
+        """Returns the link-out URI for objects of "Leishmania major GeneDB".
+        """
+        RDF::URI.new("http://www.genedb.org/genedb/Search?organism=leish&name=")
+
+    @classmethod
+    def GeneDB_Pfalciparum(cls):
+        """Returns the link-out URI for objects of "Plasmodium falciparum GeneDB".
+        """
+        RDF::URI.new("http://www.genedb.org/genedb/Search?organism=malaria&name=")
+
+    @classmethod
+    def GeneDB_Spombe(cls):
+        """Returns the link-out URI for objects of "Schizosaccharomyces pombe GeneDB".
+        """
+        RDF::URI.new("http://old.genedb.org/genedb/Search?organism=pombe&name=")
+
+    @classmethod
+    def GeneDB_Tbrucei(cls):
+        """Returns the link-out URI for objects of "Trypanosoma brucei GeneDB".
+        """
+        RDF::URI.new("http://www.genedb.org/genedb/Search?organism=tryp&name=")
+
+    @classmethod
+    def GEO(cls):
+        """Returns the link-out URI for objects of "NCBI Gene Expression Omnibus".
+        """
+        RDF::URI.new("http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=")
+
+    @classmethod
+    def GO(cls):
+        """Returns the link-out URI for objects of "Gene Ontology Database".
+        """
+        RDF::URI.new("http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:")
+
+    @classmethod
+    def GO_REF(cls):
+        """Returns the link-out URI for objects of "Gene Ontology Database references".
+        """
+        RDF::URI.new("http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:")
+
+    @classmethod
+    def GONUTS(cls):
+        """Returns the link-out URI for objects of "Gene Ontology Normal Usage Tracking System (cls, GONUTS)".
+        """
+        RDF::URI.new("http://gowiki.tamu.edu/wiki/index.php/")
+
+    @classmethod
+    def GR(cls):
+        """Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains".
+        """
+        RDF::URI.new("http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=")
+
+    @classmethod
+    def GR_GENE(cls):
+        """Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains".
+        """
+        RDF::URI.new("http://www.gramene.org/db/genes/search_gene?acc=")
+
+    @classmethod
+    def GR_PROTEIN(cls):
+        """Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains".
+        """
+        RDF::URI.new("http://www.gramene.org/db/protein/protein_search?acc=")
+
+    @classmethod
+    def GR_QTL(cls):
+        """Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains".
+        """
+        RDF::URI.new("http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=")
+
+    @classmethod
+    def GR_REF(cls):
+        """Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains".
+        """
+        RDF::URI.new("http://www.gramene.org/db/literature/pub_search?ref_id=")
+
+    @classmethod
+    def H_invDB_cDNA(cls):
+        """Returns the link-out URI for objects of "H-invitational Database".
+        """
+        RDF::URI.new("http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id=")
+
+    @classmethod
+    def H_invDB_locus(cls):
+        """Returns the link-out URI for objects of "H-invitational Database".
+        """
+        RDF::URI.new("http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=")
+
+    @classmethod
+    def HAMAP(cls):
+        """Returns the link-out URI for objects of "High-quality Automated and Manual Annotation of microbial Proteomes".
+        """
+        RDF::URI.new("http://us.expasy.org/unirules/")
+
+    @classmethod
+    def HGNC(cls):
+        """Returns the link-out URI for objects of "HUGO Gene Nomenclature Committee".
+        """
+        RDF::URI.new("http://www.genenames.org/data/hgnc_data.php?hgnc_id=HGNC:")
+
+    @classmethod
+    def HGNC_gene(cls):
+        """Returns the link-out URI for objects of "HUGO Gene Nomenclature Committee".
+        """
+        RDF::URI.new("http://www.genenames.org/data/hgnc_data.php?app_sym=")
+
+    @classmethod
+    def HPA(cls):
+        """Returns the link-out URI for objects of "Human Protein Atlas tissue profile information".
+        """
+        RDF::URI.new("http://www.proteinatlas.org/tissue_profile.php?antibody_id=")
+
+    @classmethod
+    def HPA_antibody(cls):
+        """Returns the link-out URI for objects of "Human Protein Atlas antibody information".
+        """
+        RDF::URI.new("http://www.proteinatlas.org/antibody_info.php?antibody_id=")
+
+    @classmethod
+    def IMG(cls):
+        """Returns the link-out URI for objects of "Integrated Microbial Genomes; JGI web site for genome annotation".
+        """
+        RDF::URI.new("http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=")
+
+    @classmethod
+    def IntAct(cls):
+        """Returns the link-out URI for objects of "IntAct protein interaction database".
+        """
+        RDF::URI.new("http://www.ebi.ac.uk/intact/search/do/search?searchString=")
+
+    @classmethod
+    def InterPro(cls):
+        """Returns the link-out URI for objects of "InterPro database of protein domains and motifs".
+        """
+        RDF::URI.new("http://www.ebi.ac.uk/interpro/IEntry?ac=")
+
+    @classmethod
+    def ISBN(cls):
+        """Returns the link-out URI for objects of "International Standard Book Number".
+        """
+        RDF::URI.new("http://my.linkbaton.com/get?lbCC=q&nC=q&genre=book&item=")
+
+    @classmethod
+    def IUPHAR_GPCR(cls):
+        """Returns the link-out URI for objects of "International Union of Pharmacology".
+        """
+        RDF::URI.new("http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId=")
+
+    @classmethod
+    def IUPHAR_RECEPTOR(cls):
+        """Returns the link-out URI for objects of "International Union of Pharmacology".
+        """
+        RDF::URI.new("http://www.iuphar-db.org/DATABASE/ObjectDisplayForward?objectId=")
+
+    @classmethod
+    def JCVI_CMR(cls):
+        """Returns the link-out URI for objects of "Comprehensive Microbial Resource at the J. Craig Venter Institute".
+        """
+        RDF::URI.new("http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=")
+
+    @classmethod
+    def JCVI_EGAD(cls):
+        """Returns the link-out URI for objects of "Comprehensive Microbial Resource at the J. Craig Venter Institute".
+        """
+        RDF::URI.new("http://cmr.jcvi.org/cgi-bin/CMR/EgadSearch.cgi?search_string=")
+
+    @classmethod
+    def JCVI_GenProp(cls):
+        """Returns the link-out URI for objects of "Genome Properties database at the J. Craig Venter Institute".
+        """
+        RDF::URI.new("http://cmr.jcvi.org/cgi-bin/CMR/shared/GenomePropDefinition.cgi?prop_acc=")
+
+    @classmethod
+    def JCVI_Medtr(cls):
+        """Returns the link-out URI for objects of "Medicago truncatula genome database at the J. Craig Venter Institute ".
+        """
+        RDF::URI.new("http://medicago.jcvi.org/cgi-bin/medicago/search/shared/ORF_infopage.cgi?orf=")
+
+    @classmethod
+    def JCVI_TIGRFAMS(cls):
+        """Returns the link-out URI for objects of "TIGRFAMs HMM collection at the J. Craig Venter Institute".
+        """
+        RDF::URI.new("http://search.jcvi.org/search?p&q=")
+
+    @classmethod
+    def JSTOR(cls):
+        """Returns the link-out URI for objects of "Digital archive of scholarly articles".
+        """
+        RDF::URI.new("http://www.jstor.org/stable/")
+
+    @classmethod
+    def KEGG_ENZYME(cls):
+        """Returns the link-out URI for objects of "KEGG Enzyme Database".
+        """
+        RDF::URI.new("http://www.genome.jp/dbget-bin/www_bget?ec:")
+
+    @classmethod
+    def KEGG_LIGAND(cls):
+        """Returns the link-out URI for objects of "KEGG LIGAND Database".
+        """
+        RDF::URI.new("http://www.genome.jp/dbget-bin/www_bget?cpd:")
+
+    @classmethod
+    def KEGG_PATHWAY(cls):
+        """Returns the link-out URI for objects of "KEGG Pathways Database".
+        """
+        RDF::URI.new("http://www.genome.jp/dbget-bin/www_bget?path:")
+
+    @classmethod
+    def KEGG_REACTION(cls):
+        """Returns the link-out URI for objects of "KEGG Reaction Database".
+        """
+        RDF::URI.new("http://www.genome.jp/dbget-bin/www_bget?rn:")
+
+    @classmethod
+    def LIFEdb(cls):
+        """Returns the link-out URI for objects of "LifeDB".
+        """
+        RDF::URI.new("http://www.dkfz.de/LIFEdb/LIFEdb.aspx?ID=")
+
+    @classmethod
+    def MA(cls):
+        """Returns the link-out URI for objects of "Adult Mouse Anatomical Dictionary".
+        """
+        RDF::URI.new("http://www.informatics.jax.org/searches/AMA.cgi?id=MA:")
+
+    @classmethod
+    def MaizeGDB(cls):
+        """Returns the link-out URI for objects of "MaizeGDB".
+        """
+        RDF::URI.new("http://www.maizegdb.org/cgi-bin/id_search.cgi?id=")
+
+    @classmethod
+    def MaizeGDB_Locus(cls):
+        """Returns the link-out URI for objects of "MaizeGDB".
+        """
+        RDF::URI.new("http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=")
+
+    @classmethod
+    def MEROPS(cls):
+        """Returns the link-out URI for objects of "MEROPS peptidase database".
+        """
+        RDF::URI.new("http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=")
+
+    @classmethod
+    def MEROPS_fam(cls):
+        """Returns the link-out URI for objects of "MEROPS peptidase database".
+        """
+        RDF::URI.new("http://merops.sanger.ac.uk/cgi-bin/famsum?family=")
+
+    @classmethod
+    def MeSH(cls):
+        """Returns the link-out URI for objects of "Medical Subject Headings".
+        """
+        RDF::URI.new("http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=")
+
+    @classmethod
+    def MetaCyc(cls):
+        """Returns the link-out URI for objects of "Metabolic Encyclopedia of metabolic and other pathways".
+        """
+        RDF::URI.new("http://biocyc.org/META/NEW-IMAGE?type=NIL&object=")
+
+    @classmethod
+    def MGI(cls):
+        """Returns the link-out URI for objects of "Mouse Genome Informatics".
+        """
+        RDF::URI.new("http://www.informatics.jax.org/accession/")
+
+    @classmethod
+    def MIPS_funcat(cls):
+        """Returns the link-out URI for objects of "MIPS Functional Catalogue".
+        """
+        RDF::URI.new("http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=")
+
+    @classmethod
+    def MO(cls):
+        """Returns the link-out URI for objects of "MGED Ontology".
+        """
+        RDF::URI.new("http://mged.sourceforge.net/ontologies/MGEDontology.php#")
+
+    @classmethod
+    def ModBase(cls):
+        """Returns the link-out URI for objects of "ModBase comprehensive Database of Comparative Protein Structure Models".
+        """
+        RDF::URI.new("http://salilab.org/modbase/searchbyid?databaseID=")
+
+    @classmethod
+    def NASC_code(cls):
+        """Returns the link-out URI for objects of "Nottingham Arabidopsis Stock Centre Seeds Database".
+        """
+        RDF::URI.new("http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=")
+
+    @classmethod
+    def NCBI_Gene(cls):
+        """Returns the link-out URI for objects of "NCBI Gene".
+        """
+        RDF::URI.new("http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=gene&list_uids=")
+
+    @classmethod
+    def NCBI_gi(cls):
+        """Returns the link-out URI for objects of "NCBI databases".
+        """
+        RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=")
+
+    @classmethod
+    def NCBI_GP(cls):
+        """Returns the link-out URI for objects of "NCBI GenPept".
+        """
+        RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=")
+
+    @classmethod
+    def NIF_Subcellular(cls):
+        """Returns the link-out URI for objects of "Neuroscience Information Framework standard ontology, subcellular hierarchy".
+        """
+        RDF::URI.new("http://www.neurolex.org/wiki/")
+
+    @classmethod
+    def NMPDR(cls):
+        """Returns the link-out URI for objects of "National Microbial Pathogen Data Resource".
+        """
+        RDF::URI.new("http://www.nmpdr.org/linkin.cgi?id=")
+
+    @classmethod
+    def OMIM(cls):
+        """Returns the link-out URI for objects of "Mendelian Inheritance in Man".
+        """
+        RDF::URI.new("http://omim.org/entry/")
+
+    @classmethod
+    def PAMGO_GAT(cls):
+        """Returns the link-out URI for objects of "Genome Annotation Tool (cls, Agrobacterium tumefaciens C58); PAMGO Interest Group".
+        """
+        RDF::URI.new("http://agro.vbi.vt.edu/public/servlet/GeneEdit?&Search=Search&level=2&genename=")
+
+    @classmethod
+    def PAMGO_MGG(cls):
+        """Returns the link-out URI for objects of "Magnaporthe grisea database".
+        """
+        RDF::URI.new("http://scotland.fgl.ncsu.edu/cgi-bin/adHocQuery.cgi?adHocQuery_dbName=smeng_goannotation&Action=Data&QueryName=Functional+Categorization+of+MGG+GO+Annotation&P_KeyWord=")
+
+    @classmethod
+    def PAMGO_VMD(cls):
+        """Returns the link-out URI for objects of "Virginia Bioinformatics Institute Microbial Database".
+        """
+        RDF::URI.new("http://vmd.vbi.vt.edu/cgi-bin/browse/go_detail.cgi?gene_id=")
+
+    @classmethod
+    def PANTHER(cls):
+        """Returns the link-out URI for objects of "Protein ANalysis THrough Evolutionary Relationships".
+        """
+        RDF::URI.new("http://pantree.org/node/annotationNode.jsp?id=")
+
+    @classmethod
+    def PATRIC(cls):
+        """Returns the link-out URI for objects of "PathoSystems Resource Integration Center".
+        """
+        RDF::URI.new("http://patric.vbi.vt.edu/gene/overview.php?fid=")
+
+    @classmethod
+    def PDB(cls):
+        """Returns the link-out URI for objects of "Protein Data Bank".
+        """
+        RDF::URI.new("http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=")
+
+    @classmethod
+    def Pfam(cls):
+        """Returns the link-out URI for objects of "Pfam database of protein families".
+        """
+        RDF::URI.new("http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?")
+
+    @classmethod
+    def PharmGKB(cls):
+        """Returns the link-out URI for objects of "Pharmacogenetics and Pharmacogenomics Knowledge Base".
+        """
+        RDF::URI.new("http://www.pharmgkb.org/do/serve?objId=")
+
+    @classmethod
+    def PIR(cls):
+        """Returns the link-out URI for objects of "Protein Information Resource".
+        """
+        RDF::URI.new("http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid=")
+
+    @classmethod
+    def PIRSF(cls):
+        """Returns the link-out URI for objects of "PIR Superfamily Classification System".
+        """
+        RDF::URI.new("http://pir.georgetown.edu/cgi-bin/ipcSF?id=")
+
+    @classmethod
+    def PMCID(cls):
+        """Returns the link-out URI for objects of "Pubmed Central".
+        """
+        RDF::URI.new("http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=")
+
+    @classmethod
+    def PMID(cls):
+        """Returns the link-out URI for objects of "PubMed".
+        """
+        RDF::URI.new("http://www.ncbi.nlm.nih.gov/pubmed/")
+
+    @classmethod
+    def PO(cls):
+        """Returns the link-out URI for objects of "Plant Ontology Consortium Database".
+        """
+        RDF::URI.new("http://www.plantontology.org/amigo/go.cgi?action=query&view=query&search_constraint=terms&query=PO:")
+
+    @classmethod
+    def PO_REF(cls):
+        """Returns the link-out URI for objects of "Plant Ontology custom references".
+        """
+        RDF::URI.new("http://wiki.plantontology.org:8080/index.php/PO_REF:")
+
+    @classmethod
+    def PomBase(cls):
+        """Returns the link-out URI for objects of "PomBase".
+        """
+        RDF::URI.new("http://www.pombase.org/spombe/result/")
+
+    @classmethod
+    def PR(cls):
+        """Returns the link-out URI for objects of "Protein Ontology".
+        """
+        RDF::URI.new("http://www.proconsortium.org/cgi-bin/pro/entry_pro?id=PR:")
+
+    @classmethod
+    def PRINTS(cls):
+        """Returns the link-out URI for objects of "PRINTS compendium of protein fingerprints".
+        """
+        RDF::URI.new("http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=False&regexpr=off&prints_accn=")
+
+    @classmethod
+    def ProDom(cls):
+        """Returns the link-out URI for objects of "ProDom protein domain families".
+        """
+        RDF::URI.new("http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=")
+
+    @classmethod
+    def Prosite(cls):
+        """Returns the link-out URI for objects of "Prosite database of protein families and domains".
+        """
+        RDF::URI.new("http://www.expasy.ch/cgi-bin/prosite-search-ac?")
+
+    @classmethod
+    def PseudoCAP(cls):
+        """Returns the link-out URI for objects of "Pseudomonas Genome Project".
+        """
+        RDF::URI.new("http://v2.pseudomonas.com/getAnnotation.do?locusID=")
+
+    @classmethod
+    def PSI_MOD(cls):
+        """Returns the link-out URI for objects of "Proteomics Standards Initiative protein modification ontology".
+        """
+        RDF::URI.new("http://www.ebi.ac.uk/ontology-lookup/?termId=MOD:")
+
+    @classmethod
+    def PubChem_BioAssay(cls):
+        """Returns the link-out URI for objects of "NCBI PubChem database of bioassay records".
+        """
+        RDF::URI.new("http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=")
+
+    @classmethod
+    def PubChem_Compound(cls):
+        """Returns the link-out URI for objects of "NCBI PubChem database of chemical structures".
+        """
+        RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=")
+
+    @classmethod
+    def PubChem_Substance(cls):
+        """Returns the link-out URI for objects of "NCBI PubChem database of chemical substances".
+        """
+        RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term=")
+
+    @classmethod
+    def Reactome(cls):
+        """Returns the link-out URI for objects of "Reactome - a curated knowledgebase of biological pathways".
+        """
+        RDF::URI.new("http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=")
+
+    @classmethod
+    def RefSeq(cls):
+        """Returns the link-out URI for objects of "RefSeq".
+        """
+        RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=")
+
+    @classmethod
+    def RefSeq_NA(cls):
+        """Returns the link-out URI for objects of "RefSeq (cls, Nucleic Acid)".
+        """
+        RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=")
+
+    @classmethod
+    def RefSeq_Prot(cls):
+        """Returns the link-out URI for objects of "RefSeq (cls, Protein)".
+        """
+        RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=")
+
+    @classmethod
+    def Rfam(cls):
+        """Returns the link-out URI for objects of "Rfam database of RNA families".
+        """
+        RDF::URI.new("http://rfam.sanger.ac.uk/family/")
+
+    @classmethod
+    def RGD(cls):
+        """Returns the link-out URI for objects of "Rat Genome Database".
+        """
+        RDF::URI.new("http://rgd.mcw.edu/generalSearch/RgdSearch.jsp?quickSearch=1&searchKeyword=")
+
+    @classmethod
+    def RHEA(cls):
+        """Returns the link-out URI for objects of "Rhea, the Annotated Reactions Database".
+        """
+        RDF::URI.new("http://www.ebi.ac.uk/rhea/reaction.xhtml?id=")
+
+    @classmethod
+    def RNAmods(cls):
+        """Returns the link-out URI for objects of "RNA Modification Database".
+        """
+        RDF::URI.new("http://s59.cas.albany.edu/RNAmods/cgi-bin/rnashow.cgi?")
+
+    @classmethod
+    def RO(cls):
+        """Returns the link-out URI for objects of "OBO Relation Ontology Ontology".
+        """
+        RDF::URI.new("http://purl.obolibrary.org/obo/RO_")
+
+    @classmethod
+    def SABIO_RK(cls):
+        """Returns the link-out URI for objects of "SABIO Reaction Kinetics".
+        """
+        RDF::URI.new("http://sabio.villa-bosch.de/reacdetails.jsp?reactid=")
+
+    @classmethod
+    def SEED(cls):
+        """Returns the link-out URI for objects of "The SEED;".
+        """
+        RDF::URI.new("http://www.theseed.org/linkin.cgi?id=")
+
+    @classmethod
+    def SGD(cls):
+        """Returns the link-out URI for objects of "Saccharomyces Genome Database".
+        """
+        RDF::URI.new("http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=")
+
+    @classmethod
+    def SGD_LOCUS(cls):
+        """Returns the link-out URI for objects of "Saccharomyces Genome Database".
+        """
+        RDF::URI.new("http://db.yeastgenome.org/cgi-bin/locus.pl?locus=")
+
+    @classmethod
+    def SGD_REF(cls):
+        """Returns the link-out URI for objects of "Saccharomyces Genome Database".
+        """
+        RDF::URI.new("http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=")
+
+    @classmethod
+    def SGN(cls):
+        """Returns the link-out URI for objects of "Sol Genomics Network".
+        """
+        RDF::URI.new("http://www.sgn.cornell.edu/phenome/locus_display.pl?locus_id=")
+
+    @classmethod
+    def SGN_ref(cls):
+        """Returns the link-out URI for objects of "Sol Genomics Network".
+        """
+        RDF::URI.new("http://www.sgn.cornell.edu/chado/publication.pl?pub_id=")
+
+    @classmethod
+    def SMART(cls):
+        """Returns the link-out URI for objects of "Simple Modular Architecture Research Tool".
+        """
+        RDF::URI.new("http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=")
+
+    @classmethod
+    def SO(cls):
+        """Returns the link-out URI for objects of "Sequence Ontology".
+        """
+        RDF::URI.new("http://song.sourceforge.net/SOterm_tables.html#SO:")
+
+    @classmethod
+    def SUPERFAMILY(cls):
+        """Returns the link-out URI for objects of "SUPERFAMILY protein annotation database".
+        """
+        RDF::URI.new("http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/scop.cgi?ipid=SSF")
+
+    @classmethod
+    def Swiss_Prot(cls):
+        """Returns the link-out URI for objects of "UniProtKB/Swiss-Prot".
+        """
+        RDF::URI.new("http://www.uniprot.org/uniprot/")
+
+    @classmethod
+    def TAIR(cls):
+        """Returns the link-out URI for objects of "The Arabidopsis Information Resource".
+        """
+        RDF::URI.new("http://arabidopsis.org/servlets/TairObject?accession=")
+
+    @classmethod
+    def taxon(cls):
+        """Returns the link-out URI for objects of "NCBI Taxonomy".
+        """
+        RDF::URI.new("http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=")
+
+    @classmethod
+    def TC(cls):
+        """Returns the link-out URI for objects of "Transport Protein Database".
+        """
+        RDF::URI.new("http://www.tcdb.org/tcdb/index.php?tc=")
+
+    @classmethod
+    def TGD_LOCUS(cls):
+        """Returns the link-out URI for objects of "Tetrahymena Genome Database".
+        """
+        RDF::URI.new("http://db.ciliate.org/cgi-bin/locus.pl?locus=")
+
+    @classmethod
+    def TGD_REF(cls):
+        """Returns the link-out URI for objects of "Tetrahymena Genome Database".
+        """
+        RDF::URI.new("http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=")
+
+    @classmethod
+    def TrEMBL(cls):
+        """Returns the link-out URI for objects of "UniProtKB-TrEMBL protein sequence database".
+        """
+        RDF::URI.new("http://www.uniprot.org/uniprot/")
+
+    @classmethod
+    def UBERON(cls):
+        """Returns the link-out URI for objects of "Uber-anatomy ontology".
+        """
+        RDF::URI.new("http://purl.obolibrary.org/obo/UBERON_")
+
+    @classmethod
+    def UM_BBD_enzymeID(cls):
+        """Returns the link-out URI for objects of "University of Minnesota Biocatalysis/Biodegradation Database".
+        """
+        RDF::URI.new("http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=ep&enzymeID=")
+
+    @classmethod
+    def UM_BBD_reactionID(cls):
+        """Returns the link-out URI for objects of "University of Minnesota Biocatalysis/Biodegradation Database".
+        """
+        RDF::URI.new("http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=r&reacID=")
+
+    @classmethod
+    def UM_BBD_ruleID(cls):
+        """Returns the link-out URI for objects of "University of Minnesota Biocatalysis/Biodegradation Database".
+        """
+        RDF::URI.new("http://umbbd.msi.umn.edu/servlets/rule.jsp?rule=")
+
+    @classmethod
+    def UniMod(cls):
+        """Returns the link-out URI for objects of "UniMod".
+        """
+        RDF::URI.new("http://www.unimod.org/modifications_view.php?editid1=")
+
+    @classmethod
+    def UniParc(cls):
+        """Returns the link-out URI for objects of "UniProt Archive".
+        """
+        RDF::URI.new("http://www.uniprot.org/uniparc/")
+
+    @classmethod
+    def UniPathway(cls):
+        """Returns the link-out URI for objects of "UniPathway".
+        """
+        RDF::URI.new("http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=")
+
+    @classmethod
+    def UniProtKB(cls):
+        """Returns the link-out URI for objects of "Universal Protein Knowledgebase".
+        """
+        RDF::URI.new("http://www.uniprot.org/uniprot/")
+
+    @classmethod
+    def UniProtKB_KW(cls):
+        """Returns the link-out URI for objects of "UniProt Knowledgebase keywords".
+        """
+        RDF::URI.new("http://www.uniprot.org/keywords/")
+
+    @classmethod
+    def UniProtKB_SubCell(cls):
+        """Returns the link-out URI for objects of "UniProt Knowledgebase Subcellular Location vocabulary".
+        """
+        RDF::URI.new("http://www.uniprot.org/locations/")
+
+    @classmethod
+    def VBRC(cls):
+        """Returns the link-out URI for objects of "Viral Bioinformatics Resource Center".
+        """
+        RDF::URI.new("http://vbrc.org/query.asp?web_id=VBRC:")
+
+    @classmethod
+    def VEGA(cls):
+        """Returns the link-out URI for objects of "Vertebrate Genome Annotation database".
+        """
+        RDF::URI.new("http://vega.sanger.ac.uk/perl/searchview?species=all&idx=All&q=")
+
+    @classmethod
+    def VMD(cls):
+        """Returns the link-out URI for objects of "Virginia Bioinformatics Institute Microbial Database".
+        """
+        RDF::URI.new("http://vmd.vbi.vt.edu/cgi-bin/browse/browserDetail_new.cgi?gene_id=")
+
+    @classmethod
+    def WB(cls):
+        """Returns the link-out URI for objects of "WormBase database of nematode biology".
+        """
+        RDF::URI.new("http://www.wormbase.org/db/gene/gene?name=")
+
+    @classmethod
+    def WB_REF(cls):
+        """Returns the link-out URI for objects of "WormBase database of nematode biology".
+        """
+        RDF::URI.new("http://www.wormbase.org/db/misc/paper?name=")
+
+    @classmethod
+    def Wikipedia(cls):
+        """Returns the link-out URI for objects of "Wikipedia".
+        """
+        RDF::URI.new("http://en.wikipedia.org/wiki/")
+
+    @classmethod
+    def WP(cls):
+        """Returns the link-out URI for objects of "Wormpep database of proteins of C. elegans".
+        """
+        RDF::URI.new("http://www.wormbase.org/db/get?class=Protein;name=WP:")
+
+    @classmethod
+    def ZFIN(cls):
+        """Returns the link-out URI for objects of "Zebrafish Information Network".
+        """
+        RDF::URI.new("http://zfin.org/cgi-bin/ZFIN_jump?record=")
+
+