biointerchange 0.1.0 → 0.1.2

data/supplemental/python/biointerchange/sofa.py

@@ -0,0 +1,2422 @@
+import rdflib
+
+from rdflib import Namespace
+
+__namespace_SOFO = Namespace('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:adjacent_to')
+
+def _namespace_SOFO(accession):
+    return __namespace_SOFO[accession]
+
+class SOFO:
+
+    @classmethod
+    def adjacent_to(cls):
+        return _namespace_SOFO('')
+
+    @classmethod
+    def complete_evidence_for_feature(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:complete_evidence_for_feature')
+
+    @classmethod
+    def contained_by(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:contained_by')
+
+    @classmethod
+    def contains(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:contains')
+
+    @classmethod
+    def derives_from(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:derives_from')
+
+    @classmethod
+    def evidence_for_feature(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:evidence_for_feature')
+
+    @classmethod
+    def has_integral_part(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:has_integral_part')
+
+    @classmethod
+    def has_part(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:has_part')
+
+    @classmethod
+    def homologous_to(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:homologous_to')
+
+    @classmethod
+    def integral_part_of(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:integral_part_of')
+
+    @classmethod
+    def member_of(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:member_of')
+
+    @classmethod
+    def non_functional_homolog_of(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:non_functional_homolog_of')
+
+    @classmethod
+    def orthologous_to(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:orthologous_to')
+
+    @classmethod
+    def paralogous_to(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:paralogous_to')
+
+    @classmethod
+    def part_of(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:part_of')
+
+    @classmethod
+    def partial_evidence_for_feature(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:partial_evidence_for_feature')
+
+    @classmethod
+    def similar_to(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:similar_to')
+
+    @classmethod
+    def Sequence_Ontology(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000000')
+
+    @classmethod
+    def region(cls):
+        """A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000001)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000001')
+
+    @classmethod
+    def interior_coding_exon(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000004')
+
+    @classmethod
+    def satellite_DNA(cls):
+        """The many tandem repeats (cls, identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
+        (http://purl.obolibrary.org/obo/SO_0000005)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000005')
+
+    @classmethod
+    def PCR_product(cls):
+        """A region amplified by a PCR reaction. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000006)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000006')
+
+    @classmethod
+    def read_pair(cls):
+        """One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert. (cls, SO:ls)
+        (http://purl.obolibrary.org/obo/SO_0000007)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000007')
+
+    @classmethod
+    def scRNA(cls):
+        """A small non coding RNA sequence, present in the cytoplasm. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000013)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000013')
+
+    @classmethod
+    def match_set(cls):
+        """A collection of match parts. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000038)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000038')
+
+    @classmethod
+    def match_part(cls):
+        """A part of a match, for example an hsp from blast is a match_part. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000039)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000039')
+
+    @classmethod
+    def gene_part(cls):
+        """A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000050)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000050')
+
+    @classmethod
+    def operator(cls):
+        """A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon. (cls, SO:ma)
+        (http://purl.obolibrary.org/obo/SO_0000057)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000057')
+
+    @classmethod
+    def nuclease_binding_site(cls):
+        """A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease. (cls, SO:cb)
+        (http://purl.obolibrary.org/obo/SO_0000059)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000059')
+
+    @classmethod
+    def transposable_element(cls):
+        """A transposon or insertion sequence. An element that can insert in a variety of DNA sequences. (cls, http://www.sci.sdsu.edu/~smaloy/Glossary/T.html)
+        (http://purl.obolibrary.org/obo/SO_0000101)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000101')
+
+    @classmethod
+    def expressed_sequence_match(cls):
+        """A match to an EST or cDNA sequence. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000102)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000102')
+
+    @classmethod
+    def clone_insert_end(cls):
+        """The end of the clone insert. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000103)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000103')
+
+    @classmethod
+    def polypeptide(cls):
+        """A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. (cls, SO:ma)
+        (http://purl.obolibrary.org/obo/SO_0000104)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000104')
+
+    @classmethod
+    def sequence_variant_obs(cls):
+        """A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000109)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000109')
+
+    @classmethod
+    def sequence_feature(cls):
+        """An extent of biological sequence. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000110)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000110')
+
+    @classmethod
+    def primer(cls):
+        """An oligo to which new deoxyribonucleotides can be added by DNA polymerase. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000112)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000112')
+
+    @classmethod
+    def proviral_region(cls):
+        """A viral sequence which has integrated into a host genome. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000113)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000113')
+
+    @classmethod
+    def methylated_C(cls):
+        """A methylated deoxy-cytosine. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000114)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000114')
+
+    @classmethod
+    def protein_coding_primary_transcript(cls):
+        """A primary transcript that, at least in part, encodes one or more proteins. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000120)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000120')
+
+    @classmethod
+    def ribosome_entry_site(cls):
+        """Region in mRNA where ribosome assembles. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000139)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000139')
+
+    @classmethod
+    def attenuator(cls):
+        """A sequence segment located within the five prime end of an mRNA that causes premature termination of translation. (cls, SO:as)
+        (http://purl.obolibrary.org/obo/SO_0000140)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000140')
+
+    @classmethod
+    def terminator(cls):
+        """The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription. (cls, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
+        (http://purl.obolibrary.org/obo/SO_0000141)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000141')
+
+    @classmethod
+    def assembly_component(cls):
+        """A region of known length which may be used to manufacture a longer region. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000143)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000143')
+
+    @classmethod
+    def exon(cls):
+        """A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000147)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000147')
+
+    @classmethod
+    def supercontig(cls):
+        """One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's. (cls, SO:ls)
+        (http://purl.obolibrary.org/obo/SO_0000148)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000148')
+
+    @classmethod
+    def contig(cls):
+        """A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. (cls, SO:ls)
+        (http://purl.obolibrary.org/obo/SO_0000149)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000149')
+
+    @classmethod
+    def read(cls):
+        """A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine. (cls, SO:rd)
+        (http://purl.obolibrary.org/obo/SO_0000150)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000150')
+
+    @classmethod
+    def clone(cls):
+        """A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000151)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000151')
+
+    @classmethod
+    def deletion(cls):
+        """The point at which one or more contiguous nucleotides were excised. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000159)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000159')
+
+    @classmethod
+    def methylated_A(cls):
+        """A modified RNA base in which adenine has been methylated. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000161)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000161')
+
+    @classmethod
+    def splice_site(cls):
+        """Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction. (cls, SO:cjm, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000162)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000162')
+
+    @classmethod
+    def five_prime_cis_splice_site(cls):
+        """Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron. (cls, http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000163)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000163')
+
+    @classmethod
+    def three_prime_cis_splice_site(cls):
+        """Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron. (cls, http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000164)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000164')
+
+    @classmethod
+    def enhancer(cls):
+        """A cis-acting sequence that increases the utilization of (cls, some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
+        (http://purl.obolibrary.org/obo/SO_0000165)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000165')
+
+    @classmethod
+    def promoter(cls):
+        """A regulatory_region composed of the TSS(cls, s) and binding sites for TF_complexes of the basal transcription machinery. (SO:regcreative)
+        (http://purl.obolibrary.org/obo/SO_0000167)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000167')
+
+    @classmethod
+    def cross_genome_match(cls):
+        """A nucleotide match against a sequence from another organism. (cls, SO:ma)
+        (http://purl.obolibrary.org/obo/SO_0000177)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000177')
+
+    @classmethod
+    def operon(cls):
+        """A group of contiguous genes transcribed as a single (cls, polycistronic) mRNA from a single regulatory region. (SO:ma)
+        (http://purl.obolibrary.org/obo/SO_0000178)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000178')
+
+    @classmethod
+    def clone_insert_start(cls):
+        """The start of the clone insert. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000179)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000179')
+
+    @classmethod
+    def translated_nucleotide_match(cls):
+        """A match against a translated sequence. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000181)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000181')
+
+    @classmethod
+    def non_transcribed_region(cls):
+        """A region of the gene which is not transcribed. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000183)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000183')
+
+    @classmethod
+    def primary_transcript(cls):
+        """A transcript that in its initial state requires modification to be functional. (cls, SO:ma)
+        (http://purl.obolibrary.org/obo/SO_0000185)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000185')
+
+    @classmethod
+    def repeat_family(cls):
+        """A group of characterized repeat sequences. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000187)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000187')
+
+    @classmethod
+    def intron(cls):
+        """A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (cls, exons) on either side of it. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
+        (http://purl.obolibrary.org/obo/SO_0000188)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000188')
+
+    @classmethod
+    def RFLP_fragment(cls):
+        """A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme. (cls, GOC:pj)
+        (http://purl.obolibrary.org/obo/SO_0000193)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000193')
+
+    @classmethod
+    def coding_exon(cls):
+        """An exon whereby at least one base is part of a codon (cls, here, 'codon' is inclusive of the stop_codon). (SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000195)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000195')
+
+    @classmethod
+    def five_prime_coding_exon_coding_region(cls):
+        """The sequence of the five_prime_coding_exon that codes for protein. (cls, SO:cjm)
+        (http://purl.obolibrary.org/obo/SO_0000196)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000196')
+
+    @classmethod
+    def three_prime_coding_exon_coding_region(cls):
+        """The sequence of the three_prime_coding_exon that codes for protein. (cls, SO:cjm)
+        (http://purl.obolibrary.org/obo/SO_0000197)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000197')
+
+    @classmethod
+    def noncoding_exon(cls):
+        """An exon that does not contain any codons. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000198)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000198')
+
+    @classmethod
+    def five_prime_coding_exon(cls):
+        """The 5' most coding exon. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000200)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000200')
+
+    @classmethod
+    def UTR(cls):
+        """Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000203)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000203')
+
+    @classmethod
+    def five_prime_UTR(cls):
+        """A region at the 5' end of a mature transcript (cls, preceding the initiation codon) that is not translated into a protein. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
+        (http://purl.obolibrary.org/obo/SO_0000204)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000204')
+
+    @classmethod
+    def three_prime_UTR(cls):
+        """A region at the 3' end of a mature transcript (cls, following the stop codon) that is not translated into a protein. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
+        (http://purl.obolibrary.org/obo/SO_0000205)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000205')
+
+    @classmethod
+    def rRNA_primary_transcript(cls):
+        """A primary transcript encoding a ribosomal RNA. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000209)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000209')
+
+    @classmethod
+    def mature_transcript(cls):
+        """A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000233)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000233')
+
+    @classmethod
+    def mRNA(cls):
+        """Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns. (cls, SO:ma)
+        (http://purl.obolibrary.org/obo/SO_0000234)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000234')
+
+    @classmethod
+    def TF_binding_site(cls):
+        """A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000235)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000235')
+
+    @classmethod
+    def ORF(cls):
+        """The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(cls, NNN)nTER. (SGD:rb, SO:ma)
+        (http://purl.obolibrary.org/obo/SO_0000236)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000236')
+
+    @classmethod
+    def flanking_region(cls):
+        """The sequences extending on either side of a specific region. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000239)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000239')
+
+    @classmethod
+    def rRNA(cls):
+        """RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity. (cls, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732)
+        (http://purl.obolibrary.org/obo/SO_0000252)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000252')
+
+    @classmethod
+    def tRNA(cls):
+        """Transfer RNA (cls, tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732)
+        (http://purl.obolibrary.org/obo/SO_0000253)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000253')
+
+    @classmethod
+    def snRNA(cls):
+        """A small nuclear RNA molecule involved in pre-mRNA splicing and processing. (cls, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems)
+        (http://purl.obolibrary.org/obo/SO_0000274)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000274')
+
+    @classmethod
+    def snoRNA(cls):
+        """A snoRNA (cls, small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA. (GOC:kgc)
+        (http://purl.obolibrary.org/obo/SO_0000275)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000275')
+
+    @classmethod
+    def miRNA(cls):
+        """Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (cls, SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. (PMID:12592000)
+        (http://purl.obolibrary.org/obo/SO_0000276)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000276')
+
+    @classmethod
+    def microsatellite(cls):
+        """A repeat_region containing repeat_units (cls, 2 to 4 bp) that is repeated multiple times in tandem. (http://www.informatics.jax.org/silver/glossary.shtml)
+        (http://purl.obolibrary.org/obo/SO_0000289)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000289')
+
+    @classmethod
+    def inverted_repeat(cls):
+        """The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000294)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000294')
+
+    @classmethod
+    def origin_of_replication(cls):
+        """The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies. (cls, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
+        (http://purl.obolibrary.org/obo/SO_0000296)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000296')
+
+    @classmethod
+    def clip(cls):
+        """Part of the primary transcript that is clipped off during processing. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000303)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000303')
+
+    @classmethod
+    def modified_base(cls):
+        """A modified nucleotide, i.e. a nucleotide other than A, T, C. G. (cls, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
+        (http://purl.obolibrary.org/obo/SO_0000305)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000305')
+
+    @classmethod
+    def methylated_base_feature(cls):
+        """A nucleotide modified by methylation. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000306)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000306')
+
+    @classmethod
+    def CpG_island(cls):
+        """Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes. (cls, SO:rd)
+        (http://purl.obolibrary.org/obo/SO_0000307)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000307')
+
+    @classmethod
+    def direct_repeat(cls):
+        """A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000314)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000314')
+
+    @classmethod
+    def TSS(cls):
+        """The first base where RNA polymerase begins to synthesize the RNA transcript. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000315)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000315')
+
+    @classmethod
+    def CDS(cls):
+        """A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon. (cls, SO:ma)
+        (http://purl.obolibrary.org/obo/SO_0000316)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000316')
+
+    @classmethod
+    def start_codon(cls):
+        """First codon to be translated by a ribosome. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000318)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000318')
+
+    @classmethod
+    def stop_codon(cls):
+        """In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000319)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000319')
+
+    @classmethod
+    def tag(cls):
+        """A nucleotide sequence that may be used to identify a larger sequence. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000324)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000324')
+
+    @classmethod
+    def rRNA_large_subunit_primary_transcript(cls):
+        """A primary transcript encoding a large ribosomal subunit RNA. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000325)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000325')
+
+    @classmethod
+    def SAGE_tag(cls):
+        """A short diagnostic sequence tag, serial analysis of gene expression (cls, SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract)
+        (http://purl.obolibrary.org/obo/SO_0000326)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000326')
+
+    @classmethod
+    def conserved_region(cls):
+        """Region of sequence similarity by descent from a common ancestor. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000330)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000330')
+
+    @classmethod
+    def STS(cls):
+        """Short (cls, typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known. (http://www.biospace.com)
+        (http://purl.obolibrary.org/obo/SO_0000331)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000331')
+
+    @classmethod
+    def coding_conserved_region(cls):
+        """Coding region of sequence similarity by descent from a common ancestor. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000332)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000332')
+
+    @classmethod
+    def exon_junction(cls):
+        """The boundary between two exons in a processed transcript. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000333)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000333')
+
+    @classmethod
+    def nc_conserved_region(cls):
+        """Non-coding region of sequence similarity by descent from a common ancestor. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000334)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000334')
+
+    @classmethod
+    def pseudogene(cls):
+        """A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (cls, usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog). (http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html)
+        (http://purl.obolibrary.org/obo/SO_0000336)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000336')
+
+    @classmethod
+    def RNAi_reagent(cls):
+        """A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference. (cls, SO:rd)
+        (http://purl.obolibrary.org/obo/SO_0000337)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000337')
+
+    @classmethod
+    def chromosome(cls):
+        """Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication. (cls, SO:ma)
+        (http://purl.obolibrary.org/obo/SO_0000340)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000340')
+
+    @classmethod
+    def chromosome_band(cls):
+        """A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark. (cls, SO:ma)
+        (http://purl.obolibrary.org/obo/SO_0000341)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000341')
+
+    @classmethod
+    def match(cls):
+        """A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000343)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000343')
+
+    @classmethod
+    def splice_enhancer(cls):
+        """Region of a transcript that regulates splicing. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000344)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000344')
+
+    @classmethod
+    def EST(cls):
+        """A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000345)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000345')
+
+    @classmethod
+    def nucleotide_match(cls):
+        """A match against a nucleotide sequence. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000347)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000347')
+
+    @classmethod
+    def protein_match(cls):
+        """A match against a protein sequence. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000349)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000349')
+
+    @classmethod
+    def sequence_assembly(cls):
+        """A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. (cls, SO:ma)
+        (http://purl.obolibrary.org/obo/SO_0000353)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000353')
+
+    @classmethod
+    def codon(cls):
+        """A set of (cls, usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS. (http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000360)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000360')
+
+    @classmethod
+    def insertion_site(cls):
+        """The junction where an insertion occurred. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000366)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000366')
+
+    @classmethod
+    def transposable_element_insertion_site(cls):
+        """The junction in a genome where a transposable_element has inserted. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000368)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000368')
+
+    @classmethod
+    def small_regulatory_ncRNA(cls):
+        """A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression. (cls, SO:ma)
+        (http://purl.obolibrary.org/obo/SO_0000370)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000370')
+
+    @classmethod
+    def enzymatic_RNA(cls):
+        """An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein. (cls, RSC:cb)
+        (http://purl.obolibrary.org/obo/SO_0000372)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000372')
+
+    @classmethod
+    def ribozyme(cls):
+        """An RNA with catalytic activity. (cls, SO:ma)
+        (http://purl.obolibrary.org/obo/SO_0000374)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000374')
+
+    @classmethod
+    def rRNA_5_8S(cls):
+        """5_8S ribosomal RNA (cls, 5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002)
+        (http://purl.obolibrary.org/obo/SO_0000375)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000375')
+
+    @classmethod
+    def hammerhead_ribozyme(cls):
+        """A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs. (cls, PMID:2436805)
+        (http://purl.obolibrary.org/obo/SO_0000380)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000380')
+
+    @classmethod
+    def RNase_MRP_RNA(cls):
+        """The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs. (cls, http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030)
+        (http://purl.obolibrary.org/obo/SO_0000385)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000385')
+
+    @classmethod
+    def RNase_P_RNA(cls):
+        """The RNA component of Ribonuclease P (cls, RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010)
+        (http://purl.obolibrary.org/obo/SO_0000386)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000386')
+
+    @classmethod
+    def telomerase_RNA(cls):
+        """The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA. (cls, http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025)
+        (http://purl.obolibrary.org/obo/SO_0000390)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000390')
+
+    @classmethod
+    def U1_snRNA(cls):
+        """U1 is a small nuclear RNA (cls, snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003)
+        (http://purl.obolibrary.org/obo/SO_0000391)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000391')
+
+    @classmethod
+    def U2_snRNA(cls):
+        """U2 is a small nuclear RNA (cls, snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004)
+        (http://purl.obolibrary.org/obo/SO_0000392)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000392')
+
+    @classmethod
+    def U4_snRNA(cls):
+        """U4 small nuclear RNA (cls, U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015)
+        (http://purl.obolibrary.org/obo/SO_0000393)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000393')
+
+    @classmethod
+    def U4atac_snRNA(cls):
+        """An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (cls, SO:0000397). (PMID:=12409455)
+        (http://purl.obolibrary.org/obo/SO_0000394)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000394')
+
+    @classmethod
+    def U5_snRNA(cls):
+        """U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation. (cls, http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020)
+        (http://purl.obolibrary.org/obo/SO_0000395)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000395')
+
+    @classmethod
+    def U6_snRNA(cls):
+        """U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA. (cls, http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015)
+        (http://purl.obolibrary.org/obo/SO_0000396)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000396')
+
+    @classmethod
+    def U6atac_snRNA(cls):
+        """U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (cls, SO:0000394). (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract)
+        (http://purl.obolibrary.org/obo/SO_0000397)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000397')
+
+    @classmethod
+    def U11_snRNA(cls):
+        """U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence. (cls, PMID:9622129)
+        (http://purl.obolibrary.org/obo/SO_0000398)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000398')
+
+    @classmethod
+    def U12_snRNA(cls):
+        """The U12 small nuclear (cls, snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007)
+        (http://purl.obolibrary.org/obo/SO_0000399)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000399')
+
+    @classmethod
+    def U14_snoRNA(cls):
+        """U14 small nucleolar RNA (cls, U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119)
+        (http://purl.obolibrary.org/obo/SO_0000403)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000403')
+
+    @classmethod
+    def vault_RNA(cls):
+        """A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (cls, MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006)
+        (http://purl.obolibrary.org/obo/SO_0000404)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000404')
+
+    @classmethod
+    def Y_RNA(cls):
+        """Y RNAs are components of the Ro ribonucleoprotein particle (cls, Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019)
+        (http://purl.obolibrary.org/obo/SO_0000405)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000405')
+
+    @classmethod
+    def rRNA_18S(cls):
+        """A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000407)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000407')
+
+    @classmethod
+    def binding_site(cls):
+        """A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. (cls, EBIBS:GAR, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000409)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000409')
+
+    @classmethod
+    def protein_binding_site(cls):
+        """A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000410)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000410')
+
+    @classmethod
+    def restriction_fragment(cls):
+        """A region of polynucleotide sequence produced by digestion with a restriction endonuclease. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000412)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000412')
+
+    @classmethod
+    def sequence_difference(cls):
+        """A region where the sequence differs from that of a specified sequence. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000413)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000413')
+
+    @classmethod
+    def signal_peptide(cls):
+        """The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components. (cls, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
+        (http://purl.obolibrary.org/obo/SO_0000418)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000418')
+
+    @classmethod
+    def mature_protein_region(cls):
+        """The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide. (cls, EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb)
+        (http://purl.obolibrary.org/obo/SO_0000419)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000419')
+
+    @classmethod
+    def ARS(cls):
+        """A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host. (cls, SO:ma)
+        (http://purl.obolibrary.org/obo/SO_0000436)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000436')
+
+    @classmethod
+    def ss_oligo(cls):
+        """A single stranded oligonucleotide. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000441)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000441')
+
+    @classmethod
+    def ds_oligo(cls):
+        """A double stranded oligonucleotide. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000442)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000442')
+
+    @classmethod
+    def rasiRNA(cls):
+        """A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements. (cls, http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284)
+        (http://purl.obolibrary.org/obo/SO_0000454)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000454')
+
+    @classmethod
+    def pseudogenic_region(cls):
+        """A non-functional descendent of a functional entity. (cls, SO:cjm)
+        (http://purl.obolibrary.org/obo/SO_0000462)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000462')
+
+    @classmethod
+    def decayed_exon(cls):
+        """A non-functional descendant of an exon. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000464)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000464')
+
+    @classmethod
+    def golden_path_fragment(cls):
+        """One of the pieces of sequence that make up a golden path. (cls, SO:rd)
+        (http://purl.obolibrary.org/obo/SO_0000468)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000468')
+
+    @classmethod
+    def tiling_path(cls):
+        """A set of regions which overlap with minimal polymorphism to form a linear sequence. (cls, SO:cjm)
+        (http://purl.obolibrary.org/obo/SO_0000472)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000472')
+
+    @classmethod
+    def tiling_path_fragment(cls):
+        """A piece of sequence that makes up a tiling_path (cls, SO:0000472). (SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000474)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000474')
+
+    @classmethod
+    def nc_primary_transcript(cls):
+        """A primary transcript that is never translated into a protein. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000483)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000483')
+
+    @classmethod
+    def three_prime_coding_exon_noncoding_region(cls):
+        """The sequence of the 3' exon that is not coding. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000484)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000484')
+
+    @classmethod
+    def five_prime_coding_exon_noncoding_region(cls):
+        """The sequence of the 5' exon preceding the start codon. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000486)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000486')
+
+    @classmethod
+    def virtual_sequence(cls):
+        """A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000499)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000499')
+
+    @classmethod
+    def transcribed_region(cls):
+        """A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000502)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000502')
+
+    @classmethod
+    def polyA_signal_sequence(cls):
+        """The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA. (cls, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
+        (http://purl.obolibrary.org/obo/SO_0000551)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000551')
+
+    @classmethod
+    def polyA_site(cls):
+        """The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence. (cls, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
+        (http://purl.obolibrary.org/obo/SO_0000553)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000553')
+
+    @classmethod
+    def centromere(cls):
+        """A region of chromosome where the spindle fibers attach during mitosis and meiosis. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000577)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000577')
+
+    @classmethod
+    def cap(cls):
+        """A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA. (cls, http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html)
+        (http://purl.obolibrary.org/obo/SO_0000581)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000581')
+
+    @classmethod
+    def group_I_intron(cls):
+        """Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (cls, P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028)
+        (http://purl.obolibrary.org/obo/SO_0000587)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000587')
+
+    @classmethod
+    def autocatalytically_spliced_intron(cls):
+        """A self spliced intron. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000588)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000588')
+
+    @classmethod
+    def SRP_RNA(cls):
+        """The signal recognition particle (cls, SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017)
+        (http://purl.obolibrary.org/obo/SO_0000590)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000590')
+
+    @classmethod
+    def C_D_box_snoRNA(cls):
+        """Most box C/D snoRNAs also contain long (cls, >10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'. (http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html)
+        (http://purl.obolibrary.org/obo/SO_0000593)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000593')
+
+    @classmethod
+    def guide_RNA(cls):
+        """A short 3'-uridylated RNA that can form a duplex (cls, except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA. (http://www.rna.ucla.edu/index.html)
+        (http://purl.obolibrary.org/obo/SO_0000602)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000602')
+
+    @classmethod
+    def group_II_intron(cls):
+        """Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (cls, usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny. (http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml)
+        (http://purl.obolibrary.org/obo/SO_0000603)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000603')
+
+    @classmethod
+    def intergenic_region(cls):
+        """A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome. (cls, SO:cjm)
+        (http://purl.obolibrary.org/obo/SO_0000605)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000605')
+
+    @classmethod
+    def polyA_sequence(cls):
+        """Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000610)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000610')
+
+    @classmethod
+    def branch_site(cls):
+        """A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000611)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000611')
+
+    @classmethod
+    def polypyrimidine_tract(cls):
+        """The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing. (cls, http://nar.oupjournals.org/cgi/content/full/25/4/888)
+        (http://purl.obolibrary.org/obo/SO_0000612)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000612')
+
+    @classmethod
+    def transcription_end_site(cls):
+        """The base where transcription ends. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000616)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000616')
+
+    @classmethod
+    def telomere(cls):
+        """A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end. (cls, SO:ma)
+        (http://purl.obolibrary.org/obo/SO_0000624)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000624')
+
+    @classmethod
+    def silencer(cls):
+        """A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000625)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000625')
+
+    @classmethod
+    def insulator(cls):
+        """A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression. (cls, SO:regcreative)
+        (http://purl.obolibrary.org/obo/SO_0000627)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000627')
+
+    @classmethod
+    def chromosomal_structural_element(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000628')
+
+    @classmethod
+    def minisatellite(cls):
+        """A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp. (cls, http://www.informatics.jax.org/silver/glossary.shtml)
+        (http://purl.obolibrary.org/obo/SO_0000643)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000643')
+
+    @classmethod
+    def antisense_RNA(cls):
+        """Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000644)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000644')
+
+    @classmethod
+    def antisense_primary_transcript(cls):
+        """The reverse complement of the primary transcript. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000645)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000645')
+
+    @classmethod
+    def siRNA(cls):
+        """A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (cls, via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules. (PMID:12592000)
+        (http://purl.obolibrary.org/obo/SO_0000646)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000646')
+
+    @classmethod
+    def stRNA(cls):
+        """Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans. (cls, PMID:11081512)
+        (http://purl.obolibrary.org/obo/SO_0000649)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000649')
+
+    @classmethod
+    def small_subunit_rRNA(cls):
+        """Ribosomal RNA transcript that structures the small subunit of the ribosome. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000650)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000650')
+
+    @classmethod
+    def large_subunit_rRNA(cls):
+        """Ribosomal RNA transcript that structures the large subunit of the ribosome. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000651)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000651')
+
+    @classmethod
+    def rRNA_5S(cls):
+        """5S ribosomal RNA (cls, 5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001)
+        (http://purl.obolibrary.org/obo/SO_0000652)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000652')
+
+    @classmethod
+    def rRNA_28S(cls):
+        """A component of the large ribosomal subunit. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000653)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000653')
+
+    @classmethod
+    def ncRNA(cls):
+        """An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000655)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000655')
+
+    @classmethod
+    def repeat_region(cls):
+        """A region of sequence containing one or more repeat units. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000657)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000657')
+
+    @classmethod
+    def dispersed_repeat(cls):
+        """A repeat that is located at dispersed sites in the genome. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000658)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000658')
+
+    @classmethod
+    def spliceosomal_intron(cls):
+        """An intron which is spliced by the spliceosome. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000662)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000662')
+
+    @classmethod
+    def insertion(cls):
+        """The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000667)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000667')
+
+    @classmethod
+    def EST_match(cls):
+        """A match against an EST sequence. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000668)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000668')
+
+    @classmethod
+    def transcript(cls):
+        """An RNA synthesized on a DNA or RNA template by an RNA polymerase. (cls, SO:ma)
+        (http://purl.obolibrary.org/obo/SO_0000673)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000673')
+
+    @classmethod
+    def nuclease_sensitive_site(cls):
+        """A region of nucleotide sequence targeted by a nuclease enzyme. (cls, SO:ma)
+        (http://purl.obolibrary.org/obo/SO_0000684)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000684')
+
+    @classmethod
+    def deletion_junction(cls):
+        """The space between two bases in a sequence which marks the position where a deletion has occurred. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000687)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000687')
+
+    @classmethod
+    def golden_path(cls):
+        """A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence. (cls, SO:ls)
+        (http://purl.obolibrary.org/obo/SO_0000688)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000688')
+
+    @classmethod
+    def cDNA_match(cls):
+        """A match against cDNA sequence. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000689)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000689')
+
+    @classmethod
+    def SNP(cls):
+        """SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(cls, s), wherein the least frequent variant has an abundance of 1% or greater. (SO:cb)
+        (http://purl.obolibrary.org/obo/SO_0000694)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000694')
+
+    @classmethod
+    def reagent(cls):
+        """A sequence used in experiment. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000695)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000695')
+
+    @classmethod
+    def oligo(cls):
+        """A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. (cls, SO:ma)
+        (http://purl.obolibrary.org/obo/SO_0000696)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000696')
+
+    @classmethod
+    def junction(cls):
+        """A sequence_feature with an extent of zero. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000699)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000699')
+
+    @classmethod
+    def remark(cls):
+        """A comment about the sequence. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000700)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000700')
+
+    @classmethod
+    def possible_base_call_error(cls):
+        """A region of sequence where the validity of the base calling is questionable. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000701)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000701')
+
+    @classmethod
+    def possible_assembly_error(cls):
+        """A region of sequence where there may have been an error in the assembly. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000702)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000702')
+
+    @classmethod
+    def experimental_result_region(cls):
+        """A region of sequence implicated in an experimental result. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000703)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000703')
+
+    @classmethod
+    def gene(cls):
+        """A region (cls, or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. (SO:immuno_workshop)
+        (http://purl.obolibrary.org/obo/SO_0000704)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000704')
+
+    @classmethod
+    def tandem_repeat(cls):
+        """Two or more adjcent copies of a region (cls, of length greater than 1). (SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000705)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000705')
+
+    @classmethod
+    def trans_splice_acceptor_site(cls):
+        """The 3' splice site of the acceptor primary transcript. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000706)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000706')
+
+    @classmethod
+    def nucleotide_motif(cls):
+        """A region of nucleotide sequence corresponding to a known motif. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000714)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000714')
+
+    @classmethod
+    def RNA_motif(cls):
+        """A motif that is active in RNA sequence. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000715)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000715')
+
+    @classmethod
+    def reading_frame(cls):
+        """A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon. (cls, SGD:rb)
+        (http://purl.obolibrary.org/obo/SO_0000717)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000717')
+
+    @classmethod
+    def ultracontig(cls):
+        """An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers. (cls, FB:WG)
+        (http://purl.obolibrary.org/obo/SO_0000719)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000719')
+
+    @classmethod
+    def oriT(cls):
+        """A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization. (cls, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
+        (http://purl.obolibrary.org/obo/SO_0000724)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000724')
+
+    @classmethod
+    def transit_peptide(cls):
+        """The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (cls, chloroplast, mitochondrion, microbody or cyanelle). (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
+        (http://purl.obolibrary.org/obo/SO_0000725)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000725')
+
+    @classmethod
+    def CRM(cls):
+        """A regulatory_region where more than 1 TF_binding_site together are regulatorily active. (cls, SO:SG)
+        (http://purl.obolibrary.org/obo/SO_0000727)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000727')
+
+    @classmethod
+    def gap(cls):
+        """A gap in the sequence of known length. The unknown bases are filled in with N's. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000730)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000730')
+
+    @classmethod
+    def gene_group_regulatory_region(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000752')
+
+    @classmethod
+    def clone_insert(cls):
+        """The region of sequence that has been inserted and is being propagated by the clone. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000753)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000753')
+
+    @classmethod
+    def pseudogenic_rRNA(cls):
+        """A non functional descendent of an rRNA. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000777)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000777')
+
+    @classmethod
+    def pseudogenic_tRNA(cls):
+        """A non functional descendent of a tRNA. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000778)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000778')
+
+    @classmethod
+    def chromosome_part(cls):
+        """A region of a chromosome. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000830)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000830')
+
+    @classmethod
+    def gene_member_region(cls):
+        """A region of a gene. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000831)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000831')
+
+    @classmethod
+    def transcript_region(cls):
+        """A region of a transcript. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000833)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000833')
+
+    @classmethod
+    def mature_transcript_region(cls):
+        """A region of a mature transcript. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000834)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000834')
+
+    @classmethod
+    def primary_transcript_region(cls):
+        """A part of a primary transcript. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000835)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000835')
+
+    @classmethod
+    def mRNA_region(cls):
+        """A region of an mRNA. (cls, SO:cb)
+        (http://purl.obolibrary.org/obo/SO_0000836)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000836')
+
+    @classmethod
+    def UTR_region(cls):
+        """A region of UTR. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000837)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000837')
+
+    @classmethod
+    def polypeptide_region(cls):
+        """Biological sequence region that can be assigned to a specific subsequence of a polypeptide. (cls, SO:GAR, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000839)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000839')
+
+    @classmethod
+    def spliceosomal_intron_region(cls):
+        """A region within an intron. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0000841)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000841')
+
+    @classmethod
+    def gene_component_region(cls):
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000842')
+
+    @classmethod
+    def CDS_region(cls):
+        """A region of a CDS. (cls, SO:cb)
+        (http://purl.obolibrary.org/obo/SO_0000851)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000851')
+
+    @classmethod
+    def exon_region(cls):
+        """A region of an exon. (cls, RSC:cb)
+        (http://purl.obolibrary.org/obo/SO_0000852)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000852')
+
+    @classmethod
+    def rRNA_16S(cls):
+        """A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0001000)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001000')
+
+    @classmethod
+    def rRNA_23S(cls):
+        """A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0001001)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001001')
+
+    @classmethod
+    def rRNA_25S(cls):
+        """A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes. (cls, RSC:cb)
+        (http://purl.obolibrary.org/obo/SO_0001002)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001002')
+
+    @classmethod
+    def copy_number_variation(cls):
+        """A variation that increases or decreases the copy number of a given region. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0001019)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001019')
+
+    @classmethod
+    def mobile_genetic_element(cls):
+        """A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome. (cls, PMID:14681355)
+        (http://purl.obolibrary.org/obo/SO_0001037)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001037')
+
+    @classmethod
+    def integrated_mobile_genetic_element(cls):
+        """An MGE that is integrated into the host chromosome. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0001039)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001039')
+
+    @classmethod
+    def transcriptional_cis_regulatory_region(cls):
+        """A regulatory_region that modulates the transcription of a gene or genes. (cls, SO:regcreative)
+        (http://purl.obolibrary.org/obo/SO_0001055)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001055')
+
+    @classmethod
+    def splicing_regulatory_region(cls):
+        """A regulatory_region that modulates splicing. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0001056)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001056')
+
+    @classmethod
+    def sequence_alteration(cls):
+        """A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0001059)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001059')
+
+    @classmethod
+    def immature_peptide_region(cls):
+        """An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs. (cls, EBIBS:GAR)
+        (http://purl.obolibrary.org/obo/SO_0001063)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001063')
+
+    @classmethod
+    def noncoding_region_of_exon(cls):
+        """The maximal intersection of exon and UTR. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0001214)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001214')
+
+    @classmethod
+    def coding_region_of_exon(cls):
+        """The region of an exon that encodes for protein sequence. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0001215)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001215')
+
+    @classmethod
+    def replicon(cls):
+        """A region containing at least one unique origin of replication and a unique termination site. (cls, ISBN:0716719207)
+        (http://purl.obolibrary.org/obo/SO_0001235)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001235')
+
+    @classmethod
+    def base(cls):
+        """A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0001236)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001236')
+
+    @classmethod
+    def assembly(cls):
+        """A region of the genome of known length that is composed by ordering and aligning two or more different regions. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0001248)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001248')
+
+    @classmethod
+    def biomaterial_region(cls):
+        """A region which is intended for use in an experiment. (cls, SO:cb)
+        (http://purl.obolibrary.org/obo/SO_0001409)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001409')
+
+    @classmethod
+    def experimental_feature(cls):
+        """A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. (cls, SO:cb)
+        (http://purl.obolibrary.org/obo/SO_0001410)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001410')
+
+    @classmethod
+    def biological_region(cls):
+        """A region defined by its disposition to be involved in a biological process. (cls, SO:cb)
+        (http://purl.obolibrary.org/obo/SO_0001411)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001411')
+
+    @classmethod
+    def topologically_defined_region(cls):
+        """A region that is defined according to its relations with other regions within the same sequence. (cls, SO:cb)
+        (http://purl.obolibrary.org/obo/SO_0001412)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001412')
+
+    @classmethod
+    def cis_splice_site(cls):
+        """Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron. (cls, SO:cjm, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0001419)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001419')
+
+    @classmethod
+    def trans_splice_site(cls):
+        """Primary transcript region bordering trans-splice junction. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0001420)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001420')
+
+    @classmethod
+    def SNV(cls):
+        """SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist. (cls, SO:bm)
+        (http://purl.obolibrary.org/obo/SO_0001483)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001483')
+
+    @classmethod
+    def peptide_localization_signal(cls):
+        """A region of peptide sequence used to target the polypeptide molecule to a specific organelle. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0001527)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001527')
+
+    @classmethod
+    def kozak_sequence(cls):
+        """A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0001647)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001647')
+
+    @classmethod
+    def nucleotide_to_protein_binding_site(cls):
+        """A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0001654)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001654')
+
+    @classmethod
+    def transcription_regulatory_region(cls):
+        """A regulatory region that is involved in the control of the process of transcription. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0001679)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001679')
+
+    @classmethod
+    def sequence_motif(cls):
+        """A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance. (cls, http://en.wikipedia.org/wiki/Sequence_motif)
+        (http://purl.obolibrary.org/obo/SO_0001683)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001683')
+
+    @classmethod
+    def epigenetically_modified_region(cls):
+        """A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence. (cls, http://en.wikipedia.org/wiki/Epigenetics, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0001720)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001720')
+
+    @classmethod
+    def paired_end_fragment(cls):
+        """An assembly region that has been sequenced from both ends resulting in a read_pair (cls, mate_pair). (SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0001790)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001790')
+
+    @classmethod
+    def regulatory_region(cls):
+        """A region of sequence that is involved in the control of a biological process. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_0005836)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0005836')
+
+    @classmethod
+    def gene_group(cls):
+        """A collection of related genes. (cls, SO:ma)
+        (http://purl.obolibrary.org/obo/SO_0005855)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0005855')
+
+    @classmethod
+    def cleaved_peptide_region(cls):
+        """The cleaved_peptide_regon is the a region of peptide sequence that is cleaved during maturation. (cls, EBIBS:GAR)
+        (http://purl.obolibrary.org/obo/SO_0100011)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0100011')
+
+    @classmethod
+    def substitution(cls):
+        """A sequence alteration where the length of the change in the variant is the same as that of the reference. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_1000002)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_1000002')
+
+    @classmethod
+    def complex_substitution(cls):
+        """When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change. (cls, EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html)
+        (http://purl.obolibrary.org/obo/SO_1000005)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_1000005')
+
+    @classmethod
+    def point_mutation(cls):
+        """A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. (cls, SO:immuno_workshop)
+        (http://purl.obolibrary.org/obo/SO_1000008)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_1000008')
+
+    @classmethod
+    def inversion(cls):
+        """A continuous nucleotide sequence is inverted in the same position. (cls, EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html)
+        (http://purl.obolibrary.org/obo/SO_1000036)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_1000036')
+
+    @classmethod
+    def regulon(cls):
+        """A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal. (cls, ISBN:0198506732)
+        (http://purl.obolibrary.org/obo/SO_1001284)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_1001284')
+
+    @classmethod
+    def databank_entry(cls):
+        """The sequence referred to by an entry in a databank such as Genbank or SwissProt. (cls, SO:ke)
+        (http://purl.obolibrary.org/obo/SO_2000061)
+        """
+        return _namespace_SOFO('http://purl.obolibrary.org/obo/SO_2000061')
+
+    @classmethod
+    def is_object_property(cls, uri):
+        """Determines whether the given URI is an object property.
+        
+        uri -- URI that is tested for being an object property
+        """
+        if uri == _namespace_SOFO(''):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:complete_evidence_for_feature'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:contained_by'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:contains'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:derives_from'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:evidence_for_feature'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:has_integral_part'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:has_part'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:homologous_to'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:integral_part_of'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:member_of'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:non_functional_homolog_of'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:orthologous_to'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:paralogous_to'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:part_of'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:partial_evidence_for_feature'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:similar_to'):
+            return True
+        return False
+
+    @classmethod
+    def is_datatype_property(cls, uri):
+        """Determines whether the given URI is a datatype property.
+        
+        uri -- URI that is tested for being a datatype property
+        """
+        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_SOFO('http://purl.obolibrary.org/obo/SO_0000000'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000001'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000004'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000005'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000006'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000007'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000013'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000038'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000039'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000050'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000057'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000059'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000101'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000102'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000103'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000104'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000109'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000110'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000112'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000113'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000114'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000120'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000139'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000140'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000141'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000143'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000147'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000148'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000149'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000150'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000151'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000159'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000161'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000162'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000163'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000164'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000165'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000167'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000177'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000178'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000179'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000181'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000183'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000185'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000187'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000188'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000193'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000195'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000196'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000197'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000198'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000200'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000203'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000204'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000205'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000209'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000233'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000234'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000235'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000236'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000239'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000252'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000253'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000274'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000275'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000276'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000289'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000294'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000296'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000303'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000305'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000306'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000307'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000314'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000315'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000316'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000318'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000319'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000324'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000325'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000326'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000330'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000331'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000332'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000333'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000334'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000336'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000337'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000340'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000341'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000343'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000344'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000345'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000347'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000349'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000353'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000360'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000366'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000368'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000370'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000372'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000374'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000375'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000380'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000385'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000386'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000390'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000391'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000392'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000393'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000394'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000395'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000396'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000397'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000398'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000399'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000403'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000404'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000405'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000407'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000409'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000410'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000412'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000413'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000418'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000419'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000436'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000441'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000442'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000454'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000462'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000464'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000468'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000472'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000474'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000483'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000484'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000486'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000499'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000502'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000551'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000553'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000577'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000581'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000587'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000588'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000590'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000593'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000602'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000603'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000605'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000610'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000611'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000612'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000616'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000624'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000625'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000627'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000628'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000643'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000644'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000645'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000646'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000649'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000650'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000651'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000652'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000653'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000655'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000657'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000658'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000662'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000667'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000668'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000673'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000684'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000687'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000688'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000689'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000694'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000695'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000696'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000699'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000700'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000701'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000702'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000703'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000704'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000705'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000706'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000714'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000715'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000717'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000719'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000724'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000725'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000727'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000730'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000752'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000753'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000777'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000778'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000830'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000831'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000833'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000834'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000835'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000836'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000837'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000839'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000841'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000842'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000851'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000852'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001000'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001001'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001002'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001019'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001037'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001039'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001055'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001056'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001059'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001063'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001214'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001215'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001235'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001236'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001248'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001409'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001410'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001411'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001412'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001419'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001420'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001483'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001527'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001647'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001654'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001679'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001683'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001720'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001790'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0005836'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0005855'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0100011'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_1000002'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_1000005'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_1000008'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_1000036'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_1001284'):
+            return True
+        if uri == _namespace_SOFO('http://purl.obolibrary.org/obo/SO_2000061'):
+            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
+
+    __parent_properties = { _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:complete_evidence_for_feature') : _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:evidence_for_feature') , _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:has_integral_part') : _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:has_part') , _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:homologous_to') : _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:similar_to') , _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:integral_part_of') : _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:part_of') , _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:member_of') : _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:part_of') , _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:non_functional_homolog_of') : _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:homologous_to') , _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:orthologous_to') : _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:homologous_to') , _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:paralogous_to') : _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:homologous_to') , _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:partial_evidence_for_feature') : _namespace_SOFO('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:evidence_for_feature') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000001') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000110') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000004') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000195') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000005') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000705') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000006') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000695') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000057') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000752') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000059') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001654') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000101') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001039') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000102') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000347') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000112') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000441') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000113') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001039') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000114') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000306') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000120') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000185') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000139') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000836') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000143') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001410') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000147') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000833') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000151') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000695') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000159') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001411') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000161') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000306') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000162') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000835') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000163') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001419') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000164') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001419') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000165') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000727') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000167') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001055') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000177') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000347') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000178') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0005855') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000181') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000347') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000183') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000842') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000185') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000673') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000188') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000835') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000193') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000412') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000195') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000147') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000198') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000147') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000200') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000195') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000203') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000836') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000204') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000203') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000205') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000203') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000209') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000483') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000234') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000233') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000235') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001679') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000236') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000717') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000239') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001412') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000289') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000005') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000294') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000657') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000303') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000835') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000305') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001720') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000306') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000305') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000307') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001411') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000314') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000657') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000315') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000835') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000316') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000836') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000318') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000360') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000319') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000360') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000324') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000696') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000325') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000209') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000326') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000324') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000330') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001410') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000331') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000324') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000332') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000330') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000334') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000330') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000337') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000442') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000340') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001235') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000341') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000830') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000343') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001410') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000344') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001056') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000347') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000343') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000349') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000343') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000353') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0001248') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000360') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000851') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000366') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000699') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000368') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000366') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000370') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000655') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000372') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000673') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000374') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000372') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000375') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000651') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000380') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000715') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000385') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000655') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000386') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000655') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000390') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000655') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000391') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000274') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000392') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000274') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000393') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000274') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000394') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000274') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000395') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000274') , _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000396') : _namespace_SOFO('http://purl.obolibrary.org/obo/SO_0000274') , 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