Level Rule Name Subject Property Value ERROR deprecated_class_reference SO:0001058 rdfs:subClassOf SO:0001055 ERROR duplicate_definition SO:0000428 IAO:0000115 The U5 segment of the three-prime long terminal repeat. ERROR duplicate_definition SO:0000432 IAO:0000115 The U5 segment of the three-prime long terminal repeat. ERROR duplicate_definition SO:0000429 IAO:0000115 The U3 segment of the three-prime long terminal repeat. ERROR duplicate_definition SO:0000431 IAO:0000115 The U3 segment of the three-prime long terminal repeat. ERROR duplicate_definition SO:0000753 IAO:0000115 The region of sequence that has been inserted and is being propagated by the clone. ERROR duplicate_definition SO:0000785 IAO:0000115 The region of sequence that has been inserted and is being propagated by the clone. ERROR duplicate_definition SO:0000427 IAO:0000115 The R segment of the three-prime long terminal repeat. ERROR duplicate_definition SO:0000430 IAO:0000115 The R segment of the three-prime long terminal repeat. ERROR duplicate_definition SO:0002195 IAO:0000115 The pseudogene has no parent. It is the original gene, which is functional in some species but disrupted in some way (indels, mutation, recombination) in another species or strain. ERROR duplicate_definition SO:0002199 IAO:0000115 The pseudogene has no parent. It is the original gene, which is functional in some species but disrupted in some way (indels, mutation, recombination) in another species or strain. ERROR duplicate_definition SO:0002194 IAO:0000115 The pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutation. The changes, compared to their functional homolog, include insertions, deletions, premature stop codons, frameshifts and a higher proportion of non-synonymous versus synonymous substitutions. ERROR duplicate_definition SO:0002198 IAO:0000115 The pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutation. The changes, compared to their functional homolog, include insertions, deletions, premature stop codons, frameshifts and a higher proportion of non-synonymous versus synonymous substitutions. ERROR duplicate_definition SO:0002193 IAO:0000115 The pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. Therefore, it has lost any intron/exon structure, and it might have a pseudo-polyA-tail. ERROR duplicate_definition SO:0002197 IAO:0000115 The pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. Therefore, it has lost any intron/exon structure, and it might have a pseudo-polyA-tail. ERROR duplicate_definition SO:0000960 IAO:0000115 Structural unit composed of a self-replicating, single-stranded, circular DNA molecule. ERROR duplicate_definition SO:0000966 IAO:0000115 Structural unit composed of a self-replicating, single-stranded, circular DNA molecule. ERROR duplicate_definition SO:0000737 IAO:0000115 DNA belonging to the genome of a mitochondria. ERROR duplicate_definition SO:0001032 IAO:0000115 DNA belonging to the genome of a mitochondria. ERROR duplicate_definition SO:0000030 IAO:0000115 A type of non-canonical base-pairing. ERROR duplicate_definition SO:0000501 IAO:0000115 A type of non-canonical base-pairing. ERROR duplicate_definition SO:0000283 IAO:0000115 A transposable_element that is engineered and foreign. ERROR duplicate_definition SO:0000799 IAO:0000115 A transposable_element that is engineered and foreign. ERROR duplicate_definition SO:0000107 IAO:0000115 A single stranded oligo used for polymerase chain reaction. ERROR duplicate_definition SO:0000121 IAO:0000115 A single stranded oligo used for polymerase chain reaction. ERROR duplicate_definition SO:0000132 IAO:0000115 A single stranded oligo used for polymerase chain reaction. ERROR duplicate_definition SO:0001599 IAO:0000115 A sequence variant that changes the resulting polypeptide structure. ERROR duplicate_definition SO:0001600 IAO:0000115 A sequence variant that changes the resulting polypeptide structure. ERROR duplicate_definition SO:0001898 IAO:0000115 A repeat region which is part of the regional centromere outer repeat region. ERROR duplicate_definition SO:0001899 IAO:0000115 A repeat region which is part of the regional centromere outer repeat region. ERROR duplicate_definition SO:0000226 IAO:0000115 A primary transcript encoding seryl tRNA (SO:000269). ERROR duplicate_definition SO:0005856 IAO:0000115 A primary transcript encoding seryl tRNA (SO:000269). ERROR duplicate_definition SO:0001763 IAO:0000115 A physical quality which inheres to the variant by virtue of the number instances of the variant within a population. ERROR duplicate_definition SO:0001764 IAO:0000115 A physical quality which inheres to the variant by virtue of the number instances of the variant within a population. ERROR duplicate_definition SO:0100004 IAO:0000115 A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1. ERROR duplicate_definition SO:0100006 IAO:0000115 A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1. ERROR duplicate_definition SO:0000054 IAO:0000115 A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. ERROR duplicate_definition SO:1000182 IAO:0000115 A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. ERROR duplicate_definition SO:0000816 IAO:0000115 A gene that rescues. ERROR duplicate_definition SO:0000818 IAO:0000115 A gene that rescues. ERROR duplicate_definition SO:0000456 IAO:0000115 A gene that is recombinationally rearranged. ERROR duplicate_definition SO:0000940 IAO:0000115 A gene that is recombinationally rearranged. ERROR duplicate_definition SO:0005847 IAO:0000115 A gene that is a member of a gene cassette, which is a mobile genetic element. ERROR duplicate_definition SO:0005848 IAO:0000115 A gene that is a member of a gene cassette, which is a mobile genetic element. ERROR duplicate_definition SO:0000051 IAO:0000115 A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid. ERROR duplicate_definition SO:0000328 IAO:0000115 A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid. ERROR duplicate_definition SO:0001914 IAO:0000115 A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing. ERROR duplicate_definition SO:0002021 IAO:0000115 A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing. ERROR duplicate_definition SO:0002189 IAO:0000115 A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes. ERROR duplicate_definition SO:0002196 IAO:0000115 A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes. ERROR duplicate_definition SO:0002200 IAO:0000115 A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes. ERROR duplicate_label SO:0001957 rdfs:label RNA_stability_element ERROR duplicate_label SO:0001979 rdfs:label RNA_stability_element ERROR duplicate_label SO:0001053 rdfs:label nested_transposon ERROR duplicate_label SO:0001648 rdfs:label nested_transposon ERROR duplicate_label SO:0001052 rdfs:label nested_repeat ERROR duplicate_label SO:0001649 rdfs:label nested_repeat ERROR duplicate_label SO:0000179 rdfs:label clone_insert_start ERROR duplicate_label SO:0000767 rdfs:label clone_insert_start ERROR duplicate_label SO:0000437 rdfs:label assortment_derived_duplication ERROR duplicate_label SO:0000800 rdfs:label assortment_derived_duplication ERROR duplicate_label SO:0000554 rdfs:label assortment_derived_deficiency_plus_duplication ERROR duplicate_label SO:0000801 rdfs:label assortment_derived_deficiency_plus_duplication ERROR duplicate_label SO:0000052 rdfs:label assortment_derived_deficiency ERROR duplicate_label SO:0000802 rdfs:label assortment_derived_deficiency ERROR duplicate_label SO:0000058 rdfs:label assortment_derived_aneuploid ERROR duplicate_label SO:0000803 rdfs:label assortment_derived_aneuploid ERROR missing_ontology_description http://purl.obolibrary.org/obo/so.owl dc:description ERROR missing_ontology_license http://purl.obolibrary.org/obo/so.owl dc:license ERROR missing_ontology_title http://purl.obolibrary.org/obo/so.owl dc:title WARN annotation_whitespace SO:0000621 IAO:0000115 This type of promoter recruits RNA pol III to transcribe predominantly noncoding RNAs. This promoter contains a proximal sequence element (PSE) and a TATA box upstream of the gene that it regulates. Transcription can also be activated by a distal sequence element (DSE), which is located further upstream. WARN annotation_whitespace SO:0001228 oboInOwl:hasExactSynonym D WARN annotation_whitespace SO:0001229 oboInOwl:hasExactSynonym Y WARN annotation_whitespace SO:0001317 oboInOwl:hasExactSynonym Q WARN annotation_whitespace SO:0001401 oboInOwl:hasExactSynonym modified L-leucine WARN annotation_whitespace SO:0001404 oboInOwl:hasExactSynonym modified L-proline WARN annotation_whitespace SO:0001448 IAO:0000115 A polar, hydorophilic amino acid encoded by the codons CAA and CAG. WARN annotation_whitespace SO:0001473 oboInOwl:hasExactSynonym miRNA antiguide WARN annotation_whitespace SO:0001888 oboInOwl:hasExactSynonym TFBS fusion WARN annotation_whitespace SO:0001892 oboInOwl:hasExactSynonym TFBS amplification WARN annotation_whitespace SO:0001913 oboInOwl:hasExactSynonym bacterial RNApol promoter sigma ecf WARN annotation_whitespace SO:0001947 oboInOwl:hasExactSynonym H3R2me1 WARN annotation_whitespace SO:0001950 oboInOwl:hasExactSynonym H4K4me3 WARN annotation_whitespace SO:0001996 oboInOwl:hasExactSynonym extended intronic splice region WARN annotation_whitespace SO:0002044 oboInOwl:hasExactSynonym TEA Consensus Sequence WARN annotation_whitespace SO:0002254 IAO:0000115 The loop portion of a stem loop, which is not folded back upon itself. WARN annotation_whitespace SO:0002255 IAO:0000115 The portion of a stem loop where the RNA is folded back upon itself. WARN annotation_whitespace SO:0002296 IAO:0000115 The possible discontinuous stretch of DNA that is the combination of one or several TFRSs whose bound TFs work jointly in the regulation of a promoter. WARN duplicate_exact_synonym SO:0002302 oboInOwl:hasExactSynonym simple regulon WARN duplicate_exact_synonym SO:0002303 oboInOwl:hasExactSynonym simple regulon WARN duplicate_exact_synonym SO:0001297 oboInOwl:hasExactSynonym m6A WARN duplicate_exact_synonym SO:0001920 oboInOwl:hasExactSynonym m6a WARN duplicate_exact_synonym SO:0001282 oboInOwl:hasExactSynonym m5C WARN duplicate_exact_synonym SO:0001918 oboInOwl:hasExactSynonym m5c WARN duplicate_exact_synonym SO:0001290 oboInOwl:hasExactSynonym m4C WARN duplicate_exact_synonym SO:0001919 oboInOwl:hasExactSynonym m4c WARN duplicate_exact_synonym SO:0001760 oboInOwl:hasExactSynonym INSDC_qualifier:unprocessed WARN duplicate_exact_synonym SO:0002194 oboInOwl:hasExactSynonym INSDC_qualifier:unprocessed WARN duplicate_exact_synonym SO:0002198 oboInOwl:hasExactSynonym INSDC_qualifier:unprocessed WARN duplicate_exact_synonym SO:0001759 oboInOwl:hasExactSynonym INSDC_qualifier:unitary WARN duplicate_exact_synonym SO:0002195 oboInOwl:hasExactSynonym INSDC_qualifier:unitary WARN duplicate_exact_synonym SO:0002199 oboInOwl:hasExactSynonym INSDC_qualifier:unitary WARN duplicate_exact_synonym SO:0000336 oboInOwl:hasExactSynonym INSDC_qualifier:pseudo WARN duplicate_exact_synonym SO:0000516 oboInOwl:hasExactSynonym INSDC_qualifier:pseudo WARN duplicate_exact_synonym SO:0000777 oboInOwl:hasExactSynonym INSDC_qualifier:pseudo WARN duplicate_exact_synonym SO:0000778 oboInOwl:hasExactSynonym INSDC_qualifier:pseudo WARN duplicate_exact_synonym SO:0002087 oboInOwl:hasExactSynonym INSDC_qualifier:pseudo WARN duplicate_exact_synonym SO:0000043 oboInOwl:hasExactSynonym INSDC_qualifier:processed WARN duplicate_exact_synonym SO:0002193 oboInOwl:hasExactSynonym INSDC_qualifier:processed WARN duplicate_exact_synonym SO:0002197 oboInOwl:hasExactSynonym INSDC_qualifier:processed WARN duplicate_exact_synonym SO:0000298 oboInOwl:hasExactSynonym INSDC_qualifier:other WARN duplicate_exact_synonym SO:0000657 oboInOwl:hasExactSynonym INSDC_qualifier:other WARN duplicate_exact_synonym SO:0005836 oboInOwl:hasExactSynonym INSDC_qualifier:other WARN duplicate_exact_synonym SO:0002189 oboInOwl:hasExactSynonym INSDC_qualifier:allelic WARN duplicate_exact_synonym SO:0002196 oboInOwl:hasExactSynonym INSDC_qualifier:allelic WARN duplicate_exact_synonym SO:0002200 oboInOwl:hasExactSynonym INSDC_qualifier:allelic WARN duplicate_exact_synonym SO:0000253 oboInOwl:hasExactSynonym INSDC_feature:tRNA WARN duplicate_exact_synonym SO:0002200 oboInOwl:hasExactSynonym INSDC_feature:tRNA WARN duplicate_exact_synonym SO:0000725 oboInOwl:hasExactSynonym INSDC_feature:transit_peptide WARN duplicate_exact_synonym SO:0002252 oboInOwl:hasExactSynonym INSDC_feature:transit_peptide WARN duplicate_exact_synonym SO:0000418 oboInOwl:hasExactSynonym INSDC_feature:sig_peptide WARN duplicate_exact_synonym SO:0002251 oboInOwl:hasExactSynonym INSDC_feature:sig_peptide WARN duplicate_exact_synonym SO:0001062 oboInOwl:hasExactSynonym INSDC_feature:propeptide WARN duplicate_exact_synonym SO:0002250 oboInOwl:hasExactSynonym INSDC_feature:propeptide WARN duplicate_exact_synonym SO:0000419 oboInOwl:hasExactSynonym INSDC_feature:mat_peptide WARN duplicate_exact_synonym SO:0002249 oboInOwl:hasExactSynonym INSDC_feature:mat_peptide WARN duplicate_exact_synonym SO:0000382 oboInOwl:hasExactSynonym group IIB intron WARN duplicate_exact_synonym SO:0002226 oboInOwl:hasExactSynonym group IIB intron WARN duplicate_exact_synonym SO:0001533 oboInOwl:hasExactSynonym cryptic splice site WARN duplicate_exact_synonym SO:0001569 oboInOwl:hasExactSynonym cryptic splice site WARN duplicate_exact_synonym SO:0002185 oboInOwl:hasExactSynonym bidirectional promoter lncRNA WARN duplicate_exact_synonym SO:0002381 oboInOwl:hasExactSynonym bidirectional promoter lncRNA WARN duplicate_label_synonym SO:0000667 oboInOwl:hasExactSynonym insertion WARN duplicate_label_synonym SO:0001744 oboInOwl:hasExactSynonym UPD WARN duplicate_label_synonym SO:0001792 oboInOwl:hasExactSynonym non_coding_transcript_exon_variant WARN duplicate_label_synonym SO:0002114 oboInOwl:hasExactSynonym NMD_transcript WARN duplicate_label_synonym SO:0002131 oboInOwl:hasExactSynonym sense_intronic_lncRNA WARN duplicate_label_synonym SO:0002132 oboInOwl:hasExactSynonym sense_overlap_lncRNA WARN duplicate_label_synonym SO:0002183 oboInOwl:hasExactSynonym sense_overlap_lncRNA_gene WARN duplicate_label_synonym SO:0002184 oboInOwl:hasExactSynonym sense_intronic_lncRNA_gene WARN duplicate_label_synonym SO:0002185 oboInOwl:hasExactSynonym bidirectional_promoter_lncRNA_gene WARN duplicate_label_synonym SO:0002220 oboInOwl:hasExactSynonym function_uncertain_variant WARN duplicate_label_synonym SO:1000036 oboInOwl:hasExactSynonym inversion WARN missing_definition SO:0000026 IAO:0000115 WARN missing_definition SO:0000027 IAO:0000115 WARN missing_definition SO:0000067 IAO:0000115 WARN missing_definition SO:0000081 IAO:0000115 WARN missing_definition SO:0000977 IAO:0000115 WARN missing_definition obo:so#AAMOD IAO:0000115 WARN missing_definition obo:so#AGR IAO:0000115 WARN missing_definition obo:so#BS IAO:0000115 WARN missing_definition obo:so#RNAMOD IAO:0000115 WARN missing_definition obo:so#VAR IAO:0000115 WARN missing_definition obo:so#aa1 IAO:0000115 WARN missing_definition obo:so#aa3 IAO:0000115 WARN missing_definition obo:so#associated_with IAO:0000115 WARN missing_definition obo:so#dbsnp IAO:0000115 WARN missing_definition obo:so#dbvar IAO:0000115 WARN missing_definition obo:so#derives_from IAO:0000115 WARN missing_definition obo:so#ebi_variants IAO:0000115 WARN missing_definition obo:so#edited_from IAO:0000115 WARN missing_definition obo:so#edited_to IAO:0000115 WARN missing_definition obo:so#genome_of IAO:0000115 WARN missing_definition obo:so#guided_by IAO:0000115 WARN missing_definition obo:so#guides IAO:0000115 WARN missing_definition obo:so#has_origin IAO:0000115 WARN missing_definition obo:so#has_quality IAO:0000115 WARN missing_definition obo:so#homologous_to IAO:0000115 WARN missing_definition obo:so#member_of IAO:0000115 WARN missing_definition obo:so#orthologous_to IAO:0000115 WARN missing_definition obo:so#paralogous_to IAO:0000115 WARN missing_definition obo:so#position_of IAO:0000115 WARN missing_definition obo:so#recombined_from IAO:0000115 WARN missing_definition obo:so#recombined_to IAO:0000115 WARN missing_definition obo:so#sequence_of IAO:0000115 WARN missing_definition obo:so#similar_to IAO:0000115 WARN missing_definition obo:so#trans_spliced_from IAO:0000115 WARN missing_definition obo:so#trans_spliced_to IAO:0000115 WARN missing_obsolete_label SO:0000000 rdfs:label Sequence_Ontology WARN missing_obsolete_label SO:0000008 rdfs:label gene_sensu_your_favorite_organism WARN missing_obsolete_label SO:0000009 rdfs:label gene_class WARN missing_obsolete_label SO:0000038 rdfs:label match_set WARN missing_obsolete_label SO:0000041 rdfs:label sequence_operation WARN missing_obsolete_label SO:0000042 rdfs:label pseudogene_attribute WARN missing_obsolete_label SO:0000045 rdfs:label delete WARN missing_obsolete_label SO:0000046 rdfs:label insert WARN missing_obsolete_label SO:0000047 rdfs:label invert WARN missing_obsolete_label SO:0000048 rdfs:label substitute WARN missing_obsolete_label SO:0000049 rdfs:label translocate WARN missing_obsolete_label SO:0000050 rdfs:label gene_part WARN missing_obsolete_label SO:0000052 rdfs:label assortment_derived_deficiency WARN missing_obsolete_label SO:0000053 rdfs:label sequence_variant_affecting_regulatory_region WARN missing_obsolete_label SO:0000058 rdfs:label assortment_derived_aneuploid WARN missing_obsolete_label SO:0000064 rdfs:label gene_by_transcript_attribute WARN missing_obsolete_label SO:0000066 rdfs:label gene_by_polyadenylation_attribute WARN missing_obsolete_label SO:0000072 rdfs:label end_overlapping_gene WARN missing_obsolete_label SO:0000082 rdfs:label processed_transcript_attribute WARN missing_obsolete_label SO:0000085 rdfs:label gene_by_genome_location WARN missing_obsolete_label SO:0000086 rdfs:label gene_by_organelle_of_genome