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The-Sequence-Ontology / SO-Ontologies

Collect of SO Ontologies
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terms with a single subtype [sf#79] #79

Open srynobio opened 9 years ago

srynobio commented 9 years ago

Reported by cmungall on 2008-01-29 00:45 UTC in general a class should have zero, two or more subtypes.

eg

single_is_a_child SO:0000872-trans_spliced_mRNA SO:0000479-trans_spliced_transcript

is really begging for a trans-spliced-ncRNA

srynobio commented 9 years ago

Commented by cmungall on 2008-01-29 00:45 UTC

Attached file so-single_is_a_child.txt:

single_is_a_child   SO:0000027-RNA_hook_turn    SO:0000026-RNA_junction_loop
single_is_a_child   SO:0000036-matrix_attachment_site   SO:0000626-chromosomal_regulatory_element
single_is_a_child   SO:0000054-aneuploid    SO:1000182-chromosome_number_variation
single_is_a_child   SO:0000061-restriction_enzyme_binding_site  SO:0000059-nuclease_binding_site
single_is_a_child   SO:0000068-overlapping  SO:0000067-gene_to_gene_feature
single_is_a_child   SO:0000089-kinetoplast_gene SO:0000088-mt_gene
single_is_a_child   SO:0000100-endogenous_retroviral_gene   SO:0000099-proviral_gene
single_is_a_child   SO:0000128-gene_silenced_by_DNA_modification    SO:0000127-silenced_gene
single_is_a_child   SO:0000129-gene_silenced_by_DNA_methylation SO:0000128-gene_silenced_by_DNA_modification
single_is_a_child   SO:0000161-methylated_A SO:0000250-modified_RNA_base_feature
single_is_a_child   SO:0000193-RFLP_fragment    SO:0000412-restriction_fragment
single_is_a_child   SO:0000207-simple_sequence_length_variation SO:0000248-sequence_length_variation
single_is_a_child   SO:0000281-engineered_foreign_gene  SO:0000285-foreign_gene
single_is_a_child   SO:0000283-engineered_foreign_transposable_element_gene SO:0000111-transposable_element_gene
single_is_a_child   SO:0000283-engineered_foreign_transposable_element_gene SO:0000281-engineered_foreign_gene
single_is_a_child   SO:0000288-engineered_fusion_gene   SO:0000287-fusion_gene
single_is_a_child   SO:0000301-vertebrate_immune_system_gene_recombination_feature  SO:0000300-recombination_feature_of_rearranged_gene
single_is_a_child   SO:0000306-methylated_base_feature  SO:0000305-modified_base_site
single_is_a_child   SO:0000312-experimentally_determined    SO:0000789-validated
single_is_a_child   SO:0000313-stem_loop    SO:0000122-RNA_sequence_secondary_structure
single_is_a_child   SO:0000328-microarray_oligo SO:0000051-probe
single_is_a_child   SO:0000344-splice_enhancer  SO:0001056-splicing_regulatory_region
single_is_a_child   SO:0000350-FRT_site SO:0000948-inversion_site
single_is_a_child   SO:0000363-floxed_gene  SO:0000902-transgene
single_is_a_child   SO:0000364-transposable_element_flanking_region SO:0000239-flanking_region
single_is_a_child   SO:0000368-transposable_element_insertion_site  SO:0000366-insertion_site
single_is_a_child   SO:0000374-ribozyme SO:0000372-enzymatic_RNA
single_is_a_child   SO:0000379-GcvB_RNA SO:0000378-DsrA_RNA
single_is_a_child   SO:0000383-MicF_RNA SO:0000644-antisense_RNA
single_is_a_child   SO:0000427-R_five_prime_LTR_region  SO:0000423-R_LTR_region
single_is_a_child   SO:0000428-U5_five_prime_LTR_region SO:0000422-U5_LTR_region
single_is_a_child   SO:0000429-U3_five_prime_LTR_region SO:0000424-U3_LTR_region
single_is_a_child   SO:0000434-target_site_duplication  SO:0000314-direct_repeat
single_is_a_child   SO:0000435-RR_tract SO:0000186-LTR_retrotransposon
single_is_a_child   SO:0000450-interband    SO:0000341-chromosome_band
single_is_a_child   SO:0000475-positively_autoregulated SO:0000125-transcriptionally_induced
single_is_a_child   SO:0000476-contig_read  SO:0000150-read
single_is_a_child   SO:0000480-tiling_path_clone    SO:0000474-tiling_path_fragment
single_is_a_child   SO:0000481-terminal_inverted_repeat SO:0000294-inverted_repeat
single_is_a_child   SO:0000615-terminator_of_type_2_RNApol_III_promoter SO:0000951-eukaryotic_terminator
single_is_a_child   SO:0000622-C_box    SO:0000845-RNApol_III_promoter_type_1_region
single_is_a_child   SO:0000638-transcribed_spacer_region    SO:0000838-rRNA_primary_transcript_region
single_is_a_child   SO:0000648-stRNA_primary_transcript SO:0000647-miRNA_primary_transcript
single_is_a_child   SO:0000680-non_canonical_start_codon    SO:0000318-start_codon
single_is_a_child   SO:0000685-DNAaseI_hypersensitive_site  SO:0000322-nuclease_hypersensitive_site
single_is_a_child   SO:0000692-gene_with_dicistronic_transcript SO:0000690-gene_with_polycistronic_transcript
single_is_a_child   SO:0000716-dicistronic_mRNA SO:0000634-polycistronic_mRNA
single_is_a_child   SO:0000779-engineered_episome   SO:0000637-engineered_plasmid
single_is_a_child   SO:0000779-engineered_episome   SO:0000768-episome
single_is_a_child   SO:0000795-rescue_mini_gene SO:0000815-mini_gene
single_is_a_child   SO:0000799-engineered_foreign_transposable_element  SO:0000720-foreign_transposable_element
single_is_a_child   SO:0000799-engineered_foreign_transposable_element  SO:0000798-engineered_transposable_element
single_is_a_child   SO:0000818-wild_type_rescue_gene    SO:0000816-rescue_gene
single_is_a_child   SO:0000826-kinetoplast_chromosome   SO:0000819-mitochondrial_chromosome
single_is_a_child   SO:0000872-trans_spliced_mRNA   SO:0000479-trans_spliced_transcript
single_is_a_child   SO:0000874-edited_transcript_by A_to_I_substitution SO:0000929-edited_mRNA
single_is_a_child   SO:0000879-dicistronic  SO:0000880-polycistronic
single_is_a_child   SO:0000883-stop_codon_read_through  SO:0000882-codon_redefined
single_is_a_child   SO:0000894-silenced_by_DNA_modification SO:0000893-silenced
single_is_a_child   SO:0000895-silenced_by_DNA_methylation  SO:0000894-silenced_by_DNA_modification
single_is_a_child   SO:0000903-endogenous_retroviral_sequence   SO:0000751-proviral_location
single_is_a_child   SO:0000929-edited_mRNA  SO:0000873-edited_transcript
single_is_a_child   SO:0000932-pre_edited_mRNA  SO:0000120-protein_coding_primary_transcript
single_is_a_child   SO:0000951-eukaryotic_terminator    SO:0000141-terminator
single_is_a_child   SO:0000976-cryptic  SO:0000116-edited
single_is_a_child   SO:0000992-BAC_cloned_genomic_insert    SO:0000914-cloned_genomic_insert
single_is_a_child   SO:0000995-consensus_mRNA   SO:0000994-consensus_region
single_is_a_child   SO:0001006-prophage SO:0000113-proviral_region
single_is_a_child   SO:0001008-tetraloop    SO:0000313-stem_loop
single_is_a_child   SO:0001009-DNA_constraint_sequence  SO:0000442-ds_oligo
single_is_a_child   SO:0001010-i_motif  SO:0000142-DNA_sequence_secondary_structure
single_is_a_child   SO:0001013-MNP  SO:1000005-complex_substitution
single_is_a_child   SO:0001016-internal_guide_sequence  SO:0001014-intron_domain
single_is_a_child   SO:0001022-inversion_breakpoint SO:0001021-chromosome_breakpoint
single_is_a_child   SO:0001028-diplotype    SO:0001027-genotype
single_is_a_child   SO:0001033-chloroplast_DNA  SO:0000745-chloroplast_sequence
single_is_a_child   SO:0001034-mitron   SO:0000276-miRNA
single_is_a_child   SO:0001064-active_peptide   SO:0000419-mature_protein_region
single_is_a_child   SO:0001186-ribozymic    SO:0001185-enzymatic
single_is_a_child   SO:0001187-pseudouridylation_guide_snoRNA   SO:0000594-H_ACA_box_snoRNA
single_is_a_child   SO:0005847-cassette_array_member    SO:0005848-gene_cassette_member
single_is_a_child   SO:1000004-partially_characterised_change_in_DNA_sequence   SO:1000007-uncharacterised_change_in_nucleotide_sequence
single_is_a_child   SO:1000012-C_to_T_transition_at_pCpG_site   SO:1000011-C_to_T_transition
single_is_a_child   SO:1000035-nucleotide_duplication   SO:1000034-nucleotide_insertion
single_is_a_child   SO:1000059-mutation_causing_missense_codon_change_in_transcript SO:1000058-mutation_causing_non_synonymous_codon_change_in_transcript
single_is_a_child   SO:1000065-frameshift_mutation  SO:1000064-mutation_affecting_reading_frame
single_is_a_child   SO:1000075-mutation_affecting_editing   SO:1000070-mutation_affecting_transcript_processing
single_is_a_child   SO:1000081-mutation_affecting_rate_of_transcription SO:1000076-mutation_affecting_transcription
single_is_a_child   SO:1000091-mutation_causing_partially_characterised_change_of_translational_product SO:1000090-mutation_causing_uncharacterised_change_of_translational_product
single_is_a_child   SO:1000114-mutation_causing_partially_characterised_3D_structural_change    SO:1000113-mutation_causing_uncharacterised_3D_structural_change
single_is_a_child   SO:1000120-mutation_causing_inactive_catalytic_site SO:1000119-mutation_causing_inactive_ligand_binding_site
single_is_a_child   SO:1000127-mutation_causing_compensatory_transcript_secondary_structure_mutation    SO:1000126-mutation_affecting_transcript_secondary_structure
single_is_a_child   SO:1000145-free_ring_duplication    SO:1000144-free_duplication
single_is_a_child   SO:1000175-partially_characterised_chromosomal_mutation SO:1000170-uncharacterised_chromosomal_mutation
single_is_a_child   SO:1000179-mutation_causing_partially_characterised_change_in_transcript    SO:1000177-mutation_causing_uncharacterised_change_in_transcript
single_is_a_child   SO:1000181-mutation_causing_gene_fusion SO:1000180-mutation_affecting_gene_structure
single_is_a_child   SO:1001196-cryptogene   SO:0000654-maxicircle_gene
single_is_a_child   SO:1001197-dicistronic_primary_transcript   SO:0000631-polycistronic_primary_transcript
single_is_a_child   SO:1001260-internal_Shine_Dalgarno_sequence SO:0000243-internal_ribosome_entry_site
srynobio commented 9 years ago

Commented by eilbeck on 2008-01-30 21:15 UTC Logged In: YES user_id=742851 Originator: NO

Are there any examples of trans spliced ncRNA? I was under the impression that the spliced leader is nc and it attaches to a coding transcript.

I agree with the first statement as far as logical ontology design goes. But what to do? Do we add a term that may or may not happen in real life or do we remove the parent?

--K

srynobio commented 9 years ago

Commented by cmungall on 2008-01-30 21:27 UTC Logged In: YES user_id=254723 Originator: YES

obsoleting the parent would seem wrong. And creating hypothetical terms doesnt seem great

I say for this example the most you should do is add something to the comment field of the parent.

See if there's anything of use in the rest of the report.. it may be that there are just too many unknowns in genomics and this sort of ontology structure is unavoidable.

srynobio commented 9 years ago

Updated by cmungall on 2008-01-30 21:27 UTC