diff --git a/src/pyobo/resources/so.py b/src/pyobo/resources/so.py new file mode 100644 index 00000000..2fb63d12 --- /dev/null +++ b/src/pyobo/resources/so.py @@ -0,0 +1,59 @@ +"""Loading of the relations ontology names.""" + +from __future__ import annotations + +import csv +import os +from collections.abc import Mapping +from functools import lru_cache + +import requests + +__all__ = [ + "get_so_name", + "load_so", +] + +HERE = os.path.abspath(os.path.dirname(__file__)) +SO_PATH = os.path.join(HERE, "so.tsv") +SO_JSON_URL = "https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/refs/heads/master/Ontology_Files/so-simple.json" +SO_URI_PREFIX = "http://purl.obolibrary.org/obo/SO_" + + +def get_so_name(so_id: str) -> str | None: + """Get the name from the identifier.""" + return load_so().get(so_id) + + +@lru_cache(maxsize=1) +def load_so() -> Mapping[tuple[str, str], str]: + """Load the Sequence Ontology names.""" + if not os.path.exists(SO_PATH): + download_so() + with open(SO_PATH) as file: + return { + (prefix, identifier): name + for prefix, identifier, name in csv.reader(file, delimiter="\t") + } + + +def download_so(): + """Download the latest version of the Relation Ontology.""" + rows = [] + res_json = requests.get(SO_JSON_URL).json() + for node in res_json["graphs"][0]["nodes"]: + uri = node["id"] + if not uri.startswith(SO_URI_PREFIX): + continue + identifier = uri.removeprefix(SO_URI_PREFIX) + name = node.get("lbl") + if name: + rows.append(("so", identifier, name)) + + with open(SO_PATH, "w") as file: + writer = csv.writer(file, delimiter="\t") + writer.writerows(sorted(rows)) + + +if __name__ == "__main__": + download_so() diff --git a/src/pyobo/resources/so.tsv b/src/pyobo/resources/so.tsv new file mode 100644 index 00000000..96964564 --- /dev/null +++ b/src/pyobo/resources/so.tsv @@ -0,0 +1,2604 @@ +so 0000000 Sequence_Ontology +so 00000000002382 5_prime_UTR_uORF_variant +so 0000001 region +so 00000010002382 5_prime_UTR_uORF_stop_codon_variant +so 0000002 sequence_secondary_structure +so 00000020002382 5_prime_UTR_uORF_frameshift_variant +so 0000003 G_quartet +so 00000030002382 5_prime_UTR_uORF_stop_codon_gain_variant +so 0000004 interior_coding_exon +so 00000040002382 5_prime_UTR_uORF_stop_codon_loss_variant +so 0000005 satellite_DNA +so 0000006 PCR_product +so 0000007 read_pair +so 0000008 gene_sensu_your_favorite_organism +so 0000009 gene_class +so 0000010 protein_coding +so 0000011 non_protein_coding +so 0000012 scRNA_primary_transcript +so 0000013 scRNA +so 0000014 INR_motif +so 0000015 DPE_motif +so 0000016 BREu_motif +so 0000017 PSE_motif +so 0000018 linkage_group +so 0000020 RNA_internal_loop +so 0000021 asymmetric_RNA_internal_loop +so 0000022 A_minor_RNA_motif +so 0000023 K_turn_RNA_motif +so 0000024 sarcin_like_RNA_motif +so 0000025 symmetric_RNA_internal_loop +so 0000026 RNA_junction_loop +so 0000027 RNA_hook_turn +so 0000028 base_pair +so 0000029 WC_base_pair +so 0000030 sugar_edge_base_pair +so 0000031 aptamer +so 0000032 DNA_aptamer +so 0000033 RNA_aptamer +so 0000034 morpholino_oligo +so 0000035 riboswitch +so 0000036 matrix_attachment_site +so 0000037 locus_control_region +so 0000038 match_set +so 0000039 match_part +so 0000040 genomic_clone +so 0000041 sequence_operation +so 0000042 pseudogene_attribute +so 0000043 processed_pseudogene +so 0000044 pseudogene_by_unequal_crossing_over +so 0000045 delete +so 0000046 insert +so 0000047 invert +so 0000048 substitute +so 0000049 translocate +so 0000050 gene_part +so 0000051 probe +so 0000052 assortment_derived_deficiency +so 0000053 sequence_variant_affecting_regulatory_region +so 0000054 aneuploid +so 0000055 hyperploid +so 0000056 hypoploid +so 0000057 operator +so 0000058 assortment_derived_aneuploid +so 0000059 nuclease_binding_site +so 0000060 compound_chromosome_arm +so 0000061 restriction_enzyme_binding_site +so 0000062 deficient_intrachromosomal_transposition +so 0000063 deficient_interchromosomal_transposition +so 0000064 gene_by_transcript_attribute +so 0000065 free_chromosome_arm +so 0000066 gene_by_polyadenylation_attribute +so 0000067 gene_to_gene_feature +so 0000068 overlapping +so 0000069 inside_intron +so 0000070 inside_intron_antiparallel +so 0000071 inside_intron_parallel +so 0000072 end_overlapping_gene +so 0000073 five_prime_three_prime_overlap +so 0000074 five_prime_five_prime_overlap +so 0000075 three_prime_three_prime_overlap +so 0000076 three_prime_five_prime_overlap +so 0000077 antisense +so 0000078 polycistronic_transcript +so 0000079 dicistronic_transcript +so 0000080 operon_member +so 0000081 gene_array_member +so 0000082 processed_transcript_attribute +so 0000083 macronuclear_sequence +so 0000084 micronuclear_sequence +so 0000085 gene_by_genome_location +so 0000086 gene_by_organelle_of_genome +so 0000087 nuclear_gene +so 0000088 mt_gene +so 0000089 kinetoplast_gene +so 0000090 plastid_gene +so 0000091 apicoplast_gene +so 0000092 ct_gene +so 0000093 chromoplast_gene +so 0000094 cyanelle_gene +so 0000095 leucoplast_gene +so 0000096 proplastid_gene +so 0000097 nucleomorph_gene +so 0000098 plasmid_gene +so 0000099 proviral_gene +so 0000100 endogenous_retroviral_gene +so 0000101 transposable_element +so 0000102 expressed_sequence_match +so 0000103 clone_insert_end +so 0000104 polypeptide +so 0000105 chromosome_arm +so 0000106 non_capped_primary_transcript +so 0000107 sequencing_primer +so 0000108 mRNA_with_frameshift +so 0000109 sequence_variant_obs +so 0000110 sequence_feature +so 0000111 transposable_element_gene +so 0000112 primer +so 0000113 proviral_region +so 0000114 methylated_cytosine +so 0000115 transcript_feature +so 0000116 edited +so 0000117 transcript_with_readthrough_stop_codon +so 0000118 transcript_with_translational_frameshift +so 0000119 regulated +so 0000120 protein_coding_primary_transcript +so 0000121 forward_primer +so 0000122 RNA_sequence_secondary_structure +so 0000123 transcriptionally_regulated +so 0000124 transcriptionally_constitutive +so 0000125 transcriptionally_induced +so 0000126 transcriptionally_repressed +so 0000127 silenced_gene +so 0000128 gene_silenced_by_DNA_modification +so 0000129 gene_silenced_by_DNA_methylation +so 0000130 post_translationally_regulated +so 0000131 translationally_regulated +so 0000132 reverse_primer +so 0000133 epigenetically_modified +so 0000134 genomically_imprinted +so 0000135 maternally_imprinted +so 0000136 paternally_imprinted +so 0000137 allelically_excluded +so 0000138 gene_rearranged_at_DNA_level +so 0000139 ribosome_entry_site +so 0000140 attenuator +so 0000141 terminator +so 0000142 DNA_sequence_secondary_structure +so 0000143 assembly_component +so 0000144 primary_transcript_attribute +so 0000145 recoded_codon +so 0000146 capped +so 0000147 exon +so 0000148 supercontig +so 0000149 contig +so 0000150 read +so 0000151 clone +so 0000152 YAC +so 0000153 BAC +so 0000154 PAC +so 0000155 plasmid +so 0000156 cosmid +so 0000157 phagemid +so 0000158 fosmid +so 0000159 deletion +so 0000160 lambda_clone +so 0000161 methylated_adenine +so 0000162 splice_site +so 0000163 five_prime_cis_splice_site +so 0000164 three_prime_cis_splice_site +so 0000165 enhancer +so 0000166 enhancer_bound_by_factor +so 0000167 promoter +so 0000168 restriction_enzyme_cut_site +so 0000169 RNApol_I_promoter +so 0000170 RNApol_II_promoter +so 0000171 RNApol_III_promoter +so 0000172 CAAT_signal +so 0000173 GC_rich_promoter_region +so 0000174 TATA_box +so 0000175 minus_10_signal +so 0000176 minus_35_signal +so 0000177 cross_genome_match +so 0000178 operon +so 0000179 clone_insert_start +so 0000180 retrotransposon +so 0000181 translated_nucleotide_match +so 0000182 DNA_transposon +so 0000183 non_transcribed_region +so 0000184 U2_intron +so 0000185 primary_transcript +so 0000186 LTR_retrotransposon +so 0000187 repeat_family +so 0000188 intron +so 0000189 non_LTR_retrotransposon +so 0000190 five_prime_intron +so 0000191 interior_intron +so 0000192 three_prime_intron +so 0000193 RFLP_fragment +so 0000194 LINE_element +so 0000195 coding_exon +so 0000196 five_prime_coding_exon_coding_region +so 0000197 three_prime_coding_exon_coding_region +so 0000198 noncoding_exon +so 0000199 translocation +so 0000200 five_prime_coding_exon +so 0000201 interior_exon +so 0000202 three_prime_coding_exon +so 0000203 UTR +so 0000204 five_prime_UTR +so 0000205 three_prime_UTR +so 0000206 SINE_element +so 0000207 simple_sequence_length_variation +so 0000208 terminal_inverted_repeat_element +so 0000209 rRNA_primary_transcript +so 0000210 tRNA_primary_transcript +so 0000211 alanine_tRNA_primary_transcript +so 0000212 arginine_tRNA_primary_transcript +so 0000213 asparagine_tRNA_primary_transcript +so 0000214 aspartic_acid_tRNA_primary_transcript +so 0000215 cysteine_tRNA_primary_transcript +so 0000216 glutamic_acid_tRNA_primary_transcript +so 0000217 glutamine_tRNA_primary_transcript +so 0000218 glycine_tRNA_primary_transcript +so 0000219 histidine_tRNA_primary_transcript +so 0000220 isoleucine_tRNA_primary_transcript +so 0000221 leucine_tRNA_primary_transcript +so 0000222 lysine_tRNA_primary_transcript +so 0000223 methionine_tRNA_primary_transcript +so 0000224 phenylalanine_tRNA_primary_transcript +so 0000225 proline_tRNA_primary_transcript +so 0000226 serine_tRNA_primary_transcript +so 0000227 threonine_tRNA_primary_transcript +so 0000228 tryptophan_tRNA_primary_transcript +so 0000229 tyrosine_tRNA_primary_transcript +so 0000230 valine_tRNA_primary_transcript +so 0000231 snRNA_primary_transcript +so 0000232 snoRNA_primary_transcript +so 0000233 mature_transcript +so 0000234 mRNA +so 0000235 TF_binding_site +so 0000236 ORF +so 0000237 transcript_attribute +so 0000238 foldback_element +so 0000239 flanking_region +so 0000240 chromosome_variation +so 0000241 internal_UTR +so 0000242 untranslated_region_polycistronic_mRNA +so 0000243 internal_ribosome_entry_site +so 0000244 four_cutter_restriction_site +so 0000245 mRNA_by_polyadenylation_status +so 0000246 polyadenylated +so 0000247 mRNA_not_polyadenylated +so 0000248 sequence_length_alteration +so 0000249 six_cutter_restriction_site +so 0000250 modified_RNA_base_feature +so 0000251 eight_cutter_restriction_site +so 0000252 rRNA +so 0000253 tRNA +so 0000254 alanyl_tRNA +so 0000255 rRNA_small_subunit_primary_transcript +so 0000256 asparaginyl_tRNA +so 0000257 aspartyl_tRNA +so 0000258 cysteinyl_tRNA +so 0000259 glutaminyl_tRNA +so 0000260 glutamyl_tRNA +so 0000261 glycyl_tRNA +so 0000262 histidyl_tRNA +so 0000263 isoleucyl_tRNA +so 0000264 leucyl_tRNA +so 0000265 lysyl_tRNA +so 0000266 methionyl_tRNA +so 0000267 phenylalanyl_tRNA +so 0000268 prolyl_tRNA +so 0000269 seryl_tRNA +so 0000270 threonyl_tRNA +so 0000271 tryptophanyl_tRNA +so 0000272 tyrosyl_tRNA +so 0000273 valyl_tRNA +so 0000274 snRNA +so 0000275 snoRNA +so 0000276 miRNA +so 0000277 bound_by_factor +so 0000278 transcript_bound_by_nucleic_acid +so 0000279 transcript_bound_by_protein +so 0000280 engineered_gene +so 0000281 engineered_foreign_gene +so 0000282 mRNA_with_minus_1_frameshift +so 0000283 engineered_foreign_transposable_element_gene +so 0000284 type_I_enzyme_restriction_site +so 0000285 foreign_gene +so 0000286 long_terminal_repeat +so 0000287 fusion_gene +so 0000288 engineered_fusion_gene +so 0000289 microsatellite +so 0000290 dinucleotide_repeat_microsatellite_feature +so 0000291 trinucleotide_repeat_microsatellite_feature +so 0000292 repetitive_element +so 0000293 engineered_foreign_repetitive_element +so 0000294 inverted_repeat +so 0000295 U12_intron +so 0000296 origin_of_replication +so 0000297 D_loop +so 0000298 recombination_feature +so 0000299 specific_recombination_site +so 0000300 recombination_feature_of_rearranged_gene +so 0000301 vertebrate_immune_system_gene_recombination_feature +so 0000302 J_gene_recombination_feature +so 0000303 clip +so 0000304 type_II_enzyme_restriction_site +so 0000305 modified_DNA_base +so 0000306 methylated_DNA_base_feature +so 0000307 CpG_island +so 0000308 sequence_feature_locating_method +so 0000309 computed_feature +so 0000310 predicted_ab_initio_computation +so 0000311 computed_feature_by_similarity +so 0000312 experimentally_determined +so 0000313 stem_loop +so 0000314 direct_repeat +so 0000315 TSS +so 0000316 CDS +so 0000317 cDNA_clone +so 0000318 start_codon +so 0000319 stop_codon +so 0000320 intronic_splice_enhancer +so 0000321 mRNA_with_plus_1_frameshift +so 0000322 nuclease_hypersensitive_site +so 0000323 coding_start +so 0000324 tag +so 0000325 rRNA_large_subunit_primary_transcript +so 0000326 SAGE_tag +so 0000327 coding_end +so 0000328 microarray_oligo +so 0000329 mRNA_with_plus_2_frameshift +so 0000330 conserved_region +so 0000331 STS +so 0000332 coding_conserved_region +so 0000333 exon_junction +so 0000334 nc_conserved_region +so 0000335 mRNA_with_minus_2_frameshift +so 0000336 pseudogene +so 0000337 RNAi_reagent +so 0000338 MITE +so 0000339 recombination_hotspot +so 0000340 chromosome +so 0000341 chromosome_band +so 0000342 site_specific_recombination_target_region +so 0000343 match +so 0000344 splice_enhancer +so 0000345 EST +so 0000346 loxP_site +so 0000347 nucleotide_match +so 0000348 nucleic_acid +so 0000349 protein_match +so 0000350 FRT_site +so 0000351 synthetic_sequence +so 0000352 DNA +so 0000353 sequence_assembly +so 0000354 group_1_intron_homing_endonuclease_target_region +so 0000355 haplotype_block +so 0000356 RNA +so 0000357 flanked +so 0000359 floxed +so 0000360 codon +so 0000361 FRT_flanked +so 0000362 invalidated_by_chimeric_cDNA +so 0000363 floxed_gene +so 0000364 transposable_element_flanking_region +so 0000365 integron +so 0000366 insertion_site +so 0000367 attI_site +so 0000368 transposable_element_insertion_site +so 0000369 integrase_coding_region +so 0000370 small_regulatory_ncRNA +so 0000371 conjugative_transposon +so 0000372 enzymatic_RNA +so 0000373 recombinationally_inverted_gene +so 0000374 ribozyme +so 0000375 cytosolic_5_8S_rRNA +so 0000376 RNA_6S +so 0000377 CsrB_RsmB_RNA +so 0000378 DsrA_RNA +so 0000379 GcvB_RNA +so 0000380 hammerhead_ribozyme +so 0000381 group_IIA_intron +so 0000382 group_IIB_intron +so 0000383 MicF_RNA +so 0000384 OxyS_RNA +so 0000385 RNase_MRP_RNA +so 0000386 RNase_P_RNA +so 0000387 RprA_RNA +so 0000388 RRE_RNA +so 0000389 spot_42_RNA +so 0000390 telomerase_RNA +so 0000391 U1_snRNA +so 0000392 U2_snRNA +so 0000393 U4_snRNA +so 0000394 U4atac_snRNA +so 0000395 U5_snRNA +so 0000396 U6_snRNA +so 0000397 U6atac_snRNA +so 0000398 U11_snRNA +so 0000399 U12_snRNA +so 0000400 sequence_attribute +so 0000401 gene_attribute +so 0000402 enhancer_attribute +so 0000403 U14_snoRNA +so 0000404 vault_RNA +so 0000405 Y_RNA +so 0000406 twintron +so 0000407 cytosolic_18S_rRNA +so 0000408 site +so 0000409 binding_site +so 0000410 protein_binding_site +so 0000411 rescue_region +so 0000412 restriction_fragment +so 0000413 sequence_difference +so 0000414 invalidated_by_genomic_contamination +so 0000415 invalidated_by_genomic_polyA_primed_cDNA +so 0000416 invalidated_by_partial_processing +so 0000417 polypeptide_domain +so 0000418 signal_peptide +so 0000419 mature_protein_region +so 0000420 five_prime_terminal_inverted_repeat +so 0000421 three_prime_terminal_inverted_repeat +so 0000422 U5_LTR_region +so 0000423 R_LTR_region +so 0000424 U3_LTR_region +so 0000425 five_prime_LTR +so 0000426 three_prime_LTR +so 0000427 R_five_prime_LTR_region +so 0000428 U5_five_prime_LTR_region +so 0000429 U3_five_prime_LTR_region +so 0000430 R_three_prime_LTR_region +so 0000431 U3_three_prime_LTR_region +so 0000432 U5_three_prime_LTR_region +so 0000433 non_LTR_retrotransposon_polymeric_tract +so 0000434 target_site_duplication +so 0000435 RR_tract +so 0000436 ARS +so 0000437 assortment_derived_duplication +so 0000438 gene_not_polyadenylated +so 0000439 inverted_ring_chromosome +so 0000440 vector_replicon +so 0000441 ss_oligo +so 0000442 ds_oligo +so 0000443 polymer_attribute +so 0000444 three_prime_noncoding_exon +so 0000445 five_prime_noncoding_exon +so 0000446 UTR_intron +so 0000447 five_prime_UTR_intron +so 0000448 three_prime_UTR_intron +so 0000449 random_sequence +so 0000450 interband +so 0000451 gene_with_polyadenylated_mRNA +so 0000452 transgene_attribute +so 0000453 chromosomal_transposition +so 0000454 rasiRNA +so 0000455 gene_with_mRNA_with_frameshift +so 0000456 recombinationally_rearranged_gene +so 0000457 interchromosomal_duplication +so 0000458 D_gene_segment +so 0000459 gene_with_trans_spliced_transcript +so 0000460 vertebrate_immunoglobulin_T_cell_receptor_segment +so 0000461 inversion_derived_bipartite_deficiency +so 0000462 pseudogenic_region +so 0000463 encodes_alternately_spliced_transcripts +so 0000464 decayed_exon +so 0000465 inversion_derived_deficiency_plus_duplication +so 0000466 V_gene_segment +so 0000467 post_translationally_regulated_by_protein_stability +so 0000468 golden_path_fragment +so 0000469 post_translationally_regulated_by_protein_modification +so 0000470 J_gene_segment +so 0000471 autoregulated +so 0000472 tiling_path +so 0000473 negatively_autoregulated +so 0000474 tiling_path_fragment +so 0000475 positively_autoregulated +so 0000476 contig_read +so 0000477 polycistronic_gene +so 0000478 C_gene_segment +so 0000479 trans_spliced_transcript +so 0000480 tiling_path_clone +so 0000481 terminal_inverted_repeat +so 0000482 vertebrate_immunoglobulin_T_cell_receptor_gene_cluster +so 0000483 nc_primary_transcript +so 0000484 three_prime_coding_exon_noncoding_region +so 0000485 DJ_J_cluster +so 0000486 five_prime_coding_exon_noncoding_region +so 0000487 VDJ_J_C_cluster +so 0000488 VDJ_J_cluster +so 0000489 VJ_C_cluster +so 0000490 VJ_J_C_cluster +so 0000491 VJ_J_cluster +so 0000492 D_gene_recombination_feature +so 0000493 three_prime_D_heptamer +so 0000494 three_prime_D_nonamer +so 0000495 three_prime_D_spacer +so 0000496 five_prime_D_heptamer +so 0000497 five_prime_D_nonamer +so 0000498 five_prime_D_spacer +so 0000499 virtual_sequence +so 0000500 Hoogsteen_base_pair +so 0000501 reverse_Hoogsteen_base_pair +so 0000502 transcribed_region +so 0000503 alternately_spliced_gene_encodeing_one_transcript +so 0000504 D_DJ_C_cluster +so 0000505 D_DJ_cluster +so 0000506 D_DJ_J_C_cluster +so 0000507 pseudogenic_exon +so 0000508 D_DJ_J_cluster +so 0000509 D_J_C_cluster +so 0000510 VD_gene_segment +so 0000511 J_C_cluster +so 0000512 inversion_derived_deficiency_plus_aneuploid +so 0000513 J_cluster +so 0000514 J_nonamer +so 0000515 J_heptamer +so 0000516 pseudogenic_transcript +so 0000517 J_spacer +so 0000518 V_DJ_cluster +so 0000519 V_DJ_J_cluster +so 0000520 V_VDJ_C_cluster +so 0000521 V_VDJ_cluster +so 0000522 V_VDJ_J_cluster +so 0000523 V_VJ_C_cluster +so 0000524 V_VJ_cluster +so 0000525 V_VJ_J_cluster +so 0000526 V_cluster +so 0000527 V_D_DJ_C_cluster +so 0000528 V_D_DJ_cluster +so 0000529 V_D_DJ_J_C_cluster +so 0000530 V_D_DJ_J_cluster +so 0000531 V_D_J_C_cluster +so 0000532 V_D_J_cluster +so 0000533 V_heptamer +so 0000534 V_J_cluster +so 0000535 V_J_C_cluster +so 0000536 V_nonamer +so 0000537 V_spacer +so 0000538 V_gene_recombination_feature +so 0000539 DJ_C_cluster +so 0000540 DJ_J_C_cluster +so 0000541 VDJ_C_cluster +so 0000542 V_DJ_C_cluster +so 0000543 alternately_spliced_gene_encoding_greater_than_one_transcript +so 0000544 helitron +so 0000545 recoding_pseudoknot +so 0000546 designed_sequence +so 0000547 inversion_derived_bipartite_duplication +so 0000548 gene_with_edited_transcript +so 0000549 inversion_derived_duplication_plus_aneuploid +so 0000550 aneuploid_chromosome +so 0000551 polyA_signal_sequence +so 0000552 Shine_Dalgarno_sequence +so 0000553 polyA_site +so 0000554 assortment_derived_deficiency_plus_duplication +so 0000555 five_prime_clip +so 0000556 five_prime_D_recombination_signal_sequence +so 0000557 three_prime_clip +so 0000558 C_cluster +so 0000559 D_cluster +so 0000560 D_J_cluster +so 0000561 heptamer_of_recombination_feature_of_vertebrate_immune_system_gene +so 0000562 nonamer_of_recombination_feature_of_vertebrate_immune_system_gene +so 0000563 vertebrate_immune_system_gene_recombination_spacer +so 0000564 V_DJ_J_C_cluster +so 0000565 V_VDJ_J_C_cluster +so 0000566 V_VJ_J_C_cluster +so 0000567 inversion_derived_aneuploid_chromosome +so 0000568 bidirectional_promoter +so 0000569 retrotransposed +so 0000570 three_prime_D_recombination_signal_sequence +so 0000571 miRNA_encoding +so 0000572 DJ_gene_segment +so 0000573 rRNA_encoding +so 0000574 VDJ_gene_segment +so 0000575 scRNA_encoding +so 0000576 VJ_gene_segment +so 0000577 centromere +so 0000578 snoRNA_encoding +so 0000579 edited_transcript_feature +so 0000580 methylation_guide_snoRNA_primary_transcript +so 0000581 cap +so 0000582 rRNA_cleavage_snoRNA_primary_transcript +so 0000583 pre_edited_region +so 0000584 tmRNA +so 0000585 C_D_box_snoRNA_encoding +so 0000586 tmRNA_primary_transcript +so 0000587 group_I_intron +so 0000588 autocatalytically_spliced_intron +so 0000589 SRP_RNA_primary_transcript +so 0000590 SRP_RNA +so 0000591 pseudoknot +so 0000592 H_pseudoknot +so 0000593 C_D_box_snoRNA +so 0000594 H_ACA_box_snoRNA +so 0000595 C_D_box_snoRNA_primary_transcript +so 0000596 H_ACA_box_snoRNA_primary_transcript +so 0000597 transcript_edited_by_U_insertion/deletion +so 0000598 edited_by_C_insertion_and_dinucleotide_insertion +so 0000599 edited_by_C_to_U_substitution +so 0000600 edited_by_A_to_I_substitution +so 0000601 edited_by_G_addition +so 0000602 guide_RNA +so 0000603 group_II_intron +so 0000604 editing_block +so 0000605 intergenic_region +so 0000606 editing_domain +so 0000607 unedited_region +so 0000608 H_ACA_box_snoRNA_encoding +so 0000609 oligo_U_tail +so 0000610 polyA_sequence +so 0000611 branch_site +so 0000612 polypyrimidine_tract +so 0000613 bacterial_RNApol_promoter +so 0000614 bacterial_terminator +so 0000615 terminator_of_type_2_RNApol_III_promoter +so 0000616 transcription_end_site +so 0000617 RNApol_III_promoter_type_1 +so 0000618 RNApol_III_promoter_type_2 +so 0000619 A_box +so 0000620 B_box +so 0000621 RNApol_III_promoter_type_3 +so 0000622 C_box +so 0000623 snRNA_encoding +so 0000624 telomere +so 0000625 silencer +so 0000626 chromosomal_regulatory_element +so 0000627 insulator +so 0000628 chromosomal_structural_element +so 0000629 five_prime_open_reading_frame +so 0000630 upstream_AUG_codon +so 0000631 polycistronic_primary_transcript +so 0000632 monocistronic_primary_transcript +so 0000633 monocistronic_mRNA +so 0000634 polycistronic_mRNA +so 0000635 mini_exon_donor_RNA +so 0000636 spliced_leader_RNA +so 0000637 engineered_plasmid +so 0000638 transcribed_spacer_region +so 0000639 internal_transcribed_spacer_region +so 0000640 external_transcribed_spacer_region +so 0000641 tetranucleotide_repeat_microsatellite_feature +so 0000642 SRP_RNA_encoding +so 0000643 minisatellite +so 0000644 antisense_RNA +so 0000645 antisense_primary_transcript +so 0000646 siRNA +so 0000647 miRNA_primary_transcript +so 0000650 cytosolic_SSU_rRNA +so 0000651 cytosolic_LSU_rRNA +so 0000652 cytosolic_5S_rRNA +so 0000653 cytosolic_28S_rRNA +so 0000654 maxicircle_gene +so 0000655 ncRNA +so 0000656 stRNA_encoding +so 0000657 repeat_region +so 0000658 dispersed_repeat +so 0000659 tmRNA_encoding +so 0000660 DNA_invertase_target_sequence +so 0000661 intron_attribute +so 0000662 spliceosomal_intron +so 0000663 tRNA_encoding +so 0000664 introgressed_chromosome_region +so 0000665 monocistronic_transcript +so 0000666 mobile_intron +so 0000667 insertion +so 0000668 EST_match +so 0000669 sequence_rearrangement_feature +so 0000670 chromosome_breakage_sequence +so 0000671 internal_eliminated_sequence +so 0000672 macronucleus_destined_segment +so 0000673 transcript +so 0000674 non_canonical_splice_site +so 0000675 canonical_splice_site +so 0000676 canonical_three_prime_splice_site +so 0000677 canonical_five_prime_splice_site +so 0000678 non_canonical_three_prime_splice_site +so 0000679 non_canonical_five_prime_splice_site +so 0000680 non_canonical_start_codon +so 0000681 aberrant_processed_transcript +so 0000682 splicing_feature +so 0000683 exonic_splice_enhancer +so 0000684 nuclease_sensitive_site +so 0000685 DNaseI_hypersensitive_site +so 0000686 translocation_element +so 0000687 deletion_junction +so 0000688 golden_path +so 0000689 cDNA_match +so 0000690 gene_with_polycistronic_transcript +so 0000691 cleaved_initiator_methionine +so 0000692 gene_with_dicistronic_transcript +so 0000693 gene_with_recoded_mRNA +so 0000694 SNP +so 0000695 reagent +so 0000696 oligo +so 0000697 gene_with_stop_codon_read_through +so 0000698 gene_with_stop_codon_redefined_as_pyrrolysine +so 0000699 junction +so 0000700 remark +so 0000701 possible_base_call_error +so 0000702 possible_assembly_error +so 0000703 experimental_result_region +so 0000704 gene +so 0000705 tandem_repeat +so 0000706 trans_splice_acceptor_site +so 0000707 trans_splice_donor_site +so 0000708 SL1_acceptor_site +so 0000709 SL2_acceptor_site +so 0000710 gene_with_stop_codon_redefined_as_selenocysteine +so 0000711 gene_with_mRNA_recoded_by_translational_bypass +so 0000712 gene_with_transcript_with_translational_frameshift +so 0000713 DNA_motif +so 0000714 nucleotide_motif +so 0000715 RNA_motif +so 0000716 dicistronic_mRNA +so 0000717 reading_frame +so 0000718 blocked_reading_frame +so 0000719 ultracontig +so 0000720 foreign_transposable_element +so 0000721 gene_with_dicistronic_primary_transcript +so 0000722 gene_with_dicistronic_mRNA +so 0000723 iDNA +so 0000724 oriT +so 0000725 transit_peptide +so 0000726 repeat_unit +so 0000727 cis_regulatory_module +so 0000728 intein +so 0000729 intein_containing +so 0000730 gap +so 0000731 fragmentary +so 0000732 predicted +so 0000733 feature_attribute +so 0000734 exemplar_mRNA +so 0000735 sequence_location +so 0000736 organelle_sequence +so 0000737 mitochondrial_sequence +so 0000738 nuclear_sequence +so 0000739 nucleomorphic_sequence +so 0000740 plastid_sequence +so 0000741 kinetoplast +so 0000742 maxicircle +so 0000743 apicoplast_sequence +so 0000744 chromoplast_sequence +so 0000745 chloroplast_sequence +so 0000746 cyanelle_sequence +so 0000747 leucoplast_sequence +so 0000748 proplastid_sequence +so 0000749 plasmid_location +so 0000750 amplification_origin +so 0000751 proviral_location +so 0000752 gene_group_regulatory_region +so 0000753 clone_insert +so 0000754 lambda_vector +so 0000755 plasmid_vector +so 0000756 cDNA +so 0000757 single_stranded_cDNA +so 0000758 double_stranded_cDNA +so 0000759 plasmid_clone +so 0000760 YAC_clone +so 0000761 phagemid_clone +so 0000762 PAC_clone +so 0000763 fosmid_clone +so 0000764 BAC_clone +so 0000765 cosmid_clone +so 0000766 pyrrolysyl_tRNA +so 0000767 clone_insert_start +so 0000768 episome +so 0000769 tmRNA_coding_piece +so 0000770 tmRNA_acceptor_piece +so 0000771 QTL +so 0000772 genomic_island +so 0000773 pathogenic_island +so 0000774 metabolic_island +so 0000775 adaptive_island +so 0000776 symbiosis_island +so 0000777 pseudogenic_rRNA +so 0000778 pseudogenic_tRNA +so 0000779 engineered_episome +so 0000780 transposable_element_attribute +so 0000781 transgenic +so 0000782 natural +so 0000783 engineered +so 0000784 foreign +so 0000785 cloned_region +so 0000786 reagent_attribute +so 0000787 clone_attribute +so 0000788 cloned +so 0000789 validated +so 0000790 invalidated +so 0000791 cloned_genomic +so 0000792 cloned_cDNA +so 0000793 engineered_DNA +so 0000794 engineered_rescue_region +so 0000795 rescue_mini_gene +so 0000796 transgenic_transposable_element +so 0000797 natural_transposable_element +so 0000798 engineered_transposable_element +so 0000799 engineered_foreign_transposable_element +so 0000800 assortment_derived_duplication +so 0000801 assortment_derived_deficiency_plus_duplication +so 0000802 assortment_derived_deficiency +so 0000803 assortment_derived_aneuploid +so 0000804 engineered_region +so 0000805 engineered_foreign_region +so 0000806 fusion +so 0000807 engineered_tag +so 0000808 validated_cDNA_clone +so 0000809 invalidated_cDNA_clone +so 0000810 chimeric_cDNA_clone +so 0000811 genomically_contaminated_cDNA_clone +so 0000812 polyA_primed_cDNA_clone +so 0000813 partially_processed_cDNA_clone +so 0000814 rescue +so 0000815 mini_gene +so 0000816 rescue_gene +so 0000817 wild_type +so 0000818 wild_type_rescue_gene +so 0000819 mitochondrial_chromosome +so 0000820 chloroplast_chromosome +so 0000821 chromoplast_chromosome +so 0000822 cyanelle_chromosome +so 0000823 leucoplast_chromosome +so 0000824 macronuclear_chromosome +so 0000825 micronuclear_chromosome +so 0000828 nuclear_chromosome +so 0000829 nucleomorphic_chromosome +so 0000830 chromosome_part +so 0000831 gene_member_region +so 0000832 promoter_region +so 0000833 transcript_region +so 0000834 mature_transcript_region +so 0000835 primary_transcript_region +so 0000836 mRNA_region +so 0000837 UTR_region +so 0000838 rRNA_primary_transcript_region +so 0000839 polypeptide_region +so 0000840 repeat_component +so 0000841 spliceosomal_intron_region +so 0000842 gene_component_region +so 0000843 bacterial_RNApol_promoter_region +so 0000844 RNApol_II_promoter_region +so 0000845 RNApol_III_promoter_type_1_region +so 0000846 RNApol_III_promoter_type_2_region +so 0000847 tmRNA_region +so 0000848 LTR_component +so 0000849 three_prime_LTR_component +so 0000850 five_prime_LTR_component +so 0000851 CDS_region +so 0000852 exon_region +so 0000853 homologous_region +so 0000854 paralogous_region +so 0000855 orthologous_region +so 0000856 conserved +so 0000857 homologous +so 0000858 orthologous +so 0000859 paralogous +so 0000860 syntenic +so 0000861 capped_primary_transcript +so 0000862 capped_mRNA +so 0000863 mRNA_attribute +so 0000864 exemplar +so 0000865 frameshift +so 0000866 minus_1_frameshift +so 0000867 minus_2_frameshift +so 0000868 plus_1_frameshift +so 0000869 plus_2_framshift +so 0000870 trans_spliced +so 0000871 polyadenylated_mRNA +so 0000872 trans_spliced_mRNA +so 0000873 edited_transcript +so 0000874 edited_transcript_by_A_to_I_substitution +so 0000875 bound_by_protein +so 0000876 bound_by_nucleic_acid +so 0000877 alternatively_spliced +so 0000878 monocistronic +so 0000879 dicistronic +so 0000880 polycistronic +so 0000881 recoded +so 0000882 codon_redefined +so 0000883 stop_codon_read_through +so 0000884 stop_codon_redefined_as_pyrrolysine +so 0000885 stop_codon_redefined_as_selenocysteine +so 0000886 recoded_by_translational_bypass +so 0000887 translationally_frameshifted +so 0000888 maternally_imprinted_gene +so 0000889 paternally_imprinted_gene +so 0000890 post_translationally_regulated_gene +so 0000891 negatively_autoregulated_gene +so 0000892 positively_autoregulated_gene +so 0000893 silenced +so 0000894 silenced_by_DNA_modification +so 0000895 silenced_by_DNA_methylation +so 0000896 translationally_regulated_gene +so 0000897 allelically_excluded_gene +so 0000898 epigenetically_modified_gene +so 0000899 nuclear_mitochondrial +so 0000900 processed +so 0000901 unequally_crossed_over +so 0000902 transgene +so 0000903 endogenous_retroviral_sequence +so 0000904 rearranged_at_DNA_level +so 0000905 status +so 0000906 independently_known +so 0000907 supported_by_sequence_similarity +so 0000908 supported_by_domain_match +so 0000909 supported_by_EST_or_cDNA +so 0000910 orphan +so 0000911 predicted_by_ab_initio_computation +so 0000912 asx_turn +so 0000913 cloned_cDNA_insert +so 0000914 cloned_genomic_insert +so 0000915 engineered_insert +so 0000916 edit_operation +so 0000917 insert_U +so 0000918 delete_U +so 0000919 substitute_A_to_I +so 0000920 insert_C +so 0000921 insert_dinucleotide +so 0000922 substitute_C_to_U +so 0000923 insert_G +so 0000924 insert_GC +so 0000925 insert_GU +so 0000926 insert_CU +so 0000927 insert_AU +so 0000928 insert_AA +so 0000929 edited_mRNA +so 0000930 guide_RNA_region +so 0000931 anchor_region +so 0000932 pre_edited_mRNA +so 0000933 intermediate +so 0000934 miRNA_target_site +so 0000935 edited_CDS +so 0000936 vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment +so 0000937 vertebrate_immune_system_feature +so 0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster +so 0000939 vertebrate_immune_system_gene_recombination_signal_feature +so 0000940 recombinationally_rearranged +so 0000941 recombinationally_rearranged_vertebrate_immune_system_gene +so 0000942 attP_site +so 0000943 attB_site +so 0000944 attL_site +so 0000945 attR_site +so 0000946 integration_excision_site +so 0000947 resolution_site +so 0000948 inversion_site +so 0000949 dif_site +so 0000950 attC_site +so 0000951 eukaryotic_terminator +so 0000952 oriV +so 0000953 oriC +so 0000954 DNA_chromosome +so 0000955 double_stranded_DNA_chromosome +so 0000956 single_stranded_DNA_chromosome +so 0000957 linear_double_stranded_DNA_chromosome +so 0000958 circular_double_stranded_DNA_chromosome +so 0000959 linear_single_stranded_DNA_chromosome +so 0000960 circular_single_stranded_DNA_chromosome +so 0000961 RNA_chromosome +so 0000962 single_stranded_RNA_chromosome +so 0000963 linear_single_stranded_RNA_chromosome +so 0000964 linear_double_stranded_RNA_chromosome +so 0000965 double_stranded_RNA_chromosome +so 0000966 circular_single_stranded_RNA_chromosome +so 0000967 circular_double_stranded_RNA_chromosome +so 0000968 sequence_replication_mode +so 0000969 rolling_circle +so 0000970 theta_replication +so 0000971 DNA_replication_mode +so 0000972 RNA_replication_mode +so 0000973 insertion_sequence +so 0000975 minicircle_gene +so 0000976 cryptic +so 0000977 anchor_binding_site +so 0000978 template_region +so 0000979 gRNA_encoding +so 0000980 minicircle +so 0000981 rho_dependent_bacterial_terminator +so 0000982 rho_independent_bacterial_terminator +so 0000983 strand_attribute +so 0000984 single +so 0000985 double +so 0000986 topology_attribute +so 0000987 linear +so 0000988 circular +so 0000989 class_II_RNA +so 0000990 class_I_RNA +so 0000991 genomic_DNA +so 0000992 BAC_cloned_genomic_insert +so 0000993 consensus +so 0000994 consensus_region +so 0000995 consensus_mRNA +so 0000996 predicted_gene +so 0000997 gene_fragment +so 0000998 recursive_splice_site +so 0000999 BAC_end +so 0001000 cytosolic_16S_rRNA +so 0001001 cytosolic_23S_rRNA +so 0001002 cytosolic_25S_rRNA +so 0001003 solo_LTR +so 0001004 low_complexity +so 0001005 low_complexity_region +so 0001006 prophage +so 0001007 cryptic_prophage +so 0001008 tetraloop +so 0001009 DNA_constraint_sequence +so 0001010 i_motif +so 0001011 PNA_oligo +so 0001012 DNAzyme +so 0001013 MNP +so 0001014 intron_domain +so 0001015 wobble_base_pair +so 0001016 internal_guide_sequence +so 0001017 silent_mutation +so 0001018 epitope +so 0001019 copy_number_variation +so 0001020 sequence_variant_affecting_copy_number +so 0001021 chromosome_breakpoint +so 0001022 inversion_breakpoint +so 0001023 allele +so 0001024 haplotype +so 0001025 polymorphic_sequence_variant +so 0001026 genome +so 0001027 genotype +so 0001028 diplotype +so 0001029 direction_attribute +so 0001030 forward +so 0001031 reverse +so 0001032 mitochondrial_DNA +so 0001033 chloroplast_DNA +so 0001034 miRtron +so 0001035 piRNA +so 0001036 arginyl_tRNA +so 0001037 mobile_genetic_element +so 0001038 extrachromosomal_mobile_genetic_element +so 0001039 integrated_mobile_genetic_element +so 0001040 integrated_plasmid +so 0001041 viral_sequence +so 0001042 phage_sequence +so 0001043 attCtn_site +so 0001044 nuclear_mt_pseudogene +so 0001045 cointegrated_plasmid +so 0001046 IRLinv_site +so 0001047 IRRinv_site +so 0001048 inversion_site_part +so 0001049 defective_conjugative_transposon +so 0001050 repeat_fragment +so 0001051 nested_region +so 0001052 nested_repeat +so 0001053 nested_transposon +so 0001054 transposon_fragment +so 0001055 transcriptional_cis_regulatory_region +so 0001056 splicing_regulatory_region +so 0001057 enhanceosome +so 0001058 promoter_targeting_sequence +so 0001059 sequence_alteration +so 0001060 sequence_variant +so 0001061 propeptide_cleavage_site +so 0001062 propeptide +so 0001063 immature_peptide_region +so 0001064 active_peptide +so 0001066 compositionally_biased_region_of_peptide +so 0001067 polypeptide_motif +so 0001068 polypeptide_repeat +so 0001070 polypeptide_structural_region +so 0001071 membrane_structure +so 0001072 extramembrane_polypeptide_region +so 0001073 cytoplasmic_polypeptide_region +so 0001074 non_cytoplasmic_polypeptide_region +so 0001075 intramembrane_polypeptide_region +so 0001076 membrane_peptide_loop +so 0001077 transmembrane_polypeptide_region +so 0001078 polypeptide_secondary_structure +so 0001079 polypeptide_structural_motif +so 0001080 coiled_coil +so 0001081 helix_turn_helix +so 0001082 polypeptide_sequencing_information +so 0001083 non_adjacent_residues +so 0001084 non_terminal_residue +so 0001085 sequence_conflict +so 0001086 sequence_uncertainty +so 0001087 cross_link +so 0001088 disulfide_bond +so 0001089 post_translationally_modified_region +so 0001090 covalent_binding_site +so 0001091 non_covalent_binding_site +so 0001092 polypeptide_metal_contact +so 0001093 protein_protein_contact +so 0001094 polypeptide_calcium_ion_contact_site +so 0001095 polypeptide_cobalt_ion_contact_site +so 0001096 polypeptide_copper_ion_contact_site +so 0001097 polypeptide_iron_ion_contact_site +so 0001098 polypeptide_magnesium_ion_contact_site +so 0001099 polypeptide_manganese_ion_contact_site +so 0001100 polypeptide_molybdenum_ion_contact_site +so 0001101 polypeptide_nickel_ion_contact_site +so 0001102 polypeptide_tungsten_ion_contact_site +so 0001103 polypeptide_zinc_ion_contact_site +so 0001104 catalytic_residue +so 0001105 polypeptide_ligand_contact +so 0001106 asx_motif +so 0001107 beta_bulge +so 0001108 beta_bulge_loop +so 0001109 beta_bulge_loop_five +so 0001110 beta_bulge_loop_six +so 0001111 beta_strand +so 0001112 antiparallel_beta_strand +so 0001113 parallel_beta_strand +so 0001114 peptide_helix +so 0001115 left_handed_peptide_helix +so 0001116 right_handed_peptide_helix +so 0001117 alpha_helix +so 0001118 pi_helix +so 0001119 three_ten_helix +so 0001120 polypeptide_nest_motif +so 0001121 polypeptide_nest_left_right_motif +so 0001122 polypeptide_nest_right_left_motif +so 0001123 schellmann_loop +so 0001124 schellmann_loop_seven +so 0001125 schellmann_loop_six +so 0001126 serine_threonine_motif +so 0001127 serine_threonine_staple_motif +so 0001128 polypeptide_turn_motif +so 0001129 asx_turn_left_handed_type_one +so 0001130 asx_turn_left_handed_type_two +so 0001131 asx_turn_right_handed_type_two +so 0001132 asx_turn_right_handed_type_one +so 0001133 beta_turn +so 0001134 beta_turn_left_handed_type_one +so 0001135 beta_turn_left_handed_type_two +so 0001136 beta_turn_right_handed_type_one +so 0001137 beta_turn_right_handed_type_two +so 0001138 gamma_turn +so 0001139 gamma_turn_classic +so 0001140 gamma_turn_inverse +so 0001141 serine_threonine_turn +so 0001142 st_turn_left_handed_type_one +so 0001143 st_turn_left_handed_type_two +so 0001144 st_turn_right_handed_type_one +so 0001145 st_turn_right_handed_type_two +so 0001146 polypeptide_variation_site +so 0001147 natural_variant_site +so 0001148 mutated_variant_site +so 0001149 alternate_sequence_site +so 0001150 beta_turn_type_six +so 0001151 beta_turn_type_six_a +so 0001152 beta_turn_type_six_a_one +so 0001153 beta_turn_type_six_a_two +so 0001154 beta_turn_type_six_b +so 0001155 beta_turn_type_eight +so 0001156 DRE_motif +so 0001157 DMv4_motif +so 0001158 E_box_motif +so 0001159 DMv5_motif +so 0001160 DMv3_motif +so 0001161 DMv2_motif +so 0001162 MTE +so 0001163 INR1_motif +so 0001164 DPE1_motif +so 0001165 DMv1_motif +so 0001166 GAGA_motif +so 0001167 NDM2_motif +so 0001168 NDM3_motif +so 0001169 ds_RNA_viral_sequence +so 0001170 polinton +so 0001171 rRNA_21S +so 0001172 tRNA_region +so 0001173 anticodon_loop +so 0001174 anticodon +so 0001175 CCA_tail +so 0001176 DHU_loop +so 0001177 T_loop +so 0001178 pyrrolysine_tRNA_primary_transcript +so 0001179 U3_snoRNA +so 0001180 AU_rich_element +so 0001181 Bruno_response_element +so 0001182 iron_responsive_element +so 0001183 morpholino_backbone +so 0001184 PNA +so 0001185 enzymatic +so 0001186 ribozymic +so 0001187 pseudouridylation_guide_snoRNA +so 0001188 LNA +so 0001189 LNA_oligo +so 0001190 TNA +so 0001191 TNA_oligo +so 0001192 GNA +so 0001193 GNA_oligo +so 0001194 R_GNA +so 0001195 R_GNA_oligo +so 0001196 S_GNA +so 0001197 S_GNA_oligo +so 0001198 ds_DNA_viral_sequence +so 0001199 ss_RNA_viral_sequence +so 0001200 negative_sense_ssRNA_viral_sequence +so 0001201 positive_sense_ssRNA_viral_sequence +so 0001202 ambisense_ssRNA_viral_sequence +so 0001203 RNA_polymerase_promoter +so 0001204 Phage_RNA_Polymerase_Promoter +so 0001205 SP6_RNA_Polymerase_Promoter +so 0001206 T3_RNA_Polymerase_Promoter +so 0001207 T7_RNA_Polymerase_Promoter +so 0001208 five_prime_EST +so 0001209 three_prime_EST +so 0001210 translational_frameshift +so 0001211 plus_1_translational_frameshift +so 0001212 plus_2_translational_frameshift +so 0001213 group_III_intron +so 0001214 noncoding_region_of_exon +so 0001215 coding_region_of_exon +so 0001216 endonuclease_spliced_intron +so 0001217 protein_coding_gene +so 0001218 transgenic_insertion +so 0001219 retrogene +so 0001220 silenced_by_RNA_interference +so 0001221 silenced_by_histone_modification +so 0001222 silenced_by_histone_methylation +so 0001223 silenced_by_histone_deacetylation +so 0001224 gene_silenced_by_RNA_interference +so 0001225 gene_silenced_by_histone_modification +so 0001226 gene_silenced_by_histone_methylation +so 0001227 gene_silenced_by_histone_deacetylation +so 0001228 dihydrouridine +so 0001229 pseudouridine +so 0001230 inosine +so 0001231 seven_methylguanine +so 0001232 ribothymidine +so 0001233 methylinosine +so 0001234 mobile +so 0001235 replicon +so 0001236 base +so 0001237 amino_acid +so 0001238 major_TSS +so 0001239 minor_TSS +so 0001240 TSS_region +so 0001241 encodes_alternate_transcription_start_sites +so 0001243 miRNA_primary_transcript_region +so 0001244 pre_miRNA +so 0001245 miRNA_stem +so 0001246 miRNA_loop +so 0001247 synthetic_oligo +so 0001248 assembly +so 0001249 fragment_assembly +so 0001250 fingerprint_map +so 0001251 STS_map +so 0001252 RH_map +so 0001253 sonicate_fragment +so 0001254 polyploid +so 0001255 autopolyploid +so 0001256 allopolyploid +so 0001257 homing_endonuclease_binding_site +so 0001258 octamer_motif +so 0001259 apicoplast_chromosome +so 0001260 sequence_collection +so 0001261 overlapping_feature_set +so 0001262 overlapping_EST_set +so 0001263 ncRNA_gene +so 0001264 gRNA_gene +so 0001265 miRNA_gene +so 0001266 scRNA_gene +so 0001267 snoRNA_gene +so 0001268 snRNA_gene +so 0001269 SRP_RNA_gene +so 0001271 tmRNA_gene +so 0001272 tRNA_gene +so 0001273 modified_adenosine +so 0001274 modified_inosine +so 0001275 modified_cytidine +so 0001276 modified_guanosine +so 0001277 modified_uridine +so 0001278 one_methylinosine +so 0001279 one_two_prime_O_dimethylinosine +so 0001280 two_prime_O_methylinosine +so 0001281 three_methylcytidine +so 0001282 five_methylcytidine +so 0001283 two_prime_O_methylcytidine +so 0001284 two_thiocytidine +so 0001285 N4_acetylcytidine +so 0001286 five_formylcytidine +so 0001287 five_two_prime_O_dimethylcytidine +so 0001288 N4_acetyl_2_prime_O_methylcytidine +so 0001289 lysidine +so 0001290 N4_methylcytidine +so 0001291 N4_2_prime_O_dimethylcytidine +so 0001292 five_hydroxymethylcytidine +so 0001293 five_formyl_two_prime_O_methylcytidine +so 0001294 N4_N4_2_prime_O_trimethylcytidine +so 0001295 one_methyladenosine +so 0001296 two_methyladenosine +so 0001297 N6_methyladenosine +so 0001298 two_prime_O_methyladenosine +so 0001299 two_methylthio_N6_methyladenosine +so 0001300 N6_isopentenyladenosine +so 0001301 two_methylthio_N6_isopentenyladenosine +so 0001302 N6_cis_hydroxyisopentenyl_adenosine +so 0001303 two_methylthio_N6_cis_hydroxyisopentenyl_adenosine +so 0001304 N6_glycinylcarbamoyladenosine +so 0001305 N6_threonylcarbamoyladenosine +so 0001306 two_methylthio_N6_threonyl_carbamoyladenosine +so 0001307 N6_methyl_N6_threonylcarbamoyladenosine +so 0001308 N6_hydroxynorvalylcarbamoyladenosine +so 0001309 two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine +so 0001310 two_prime_O_ribosyladenosine_phosphate +so 0001311 N6_N6_dimethyladenosine +so 0001312 N6_2_prime_O_dimethyladenosine +so 0001313 N6_N6_2_prime_O_trimethyladenosine +so 0001314 one_two_prime_O_dimethyladenosine +so 0001315 N6_acetyladenosine +so 0001316 seven_deazaguanosine +so 0001317 queuosine +so 0001318 epoxyqueuosine +so 0001319 galactosyl_queuosine +so 0001320 mannosyl_queuosine +so 0001321 seven_cyano_seven_deazaguanosine +so 0001322 seven_aminomethyl_seven_deazaguanosine +so 0001323 archaeosine +so 0001324 one_methylguanosine +so 0001325 N2_methylguanosine +so 0001326 seven_methylguanosine +so 0001327 two_prime_O_methylguanosine +so 0001328 N2_N2_dimethylguanosine +so 0001329 N2_2_prime_O_dimethylguanosine +so 0001330 N2_N2_2_prime_O_trimethylguanosine +so 0001331 two_prime_O_ribosylguanosine_phosphate +so 0001332 wybutosine +so 0001333 peroxywybutosine +so 0001334 hydroxywybutosine +so 0001335 undermodified_hydroxywybutosine +so 0001336 wyosine +so 0001337 methylwyosine +so 0001338 N2_7_dimethylguanosine +so 0001339 N2_N2_7_trimethylguanosine +so 0001340 one_two_prime_O_dimethylguanosine +so 0001341 four_demethylwyosine +so 0001342 isowyosine +so 0001343 N2_7_2prirme_O_trimethylguanosine +so 0001344 five_methyluridine +so 0001345 two_prime_O_methyluridine +so 0001346 five_two_prime_O_dimethyluridine +so 0001347 one_methylpseudouridine +so 0001348 two_prime_O_methylpseudouridine +so 0001349 two_thiouridine +so 0001350 four_thiouridine +so 0001351 five_methyl_2_thiouridine +so 0001352 two_thio_two_prime_O_methyluridine +so 0001353 three_three_amino_three_carboxypropyl_uridine +so 0001354 five_hydroxyuridine +so 0001355 five_methoxyuridine +so 0001356 uridine_five_oxyacetic_acid +so 0001357 uridine_five_oxyacetic_acid_methyl_ester +so 0001358 five_carboxyhydroxymethyl_uridine +so 0001359 five_carboxyhydroxymethyl_uridine_methyl_ester +so 0001360 five_methoxycarbonylmethyluridine +so 0001361 five_methoxycarbonylmethyl_two_prime_O_methyluridine +so 0001362 five_methoxycarbonylmethyl_two_thiouridine +so 0001363 five_aminomethyl_two_thiouridine +so 0001364 five_methylaminomethyluridine +so 0001365 five_methylaminomethyl_two_thiouridine +so 0001366 five_methylaminomethyl_two_selenouridine +so 0001367 five_carbamoylmethyluridine +so 0001368 five_carbamoylmethyl_two_prime_O_methyluridine +so 0001369 five_carboxymethylaminomethyluridine +so 0001370 five_carboxymethylaminomethyl_two_prime_O_methyluridine +so 0001371 five_carboxymethylaminomethyl_two_thiouridine +so 0001372 three_methyluridine +so 0001373 one_methyl_three_three_amino_three_carboxypropyl_pseudouridine +so 0001374 five_carboxymethyluridine +so 0001375 three_two_prime_O_dimethyluridine +so 0001376 five_methyldihydrouridine +so 0001377 three_methylpseudouridine +so 0001378 five_taurinomethyluridine +so 0001379 five_taurinomethyl_two_thiouridine +so 0001380 five_isopentenylaminomethyl_uridine +so 0001381 five_isopentenylaminomethyl_two_thiouridine +so 0001382 five_isopentenylaminomethyl_two_prime_O_methyluridine +so 0001383 histone_binding_site +so 0001384 CDS_fragment +so 0001385 modified_amino_acid_feature +so 0001386 modified_glycine +so 0001387 modified_L_alanine +so 0001388 modified_L_asparagine +so 0001389 modified_L_aspartic_acid +so 0001390 modified_L_cysteine +so 0001391 modified_L_glutamic_acid +so 0001392 modified_L_threonine +so 0001393 modified_L_tryptophan +so 0001394 modified_L_glutamine +so 0001395 modified_L_methionine +so 0001396 modified_L_isoleucine +so 0001397 modified_L_phenylalanine +so 0001398 modified_L_histidine +so 0001399 modified_L_serine +so 0001400 modified_L_lysine +so 0001401 modified_L_leucine +so 0001402 modified_L_selenocysteine +so 0001403 modified_L_valine +so 0001404 modified_L_proline +so 0001405 modified_L_tyrosine +so 0001406 modified_L_arginine +so 0001407 peptidyl +so 0001408 cleaved_for_gpi_anchor_region +so 0001409 biomaterial_region +so 0001410 experimental_feature +so 0001411 biological_region +so 0001412 topologically_defined_region +so 0001413 translocation_breakpoint +so 0001414 insertion_breakpoint +so 0001415 deletion_breakpoint +so 0001416 five_prime_flanking_region +so 0001417 three_prime_flanking_region +so 0001418 transcribed_fragment +so 0001419 cis_splice_site +so 0001420 trans_splice_site +so 0001421 splice_junction +so 0001422 conformational_switch +so 0001423 dye_terminator_read +so 0001424 pyrosequenced_read +so 0001425 ligation_based_read +so 0001426 polymerase_synthesis_read +so 0001427 cis_regulatory_frameshift_element +so 0001428 expressed_sequence_assembly +so 0001429 DNA_binding_site +so 0001431 cryptic_gene +so 0001432 sequence_variant_affecting_polyadenylation +so 0001433 three_prime_RACE_clone +so 0001434 cassette_pseudogene +so 0001435 alanine +so 0001436 valine +so 0001437 leucine +so 0001438 isoleucine +so 0001439 proline +so 0001440 tryptophan +so 0001441 phenylalanine +so 0001442 methionine +so 0001443 glycine +so 0001444 serine +so 0001445 threonine +so 0001446 tyrosine +so 0001447 cysteine +so 0001448 glutamine +so 0001449 asparagine +so 0001450 lysine +so 0001451 arginine +so 0001452 histidine +so 0001453 aspartic_acid +so 0001454 glutamic_acid +so 0001455 selenocysteine +so 0001456 pyrrolysine +so 0001457 transcribed_cluster +so 0001458 unigene_cluster +so 0001459 CRISPR +so 0001460 insulator_binding_site +so 0001461 enhancer_binding_site +so 0001462 contig_collection +so 0001463 lincRNA +so 0001464 UST +so 0001465 three_prime_UST +so 0001466 five_prime_UST +so 0001467 RST +so 0001468 three_prime_RST +so 0001469 five_prime_RST +so 0001470 UST_match +so 0001471 RST_match +so 0001472 primer_match +so 0001473 miRNA_antiguide +so 0001474 trans_splice_junction +so 0001475 outron +so 0001476 natural_plasmid +so 0001477 gene_trap_construct +so 0001478 promoter_trap_construct +so 0001479 enhancer_trap_construct +so 0001480 PAC_end +so 0001481 RAPD +so 0001482 shadow_enhancer +so 0001483 SNV +so 0001484 X_element_combinatorial_repeat +so 0001485 Y_prime_element +so 0001486 standard_draft +so 0001487 high_quality_draft +so 0001488 improved_high_quality_draft +so 0001489 annotation_directed_improved_draft +so 0001490 noncontiguous_finished +so 0001491 finished_genome +so 0001492 intronic_regulatory_region +so 0001493 centromere_DNA_Element_I +so 0001494 centromere_DNA_Element_II +so 0001495 centromere_DNA_Element_III +so 0001496 telomeric_repeat +so 0001497 X_element +so 0001498 YAC_end +so 0001499 whole_genome_sequence_status +so 0001500 heritable_phenotypic_marker +so 0001501 peptide_collection +so 0001502 high_identity_region +so 0001503 processed_transcript +so 0001504 assortment_derived_variation +so 0001505 reference_genome +so 0001506 variant_genome +so 0001507 variant_collection +so 0001508 alteration_attribute +so 0001509 chromosomal_variation_attribute +so 0001510 intrachromosomal +so 0001511 interchromosomal +so 0001512 insertion_attribute +so 0001513 tandem +so 0001514 direct +so 0001515 inverted +so 0001516 free +so 0001517 inversion_attribute +so 0001518 pericentric +so 0001519 paracentric +so 0001520 translocaton_attribute +so 0001521 reciprocal +so 0001522 insertional +so 0001523 duplication_attribute +so 0001524 chromosomally_aberrant_genome +so 0001525 assembly_error_correction +so 0001526 base_call_error_correction +so 0001527 peptide_localization_signal +so 0001528 nuclear_localization_signal +so 0001529 endosomal_localization_signal +so 0001530 lysosomal_localization_signal +so 0001531 nuclear_export_signal +so 0001532 recombination_signal_sequence +so 0001533 cryptic_splice_site +so 0001534 nuclear_rim_localization_signal +so 0001535 P_TIR_transposon +so 0001536 functional_effect_variant +so 0001537 structural_variant +so 0001538 transcript_function_variant +so 0001539 translational_product_function_variant +so 0001540 level_of_transcript_variant +so 0001541 decreased_transcript_level_variant +so 0001542 increased_transcript_level_variant +so 0001543 transcript_processing_variant +so 0001544 editing_variant +so 0001545 polyadenylation_variant +so 0001546 transcript_stability_variant +so 0001547 decreased_transcript_stability_variant +so 0001548 increased_transcript_stability_variant +so 0001549 transcription_variant +so 0001550 rate_of_transcription_variant +so 0001551 increased_transcription_rate_variant +so 0001552 decreased_transcription_rate_variant +so 0001553 translational_product_level_variant +so 0001554 polypeptide_function_variant +so 0001555 decreased_translational_product_level +so 0001556 increased_translational_product_level +so 0001557 polypeptide_gain_of_function_variant +so 0001558 polypeptide_localization_variant +so 0001559 polypeptide_loss_of_function_variant +so 0001560 inactive_ligand_binding_site +so 0001561 polypeptide_partial_loss_of_function +so 0001562 polypeptide_post_translational_processing_variant +so 0001563 copy_number_change +so 0001564 gene_variant +so 0001565 gene_fusion +so 0001566 regulatory_region_variant +so 0001567 stop_retained_variant +so 0001568 splicing_variant +so 0001569 cryptic_splice_site_variant +so 0001570 cryptic_splice_acceptor +so 0001571 cryptic_splice_donor +so 0001572 exon_loss_variant +so 0001573 intron_gain_variant +so 0001574 splice_acceptor_variant +so 0001575 splice_donor_variant +so 0001576 transcript_variant +so 0001577 complex_transcript_variant +so 0001578 stop_lost +so 0001579 transcript_sequence_variant +so 0001580 coding_sequence_variant +so 0001582 initiator_codon_variant +so 0001583 missense_variant +so 0001585 conservative_missense_variant +so 0001586 non_conservative_missense_variant +so 0001587 stop_gained +so 0001589 frameshift_variant +so 0001590 terminator_codon_variant +so 0001591 frame_restoring_variant +so 0001592 minus_1_frameshift_variant +so 0001593 minus_2_frameshift_variant +so 0001594 plus_1_frameshift_variant +so 0001595 plus_2_frameshift_variant +so 0001596 transcript_secondary_structure_variant +so 0001597 compensatory_transcript_secondary_structure_variant +so 0001598 translational_product_structure_variant +so 0001599 3D_polypeptide_structure_variant +so 0001600 complex_3D_structural_variant +so 0001601 conformational_change_variant +so 0001602 complex_change_of_translational_product_variant +so 0001603 polypeptide_sequence_variant +so 0001604 amino_acid_deletion +so 0001605 amino_acid_insertion +so 0001606 amino_acid_substitution +so 0001607 conservative_amino_acid_substitution +so 0001608 non_conservative_amino_acid_substitution +so 0001609 elongated_polypeptide +so 0001610 elongated_polypeptide_C_terminal +so 0001611 elongated_polypeptide_N_terminal +so 0001612 elongated_in_frame_polypeptide_C_terminal +so 0001613 elongated_out_of_frame_polypeptide_C_terminal +so 0001614 elongated_in_frame_polypeptide_N_terminal_elongation +so 0001615 elongated_out_of_frame_polypeptide_N_terminal +so 0001616 polypeptide_fusion +so 0001617 polypeptide_truncation +so 0001618 inactive_catalytic_site +so 0001619 non_coding_transcript_variant +so 0001620 mature_miRNA_variant +so 0001621 NMD_transcript_variant +so 0001622 UTR_variant +so 0001623 5_prime_UTR_variant +so 0001624 3_prime_UTR_variant +so 0001626 incomplete_terminal_codon_variant +so 0001627 intron_variant +so 0001628 intergenic_variant +so 0001629 splice_site_variant +so 0001630 splice_region_variant +so 0001631 upstream_gene_variant +so 0001632 downstream_gene_variant +so 0001633 5KB_downstream_variant +so 0001634 500B_downstream_variant +so 0001635 5KB_upstream_variant +so 0001636 2KB_upstream_variant +so 0001637 rRNA_gene +so 0001638 piRNA_gene +so 0001639 RNase_P_RNA_gene +so 0001640 RNase_MRP_RNA_gene +so 0001641 lincRNA_gene +so 0001642 mathematically_defined_repeat +so 0001643 telomerase_RNA_gene +so 0001644 targeting_vector +so 0001645 genetic_marker +so 0001646 DArT_marker +so 0001647 kozak_sequence +so 0001648 nested_transposon +so 0001649 nested_repeat +so 0001650 inframe_variant +so 0001653 retinoic_acid_responsive_element +so 0001654 nucleotide_to_protein_binding_site +so 0001655 nucleotide_binding_site +so 0001656 metal_binding_site +so 0001657 ligand_binding_site +so 0001658 nested_tandem_repeat +so 0001659 promoter_element +so 0001660 core_eukaryotic_promoter_element +so 0001661 RNA_polymerase_II_TATA_box +so 0001662 RNA_polymerase_III_TATA_box +so 0001663 BREd_motif +so 0001664 DCE +so 0001665 DCE_SI +so 0001666 DCE_SII +so 0001667 DCE_SIII +so 0001668 proximal_promoter_element +so 0001669 RNApol_II_core_promoter +so 0001670 distal_promoter_element +so 0001671 bacterial_RNApol_promoter_sigma_70_element +so 0001672 bacterial_RNApol_promoter_sigma54_element +so 0001673 minus_12_signal +so 0001674 minus_24_signal +so 0001675 A_box_type_1 +so 0001676 A_box_type_2 +so 0001677 intermediate_element +so 0001678 regulatory_promoter_element +so 0001679 transcription_regulatory_region +so 0001680 translation_regulatory_region +so 0001681 recombination_regulatory_region +so 0001682 replication_regulatory_region +so 0001683 sequence_motif +so 0001684 experimental_feature_attribute +so 0001685 score +so 0001686 quality_value +so 0001687 restriction_enzyme_recognition_site +so 0001688 restriction_enzyme_cleavage_junction +so 0001689 five_prime_restriction_enzyme_junction +so 0001690 three_prime_restriction_enzyme_junction +so 0001691 blunt_end_restriction_enzyme_cleavage_site +so 0001692 sticky_end_restriction_enzyme_cleavage_site +so 0001693 blunt_end_restriction_enzyme_cleavage_junction +so 0001694 single_strand_restriction_enzyme_cleavage_site +so 0001695 restriction_enzyme_single_strand_overhang +so 0001696 experimentally_defined_binding_region +so 0001697 ChIP_seq_region +so 0001698 ASPE_primer +so 0001699 dCAPS_primer +so 0001700 histone_modification +so 0001701 histone_methylation_site +so 0001702 histone_acetylation_site +so 0001703 H3K9_acetylation_site +so 0001704 H3K14_acetylation_site +so 0001705 H3K4_monomethylation_site +so 0001706 H3K4_trimethylation +so 0001707 H3K9_trimethylation_site +so 0001708 H3K27_monomethylation_site +so 0001709 H3K27_trimethylation_site +so 0001710 H3K79_monomethylation_site +so 0001711 H3K79_dimethylation_site +so 0001712 H3K79_trimethylation_site +so 0001713 H4K20_monomethylation_site +so 0001714 H2BK5_monomethylation_site +so 0001715 ISRE +so 0001716 histone_ubiqitination_site +so 0001717 H2B_ubiquitination_site +so 0001718 H3K18_acetylation_site +so 0001719 H3K23_acetylation_site +so 0001720 epigenetically_modified_region +so 0001721 H3K27_acylation_site +so 0001722 H3K36_monomethylation_site +so 0001723 H3K36_dimethylation_site +so 0001724 H3K36_trimethylation_site +so 0001725 H3K4_dimethylation_site +so 0001726 H3K27_dimethylation_site +so 0001727 H3K9_monomethylation_site +so 0001728 H3K9_dimethylation_site +so 0001729 H4K16_acetylation_site +so 0001730 H4K5_acetylation_site +so 0001731 H4K8_acetylation_site +so 0001732 H3K27_methylation_site +so 0001733 H3K36_methylation_site +so 0001734 H3K4_methylation_site +so 0001735 H3K79_methylation_site +so 0001736 H3K9_methylation_site +so 0001737 histone_acylation_region +so 0001738 H4K_acylation_region +so 0001739 gene_with_non_canonical_start_codon +so 0001740 gene_with_start_codon_CUG +so 0001741 pseudogenic_gene_segment +so 0001742 copy_number_gain +so 0001743 copy_number_loss +so 0001744 UPD +so 0001745 maternal_uniparental_disomy +so 0001746 paternal_uniparental_disomy +so 0001747 open_chromatin_region +so 0001748 SL3_acceptor_site +so 0001749 SL4_acceptor_site +so 0001750 SL5_acceptor_site +so 0001751 SL6_acceptor_site +so 0001752 SL7_acceptor_site +so 0001753 SL8_acceptor_site +so 0001754 SL9_acceptor_site +so 0001755 SL10_acceptor_site +so 0001756 SL11_acceptor_site +so 0001757 SL12_acceptor_site +so 0001758 duplicated_pseudogene +so 0001759 unitary_pseudogene +so 0001760 non_processed_pseudogene +so 0001761 variant_quality +so 0001762 variant_origin +so 0001763 variant_frequency +so 0001764 unique_variant +so 0001765 rare_variant +so 0001766 polymorphic_variant +so 0001767 common_variant +so 0001768 fixed_variant +so 0001769 variant_phenotype +so 0001770 benign_variant +so 0001771 disease_associated_variant +so 0001772 disease_causing_variant +so 0001773 lethal_variant +so 0001774 quantitative_variant +so 0001775 maternal_variant +so 0001776 paternal_variant +so 0001777 somatic_variant +so 0001778 germline_variant +so 0001779 pedigree_specific_variant +so 0001780 population_specific_variant +so 0001781 de_novo_variant +so 0001782 TF_binding_site_variant +so 0001784 complex_structural_alteration +so 0001785 structural_alteration +so 0001786 loss_of_heterozygosity +so 0001787 splice_donor_5th_base_variant +so 0001788 U_box +so 0001789 mating_type_region +so 0001790 paired_end_fragment +so 0001791 exon_variant +so 0001792 non_coding_transcript_exon_variant +so 0001793 clone_end +so 0001794 point_centromere +so 0001795 regional_centromere +so 0001796 regional_centromere_central_core +so 0001797 centromeric_repeat +so 0001798 regional_centromere_inner_repeat_region +so 0001799 regional_centromere_outer_repeat_region +so 0001800 tasiRNA +so 0001801 tasiRNA_primary_transcript +so 0001802 increased_polyadenylation_variant +so 0001803 decreased_polyadenylation_variant +so 0001804 DDB_box +so 0001805 destruction_box +so 0001806 ER_retention_signal +so 0001807 KEN_box +so 0001808 mitochondrial_targeting_signal +so 0001809 signal_anchor +so 0001810 PIP_box +so 0001811 phosphorylation_site +so 0001812 transmembrane_helix +so 0001813 vacuolar_sorting_signal +so 0001814 coding_variant_quality +so 0001815 synonymous +so 0001816 non_synonymous +so 0001817 inframe +so 0001818 protein_altering_variant +so 0001819 synonymous_variant +so 0001820 inframe_indel +so 0001821 inframe_insertion +so 0001822 inframe_deletion +so 0001823 conservative_inframe_insertion +so 0001824 disruptive_inframe_insertion +so 0001825 conservative_inframe_deletion +so 0001826 disruptive_inframe_deletion +so 0001827 mRNA_read +so 0001828 genomic_DNA_read +so 0001829 mRNA_contig +so 0001830 AFLP_fragment +so 0001831 protein_hmm_match +so 0001832 immunoglobulin_region +so 0001833 V_region +so 0001834 C_region +so 0001835 N_region +so 0001836 S_region +so 0001837 mobile_element_insertion +so 0001838 novel_sequence_insertion +so 0001839 CSL_response_element +so 0001840 GATA_box +so 0001841 polymorphic_pseudogene +so 0001842 AP_1_binding_site +so 0001843 CRE +so 0001844 CuRE +so 0001845 DRE +so 0001846 FLEX_element +so 0001847 forkhead_motif +so 0001848 homol_D_box +so 0001849 homol_E_box +so 0001850 HSE +so 0001851 iron_repressed_GATA_element +so 0001852 mating_type_M_box +so 0001853 androgen_response_element +so 0001854 smFISH_probe +so 0001855 MCB +so 0001856 CCAAT_motif +so 0001857 Ace2_UAS +so 0001858 TR_box +so 0001859 STREP_motif +so 0001860 rDNA_intergenic_spacer_element +so 0001861 sterol_regulatory_element +so 0001862 GT_dinucleotide_repeat +so 0001863 GTT_trinucleotide_repeat +so 0001864 Sap1_recognition_motif +so 0001865 CDRE_motif +so 0001866 BAC_read_contig +so 0001867 candidate_gene +so 0001868 positional_candidate_gene +so 0001869 functional_candidate_gene +so 0001870 enhancerRNA +so 0001871 PCB +so 0001872 rearrangement_region +so 0001873 interchromosomal_breakpoint +so 0001874 intrachromosomal_breakpoint +so 0001875 unassigned_supercontig +so 0001876 partial_genomic_sequence_assembly +so 0001877 lncRNA +so 0001878 feature_variant +so 0001879 feature_ablation +so 0001880 feature_amplification +so 0001881 feature_translocation +so 0001882 feature_fusion +so 0001883 transcript_translocation +so 0001884 regulatory_region_translocation +so 0001885 TFBS_translocation +so 0001886 transcript_fusion +so 0001887 regulatory_region_fusion +so 0001888 TFBS_fusion +so 0001889 transcript_amplification +so 0001890 transcript_regulatory_region_fusion +so 0001891 regulatory_region_amplification +so 0001892 TFBS_amplification +so 0001893 transcript_ablation +so 0001894 regulatory_region_ablation +so 0001895 TFBS_ablation +so 0001896 transposable_element_CDS +so 0001897 transposable_element_pseudogene +so 0001898 dg_repeat +so 0001899 dh_repeat +so 0001901 AACCCT_box +so 0001902 splice_region +so 0001904 antisense_lncRNA +so 0001905 regional_centromere_outer_repeat_transcript +so 0001906 feature_truncation +so 0001907 feature_elongation +so 0001908 internal_feature_elongation +so 0001909 frameshift_elongation +so 0001910 frameshift_truncation +so 0001911 copy_number_increase +so 0001912 copy_number_decrease +so 0001913 bacterial_RNApol_promoter_sigma_ecf_element +so 0001914 rDNA_replication_fork_barrier +so 0001915 transcription_start_cluster +so 0001916 CAGE_tag +so 0001917 CAGE_cluster +so 0001918 5_methylcytosine +so 0001919 4_methylcytosine +so 0001920 N6_methyladenine +so 0001921 mitochondrial_contig +so 0001922 mitochondrial_supercontig +so 0001923 TERRA +so 0001924 ARRET +so 0001925 ARIA +so 0001926 anti_ARRET +so 0001927 telomeric_transcript +so 0001928 distal_duplication +so 0001929 mitochondrial_DNA_read +so 0001930 chloroplast_DNA_read +so 0001931 consensus_gDNA +so 0001932 restriction_enzyme_five_prime_single_strand_overhang +so 0001933 restriction_enzyme_three_prime_single_strand_overhang +so 0001934 monomeric_repeat +so 0001935 H3K20_trimethylation_site +so 0001936 H3K36_acetylation_site +so 0001937 H2BK12_acetylation_site +so 0001938 H2AK5_acetylation_site +so 0001939 H4K12_acetylation_site +so 0001940 H2BK120_acetylation_site +so 0001941 H4K91_acetylation_site +so 0001942 H2BK20_acetylation_site +so 0001943 H3K4_acetylation_site +so 0001944 H2AK9_acetylation_site +so 0001945 H3K56_acetylation_site +so 0001946 H2BK15_acetylation_site +so 0001947 H3R2_monomethylation_site +so 0001948 H3R2_dimethylation_site +so 0001949 H4R3_dimethylation_site +so 0001950 H4K4_trimethylation_site +so 0001951 H3K23_dimethylation_site +so 0001952 promoter_flanking_region +so 0001953 restriction_enzyme_assembly_scar +so 0001954 restriction_enzyme_region +so 0001955 protein_stability_element +so 0001956 protease_site +so 0001957 RNA_stability_element +so 0001958 lariat_intron +so 0001959 TCT_motif +so 0001960 5_hydroxymethylcytosine +so 0001961 5_formylcytosine +so 0001962 modified_adenine +so 0001963 modified_cytosine +so 0001964 modified_guanine +so 0001965 8_oxoguanine +so 0001966 5_carboxylcytosine +so 0001967 8_oxoadenine +so 0001968 coding_transcript_variant +so 0001969 coding_transcript_intron_variant +so 0001970 non_coding_transcript_intron_variant +so 0001971 zinc_finger_binding_site +so 0001972 histone_4_acetylation_site +so 0001973 histone_3_acetylation_site +so 0001974 CTCF_binding_site +so 0001975 five_prime_sticky_end_restriction_enzyme_cleavage_site +so 0001976 three_prime_sticky_end_restriction_enzyme_cleavage_site +so 0001977 ribonuclease_site +so 0001978 signature +so 0001979 RNA_stability_element +so 0001980 G_box +so 0001981 L_box +so 0001982 I-box +so 0001983 5_prime_UTR_premature_start_codon_variant +so 0001984 silent_mating_type_cassette_array +so 0001985 Okazaki_fragment +so 0001986 upstream_transcript_variant +so 0001987 downstream_transcript_variant +so 0001988 5_prime_UTR_premature_start_codon_gain_variant +so 0001989 5_prime_UTR_premature_start_codon_loss_variant +so 0001990 five_prime_UTR_premature_start_codon_location_variant +so 0001991 consensus_AFLP_fragment +so 0001992 nonsynonymous_variant +so 0001993 extended_cis_splice_site +so 0001994 intron_base_5 +so 0001995 extended_intronic_splice_region_variant +so 0001996 extended_intronic_splice_region +so 0001997 subtelomere +so 0001998 sgRNA +so 0001999 mating_type_region_motif +so 0002001 Y_region +so 0002002 Z1_region +so 0002003 Z2_region +so 0002004 ARS_consensus_sequence +so 0002005 DSR_motif +so 0002006 zinc_repressed_element +so 0002007 MNV +so 0002008 rare_amino_acid_variant +so 0002009 selenocysteine_loss +so 0002010 pyrrolysine_loss +so 0002011 intragenic_variant +so 0002012 start_lost +so 0002013 5_prime_UTR_truncation +so 0002014 5_prime_UTR_elongation +so 0002015 3_prime_UTR_truncation +so 0002016 3_prime_UTR_elongation +so 0002017 conserved_intergenic_variant +so 0002018 conserved_intron_variant +so 0002019 start_retained_variant +so 0002020 boundary_element +so 0002021 mating_type_region_replication_fork_barrier +so 0002022 priRNA +so 0002023 multiplexing_sequence_identifier +so 0002024 W_region +so 0002025 cis_acting_homologous_chromosome_pairing_region +so 0002026 intein_encoding_region +so 0002027 uORF +so 0002028 sORF +so 0002029 tnaORF +so 0002030 X_region +so 0002031 shRNA +so 0002032 moR +so 0002033 loR +so 0002034 miR_encoding_snoRNA_primary_transcript +so 0002035 lncRNA_primary_transcript +so 0002036 miR_encoding_lncRNA_primary_transcript +so 0002037 miR_encoding_tRNA_primary_transcript +so 0002038 shRNA_primary_transcript +so 0002039 miR_encoding_shRNA_primary_transcript +so 0002040 vaultRNA_primary_transcript +so 0002041 miR_encoding_vaultRNA_primary_transcript +so 0002042 Y_RNA_primary_transcript +so 0002043 miR_encoding_Y_RNA_primary_transcript +so 0002044 TCS_element +so 0002045 pheromone_response_element +so 0002046 FRE +so 0002047 transcription_pause_site +so 0002048 disabled_reading_frame +so 0002049 H3K27_acetylation_site +so 0002050 constitutive_promoter +so 0002051 inducible_promoter +so 0002052 dominant_negative_variant +so 0002053 gain_of_function_variant +so 0002054 loss_of_function_variant +so 0002055 null_mutation +so 0002056 intronic_splicing_silencer +so 0002057 intronic_splicing_enhancer +so 0002058 exonic_splicing_silencer +so 0002059 recombination_enhancer +so 0002060 interchromosomal_translocation +so 0002061 intrachromosomal_translocation +so 0002062 complex_chromosomal_rearrangement +so 0002063 Alu_insertion +so 0002064 LINE1_insertion +so 0002065 SVA_insertion +so 0002066 mobile_element_deletion +so 0002067 HERV_deletion +so 0002068 SVA_deletion +so 0002069 LINE1_deletion +so 0002070 Alu_deletion +so 0002071 CDS_supported_by_peptide_spectrum_match +so 0002072 sequence_comparison +so 0002073 no_sequence_alteration +so 0002074 intergenic_1kb_variant +so 0002075 incomplete_transcript_variant +so 0002076 incomplete_transcript_3UTR_variant +so 0002077 incomplete_transcript_5UTR_variant +so 0002078 incomplete_transcript_intronic_variant +so 0002079 incomplete_transcript_splice_region_variant +so 0002080 incomplete_transcript_exonic_variant +so 0002081 incomplete_transcript_CDS +so 0002082 incomplete_transcript_coding_splice_variant +so 0002083 2KB_downstream_variant +so 0002084 exonic_splice_region_variant +so 0002085 unidirectional_gene_fusion +so 0002086 bidirectional_gene_fusion +so 0002087 pseudogenic_CDS +so 0002088 non_coding_transcript_splice_region_variant +so 0002089 3_prime_UTR_exon_variant +so 0002090 3_prime_UTR_intron_variant +so 0002091 5_prime_UTR_intron_variant +so 0002092 5_prime_UTR_exon_variant +so 0002093 structural_interaction_variant +so 0002094 non_allelic_homologous_recombination_region +so 0002095 scaRNA +so 0002096 short_tandem_repeat_variation +so 0002097 vertebrate_immune_system_pseudogene +so 0002098 immunoglobulin_pseudogene +so 0002099 T_cell_receptor_pseudogene +so 0002100 IG_C_pseudogene +so 0002101 IG_J_pseudogene +so 0002102 IG_V_pseudogene +so 0002103 TR_V_pseudogene +so 0002104 TR_J_pseudogene +so 0002105 translated_processed_pseudogene +so 0002106 translated_unprocessed_pseudogene +so 0002107 transcribed_unprocessed_pseudogene +so 0002108 transcribed_unitary_pseudogene +so 0002109 transcribed_processed_pseudogene +so 0002110 polymorphic_pseudogene_with_retained_intron +so 0002111 pseudogene_processed_transcript +so 0002112 coding_transcript_with_retained_intron +so 0002113 lncRNA_with_retained_intron +so 0002114 NMD_transcript +so 0002115 pseudogenic_transcript_with_retained_intron +so 0002116 polymorphic_pseudogene_processed_transcript +so 0002117 +so 0002118 NMD_polymorphic_pseudogene_transcript +so 0002119 allelic_frequency +so 0002120 three_prime_overlapping_ncrna +so 0002121 vertebrate_immune_system_gene +so 0002122 immunoglobulin_gene +so 0002123 IG_C_gene +so 0002124 IG_D_gene +so 0002125 IG_J_gene +so 0002126 IG_V_gene +so 0002127 lncRNA_gene +so 0002128 mt_rRNA +so 0002129 mt_tRNA +so 0002130 NSD_transcript +so 0002131 sense_intronic_lncRNA +so 0002132 sense_overlap_lncRNA +so 0002133 T_cell_receptor_gene +so 0002134 TR_C_Gene +so 0002135 TR_D_Gene +so 0002136 TR_J_Gene +so 0002137 TR_V_Gene +so 0002138 predicted_transcript +so 0002139 unconfirmed_transcript +so 0002140 early_origin_of_replication +so 0002141 late_origin_of_replication +so 0002142 histone_2A_acetylation_site +so 0002143 histone_2B_acetylation_site +so 0002144 histone_2AZ_acetylation_site +so 0002145 H2AZK4_acetylation_site +so 0002146 H2AZK7_acetylation_site +so 0002147 H2AZK11_acetylation_site +so 0002148 H2AZK13_acetylation_site +so 0002149 H2AZK15_acetylation_site +so 0002150 AUG_initiated_uORF +so 0002151 non_AUG_initiated_uORF +so 0002152 genic_downstream_transcript_variant +so 0002153 genic_upstream_transcript_variant +so 0002154 mitotic_recombination_region +so 0002155 meiotic_recombination_region +so 0002156 CArG_box +so 0002157 Mat2P +so 0002158 Mat3M +so 0002159 SHP_box +so 0002160 sequence_length_variant +so 0002161 short_tandem_repeat_change +so 0002162 short_tandem_repeat_expansion +so 0002163 short_tandem_repeat_contraction +so 0002164 H2BK5_acetylation_site +so 0002165 trinucleotide_repeat_expansion +so 0002166 ref_miRNA +so 0002167 isomiR +so 0002168 RNA_thermometer +so 0002169 splice_polypyrimidine_tract_variant +so 0002170 splice_donor_region_variant +so 0002171 telomeric_D_loop +so 0002172 sequence_alteration_artifact +so 0002173 indel_artifact +so 0002174 deletion_artifact +so 0002175 insertion_artifact +so 0002176 substitution_artifact +so 0002177 duplication_artifact +so 0002178 SNV_artifact +so 0002179 MNV_artifact +so 0002180 enzymatic_RNA_gene +so 0002181 ribozyme_gene +so 0002182 antisense_lncRNA_gene +so 0002183 sense_overlap_lncRNA_gene +so 0002184 sense_intronic_lncRNA_gene +so 0002185 bidirectional_promoter_lncRNA_gene +so 0002186 mutational_hotspot +so 0002187 HERV_insertion +so 0002188 functional_gene_region +so 0002189 allelic_pseudogene +so 0002190 enhancer_blocking_element +so 0002191 imprinting_control_region +so 0002192 flanking_repeat +so 0002193 processed_pseudogenic_rRNA +so 0002194 unprocessed_pseudogenic_rRNA +so 0002195 unitary_pseudogenic_rRNA +so 0002196 allelic_pseudogenic_rRNA +so 0002197 processed_pseudogenic_tRNA +so 0002198 unprocessed_pseudogenic_tRNA +so 0002199 unitary_pseudogenic_tRNA +so 0002200 allelic_pseudogenic_tRNA +so 0002201 terminal_repeat +so 0002202 repeat_instability_region +so 0002203 replication_start_site +so 0002204 nucleotide_cleavage_site +so 0002205 response_element +so 0002206 sequence_source +so 0002207 UNAAAC_motif +so 0002208 long_terminal_repeat_transcript +so 0002209 genomic_DNA_contig +so 0002210 presence_absence_variation +so 0002211 circular_plasmid +so 0002212 linear_plasmid +so 0002213 transcription_termination_signal +so 0002214 redundant_inserted_stop_gained +so 0002215 Zas1_recognition_motif +so 0002216 Pho7_binding_site +so 0002217 unspecified_indel +so 0002218 functionally_abnormal +so 0002219 functionally_normal +so 0002220 function_uncertain_variant +so 0002221 eukaryotic_promoter +so 0002222 prokaryotic_promoter +so 0002223 inert_DNA_spacer +so 0002224 2A_self_cleaving_peptide_region +so 0002225 LOZ1_response_element +so 0002226 group_IIC_intron +so 0002227 CDS_extension +so 0002228 CDS_five_prime_extension +so 0002229 CDS_three_prime_extension +so 0002230 CAAX_box +so 0002231 self_cleaving_ribozyme +so 0002232 selection_marker +so 0002233 homologous_chromosome_recognition_and_pairing_locus +so 0002234 pumilio_response_element +so 0002235 SUMO_interaction_motif +so 0002236 cytosolic_rRNA_18S_gene +so 0002237 cytosolic_rRNA_16S_gene +so 0002238 cytosolic_rRNA_5S_gene +so 0002239 cytosolic_rRNA_28S_gene +so 0002240 cytosolic_rRNA_5_8S_gene +so 0002241 rRNA_21S_gene +so 0002242 cytosolic_rRNA_25S_gene +so 0002243 cytosolic_rRNA_23S_gene +so 0002244 partially_duplicated_transcript +so 0002245 five_prime_duplicated_transcript +so 0002246 three_prime_duplicated_transcript +so 0002247 sncRNA +so 0002248 spurious_protein +so 0002249 mature_protein_region_of_CDS +so 0002250 propeptide_region_of_CDS +so 0002251 signal_peptide_region_of_CDS +so 0002252 transit_peptide_region_of_CDS +so 0002253 stem_loop_region +so 0002254 loop +so 0002255 stem +so 0002256 non_complimentary_stem +so 0002257 knob +so 0002258 teb1_recognition_motif +so 0002259 polyA_site_cluster +so 0002260 LARD +so 0002261 TRIM +so 0002262 Watson_strand +so 0002263 Crick_strand +so 0002264 Copia_LTR_retrotransposon +so 0002265 Gypsy_LTR_retrotransposon +so 0002266 Bel_Pao_LTR_retrotransposon +so 0002267 Retrovirus_LTR_retrotransposon +so 0002268 Endogenous_Retrovirus_LTR_retrotransposon +so 0002269 R2_LINE_retrotransposon +so 0002270 RTE_LINE_retrotransposon +so 0002271 Jockey_LINE_retrotransposon +so 0002272 L1_LINE_retrotransposon +so 0002273 I_LINE_retrotransposon +so 0002274 tRNA_SINE_retrotransposon +so 0002275 7SL_SINE_retrotransposon +so 0002276 5S_SINE_retrotransposon +so 0002277 Crypton_YR_transposon +so 0002278 Tc1_Mariner_TIR_transposon +so 0002279 hAT_TIR_transposon +so 0002280 Mutator_TIR_transposon +so 0002281 Merlin_TIR_transposon +so 0002282 Transib_TIR_transposon +so 0002283 piggyBac_TIR_transposon +so 0002284 PIF_Harbinger_TIR_transposon +so 0002285 CACTA_TIR_transposon +so 0002286 YR_retrotransposon +so 0002287 DIRS_YR_retrotransposon +so 0002288 Ngaro_YR_retrotransposon +so 0002289 Viper_YR_retrotransposon +so 0002290 Penelope_retrotransposon +so 0002291 circular_ncRNA +so 0002292 circular_mRNA +so 0002293 mitochondrial_control_region +so 0002294 mitochondrial_D_loop +so 0002295 transcription_factor_regulatory_site +so 0002296 TFRS_module +so 0002297 TFRS_collection +so 0002298 simple_operon +so 0002299 complex_operon +so 0002300 unit_of_gene_expression +so 0002301 transcription_unit +so 0002302 simple_regulon +so 0002303 complex_regulon +so 0002304 topologically_associated_domain +so 0002305 topologically_associated_domain_boundary +so 0002306 chromatin_regulatory_region +so 0002307 DNA_loop +so 0002308 DNA_loop_anchor +so 0002309 core_promoter_element +so 0002310 cryptic_promoter +so 0002311 viral_promoter +so 0002312 core_prokaryotic_promoter_element +so 0002313 core_viral_promoter_element +so 0002314 altered_gene_product_level +so 0002315 increased_gene_product_level +so 0002316 decreased_gene_product_level +so 0002317 absent_gene_product +so 0002318 altered_gene_product_sequence +so 0002319 NMD_triggering_variant +so 0002320 NMD_escaping_variant +so 0002321 stop_gained_NMD_triggering +so 0002322 stop_gained_NMD_escaping +so 0002323 frameshift_variant_NMD_triggering +so 0002324 frameshift_variant_NMD_escaping +so 0002325 splice_donor_variant_NMD_triggering +so 0002326 splice_donor_variant_NMD_escaping +so 0002327 splice_acceptor_variant_NMD_triggering +so 0002328 splice_acceptor_variant_NMD_escaping +so 0002329 minus_1_translational_frameshift +so 0002330 minus_2_translational_frameshift +so 0002331 accessible_DNA_region +so 0002332 epigenomically_modified_region +so 0002333 amber_stop_codon +so 0002334 ochre_stop_codon +so 0002335 opal_stop_codon +so 0002336 cytosolic_rRNA_2S_gene +so 0002337 cytosolic_2S_rRNA +so 0002338 U7_snRNA +so 0002339 scaRNA_gene +so 0002340 RNA_7SK +so 0002341 RNA_7SK_gene +so 0002342 sncRNA_gene +so 0002343 cytosolic_rRNA +so 0002344 mt_SSU_rRNA +so 0002345 mt_LSU_rRNA +so 0002346 plastid_rRNA +so 0002347 plastid_SSU_rRNA +so 0002348 plastid_LSU_rRNA +so 0002349 fragile_site +so 0002350 common_fragile_site +so 0002351 rare_fragile_site +so 0002352 sisRNA +so 0002353 sbRNA_gene +so 0002354 sbRNA +so 0002355 hpRNA_gene +so 0002356 hpRNA +so 0002357 biosynthetic_gene_cluster +so 0002358 vault_RNA_gene +so 0002359 Y_RNA_gene +so 0002360 cytosolic_rRNA_gene +so 0002361 cytosolic_LSU_rRNA_gene +so 0002362 cytosolic_SSU_rRNA_gene +so 0002363 mt_rRNA_gene +so 0002364 mt_LSU_rRNA_gene +so 0002365 mt_SSU_rRNA_gene +so 0002366 plastid_rRNA_gene +so 0002367 plastid_LSU_rRNA_gene +so 0002368 plastid_SSU_rRNA_gene +so 0002369 C_D_box_scaRNA +so 0002370 H_ACA_box_scaRNA +so 0002371 C-D_H_ACA_box_scaRNA +so 0002372 C_D_box_scaRNA_gene +so 0002373 H_ACA_box_scaRNA_gene +so 0002374 C-D_H_ACA_box_scaRNA_gene +so 0002375 C_D_box_snoRNA_gene +so 0002376 H_ACA_box_snoRNA_gene +so 0002377 U14_snoRNA_gene +so 0002378 U3_snoRNA_gene +so 0002379 methylation_guide_snoRNA_gene +so 0002380 pseudouridylation_guide_snoRNA_gene +so 0002381 bidirectional_promoter_lncRNA +so 0002382 range_extender_element +so 0002383 oncogenic_variant +so 0005836 regulatory_region +so 0005837 U14_snoRNA_primary_transcript +so 0005841 methylation_guide_snoRNA +so 0005843 rRNA_cleavage_RNA +so 0005845 exon_of_single_exon_gene +so 0005847 cassette_array_member +so 0005848 gene_cassette_member +so 0005849 gene_subarray_member +so 0005850 primer_binding_site +so 0005851 gene_array +so 0005852 gene_subarray +so 0005853 gene_cassette +so 0005854 gene_cassette_array +so 0005855 gene_group +so 0005856 selenocysteine_tRNA_primary_transcript +so 0005857 selenocysteinyl_tRNA +so 0005858 syntenic_region +so 0100001 biochemical_region_of_peptide +so 0100002 molecular_contact_region +so 0100003 intrinsically_unstructured_polypeptide_region +so 0100004 catmat_left_handed_three +so 0100005 catmat_left_handed_four +so 0100006 catmat_right_handed_three +so 0100007 catmat_right_handed_four +so 0100008 alpha_beta_motif +so 0100009 lipoprotein_signal_peptide +so 0100010 no_output +so 0100011 cleaved_peptide_region +so 0100012 peptide_coil +so 0100013 hydrophobic_region_of_peptide +so 0100014 n_terminal_region +so 0100015 c_terminal_region +so 0100016 central_hydrophobic_region_of_signal_peptide +so 0100017 polypeptide_conserved_motif +so 0100018 polypeptide_binding_motif +so 0100019 polypeptide_catalytic_motif +so 0100020 polypeptide_DNA_contact +so 0100021 polypeptide_conserved_region +so 1000002 substitution +so 1000005 complex_substitution +so 1000008 point_mutation +so 1000009 transition +so 1000010 pyrimidine_transition +so 1000011 C_to_T_transition +so 1000012 C_to_T_transition_at_pCpG_site +so 1000013 T_to_C_transition +so 1000014 purine_transition +so 1000015 A_to_G_transition +so 1000016 G_to_A_transition +so 1000017 transversion +so 1000018 pyrimidine_to_purine_transversion +so 1000019 C_to_A_transversion +so 1000020 C_to_G_transversion +so 1000021 T_to_A_transversion +so 1000022 T_to_G_transversion +so 1000023 purine_to_pyrimidine_transversion +so 1000024 A_to_C_transversion +so 1000025 A_to_T_transversion +so 1000026 G_to_C_transversion +so 1000027 G_to_T_transversion +so 1000028 intrachromosomal_mutation +so 1000029 chromosomal_deletion +so 1000030 chromosomal_inversion +so 1000031 interchromosomal_mutation +so 1000032 delins +so 1000035 duplication +so 1000036 inversion +so 1000037 chromosomal_duplication +so 1000038 intrachromosomal_duplication +so 1000039 direct_tandem_duplication +so 1000040 inverted_tandem_duplication +so 1000041 intrachromosomal_transposition +so 1000042 compound_chromosome +so 1000043 Robertsonian_fusion +so 1000044 chromosomal_translocation +so 1000045 ring_chromosome +so 1000046 pericentric_inversion +so 1000047 paracentric_inversion +so 1000048 reciprocal_chromosomal_translocation +so 1000049 sequence_variation_affecting_transcript +so 1000050 sequence_variant_causing_no_change_in_transcript +so 1000054 sequence_variation_affecting_coding_sequence +so 1000055 sequence_variant_causing_initiator_codon_change_in_transcript +so 1000056 sequence_variant_causing_amino_acid_coding_codon_change_in_transcript +so 1000057 sequence_variant_causing_synonymous_codon_change_in_transcript +so 1000058 sequence_variant_causing_non_synonymous_codon_change_in_transcript +so 1000059 sequence_variant_causing_missense_codon_change_in_transcript +so 1000060 sequence_variant_causing_conservative_missense_codon_change_in_transcript +so 1000061 sequence_variant_causing_nonconservative_missense_codon_change_in_transcript +so 1000062 sequence_variant_causing_nonsense_codon_change_in_transcript +so 1000063 sequence_variant_causing_terminator_codon_change_in_transcript +so 1000064 sequence_variation_affecting_reading_frame +so 1000065 frameshift_sequence_variation +so 1000066 sequence_variant_causing_plus_1_frameshift_mutation +so 1000067 sequence_variant_causing_minus_1_frameshift +so 1000068 sequence_variant_causing_plus_2_frameshift +so 1000069 sequence_variant_causing_minus_2_frameshift +so 1000070 sequence_variant_affecting_transcript_processing +so 1000071 sequence_variant_affecting_splicing +so 1000072 sequence_variant_affecting_splice_donor +so 1000073 sequence_variant_affecting_splice_acceptor +so 1000074 sequence_variant_causing_cryptic_splice_activation +so 1000075 sequence_variant_affecting_editing +so 1000076 sequence_variant_affecting_transcription +so 1000078 sequence_variant_decreasing_rate_of_transcription +so 1000079 sequence_variation_affecting_transcript_sequence +so 1000080 sequence_variant_increasing_rate_of_transcription +so 1000081 sequence_variant_affecting_rate_of_transcription +so 1000082 sequence variant_affecting_transcript_stability +so 1000083 sequence_variant_increasing_transcript_stability +so 1000084 sequence_variant_decreasing_transcript_stability +so 1000085 sequence_variation_affecting_level_of_transcript +so 1000086 sequence_variation_decreasing_level_of_transcript +so 1000087 sequence_variation_increasing_level_of_transcript +so 1000088 sequence_variant_affecting_translational_product +so 1000089 sequence_variant_causing_no_change_of_translational_product +so 1000092 sequence_variant_causing_complex_change_of_translational_product +so 1000093 sequence_variant_causing_amino_acid_substitution +so 1000094 sequence_variant_causing_conservative_amino_acid_substitution +so 1000095 sequence_variant_causing_nonconservative_amino_acid_substitution +so 1000096 sequence_variant_causing_amino_acid_insertion +so 1000097 sequence_variant_causing_amino_acid_deletion +so 1000098 sequence_variant_causing_polypeptide_truncation +so 1000099 sequence_variant_causing_polypeptide_elongation +so 1000100 mutation_causing_polypeptide_N_terminal_elongation +so 1000101 mutation_causing_polypeptide_C_terminal_elongation +so 1000102 sequence_variant_affecting_level_of_translational_product +so 1000103 sequence_variant_decreasing_level_of_translation_product +so 1000104 sequence_variant_increasing_level_of_translation_product +so 1000105 sequence_variant_affecting_polypeptide_amino_acid_sequence +so 1000106 mutation_causing_inframe_polypeptide_N_terminal_elongation +so 1000107 mutation_causing_out_of_frame_polypeptide_N_terminal_elongation +so 1000108 mutaton_causing_inframe_polypeptide_C_terminal_elongation +so 1000109 mutation_causing_out_of_frame_polypeptide_C_terminal_elongation +so 1000110 frame_restoring_sequence_variant +so 1000111 sequence_variant_affecting_3D_structure_of_polypeptide +so 1000112 sequence_variant_causing_no_3D_structural_change +so 1000115 sequence_variant_causing_complex_3D_structural_change +so 1000116 sequence_variant_causing_conformational_change +so 1000117 sequence_variant_affecting_polypeptide_function +so 1000118 sequence_variant_causing_loss_of_function_of_polypeptide +so 1000119 sequence_variant_causing_inactive_ligand_binding_site +so 1000120 sequence_variant_causing_inactive_catalytic_site +so 1000121 sequence_variant_causing_polypeptide_localization_change +so 1000122 sequence_variant_causing_polypeptide_post_translational_processing_change +so 1000123 polypeptide_post_translational_processing_affected +so 1000124 sequence_variant_causing_partial_loss_of_function_of_polypeptide +so 1000125 sequence_variant_causing_gain_of_function_of_polypeptide +so 1000126 sequence_variant_affecting_transcript_secondary_structure +so 1000127 sequence_variant_causing_compensatory_transcript_secondary_structure_mutation +so 1000132 sequence_variant_effect +so 1000134 sequence_variant_causing_polypeptide_fusion +so 1000136 autosynaptic_chromosome +so 1000138 homo_compound_chromosome +so 1000140 hetero_compound_chromosome +so 1000141 chromosome_fission +so 1000142 dextrosynaptic_chromosome +so 1000143 laevosynaptic_chromosome +so 1000144 free_duplication +so 1000145 free_ring_duplication +so 1000147 deficient_translocation +so 1000148 inversion_cum_translocation +so 1000149 bipartite_duplication +so 1000150 cyclic_translocation +so 1000151 bipartite_inversion +so 1000152 uninverted_insertional_duplication +so 1000153 inverted_insertional_duplication +so 1000154 insertional_duplication +so 1000155 interchromosomal_transposition +so 1000156 inverted_interchromosomal_transposition +so 1000157 uninverted_interchromosomal_transposition +so 1000158 inverted_intrachromosomal_transposition +so 1000159 uninverted_intrachromosomal_transposition +so 1000160 unoriented_insertional_duplication +so 1000161 unoriented_interchromosomal_transposition +so 1000162 unoriented_intrachromosomal_transposition +so 1000170 uncharacterized_chromosomal_mutation +so 1000171 deficient_inversion +so 1000173 tandem_duplication +so 1000175 partially_characterized_chromosomal_mutation +so 1000180 sequence_variant_affecting_gene_structure +so 1000181 sequence_variant_causing_gene_fusion +so 1000182 chromosome_number_variation +so 1000183 chromosome_structure_variation +so 1000184 sequence_variant_causes_exon_loss +so 1000185 sequence_variant_causes_intron_gain +so 1000186 sequence_variant_causing_cryptic_splice_donor_activation +so 1001186 sequence_variant_causing_cryptic_splice_acceptor_activation +so 1001187 alternatively_spliced_transcript +so 1001188 encodes_1_polypeptide +so 1001189 encodes_greater_than_1_polypeptide +so 1001190 encodes_different_polypeptides_different_stop +so 1001191 encodes_overlapping_peptides_different_start +so 1001192 encodes_disjoint_polypeptides +so 1001193 encodes_overlapping_polypeptides_different_start_and_stop +so 1001194 alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping +so 1001195 encodes_overlapping_peptides +so 1001196 cryptogene +so 1001197 dicistronic_primary_transcript +so 1001217 member_of_regulon +so 1001244 alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping +so 1001246 CDS_independently_known +so 1001247 orphan_CDS +so 1001249 CDS_supported_by_domain_match_data +so 1001251 CDS_supported_by_sequence_similarity_data +so 1001254 CDS_predicted +so 1001255 status_of_coding_sequence +so 1001259 CDS_supported_by_EST_or_cDNA_data +so 1001260 internal_Shine_Dalgarno_sequence +so 1001261 recoded_mRNA +so 1001262 minus_1_translationally_frameshifted +so 1001263 plus_1_translationally_frameshifted +so 1001264 mRNA_recoded_by_translational_bypass +so 1001265 mRNA_recoded_by_codon_redefinition +so 1001266 stop_codon_redefinition_as_selenocysteine +so 1001267 stop_codon_readthrough +so 1001268 recoding_stimulatory_region +so 1001269 four_bp_start_codon +so 1001270 stop_codon_redefinition_as_pyrrolysine +so 1001271 archaeal_intron +so 1001272 tRNA_intron +so 1001273 CTG_start_codon +so 1001274 SECIS_element +so 1001275 retron +so 1001277 three_prime_recoding_site +so 1001279 three_prime_stem_loop_structure +so 1001280 five_prime_recoding_site +so 1001281 flanking_three_prime_quadruplet_recoding_signal +so 1001282 UAG_stop_codon_signal +so 1001283 UAA_stop_codon_signal +so 1001284 regulon +so 1001285 UGA_stop_codon_signal +so 1001286 three_prime_repeat_recoding_signal +so 1001287 distant_three_prime_recoding_signal +so 1001288 stop_codon_signal +so 2000061 databank_entry +so 3000000 gene_segment diff --git a/src/pyobo/sources/flybase.py b/src/pyobo/sources/flybase.py index 0ebfb028..a088602e 100644 --- a/src/pyobo/sources/flybase.py +++ b/src/pyobo/sources/flybase.py @@ -7,6 +7,7 @@ from tqdm.auto import tqdm from pyobo import Reference +from pyobo.resources.so import get_so_name from pyobo.struct import Obo, Term, from_species, orthologous from pyobo.utils.io import multisetdict from pyobo.utils.path import ensure_df @@ -133,7 +134,7 @@ def get_terms(version: str, force: bool = False) -> Iterable[Term]: "FlyBase gene type is missing mapping to Sequence Ontology (SO): %s", gtype ) else: - so[gtype] = Reference.auto("SO", so_id) + so[gtype] = Reference(prefix="SO", identifier=so_id, name=get_so_name(so_id)) for _, reference in sorted(so.items()): yield Term(reference=reference) diff --git a/src/pyobo/sources/hgnc.py b/src/pyobo/sources/hgnc.py index 61b1db86..bd47eef6 100644 --- a/src/pyobo/sources/hgnc.py +++ b/src/pyobo/sources/hgnc.py @@ -13,6 +13,7 @@ from tqdm.auto import tqdm from pyobo.api.utils import get_version +from pyobo.resources.so import get_so_name from pyobo.struct import ( Obo, Reference, @@ -222,7 +223,7 @@ class HGNCGetter(Obo): alias_symbol_type, ] root_terms = [ - Reference(prefix="so", identifier=so_id) + Reference(prefix="SO", identifier=so_id, name=get_so_name(so_id)) for so_id in sorted(set(LOCUS_TYPE_TO_SO.values())) if so_id ] @@ -256,7 +257,7 @@ def get_terms(version: Optional[str] = None, force: bool = False) -> Iterable[Te yield Term.from_triple("NCBITaxon", "9606", "Homo sapiens") yield from sorted( { - Term(reference=Reference.auto("SO", so_id)) + Term(reference=Reference(prefix="SO", identifier=so_id, name=get_so_name(so_id))) for so_id in sorted(LOCUS_TYPE_TO_SO.values()) if so_id }, @@ -418,9 +419,11 @@ def get_terms(version: Optional[str] = None, force: bool = False) -> Iterable[Te locus_group = entry.pop("locus_group") so_id = LOCUS_TYPE_TO_SO.get(locus_type) if so_id: - term.append_parent(Reference.auto("SO", so_id)) + term.append_parent(Reference(prefix="SO", identifier=so_id, name=get_so_name(so_id))) else: - term.append_parent(Reference.auto("SO", "0000704")) # gene + term.append_parent( + Reference(prefix="SO", identifier="0000704", name=get_so_name("0000704")) + ) # gene unhandle_locus_types[locus_type][identifier] = term term.append_property("locus_type", locus_type) term.append_property("locus_group", locus_group) diff --git a/src/pyobo/sources/pombase.py b/src/pyobo/sources/pombase.py index 776de7e2..98052c0f 100644 --- a/src/pyobo/sources/pombase.py +++ b/src/pyobo/sources/pombase.py @@ -9,6 +9,7 @@ import pyobo from pyobo import Reference +from pyobo.resources.so import get_so_name from pyobo.struct import Obo, Term, from_species, has_gene_product, orthologous from pyobo.utils.path import ensure_df @@ -70,7 +71,9 @@ def get_terms(version: str, force: bool = False) -> Iterable[Term]: df = ensure_df(PREFIX, url=GENE_NAMES_URL, force=force, version=version) so = { - gtype: Reference.auto("SO", POMBASE_TO_SO[gtype]) + gtype: Reference( + prefix="SO", identifier=POMBASE_TO_SO[gtype], name=get_so_name(POMBASE_TO_SO[gtype]) + ) for gtype in sorted(df[df.columns[6]].unique()) } for _, reference in sorted(so.items()): diff --git a/src/pyobo/sources/zfin.py b/src/pyobo/sources/zfin.py index 39451f88..1c745334 100644 --- a/src/pyobo/sources/zfin.py +++ b/src/pyobo/sources/zfin.py @@ -7,6 +7,7 @@ from tqdm.auto import tqdm +from pyobo.resources.so import get_so_name from pyobo.struct import ( Obo, Reference, @@ -113,7 +114,9 @@ def get_terms(force: bool = False, version: Optional[str] = None) -> Iterable[Te ) df["sequence_ontology_id"] = df["sequence_ontology_id"].map(lambda x: x[len("SO:") :]) so = { - sequence_ontology_id: Reference.auto(prefix="SO", identifier=sequence_ontology_id) + sequence_ontology_id: Reference( + prefix="SO", identifier=sequence_ontology_id, name=get_so_name(sequence_ontology_id) + ) for sequence_ontology_id in df["sequence_ontology_id"].unique() } for _, reference in sorted(so.items()):