tripal_chado/chado_schema/parts-v1.3/default_schema-1.3.part33.sql
SET search_path = so,chado,pg_catalog;
--- *** relation: benign_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW benign_variant AS
SELECT
feature_id AS benign_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'benign_variant';
--- ************************************************
--- *** relation: disease_associated_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW disease_associated_variant AS
SELECT
feature_id AS disease_associated_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'disease_associated_variant';
--- ************************************************
--- *** relation: disease_causing_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW disease_causing_variant AS
SELECT
feature_id AS disease_causing_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'disease_causing_variant';
--- ************************************************
--- *** relation: lethal_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW lethal_variant AS
SELECT
feature_id AS lethal_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'lethal_variant';
--- ************************************************
--- *** relation: quantitative_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW quantitative_variant AS
SELECT
feature_id AS quantitative_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'quantitative_variant';
--- ************************************************
--- *** relation: maternal_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW maternal_variant AS
SELECT
feature_id AS maternal_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'maternal_variant';
--- ************************************************
--- *** relation: paternal_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW paternal_variant AS
SELECT
feature_id AS paternal_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'paternal_variant';
--- ************************************************
--- *** relation: somatic_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW somatic_variant AS
SELECT
feature_id AS somatic_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'somatic_variant';
--- ************************************************
--- *** relation: germline_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW germline_variant AS
SELECT
feature_id AS germline_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'germline_variant';
--- ************************************************
--- *** relation: pedigree_specific_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW pedigree_specific_variant AS
SELECT
feature_id AS pedigree_specific_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'pedigree_specific_variant';
--- ************************************************
--- *** relation: population_specific_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW population_specific_variant AS
SELECT
feature_id AS population_specific_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'population_specific_variant';
--- ************************************************
--- *** relation: de_novo_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW de_novo_variant AS
SELECT
feature_id AS de_novo_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'de_novo_variant';
--- ************************************************
--- *** relation: tf_binding_site_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant located within a tran ***
--- *** scription factor binding site. ***
--- ************************************************
---
CREATE VIEW tf_binding_site_variant AS
SELECT
feature_id AS tf_binding_site_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'TF_binding_site_variant';
--- ************************************************
--- *** relation: missense_codon ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant whereby at least one ***
--- *** base of a codon is changed resulting in ***
--- *** a codon that encodes for a different ami ***
--- *** no acid. ***
--- ************************************************
---
CREATE VIEW missense_codon AS
SELECT
feature_id AS missense_codon_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'missense_codon';
--- ************************************************
--- *** relation: complex_structural_alteration ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A structural sequence alteration where t ***
--- *** here are multiple equally plausible expl ***
--- *** anations for the change. ***
--- ************************************************
---
CREATE VIEW complex_structural_alteration AS
SELECT
feature_id AS complex_structural_alteration_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'complex_structural_alteration';
--- ************************************************
--- *** relation: structural_alteration ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW structural_alteration AS
SELECT
feature_id AS structural_alteration_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'complex_structural_alteration' OR cvterm.name = 'structural_alteration';
--- ************************************************
--- *** relation: loss_of_heterozygosity ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW loss_of_heterozygosity AS
SELECT
feature_id AS loss_of_heterozygosity_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'loss_of_heterozygosity';
--- ************************************************
--- *** relation: splice_donor_5th_base_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that causes a change ***
--- *** at the 5th base pair after the start of ***
--- *** the intron in the orientation of the tra ***
--- *** nscript. ***
--- ************************************************
---
CREATE VIEW splice_donor_5th_base_variant AS
SELECT
feature_id AS splice_donor_5th_base_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'splice_donor_5th_base_variant';
--- ************************************************
--- *** relation: u_box ***
--- *** relation type: VIEW ***
--- *** ***
--- *** An U-box is a conserved T-rich region up ***
--- *** stream of a retroviral polypurine tract ***
--- *** that is involved in PPT primer creation ***
--- *** during reverse transcription. ***
--- ************************************************
---
CREATE VIEW u_box AS
SELECT
feature_id AS u_box_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'U_box';
--- ************************************************
--- *** relation: mating_type_region ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A specialized region in the genomes of s ***
--- *** ome yeast and fungi, the genes of which ***
--- *** regulate mating type. ***
--- ************************************************
---
CREATE VIEW mating_type_region AS
SELECT
feature_id AS mating_type_region_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'mating_type_region';
--- ************************************************
--- *** relation: paired_end_fragment ***
--- *** relation type: VIEW ***
--- *** ***
--- *** An assembly region that has been sequenc ***
--- *** ed from both ends resulting in a read_pa ***
--- *** ir (mate_pair). ***
--- ************************************************
---
CREATE VIEW paired_end_fragment AS
SELECT
feature_id AS paired_end_fragment_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'paired_end_fragment';
--- ************************************************
--- *** relation: exon_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that changes exon seq ***
--- *** uence. ***
--- ************************************************
---
CREATE VIEW exon_variant AS
SELECT
feature_id AS exon_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'coding_sequence_variant' OR cvterm.name = 'non_coding_exon_variant' OR cvterm.name = 'codon_variant' OR cvterm.name = 'frameshift_variant' OR cvterm.name = 'inframe_variant' OR cvterm.name = 'initiator_codon_change' OR cvterm.name = 'non_synonymous_codon' OR cvterm.name = 'synonymous_codon' OR cvterm.name = 'terminal_codon_variant' OR cvterm.name = 'stop_gained' OR cvterm.name = 'missense_codon' OR cvterm.name = 'conservative_missense_codon' OR cvterm.name = 'non_conservative_missense_codon' OR cvterm.name = 'terminator_codon_variant' OR cvterm.name = 'incomplete_terminal_codon_variant' OR cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'frame_restoring_variant' OR cvterm.name = 'minus_1_frameshift_variant' OR cvterm.name = 'minus_2_frameshift_variant' OR cvterm.name = 'plus_1_frameshift_variant' OR cvterm.name = 'plus_2_frameshift variant' OR cvterm.name = 'inframe_codon_gain' OR cvterm.name = 'inframe_codon_loss' OR cvterm.name = 'exon_variant';
--- ************************************************
--- *** relation: non_coding_exon_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that changes non-codi ***
--- *** ng exon sequence. ***
--- ************************************************
---
CREATE VIEW non_coding_exon_variant AS
SELECT
feature_id AS non_coding_exon_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'non_coding_exon_variant';
--- ************************************************
--- *** relation: clone_end ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A read from an end of the clone sequence ***
--- *** . ***
--- ************************************************
---
CREATE VIEW clone_end AS
SELECT
feature_id AS clone_end_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'clone_end';
--- ************************************************
--- *** relation: point_centromere ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A point centromere is a relatively small ***
--- *** centromere (about 125 bp DNA) in discre ***
--- *** te sequence, found in some yeast includi ***
--- *** ng S. cerevisiae. ***
--- ************************************************
---
CREATE VIEW point_centromere AS
SELECT
feature_id AS point_centromere_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'point_centromere';
--- ************************************************
--- *** relation: regional_centromere ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A regional centromere is a large modular ***
--- *** centromere found in fission yeast and h ***
--- *** igher eukaryotes. It consist of a centra ***
--- *** l core region flanked by inverted inner ***
--- *** and outer repeat regions. ***
--- ************************************************
---
CREATE VIEW regional_centromere AS
SELECT
feature_id AS regional_centromere_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'regional_centromere';
--- ************************************************
--- *** relation: regional_centromere_central_core ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A conserved region within the central re ***
--- *** gion of a modular centromere, where the ***
--- *** kinetochore is formed. ***
--- ************************************************
---
CREATE VIEW regional_centromere_central_core AS
SELECT
feature_id AS regional_centromere_central_core_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'regional_centromere_central_core';
--- ************************************************
--- *** relation: centromeric_repeat ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A repeat region found within the modular ***
--- *** centromere. ***
--- ************************************************
---
CREATE VIEW centromeric_repeat AS
SELECT
feature_id AS centromeric_repeat_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'regional_centromere_inner_repeat_region' OR cvterm.name = 'regional_centromere_outer_repeat_region' OR cvterm.name = 'centromeric_repeat';
--- ************************************************
--- *** relation: regional_centromere_inner_repeat_region ***
--- *** relation type: VIEW ***
--- *** ***
--- *** The inner repeat region of a modular cen ***
--- *** tromere. This region is adjacent to the ***
--- *** central core, on each chromosome arm. ***
--- ************************************************
---
CREATE VIEW regional_centromere_inner_repeat_region AS
SELECT
feature_id AS regional_centromere_inner_repeat_region_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'regional_centromere_inner_repeat_region';
--- ************************************************
--- *** relation: regional_centromere_outer_repeat_region ***
--- *** relation type: VIEW ***
--- *** ***
--- *** The heterochromatic outer repeat region ***
--- *** of a modular centromere. These repeats e ***
--- *** xist in tandem arrays on both chromosome ***
--- *** arms. ***
--- ************************************************
---
CREATE VIEW regional_centromere_outer_repeat_region AS
SELECT
feature_id AS regional_centromere_outer_repeat_region_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'regional_centromere_outer_repeat_region';
--- ************************************************
--- *** relation: tasirna ***
--- *** relation type: VIEW ***
--- *** ***
--- *** The sequence of a 21 nucleotide double s ***
--- *** tranded, polyadenylated non coding RNA, ***
--- *** transcribed from the TAS gene. ***
--- ************************************************
---
CREATE VIEW tasirna AS
SELECT
feature_id AS tasirna_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'tasiRNA';
--- ************************************************
--- *** relation: tasirna_primary_transcript ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A primary transcript encoding a tasiRNA. ***
--- ************************************************
---
CREATE VIEW tasirna_primary_transcript AS
SELECT
feature_id AS tasirna_primary_transcript_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'tasiRNA_primary_transcript';
--- ************************************************
--- *** relation: increased_polyadenylation_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A transcript processing variant whereby ***
--- *** polyadenylation of the encoded transcrip ***
--- *** t is increased with respect to the refer ***
--- *** ence. ***
--- ************************************************
---
CREATE VIEW increased_polyadenylation_variant AS
SELECT
feature_id AS increased_polyadenylation_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'increased_polyadenylation_variant';
--- ************************************************
--- *** relation: decreased_polyadenylation_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A transcript processing variant whereby ***
--- *** polyadenylation of the encoded transcrip ***
--- *** t is decreased with respect to the refer ***
--- *** ence. ***
--- ************************************************
---
CREATE VIEW decreased_polyadenylation_variant AS
SELECT
feature_id AS decreased_polyadenylation_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'decreased_polyadenylation_variant';
--- ************************************************
--- *** relation: regulatory_region ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A region of sequence that is involved in ***
--- *** the control of a biological process. ***
--- ************************************************
---
CREATE VIEW regulatory_region AS
SELECT
feature_id AS regulatory_region_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'transcription_regulatory_region' OR cvterm.name = 'translation_regulatory_region' OR cvterm.name = 'recombination_regulatory_region' OR cvterm.name = 'replication_regulatory_region' OR cvterm.name = 'terminator' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'polyA_signal_sequence' OR cvterm.name = 'gene_group_regulatory_region' OR cvterm.name = 'transcriptional_cis_regulatory_region' OR cvterm.name = 'splicing_regulatory_region' OR cvterm.name = 'cis_regulatory_frameshift_element' OR cvterm.name = 'intronic_regulatory_region' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'eukaryotic_terminator' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'terminator_of_type_2_RNApol_III_promoter' OR cvterm.name = 'operator' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'bacterial_terminator' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'rho_dependent_bacterial_terminator' OR cvterm.name = 'rho_independent_bacterial_terminator' OR cvterm.name = 'promoter' OR cvterm.name = 'insulator' OR cvterm.name = 'CRM' OR cvterm.name = 'promoter_targeting_sequence' OR cvterm.name = 'ISRE' OR cvterm.name = 'bidirectional_promoter' OR cvterm.name = 'RNA_polymerase_promoter' OR cvterm.name = 'RNApol_I_promoter' OR cvterm.name = 'RNApol_II_promoter' OR cvterm.name = 'RNApol_III_promoter' OR cvterm.name = 'bacterial_RNApol_promoter' OR cvterm.name = 'Phage_RNA_Polymerase_Promoter' OR cvterm.name = 'RNApol_II_core_promoter' OR cvterm.name = 'RNApol_III_promoter_type_1' OR cvterm.name = 'RNApol_III_promoter_type_2' OR cvterm.name = 'RNApol_III_promoter_type_3' OR cvterm.name = 'bacterial_RNApol_promoter_sigma_70' OR cvterm.name = 'bacterial_RNApol_promoter_sigma54' OR cvterm.name = 'SP6_RNA_Polymerase_Promoter' OR cvterm.name = 'T3_RNA_Polymerase_Promoter' OR cvterm.name = 'T7_RNA_Polymerase_Promoter' OR cvterm.name = 'locus_control_region' OR cvterm.name = 'enhancer' OR cvterm.name = 'silencer' OR cvterm.name = 'enhancer_bound_by_factor' OR cvterm.name = 'shadow_enhancer' OR cvterm.name = 'splice_enhancer' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'exonic_splice_enhancer' OR cvterm.name = 'attenuator' OR cvterm.name = 'regulatory_region';
--- ************************************************
--- *** relation: u14_snorna_primary_transcript ***
--- *** relation type: VIEW ***
--- *** ***
--- *** The primary transcript of an evolutionar ***
--- *** ily conserved eukaryotic low molecular w ***
--- *** eight RNA capable of intermolecular hybr ***
--- *** idization with both homologous and heter ***
--- *** ologous 18S rRNA. ***
--- ************************************************
---
CREATE VIEW u14_snorna_primary_transcript AS
SELECT
feature_id AS u14_snorna_primary_transcript_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'U14_snoRNA_primary_transcript';
--- ************************************************
--- *** relation: methylation_guide_snorna ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A snoRNA that specifies the site of 2'-O ***
--- *** -ribose methylation in an RNA molecule b ***
--- *** y base pairing with a short sequence aro ***
--- *** und the target residue. ***
--- ************************************************
---
CREATE VIEW methylation_guide_snorna AS
SELECT
feature_id AS methylation_guide_snorna_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'methylation_guide_snoRNA';
--- ************************************************
--- *** relation: rrna_cleavage_rna ***
--- *** relation type: VIEW ***
--- *** ***
--- *** An ncRNA that is part of a ribonucleopro ***
--- *** tein that cleaves the primary pre-rRNA t ***
--- *** ranscript in the process of producing ma ***
--- *** ture rRNA molecules. ***
--- ************************************************
---
CREATE VIEW rrna_cleavage_rna AS
SELECT
feature_id AS rrna_cleavage_rna_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'rRNA_cleavage_RNA';
--- ************************************************
--- *** relation: exon_of_single_exon_gene ***
--- *** relation type: VIEW ***
--- *** ***
--- *** An exon that is the only exon in a gene. ***
--- ************************************************
---
CREATE VIEW exon_of_single_exon_gene AS
SELECT
feature_id AS exon_of_single_exon_gene_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'exon_of_single_exon_gene';
--- ************************************************
--- *** relation: cassette_array_member ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW cassette_array_member AS
SELECT
feature_id AS cassette_array_member_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'cassette_array_member';
--- ************************************************
--- *** relation: gene_cassette_member ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW gene_cassette_member AS
SELECT
feature_id AS gene_cassette_member_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'cassette_array_member' OR cvterm.name = 'gene_cassette_member';
--- ************************************************
--- *** relation: gene_subarray_member ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW gene_subarray_member AS
SELECT
feature_id AS gene_subarray_member_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'gene_subarray_member';
--- ************************************************
--- *** relation: primer_binding_site ***
--- *** relation type: VIEW ***
--- *** ***
--- *** Non-covalent primer binding site for ini ***
--- *** tiation of replication, transcription, o ***
--- *** r reverse transcription. ***
--- ************************************************
---
CREATE VIEW primer_binding_site AS
SELECT
feature_id AS primer_binding_site_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'primer_binding_site';
--- ************************************************
--- *** relation: gene_array ***
--- *** relation type: VIEW ***
--- *** ***
--- *** An array includes two or more genes, or ***
--- *** two or more gene subarrays, contiguously ***
--- *** arranged where the individual genes, or ***
--- *** subarrays, are either identical in sequ ***
--- *** ence, or essentially so. ***
--- ************************************************
---
CREATE VIEW gene_array AS
SELECT
feature_id AS gene_array_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'gene_array';
--- ************************************************
--- *** relation: gene_subarray ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A subarray is, by defintition, a member ***
--- *** of a gene array (SO:0005851); the member ***
--- *** s of a subarray may differ substantially ***
--- *** in sequence, but are closely related in ***
--- *** function. ***
--- ************************************************
---
CREATE VIEW gene_subarray AS
SELECT
feature_id AS gene_subarray_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'gene_subarray';
--- ************************************************
--- *** relation: gene_cassette ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A gene that can be substituted for a rel ***
--- *** ated gene at a different site in the gen ***
--- *** ome. ***
--- ************************************************
---
CREATE VIEW gene_cassette AS
SELECT
feature_id AS gene_cassette_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'gene_cassette';
--- ************************************************
--- *** relation: gene_cassette_array ***
--- *** relation type: VIEW ***
--- *** ***
--- *** An array of non-functional genes whose m ***
--- *** embers, when captured by recombination f ***
--- *** orm functional genes. ***
--- ************************************************
---
CREATE VIEW gene_cassette_array AS
SELECT
feature_id AS gene_cassette_array_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'gene_cassette_array';
--- ************************************************
--- *** relation: gene_group ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A collection of related genes. ***
--- ************************************************
---
CREATE VIEW gene_group AS
SELECT
feature_id AS gene_group_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'operon' OR cvterm.name = 'mating_type_region' OR cvterm.name = 'gene_array' OR cvterm.name = 'gene_subarray' OR cvterm.name = 'gene_cassette_array' OR cvterm.name = 'regulon' OR cvterm.name = 'gene_group';
--- ************************************************
--- *** relation: selenocysteine_trna_primary_transcript ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A primary transcript encoding seryl tRNA ***
--- *** (SO:000269). ***
--- ************************************************
---
CREATE VIEW selenocysteine_trna_primary_transcript AS
SELECT
feature_id AS selenocysteine_trna_primary_transcript_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'selenocysteine_tRNA_primary_transcript';
--- ************************************************
--- *** relation: selenocysteinyl_trna ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A tRNA sequence that has a selenocystein ***
--- *** e anticodon, and a 3' selenocysteine bin ***
--- *** ding region. ***
--- ************************************************
---
CREATE VIEW selenocysteinyl_trna AS
SELECT
feature_id AS selenocysteinyl_trna_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'selenocysteinyl_tRNA';
--- ************************************************
--- *** relation: syntenic_region ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A region in which two or more pairs of h ***
--- *** omologous markers occur on the same chro ***
--- *** mosome in two or more species. ***
--- ************************************************
---
CREATE VIEW syntenic_region AS
SELECT
feature_id AS syntenic_region_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'syntenic_region';
--- ************************************************
--- *** relation: biochemical_region_of_peptide ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A region of a peptide that is involved i ***
--- *** n a biochemical function. ***
--- ************************************************
---
CREATE VIEW biochemical_region_of_peptide AS
SELECT
feature_id AS biochemical_region_of_peptide_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'post_translationally_modified_region' OR cvterm.name = 'conformational_switch' OR cvterm.name = 'molecular_contact_region' OR cvterm.name = 'polypeptide_binding_motif' OR cvterm.name = 'polypeptide_catalytic_motif' OR cvterm.name = 'histone_modification' OR cvterm.name = 'histone_methylation_site' OR cvterm.name = 'histone_acetylation_site' OR cvterm.name = 'histone_ubiqitination_site' OR cvterm.name = 'histone_acylation_region' OR cvterm.name = 'H4K20_monomethylation_site' OR cvterm.name = 'H2BK5_monomethylation_site' OR cvterm.name = 'H3K27_methylation_site' OR cvterm.name = 'H3K36_methylation_site' OR cvterm.name = 'H3K4_methylation_site' OR cvterm.name = 'H3K79_methylation_site' OR cvterm.name = 'H3K9_methylation_site' OR cvterm.name = 'H3K27_monomethylation_site' OR cvterm.name = 'H3K27_trimethylation_site' OR cvterm.name = 'H3K27_dimethylation_site' OR cvterm.name = 'H3K36_monomethylation_site' OR cvterm.name = 'H3K36_dimethylation_site' OR cvterm.name = 'H3K36_trimethylation_site' OR cvterm.name = 'H3K4_monomethylation_site' OR cvterm.name = 'H3K4_trimethylation' OR cvterm.name = 'H3K4_dimethylation_site' OR cvterm.name = 'H3K79_monomethylation_site' OR cvterm.name = 'H3K79_dimethylation_site' OR cvterm.name = 'H3K79_trimethylation_site' OR cvterm.name = 'H3K9_trimethylation_site' OR cvterm.name = 'H3K9_monomethylation_site' OR cvterm.name = 'H3K9_dimethylation_site' OR cvterm.name = 'H3K9_acetylation_site' OR cvterm.name = 'H3K14_acetylation_site' OR cvterm.name = 'H3K18_acetylation_site' OR cvterm.name = 'H3K23_acylation site' OR cvterm.name = 'H3K27_acylation_site' OR cvterm.name = 'H4K16_acylation_site' OR cvterm.name = 'H4K5_acylation_site' OR cvterm.name = 'H4K8_acylation site' OR cvterm.name = 'H2B_ubiquitination_site' OR cvterm.name = 'H4K_acylation_region' OR cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'biochemical_region_of_peptide';
--- ************************************************
--- *** relation: molecular_contact_region ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A region that is involved a contact with ***
--- *** another molecule. ***
--- ************************************************
---
CREATE VIEW molecular_contact_region AS
SELECT
feature_id AS molecular_contact_region_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'polypeptide_metal_contact' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'polypeptide_ligand_contact' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_calcium_ion_contact_site' OR cvterm.name = 'polypeptide_cobalt_ion_contact_site' OR cvterm.name = 'polypeptide_copper_ion_contact_site' OR cvterm.name = 'polypeptide_iron_ion_contact_site' OR cvterm.name = 'polypeptide_magnesium_ion_contact_site' OR cvterm.name = 'polypeptide_manganese_ion_contact_site' OR cvterm.name = 'polypeptide_molybdenum_ion_contact_site' OR cvterm.name = 'polypeptide_nickel_ion_contact_site' OR cvterm.name = 'polypeptide_tungsten_ion_contact_site' OR cvterm.name = 'polypeptide_zinc_ion_contact_site' OR cvterm.name = 'molecular_contact_region';
--- ************************************************
--- *** relation: intrinsically_unstructured_polypeptide_region ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A region of polypeptide chain with high ***
--- *** conformational flexibility. ***
--- ************************************************
---
CREATE VIEW intrinsically_unstructured_polypeptide_region AS
SELECT
feature_id AS intrinsically_unstructured_polypeptide_region_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'intrinsically_unstructured_polypeptide_region';
--- ************************************************
--- *** relation: catmat_left_handed_three ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A motif of 3 consecutive residues with d ***
--- *** ihedral angles as follows: res i: phi -9 ***
--- *** 0 bounds -120 to -60, res i: psi -10 bou ***
--- *** nds -50 to 30, res i+1: phi -75 bounds - ***
--- *** 100 to -50, res i+1: psi 140 bounds 110 ***
--- *** to 170. An extra restriction of the leng ***
--- *** th of the O to O distance would be usefu ***
--- *** l, that it be less than 5 Angstrom. More ***
--- *** precisely these two oxygens are the mai ***
--- *** n chain carbonyl oxygen atoms of residue ***
--- *** s i-1 and i+1. ***
--- ************************************************
---
CREATE VIEW catmat_left_handed_three AS
SELECT
feature_id AS catmat_left_handed_three_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'catmat_left_handed_three';
--- ************************************************
--- *** relation: catmat_left_handed_four ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A motif of 4 consecutive residues with d ***
--- *** ihedral angles as follows: res i: phi -9 ***
--- *** 0 bounds -120 to -60, res i psi -10 boun ***
--- *** ds -50 to 30, res i+1: phi -90 bounds -1 ***
--- *** 20 to -60, res i+1: psi -10 bounds -50 t ***
--- *** o 30, res i+2: phi -75 bounds -100 to -5 ***
--- *** 0, res i+2: psi 140 bounds 110 to 170. ***
--- *** The extra restriction of the length of t ***
--- *** he O to O distance is similar, that it b ***
--- *** e less than 5 Angstrom. In this case the ***
--- *** se two Oxygen atoms are the main chain c ***
--- *** arbonyl oxygen atoms of residues i-1 and ***
--- *** i+2. ***
--- ************************************************
---
CREATE VIEW catmat_left_handed_four AS
SELECT
feature_id AS catmat_left_handed_four_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'catmat_left_handed_four';
--- ************************************************
--- *** relation: catmat_right_handed_three ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A motif of 3 consecutive residues with d ***
--- *** ihedral angles as follows: res i: phi -9 ***
--- *** 0 bounds -120 to -60, res i: psi -10 bou ***
--- *** nds -50 to 30, res i+1: phi -75 bounds - ***
--- *** 100 to -50, res i+1: psi 140 bounds 110 ***
--- *** to 170. An extra restriction of the leng ***
--- *** th of the O to O distance would be usefu ***
--- *** l, that it be less than 5 Angstrom. More ***
--- *** precisely these two oxygens are the mai ***
--- *** n chain carbonyl oxygen atoms of residue ***
--- *** s i-1 and i+1. ***
--- ************************************************
---
CREATE VIEW catmat_right_handed_three AS
SELECT
feature_id AS catmat_right_handed_three_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'catmat_right_handed_three';
--- ************************************************