tripal_chado/chado_schema/parts-v1.3/default_schema-1.3.part19.sql
SET search_path=so,chado,pg_catalog;
--- *** relation: rna_chromosome ***
--- *** relation type: VIEW ***
--- *** ***
--- *** Structural unit composed of a self-repli ***
--- *** cating, RNA molecule. ***
--- ************************************************
---
CREATE VIEW rna_chromosome AS
SELECT
feature_id AS rna_chromosome_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'single_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome' OR cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'RNA_chromosome';
--- ************************************************
--- *** relation: single_stranded_rna_chromosome ***
--- *** relation type: VIEW ***
--- *** ***
--- *** Structural unit composed of a self-repli ***
--- *** cating, single-stranded RNA molecule. ***
--- ************************************************
---
CREATE VIEW single_stranded_rna_chromosome AS
SELECT
feature_id AS single_stranded_rna_chromosome_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'linear_single_stranded_RNA_chromosome' OR cvterm.name = 'circular_single_stranded_RNA_chromosome' OR cvterm.name = 'single_stranded_RNA_chromosome';
--- ************************************************
--- *** relation: linear_single_stranded_rna_chromosome ***
--- *** relation type: VIEW ***
--- *** ***
--- *** Structural unit composed of a self-repli ***
--- *** cating, single-stranded, linear RNA mole ***
--- *** cule. ***
--- ************************************************
---
CREATE VIEW linear_single_stranded_rna_chromosome AS
SELECT
feature_id AS linear_single_stranded_rna_chromosome_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'linear_single_stranded_RNA_chromosome';
--- ************************************************
--- *** relation: linear_double_stranded_rna_chromosome ***
--- *** relation type: VIEW ***
--- *** ***
--- *** Structural unit composed of a self-repli ***
--- *** cating, double-stranded, linear RNA mole ***
--- *** cule. ***
--- ************************************************
---
CREATE VIEW linear_double_stranded_rna_chromosome AS
SELECT
feature_id AS linear_double_stranded_rna_chromosome_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'linear_double_stranded_RNA_chromosome';
--- ************************************************
--- *** relation: double_stranded_rna_chromosome ***
--- *** relation type: VIEW ***
--- *** ***
--- *** Structural unit composed of a self-repli ***
--- *** cating, double-stranded RNA molecule. ***
--- ************************************************
---
CREATE VIEW double_stranded_rna_chromosome AS
SELECT
feature_id AS double_stranded_rna_chromosome_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'linear_double_stranded_RNA_chromosome' OR cvterm.name = 'circular_double_stranded_RNA_chromosome' OR cvterm.name = 'double_stranded_RNA_chromosome';
--- ************************************************
--- *** relation: circular_single_stranded_rna_chromosome ***
--- *** relation type: VIEW ***
--- *** ***
--- *** Structural unit composed of a self-repli ***
--- *** cating, single-stranded, circular DNA mo ***
--- *** lecule. ***
--- ************************************************
---
CREATE VIEW circular_single_stranded_rna_chromosome AS
SELECT
feature_id AS circular_single_stranded_rna_chromosome_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'circular_single_stranded_RNA_chromosome';
--- ************************************************
--- *** relation: circular_double_stranded_rna_chromosome ***
--- *** relation type: VIEW ***
--- *** ***
--- *** Structural unit composed of a self-repli ***
--- *** cating, double-stranded, circular RNA mo ***
--- *** lecule. ***
--- ************************************************
---
CREATE VIEW circular_double_stranded_rna_chromosome AS
SELECT
feature_id AS circular_double_stranded_rna_chromosome_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'circular_double_stranded_RNA_chromosome';
--- ************************************************
--- *** relation: insertion_sequence ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A terminal_inverted_repeat_element that ***
--- *** is bacterial and only encodes the functi ***
--- *** ons required for its transposition betwe ***
--- *** en these inverted repeats. ***
--- ************************************************
---
CREATE VIEW insertion_sequence AS
SELECT
feature_id AS insertion_sequence_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'insertion_sequence';
--- ************************************************
--- *** relation: minicircle_gene ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW minicircle_gene AS
SELECT
feature_id AS minicircle_gene_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'minicircle_gene';
--- ************************************************
--- *** relation: cryptic ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A feature_attribute describing a feature ***
--- *** that is not manifest under normal condi ***
--- *** tions. ***
--- ************************************************
---
CREATE VIEW cryptic AS
SELECT
feature_id AS cryptic_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'cryptic';
--- ************************************************
--- *** relation: anchor_binding_site ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW anchor_binding_site AS
SELECT
feature_id AS anchor_binding_site_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'anchor_binding_site';
--- ************************************************
--- *** relation: template_region ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A region of a guide_RNA that specifies t ***
--- *** he insertions and deletions of bases in ***
--- *** the editing of a target mRNA. ***
--- ************************************************
---
CREATE VIEW template_region AS
SELECT
feature_id AS template_region_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'template_region';
--- ************************************************
--- *** relation: grna_encoding ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A non-protein_coding gene that encodes a ***
--- *** guide_RNA. ***
--- ************************************************
---
CREATE VIEW grna_encoding AS
SELECT
feature_id AS grna_encoding_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'gRNA_encoding';
--- ************************************************
--- *** relation: minicircle ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A minicircle is a replicon, part of a ki ***
--- *** netoplast, that encodes for guide RNAs. ***
--- ************************************************
---
CREATE VIEW minicircle AS
SELECT
feature_id AS minicircle_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'minicircle';
--- ************************************************
--- *** relation: rho_dependent_bacterial_terminator ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW rho_dependent_bacterial_terminator AS
SELECT
feature_id AS rho_dependent_bacterial_terminator_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'rho_dependent_bacterial_terminator';
--- ************************************************
--- *** relation: rho_independent_bacterial_terminator ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW rho_independent_bacterial_terminator AS
SELECT
feature_id AS rho_independent_bacterial_terminator_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'rho_independent_bacterial_terminator';
--- ************************************************
--- *** relation: strand_attribute ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW strand_attribute AS
SELECT
feature_id AS strand_attribute_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'single' OR cvterm.name = 'double' OR cvterm.name = 'strand_attribute';
--- ************************************************
--- *** relation: single ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW single AS
SELECT
feature_id AS single_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'single';
--- ************************************************
--- *** relation: double ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW double AS
SELECT
feature_id AS double_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'double';
--- ************************************************
--- *** relation: topology_attribute ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW topology_attribute AS
SELECT
feature_id AS topology_attribute_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'linear' OR cvterm.name = 'circular' OR cvterm.name = 'topology_attribute';
--- ************************************************
--- *** relation: linear ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A quality of a nucleotide polymer that h ***
--- *** as a 3'-terminal residue and a 5'-termin ***
--- *** al residue. ***
--- ************************************************
---
CREATE VIEW linear AS
SELECT
feature_id AS linear_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'linear';
--- ************************************************
--- *** relation: circular ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A quality of a nucleotide polymer that h ***
--- *** as no terminal nucleotide residues. ***
--- ************************************************
---
CREATE VIEW circular AS
SELECT
feature_id AS circular_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'circular';
--- ************************************************
--- *** relation: class_ii_rna ***
--- *** relation type: VIEW ***
--- *** ***
--- *** Small non-coding RNA (59-60 nt long) con ***
--- *** taining 5' and 3' ends that are predicte ***
--- *** d to come together to form a stem struct ***
--- *** ure. Identified in the social amoeba Dic ***
--- *** tyostelium discoideum and localized in t ***
--- *** he cytoplasm. ***
--- ************************************************
---
CREATE VIEW class_ii_rna AS
SELECT
feature_id AS class_ii_rna_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'class_II_RNA';
--- ************************************************
--- *** relation: class_i_rna ***
--- *** relation type: VIEW ***
--- *** ***
--- *** Small non-coding RNA (55-65 nt long) con ***
--- *** taining highly conserved 5' and 3' ends ***
--- *** (16 and 8 nt, respectively) that are pre ***
--- *** dicted to come together to form a stem s ***
--- *** tructure. Identified in the social amoeb ***
--- *** a Dictyostelium discoideum and localized ***
--- *** in the cytoplasm. ***
--- ************************************************
---
CREATE VIEW class_i_rna AS
SELECT
feature_id AS class_i_rna_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'class_I_RNA';
--- ************************************************
--- *** relation: genomic_dna ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW genomic_dna AS
SELECT
feature_id AS genomic_dna_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'genomic_DNA';
--- ************************************************
--- *** relation: bac_cloned_genomic_insert ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW bac_cloned_genomic_insert AS
SELECT
feature_id AS bac_cloned_genomic_insert_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'BAC_cloned_genomic_insert';
--- ************************************************
--- *** relation: consensus ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW consensus AS
SELECT
feature_id AS consensus_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'consensus';
--- ************************************************
--- *** relation: consensus_region ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW consensus_region AS
SELECT
feature_id AS consensus_region_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'consensus_mRNA' OR cvterm.name = 'consensus_region';
--- ************************************************
--- *** relation: consensus_mrna ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW consensus_mrna AS
SELECT
feature_id AS consensus_mrna_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'consensus_mRNA';
--- ************************************************
--- *** relation: predicted_gene ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW predicted_gene AS
SELECT
feature_id AS predicted_gene_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'predicted_gene';
--- ************************************************
--- *** relation: gene_fragment ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW gene_fragment AS
SELECT
feature_id AS gene_fragment_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'gene_fragment';
--- ************************************************
--- *** relation: recursive_splice_site ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A recursive splice site is a splice site ***
--- *** which subdivides a large intron. Recurs ***
--- *** ive splicing is a mechanism that splices ***
--- *** large introns by sub dividing the intro ***
--- *** n at non exonic elements and alternate e ***
--- *** xons. ***
--- ************************************************
---
CREATE VIEW recursive_splice_site AS
SELECT
feature_id AS recursive_splice_site_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'recursive_splice_site';
--- ************************************************
--- *** relation: bac_end ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A region of sequence from the end of a B ***
--- *** AC clone that may provide a highly speci ***
--- *** fic marker. ***
--- ************************************************
---
CREATE VIEW bac_end AS
SELECT
feature_id AS bac_end_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'BAC_end';
--- ************************************************
--- *** relation: rrna_16s ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A large polynucleotide in Bacteria and A ***
--- *** rchaea, which functions as the small sub ***
--- *** unit of the ribosome. ***
--- ************************************************
---
CREATE VIEW rrna_16s AS
SELECT
feature_id AS rrna_16s_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'rRNA_16S';
--- ************************************************
--- *** relation: rrna_23s ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A large polynucleotide in Bacteria and A ***
--- *** rchaea, which functions as the large sub ***
--- *** unit of the ribosome. ***
--- ************************************************
---
CREATE VIEW rrna_23s AS
SELECT
feature_id AS rrna_23s_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'rRNA_23S';
--- ************************************************
--- *** relation: rrna_25s ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A large polynucleotide which functions a ***
--- *** s part of the large subunit of the ribos ***
--- *** ome in some eukaryotes. ***
--- ************************************************
---
CREATE VIEW rrna_25s AS
SELECT
feature_id AS rrna_25s_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'rRNA_25S';
--- ************************************************
--- *** relation: solo_ltr ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A recombination product between the 2 LT ***
--- *** R of the same element. ***
--- ************************************************
---
CREATE VIEW solo_ltr AS
SELECT
feature_id AS solo_ltr_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'solo_LTR';
--- ************************************************
--- *** relation: low_complexity ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW low_complexity AS
SELECT
feature_id AS low_complexity_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'low_complexity';
--- ************************************************
--- *** relation: low_complexity_region ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW low_complexity_region AS
SELECT
feature_id AS low_complexity_region_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'low_complexity_region';
--- ************************************************
--- *** relation: prophage ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A phage genome after it has established ***
--- *** in the host genome in a latent/immune st ***
--- *** ate either as a plasmid or as an integra ***
--- *** ted "island". ***
--- ************************************************
---
CREATE VIEW prophage AS
SELECT
feature_id AS prophage_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'prophage';
--- ************************************************
--- *** relation: cryptic_prophage ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A remnant of an integrated prophage in t ***
--- *** he host genome or an "island" in the hos ***
--- *** t genome that includes phage like-genes. ***
--- ************************************************
---
CREATE VIEW cryptic_prophage AS
SELECT
feature_id AS cryptic_prophage_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'cryptic_prophage';
--- ************************************************
--- *** relation: tetraloop ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A base-paired stem with loop of 4 non-hy ***
--- *** drogen bonded nucleotides. ***
--- ************************************************
---
CREATE VIEW tetraloop AS
SELECT
feature_id AS tetraloop_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'tetraloop';
--- ************************************************
--- *** relation: dna_constraint_sequence ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A double-stranded DNA used to control ma ***
--- *** cromolecular structure and function. ***
--- ************************************************
---
CREATE VIEW dna_constraint_sequence AS
SELECT
feature_id AS dna_constraint_sequence_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'DNA_constraint_sequence';
--- ************************************************
--- *** relation: i_motif ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A cytosine rich domain whereby strands a ***
--- *** ssociate both inter- and intramolecularl ***
--- *** y at moderately acidic pH. ***
--- ************************************************
---
CREATE VIEW i_motif AS
SELECT
feature_id AS i_motif_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'i_motif';
--- ************************************************
--- *** relation: pna_oligo ***
--- *** relation type: VIEW ***
--- *** ***
--- *** Peptide nucleic acid, is a chemical not ***
--- *** known to occur naturally but is artifici ***
--- *** ally synthesized and used in some biolog ***
--- *** ical research and medical treatments. Th ***
--- *** e PNA backbone is composed of repeating ***
--- *** N-(2-aminoethyl)-glycine units linked by ***
--- *** peptide bonds. The purine and pyrimidin ***
--- *** e bases are linked to the backbone by me ***
--- *** thylene carbonyl bonds. ***
--- ************************************************
---
CREATE VIEW pna_oligo AS
SELECT
feature_id AS pna_oligo_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'PNA_oligo';
--- ************************************************
--- *** relation: dnazyme ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A DNA sequence with catalytic activity. ***
--- ************************************************
---
CREATE VIEW dnazyme AS
SELECT
feature_id AS dnazyme_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'DNAzyme';
--- ************************************************
--- *** relation: mnp ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A multiple nucleotide polymorphism with ***
--- *** alleles of common length > 1, for exampl ***
--- *** e AAA/TTT. ***
--- ************************************************
---
CREATE VIEW mnp AS
SELECT
feature_id AS mnp_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'MNP';
--- ************************************************
--- *** relation: intron_domain ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW intron_domain AS
SELECT
feature_id AS intron_domain_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'intron_domain';
--- ************************************************
--- *** relation: wobble_base_pair ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A type of non-canonical base pairing, mo ***
--- *** st commonly between G and U, which is im ***
--- *** portant for the secondary structure of R ***
--- *** NAs. It has similar thermodynamic stabil ***
--- *** ity to the Watson-Crick pairing. Wobble ***
--- *** base pairs only have two hydrogen bonds. ***
--- *** Other wobble base pair possibilities ar ***
--- *** e I-A, I-U and I-C. ***
--- ************************************************
---
CREATE VIEW wobble_base_pair AS
SELECT
feature_id AS wobble_base_pair_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'wobble_base_pair';
--- ************************************************
--- *** relation: internal_guide_sequence ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A purine-rich sequence in the group I in ***
--- *** trons which determines the locations of ***
--- *** the splice sites in group I intron splic ***
--- *** ing and has catalytic activity. ***
--- ************************************************
---
CREATE VIEW internal_guide_sequence AS
SELECT
feature_id AS internal_guide_sequence_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'internal_guide_sequence';
--- ************************************************
--- *** relation: silent_mutation ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that does not affect ***
--- *** protein function. Silent mutations may o ***
--- *** ccur in genic ( CDS, UTR, intron etc) an ***
--- *** d intergenic regions. Silent mutations m ***
--- *** ay have affects on processes such as spl ***
--- *** icing and regulation. ***
--- ************************************************
---
CREATE VIEW silent_mutation AS
SELECT
feature_id AS silent_mutation_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'silent_mutation';
--- ************************************************
--- *** relation: epitope ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A binding site that, in the molecule, in ***
--- *** teracts selectively and non-covalently w ***
--- *** ith antibodies, B cells or T cells. ***
--- ************************************************
---
CREATE VIEW epitope AS
SELECT
feature_id AS epitope_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'epitope';
--- ************************************************
--- *** relation: copy_number_variation ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A variation that increases or decreases ***
--- *** the copy number of a given region. ***
--- ************************************************
---
CREATE VIEW copy_number_variation AS
SELECT
feature_id AS copy_number_variation_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'copy_number_gain' OR cvterm.name = 'copy_number_loss' OR cvterm.name = 'copy_number_variation';
--- ************************************************
--- *** relation: chromosome_breakpoint ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW chromosome_breakpoint AS
SELECT
feature_id AS chromosome_breakpoint_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'inversion_breakpoint' OR cvterm.name = 'translocation_breakpoint' OR cvterm.name = 'insertion_breakpoint' OR cvterm.name = 'deletion_breakpoint' OR cvterm.name = 'chromosome_breakpoint';
--- ************************************************
--- *** relation: inversion_breakpoint ***
--- *** relation type: VIEW ***
--- *** ***
--- *** The point within a chromosome where an i ***
--- *** nversion begins or ends. ***
--- ************************************************
---
CREATE VIEW inversion_breakpoint AS
SELECT
feature_id AS inversion_breakpoint_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'inversion_breakpoint';
--- ************************************************
--- *** relation: allele ***
--- *** relation type: VIEW ***
--- *** ***
--- *** An allele is one of a set of coexisting ***
--- *** sequence variants of a gene. ***
--- ************************************************
---
CREATE VIEW allele AS
SELECT
feature_id AS allele_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'polymorphic_sequence_variant' OR cvterm.name = 'allele';
--- ************************************************
--- *** relation: haplotype ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A haplotype is one of a set of coexistin ***
--- *** g sequence variants of a haplotype block ***
--- *** . ***
--- ************************************************
---
CREATE VIEW haplotype AS
SELECT
feature_id AS haplotype_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'haplotype';
--- ************************************************
--- *** relation: polymorphic_sequence_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that is segregating i ***
--- *** n one or more natural populations of a s ***
--- *** pecies. ***
--- ************************************************
---
CREATE VIEW polymorphic_sequence_variant AS
SELECT
feature_id AS polymorphic_sequence_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'polymorphic_sequence_variant';
--- ************************************************
--- *** relation: genome ***