tripal_chado/chado_schema/parts-v1.3/default_schema-1.3.part29.sql
SET search_path = so,chado,pg_catalog;
--- *** relation type: VIEW ***
--- *** ***
--- *** A transcript processing variant whereby ***
--- *** the process of editing is disrupted with ***
--- *** respect to the reference. ***
--- ************************************************
---
CREATE VIEW editing_variant AS
SELECT
feature_id AS editing_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'editing_variant';
--- ************************************************
--- *** relation: polyadenylation_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that changes polyaden ***
--- *** ylation with respect to a reference sequ ***
--- *** ence. ***
--- ************************************************
---
CREATE VIEW polyadenylation_variant AS
SELECT
feature_id AS polyadenylation_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'increased_polyadenylation_variant' OR cvterm.name = 'decreased_polyadenylation_variant' OR cvterm.name = 'polyadenylation_variant';
--- ************************************************
--- *** relation: transcript_stability_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A variant that changes the stability of ***
--- *** a transcript with respect to a reference ***
--- *** sequence. ***
--- ************************************************
---
CREATE VIEW transcript_stability_variant AS
SELECT
feature_id AS transcript_stability_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'decreased_transcript_stability_variant' OR cvterm.name = 'increased_transcript_stability_variant' OR cvterm.name = 'transcript_stability_variant';
--- ************************************************
--- *** relation: decreased_transcript_stability_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that decreases transc ***
--- *** ript stability with respect to a referen ***
--- *** ce sequence. ***
--- ************************************************
---
CREATE VIEW decreased_transcript_stability_variant AS
SELECT
feature_id AS decreased_transcript_stability_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'decreased_transcript_stability_variant';
--- ************************************************
--- *** relation: increased_transcript_stability_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that increases transc ***
--- *** ript stability with respect to a referen ***
--- *** ce sequence. ***
--- ************************************************
---
CREATE VIEW increased_transcript_stability_variant AS
SELECT
feature_id AS increased_transcript_stability_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'increased_transcript_stability_variant';
--- ************************************************
--- *** relation: transcription_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A variant that changes alters the transc ***
--- *** ription of a transcript with respect to ***
--- *** a reference sequence. ***
--- ************************************************
---
CREATE VIEW transcription_variant AS
SELECT
feature_id AS transcription_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'rate_of_transcription_variant' OR cvterm.name = 'increased_transcription_rate_variant' OR cvterm.name = 'decreased_transcription_rate_variant' OR cvterm.name = 'transcription_variant';
--- ************************************************
--- *** relation: rate_of_transcription_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that changes the rate ***
--- *** of transcription with respect to a refe ***
--- *** rence sequence. ***
--- ************************************************
---
CREATE VIEW rate_of_transcription_variant AS
SELECT
feature_id AS rate_of_transcription_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'increased_transcription_rate_variant' OR cvterm.name = 'decreased_transcription_rate_variant' OR cvterm.name = 'rate_of_transcription_variant';
--- ************************************************
--- *** relation: increased_transcription_rate_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that increases the ra ***
--- *** te of transcription with respect to a re ***
--- *** ference sequence. ***
--- ************************************************
---
CREATE VIEW increased_transcription_rate_variant AS
SELECT
feature_id AS increased_transcription_rate_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'increased_transcription_rate_variant';
--- ************************************************
--- *** relation: decreased_transcription_rate_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that decreases the ra ***
--- *** te of transcription with respect to a re ***
--- *** ference sequence. ***
--- ************************************************
---
CREATE VIEW decreased_transcription_rate_variant AS
SELECT
feature_id AS decreased_transcription_rate_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'decreased_transcription_rate_variant';
--- ************************************************
--- *** relation: translational_product_level_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A functional variant that changes the tr ***
--- *** anslational product level with respect t ***
--- *** o a reference sequence. ***
--- ************************************************
---
CREATE VIEW translational_product_level_variant AS
SELECT
feature_id AS translational_product_level_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'decreased_translational_product_level' OR cvterm.name = 'increased_translational_product_level' OR cvterm.name = 'translational_product_level_variant';
--- ************************************************
--- *** relation: polypeptide_function_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant which changes polypep ***
--- *** tide functioning with respect to a refer ***
--- *** ence sequence. ***
--- ************************************************
---
CREATE VIEW polypeptide_function_variant AS
SELECT
feature_id AS polypeptide_function_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'polypeptide_gain_of_function_variant' OR cvterm.name = 'polypeptide_localization_variant' OR cvterm.name = 'polypeptide_loss_of_function_variant' OR cvterm.name = 'polypeptide_post_translational_processing_variant' OR cvterm.name = 'inactive_ligand_binding_site' OR cvterm.name = 'polypeptide_partial_loss_of_function' OR cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'polypeptide_function_variant';
--- ************************************************
--- *** relation: decreased_translational_product_level ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant which decreases the t ***
--- *** ranslational product level with respect ***
--- *** to a reference sequence. ***
--- ************************************************
---
CREATE VIEW decreased_translational_product_level AS
SELECT
feature_id AS decreased_translational_product_level_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'decreased_translational_product_level';
--- ************************************************
--- *** relation: increased_translational_product_level ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant which increases the t ***
--- *** ranslational product level with respect ***
--- *** to a reference sequence. ***
--- ************************************************
---
CREATE VIEW increased_translational_product_level AS
SELECT
feature_id AS increased_translational_product_level_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'increased_translational_product_level';
--- ************************************************
--- *** relation: polypeptide_gain_of_function_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant which causes gain of ***
--- *** polypeptide function with respect to a r ***
--- *** eference sequence. ***
--- ************************************************
---
CREATE VIEW polypeptide_gain_of_function_variant AS
SELECT
feature_id AS polypeptide_gain_of_function_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'polypeptide_gain_of_function_variant';
--- ************************************************
--- *** relation: polypeptide_localization_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant which changes the loc ***
--- *** alization of a polypeptide with respect ***
--- *** to a reference sequence. ***
--- ************************************************
---
CREATE VIEW polypeptide_localization_variant AS
SELECT
feature_id AS polypeptide_localization_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'polypeptide_localization_variant';
--- ************************************************
--- *** relation: polypeptide_loss_of_function_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that causes the loss ***
--- *** of a polypeptide function with respect t ***
--- *** o a reference sequence. ***
--- ************************************************
---
CREATE VIEW polypeptide_loss_of_function_variant AS
SELECT
feature_id AS polypeptide_loss_of_function_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'inactive_ligand_binding_site' OR cvterm.name = 'polypeptide_partial_loss_of_function' OR cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'polypeptide_loss_of_function_variant';
--- ************************************************
--- *** relation: inactive_ligand_binding_site ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that causes the inact ***
--- *** ivation of a ligand binding site with re ***
--- *** spect to a reference sequence. ***
--- ************************************************
---
CREATE VIEW inactive_ligand_binding_site AS
SELECT
feature_id AS inactive_ligand_binding_site_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'inactive_catalytic_site' OR cvterm.name = 'inactive_ligand_binding_site';
--- ************************************************
--- *** relation: polypeptide_partial_loss_of_function ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that causes some but ***
--- *** not all loss of polypeptide function wit ***
--- *** h respect to a reference sequence. ***
--- ************************************************
---
CREATE VIEW polypeptide_partial_loss_of_function AS
SELECT
feature_id AS polypeptide_partial_loss_of_function_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'polypeptide_partial_loss_of_function';
--- ************************************************
--- *** relation: polypeptide_post_translational_processing_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that causes a change ***
--- *** in post translational processing of the ***
--- *** peptide with respect to a reference sequ ***
--- *** ence. ***
--- ************************************************
---
CREATE VIEW polypeptide_post_translational_processing_variant AS
SELECT
feature_id AS polypeptide_post_translational_processing_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'polypeptide_post_translational_processing_variant';
--- ************************************************
--- *** relation: copy_number_change ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant where copies of a fea ***
--- *** ture (CNV) are either increased or decre ***
--- *** ased. ***
--- ************************************************
---
CREATE VIEW copy_number_change AS
SELECT
feature_id AS copy_number_change_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'copy_number_change';
--- ************************************************
--- *** relation: gene_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant where the structure o ***
--- *** f the gene is changed. ***
--- ************************************************
---
CREATE VIEW gene_variant AS
SELECT
feature_id AS gene_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'gene_fusion' OR cvterm.name = 'splicing_variant' OR cvterm.name = 'transcript_variant' OR cvterm.name = 'translational_product_structure_variant' OR cvterm.name = 'cryptic_splice_site_variant' OR cvterm.name = 'exon_loss' OR cvterm.name = 'intron_gain' OR cvterm.name = 'splice_region_variant' OR cvterm.name = 'cryptic_splice_acceptor' OR cvterm.name = 'cryptic_splice_donor' OR cvterm.name = 'complex_change_in_transcript' OR cvterm.name = 'transcript_secondary_structure_variant' OR cvterm.name = 'nc_transcript_variant' OR cvterm.name = 'NMD_transcript_variant' OR cvterm.name = 'UTR_variant' OR cvterm.name = 'intron_variant' OR cvterm.name = 'exon_variant' OR cvterm.name = 'compensatory_transcript_secondary_structure_variant' OR cvterm.name = 'mature_miRNA_variant' OR cvterm.name = '5_prime_UTR_variant' OR cvterm.name = '3_prime_UTR_variant' OR cvterm.name = 'splice_site_variant' OR cvterm.name = 'splice_acceptor_variant' OR cvterm.name = 'splice_donor_variant' OR cvterm.name = 'splice_donor_5th_base_variant' OR 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 = '3D_polypeptide_structure_variant' OR cvterm.name = 'complex_change_of_translational_product_variant' OR cvterm.name = 'polypeptide_sequence_variant' OR cvterm.name = 'complex_3D_structural_variant' OR cvterm.name = 'conformational_change_variant' OR cvterm.name = 'amino_acid_deletion' OR cvterm.name = 'amino_acid_insertion' OR cvterm.name = 'amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide' OR cvterm.name = 'polypeptide_fusion' OR cvterm.name = 'polypeptide_truncation' OR cvterm.name = 'conservative_amino_acid_substitution' OR cvterm.name = 'non_conservative_amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'gene_variant';
--- ************************************************
--- *** relation: gene_fusion ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant whereby a two genes h ***
--- *** ave become joined. ***
--- ************************************************
---
CREATE VIEW gene_fusion AS
SELECT
feature_id AS gene_fusion_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'gene_fusion';
--- ************************************************
--- *** relation: regulatory_region_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant located within a regu ***
--- *** latory region. ***
--- ************************************************
---
CREATE VIEW regulatory_region_variant AS
SELECT
feature_id AS regulatory_region_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'TF_binding_site_variant' OR cvterm.name = 'regulatory_region_variant';
--- ************************************************
--- *** relation: stop_retained_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant where at least one ba ***
--- *** se in the terminator codon is changed, b ***
--- *** ut the terminator remains. ***
--- ************************************************
---
CREATE VIEW stop_retained_variant AS
SELECT
feature_id AS stop_retained_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'stop_retained_variant';
--- ************************************************
--- *** relation: splicing_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that changes the proc ***
--- *** ess of splicing. ***
--- ************************************************
---
CREATE VIEW splicing_variant AS
SELECT
feature_id AS splicing_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'cryptic_splice_site_variant' OR cvterm.name = 'exon_loss' OR cvterm.name = 'intron_gain' OR cvterm.name = 'splice_region_variant' OR cvterm.name = 'cryptic_splice_acceptor' OR cvterm.name = 'cryptic_splice_donor' OR cvterm.name = 'splicing_variant';
--- ************************************************
--- *** relation: cryptic_splice_site_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant causing a new (functi ***
--- *** onal) splice site. ***
--- ************************************************
---
CREATE VIEW cryptic_splice_site_variant AS
SELECT
feature_id AS cryptic_splice_site_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'cryptic_splice_acceptor' OR cvterm.name = 'cryptic_splice_donor' OR cvterm.name = 'cryptic_splice_site_variant';
--- ************************************************
--- *** relation: cryptic_splice_acceptor ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant whereby a new splice ***
--- *** site is created due to the activation of ***
--- *** a new acceptor. ***
--- ************************************************
---
CREATE VIEW cryptic_splice_acceptor AS
SELECT
feature_id AS cryptic_splice_acceptor_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'cryptic_splice_acceptor';
--- ************************************************
--- *** relation: cryptic_splice_donor ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant whereby a new splice ***
--- *** site is created due to the activation of ***
--- *** a new donor. ***
--- ************************************************
---
CREATE VIEW cryptic_splice_donor AS
SELECT
feature_id AS cryptic_splice_donor_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'cryptic_splice_donor';
--- ************************************************
--- *** relation: exon_loss ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant whereby an exon is lo ***
--- *** st from the transcript. ***
--- ************************************************
---
CREATE VIEW exon_loss AS
SELECT
feature_id AS exon_loss_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'exon_loss';
--- ************************************************
--- *** relation: intron_gain ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant whereby an intron is ***
--- *** gained by the processed transcript; usua ***
--- *** lly a result of an alteration of the don ***
--- *** or or acceptor. ***
--- ************************************************
---
CREATE VIEW intron_gain AS
SELECT
feature_id AS intron_gain_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'intron_gain';
--- ************************************************
--- *** relation: splice_acceptor_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A splice variant that changes the 2 base ***
--- *** region at the 3' end of an intron. ***
--- ************************************************
---
CREATE VIEW splice_acceptor_variant AS
SELECT
feature_id AS splice_acceptor_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'splice_acceptor_variant';
--- ************************************************
--- *** relation: splice_donor_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A splice variant that changes the2 base ***
--- *** region at the 5' end of an intron. ***
--- ************************************************
---
CREATE VIEW splice_donor_variant AS
SELECT
feature_id AS splice_donor_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'splice_donor_variant';
--- ************************************************
--- *** relation: transcript_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that changes the stru ***
--- *** cture of the transcript. ***
--- ************************************************
---
CREATE VIEW transcript_variant AS
SELECT
feature_id AS transcript_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'complex_change_in_transcript' OR cvterm.name = 'transcript_secondary_structure_variant' OR cvterm.name = 'nc_transcript_variant' OR cvterm.name = 'NMD_transcript_variant' OR cvterm.name = 'UTR_variant' OR cvterm.name = 'intron_variant' OR cvterm.name = 'exon_variant' OR cvterm.name = 'compensatory_transcript_secondary_structure_variant' OR cvterm.name = 'mature_miRNA_variant' OR cvterm.name = '5_prime_UTR_variant' OR cvterm.name = '3_prime_UTR_variant' OR cvterm.name = 'splice_site_variant' OR cvterm.name = 'splice_acceptor_variant' OR cvterm.name = 'splice_donor_variant' OR cvterm.name = 'splice_donor_5th_base_variant' OR 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 = 'transcript_variant';
--- ************************************************
--- *** relation: complex_change_in_transcript ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A transcript variant with a complex INDE ***
--- *** L- Insertion or deletion that spans an e ***
--- *** xon/intron border or a coding sequence/U ***
--- *** TR border. ***
--- ************************************************
---
CREATE VIEW complex_change_in_transcript AS
SELECT
feature_id AS complex_change_in_transcript_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'complex_change_in_transcript';
--- ************************************************
--- *** relation: stop_lost ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant where at least one ba ***
--- *** se of the terminator codon (stop) is cha ***
--- *** nged, resulting in an elongated transcri ***
--- *** pt. ***
--- ************************************************
---
CREATE VIEW stop_lost AS
SELECT
feature_id AS stop_lost_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'stop_lost';
--- ************************************************
--- *** relation: coding_sequence_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that changes the codi ***
--- *** ng sequence. ***
--- ************************************************
---
CREATE VIEW coding_sequence_variant AS
SELECT
feature_id AS coding_sequence_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE 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 = 'coding_sequence_variant';
--- ************************************************
--- *** relation: codon_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that changes at least ***
--- *** one base in a codon. ***
--- ************************************************
---
CREATE VIEW codon_variant AS
SELECT
feature_id AS codon_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE 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 = 'codon_variant';
--- ************************************************
--- *** relation: initiator_codon_change ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A codon variant that changes at least on ***
--- *** e base of the first codon of a transcrip ***
--- *** t. ***
--- ************************************************
---
CREATE VIEW initiator_codon_change AS
SELECT
feature_id AS initiator_codon_change_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'initiator_codon_change';
--- ************************************************
--- *** relation: non_synonymous_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 or stop codon. ***
--- ************************************************
---
CREATE VIEW non_synonymous_codon AS
SELECT
feature_id AS non_synonymous_codon_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE 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 = 'non_synonymous_codon';
--- ************************************************
--- *** relation: conservative_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 but ***
--- *** similar amino acid. These variants may ***
--- *** or may not be deleterious. ***
--- ************************************************
---
CREATE VIEW conservative_missense_codon AS
SELECT
feature_id AS conservative_missense_codon_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'conservative_missense_codon';
--- ************************************************
--- *** relation: non_conservative_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 an amino acid w ***
--- *** ith different biochemical properties. ***
--- ************************************************
---
CREATE VIEW non_conservative_missense_codon AS
SELECT
feature_id AS non_conservative_missense_codon_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'non_conservative_missense_codon';
--- ************************************************
--- *** relation: stop_gained ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant whereby at least one ***
--- *** base of a codon is changed, resulting in ***
--- *** a premature stop codon, leading to a sh ***
--- *** ortened transcript. ***
--- ************************************************
---
CREATE VIEW stop_gained AS
SELECT
feature_id AS stop_gained_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'stop_gained';
--- ************************************************
--- *** relation: synonymous_codon ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant whereby a base of a c ***
--- *** odon is changed, but there is no resulti ***
--- *** ng change to the encoded amino acid. ***
--- ************************************************
---
CREATE VIEW synonymous_codon AS
SELECT
feature_id AS synonymous_codon_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'synonymous_codon';
--- ************************************************
--- *** relation: frameshift_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant which causes a disrup ***
--- *** tion of the translational reading frame, ***
--- *** because the number of nucleotides inser ***
--- *** ted or deleted is not a multiple of thre ***
--- *** e. ***
--- ************************************************
---
CREATE VIEW frameshift_variant AS
SELECT
feature_id AS frameshift_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE 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 = 'frameshift_variant';
--- ************************************************
--- *** relation: terminator_codon_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant whereby at least one ***
--- *** of the bases in the terminator codon is ***
--- *** changed. ***
--- ************************************************
---
CREATE VIEW terminator_codon_variant AS
SELECT
feature_id AS terminator_codon_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'stop_retained_variant' OR cvterm.name = 'stop_lost' OR cvterm.name = 'terminator_codon_variant';
--- ************************************************
--- *** relation: frame_restoring_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that reverts the sequ ***
--- *** ence of a previous frameshift mutation b ***
--- *** ack to the initial frame. ***
--- ************************************************
---
CREATE VIEW frame_restoring_variant AS
SELECT
feature_id AS frame_restoring_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'frame_restoring_variant';
--- ************************************************
--- *** relation: minus_1_frameshift_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant which causes a disrup ***
--- *** tion of the translational reading frame, ***
--- *** by shifting one base ahead. ***
--- ************************************************
---
CREATE VIEW minus_1_frameshift_variant AS
SELECT
feature_id AS minus_1_frameshift_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'minus_1_frameshift_variant';
--- ************************************************
--- *** relation: minus_2_frameshift_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW minus_2_frameshift_variant AS
SELECT
feature_id AS minus_2_frameshift_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'minus_2_frameshift_variant';
--- ************************************************
--- *** relation: plus_1_frameshift_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant which causes a disrup ***
--- *** tion of the translational reading frame, ***
--- *** by shifting one base backward. ***
--- ************************************************
---
CREATE VIEW plus_1_frameshift_variant AS
SELECT
feature_id AS plus_1_frameshift_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'plus_1_frameshift_variant';
--- ************************************************
--- *** relation: plus_2_frameshift_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- ************************************************
---
CREATE VIEW plus_2_frameshift_variant AS
SELECT
feature_id AS plus_2_frameshift_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'plus_2_frameshift variant';
--- ************************************************
--- *** relation: transcript_secondary_structure_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant within a transcript t ***
--- *** hat changes the secondary structure of t ***
--- *** he RNA product. ***
--- ************************************************
---
CREATE VIEW transcript_secondary_structure_variant AS
SELECT
feature_id AS transcript_secondary_structure_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'compensatory_transcript_secondary_structure_variant' OR cvterm.name = 'transcript_secondary_structure_variant';
--- ************************************************
--- *** relation: compensatory_transcript_secondary_structure_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A secondary structure variant that compe ***
--- *** nsate for the change made by a previous ***
--- *** variant. ***
--- ************************************************
---
CREATE VIEW compensatory_transcript_secondary_structure_variant AS
SELECT
feature_id AS compensatory_transcript_secondary_structure_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'compensatory_transcript_secondary_structure_variant';
--- ************************************************
--- *** relation: translational_product_structure_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant within the transcript ***
--- *** that changes the structure of the trans ***
--- *** lational product. ***
--- ************************************************
---
CREATE VIEW translational_product_structure_variant AS
SELECT
feature_id AS translational_product_structure_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = '3D_polypeptide_structure_variant' OR cvterm.name = 'complex_change_of_translational_product_variant' OR cvterm.name = 'polypeptide_sequence_variant' OR cvterm.name = 'complex_3D_structural_variant' OR cvterm.name = 'conformational_change_variant' OR cvterm.name = 'amino_acid_deletion' OR cvterm.name = 'amino_acid_insertion' OR cvterm.name = 'amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide' OR cvterm.name = 'polypeptide_fusion' OR cvterm.name = 'polypeptide_truncation' OR cvterm.name = 'conservative_amino_acid_substitution' OR cvterm.name = 'non_conservative_amino_acid_substitution' OR cvterm.name = 'elongated_polypeptide_C_terminal' OR cvterm.name = 'elongated_polypeptide_N_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_out_of_frame_polypeptide_C_terminal' OR cvterm.name = 'elongated_in_frame_polypeptide_N_terminal_elongation' OR cvterm.name = 'elongated_out_of_frame_polypeptide_N_terminal' OR cvterm.name = 'translational_product_structure_variant';
--- ************************************************
--- *** relation: threed_polypeptide_structure_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that changes the resu ***
--- *** lting polypeptide structure. ***
--- ************************************************
---
CREATE VIEW threed_polypeptide_structure_variant AS
SELECT
feature_id AS threed_polypeptide_structure_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'complex_3D_structural_variant' OR cvterm.name = 'conformational_change_variant' OR cvterm.name = '3D_polypeptide_structure_variant';
--- ************************************************
--- *** relation: complex_3d_structural_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant that changes the resu ***
--- *** lting polypeptide structure. ***
--- ************************************************
---
CREATE VIEW complex_3d_structural_variant AS
SELECT
feature_id AS complex_3d_structural_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'complex_3D_structural_variant';
--- ************************************************
--- *** relation: conformational_change_variant ***
--- *** relation type: VIEW ***
--- *** ***
--- *** A sequence variant in the CDS region tha ***
--- *** t causes a conformational change in the ***
--- *** resulting polypeptide sequence. ***
--- ************************************************
---
CREATE VIEW conformational_change_variant AS
SELECT
feature_id AS conformational_change_variant_id,
feature.*
FROM
feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
WHERE cvterm.name = 'conformational_change_variant';
--- ************************************************
--- *** relation: complex_change_of_translational_product_variant ***
--- *** relation type: VIEW ***