tripal/t4d8

SET search_path = chado,public;
-- TABLE: feature_cvterm
-- ================================================

create table feature_cvterm (
    feature_cvterm_id bigserial not null,
    primary key (feature_cvterm_id),
    feature_id bigint not null,
    foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED,
    cvterm_id bigint not null,
    foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
    pub_id bigint not null,
    foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
    is_not boolean not null default false,
    rank int not null default 0,
    constraint feature_cvterm_c1 unique (feature_id,cvterm_id,pub_id,rank)
);
create index feature_cvterm_idx1 on feature_cvterm (feature_id);
create index feature_cvterm_idx2 on feature_cvterm (cvterm_id);
create index feature_cvterm_idx3 on feature_cvterm (pub_id);

COMMENT ON TABLE feature_cvterm IS 'Associate a term from a cv with a feature, for example, GO annotation.';

COMMENT ON COLUMN feature_cvterm.pub_id IS 'Provenance for the annotation. Each annotation should have a single primary publication (which may be of the appropriate type for computational analyses) where more details can be found. Additional provenance dbxrefs can be attached using feature_cvterm_dbxref.';

COMMENT ON COLUMN feature_cvterm.is_not IS 'If this is set to true, then this annotation is interpreted as a NEGATIVE annotation - i.e. the feature does NOT have the specified function, process, component, part, etc. See GO docs for more details.';


-- ================================================
-- TABLE: feature_cvtermprop
-- ================================================

create table feature_cvtermprop (
    feature_cvtermprop_id bigserial not null,
    primary key (feature_cvtermprop_id),
    feature_cvterm_id bigint not null,
    foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade,
    type_id bigint not null,
    foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
    value text null,
    rank int not null default 0,
    constraint feature_cvtermprop_c1 unique (feature_cvterm_id,type_id,rank)
);
create index feature_cvtermprop_idx1 on feature_cvtermprop (feature_cvterm_id);
create index feature_cvtermprop_idx2 on feature_cvtermprop (type_id);

COMMENT ON TABLE feature_cvtermprop IS 'Extensible properties for
feature to cvterm associations. Examples: GO evidence codes;
qualifiers; metadata such as the date on which the entry was curated
and the source of the association. See the featureprop table for
meanings of type_id, value and rank.';

COMMENT ON COLUMN feature_cvtermprop.type_id IS 'The name of the
property/slot is a cvterm. The meaning of the property is defined in
that cvterm. cvterms may come from the OBO evidence code cv.';

COMMENT ON COLUMN feature_cvtermprop.value IS 'The value of the
property, represented as text. Numeric values are converted to their
text representation. This is less efficient than using native database
types, but is easier to query.';

COMMENT ON COLUMN feature_cvtermprop.rank IS 'Property-Value
ordering. Any feature_cvterm can have multiple values for any particular
property type - these are ordered in a list using rank, counting from
zero. For properties that are single-valued rather than multi-valued,
the default 0 value should be used.';


-- ================================================
-- TABLE: feature_cvterm_dbxref
-- ================================================

create table feature_cvterm_dbxref (
    feature_cvterm_dbxref_id bigserial not null,
    primary key (feature_cvterm_dbxref_id),
    feature_cvterm_id bigint not null,
    foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade,
    dbxref_id bigint not null,
    foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED,
    constraint feature_cvterm_dbxref_c1 unique (feature_cvterm_id,dbxref_id)
);
create index feature_cvterm_dbxref_idx1 on feature_cvterm_dbxref (feature_cvterm_id);
create index feature_cvterm_dbxref_idx2 on feature_cvterm_dbxref (dbxref_id);

COMMENT ON TABLE feature_cvterm_dbxref IS 'Additional dbxrefs for an association. Rows in the feature_cvterm table may be backed up by dbxrefs. For example, a feature_cvterm association that was inferred via a protein-protein interaction may be backed by by refering to the dbxref for the alternate protein. Corresponds to the WITH column in a GO gene association file (but can also be used for other analagous associations). See http://www.geneontology.org/doc/GO.annotation.shtml#file for more details.';

-- ================================================
-- TABLE: feature_cvterm_pub
-- ================================================

create table feature_cvterm_pub (
    feature_cvterm_pub_id bigserial not null,
    primary key (feature_cvterm_pub_id),
    feature_cvterm_id bigint not null,
    foreign key (feature_cvterm_id) references feature_cvterm (feature_cvterm_id) on delete cascade,
    pub_id bigint not null,
    foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
    constraint feature_cvterm_pub_c1 unique (feature_cvterm_id,pub_id)
);
create index feature_cvterm_pub_idx1 on feature_cvterm_pub (feature_cvterm_id);
create index feature_cvterm_pub_idx2 on feature_cvterm_pub (pub_id);

COMMENT ON TABLE feature_cvterm_pub IS 'Secondary pubs for an
association. Each feature_cvterm association is supported by a single
primary publication. Additional secondary pubs can be added using this
linking table (in a GO gene association file, these corresponding to
any IDs after the pipe symbol in the publications column.';

-- ================================================
-- TABLE: synonym
-- ================================================

create table synonym (
    synonym_id bigserial not null,
    primary key (synonym_id),
    name varchar(255) not null,
    type_id bigint not null,
    foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
    synonym_sgml varchar(255) not null,
    constraint synonym_c1 unique (name,type_id)
);
create index synonym_idx1 on synonym (type_id);
create index synonym_idx2 on synonym ((lower(synonym_sgml)));

COMMENT ON TABLE synonym IS 'A synonym for a feature. One feature can have multiple synonyms, and the same synonym can apply to multiple features.';

COMMENT ON COLUMN synonym.name IS 'The synonym itself. Should be human-readable machine-searchable ascii text.';

COMMENT ON COLUMN synonym.synonym_sgml IS 'The fully specified synonym, with any non-ascii characters encoded in SGML.';

COMMENT ON COLUMN synonym.type_id IS 'Types would be symbol and fullname for now.';


-- ================================================
-- TABLE: feature_synonym
-- ================================================

create table feature_synonym (
    feature_synonym_id bigserial not null,
    primary key (feature_synonym_id),
    synonym_id bigint not null,
    foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED,
    feature_id bigint not null,
    foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED,
    pub_id bigint not null,
    foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
    is_current boolean not null default 'false',
    is_internal boolean not null default 'false',
    constraint feature_synonym_c1 unique (synonym_id,feature_id,pub_id)
);
create index feature_synonym_idx1 on feature_synonym (synonym_id);
create index feature_synonym_idx2 on feature_synonym (feature_id);
create index feature_synonym_idx3 on feature_synonym (pub_id);

COMMENT ON TABLE feature_synonym IS 'Linking table between feature and synonym.';

COMMENT ON COLUMN feature_synonym.pub_id IS 'The pub_id link is for relating the usage of a given synonym to the publication in which it was used.';

COMMENT ON COLUMN feature_synonym.is_current IS 'The is_current boolean indicates whether the linked synonym is the  current -official- symbol for the linked feature.';

COMMENT ON COLUMN feature_synonym.is_internal IS 'Typically a synonym exists so that somebody querying the db with an obsolete name can find the object theyre looking for (under its current name.  If the synonym has been used publicly and deliberately (e.g. in a paper), it may also be listed in reports as a synonym. If the synonym was not used deliberately (e.g. there was a typo which went public), then the is_internal boolean may be set to -true- so that it is known that the synonym is -internal- and should be queryable but should not be listed in reports as a valid synonym.';

-- ================================================
-- TABLE: feature_contact
-- ================================================

CREATE TABLE feature_contact (
    feature_contact_id bigserial primary key NOT NULL,
    feature_id bigint NOT NULL,
    contact_id bigint NOT NULL,
    CONSTRAINT feature_contact_c1 UNIQUE (feature_id, contact_id),
    FOREIGN KEY (contact_id) REFERENCES contact(contact_id) ON DELETE CASCADE,
    FOREIGN KEY (feature_id) REFERENCES feature(feature_id) ON DELETE CASCADE
);

CREATE INDEX feature_contact_idx1 ON feature_contact USING btree (feature_id);
CREATE INDEX feature_contact_idx2 ON feature_contact USING btree (contact_id);

COMMENT ON TABLE feature_contact IS 'Links contact(s) with a feature.  Used to indicate a particular
person or organization responsible for discovery or that can provide more information on a particular feature.';
CREATE VIEW type_feature_count AS
  SELECT t.name AS type,count(*) AS num_features
   FROM cvterm AS t INNER JOIN feature ON (type_id=t.cvterm_id)
  GROUP BY t.name;
COMMENT ON VIEW type_feature_count IS 'per-feature-type feature counts';
CREATE SCHEMA genetic_code;
SET search_path = genetic_code,chado,pg_catalog;

CREATE TABLE gencode (
        gencode_id      BIGINT PRIMARY KEY NOT NULL,
        organismstr     VARCHAR(512) NOT NULL
);

CREATE TABLE gencode_codon_aa (
        gencode_id      BIGINT NOT NULL REFERENCES gencode(gencode_id),
        codon           CHAR(3) NOT NULL,
        aa              CHAR(1) NOT NULL,
        CONSTRAINT gencode_codon_unique UNIQUE( gencode_id, codon )
);
CREATE INDEX gencode_codon_aa_i1 ON gencode_codon_aa(gencode_id,codon,aa);

CREATE TABLE gencode_startcodon (
        gencode_id      BIGINT NOT NULL REFERENCES gencode(gencode_id),
        codon           CHAR(3),
        CONSTRAINT gencode_startcodon_unique UNIQUE( gencode_id, codon )
);
SET search_path = chado,pg_catalog;
--
-- functions operating on featureloc ranges
--

-- create a point
CREATE OR REPLACE FUNCTION create_point (bigint, bigint) RETURNS point AS
 'SELECT point ($1, $2)'
LANGUAGE 'sql';

-- create a range box
-- (make this immutable so we can index it)
CREATE OR REPLACE FUNCTION boxrange (bigint, bigint) RETURNS box AS
 'SELECT box (create_point(0, $1), create_point($2,500000000))'
LANGUAGE 'sql' IMMUTABLE;

-- create a query box
CREATE OR REPLACE FUNCTION boxquery (bigint, bigint) RETURNS box AS
 'SELECT box (create_point($1, $2), create_point($1, $2))'
LANGUAGE 'sql' IMMUTABLE;

--functional index that depends on the above functions
CREATE INDEX binloc_boxrange ON featureloc USING GIST (boxrange(fmin, fmax));


CREATE OR REPLACE FUNCTION featureloc_slice(bigint, bigint) RETURNS setof featureloc AS
  'SELECT * from featureloc where boxquery($1, $2) <@ boxrange(fmin,fmax)'
LANGUAGE 'sql';

CREATE OR REPLACE FUNCTION featureloc_slice(varchar, bigint, bigint)
  RETURNS setof featureloc AS
  'SELECT featureloc.*
   FROM featureloc
   INNER JOIN feature AS srcf ON (srcf.feature_id = featureloc.srcfeature_id)
   WHERE boxquery($2, $3) <@ boxrange(fmin,fmax)
   AND srcf.name = $1 '
LANGUAGE 'sql';

CREATE OR REPLACE FUNCTION featureloc_slice(bigint, bigint, bigint)
  RETURNS setof featureloc AS
  'SELECT *
   FROM featureloc
   WHERE boxquery($2, $3) <@ boxrange(fmin,fmax)
   AND srcfeature_id = $1 '
LANGUAGE 'sql';


-- can we not just do these as views?
CREATE OR REPLACE FUNCTION feature_overlaps(bigint)
 RETURNS setof feature AS
 'SELECT feature.*
  FROM feature
   INNER JOIN featureloc AS x ON (x.feature_id=feature.feature_id)
   INNER JOIN featureloc AS y ON (y.feature_id = $1)
  WHERE
   x.srcfeature_id = y.srcfeature_id            AND
   ( x.fmax >= y.fmin AND x.fmin <= y.fmax ) '
LANGUAGE 'sql';

CREATE OR REPLACE FUNCTION feature_disjoint_from(bigint)
 RETURNS setof feature AS
 'SELECT feature.*
  FROM feature
   INNER JOIN featureloc AS x ON (x.feature_id=feature.feature_id)
   INNER JOIN featureloc AS y ON (y.feature_id = $1)
  WHERE
   x.srcfeature_id = y.srcfeature_id            AND
   ( x.fmax < y.fmin OR x.fmin > y.fmax ) '
LANGUAGE 'sql';



--Evolution of the methods found in range.plpgsql (C. Pommier)
--Goal : increase performances of segment fetching
--       Implies to optimise featureloc_slice

--Background : The existing featureloc_slice uses uses a spatial rtree index. The spatial objects used are a boxrange ((0,fmin), (fmax,500000000)) and a boxquery ((fmin,fmax),(fmin,fmax)) . The boxranges are indexed.
--             To speed up things (for gbrowse) featureloc_slice has been overiden to filter simultaneously on the boxrange and the srcfeature_id. This gives good results.
--             The goal here is to push this logic further and to include the srcfeature_id filter directly into the boxrange object. We propose to consider the following boxs :
--             boxrange : ((srcfeature_id,fmin),(srcfeature_id,fmax))
--             boxquery : ((srcfeature_id,fmin),(srcfeature_id,fmax))



CREATE OR REPLACE FUNCTION boxrange (bigint, bigint, bigint) RETURNS box AS
 'SELECT box (create_point($1, $2), create_point($1,$3))'
LANGUAGE 'sql' IMMUTABLE;

-- create a query box
CREATE OR REPLACE FUNCTION boxquery (bigint, bigint, bigint) RETURNS box AS
 'SELECT box (create_point($1, $2), create_point($1, $3))'
LANGUAGE 'sql' IMMUTABLE;

CREATE INDEX binloc_boxrange_src ON featureloc USING GIST (boxrange(srcfeature_id,fmin, fmax));

CREATE OR REPLACE FUNCTION featureloc_slice(bigint, bigint, bigint)
  RETURNS setof featureloc AS
  'SELECT *
   FROM featureloc
   WHERE boxquery($1, $2, $3) && boxrange(srcfeature_id,fmin,fmax)'
LANGUAGE 'sql';

-- reverse_string
CREATE OR REPLACE FUNCTION reverse_string(TEXT) RETURNS TEXT AS
'
 DECLARE
  reversed_string TEXT;
  incoming ALIAS FOR $1;
 BEGIN
   reversed_string = '''';
   FOR i IN REVERSE char_length(incoming)..1 loop
     reversed_string = reversed_string || substring(incoming FROM i FOR 1);
   END loop;
 RETURN reversed_string;
END'
language plpgsql;

-- complements DNA
CREATE OR REPLACE FUNCTION complement_residues(text) RETURNS text AS
 'SELECT (translate($1,
                   ''acgtrymkswhbvdnxACGTRYMKSWHBVDNX'',
                   ''tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX''))'
LANGUAGE 'sql';

-- revcomp
CREATE OR REPLACE FUNCTION reverse_complement(TEXT) RETURNS TEXT AS
 'SELECT reverse_string(complement_residues($1))'
LANGUAGE 'sql';

-- DNA to AA
CREATE OR REPLACE FUNCTION translate_dna(TEXT,BIGINT) RETURNS TEXT AS
'
 DECLARE
  dnaseq ALIAS FOR $1;
  gcode ALIAS FOR $2;
  translation TEXT;
  dnaseqlen BIGINT;
  codon CHAR(3);
  aa CHAR(1);
  i INT;
 BEGIN
   translation = '''';
   dnaseqlen = char_length(dnaseq);
   i=1;
   WHILE i+1 < dnaseqlen loop
     codon = substring(dnaseq,i,3);
     aa = translate_codon(codon,gcode);
     translation = translation || aa;
     i = i+3;
   END loop;
 RETURN translation;
END'
language plpgsql;

-- DNA to AA, default genetic code
CREATE OR REPLACE FUNCTION translate_dna(TEXT) RETURNS TEXT AS
 'SELECT translate_dna($1,1)'
LANGUAGE 'sql';


CREATE OR REPLACE FUNCTION translate_codon(TEXT,BIGINT) RETURNS CHAR AS
 'SELECT aa FROM genetic_code.gencode_codon_aa WHERE codon=$1 AND gencode_id=$2'
LANGUAGE 'sql';



CREATE OR REPLACE FUNCTION concat_pair (text, text) RETURNS text AS
 'SELECT $1 || $2'
LANGUAGE 'sql';

CREATE AGGREGATE concat (
sfunc = concat_pair,
basetype = text,
stype = text,
initcond = ''
);


--function to 'unshare' exons.  It looks for exons that have the same fmin
--and fmax and belong to the same gene and only keeps one.  The other,
--redundant exons are marked obsolete in the feature table.  Nothing
--is done with those features' entries in the featureprop, feature_dbxref,
--feature_pub, or feature_cvterm tables.  For the moment, I'm assuming
--that any annotations that they have when this script is run are
--identical to their non-obsoleted doppelgangers.  If that's not the case,
--they could be merged via query.
--
--The bulk of this code was contributed by Robin Houston at
--GeneDB/Sanger Centre.

CREATE OR REPLACE FUNCTION share_exons () RETURNS void AS '
  DECLARE
  BEGIN
    /* Generate a table of shared exons */
    CREATE temporary TABLE shared_exons AS
      SELECT gene.feature_id as gene_feature_id
           , gene.uniquename as gene_uniquename
           , transcript1.uniquename as transcript1
           , exon1.feature_id as exon1_feature_id
           , exon1.uniquename as exon1_uniquename
           , transcript2.uniquename as transcript2
           , exon2.feature_id as exon2_feature_id
           , exon2.uniquename as exon2_uniquename
           , exon1_loc.fmin /* = exon2_loc.fmin */
           , exon1_loc.fmax /* = exon2_loc.fmax */
      FROM feature gene
        JOIN cvterm gene_type ON gene.type_id = gene_type.cvterm_id
        JOIN cv gene_type_cv USING (cv_id)
        JOIN feature_relationship gene_transcript1 ON gene.feature_id = gene_transcript1.object_id
        JOIN feature transcript1 ON gene_transcript1.subject_id = transcript1.feature_id
        JOIN cvterm transcript1_type ON transcript1.type_id = transcript1_type.cvterm_id
        JOIN cv transcript1_type_cv ON transcript1_type.cv_id = transcript1_type_cv.cv_id
        JOIN feature_relationship transcript1_exon1 ON transcript1_exon1.object_id = transcript1.feature_id
        JOIN feature exon1 ON transcript1_exon1.subject_id = exon1.feature_id
        JOIN cvterm exon1_type ON exon1.type_id = exon1_type.cvterm_id
        JOIN cv exon1_type_cv ON exon1_type.cv_id = exon1_type_cv.cv_id
        JOIN featureloc exon1_loc ON exon1_loc.feature_id = exon1.feature_id
        JOIN feature_relationship gene_transcript2 ON gene.feature_id = gene_transcript2.object_id
        JOIN feature transcript2 ON gene_transcript2.subject_id = transcript2.feature_id
        JOIN cvterm transcript2_type ON transcript2.type_id = transcript2_type.cvterm_id
        JOIN cv transcript2_type_cv ON transcript2_type.cv_id = transcript2_type_cv.cv_id
        JOIN feature_relationship transcript2_exon2 ON transcript2_exon2.object_id = transcript2.feature_id
        JOIN feature exon2 ON transcript2_exon2.subject_id = exon2.feature_id
        JOIN cvterm exon2_type ON exon2.type_id = exon2_type.cvterm_id
        JOIN cv exon2_type_cv ON exon2_type.cv_id = exon2_type_cv.cv_id
        JOIN featureloc exon2_loc ON exon2_loc.feature_id = exon2.feature_id
      WHERE gene_type_cv.name = ''sequence''
        AND gene_type.name = ''gene''
        AND transcript1_type_cv.name = ''sequence''
        AND transcript1_type.name = ''mRNA''
        AND transcript2_type_cv.name = ''sequence''
        AND transcript2_type.name = ''mRNA''
        AND exon1_type_cv.name = ''sequence''
        AND exon1_type.name = ''exon''
        AND exon2_type_cv.name = ''sequence''
        AND exon2_type.name = ''exon''
        AND exon1.feature_id < exon2.feature_id
        AND exon1_loc.rank = 0
        AND exon2_loc.rank = 0
        AND exon1_loc.fmin = exon2_loc.fmin
        AND exon1_loc.fmax = exon2_loc.fmax
    ;

    /* Choose one of the shared exons to be the canonical representative.
       We pick the one with the smallest feature_id.
     */
    CREATE temporary TABLE canonical_exon_representatives AS
      SELECT gene_feature_id, min(exon1_feature_id) AS canonical_feature_id, fmin
      FROM shared_exons
      GROUP BY gene_feature_id,fmin
    ;

    CREATE temporary TABLE exon_replacements AS
      SELECT DISTINCT shared_exons.exon2_feature_id AS actual_feature_id
                    , canonical_exon_representatives.canonical_feature_id
                    , canonical_exon_representatives.fmin
      FROM shared_exons
        JOIN canonical_exon_representatives USING (gene_feature_id)
      WHERE shared_exons.exon2_feature_id <> canonical_exon_representatives.canonical_feature_id
        AND shared_exons.fmin = canonical_exon_representatives.fmin
    ;

    UPDATE feature_relationship
      SET subject_id = (
            SELECT canonical_feature_id
            FROM exon_replacements
            WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id)
      WHERE subject_id IN (
        SELECT actual_feature_id FROM exon_replacements
    );

    UPDATE feature_relationship
      SET object_id = (
            SELECT canonical_feature_id
            FROM exon_replacements
            WHERE feature_relationship.subject_id = exon_replacements.actual_feature_id)
      WHERE object_id IN (
        SELECT actual_feature_id FROM exon_replacements
    );

    UPDATE feature
      SET is_obsolete = true
      WHERE feature_id IN (
        SELECT actual_feature_id FROM exon_replacements
    );
  END;
' LANGUAGE 'plpgsql';

--This is a function to seek out exons of transcripts and orders them,
--using feature_relationship.rank, in "transcript order" numbering
--from 0, taking strand into account. It will not touch transcripts that
--already have their exons ordered (in case they have a non-obvious
--ordering due to trans splicing). It takes as an argument the
--feature.type_id of the parent transcript type (typically, mRNA, although
--non coding transcript types should work too).

CREATE OR REPLACE FUNCTION order_exons (bigint) RETURNS void AS '
  DECLARE
    parent_type      ALIAS FOR $1;
    exon_id          bigint;
    part_of          bigint;
    exon_type        bigint;
    strand           int;
    arow             RECORD;
    order_by         varchar;
    rowcount         int;
    exon_count       int;
    ordered_exons    int;
    transcript_id    bigint;
    transcript_row   feature%ROWTYPE;
  BEGIN
    SELECT INTO part_of cvterm_id FROM cvterm WHERE name=''part_of''
      AND cv_id IN (SELECT cv_id FROM cv WHERE name=''relationship'');
    --SELECT INTO exon_type cvterm_id FROM cvterm WHERE name=''exon''
    --  AND cv_id IN (SELECT cv_id FROM cv WHERE name=''sequence'');

    --RAISE NOTICE ''part_of %, exon %'',part_of,exon_type;

    FOR transcript_row IN
      SELECT * FROM feature WHERE type_id = parent_type
    LOOP
      transcript_id = transcript_row.feature_id;
      SELECT INTO rowcount count(*) FROM feature_relationship
        WHERE object_id = transcript_id
          AND rank = 0;

      --Dont modify this transcript if there are already numbered exons or
      --if there is only one exon
      IF rowcount = 1 THEN
        --RAISE NOTICE ''skipping transcript %, row count %'',transcript_id,rowcount;
        CONTINUE;
      END IF;

      --need to reverse the order if the strand is negative
      SELECT INTO strand strand FROM featureloc WHERE feature_id=transcript_id;
      IF strand > 0 THEN
          order_by = ''fl.fmin'';
      ELSE
          order_by = ''fl.fmax desc'';
      END IF;

      exon_count = 0;
      FOR arow IN EXECUTE
        ''SELECT fr.*, fl.fmin, fl.fmax
          FROM feature_relationship fr, featureloc fl
          WHERE fr.object_id  = ''||transcript_id||''
            AND fr.subject_id = fl.feature_id
            AND fr.type_id    = ''||part_of||''
            ORDER BY ''||order_by
      LOOP
        --number the exons for a given transcript
        UPDATE feature_relationship
          SET rank = exon_count
          WHERE feature_relationship_id = arow.feature_relationship_id;
        exon_count = exon_count + 1;
      END LOOP;

    END LOOP;

  END;
' LANGUAGE 'plpgsql';
-- down the graph: eg from  chromosome to contig
CREATE OR REPLACE FUNCTION project_point_up(bigint,bigint,bigint,bigint)
 RETURNS bigint AS
'SELECT
  CASE WHEN $4<0
   THEN $3-$1             -- rev strand
   ELSE $1-$2             -- fwd strand
  END AS p'
LANGUAGE 'sql';

-- down the graph: eg from contig to chromosome
CREATE OR REPLACE FUNCTION project_point_down(bigint,bigint,bigint,bigint)
 RETURNS bigint AS
'SELECT
  CASE WHEN $4<0
   THEN $3-$1
   ELSE $1+$2
  END AS p'
LANGUAGE 'sql';

CREATE OR REPLACE FUNCTION project_featureloc_up(bigint,bigint)
 RETURNS featureloc AS
'
DECLARE
    in_featureloc_id alias for $1;
    up_srcfeature_id alias for $2;
    in_featureloc featureloc%ROWTYPE;
    up_featureloc featureloc%ROWTYPE;
    nu_featureloc featureloc%ROWTYPE;
    nu_fmin BIGINT;
    nu_fmax BIGINT;
    nu_strand INT;
BEGIN
 SELECT INTO in_featureloc
   featureloc.*
  FROM featureloc
  WHERE featureloc_id = in_featureloc_id;

 SELECT INTO up_featureloc
   up_fl.*
  FROM featureloc AS in_fl
  INNER JOIN featureloc AS up_fl
    ON (in_fl.srcfeature_id = up_fl.feature_id)
  WHERE
   in_fl.featureloc_id = in_featureloc_id AND
   up_fl.srcfeature_id = up_srcfeature_id;

  IF up_featureloc.strand IS NULL
   THEN RETURN NULL;
  END IF;

  IF up_featureloc.strand < 0
  THEN
   nu_fmin = project_point_up(in_featureloc.fmax,
                              up_featureloc.fmin,up_featureloc.fmax,-1);
   nu_fmax = project_point_up(in_featureloc.fmin,
                              up_featureloc.fmin,up_featureloc.fmax,-1);
   nu_strand = -in_featureloc.strand;
  ELSE
   nu_fmin = project_point_up(in_featureloc.fmin,
                              up_featureloc.fmin,up_featureloc.fmax,1);
   nu_fmax = project_point_up(in_featureloc.fmax,
                              up_featureloc.fmin,up_featureloc.fmax,1);
   nu_strand = in_featureloc.strand;
  END IF;
  in_featureloc.fmin = nu_fmin;
  in_featureloc.fmax = nu_fmax;
  in_featureloc.strand = nu_strand;
  in_featureloc.srcfeature_id = up_featureloc.srcfeature_id;
  RETURN in_featureloc;
END
'
LANGUAGE 'plpgsql';

CREATE OR REPLACE FUNCTION project_point_g2t(bigint,bigint,bigint)
 RETURNS BIGINT AS '
 DECLARE
    in_p             alias for $1;
    srcf_id          alias for $2;
    t_id             alias for $3;
    e_floc           featureloc%ROWTYPE;
    out_p            BIGINT;
    exon_cvterm_id   BIGINT;
BEGIN
 SELECT INTO exon_cvterm_id get_feature_type_id(''exon'');
 SELECT INTO out_p
  CASE
   WHEN strand<0 THEN fmax-p
   ELSE p-fmin
   END AS p
  FROM featureloc
   INNER JOIN feature USING (feature_id)
   INNER JOIN feature_relationship ON (feature.feature_id=subject_id)
  WHERE
   object_id = t_id                     AND
   feature.type_id = exon_cvterm_id     AND
   featureloc.srcfeature_id = srcf_id   AND
   in_p >= fmin                         AND
   in_p <= fmax;
  RETURN in_featureloc;
END
'
LANGUAGE 'plpgsql';


CREATE OR REPLACE FUNCTION get_cv_id_for_feature() RETURNS BIGINT
 AS 'SELECT cv_id FROM cv WHERE name=''sequence''' LANGUAGE 'sql';
CREATE OR REPLACE FUNCTION get_cv_id_for_featureprop() RETURNS BIGINT
 AS 'SELECT cv_id FROM cv WHERE name=''feature_property''' LANGUAGE 'sql';
CREATE OR REPLACE FUNCTION get_cv_id_for_feature_relationsgip() RETURNS BIGINT
 AS 'SELECT cv_id FROM cv WHERE name=''relationship''' LANGUAGE 'sql';

CREATE OR REPLACE FUNCTION get_feature_type_id(VARCHAR) RETURNS BIGINT
 AS '
  SELECT cvterm_id
  FROM cv INNER JOIN cvterm USING (cv_id)
  WHERE cvterm.name=$1 AND cv.name=''sequence''
 ' LANGUAGE 'sql';

CREATE OR REPLACE FUNCTION get_featureprop_type_id(VARCHAR) RETURNS BIGINT
 AS '
  SELECT cvterm_id
  FROM cv INNER JOIN cvterm USING (cv_id)
  WHERE cvterm.name=$1 AND cv.name=''feature_property''
 ' LANGUAGE 'sql';

CREATE OR REPLACE FUNCTION get_feature_relationship_type_id(VARCHAR) RETURNS BIGINT
 AS '
  SELECT cvterm_id
  FROM cv INNER JOIN cvterm USING (cv_id)
  WHERE cvterm.name=$1 AND cv.name=''relationship''
 ' LANGUAGE 'sql';

-- depends on sequence-cv-helper
CREATE OR REPLACE FUNCTION get_feature_id(VARCHAR,VARCHAR,VARCHAR) RETURNS BIGINT
 AS '
  SELECT feature_id
  FROM feature
  WHERE uniquename=$1
    AND type_id=get_feature_type_id($2)
    AND organism_id=get_organism_id($3)
 ' LANGUAGE 'sql';
--This is an automatically generated file; do not edit it as changes will not
--be saved.  Instead, modify bin/create-so-bridge.pl, which creates this file.


CREATE SCHEMA so;
SET search_path=so,chado,pg_catalog;

--- ************************************************
--- *** relation: region ***
--- *** relation type: VIEW                      ***
--- ***                                          ***
--- *** A sequence_feature with an extent greate ***
--- *** r than zero. A nucleotide region is comp ***
--- *** osed of bases and a polypeptide region i ***
--- *** s composed of amino acids.               ***
--- ************************************************
---

CREATE VIEW region AS
  SELECT
    feature_id AS region_id,
    feature.*
  FROM
    feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
  WHERE cvterm.name = 'biomaterial_region' OR cvterm.name = 'experimental_feature' OR cvterm.name = 'biological_region' OR cvterm.name = 'topologically_defined_region' OR cvterm.name = 'reagent' OR cvterm.name = 'engineered_region' OR cvterm.name = 'PCR_product' OR cvterm.name = 'clone' OR cvterm.name = 'rescue_region' OR cvterm.name = 'oligo' OR cvterm.name = 'clone_insert' OR cvterm.name = 'cloned_region' OR cvterm.name = 'databank_entry' OR cvterm.name = 'RAPD' OR cvterm.name = 'genomic_clone' OR cvterm.name = 'cDNA_clone' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'validated_cDNA_clone' OR cvterm.name = 'invalidated_cDNA_clone' OR cvterm.name = 'three_prime_RACE_clone' OR cvterm.name = 'chimeric_cDNA_clone' OR cvterm.name = 'genomically_contaminated_cDNA_clone' OR cvterm.name = 'polyA_primed_cDNA_clone' OR cvterm.name = 'partially_processed_cDNA_clone' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'aptamer' OR cvterm.name = 'probe' OR cvterm.name = 'tag' OR cvterm.name = 'ss_oligo' OR cvterm.name = 'ds_oligo' OR cvterm.name = 'DNAzyme' OR cvterm.name = 'synthetic_oligo' OR cvterm.name = 'DNA_aptamer' OR cvterm.name = 'RNA_aptamer' OR cvterm.name = 'microarray_oligo' OR cvterm.name = 'SAGE_tag' OR cvterm.name = 'STS' OR cvterm.name = 'EST' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'five_prime_EST' OR cvterm.name = 'three_prime_EST' OR cvterm.name = 'UST' OR cvterm.name = 'RST' OR cvterm.name = 'three_prime_UST' OR cvterm.name = 'five_prime_UST' OR cvterm.name = 'three_prime_RST' OR cvterm.name = 'five_prime_RST' OR cvterm.name = 'primer' OR cvterm.name = 'sequencing_primer' OR cvterm.name = 'forward_primer' OR cvterm.name = 'reverse_primer' OR cvterm.name = 'ASPE_primer' OR cvterm.name = 'dCAPS_primer' OR cvterm.name = 'RNAi_reagent' OR cvterm.name = 'DNA_constraint_sequence' OR cvterm.name = 'morpholino_oligo' OR cvterm.name = 'PNA_oligo' OR cvterm.name = 'LNA_oligo' OR cvterm.name = 'TNA_oligo' OR cvterm.name = 'GNA_oligo' OR cvterm.name = 'R_GNA_oligo' OR cvterm.name = 'S_GNA_oligo' OR cvterm.name = 'cloned_cDNA_insert' OR cvterm.name = 'cloned_genomic_insert' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'BAC_cloned_genomic_insert' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'engineered_rescue_region' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'engineered_foreign_region' OR cvterm.name = 'engineered_tag' OR cvterm.name = 'engineered_insert' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'match_part' OR cvterm.name = 'assembly_component' OR cvterm.name = 'conserved_region' OR cvterm.name = 'match' OR cvterm.name = 'remark' OR cvterm.name = 'reading_frame' OR cvterm.name = 'consensus_region' OR cvterm.name = 'low_complexity_region' OR cvterm.name = 'assembly' OR cvterm.name = 'transcribed_fragment' OR cvterm.name = 'transcribed_cluster' OR cvterm.name = 'high_identity_region' OR cvterm.name = 'mathematically_defined_repeat' OR cvterm.name = 'experimentally_defined_binding_region' OR cvterm.name = 'contig' OR cvterm.name = 'read' OR cvterm.name = 'restriction_fragment' OR cvterm.name = 'golden_path_fragment' OR cvterm.name = 'tiling_path_fragment' OR cvterm.name = 'gap' OR cvterm.name = 'sonicate_fragment' OR cvterm.name = 'paired_end_fragment' OR cvterm.name = 'read_pair' OR cvterm.name = 'contig_read' OR cvterm.name = 'BAC_end' OR cvterm.name = 'dye_terminator_read' OR cvterm.name = 'pyrosequenced_read' OR cvterm.name = 'ligation_based_read' OR cvterm.name = 'polymerase_synthesis_read' OR cvterm.name = 'PAC_end' OR cvterm.name = 'YAC_end' OR cvterm.name = 'clone_end' OR cvterm.name = 'RFLP_fragment' OR cvterm.name = 'tiling_path_clone' OR cvterm.name = 'coding_conserved_region' OR cvterm.name = 'nc_conserved_region' OR cvterm.name = 'RR_tract' OR cvterm.name = 'homologous_region' OR cvterm.name = 'centromere_DNA_Element_I' OR cvterm.name = 'centromere_DNA_Element_II' OR cvterm.name = 'centromere_DNA_Element_III' OR cvterm.name = 'X_element' OR cvterm.name = 'U_box' OR cvterm.name = 'regional_centromere_central_core' OR cvterm.name = 'syntenic_region' OR cvterm.name = 'paralogous_region' OR cvterm.name = 'orthologous_region' OR cvterm.name = 'nucleotide_match' OR cvterm.name = 'protein_match' OR cvterm.name = 'expressed_sequence_match' OR cvterm.name = 'cross_genome_match' OR cvterm.name = 'translated_nucleotide_match' OR cvterm.name = 'primer_match' OR cvterm.name = 'EST_match' OR cvterm.name = 'cDNA_match' OR cvterm.name = 'UST_match' OR cvterm.name = 'RST_match' OR cvterm.name = 'sequence_difference' OR cvterm.name = 'experimental_result_region' OR cvterm.name = 'polypeptide_sequencing_information' OR cvterm.name = 'possible_base_call_error' OR cvterm.name = 'possible_assembly_error' OR cvterm.name = 'assembly_error_correction' OR cvterm.name = 'base_call_error_correction' OR cvterm.name = 'overlapping_feature_set' OR cvterm.name = 'no_output' OR cvterm.name = 'overlapping_EST_set' OR cvterm.name = 'non_adjacent_residues' OR cvterm.name = 'non_terminal_residue' OR cvterm.name = 'sequence_conflict' OR cvterm.name = 'sequence_uncertainty' OR cvterm.name = 'contig_collection' OR cvterm.name = 'ORF' OR cvterm.name = 'blocked_reading_frame' OR cvterm.name = 'mini_gene' OR cvterm.name = 'rescue_mini_gene' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'sequence_assembly' OR cvterm.name = 'fragment_assembly' OR cvterm.name = 'supercontig' OR cvterm.name = 'contig' OR cvterm.name = 'tiling_path' OR cvterm.name = 'virtual_sequence' OR cvterm.name = 'golden_path' OR cvterm.name = 'ultracontig' OR cvterm.name = 'expressed_sequence_assembly' OR cvterm.name = 'fingerprint_map' OR cvterm.name = 'STS_map' OR cvterm.name = 'RH_map' OR cvterm.name = 'unigene_cluster' OR cvterm.name = 'CHiP_seq_region' OR cvterm.name = 'sequence_secondary_structure' OR cvterm.name = 'linkage_group' OR cvterm.name = 'polypeptide' OR cvterm.name = 'deletion' OR cvterm.name = 'origin_of_replication' OR cvterm.name = 'recombination_feature' OR cvterm.name = 'CpG_island' OR cvterm.name = 'pseudogene' OR cvterm.name = 'binding_site' OR cvterm.name = 'pseudogenic_region' OR cvterm.name = 'cap' OR cvterm.name = 'intergenic_region' OR cvterm.name = 'oligo_U_tail' OR cvterm.name = 'polyA_sequence' OR cvterm.name = 'repeat_region' OR cvterm.name = 'insertion' OR cvterm.name = 'gene' OR cvterm.name = 'repeat_unit' OR cvterm.name = 'QTL' OR cvterm.name = 'chromosome_part' OR cvterm.name = 'gene_member_region' OR cvterm.name = 'transcript_region' OR cvterm.name = 'polypeptide_region' OR cvterm.name = 'gene_component_region' OR cvterm.name = 'mobile_genetic_element' OR cvterm.name = 'replicon' OR cvterm.name = 'base' OR cvterm.name = 'amino_acid' OR cvterm.name = 'genetic_marker' OR cvterm.name = 'sequence_motif' OR cvterm.name = 'restriction_enzyme_recognition_site' OR cvterm.name = 'restriction_enzyme_single_strand_overhang' OR cvterm.name = 'epigenetically_modified_region' OR cvterm.name = 'open_chromatin_region' OR cvterm.name = 'gene_group' OR cvterm.name = 'substitution' OR cvterm.name = 'inversion' OR cvterm.name = 'retron' OR cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'D_loop' OR cvterm.name = 'ARS' OR cvterm.name = 'oriT' OR cvterm.name = 'amplification_origin' OR cvterm.name = 'oriV' OR cvterm.name = 'oriC' OR cvterm.name = 'recombination_hotspot' OR cvterm.name = 'haplotype_block' OR cvterm.name = 'sequence_rearrangement_feature' OR cvterm.name = 'iDNA' OR cvterm.name = 'specific_recombination_site' OR cvterm.name = 'chromosome_breakage_sequence' OR cvterm.name = 'internal_eliminated_sequence' OR cvterm.name = 'macronucleus_destined_segment' OR cvterm.name = 'recombination_feature_of_rearranged_gene' OR cvterm.name = 'site_specific_recombination_target_region' OR cvterm.name = 'recombination_signal_sequence' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_feature' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_spacer' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment' OR cvterm.name = 'vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster' OR cvterm.name = 'vertebrate_immune_system_gene_recombination_signal_feature' OR cvterm.name = 'D_gene' OR cvterm.name = 'V_gene' OR cvterm.name = 'J_gene' OR cvterm.name = 'C_gene' OR cvterm.name = 'D_J_C_cluster' OR cvterm.name = 'J_C_cluster' OR cvterm.name = 'J_cluster' OR cvterm.name = 'V_cluster' OR cvterm.name = 'V_J_cluster' OR cvterm.name = 'V_J_C_cluster' OR cvterm.name = 'C_cluster' OR cvterm.name = 'D_cluster' OR cvterm.name = 'D_J_cluster' OR cvterm.name = 'three_prime_D_spacer' OR cvterm.name = 'five_prime_D_spacer' OR cvterm.name = 'J_spacer' OR cvterm.name = 'V_spacer' OR cvterm.name = 'VD_gene' OR cvterm.name = 'DJ_gene' OR cvterm.name = 'VDJ_gene' OR cvterm.name = 'VJ_gene' OR cvterm.name = 'DJ_J_cluster' OR cvterm.name = 'VDJ_J_C_cluster' OR cvterm.name = 'VDJ_J_cluster' OR cvterm.name = 'VJ_C_cluster' OR cvterm.name = 'VJ_J_C_cluster' OR cvterm.name = 'VJ_J_cluster' OR cvterm.name = 'D_DJ_C_cluster' OR cvterm.name = 'D_DJ_cluster' OR cvterm.name = 'D_DJ_J_C_cluster' OR cvterm.name = 'D_DJ_J_cluster' OR cvterm.name = 'V_DJ_cluster' OR cvterm.name = 'V_DJ_J_cluster' OR cvterm.name = 'V_VDJ_C_cluster' OR cvterm.name = 'V_VDJ_cluster' OR cvterm.name = 'V_VDJ_J_cluster' OR cvterm.name = 'V_VJ_C_cluster' OR cvterm.name = 'V_VJ_cluster' OR cvterm.name = 'V_VJ_J_cluster' OR cvterm.name = 'V_D_DJ_C_cluster' OR cvterm.name = 'V_D_DJ_cluster' OR cvterm.name = 'V_D_DJ_J_C_cluster' OR cvterm.name = 'V_D_DJ_J_cluster' OR cvterm.name = 'V_D_J_C_cluster' OR cvterm.name = 'V_D_J_cluster' OR cvterm.name = 'DJ_C_cluster' OR cvterm.name = 'DJ_J_C_cluster' OR cvterm.name = 'VDJ_C_cluster' OR cvterm.name = 'V_DJ_C_cluster' OR cvterm.name = 'V_DJ_J_C_cluster' OR cvterm.name = 'V_VDJ_J_C_cluster' OR cvterm.name = 'V_VJ_J_C_cluster' OR cvterm.name = 'J_gene_recombination_feature' OR cvterm.name = 'D_gene_recombination_feature' OR cvterm.name = 'V_gene_recombination_feature' OR cvterm.name = 'heptamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'nonamer_of_recombination_feature_of_vertebrate_immune_system_gene' OR cvterm.name = 'five_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_recombination_signal_sequence' OR cvterm.name = 'three_prime_D_heptamer' OR cvterm.name = 'five_prime_D_heptamer' OR cvterm.name = 'J_heptamer' OR cvterm.name = 'V_heptamer' OR cvterm.name = 'three_prime_D_nonamer' OR cvterm.name = 'five_prime_D_nonamer' OR cvterm.name = 'J_nonamer' OR cvterm.name = 'V_nonamer' OR cvterm.name = 'integration_excision_site' OR cvterm.name = 'resolution_site' OR cvterm.name = 'inversion_site' OR cvterm.name = 'inversion_site_part' OR cvterm.name = 'attI_site' OR cvterm.name = 'attP_site' OR cvterm.name = 'attB_site' OR cvterm.name = 'attL_site' OR cvterm.name = 'attR_site' OR cvterm.name = 'attC_site' OR cvterm.name = 'attCtn_site' OR cvterm.name = 'loxP_site' OR cvterm.name = 'dif_site' OR cvterm.name = 'FRT_site' OR cvterm.name = 'IRLinv_site' OR cvterm.name = 'IRRinv_site' OR cvterm.name = 'processed_pseudogene' OR cvterm.name = 'non_processed_pseudogene' OR cvterm.name = 'pseudogene_by_unequal_crossing_over' OR cvterm.name = 'nuclear_mt_pseudogene' OR cvterm.name = 'cassette_pseudogene' OR cvterm.name = 'duplicated_pseudogene' OR cvterm.name = 'unitary_pseudogene' OR cvterm.name = 'protein_binding_site' OR cvterm.name = 'epitope' OR cvterm.name = 'nucleotide_binding_site' OR cvterm.name = 'metal_binding_site' OR cvterm.name = 'ligand_binding_site' OR cvterm.name = 'protein_protein_contact' OR cvterm.name = 'nucleotide_to_protein_binding_site' OR cvterm.name = 'nuclease_binding_site' OR cvterm.name = 'TF_binding_site' OR cvterm.name = 'histone_binding_site' OR cvterm.name = 'insulator_binding_site' OR cvterm.name = 'enhancer_binding_site' OR cvterm.name = 'restriction_enzyme_binding_site' OR cvterm.name = 'nuclease_sensitive_site' OR cvterm.name = 'homing_endonuclease_binding_site' OR cvterm.name = 'nuclease_hypersensitive_site' OR cvterm.name = 'group_1_intron_homing_endonuclease_target_region' OR cvterm.name = 'DNAseI_hypersensitive_site' OR cvterm.name = 'miRNA_target_site' OR cvterm.name = 'DNA_binding_site' OR cvterm.name = 'primer_binding_site' OR cvterm.name = 'polypeptide_DNA_contact' OR cvterm.name = 'polypeptide_metal_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 = 'polypeptide_ligand_contact' OR cvterm.name = 'decayed_exon' OR cvterm.name = 'pseudogenic_exon' OR cvterm.name = 'pseudogenic_transcript' OR cvterm.name = 'pseudogenic_rRNA' OR cvterm.name = 'pseudogenic_tRNA' OR cvterm.name = 'long_terminal_repeat' OR cvterm.name = 'engineered_foreign_repetitive_element' OR cvterm.name = 'inverted_repeat' OR cvterm.name = 'direct_repeat' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'dispersed_repeat' OR cvterm.name = 'tandem_repeat' OR cvterm.name = 'X_element_combinatorial_repeat' OR cvterm.name = 'Y_prime_element' OR cvterm.name = 'telomeric_repeat' OR cvterm.name = 'nested_repeat' OR cvterm.name = 'centromeric_repeat' OR cvterm.name = 'five_prime_LTR' OR cvterm.name = 'three_prime_LTR' OR cvterm.name = 'solo_LTR' OR cvterm.name = 'terminal_inverted_repeat' OR cvterm.name = 'five_prime_terminal_inverted_repeat' OR cvterm.name = 'three_prime_terminal_inverted_repeat' OR cvterm.name = 'target_site_duplication' OR cvterm.name = 'CRISPR' OR cvterm.name = 'satellite_DNA' OR cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'nested_tandem_repeat' OR cvterm.name = 'regional_centromere_inner_repeat_region' OR cvterm.name = 'regional_centromere_outer_repeat_region' OR cvterm.name = 'transgenic_insertion' OR cvterm.name = 'duplication' OR cvterm.name = 'tandem_duplication' OR cvterm.name = 'direct_tandem_duplication' OR cvterm.name = 'inverted_tandem_duplication' OR cvterm.name = 'nuclear_gene' OR cvterm.name = 'mt_gene' OR cvterm.name = 'plastid_gene' OR cvterm.name = 'nucleomorph_gene' OR cvterm.name = 'plasmid_gene' OR cvterm.name = 'proviral_gene' OR cvterm.name = 'transposable_element_gene' OR cvterm.name = 'silenced_gene' OR cvterm.name = 'engineered_gene' OR cvterm.name = 'foreign_gene' OR cvterm.name = 'fusion_gene' OR cvterm.name = 'recombinationally_rearranged_gene' OR cvterm.name = 'gene_with_trans_spliced_transcript' OR cvterm.name = 'gene_with_polycistronic_transcript' OR cvterm.name = 'rescue_gene' OR cvterm.name = 'post_translationally_regulated_gene' OR cvterm.name = 'negatively_autoregulated_gene' OR cvterm.name = 'positively_autoregulated_gene' OR cvterm.name = 'translationally_regulated_gene' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'transgene' OR cvterm.name = 'predicted_gene' OR cvterm.name = 'protein_coding_gene' OR cvterm.name = 'retrogene' OR cvterm.name = 'ncRNA_gene' OR cvterm.name = 'cryptic_gene' OR cvterm.name = 'gene_with_non_canonical_start_codon' OR cvterm.name = 'gene_cassette' OR cvterm.name = 'kinetoplast_gene' OR cvterm.name = 'maxicircle_gene' OR cvterm.name = 'minicircle_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'apicoplast_gene' OR cvterm.name = 'ct_gene' OR cvterm.name = 'chromoplast_gene' OR cvterm.name = 'cyanelle_gene' OR cvterm.name = 'leucoplast_gene' OR cvterm.name = 'proplastid_gene' OR cvterm.name = 'endogenous_retroviral_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'gene_silenced_by_DNA_modification' OR cvterm.name = 'gene_silenced_by_RNA_interference' OR cvterm.name = 'gene_silenced_by_histone_modification' OR cvterm.name = 'gene_silenced_by_DNA_methylation' OR cvterm.name = 'gene_silenced_by_histone_methylation' OR cvterm.name = 'gene_silenced_by_histone_deacetylation' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_foreign_gene' OR cvterm.name = 'engineered_foreign_transposable_element_gene' OR cvterm.name = 'engineered_fusion_gene' OR cvterm.name = 'recombinationally_inverted_gene' OR cvterm.name = 'recombinationally_rearranged_vertebrate_immune_system_gene' OR cvterm.name = 'gene_with_dicistronic_transcript' OR cvterm.name = 'gene_with_dicistronic_primary_transcript' OR cvterm.name = 'gene_with_dicistronic_mRNA' OR cvterm.name = 'wild_type_rescue_gene' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' OR cvterm.name = 'floxed_gene' OR cvterm.name = 'gene_with_polyadenylated_mRNA' OR cvterm.name = 'gene_with_mRNA_with_frameshift' OR cvterm.name = 'gene_with_edited_transcript' OR cvterm.name = 'gene_with_recoded_mRNA' OR cvterm.name = 'gene_with_stop_codon_read_through' OR cvterm.name = 'gene_with_mRNA_recoded_by_translational_bypass' OR cvterm.name = 'gene_with_transcript_with_translational_frameshift' OR cvterm.name = 'gene_with_stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'gene_with_stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'gRNA_gene' OR cvterm.name = 'miRNA_gene' OR cvterm.name = 'scRNA_gene' OR cvterm.name = 'snoRNA_gene' OR cvterm.name = 'snRNA_gene' OR cvterm.name = 'SRP_RNA_gene' OR cvterm.name = 'stRNA_gene' OR cvterm.name = 'tmRNA_gene' OR cvterm.name = 'tRNA_gene' OR cvterm.name = 'rRNA_gene' OR cvterm.name = 'piRNA_gene' OR cvterm.name = 'RNase_P_RNA_gene' OR cvterm.name = 'RNase_MRP_RNA_gene' OR cvterm.name = 'lincRNA_gene' OR cvterm.name = 'telomerase_RNA_gene' OR cvterm.name = 'cryptogene' OR cvterm.name = 'gene_with_start_codon_CUG' OR cvterm.name = 'chromosome_arm' OR cvterm.name = 'chromosome_band' OR cvterm.name = 'interband' OR cvterm.name = 'chromosomal_regulatory_element' OR cvterm.name = 'chromosomal_structural_element' OR cvterm.name = 'introgressed_chromosome_region' OR cvterm.name = 'matrix_attachment_site' OR cvterm.name = 'centromere' OR cvterm.name = 'telomere' OR cvterm.name = 'point_centromere' OR cvterm.name = 'regional_centromere' OR cvterm.name = 'transcript' OR cvterm.name = 'regulatory_region' OR cvterm.name = 'polycistronic_transcript' OR cvterm.name = 'transcript_with_translational_frameshift' OR cvterm.name = 'primary_transcript' OR cvterm.name = 'mature_transcript' OR cvterm.name = 'transcript_bound_by_nucleic_acid' OR cvterm.name = 'transcript_bound_by_protein' OR cvterm.name = 'enzymatic_RNA' OR cvterm.name = 'trans_spliced_transcript' OR cvterm.name = 'monocistronic_transcript' OR cvterm.name = 'aberrant_processed_transcript' OR cvterm.name = 'edited_transcript' OR cvterm.name = 'processed_transcript' OR cvterm.name = 'alternatively_spliced_transcript' OR cvterm.name = 'dicistronic_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'protein_coding_primary_transcript' OR cvterm.name = 'nc_primary_transcript' OR cvterm.name = 'polycistronic_primary_transcript' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'mini_exon_donor_RNA' OR cvterm.name = 'antisense_primary_transcript' OR cvterm.name = 'capped_primary_transcript' OR cvterm.name = 'pre_edited_mRNA' OR cvterm.name = 'scRNA_primary_transcript' OR cvterm.name = 'rRNA_primary_transcript' OR cvterm.name = 'tRNA_primary_transcript' OR cvterm.name = 'snRNA_primary_transcript' OR cvterm.name = 'snoRNA_primary_transcript' OR cvterm.name = 'tmRNA_primary_transcript' OR cvterm.name = 'SRP_RNA_primary_transcript' OR cvterm.name = 'miRNA_primary_transcript' OR cvterm.name = 'tasiRNA_primary_transcript' OR cvterm.name = 'rRNA_small_subunit_primary_transcript' OR cvterm.name = 'rRNA_large_subunit_primary_transcript' OR cvterm.name = 'alanine_tRNA_primary_transcript' OR cvterm.name = 'arginine_tRNA_primary_transcript' OR cvterm.name = 'asparagine_tRNA_primary_transcript' OR cvterm.name = 'aspartic_acid_tRNA_primary_transcript' OR cvterm.name = 'cysteine_tRNA_primary_transcript' OR cvterm.name = 'glutamic_acid_tRNA_primary_transcript' OR cvterm.name = 'glutamine_tRNA_primary_transcript' OR cvterm.name = 'glycine_tRNA_primary_transcript' OR cvterm.name = 'histidine_tRNA_primary_transcript' OR cvterm.name = 'isoleucine_tRNA_primary_transcript' OR cvterm.name = 'leucine_tRNA_primary_transcript' OR cvterm.name = 'lysine_tRNA_primary_transcript' OR cvterm.name = 'methionine_tRNA_primary_transcript' OR cvterm.name = 'phenylalanine_tRNA_primary_transcript' OR cvterm.name = 'proline_tRNA_primary_transcript' OR cvterm.name = 'serine_tRNA_primary_transcript' OR cvterm.name = 'threonine_tRNA_primary_transcript' OR cvterm.name = 'tryptophan_tRNA_primary_transcript' OR cvterm.name = 'tyrosine_tRNA_primary_transcript' OR cvterm.name = 'valine_tRNA_primary_transcript' OR cvterm.name = 'pyrrolysine_tRNA_primary_transcript' OR cvterm.name = 'selenocysteine_tRNA_primary_transcript' OR cvterm.name = 'methylation_guide_snoRNA_primary_transcript' OR cvterm.name = 'rRNA_cleavage_snoRNA_primary_transcript' OR cvterm.name = 'C_D_box_snoRNA_primary_transcript' OR cvterm.name = 'H_ACA_box_snoRNA_primary_transcript' OR cvterm.name = 'U14_snoRNA_primary_transcript' OR cvterm.name = 'stRNA_primary_transcript' OR cvterm.name = 'dicistronic_primary_transcript' OR cvterm.name = 'mRNA' OR cvterm.name = 'ncRNA' OR cvterm.name = 'mRNA_with_frameshift' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'polycistronic_mRNA' OR cvterm.name = 'exemplar_mRNA' OR cvterm.name = 'capped_mRNA' OR cvterm.name = 'polyadenylated_mRNA' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'edited_mRNA' OR cvterm.name = 'consensus_mRNA' OR cvterm.name = 'recoded_mRNA' OR cvterm.name = 'mRNA_with_minus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_1_frameshift' OR cvterm.name = 'mRNA_with_plus_2_frameshift' OR cvterm.name = 'mRNA_with_minus_2_frameshift' OR cvterm.name = 'dicistronic_mRNA' OR cvterm.name = 'mRNA_recoded_by_translational_bypass' OR cvterm.name = 'mRNA_recoded_by_codon_redefinition' OR cvterm.name = 'scRNA' OR cvterm.name = 'rRNA' OR cvterm.name = 'tRNA' OR cvterm.name = 'snRNA' OR cvterm.name = 'snoRNA' OR cvterm.name = 'small_regulatory_ncRNA' OR cvterm.name = 'RNase_MRP_RNA' OR cvterm.name = 'RNase_P_RNA' OR cvterm.name = 'telomerase_RNA' OR cvterm.name = 'vault_RNA' OR cvterm.name = 'Y_RNA' OR cvterm.name = 'rasiRNA' OR cvterm.name = 'SRP_RNA' OR cvterm.name = 'guide_RNA' OR cvterm.name = 'antisense_RNA' OR cvterm.name = 'siRNA' OR cvterm.name = 'stRNA' OR cvterm.name = 'class_II_RNA' OR cvterm.name = 'class_I_RNA' OR cvterm.name = 'piRNA' OR cvterm.name = 'lincRNA' OR cvterm.name = 'tasiRNA' OR cvterm.name = 'rRNA_cleavage_RNA' OR cvterm.name = 'small_subunit_rRNA' OR cvterm.name = 'large_subunit_rRNA' OR cvterm.name = 'rRNA_18S' OR cvterm.name = 'rRNA_16S' OR cvterm.name = 'rRNA_5_8S' OR cvterm.name = 'rRNA_5S' OR cvterm.name = 'rRNA_28S' OR cvterm.name = 'rRNA_23S' OR cvterm.name = 'rRNA_25S' OR cvterm.name = 'rRNA_21S' OR cvterm.name = 'alanyl_tRNA' OR cvterm.name = 'asparaginyl_tRNA' OR cvterm.name = 'aspartyl_tRNA' OR cvterm.name = 'cysteinyl_tRNA' OR cvterm.name = 'glutaminyl_tRNA' OR cvterm.name = 'glutamyl_tRNA' OR cvterm.name = 'glycyl_tRNA' OR cvterm.name = 'histidyl_tRNA' OR cvterm.name = 'isoleucyl_tRNA' OR cvterm.name = 'leucyl_tRNA' OR cvterm.name = 'lysyl_tRNA' OR cvterm.name = 'methionyl_tRNA' OR cvterm.name = 'phenylalanyl_tRNA' OR cvterm.name = 'prolyl_tRNA' OR cvterm.name = 'seryl_tRNA' OR cvterm.name = 'threonyl_tRNA' OR cvterm.name = 'tryptophanyl_tRNA' OR cvterm.name = 'tyrosyl_tRNA' OR cvterm.name = 'valyl_tRNA' OR cvterm.name = 'pyrrolysyl_tRNA' OR cvterm.name = 'arginyl_tRNA' OR cvterm.name = 'selenocysteinyl_tRNA' OR cvterm.name = 'U1_snRNA' OR cvterm.name = 'U2_snRNA' OR cvterm.name = 'U4_snRNA' OR cvterm.name = 'U4atac_snRNA' OR cvterm.name = 'U5_snRNA' OR cvterm.name = 'U6_snRNA' OR cvterm.name = 'U6atac_snRNA' OR cvterm.name = 'U11_snRNA' OR cvterm.name = 'U12_snRNA' OR cvterm.name = 'C_D_box_snoRNA' OR cvterm.name = 'H_ACA_box_snoRNA' OR cvterm.name = 'U14_snoRNA' OR cvterm.name = 'U3_snoRNA' OR cvterm.name = 'methylation_guide_snoRNA' OR cvterm.name = 'pseudouridylation_guide_snoRNA' OR cvterm.name = 'miRNA' OR cvterm.name = 'RNA_6S' OR cvterm.name = 'CsrB_RsmB_RNA' OR cvterm.name = 'DsrA_RNA' OR cvterm.name = 'OxyS_RNA' OR cvterm.name = 'RprA_RNA' OR cvterm.name = 'RRE_RNA' OR cvterm.name = 'spot_42_RNA' OR cvterm.name = 'tmRNA' OR cvterm.name = 'GcvB_RNA' OR cvterm.name = 'MicF_RNA' OR cvterm.name = 'ribozyme' OR cvterm.name = 'trans_spliced_mRNA' OR cvterm.name = 'monocistronic_primary_transcript' OR cvterm.name = 'monocistronic_mRNA' OR cvterm.name = 'edited_transcript_by_A_to_I_substitution' OR cvterm.name = 'edited_mRNA' OR 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 = 'exon' OR cvterm.name = 'edited_transcript_feature' OR cvterm.name = 'mature_transcript_region' OR cvterm.name = 'primary_transcript_region' OR cvterm.name = 'exon_region' OR cvterm.name = 'anchor_binding_site' OR cvterm.name = 'coding_exon' OR cvterm.name = 'noncoding_exon' OR cvterm.name = 'interior_exon' OR cvterm.name = 'exon_of_single_exon_gene' OR cvterm.name = 'interior_coding_exon' OR cvterm.name = 'five_prime_coding_exon' OR cvterm.name = 'three_prime_coding_exon' OR cvterm.name = 'three_prime_noncoding_exon' OR cvterm.name = 'five_prime_noncoding_exon' OR cvterm.name = 'pre_edited_region' OR cvterm.name = 'editing_block' OR cvterm.name = 'editing_domain' OR cvterm.name = 'unedited_region' OR cvterm.name = 'mRNA_region' OR cvterm.name = 'tmRNA_region' OR cvterm.name = 'guide_RNA_region' OR cvterm.name = 'tRNA_region' OR cvterm.name = 'riboswitch' OR cvterm.name = 'ribosome_entry_site' OR cvterm.name = 'UTR' OR cvterm.name = 'CDS' OR cvterm.name = 'five_prime_open_reading_frame' OR cvterm.name = 'UTR_region' OR cvterm.name = 'CDS_region' OR cvterm.name = 'translational_frameshift' OR cvterm.name = 'recoding_stimulatory_region' OR cvterm.name = 'internal_ribosome_entry_site' OR cvterm.name = 'Shine_Dalgarno_sequence' OR cvterm.name = 'kozak_sequence' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'five_prime_UTR' OR cvterm.name = 'three_prime_UTR' OR cvterm.name = 'internal_UTR' OR cvterm.name = 'untranslated_region_polycistronic_mRNA' OR cvterm.name = 'edited_CDS' OR cvterm.name = 'CDS_fragment' OR cvterm.name = 'CDS_independently_known' OR cvterm.name = 'CDS_predicted' OR cvterm.name = 'orphan_CDS' OR cvterm.name = 'CDS_supported_by_sequence_similarity_data' OR cvterm.name = 'CDS_supported_by_domain_match_data' OR cvterm.name = 'CDS_supported_by_EST_or_cDNA_data' OR cvterm.name = 'upstream_AUG_codon' OR cvterm.name = 'AU_rich_element' OR cvterm.name = 'Bruno_response_element' OR cvterm.name = 'iron_responsive_element' OR cvterm.name = 'coding_start' OR cvterm.name = 'coding_end' OR cvterm.name = 'codon' OR cvterm.name = 'recoded_codon' OR cvterm.name = 'start_codon' OR cvterm.name = 'stop_codon' OR cvterm.name = 'stop_codon_read_through' OR cvterm.name = 'stop_codon_redefined_as_pyrrolysine' OR cvterm.name = 'stop_codon_redefined_as_selenocysteine' OR cvterm.name = 'non_canonical_start_codon' OR cvterm.name = 'four_bp_start_codon' OR cvterm.name = 'CTG_start_codon' OR cvterm.name = 'plus_1_translational_frameshift' OR cvterm.name = 'plus_2_translational_frameshift' OR cvterm.name = 'internal_Shine_Dalgarno_sequence' OR cvterm.name = 'SECIS_element' OR cvterm.name = 'three_prime_recoding_site' OR cvterm.name = 'five_prime_recoding_site' OR cvterm.name = 'stop_codon_signal' OR cvterm.name = 'three_prime_stem_loop_structure' OR cvterm.name = 'flanking_three_prime_quadruplet_recoding_signal' OR cvterm.name = 'three_prime_repeat_recoding_signal' OR cvterm.name = 'distant_three_prime_recoding_signal' OR cvterm.name = 'UAG_stop_codon_signal' OR cvterm.name = 'UAA_stop_codon_signal' OR cvterm.name = 'UGA_stop_codon_signal' OR cvterm.name = 'tmRNA_coding_piece' OR cvterm.name = 'tmRNA_acceptor_piece' OR cvterm.name = 'anchor_region' OR cvterm.name = 'template_region' OR cvterm.name = 'anticodon_loop' OR cvterm.name = 'anticodon' OR cvterm.name = 'CCA_tail' OR cvterm.name = 'DHU_loop' OR cvterm.name = 'T_loop' OR cvterm.name = 'splice_site' OR cvterm.name = 'intron' OR cvterm.name = 'clip' OR cvterm.name = 'TSS' OR cvterm.name = 'transcription_end_site' OR cvterm.name = 'spliced_leader_RNA' OR cvterm.name = 'rRNA_primary_transcript_region' OR cvterm.name = 'spliceosomal_intron_region' OR cvterm.name = 'intron_domain' OR cvterm.name = 'miRNA_primary_transcript_region' OR cvterm.name = 'outron' OR cvterm.name = 'cis_splice_site' OR cvterm.name = 'trans_splice_site' OR cvterm.name = 'cryptic_splice_site' OR cvterm.name = 'five_prime_cis_splice_site' OR cvterm.name = 'three_prime_cis_splice_site' OR cvterm.name = 'recursive_splice_site' OR cvterm.name = 'canonical_five_prime_splice_site' OR cvterm.name = 'non_canonical_five_prime_splice_site' OR cvterm.name = 'canonical_three_prime_splice_site' OR cvterm.name = 'non_canonical_three_prime_splice_site' OR cvterm.name = 'trans_splice_acceptor_site' OR cvterm.name = 'trans_splice_donor_site' OR cvterm.name = 'SL1_acceptor_site' OR cvterm.name = 'SL2_acceptor_site' OR cvterm.name = 'SL3_acceptor_site' OR cvterm.name = 'SL4_acceptor_site' OR cvterm.name = 'SL5_acceptor_site' OR cvterm.name = 'SL6_acceptor_site' OR cvterm.name = 'SL7_acceptor_site' OR cvterm.name = 'SL8_acceptor_site' OR cvterm.name = 'SL9_acceptor_site' OR cvterm.name = 'SL10_accceptor_site' OR cvterm.name = 'SL11_acceptor_site' OR cvterm.name = 'SL12_acceptor_site' OR cvterm.name = 'five_prime_intron' OR cvterm.name = 'interior_intron' OR cvterm.name = 'three_prime_intron' OR cvterm.name = 'twintron' OR cvterm.name = 'UTR_intron' OR cvterm.name = 'autocatalytically_spliced_intron' OR cvterm.name = 'spliceosomal_intron' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'endonuclease_spliced_intron' OR cvterm.name = 'five_prime_UTR_intron' OR cvterm.name = 'three_prime_UTR_intron' OR cvterm.name = 'group_I_intron' OR cvterm.name = 'group_II_intron' OR cvterm.name = 'group_III_intron' OR cvterm.name = 'group_IIA_intron' OR cvterm.name = 'group_IIB_intron' OR cvterm.name = 'U2_intron' OR cvterm.name = 'U12_intron' OR cvterm.name = 'archaeal_intron' OR cvterm.name = 'tRNA_intron' OR cvterm.name = 'five_prime_clip' OR cvterm.name = 'three_prime_clip' OR cvterm.name = 'major_TSS' OR cvterm.name = 'minor_TSS' OR cvterm.name = 'transcribed_spacer_region' OR cvterm.name = 'internal_transcribed_spacer_region' OR cvterm.name = 'external_transcribed_spacer_region' OR cvterm.name = 'intronic_splice_enhancer' OR cvterm.name = 'branch_site' OR cvterm.name = 'polypyrimidine_tract' OR cvterm.name = 'internal_guide_sequence' OR cvterm.name = 'mirtron' OR cvterm.name = 'pre_miRNA' OR cvterm.name = 'miRNA_stem' OR cvterm.name = 'miRNA_loop' OR cvterm.name = 'miRNA_antiguide' OR cvterm.name = 'noncoding_region_of_exon' OR cvterm.name = 'coding_region_of_exon' OR cvterm.name = 'three_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_noncoding_region' OR cvterm.name = 'five_prime_coding_exon_coding_region' OR cvterm.name = 'three_prime_coding_exon_coding_region' OR cvterm.name = 'mature_protein_region' OR cvterm.name = 'immature_peptide_region' OR cvterm.name = 'compositionally_biased_region_of_peptide' OR cvterm.name = 'polypeptide_structural_region' OR cvterm.name = 'polypeptide_variation_site' OR cvterm.name = 'peptide_localization_signal' OR cvterm.name = 'cleaved_peptide_region' OR cvterm.name = 'hydrophobic_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_region' OR cvterm.name = 'active_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'membrane_structure' OR cvterm.name = 'extramembrane_polypeptide_region' OR cvterm.name = 'intramembrane_polypeptide_region' OR cvterm.name = 'polypeptide_secondary_structure' OR cvterm.name = 'polypeptide_structural_motif' OR cvterm.name = 'intrinsically_unstructured_polypeptide_region' OR cvterm.name = 'cytoplasmic_polypeptide_region' OR cvterm.name = 'non_cytoplasmic_polypeptide_region' OR cvterm.name = 'membrane_peptide_loop' OR cvterm.name = 'transmembrane_polypeptide_region' OR cvterm.name = 'asx_motif' OR cvterm.name = 'beta_bulge' OR cvterm.name = 'beta_bulge_loop' OR cvterm.name = 'beta_strand' OR cvterm.name = 'peptide_helix' OR cvterm.name = 'polypeptide_nest_motif' OR cvterm.name = 'schellmann_loop' OR cvterm.name = 'serine_threonine_motif' OR cvterm.name = 'serine_threonine_staple_motif' OR cvterm.name = 'polypeptide_turn_motif' OR cvterm.name = 'catmat_left_handed_three' OR cvterm.name = 'catmat_left_handed_four' OR cvterm.name = 'catmat_right_handed_three' OR cvterm.name = 'catmat_right_handed_four' OR cvterm.name = 'alpha_beta_motif' OR cvterm.name = 'peptide_coil' OR cvterm.name = 'beta_bulge_loop_five' OR cvterm.name = 'beta_bulge_loop_six' OR cvterm.name = 'antiparallel_beta_strand' OR cvterm.name = 'parallel_beta_strand' OR cvterm.name = 'left_handed_peptide_helix' OR cvterm.name = 'right_handed_peptide_helix' OR cvterm.name = 'alpha_helix' OR cvterm.name = 'pi_helix' OR cvterm.name = 'three_ten_helix' OR cvterm.name = 'polypeptide_nest_left_right_motif' OR cvterm.name = 'polypeptide_nest_right_left_motif' OR cvterm.name = 'schellmann_loop_seven' OR cvterm.name = 'schellmann_loop_six' OR cvterm.name = 'asx_turn' OR cvterm.name = 'beta_turn' OR cvterm.name = 'gamma_turn' OR cvterm.name = 'serine_threonine_turn' OR cvterm.name = 'asx_turn_left_handed_type_one' OR cvterm.name = 'asx_turn_left_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_two' OR cvterm.name = 'asx_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_one' OR cvterm.name = 'beta_turn_left_handed_type_two' OR cvterm.name = 'beta_turn_right_handed_type_one' OR cvterm.name = 'beta_turn_right_handed_type_two' OR cvterm.name = 'beta_turn_type_six' OR cvterm.name = 'beta_turn_type_eight' OR cvterm.name = 'beta_turn_type_six_a' OR cvterm.name = 'beta_turn_type_six_b' OR cvterm.name = 'beta_turn_type_six_a_one' OR cvterm.name = 'beta_turn_type_six_a_two' OR cvterm.name = 'gamma_turn_classic' OR cvterm.name = 'gamma_turn_inverse' OR cvterm.name = 'st_turn_left_handed_type_one' OR cvterm.name = 'st_turn_left_handed_type_two' OR cvterm.name = 'st_turn_right_handed_type_one' OR cvterm.name = 'st_turn_right_handed_type_two' OR cvterm.name = 'coiled_coil' OR cvterm.name = 'helix_turn_helix' OR cvterm.name = 'natural_variant_site' OR cvterm.name = 'mutated_variant_site' OR cvterm.name = 'alternate_sequence_site' OR cvterm.name = 'signal_peptide' OR cvterm.name = 'transit_peptide' OR cvterm.name = 'nuclear_localization_signal' OR cvterm.name = 'endosomal_localization_signal' OR cvterm.name = 'lysosomal_localization_signal' OR cvterm.name = 'nuclear_export_signal' OR cvterm.name = 'nuclear_rim_localization_signal' OR cvterm.name = 'cleaved_initiator_methionine' OR cvterm.name = 'intein' OR cvterm.name = 'propeptide_cleavage_site' OR cvterm.name = 'propeptide' OR cvterm.name = 'cleaved_for_gpi_anchor_region' OR cvterm.name = 'lipoprotein_signal_peptide' OR cvterm.name = 'n_terminal_region' OR cvterm.name = 'c_terminal_region' OR cvterm.name = 'central_hydrophobic_region_of_signal_peptide' OR cvterm.name = 'polypeptide_domain' OR cvterm.name = 'polypeptide_motif' OR cvterm.name = 'polypeptide_repeat' OR cvterm.name = 'biochemical_region_of_peptide' OR cvterm.name = 'polypeptide_conserved_motif' OR 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 = 'non_transcribed_region' OR cvterm.name = 'gene_fragment' OR cvterm.name = 'TSS_region' OR cvterm.name = 'gene_segment' OR cvterm.name = 'pseudogenic_gene_segment' OR cvterm.name = 'mobile_intron' OR cvterm.name = 'extrachromosomal_mobile_genetic_element' OR cvterm.name = 'integrated_mobile_genetic_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'transposable_element' OR cvterm.name = 'proviral_region' OR cvterm.name = 'integron' OR cvterm.name = 'genomic_island' OR cvterm.name = 'integrated_plasmid' OR cvterm.name = 'cointegrated_plasmid' OR cvterm.name = 'retrotransposon' OR cvterm.name = 'DNA_transposon' OR cvterm.name = 'foreign_transposable_element' OR cvterm.name = 'transgenic_transposable_element' OR cvterm.name = 'natural_transposable_element' OR cvterm.name = 'engineered_transposable_element' OR cvterm.name = 'nested_transposon' OR cvterm.name = 'LTR_retrotransposon' OR cvterm.name = 'non_LTR_retrotransposon' OR cvterm.name = 'LINE_element' OR cvterm.name = 'SINE_element' OR cvterm.name = 'terminal_inverted_repeat_element' OR cvterm.name = 'foldback_element' OR cvterm.name = 'conjugative_transposon' OR cvterm.name = 'helitron' OR cvterm.name = 'p_element' OR cvterm.name = 'MITE' OR cvterm.name = 'insertion_sequence' OR cvterm.name = 'polinton' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'engineered_foreign_transposable_element' OR cvterm.name = 'prophage' OR cvterm.name = 'pathogenic_island' OR cvterm.name = 'metabolic_island' OR cvterm.name = 'adaptive_island' OR cvterm.name = 'symbiosis_island' OR cvterm.name = 'cryptic_prophage' OR cvterm.name = 'defective_conjugative_transposon' OR cvterm.name = 'plasmid' OR cvterm.name = 'chromosome' OR cvterm.name = 'vector_replicon' OR cvterm.name = 'maxicircle' OR cvterm.name = 'minicircle' OR cvterm.name = 'viral_sequence' OR cvterm.name = 'engineered_plasmid' OR cvterm.name = 'episome' OR cvterm.name = 'natural_plasmid' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'gene_trap_construct' OR cvterm.name = 'promoter_trap_construct' OR cvterm.name = 'enhancer_trap_construct' OR cvterm.name = 'engineered_episome' OR cvterm.name = 'mitochondrial_chromosome' OR cvterm.name = 'chloroplast_chromosome' OR cvterm.name = 'chromoplast_chromosome' OR cvterm.name = 'cyanelle_chromosome' OR cvterm.name = 'leucoplast_chromosome' OR cvterm.name = 'macronuclear_chromosome' OR cvterm.name = 'micronuclear_chromosome' OR cvterm.name = 'nuclear_chromosome' OR cvterm.name = 'nucleomorphic_chromosome' OR cvterm.name = 'DNA_chromosome' OR cvterm.name = 'RNA_chromosome' OR cvterm.name = 'apicoplast_chromosome' OR cvterm.name = 'double_stranded_DNA_chromosome' OR cvterm.name = 'single_stranded_DNA_chromosome' OR cvterm.name = 'linear_double_stranded_DNA_chromosome' OR cvterm.name = 'circular_double_stranded_DNA_chromosome' OR cvterm.name = 'linear_single_stranded_DNA_chromosome' OR cvterm.name = 'circular_single_stranded_DNA_chromosome' OR 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 = 'YAC' OR cvterm.name = 'BAC' OR cvterm.name = 'PAC' OR cvterm.name = 'cosmid' OR cvterm.name = 'phagemid' OR cvterm.name = 'fosmid' OR cvterm.name = 'lambda_vector' OR cvterm.name = 'plasmid_vector' OR cvterm.name = 'targeting_vector' OR cvterm.name = 'phage_sequence' OR cvterm.name = 'ds_RNA_viral_sequence' OR cvterm.name = 'ds_DNA_viral_sequence' OR cvterm.name = 'ss_RNA_viral_sequence' OR cvterm.name = 'negative_sense_ssRNA_viral_sequence' OR cvterm.name = 'positive_sense_ssRNA_viral_sequence' OR cvterm.name = 'ambisense_ssRNA_viral_sequence' OR cvterm.name = 'modified_RNA_base_feature' OR cvterm.name = 'inosine' OR cvterm.name = 'seven_methylguanine' OR cvterm.name = 'ribothymidine' OR cvterm.name = 'modified_adenosine' OR cvterm.name = 'modified_cytidine' OR cvterm.name = 'modified_guanosine' OR cvterm.name = 'modified_uridine' OR cvterm.name = 'modified_inosine' OR cvterm.name = 'methylinosine' OR cvterm.name = 'one_methylinosine' OR cvterm.name = 'one_two_prime_O_dimethylinosine' OR cvterm.name = 'two_prime_O_methylinosine' OR cvterm.name = 'one_methyladenosine' OR cvterm.name = 'two_methyladenosine' OR cvterm.name = 'N6_methyladenosine' OR cvterm.name = 'two_prime_O_methyladenosine' OR cvterm.name = 'two_methylthio_N6_methyladenosine' OR cvterm.name = 'N6_isopentenyladenosine' OR cvterm.name = 'two_methylthio_N6_isopentenyladenosine' OR cvterm.name = 'N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'two_methylthio_N6_cis_hydroxyisopentenyl_adenosine' OR cvterm.name = 'N6_glycinylcarbamoyladenosine' OR cvterm.name = 'N6_threonylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_threonyl_carbamoyladenosine' OR cvterm.name = 'N6_methyl_N6_threonylcarbamoyladenosine' OR cvterm.name = 'N6_hydroxynorvalylcarbamoyladenosine' OR cvterm.name = 'two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine' OR cvterm.name = 'two_prime_O_ribosyladenosine_phosphate' OR cvterm.name = 'N6_N6_dimethyladenosine' OR cvterm.name = 'N6_2_prime_O_dimethyladenosine' OR cvterm.name = 'N6_N6_2_prime_O_trimethyladenosine' OR cvterm.name = 'one_two_prime_O_dimethyladenosine' OR cvterm.name = 'N6_acetyladenosine' OR cvterm.name = 'three_methylcytidine' OR cvterm.name = 'five_methylcytidine' OR cvterm.name = 'two_prime_O_methylcytidine' OR cvterm.name = 'two_thiocytidine' OR cvterm.name = 'N4_acetylcytidine' OR cvterm.name = 'five_formylcytidine' OR cvterm.name = 'five_two_prime_O_dimethylcytidine' OR cvterm.name = 'N4_acetyl_2_prime_O_methylcytidine' OR cvterm.name = 'lysidine' OR cvterm.name = 'N4_methylcytidine' OR cvterm.name = 'N4_2_prime_O_dimethylcytidine' OR cvterm.name = 'five_hydroxymethylcytidine' OR cvterm.name = 'five_formyl_two_prime_O_methylcytidine' OR cvterm.name = 'N4_N4_2_prime_O_trimethylcytidine' OR cvterm.name = 'seven_deazaguanosine' OR cvterm.name = 'one_methylguanosine' OR cvterm.name = 'N2_methylguanosine' OR cvterm.name = 'seven_methylguanosine' OR cvterm.name = 'two_prime_O_methylguanosine' OR cvterm.name = 'N2_N2_dimethylguanosine' OR cvterm.name = 'N2_2_prime_O_dimethylguanosine' OR cvterm.name = 'N2_N2_2_prime_O_trimethylguanosine' OR cvterm.name = 'two_prime_O_ribosylguanosine_phosphate' OR cvterm.name = 'wybutosine' OR cvterm.name = 'peroxywybutosine' OR cvterm.name = 'hydroxywybutosine' OR cvterm.name = 'undermodified_hydroxywybutosine' OR cvterm.name = 'wyosine' OR cvterm.name = 'methylwyosine' OR cvterm.name = 'N2_7_dimethylguanosine' OR cvterm.name = 'N2_N2_7_trimethylguanosine' OR cvterm.name = 'one_two_prime_O_dimethylguanosine' OR cvterm.name = 'four_demethylwyosine' OR cvterm.name = 'isowyosine' OR cvterm.name = 'N2_7_2prirme_O_trimethylguanosine' OR cvterm.name = 'queuosine' OR cvterm.name = 'epoxyqueuosine' OR cvterm.name = 'galactosyl_queuosine' OR cvterm.name = 'mannosyl_queuosine' OR cvterm.name = 'seven_cyano_seven_deazaguanosine' OR cvterm.name = 'seven_aminomethyl_seven_deazaguanosine' OR cvterm.name = 'archaeosine' OR cvterm.name = 'dihydrouridine' OR cvterm.name = 'pseudouridine' OR cvterm.name = 'five_methyluridine' OR cvterm.name = 'two_prime_O_methyluridine' OR cvterm.name = 'five_two_prime_O_dimethyluridine' OR cvterm.name = 'one_methylpseudouridine' OR cvterm.name = 'two_prime_O_methylpseudouridine' OR cvterm.name = 'two_thiouridine' OR cvterm.name = 'four_thiouridine' OR cvterm.name = 'five_methyl_2_thiouridine' OR cvterm.name = 'two_thio_two_prime_O_methyluridine' OR cvterm.name = 'three_three_amino_three_carboxypropyl_uridine' OR cvterm.name = 'five_hydroxyuridine' OR cvterm.name = 'five_methoxyuridine' OR cvterm.name = 'uridine_five_oxyacetic_acid' OR cvterm.name = 'uridine_five_oxyacetic_acid_methyl_ester' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine' OR cvterm.name = 'five_carboxyhydroxymethyl_uridine_methyl_ester' OR cvterm.name = 'five_methoxycarbonylmethyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_methoxycarbonylmethyl_two_thiouridine' OR cvterm.name = 'five_aminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyluridine' OR cvterm.name = 'five_methylaminomethyl_two_thiouridine' OR cvterm.name = 'five_methylaminomethyl_two_selenouridine' OR cvterm.name = 'five_carbamoylmethyluridine' OR cvterm.name = 'five_carbamoylmethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'five_carboxymethylaminomethyl_two_thiouridine' OR cvterm.name = 'three_methyluridine' OR cvterm.name = 'one_methyl_three_three_amino_three_carboxypropyl_pseudouridine' OR cvterm.name = 'five_carboxymethyluridine' OR cvterm.name = 'three_two_prime_O_dimethyluridine' OR cvterm.name = 'five_methyldihydrouridine' OR cvterm.name = 'three_methylpseudouridine' OR cvterm.name = 'five_taurinomethyluridine' OR cvterm.name = 'five_taurinomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_uridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_thiouridine' OR cvterm.name = 'five_isopentenylaminomethyl_two_prime_O_methyluridine' OR cvterm.name = 'catalytic_residue' OR cvterm.name = 'modified_amino_acid_feature' OR cvterm.name = 'alanine' OR cvterm.name = 'valine' OR cvterm.name = 'leucine' OR cvterm.name = 'isoleucine' OR cvterm.name = 'proline' OR cvterm.name = 'tryptophan' OR cvterm.name = 'phenylalanine' OR cvterm.name = 'methionine' OR cvterm.name = 'glycine' OR cvterm.name = 'serine' OR cvterm.name = 'threonine' OR cvterm.name = 'tyrosine' OR cvterm.name = 'cysteine' OR cvterm.name = 'glutamine' OR cvterm.name = 'asparagine' OR cvterm.name = 'lysine' OR cvterm.name = 'arginine' OR cvterm.name = 'histidine' OR cvterm.name = 'aspartic_acid' OR cvterm.name = 'glutamic_acid' OR cvterm.name = 'selenocysteine' OR cvterm.name = 'pyrrolysine' OR cvterm.name = 'modified_glycine' OR cvterm.name = 'modified_L_alanine' OR cvterm.name = 'modified_L_asparagine' OR cvterm.name = 'modified_L_aspartic_acid' OR cvterm.name = 'modified_L_cysteine' OR cvterm.name = 'modified_L_glutamic_acid' OR cvterm.name = 'modified_L_threonine' OR cvterm.name = 'modified_L_tryptophan' OR cvterm.name = 'modified_L_glutamine' OR cvterm.name = 'modified_L_methionine' OR cvterm.name = 'modified_L_isoleucine' OR cvterm.name = 'modified_L_phenylalanine' OR cvterm.name = 'modified_L_histidine' OR cvterm.name = 'modified_L_serine' OR cvterm.name = 'modified_L_lysine' OR cvterm.name = 'modified_L_leucine' OR cvterm.name = 'modified_L_selenocysteine' OR cvterm.name = 'modified_L_valine' OR cvterm.name = 'modified_L_proline' OR cvterm.name = 'modified_L_tyrosine' OR cvterm.name = 'modified_L_arginine' OR cvterm.name = 'heritable_phenotypic_marker' OR cvterm.name = 'DArT_marker' OR cvterm.name = 'nucleotide_motif' OR cvterm.name = 'DNA_motif' OR cvterm.name = 'RNA_motif' OR cvterm.name = 'PSE_motif' OR cvterm.name = 'CAAT_signal' OR cvterm.name = 'minus_10_signal' OR cvterm.name = 'minus_35_signal' OR cvterm.name = 'DRE_motif' OR cvterm.name = 'E_box_motif' OR cvterm.name = 'INR1_motif' OR cvterm.name = 'GAGA_motif' OR cvterm.name = 'octamer_motif' OR cvterm.name = 'retinoic_acid_responsive_element' OR cvterm.name = 'promoter_element' OR cvterm.name = 'DCE_SI' OR cvterm.name = 'DCE_SII' OR cvterm.name = 'DCE_SIII' OR cvterm.name = 'minus_12_signal' OR cvterm.name = 'minus_24_signal' OR cvterm.name = 'GC_rich_promoter_region' OR cvterm.name = 'DMv4_motif' OR cvterm.name = 'DMv5_motif' OR cvterm.name = 'DMv3_motif' OR cvterm.name = 'DMv2_motif' OR cvterm.name = 'DPE1_motif' OR cvterm.name = 'DMv1_motif' OR cvterm.name = 'NDM2_motif' OR cvterm.name = 'NDM3_motif' OR cvterm.name = 'core_promoter_element' OR cvterm.name = 'regulatory_promoter_element' OR cvterm.name = 'INR_motif' OR cvterm.name = 'DPE_motif' OR cvterm.name = 'BREu_motif' OR cvterm.name = 'TATA_box' OR cvterm.name = 'A_box' OR cvterm.name = 'B_box' OR cvterm.name = 'C_box' OR cvterm.name = 'MTE' OR cvterm.name = 'BREd_motif' OR cvterm.name = 'DCE' OR cvterm.name = 'intermediate_element' OR cvterm.name = 'RNA_polymerase_II_TATA_box' OR cvterm.name = 'RNA_polymerase_III_TATA_box' OR cvterm.name = 'A_box_type_1' OR cvterm.name = 'A_box_type_2' OR cvterm.name = 'proximal_promoter_element' OR cvterm.name = 'distal_promoter_element' OR cvterm.name = 'RNA_internal_loop' OR cvterm.name = 'A_minor_RNA_motif' OR cvterm.name = 'RNA_junction_loop' OR cvterm.name = 'hammerhead_ribozyme' OR cvterm.name = 'asymmetric_RNA_internal_loop' OR cvterm.name = 'symmetric_RNA_internal_loop' OR cvterm.name = 'K_turn_RNA_motif' OR cvterm.name = 'sarcin_like_RNA_motif' OR cvterm.name = 'RNA_hook_turn' OR cvterm.name = 'blunt_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'sticky_end_restriction_enzyme_cleavage_site' OR cvterm.name = 'modified_base' OR cvterm.name = 'epigenetically_modified_gene' OR cvterm.name = 'histone_modification' OR cvterm.name = 'methylated_base_feature' OR cvterm.name = 'methylated_C' OR cvterm.name = 'methylated_A' OR cvterm.name = 'gene_rearranged_at_DNA_level' OR cvterm.name = 'maternally_imprinted_gene' OR cvterm.name = 'paternally_imprinted_gene' OR cvterm.name = 'allelically_excluded_gene' 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 = '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 = 'sequence_length_variation' OR cvterm.name = 'MNP' OR cvterm.name = 'SNV' OR cvterm.name = 'complex_substitution' OR cvterm.name = 'simple_sequence_length_variation' OR cvterm.name = 'SNP' OR cvterm.name = 'point_mutation' OR cvterm.name = 'transition' OR cvterm.name = 'transversion' OR cvterm.name = 'pyrimidine_transition' OR cvterm.name = 'purine_transition' OR cvterm.name = 'C_to_T_transition' OR cvterm.name = 'T_to_C_transition' OR cvterm.name = 'C_to_T_transition_at_pCpG_site' OR cvterm.name = 'A_to_G_transition' OR cvterm.name = 'G_to_A_transition' OR cvterm.name = 'pyrimidine_to_purine_transversion' OR cvterm.name = 'purine_to_pyrimidine_transversion' OR cvterm.name = 'C_to_A_transversion' OR cvterm.name = 'C_to_G_transversion' OR cvterm.name = 'T_to_A_transversion' OR cvterm.name = 'T_to_G_transversion' OR cvterm.name = 'A_to_C_transversion' OR cvterm.name = 'A_to_T_transversion' OR cvterm.name = 'G_to_C_transversion' OR cvterm.name = 'G_to_T_transversion' OR cvterm.name = 'flanking_region' OR cvterm.name = 'repeat_component' OR cvterm.name = 'transposable_element_flanking_region' OR cvterm.name = 'five_prime_flanking_region' OR cvterm.name = 'three_prime_flanking_region' OR cvterm.name = 'non_LTR_retrotransposon_polymeric_tract' OR cvterm.name = 'LTR_component' OR cvterm.name = 'repeat_fragment' OR cvterm.name = 'transposon_fragment' OR cvterm.name = 'U5_LTR_region' OR cvterm.name = 'R_LTR_region' OR cvterm.name = 'U3_LTR_region' OR cvterm.name = 'three_prime_LTR_component' OR cvterm.name = 'five_prime_LTR_component' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'R_three_prime_LTR_region' OR cvterm.name = 'U3_three_prime_LTR_region' OR cvterm.name = 'U5_three_prime_LTR_region' OR cvterm.name = 'R_five_prime_LTR_region' OR cvterm.name = 'U5_five_prime_LTR_region' OR cvterm.name = 'U3_five_prime_LTR_region' OR cvterm.name = 'region';

--- ************************************************
--- *** relation: sequence_secondary_structure ***
--- *** relation type: VIEW                      ***
--- ***                                          ***
--- *** A folded sequence.                       ***
--- ************************************************
---

CREATE VIEW sequence_secondary_structure AS
  SELECT
    feature_id AS sequence_secondary_structure_id,
    feature.*
  FROM
    feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
  WHERE cvterm.name = 'G_quartet' OR cvterm.name = 'base_pair' OR cvterm.name = 'RNA_sequence_secondary_structure' OR cvterm.name = 'DNA_sequence_secondary_structure' OR cvterm.name = 'pseudoknot' OR cvterm.name = 'WC_base_pair' OR cvterm.name = 'sugar_edge_base_pair' OR cvterm.name = 'Hoogsteen_base_pair' OR cvterm.name = 'reverse_Hoogsteen_base_pair' OR cvterm.name = 'wobble_base_pair' OR cvterm.name = 'stem_loop' OR cvterm.name = 'tetraloop' OR cvterm.name = 'i_motif' OR cvterm.name = 'recoding_pseudoknot' OR cvterm.name = 'H_pseudoknot' OR cvterm.name = 'sequence_secondary_structure';

--- ************************************************
--- *** relation: g_quartet ***
--- *** relation type: VIEW                      ***
--- ***                                          ***
--- *** G-quartets are unusual nucleic acid stru ***
--- *** ctures consisting of a planar arrangemen ***
--- *** t where each guanine is hydrogen bonded  ***
--- *** by hoogsteen pairing to another guanine  ***
--- *** in the quartet.                          ***
--- ************************************************
---

CREATE VIEW g_quartet AS
  SELECT
    feature_id AS g_quartet_id,
    feature.*
  FROM
    feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
  WHERE cvterm.name = 'G_quartet';

--- ************************************************
--- *** relation: interior_coding_exon ***
--- *** relation type: VIEW                      ***
--- ***                                          ***
--- ************************************************
---

CREATE VIEW interior_coding_exon AS
  SELECT
    feature_id AS interior_coding_exon_id,
    feature.*
  FROM
    feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
  WHERE cvterm.name = 'interior_coding_exon';

--- ************************************************
--- *** relation: satellite_dna ***
--- *** relation type: VIEW                      ***
--- ***                                          ***
--- *** The many tandem repeats (identical or re ***
--- *** lated) of a short basic repeating unit;  ***
--- *** many have a base composition or other pr ***
--- *** operty different from the genome average ***
--- ***  that allows them to be separated from t ***
--- *** he bulk (main band) genomic DNA.         ***
--- ************************************************
---

CREATE VIEW satellite_dna AS
  SELECT
    feature_id AS satellite_dna_id,
    feature.*
  FROM
    feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
  WHERE cvterm.name = 'microsatellite' OR cvterm.name = 'minisatellite' OR cvterm.name = 'dinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'trinucleotide_repeat_microsatellite_feature' OR cvterm.name = 'tetranucleotide_repeat_microsatellite_feature' OR cvterm.name = 'satellite_DNA';

--- ************************************************
--- *** relation: pcr_product ***
--- *** relation type: VIEW                      ***
--- ***                                          ***
--- *** A region amplified by a PCR reaction.    ***
--- ************************************************
---

CREATE VIEW pcr_product AS
  SELECT
    feature_id AS pcr_product_id,
    feature.*
  FROM
    feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
  WHERE cvterm.name = 'RAPD' OR cvterm.name = 'PCR_product';

--- ************************************************
--- *** relation: read_pair ***
--- *** relation type: VIEW                      ***
--- ***                                          ***
--- *** One of a pair of sequencing reads in whi ***
--- *** ch the two members of the pair are relat ***
--- *** ed by originating at either end of a clo ***
--- *** ne insert.                               ***
--- ************************************************
---

CREATE VIEW read_pair AS
  SELECT
    feature_id AS read_pair_id,
    feature.*
  FROM
    feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
  WHERE cvterm.name = 'read_pair';

--- ************************************************
--- *** relation: protein_coding ***
--- *** relation type: VIEW                      ***
--- ***                                          ***
--- ************************************************
---

CREATE VIEW protein_coding AS
  SELECT
    feature_id AS protein_coding_id,
    feature.*
  FROM
    feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
  WHERE cvterm.name = 'intein_containing' OR cvterm.name = 'protein_coding';

--- ************************************************
--- *** relation: non_protein_coding ***
--- *** relation type: VIEW                      ***
--- ***                                          ***
--- ************************************************
---

CREATE VIEW non_protein_coding AS
  SELECT
    feature_id AS non_protein_coding_id,
    feature.*
  FROM
    feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
  WHERE cvterm.name = 'miRNA_encoding' OR cvterm.name = 'rRNA_encoding' OR cvterm.name = 'scRNA_encoding' OR cvterm.name = 'snoRNA_encoding' OR cvterm.name = 'snRNA_encoding' OR cvterm.name = 'SRP_RNA_encoding' OR cvterm.name = 'stRNA_encoding' OR cvterm.name = 'tmRNA_encoding' OR cvterm.name = 'tRNA_encoding' OR cvterm.name = 'gRNA_encoding' OR cvterm.name = 'C_D_box_snoRNA_encoding' OR cvterm.name = 'H_ACA_box_snoRNA_encoding' OR cvterm.name = 'non_protein_coding';

--- ************************************************
--- *** relation: scrna_primary_transcript ***
--- *** relation type: VIEW                      ***
--- ***                                          ***
--- *** The primary transcript of any one of sev ***
--- *** eral small cytoplasmic RNA molecules pre ***
--- *** sent in the cytoplasm and sometimes nucl ***
--- *** eus of a eukaryote.                      ***
--- ************************************************
---

CREATE VIEW scrna_primary_transcript AS
  SELECT
    feature_id AS scrna_primary_transcript_id,
    feature.*
  FROM
    feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
  WHERE cvterm.name = 'scRNA_primary_transcript';

--- ************************************************
--- *** relation: scrna ***
--- *** relation type: VIEW                      ***
--- ***                                          ***
--- *** A small non coding RNA sequence, present ***
--- ***  in the cytoplasm.                       ***
--- ************************************************
---

CREATE VIEW scrna AS
  SELECT
    feature_id AS scrna_id,
    feature.*
  FROM
    feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
  WHERE cvterm.name = 'scRNA';

--- ************************************************
--- *** relation: inr_motif ***
--- *** relation type: VIEW                      ***
--- ***                                          ***
--- *** A sequence element characteristic of som ***
--- *** e RNA polymerase II promoters required f ***
--- *** or the correct positioning of the polyme ***
--- *** rase for the start of transcription. Ove ***
--- *** rlaps the TSS. The mammalian consensus s ***
--- *** equence is YYAN(T|A)YY; the Drosophila c ***
--- *** onsensus sequence is TCA(G|T)t(T|C). In  ***
--- *** each the A is at position +1 with respec ***
--- *** t to the TSS. Functionally similar to th ***
--- *** e TATA box element.                      ***
--- ************************************************
---

CREATE VIEW inr_motif AS
  SELECT
    feature_id AS inr_motif_id,
    feature.*
  FROM
    feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
  WHERE cvterm.name = 'INR_motif';

--- ************************************************
--- *** relation: dpe_motif ***
--- *** relation type: VIEW                      ***
--- ***                                          ***
--- *** A sequence element characteristic of som ***
--- *** e RNA polymerase II promoters; Positione ***
--- *** d from +28 to +32 with respect to the TS ***
--- *** S (+1). Experimental results suggest tha ***
--- *** t the DPE acts in conjunction with the I ***
--- *** NR_motif to provide a binding site for T ***
--- *** FIID in the absence of a TATA box to med ***
--- *** iate transcription of TATA-less promoter ***
--- *** s. Consensus sequence (A|G)G(A|T)(C|T)(G ***
--- *** |A|C).                                   ***
--- ************************************************
---

CREATE VIEW dpe_motif AS
  SELECT
    feature_id AS dpe_motif_id,
    feature.*
  FROM
    feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
  WHERE cvterm.name = 'DPE_motif';

--- ************************************************
--- *** relation: breu_motif ***
--- *** relation type: VIEW                      ***
--- ***                                          ***
--- *** A sequence element characteristic of som ***
--- *** e RNA polymerase II promoters, located i ***
--- *** mmediately upstream of some TATA box ele ***
--- *** ments at -37 to -32 with respect to the  ***
--- *** TSS (+1). Consensus sequence is (G|C)(G| ***
--- *** C)(G|A)CGCC. Binds TFIIB.                ***
--- ************************************************
---

CREATE VIEW breu_motif AS
  SELECT
    feature_id AS breu_motif_id,
    feature.*
  FROM
    feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
  WHERE cvterm.name = 'BREu_motif';

--- ************************************************
--- *** relation: pse_motif ***
--- *** relation type: VIEW                      ***
--- ***                                          ***
--- *** A sequence element characteristic of the ***
--- ***  promoters of snRNA genes transcribed by ***
--- ***  RNA polymerase II or by RNA polymerase  ***
--- *** III. Located between -45 and -60 relativ ***
--- *** e to the TSS. The human PSE_motif consen ***
--- *** sus sequence is TCACCNTNA(C|G)TNAAAAG(T| ***
--- *** G).                                      ***
--- ************************************************
---

CREATE VIEW pse_motif AS
  SELECT
    feature_id AS pse_motif_id,
    feature.*
  FROM
    feature INNER JOIN cvterm ON (feature.type_id = cvterm.cvterm_id)
  WHERE cvterm.name = 'PSE_motif';

--- ************************************************