Table cxgn.public.feature

A feature is a biological sequence or a
section of a biological sequence, or a collection of such
sections. Examples include genes, exons, transcripts, regulatory
regions, polypeptides, protein domains, chromosome sequences, sequence
variations, cross-genome match regions such as hits and HSPs and so
on; see the Sequence Ontology for more

 Generated by
SchemaSpy
Related columns Constraint names Comments Legend
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Primary key columns
Columns with indexes
Implied relationships
Excluded column relationships
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implied relationships
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Column Type Size Nulls Auto Default Children Parents Comments
feature_id serial 10  √  nextval('feature_feature_id_seq'::regclass)
analysisfeature.feature_id analysisfeature_feature_id_fkey
clone_feature.feature_id clone_feature_feature_id_fkey
feature_cvterm.feature_id feature_cvterm_feature_id_fkey
feature_dbxref.feature_id feature_dbxref_feature_id_fkey
feature_pub.feature_id feature_pub_feature_id_fkey
feature_relationship.object_id feature_relationship_object_id_fkey
feature_relationship.subject_id feature_relationship_subject_id_fkey
feature_synonym.feature_id feature_synonym_feature_id_fkey
featureloc.feature_id featureloc_feature_id_fkey
featureloc.srcfeature_id featureloc_srcfeature_id_fkey
featureprop.feature_id featureprop_feature_id_fkey
dbxref_id int4 10  √  null
dbxref.dbxref_id feature_dbxref_id_fkey
An optional primary public stable
identifier for this feature. Secondary identifiers and external
dbxrefs go in table:feature_dbxref
organism_id int4 10
organism.organism_id feature_organism_id_fkey
The organism to which this feature
belongs. This column is mandatory
name varchar 255  √  null The optional human-readable common name for
a feature, for display purposes
uniquename text 2147483647 The unique name for a feature; may
not be necessarily be particularly human-readable, although this is
prefered. This name must be unique for this type of feature within
this organism
residues text 2147483647  √  null A sequence of alphabetic characters
representing biological residues (nucleic acids, amino acids). This
column does not need to be manifested for all features; it is optional
for features such as exons where the residues can be derived from the
featureloc. It is recommended that the value for this column be
manifested for features which may may non-contiguous sublocations (eg
transcripts), since derivation at query time is non-trivial. For
expressed sequence, the DNA sequence should be used rather than the
RNA sequence
seqlen int4 10  √  null The length of the residue feature. See
column:residues. This column is partially redundant with the residues
column, and also with featureloc. This column is required because the
location may be unknown and the residue sequence may not be
manifested, yet it may be desirable to store and query the length of
the feature. The seqlen should always be manifested where the length
of the sequence is known
md5checksum bpchar 32  √  null The 32-character checksum of the sequence,
calculated using the MD5 algorithm. This is practically guaranteed to
be unique for any feature. This column thus acts as a unique
identifier on the mathematical sequence
type_id int4 10
cvterm.cvterm_id feature_type_id_fkey
A required reference to a table:cvterm
giving the feature type. This will typically be a Sequence Ontology
identifier. This column is thus used to subclass the feature table
is_analysis bool 1 false Boolean indicating whether this
feature is annotated or the result of an automated analysis. Analysis
results also use the companalysis module. Note that the dividing line
between analysis/annotation may be fuzzy, this should be determined on
a per-project basis in a consistent manner. One requirement is that
there should only be one non-analysis version of each wild-type gene
feature in a genome, whereas the same gene feature can be predicted
multiple times in different analyses
is_obsolete bool 1 false Boolean indicating whether this
feature has been obsoleted. Some chado instances may choose to simply
remove the feature altogether, others may choose to keep an obsolete
row in the table
timeaccessioned timestamp 29,6 ('now'::text)::timestamp(6) with time zone for handling object
accession/modification timestamps (as opposed to db auditing info,
handled elsewhere). The expectation is that these fields would be
available to software interacting with chado
timelastmodified timestamp 29,6 ('now'::text)::timestamp(6) with time zone for handling object
accession/modification timestamps (as opposed to db auditing info,
handled elsewhere). The expectation is that these fields would be
available to software interacting with chado

Table contained 358,674 rows at Wed May 20 01:40 EDT 2009

Indexes:
Column(s) Type Sort Constraint Name
feature_id Primary key Asc feature_pkey
organism_id + uniquename + type_id Must be unique Asc/Asc/Asc feature_c1
dbxref_id Performance Asc feature_idx1
organism_id Performance Asc feature_idx2
type_id Performance Asc feature_idx3
uniquename Performance Asc feature_idx4
Performance feature_idx5
name Performance Asc feature_name_ind1

Close relationships  within one two degrees of separation :