feature

0 rows


Description

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

Columns

Column Type Size Nulls Auto Default Children Parents Comments
feature_id serial 10 √ nextval('feature_feature_id_seq'::regclass)
clone_feature.feature_id clone_feature_feature_id_fkey C
analysisfeature.feature_id analysisfeature_feature_id_fkey C
feature_cvterm.feature_id feature_cvterm_feature_id_fkey C
feature_dbxref.feature_id feature_dbxref_feature_id_fkey C
feature_genotype.chromosome_id feature_genotype_chromosome_id_fkey N
feature_genotype.feature_id feature_genotype_feature_id_fkey C
feature_pub.feature_id feature_pub_feature_id_fkey C
feature_relationship.object_id feature_relationship_object_id_fkey C
feature_relationship.subject_id feature_relationship_subject_id_fkey C
feature_synonym.feature_id feature_synonym_feature_id_fkey C
featureloc.feature_id featureloc_feature_id_fkey C
featureloc.srcfeature_id featureloc_srcfeature_id_fkey N
featureprop.feature_id featureprop_feature_id_fkey C
featureprop_json.feature_id featureprop_json_feature_id_fkey R
gff3atts.feature_id Implied Constraint R
gff3view.feature_id Implied Constraint R
gffatts.feature_id Implied Constraint R
nd_reagent.feature_id Implied Constraint R
phylonode.feature_id phylonode_feature_id_fkey C
tmp_gff_load_cache.feature_id Implied Constraint R
cds.protein_feature_id cds_protein_feature_id_fkey R
dbxref_id int4 10 √ null
dbxref.dbxref_id feature_dbxref_id_fkey N

An optional primary public stable identifier for this feature. Secondary identifiers and external dbxrefs go in table:feature_dbxref
organism_id int4 10 null
organism.organism_id feature_organism_id_fkey C

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 null

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 null
cvterm.cvterm_id feature_type_id_fkey C

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

Indexes

Constraint Name Type Sort Column(s)
feature_pkey Primary key Asc feature_id
feature_c1 Must be unique Asc/Asc/Asc organism_id + uniquename + type_id
feature_idx1 Performance Asc dbxref_id
feature_idx2 Performance Asc organism_id
feature_idx3 Performance Asc type_id
feature_idx4 Performance Asc uniquename
feature_idx5 Performance
feature_idx6 Performance
feature_name_ind1 Performance Asc name

Relationships

Close relationships within degrees of separation