Difference between revisions of "Template:ChadoTable featureloc"
(Table definition, first upload on 2010/11/22.) |
(Table definition for Chado on 2010/11/24) |
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− | <noinclude>{{ChadoTableTemplateHeader}}</noinclude> | + | <protect><noinclude>{{ChadoTableTemplateHeader}}</noinclude> |
+ | {{ChadoTableDesc|Sequence|featureloc|The location of a feature relative to | ||
another feature. Important: interbase coordinates are used. This is | another feature. Important: interbase coordinates are used. This is | ||
vital as it allows us to represent zero-length features e.g. splice | vital as it allows us to represent zero-length features e.g. splice | ||
Line 19: | Line 20: | ||
never be stored - this is for -proper- (i.e. non-self) locations only; nothing should be located relative to itself.}} | never be stored - this is for -proper- (i.e. non-self) locations only; nothing should be located relative to itself.}} | ||
{{ChadoColumnsHeader|Sequence|featureloc}} | {{ChadoColumnsHeader|Sequence|featureloc}} | ||
− | {{ChadoColumnDesc||featureloc_id|serial|''PRIMARY KEY'' | + | {{ChadoColumnDesc||featureloc_id|serial|''PRIMARY KEY''<br /> |
− | + | ||
}} | }} | ||
− | {{ChadoColumnDesc|{{ChadoModuleTableLink|Sequence|feature}}|feature_id|integer|''UNIQUE#1'' | + | {{ChadoColumnDesc|{{ChadoModuleTableLink|Sequence|feature}}|feature_id|integer|''UNIQUE#1''<br /> |
− | + | ''NOT NULL''<br /> | |
− | ''NOT NULL'' | + | |
− | + | ||
The feature that is being located. Any feature can have zero or more featurelocs.}} | The feature that is being located. Any feature can have zero or more featurelocs.}} | ||
{{ChadoColumnDesc|{{ChadoModuleTableLink|Sequence|feature}}|srcfeature_id|integer|The source feature which this location is relative to. Every location is relative to another feature (however, this column is nullable, because the srcfeature may not be known). All locations are -proper- that is, nothing should be located relative to itself. No cycles are allowed in the featureloc graph.}} | {{ChadoColumnDesc|{{ChadoModuleTableLink|Sequence|feature}}|srcfeature_id|integer|The source feature which this location is relative to. Every location is relative to another feature (however, this column is nullable, because the srcfeature may not be known). All locations are -proper- that is, nothing should be located relative to itself. No cycles are allowed in the featureloc graph.}} | ||
{{ChadoColumnDesc||fmin|integer|The leftmost/minimal boundary in the linear range represented by the featureloc. Sometimes (e.g. in Bioperl) this is called -start- although this is confusing because it does not necessarily represent the 5-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. To convert this to the leftmost position in a base-oriented system (eg GFF, Bioperl), add 1 to fmin.}} | {{ChadoColumnDesc||fmin|integer|The leftmost/minimal boundary in the linear range represented by the featureloc. Sometimes (e.g. in Bioperl) this is called -start- although this is confusing because it does not necessarily represent the 5-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. To convert this to the leftmost position in a base-oriented system (eg GFF, Bioperl), add 1 to fmin.}} | ||
− | {{ChadoColumnDesc||is_fmin_partial|boolean|''NOT NULL'' | + | {{ChadoColumnDesc||is_fmin_partial|boolean|''NOT NULL''<br /> |
− | + | ''DEFAULT ''false<br /> | |
− | ''DEFAULT ''false | + | |
− | + | ||
This is typically | This is typically | ||
false, but may be true if the value for column:fmin is inaccurate or | false, but may be true if the value for column:fmin is inaccurate or | ||
the leftmost part of the range is unknown/unbounded.}} | the leftmost part of the range is unknown/unbounded.}} | ||
{{ChadoColumnDesc||fmax|integer|The rightmost/maximal boundary in the linear range represented by the featureloc. Sometimes (e.g. in bioperl) this is called -end- although this is confusing because it does not necessarily represent the 3-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. No conversion is required to go from fmax to the rightmost coordinate in a base-oriented system that counts from 1 (e.g. GFF, Bioperl).}} | {{ChadoColumnDesc||fmax|integer|The rightmost/maximal boundary in the linear range represented by the featureloc. Sometimes (e.g. in bioperl) this is called -end- although this is confusing because it does not necessarily represent the 3-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. No conversion is required to go from fmax to the rightmost coordinate in a base-oriented system that counts from 1 (e.g. GFF, Bioperl).}} | ||
− | {{ChadoColumnDesc||is_fmax_partial|boolean|''NOT NULL'' | + | {{ChadoColumnDesc||is_fmax_partial|boolean|''NOT NULL''<br /> |
− | + | ''DEFAULT ''false<br /> | |
− | ''DEFAULT ''false | + | |
− | + | ||
This is typically | This is typically | ||
false, but may be true if the value for column:fmax is inaccurate or | false, but may be true if the value for column:fmax is inaccurate or | ||
Line 60: | Line 54: | ||
locations, one (rank 0) on the genome, the other (rank 1) would have | locations, one (rank 0) on the genome, the other (rank 1) would have | ||
most fields null, except for alternative residues.}} | most fields null, except for alternative residues.}} | ||
− | {{ChadoColumnDesc||locgroup|integer|''UNIQUE#1'' | + | {{ChadoColumnDesc||locgroup|integer|''UNIQUE#1''<br /> |
− | + | ''NOT NULL''<br /> | |
− | ''NOT NULL'' | + | |
− | + | ||
This is used to manifest redundant, | This is used to manifest redundant, | ||
derivable extra locations for a feature. The default locgroup=0 is | derivable extra locations for a feature. The default locgroup=0 is | ||
Line 84: | Line 76: | ||
conserved region feature - two distinct locgroups (contig level and | conserved region feature - two distinct locgroups (contig level and | ||
chromosome level) and two distinct ranks (for the two species).}} | chromosome level) and two distinct ranks (for the two species).}} | ||
− | {{ChadoColumnDesc||rank|integer|''UNIQUE#1'' | + | {{ChadoColumnDesc||rank|integer|''UNIQUE#1''<br /> |
− | + | ''NOT NULL''<br /> | |
− | ''NOT NULL'' | + | |
− | + | ||
Used when a feature has >1 | Used when a feature has >1 | ||
location, otherwise the default rank 0 is used. Some features (e.g. | location, otherwise the default rank 0 is used. Some features (e.g. | ||
Line 99: | Line 89: | ||
{{ChadoTablesReferencingHeader|featureloc}} | {{ChadoTablesReferencingHeader|featureloc}} | ||
− | + | {{ChadoReferencingTable|Sequence|featureloc_pub}} | |
− | + | ||
</protect> | </protect> |
Latest revision as of 19:58, 24 November 2010
This template is a Chado Table Template. It defines a single table from the Chado schema, and every Chado table has a template like this one. This template is automatically included in two places:
- The module page for the module the table is a part of. This is where updates and comments should be posted.
- The Chado Tables page, which lists all tables.
You can include this template anywhere you want to show the table description.
Table: | featureloc |
Module: | Sequence |
The location of a feature relative to another feature. Important: interbase coordinates are used. This is vital as it allows us to represent zero-length features e.g. splice sites, insertion points without an awkward fuzzy system. Features typically have exactly ONE location, but this need not be the case. Some features may not be localized (e.g. a gene that has been characterized genetically but no sequence or molecular information is available). Note on multiple locations: Each feature can have 0 or more locations. Multiple locations do NOT indicate non-contiguous locations (if a feature such as a transcript has a non-contiguous location, then the subfeatures such as exons should always be manifested). Instead, multiple featurelocs for a feature designate alternate locations or grouped locations; for instance, a feature designating a blast hit or hsp will have two locations, one on the query feature, one on the subject feature. Features representing sequence variation could have alternate locations instantiated on a feature on the mutant strain. The column:rank is used to differentiate these different locations. Reflexive locations should never be stored - this is for -proper- (i.e. non-self) locations only; nothing should be located relative to itself.
FK | Name | Type | Description |
---|---|---|---|
featureloc_id | serial | PRIMARY KEY | |
feature | feature_id | integer | UNIQUE#1 NOT NULL |
feature | srcfeature_id | integer | The source feature which this location is relative to. Every location is relative to another feature (however, this column is nullable, because the srcfeature may not be known). All locations are -proper- that is, nothing should be located relative to itself. No cycles are allowed in the featureloc graph. |
fmin | integer | The leftmost/minimal boundary in the linear range represented by the featureloc. Sometimes (e.g. in Bioperl) this is called -start- although this is confusing because it does not necessarily represent the 5-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. To convert this to the leftmost position in a base-oriented system (eg GFF, Bioperl), add 1 to fmin. | |
is_fmin_partial | boolean | NOT NULL DEFAULT false | |
fmax | integer | The rightmost/maximal boundary in the linear range represented by the featureloc. Sometimes (e.g. in bioperl) this is called -end- although this is confusing because it does not necessarily represent the 3-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. No conversion is required to go from fmax to the rightmost coordinate in a base-oriented system that counts from 1 (e.g. GFF, Bioperl). | |
is_fmax_partial | boolean | NOT NULL DEFAULT false | |
strand | smallint | The orientation/directionality of the
location. Should be 0, -1 or +1. | |
phase | integer | Phase of translation with
respect to srcfeature_id. Values are 0, 1, 2. It may not be possible to manifest this column for some features such as exons, because the phase is dependant on the spliceform (the same exon can appear in multiple spliceforms). This column is mostly useful for predicted exons and CDSs. | |
residue_info | text | Alternative residues,
when these differ from feature.residues. For instance, a SNP feature located on a wild and mutant protein would have different alternative residues. for alignment/similarity features, the alternative residues is used to represent the alignment string (CIGAR format). Note on variation features; even if we do not want to instantiate a mutant chromosome/contig feature, we can still represent a SNP etc with 2 locations, one (rank 0) on the genome, the other (rank 1) would have most fields null, except for alternative residues. | |
locgroup | integer | UNIQUE#1 NOT NULL | |
rank | integer | UNIQUE#1 NOT NULL |
Tables referencing featureloc via foreign key constraints: