User:Clements/AllTables
Contents
- 1 Module: General
- 2 Module: CV
- 3 Module: Publication
- 4 Module: Organism
- 5 Module: Sequence
- 5.1 Table: feature
- 5.2 Table: featureloc
- 5.3 Table: featureloc_pub
- 5.4 Table: feature_pub
- 5.5 Table: feature_pubprop
- 5.6 Table: featureprop
- 5.7 Table: featureprop_pub
- 5.8 Table: feature_dbxref
- 5.9 Table: feature_relationship
- 5.10 Table: feature_relationship_pub
- 5.11 Table: feature_relationshipprop
- 5.12 Table: feature_relationshipprop_pub
- 5.13 Table: feature_cvterm
- 5.14 Table: feature_cvtermprop
- 5.15 Table: feature_cvterm_dbxref
- 5.16 Table: feature_cvterm_pub
- 5.17 Table: synonym
- 5.18 Table: feature_synonym
- 5.19 Table: gencode
- 5.20 Table: gencode_codon_aa
- 5.21 Table: gencode_startcodon
- 6 Module: Companalysis
- 7 Module: Cell Line
- 7.1 Table: cell_line
- 7.2 Table: cell_line_relationship
- 7.3 Table: cell_line_synonym
- 7.4 Table: cell_line_cvterm
- 7.5 Table: cell_line_dbxref
- 7.6 Table: cell_lineprop
- 7.7 Table: cell_lineprop_pub
- 7.8 Table: cell_line_feature
- 7.9 Table: cell_line_cvtermprop
- 7.10 Table: cell_line_pub
- 7.11 Table: cell_line_library
- 8 Module: Contact
- 9 Module: Expression
- 10 Module: Genetic
- 11 Module: Library
- 12 Module: Mage
- 12.1 Table: mageml
- 12.2 Table: magedocumentation
- 12.3 Table: protocol
- 12.4 Table: protocolparam
- 12.5 Table: channel
- 12.6 Table: arraydesign
- 12.7 Table: arraydesignprop
- 12.8 Table: assay
- 12.9 Table: assayprop
- 12.10 Table: assay_project
- 12.11 Table: biomaterial
- 12.12 Table: biomaterial_relationship
- 12.13 Table: biomaterialprop
- 12.14 Table: biomaterial_dbxref
- 12.15 Table: treatment
- 12.16 Table: biomaterial_treatment
- 12.17 Table: assay_biomaterial
- 12.18 Table: acquisition
- 12.19 Table: acquisitionprop
- 12.20 Table: acquisition_relationship
- 12.21 Table: quantification
- 12.22 Table: quantificationprop
- 12.23 Table: quantification_relationship
- 12.24 Table: control
- 12.25 Table: element
- 12.26 Table: elementresult
- 12.27 Table: element_relationship
- 12.28 Table: elementresult_relationship
- 12.29 Table: study
- 12.30 Table: study_assay
- 12.31 Table: studydesign
- 12.32 Table: studydesignprop
- 12.33 Table: studyfactor
- 12.34 Table: studyfactorvalue
- 12.35 Table: studyprop
- 12.36 Table: studyprop_feature
- 13 Module: Map
- 14 Module: Natural Diversity
- 14.1 Table: nd_geolocation
- 14.2 Table: nd_experiment
- 14.3 Table: nd_experiment_project
- 14.4 Table: nd_experimentprop
- 14.5 Table: nd_experiment_pub
- 14.6 Table: nd_geolocationprop
- 14.7 Table: nd_protocol
- 14.8 Table: nd_reagent
- 14.9 Table: nd_protocol_reagent
- 14.10 Table: nd_protocolprop
- 14.11 Table: nd_experiment_stock
- 14.12 Table: nd_experiment_protocol
- 14.13 Table: nd_experiment_phenotype
- 14.14 Table: nd_experiment_genotype
- 14.15 Table: nd_reagent_relationship
- 14.16 Table: nd_reagentprop
- 14.17 Table: nd_experiment_stockprop
- 14.18 Table: nd_experiment_stock_dbxref
- 14.19 Table: nd_experiment_dbxref
- 14.20 Table: nd_experiment_contact
- 15 Module: Phenotype
- 16 Module: Phylogeny
- 17 Module: Project
- 18 Module: Stock
- 18.1 Table: stock
- 18.2 Table: stock_pub
- 18.3 Table: stockprop
- 18.4 Table: stockprop_pub
- 18.5 Table: stock_relationship
- 18.6 Table: stock_relationship_cvterm
- 18.7 Table: stock_relationship_pub
- 18.8 Table: stock_dbxref
- 18.9 Table: stock_cvterm
- 18.10 Table: stock_genotype
- 18.11 Table: stockcollection
- 18.12 Table: stockcollectionprop
- 18.13 Table: stockcollection_stock
- 18.14 Table: stock_dbxrefprop
- 19 Module: WWW
- 19.1 Table: wwwuser
- 19.2 Table: wwwuser_project
- 19.3 Table: wwwuser_author
- 19.4 Table: wwwuser_cvterm
- 19.5 Table: wwwuser_expression
- 19.6 Table: wwwuser_feature
- 19.7 Table: wwwuser_genotype
- 19.8 Table: wwwuser_interaction
- 19.9 Table: wwwuser_organism
- 19.10 Table: wwwuser_phenotype
- 19.11 Table: wwwuser_pub
- 19.12 Table: wwwuserrelationship
- 20 Module: Audit
- 20.1 Table: audit_tableinfo
- 20.2 Table: audit_db
- 20.3 Table: audit_dbxref
- 20.4 Table: audit_cv
- 20.5 Table: audit_cvterm
- 20.6 Table: audit_cvterm_relationship
- 20.7 Table: audit_cvtermpath
- 20.8 Table: audit_cvtermsynonym
- 20.9 Table: audit_cvterm_dbxref
- 20.10 Table: audit_cvtermprop
- 20.11 Table: audit_dbxrefprop
- 20.12 Table: audit_pub
- 20.13 Table: audit_pub_relationship
- 20.14 Table: audit_pub_dbxref
- 20.15 Table: audit_pubauthor
- 20.16 Table: audit_pubprop
- 20.17 Table: audit_organism
- 20.18 Table: audit_organism_dbxref
- 20.19 Table: audit_organismprop
- 20.20 Table: audit_feature
- 20.21 Table: audit_featureloc
- 20.22 Table: audit_featureloc_pub
- 20.23 Table: audit_feature_pub
- 20.24 Table: audit_feature_pubprop
- 20.25 Table: audit_featureprop
- 20.26 Table: audit_featureprop_pub
- 20.27 Table: audit_feature_dbxref
- 20.28 Table: audit_feature_relationship
- 20.29 Table: audit_feature_relationship_pub
- 20.30 Table: audit_feature_relationshipprop
- 20.31 Table: audit_feature_relationshipprop_pub
- 20.32 Table: audit_feature_cvterm
- 20.33 Table: audit_feature_cvtermprop
- 20.34 Table: audit_feature_cvterm_dbxref
- 20.35 Table: audit_feature_cvterm_pub
- 20.36 Table: audit_synonym
- 20.37 Table: audit_feature_synonym
- 20.38 Table: audit_gencode
- 20.39 Table: audit_gencode_codon_aa
- 20.40 Table: audit_gencode_startcodon
- 20.41 Table: audit_analysis
- 20.42 Table: audit_analysisprop
- 20.43 Table: audit_analysisfeature
- 20.44 Table: audit_analysisfeatureprop
- 20.45 Table: audit_phenotype
- 20.46 Table: audit_phenotype_cvterm
- 20.47 Table: audit_feature_phenotype
- 20.48 Table: audit_genotype
- 20.49 Table: audit_feature_genotype
- 20.50 Table: audit_environment
- 20.51 Table: audit_environment_cvterm
- 20.52 Table: audit_phenstatement
- 20.53 Table: audit_phendesc
- 20.54 Table: audit_phenotype_comparison
- 20.55 Table: audit_phenotype_comparison_cvterm
- 20.56 Table: audit_featuremap
- 20.57 Table: audit_featurerange
- 20.58 Table: audit_featurepos
- 20.59 Table: audit_featuremap_pub
- 20.60 Table: audit_phylotree
- 20.61 Table: audit_phylotree_pub
- 20.62 Table: audit_phylonode
- 20.63 Table: audit_phylonode_dbxref
- 20.64 Table: audit_phylonode_pub
- 20.65 Table: audit_phylonode_organism
- 20.66 Table: audit_phylonodeprop
- 20.67 Table: audit_phylonode_relationship
- 20.68 Table: audit_contact
- 20.69 Table: audit_contact_relationship
- 20.70 Table: audit_expression
- 20.71 Table: audit_expression_cvterm
- 20.72 Table: audit_expression_cvtermprop
- 20.73 Table: audit_expressionprop
- 20.74 Table: audit_expression_pub
- 20.75 Table: audit_feature_expression
- 20.76 Table: audit_feature_expressionprop
- 20.77 Table: audit_eimage
- 20.78 Table: audit_expression_image
- 20.79 Table: audit_project
- 20.80 Table: audit_projectprop
- 20.81 Table: audit_project_relationship
- 20.82 Table: audit_project_pub
- 20.83 Table: audit_project_contact
- 20.84 Table: audit_mageml
- 20.85 Table: audit_magedocumentation
- 20.86 Table: audit_protocol
- 20.87 Table: audit_protocolparam
- 20.88 Table: audit_channel
- 20.89 Table: audit_arraydesign
- 20.90 Table: audit_arraydesignprop
- 20.91 Table: audit_assay
- 20.92 Table: audit_assayprop
- 20.93 Table: audit_assay_project
- 20.94 Table: audit_biomaterial
- 20.95 Table: audit_biomaterial_relationship
- 20.96 Table: audit_biomaterialprop
- 20.97 Table: audit_biomaterial_dbxref
- 20.98 Table: audit_treatment
- 20.99 Table: audit_biomaterial_treatment
- 20.100 Table: audit_assay_biomaterial
- 20.101 Table: audit_acquisition
- 20.102 Table: audit_acquisitionprop
- 20.103 Table: audit_acquisition_relationship
- 20.104 Table: audit_quantification
- 20.105 Table: audit_quantificationprop
- 20.106 Table: audit_quantification_relationship
- 20.107 Table: audit_control
- 20.108 Table: audit_element
- 20.109 Table: audit_elementresult
- 20.110 Table: audit_element_relationship
- 20.111 Table: audit_elementresult_relationship
- 20.112 Table: audit_study
- 20.113 Table: audit_study_assay
- 20.114 Table: audit_studydesign
- 20.115 Table: audit_studydesignprop
- 20.116 Table: audit_studyfactor
- 20.117 Table: audit_studyfactorvalue
- 20.118 Table: audit_studyprop
- 20.119 Table: audit_studyprop_feature
- 20.120 Table: audit_stock
- 20.121 Table: audit_stock_pub
- 20.122 Table: audit_stockprop
- 20.123 Table: audit_stockprop_pub
- 20.124 Table: audit_stock_relationship
- 20.125 Table: audit_stock_relationship_cvterm
- 20.126 Table: audit_stock_relationship_pub
- 20.127 Table: audit_stock_dbxref
- 20.128 Table: audit_stock_cvterm
- 20.129 Table: audit_stock_genotype
- 20.130 Table: audit_stockcollection
- 20.131 Table: audit_stockcollectionprop
- 20.132 Table: audit_stockcollection_stock
- 20.133 Table: audit_stock_dbxrefprop
- 20.134 Table: audit_library
- 20.135 Table: audit_library_synonym
- 20.136 Table: audit_library_pub
- 20.137 Table: audit_libraryprop
- 20.138 Table: audit_libraryprop_pub
- 20.139 Table: audit_library_cvterm
- 20.140 Table: audit_library_feature
- 20.141 Table: audit_library_dbxref
- 20.142 Table: audit_cell_line
- 20.143 Table: audit_cell_line_relationship
- 20.144 Table: audit_cell_line_synonym
- 20.145 Table: audit_cell_line_cvterm
- 20.146 Table: audit_cell_line_dbxref
- 20.147 Table: audit_cell_lineprop
- 20.148 Table: audit_cell_lineprop_pub
- 20.149 Table: audit_cell_line_feature
- 20.150 Table: audit_cell_line_cvtermprop
- 20.151 Table: audit_cell_line_pub
- 20.152 Table: audit_cell_line_library
- 20.153 Table: audit_nd_geolocation
- 20.154 Table: audit_nd_experiment
- 20.155 Table: audit_nd_experiment_project
- 20.156 Table: audit_nd_experimentprop
- 20.157 Table: audit_nd_experiment_pub
- 20.158 Table: audit_nd_geolocationprop
- 20.159 Table: audit_nd_protocol
- 20.160 Table: audit_nd_reagent
- 20.161 Table: audit_nd_protocol_reagent
- 20.162 Table: audit_nd_protocolprop
- 20.163 Table: audit_nd_experiment_stock
- 20.164 Table: audit_nd_experiment_protocol
- 20.165 Table: audit_nd_experiment_phenotype
- 20.166 Table: audit_nd_experiment_genotype
- 20.167 Table: audit_nd_reagent_relationship
- 20.168 Table: audit_nd_reagentprop
- 20.169 Table: audit_nd_experiment_stockprop
- 20.170 Table: audit_nd_experiment_stock_dbxref
- 20.171 Table: audit_nd_experiment_dbxref
- 20.172 Table: audit_nd_experiment_contact
Module: General
Table: tableinfo
<protect>
Table: | tableinfo |
Module: | General |
FK | Name | Type | Description |
---|---|---|---|
tableinfo_id | serial | PRIMARY KEY | |
name | character varying(30) | UNIQUE NOT NULL | |
primary_key_column | character varying(30) | ||
is_view | integer | NOT NULL | |
view_on_table_id | integer | ||
superclass_table_id | integer | ||
is_updateable | integer | NOT NULL DEFAULT 1 | |
modification_date | date | NOT NULL DEFAULT now()
|
Tables referencing tableinfo via foreign key constraints:
</protect>
Table: db
<protect>
Table: | db |
Module: | General |
A database authority. Typical databases in bioinformatics are FlyBase, GO, UniProt, NCBI, MGI, etc. The authority is generally known by this shortened form, which is unique within the bioinformatics and biomedical realm. To Do - add support for URIs, URNs (e.g. LSIDs). We can do this by treating the URL as a URI - however, some applications may expect this to be resolvable - to be decided.
FK | Name | Type | Description |
---|---|---|---|
db_id | serial | PRIMARY KEY | |
name | character varying(255) | UNIQUE NOT NULL | |
description | character varying(255) | ||
urlprefix | character varying(255) | ||
url | character varying(255) |
Tables referencing db via foreign key constraints:
</protect>
Table: dbxref
<protect>
Table: | dbxref |
Module: | General |
A unique, global, public, stable identifier. Not necessarily an external reference - can reference data items inside the particular chado instance being used. Typically a row in a table can be uniquely identified with a primary identifier (called dbxref_id); a table may also have secondary identifiers (in a linking table <T>_dbxref). A dbxref is generally written as <DB>:<ACCESSION> or as <DB>:<ACCESSION>:<VERSION>.
FK | Name | Type | Description |
---|---|---|---|
dbxref_id | serial | PRIMARY KEY | |
db | db_id | integer | UNIQUE#1 NOT NULL |
accession | character varying(255) | UNIQUE#1 NOT NULL | |
version | character varying(255) | UNIQUE#1 NOT NULL | |
description | text |
Tables referencing dbxref via foreign key constraints:
- arraydesign
- assay
- biomaterial
- biomaterial_dbxref
- cell_line_dbxref
- cvterm
- cvterm_dbxref
- dbxrefprop
- element
- feature
- feature_cvterm_dbxref
- feature_dbxref
- library_dbxref
- nd_experiment_dbxref
- nd_experiment_stock_dbxref
- organism_dbxref
- phylonode_dbxref
- phylotree
- protocol
- pub_dbxref
- stock
- stock_dbxref
- study
</protect>
Table: dbxrefprop
<protect>
Table: | dbxrefprop |
Module: | General |
Metadata about a dbxref. Note that this is not defined in the dbxref module, as it depends on the cvterm table. This table has a structure analagous to cvtermprop.
FK | Name | Type | Description |
---|---|---|---|
dbxrefprop_id | serial | PRIMARY KEY | |
dbxref | dbxref_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | NOT NULL DEFAULT ''::text | |
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing dbxrefprop via foreign key constraints:
- None.</protect>
Module: CV
Table: cv
<protect>
Table: | cv |
Module: | CV |
A controlled vocabulary or ontology. A cv is composed of cvterms (AKA terms, classes, types, universals - relations and properties are also stored in cvterm) and the relationships between them.
FK | Name | Type | Description |
---|---|---|---|
cv_id | serial | PRIMARY KEY | |
name | character varying(255) | UNIQUE NOT NULL | |
definition | text | A text description of the criteria for
membership of this ontology. |
Tables referencing cv via foreign key constraints:
</protect>
Table: cvterm
<protect>
Table: | cvterm |
Module: | CV |
A term, class, universal or type within an ontology or controlled vocabulary. This table is also used for relations and properties. cvterms constitute nodes in the graph defined by the collection of cvterms and cvterm_relationships.
FK | Name | Type | Description |
---|---|---|---|
cvterm_id | serial | PRIMARY KEY | |
cv | cv_id | integer | UNIQUE#1 NOT NULL |
name | character varying(1024) | UNIQUE#1 NOT NULL | |
definition | text | A human-readable text
definition. | |
dbxref | dbxref_id | integer | UNIQUE NOT NULL |
is_obsolete | integer | UNIQUE#1 NOT NULL | |
is_relationshiptype | integer | NOT NULL Boolean 0=false,1=true relations or relationship types (also known as Typedefs in OBO format, or as properties or slots) form a cv/ontology in themselves. We use this flag to indicate whether this cvterm is an actual term/class/universal or a relation. Relations may be drawn from the OBO Relations ontology, but are not exclusively drawn from there. |
Tables referencing cvterm via foreign key constraints:
- acquisition_relationship
- acquisitionprop
- analysisfeatureprop
- analysisprop
- arraydesign
- arraydesignprop
- assayprop
- biomaterial_relationship
- biomaterial_treatment
- biomaterialprop
- cell_line_cvterm
- cell_line_cvtermprop
- cell_line_relationship
- cell_lineprop
- contact
- contact_relationship
- control
- cvterm_dbxref
- cvterm_relationship
- cvtermpath
- cvtermprop
- cvtermsynonym
- dbxrefprop
- element
- element_relationship
- elementresult_relationship
- environment_cvterm
- expression_cvterm
- expression_cvtermprop
- expressionprop
- feature
- feature_cvterm
- feature_cvtermprop
- feature_expressionprop
- feature_genotype
- feature_pubprop
- feature_relationship
- feature_relationshipprop
- featuremap
- featureprop
- library
- library_cvterm
- libraryprop
- nd_experiment
- nd_experiment_stock
- nd_experiment_stockprop
- nd_experimentprop
- nd_geolocationprop
- nd_protocol_reagent
- nd_protocolprop
- nd_reagent
- nd_reagent_relationship
- nd_reagentprop
- organismprop
- phendesc
- phenotype
- phenotype_comparison_cvterm
- phenotype_cvterm
- phenstatement
- phylonode
- phylonode_relationship
- phylonodeprop
- phylotree
- project_relationship
- projectprop
- protocol
- protocolparam
- pub
- pub_relationship
- pubprop
- quantification_relationship
- quantificationprop
- stock
- stock_cvterm
- stock_dbxrefprop
- stock_relationship
- stock_relationship_cvterm
- stockcollection
- stockcollectionprop
- stockprop
- studydesignprop
- studyfactor
- studyprop
- studyprop_feature
- synonym
- treatment
</protect>
Table: cvterm_relationship
<protect>
Table: | cvterm_relationship |
Module: | CV |
A relationship linking two cvterms. Each cvterm_relationship constitutes an edge in the graph defined by the collection of cvterms and cvterm_relationships. The meaning of the cvterm_relationship depends on the definition of the cvterm R refered to by type_id. However, in general the definitions are such that the statement "all SUBJs REL some OBJ" is true. The cvterm_relationship statement is about the subject, not the object. For example "insect wing part_of thorax".
FK | Name | Type | Description |
---|---|---|---|
cvterm_relationship_id | serial | PRIMARY KEY | |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
cvterm | subject_id | integer | UNIQUE#1 NOT NULL |
cvterm | object_id | integer | UNIQUE#1 NOT NULL |
Tables referencing cvterm_relationship via foreign key constraints:
- None.</protect>
Table: cvtermpath
<protect>
Table: | cvtermpath |
Module: | CV |
The reflexive transitive closure of the cvterm_relationship relation.
FK | Name | Type | Description |
---|---|---|---|
cvtermpath_id | serial | PRIMARY KEY | |
cvterm | type_id | integer | UNIQUE#1 The relationship type that this is a closure over. If null, then this is a closure over ALL relationship types. If non-null, then this references a relationship cvterm - note that the closure will apply to both this relationship AND the OBO_REL:is_a (subclass) relationship. |
cvterm | subject_id | integer | UNIQUE#1 NOT NULL |
cvterm | object_id | integer | UNIQUE#1 NOT NULL |
cv | cv_id | integer | NOT NULL Closures will mostly be within one cv. If the closure of a relationship traverses a cv, then this refers to the cv of the object_id cvterm. |
pathdistance | integer | UNIQUE#1 The number of steps required to get from the subject cvterm to the object cvterm, counting from zero (reflexive relationship). |
Tables referencing cvtermpath via foreign key constraints:
- None.</protect>
Table: cvtermsynonym
<protect>
Table: | cvtermsynonym |
Module: | CV |
A cvterm actually represents a distinct class or concept. A concept can be refered to by different phrases or names. In addition to the primary name (cvterm.name) there can be a number of alternative aliases or synonyms. For example, "T cell" as a synonym for "T lymphocyte".
FK | Name | Type | Description |
---|---|---|---|
cvtermsynonym_id | serial | PRIMARY KEY | |
cvterm | cvterm_id | integer | UNIQUE#1 NOT NULL |
synonym | character varying(1024) | UNIQUE#1 NOT NULL | |
cvterm | type_id | integer | A synonym can be exact,
narrower, or broader than. |
Tables referencing cvtermsynonym via foreign key constraints:
- None.</protect>
Table: cvterm_dbxref
<protect>
Table: | cvterm_dbxref |
Module: | CV |
In addition to the primary identifier (cvterm.dbxref_id) a cvterm can have zero or more secondary identifiers/dbxrefs, which may refer to records in external databases. The exact semantics of cvterm_dbxref are not fixed. For example: the dbxref could be a pubmed ID that is pertinent to the cvterm, or it could be an equivalent or similar term in another ontology. For example, GO cvterms are typically linked to InterPro IDs, even though the nature of the relationship between them is largely one of statistical association. The dbxref may be have data records attached in the same database instance, or it could be a "hanging" dbxref pointing to some external database. NOTE: If the desired objective is to link two cvterms together, and the nature of the relation is known and holds for all instances of the subject cvterm then consider instead using cvterm_relationship together with a well-defined relation.
FK | Name | Type | Description |
---|---|---|---|
cvterm_dbxref_id | serial | PRIMARY KEY | |
cvterm | cvterm_id | integer | UNIQUE#1 NOT NULL |
dbxref | dbxref_id | integer | UNIQUE#1 NOT NULL |
is_for_definition | integer | NOT NULL A cvterm.definition should be supported by one or more references. If this column is true, the dbxref is not for a term in an external database - it is a dbxref for provenance information for the definition. |
Tables referencing cvterm_dbxref via foreign key constraints:
- None.</protect>
Table: cvtermprop
<protect>
Table: | cvtermprop |
Module: | CV |
Additional extensible properties can be attached to a cvterm using this table. Corresponds to -AnnotationProperty- in W3C OWL format.
FK | Name | Type | Description |
---|---|---|---|
cvtermprop_id | serial | PRIMARY KEY | |
cvterm | cvterm_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | UNIQUE#1 NOT NULL | |
rank | integer | UNIQUE#1 NOT NULL |
Tables referencing cvtermprop via foreign key constraints:
- None.</protect>
Module: Publication
Table: pub
<protect>
Table: | pub |
Module: | Publication |
A documented provenance artefact - publications, documents, personal communication.
FK | Name | Type | Description |
---|---|---|---|
pub_id | serial | PRIMARY KEY | |
title | text | Descriptive general heading. | |
volumetitle | text | Title of part if one of a series. | |
volume | character varying(255) | ||
series_name | character varying(255) | Full name of (journal) series. | |
issue | character varying(255) | ||
pyear | character varying(255) | ||
pages | character varying(255) | Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii. | |
miniref | character varying(255) | ||
uniquename | text | UNIQUE NOT NULL | |
cvterm | type_id | integer | NOT NULL The type of the publication (book, journal, poem, graffiti, etc). Uses pub cv. |
is_obsolete | boolean | DEFAULT false | |
publisher | character varying(255) | ||
pubplace | character varying(255) |
Tables referencing pub via foreign key constraints:
- cell_line_cvterm
- cell_line_feature
- cell_line_library
- cell_line_pub
- cell_line_synonym
- cell_lineprop_pub
- expression_pub
- feature_cvterm
- feature_cvterm_pub
- feature_expression
- feature_pub
- feature_relationship_pub
- feature_relationshipprop_pub
- feature_synonym
- featureloc_pub
- featuremap_pub
- featureprop_pub
- library_cvterm
- library_pub
- library_synonym
- libraryprop_pub
- nd_experiment_pub
- phendesc
- phenotype_comparison
- phenotype_comparison_cvterm
- phenstatement
- phylonode_pub
- phylotree_pub
- project_pub
- protocol
- pub_dbxref
- pub_relationship
- pubauthor
- pubprop
- stock_cvterm
- stock_pub
- stock_relationship_cvterm
- stock_relationship_pub
- stockprop_pub
- study
</protect>
Table: pub_relationship
<protect>
Table: | pub_relationship |
Module: | Publication |
Handle relationships between publications, e.g. when one publication makes others obsolete, when one publication contains errata with respect to other publication(s), or when one publication also appears in another pub.
FK | Name | Type | Description |
---|---|---|---|
pub_relationship_id | serial | PRIMARY KEY | |
pub | subject_id | integer | UNIQUE#1 NOT NULL |
pub | object_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing pub_relationship via foreign key constraints:
- None.</protect>
Table: pub_dbxref
<protect>
Table: | pub_dbxref |
Module: | Publication |
Handle links to repositories, e.g. Pubmed, Biosis, zoorec, OCLC, Medline, ISSN, coden...
FK | Name | Type | Description |
---|---|---|---|
pub_dbxref_id | serial | PRIMARY KEY | |
pub | pub_id | integer | UNIQUE#1 NOT NULL |
dbxref | dbxref_id | integer | UNIQUE#1 NOT NULL |
is_current | boolean | NOT NULL DEFAULT true
|
Tables referencing pub_dbxref via foreign key constraints:
- None.</protect>
Table: pubauthor
<protect>
Table: | pubauthor |
Module: | Publication |
An author for a publication. Note the denormalisation (hence lack of _ in table name) - this is deliberate as it is in general too hard to assign IDs to authors.
FK | Name | Type | Description |
---|---|---|---|
pubauthor_id | serial | PRIMARY KEY | |
pub | pub_id | integer | UNIQUE#1 NOT NULL |
rank | integer | UNIQUE#1 NOT NULL | |
editor | boolean | DEFAULT false Indicates whether the author is an editor for linked publication. Note: this is a boolean field but does not follow the normal chado convention for naming booleans. | |
surname | character varying(100) | NOT NULL | |
givennames | character varying(100) | First name, initials | |
suffix | character varying(100) | Jr., Sr., etc |
Tables referencing pubauthor via foreign key constraints:
- None.</protect>
Table: pubprop
<protect>
Table: | pubprop |
Module: | Publication |
Property-value pairs for a pub. Follows standard chado pattern.
FK | Name | Type | Description |
---|---|---|---|
pubprop_id | serial | PRIMARY KEY | |
pub | pub_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | NOT NULL | |
rank | integer | UNIQUE#1
|
Tables referencing pubprop via foreign key constraints:
- None.</protect>
Module: Organism
Table: organism
<protect>
Table: | organism |
Module: | Organism |
The organismal taxonomic classification. Note that phylogenies are represented using the phylogeny module, and taxonomies can be represented using the cvterm module or the phylogeny module.
FK | Name | Type | Description |
---|---|---|---|
organism_id | serial | PRIMARY KEY | |
abbreviation | character varying(255) | ||
genus | character varying(255) | UNIQUE#1 NOT NULL | |
species | character varying(255) | UNIQUE#1 NOT NULL | |
common_name | character varying(255) | ||
comment | text |
Tables referencing organism via foreign key constraints:
- biomaterial
- cell_line
- feature
- library
- organism_dbxref
- organismprop
- phenotype_comparison
- phylonode_organism
- stock
</protect>
Table: organism_dbxref
<protect>
Table: | organism_dbxref |
Module: | Organism |
FK | Name | Type | Description |
---|---|---|---|
organism_dbxref_id | serial | PRIMARY KEY | |
organism | organism_id | integer | UNIQUE#1 NOT NULL |
dbxref | dbxref_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing organism_dbxref via foreign key constraints:
- None.</protect>
Table: organismprop
<protect>
Table: | organismprop |
Module: | Organism |
Tag-value properties - follows standard chado model.
FK | Name | Type | Description |
---|---|---|---|
organismprop_id | serial | PRIMARY KEY | |
organism | organism_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing organismprop via foreign key constraints:
- None.</protect>
Module: Sequence
Table: feature
<protect>
Table: | feature |
Module: | Sequence |
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. The combination of organism_id, uniquename and type_id should be unique.
FK | Name | Type | Description |
---|---|---|---|
feature_id | serial | PRIMARY KEY | |
dbxref | dbxref_id | integer | An optional primary public stable
identifier for this feature. Secondary identifiers and external dbxrefs go in the table feature_dbxref. |
organism | organism_id | integer | UNIQUE#1 NOT NULL |
name | character varying(255) | The optional human-readable common name for
a feature, for display purposes. | |
uniquename | text | UNIQUE#1 NOT NULL | |
residues | text | 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 (e.g. transcripts), since derivation at query time is non-trivial. For expressed sequence, the DNA sequence should be used rather than the RNA sequence. The default storage method for the residues column is EXTERNAL, which will store it uncompressed to make substring operations faster. | |
seqlen | integer | 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 | character(32) | 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. | |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
is_analysis | boolean | NOT NULL DEFAULT false | |
is_obsolete | boolean | NOT NULL DEFAULT false | |
timeaccessioned | timestamp without time zone | NOT NULL DEFAULT now() | |
timelastmodified | timestamp without time zone | NOT NULL DEFAULT now() |
Tables referencing feature via foreign key constraints:
- featuregroup
- analysisfeature
- cell_line_feature
- element
- feature_cvterm
- feature_dbxref
- feature_expression
- feature_genotype
- feature_phenotype
- feature_pub
- feature_relationship
- feature_synonym
- featureloc
- featurepos
- featureprop
- featurerange
- library_feature
- phylonode
- studyprop_feature
</protect>
Table: featureloc
<protect>
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:
</protect>
Table: featureloc_pub
<protect>
Table: | featureloc_pub |
Module: | Sequence |
Provenance of featureloc. Linking table between featurelocs and publications that mention them.
FK | Name | Type | Description |
---|---|---|---|
featureloc_pub_id | serial | PRIMARY KEY | |
featureloc | featureloc_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing featureloc_pub via foreign key constraints:
- None.</protect>
Table: feature_pub
<protect>
Table: | feature_pub |
Module: | Sequence |
Provenance. Linking table between features and publications that mention them.
FK | Name | Type | Description |
---|---|---|---|
feature_pub_id | serial | PRIMARY KEY | |
feature | feature_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing feature_pub via foreign key constraints:
</protect>
Table: feature_pubprop
<protect>
Table: | feature_pubprop |
Module: | Sequence |
Property or attribute of a feature_pub link.
FK | Name | Type | Description |
---|---|---|---|
feature_pubprop_id | serial | PRIMARY KEY | |
feature_pub | feature_pub_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing feature_pubprop via foreign key constraints:
- None.</protect>
Table: featureprop
<protect>
Table: | featureprop |
Module: | Sequence |
A feature can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible.
FK | Name | Type | Description |
---|---|---|---|
featureprop_id | serial | PRIMARY KEY | |
feature | feature_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | 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. | |
rank | integer | UNIQUE#1 NOT NULL |
Tables referencing featureprop via foreign key constraints:
</protect>
Table: featureprop_pub
<protect>
Table: | featureprop_pub |
Module: | Sequence |
Provenance. Any featureprop assignment can optionally be supported by a publication.
FK | Name | Type | Description |
---|---|---|---|
featureprop_pub_id | serial | PRIMARY KEY | |
featureprop | featureprop_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing featureprop_pub via foreign key constraints:
- None.</protect>
Table: feature_dbxref
<protect>
Table: | feature_dbxref |
Module: | Sequence |
Links a feature to dbxrefs. This is for secondary identifiers; primary identifiers should use feature.dbxref_id.
FK | Name | Type | Description |
---|---|---|---|
feature_dbxref_id | serial | PRIMARY KEY | |
feature | feature_id | integer | UNIQUE#1 NOT NULL |
dbxref | dbxref_id | integer | UNIQUE#1 NOT NULL |
is_current | boolean | NOT NULL DEFAULT true |
Tables referencing feature_dbxref via foreign key constraints:
- None.</protect>
Table: feature_relationship
<protect>
Table: | feature_relationship |
Module: | Sequence |
Features can be arranged in graphs, e.g. "exon part_of transcript part_of gene"; If type is thought of as a verb, the each arc or edge makes a statement [Subject Verb Object]. The object can also be thought of as parent (containing feature), and subject as child (contained feature or subfeature). We include the relationship rank/order, because even though most of the time we can order things implicitly by sequence coordinates, we can not always do this - e.g. transpliced genes. It is also useful for quickly getting implicit introns.
FK | Name | Type | Description |
---|---|---|---|
feature_relationship_id | serial | PRIMARY KEY | |
feature | subject_id | integer | UNIQUE#1 NOT NULL |
feature | object_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | Additional notes or comments. | |
rank | integer | UNIQUE#1 NOT NULL |
Tables referencing feature_relationship via foreign key constraints:
</protect>
Table: feature_relationship_pub
<protect>
Table: | feature_relationship_pub |
Module: | Sequence |
Provenance. Attach optional evidence to a feature_relationship in the form of a publication.
FK | Name | Type | Description |
---|---|---|---|
feature_relationship_pub_id | serial | PRIMARY KEY | |
feature_relationship | feature_relationship_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing feature_relationship_pub via foreign key constraints:
- None.</protect>
Table: feature_relationshipprop
<protect>
Table: | feature_relationshipprop |
Module: | Sequence |
Extensible properties for feature_relationships. Analagous structure to featureprop. This table is largely optional and not used with a high frequency. Typical scenarios may be if one wishes to attach additional data to a feature_relationship - for example to say that the feature_relationship is only true in certain contexts.
FK | Name | Type | Description |
---|---|---|---|
feature_relationshipprop_id | serial | PRIMARY KEY | |
feature_relationship | feature_relationship_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | 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. | |
rank | integer | UNIQUE#1 NOT NULL |
Tables referencing feature_relationshipprop via foreign key constraints:
</protect>
Table: feature_relationshipprop_pub
<protect>
Table: | feature_relationshipprop_pub |
Module: | Sequence |
Provenance for feature_relationshipprop.
FK | Name | Type | Description |
---|---|---|---|
feature_relationshipprop_pub_id | serial | PRIMARY KEY | |
feature_relationshipprop | feature_relationshipprop_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing feature_relationshipprop_pub via foreign key constraints:
- None.</protect>
Table: feature_cvterm
<protect>
Table: | feature_cvterm |
Module: | Sequence |
Associate a term from a cv with a feature, for example, GO annotation.
FK | Name | Type | Description |
---|---|---|---|
feature_cvterm_id | serial | PRIMARY KEY | |
feature | feature_id | integer | UNIQUE#1 NOT NULL |
cvterm | cvterm_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL |
is_not | boolean | NOT NULL DEFAULT false | |
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing feature_cvterm via foreign key constraints:
</protect>
Table: feature_cvtermprop
<protect>
Table: | feature_cvtermprop |
Module: | Sequence |
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.
FK | Name | Type | Description |
---|---|---|---|
feature_cvtermprop_id | serial | PRIMARY KEY | |
feature_cvterm | feature_cvterm_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | 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. | |
rank | integer | UNIQUE#1 NOT NULL |
Tables referencing feature_cvtermprop via foreign key constraints:
- None.</protect>
Table: feature_cvterm_dbxref
<protect>
Table: | feature_cvterm_dbxref |
Module: | Sequence |
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.
FK | Name | Type | Description |
---|---|---|---|
feature_cvterm_dbxref_id | serial | PRIMARY KEY | |
feature_cvterm | feature_cvterm_id | integer | UNIQUE#1 NOT NULL |
dbxref | dbxref_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing feature_cvterm_dbxref via foreign key constraints:
- None.</protect>
Table: feature_cvterm_pub
<protect>
Table: | feature_cvterm_pub |
Module: | Sequence |
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.
FK | Name | Type | Description |
---|---|---|---|
feature_cvterm_pub_id | serial | PRIMARY KEY | |
feature_cvterm | feature_cvterm_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing feature_cvterm_pub via foreign key constraints:
- None.</protect>
Table: synonym
<protect>
Table: | synonym |
Module: | Sequence |
A synonym for a feature. One feature can have multiple synonyms, and the same synonym can apply to multiple features.
FK | Name | Type | Description |
---|---|---|---|
synonym_id | serial | PRIMARY KEY | |
name | character varying(255) | UNIQUE#1 NOT NULL | |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
synonym_sgml | character varying(255) | NOT NULL The fully specified synonym, with any non-ascii characters encoded in SGML. |
Tables referencing synonym via foreign key constraints:
</protect>
Table: feature_synonym
<protect>
Table: | feature_synonym |
Module: | Sequence |
Linking table between feature and synonym.
FK | Name | Type | Description |
---|---|---|---|
feature_synonym_id | serial | PRIMARY KEY | |
synonym | synonym_id | integer | UNIQUE#1 NOT NULL |
feature | feature_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL |
is_current | boolean | NOT NULL DEFAULT false | |
is_internal | boolean | NOT NULL DEFAULT false |
Tables referencing feature_synonym via foreign key constraints:
- None.</protect>
Table: gencode
<protect>
Table: | gencode |
Module: | Sequence |
FK | Name | Type | Description |
---|---|---|---|
gencode_id | integer | PRIMARY KEY | |
organismstr | character varying(512) | NOT NULL
|
Tables referencing gencode via foreign key constraints:
</protect>
Table: gencode_codon_aa
<protect>
Table: | gencode_codon_aa |
Module: | Sequence |
FK | Name | Type | Description |
---|---|---|---|
gencode | gencode_id | integer | NOT NULL |
codon | character(3) | NOT NULL | |
aa | character(1) | NOT NULL
|
Tables referencing gencode_codon_aa via foreign key constraints:
- None.</protect>
Table: gencode_startcodon
<protect>
Table: | gencode_startcodon |
Module: | Sequence |
FK | Name | Type | Description |
---|---|---|---|
gencode | gencode_id | integer | NOT NULL |
codon | character(3) |
Tables referencing gencode_startcodon via foreign key constraints:
- None.</protect>
Module: Companalysis
Table: analysis
<protect>
Table: | analysis |
Module: | Companalysis |
An analysis is a particular type of a
computational analysis; it may be a blast of one sequence against another, or an all by all blast, or a different kind of analysis altogether. It is a single unit of computation.
FK | Name | Type | Description |
---|---|---|---|
analysis_id | serial | PRIMARY KEY | |
name | character varying(255) | A way of grouping analyses. This
should be a handy short identifier that can help people find an analysis they want. For instance "tRNAscan", "cDNA", "FlyPep", "SwissProt", and it should not be assumed to be unique. For instance, there may be lots of separate analyses done against a cDNA database. | |
description | text | ||
program | character varying(255) | UNIQUE#1 NOT NULL | |
programversion | character varying(255) | UNIQUE#1 NOT NULL | |
algorithm | character varying(255) | Algorithm name, e.g. blast. | |
sourcename | character varying(255) | UNIQUE#1 Source name, e.g. cDNA, SwissProt. | |
sourceversion | character varying(255) | ||
sourceuri | text | This is an optional, permanent URL or URI for the source of the analysis. The idea is that someone could recreate the analysis directly by going to this URI and fetching the source data (e.g. the blast database, or the training model). | |
timeexecuted | timestamp without time zone | NOT NULL DEFAULT now()
|
Tables referencing analysis via foreign key constraints:
</protect>
Table: analysisprop
<protect>
Table: | analysisprop |
Module: | Companalysis |
FK | Name | Type | Description |
---|---|---|---|
analysisprop_id | serial | PRIMARY KEY | |
analysis | analysis_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing analysisprop via foreign key constraints:
- None.</protect>
Table: analysisfeature
<protect>
Table: | analysisfeature |
Module: | Companalysis |
Computational analyses generate features (e.g. Genscan generates transcripts and exons; sim4 alignments generate similarity/match features). analysisfeatures are stored using the feature table from the sequence module. The analysisfeature table is used to decorate these features, with analysis specific attributes. A feature is an analysisfeature if and only if there is a corresponding entry in the analysisfeature table. analysisfeatures will have two or more featureloc entries,
with rank indicating query/subject
FK | Name | Type | Description |
---|---|---|---|
analysisfeature_id | serial | PRIMARY KEY | |
feature | feature_id | integer | UNIQUE#1 NOT NULL |
analysis | analysis_id | integer | UNIQUE#1 NOT NULL |
rawscore | double precision | This is the native score generated by the program; for example, the bitscore generated by blast, sim4 or genscan scores. One should not assume that high is necessarily better than low. | |
normscore | double precision | This is the rawscore but
semi-normalized. Complete normalization to allow comparison of features generated by different programs would be nice but too difficult. Instead the normalization should strive to enforce the following semantics: * normscores are floating point numbers >= 0, * high normscores are better than low one. For most programs, it would be sufficient to make the normscore the same as this rawscore, providing these semantics are satisfied. | |
significance | double precision | This is some kind of expectation or probability metric, representing the probability that the analysis would appear randomly given the model. As such, any program or person querying this table can assume the following semantics:
* 0 <= significance <= n, where n is a positive number, theoretically unbounded but unlikely to be more than 10 * low numbers are better than high numbers. | |
identity | double precision | Percent identity between the locations compared. Note that these 4 metrics do not cover the full range of scores possible; it would be undesirable to list every score possible, as this should be kept extensible. instead, for non-standard scores, use the analysisprop table. |
Tables referencing analysisfeature via foreign key constraints:
</protect>
Table: analysisfeatureprop
<protect>
Table: | analysisfeatureprop |
Module: | Companalysis |
FK | Name | Type | Description |
---|---|---|---|
analysisfeatureprop_id | serial | PRIMARY KEY | |
analysisfeature | analysisfeature_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing analysisfeatureprop via foreign key constraints:
- None.</protect>
Module: Cell Line
Table: cell_line
<protect>
Table: | cell_line |
Module: | Cell Line |
FK | Name | Type | Description |
---|---|---|---|
cell_line_id | serial | PRIMARY KEY | |
name | character varying(255) | ||
uniquename | character varying(255) | UNIQUE#1 NOT NULL | |
organism | organism_id | integer | UNIQUE#1 NOT NULL |
timeaccessioned | timestamp without time zone | NOT NULL DEFAULT now() | |
timelastmodified | timestamp without time zone | NOT NULL DEFAULT now()
|
Tables referencing cell_line via foreign key constraints:
- cell_line_cvterm
- cell_line_dbxref
- cell_line_feature
- cell_line_library
- cell_line_pub
- cell_line_relationship
- cell_line_synonym
- cell_lineprop
</protect>
Table: cell_line_relationship
<protect>
Table: | cell_line_relationship |
Module: | Cell Line |
FK | Name | Type | Description |
---|---|---|---|
cell_line_relationship_id | serial | PRIMARY KEY | |
cell_line | subject_id | integer | UNIQUE#1 NOT NULL |
cell_line | object_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing cell_line_relationship via foreign key constraints:
- None.</protect>
Table: cell_line_synonym
<protect>
Table: | cell_line_synonym |
Module: | Cell Line |
FK | Name | Type | Description |
---|---|---|---|
cell_line_synonym_id | serial | PRIMARY KEY | |
cell_line | cell_line_id | integer | UNIQUE#1 NOT NULL |
synonym | synonym_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL |
is_current | boolean | NOT NULL DEFAULT false | |
is_internal | boolean | NOT NULL DEFAULT false
|
Tables referencing cell_line_synonym via foreign key constraints:
- None.</protect>
Table: cell_line_cvterm
<protect>
Table: | cell_line_cvterm |
Module: | Cell Line |
FK | Name | Type | Description |
---|---|---|---|
cell_line_cvterm_id | serial | PRIMARY KEY | |
cell_line | cell_line_id | integer | UNIQUE#1 NOT NULL |
cvterm | cvterm_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL |
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing cell_line_cvterm via foreign key constraints:
</protect>
Table: cell_line_dbxref
<protect>
Table: | cell_line_dbxref |
Module: | Cell Line |
FK | Name | Type | Description |
---|---|---|---|
cell_line_dbxref_id | serial | PRIMARY KEY | |
cell_line | cell_line_id | integer | UNIQUE#1 NOT NULL |
dbxref | dbxref_id | integer | UNIQUE#1 NOT NULL |
is_current | boolean | NOT NULL DEFAULT true
|
Tables referencing cell_line_dbxref via foreign key constraints:
- None.</protect>
Table: cell_lineprop
<protect>
Table: | cell_lineprop |
Module: | Cell Line |
FK | Name | Type | Description |
---|---|---|---|
cell_lineprop_id | serial | PRIMARY KEY | |
cell_line | cell_line_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing cell_lineprop via foreign key constraints:
</protect>
Table: cell_lineprop_pub
<protect>
Table: | cell_lineprop_pub |
Module: | Cell Line |
FK | Name | Type | Description |
---|---|---|---|
cell_lineprop_pub_id | serial | PRIMARY KEY | |
cell_lineprop | cell_lineprop_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing cell_lineprop_pub via foreign key constraints:
- None.</protect>
Table: cell_line_feature
<protect>
Table: | cell_line_feature |
Module: | Cell Line |
FK | Name | Type | Description |
---|---|---|---|
cell_line_feature_id | serial | PRIMARY KEY | |
cell_line | cell_line_id | integer | UNIQUE#1 NOT NULL |
feature | feature_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing cell_line_feature via foreign key constraints:
- None.</protect>
Table: cell_line_cvtermprop
<protect>
Table: | cell_line_cvtermprop |
Module: | Cell Line |
FK | Name | Type | Description |
---|---|---|---|
cell_line_cvtermprop_id | serial | PRIMARY KEY | |
cell_line_cvterm | cell_line_cvterm_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing cell_line_cvtermprop via foreign key constraints:
- None.</protect>
Table: cell_line_pub
<protect>
Table: | cell_line_pub |
Module: | Cell Line |
FK | Name | Type | Description |
---|---|---|---|
cell_line_pub_id | serial | PRIMARY KEY | |
cell_line | cell_line_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing cell_line_pub via foreign key constraints:
- None.</protect>
Table: cell_line_library
<protect>
Table: | cell_line_library |
Module: | Cell Line |
FK | Name | Type | Description |
---|---|---|---|
cell_line_library_id | serial | PRIMARY KEY | |
cell_line | cell_line_id | integer | UNIQUE#1 NOT NULL |
library | library_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing cell_line_library via foreign key constraints:
- None.</protect>
Module: Contact
Table: contactprop
Table: contact
<protect>
Table: | contact |
Module: | Contact |
Model persons, institutes, groups, organizations, etc.
FK | Name | Type | Description |
---|---|---|---|
contact_id | serial | PRIMARY KEY | |
cvterm | type_id | integer | What type of contact is this? E.g. "person", "lab". |
name | character varying(255) | UNIQUE NOT NULL | |
description | character varying(255) |
Tables referencing contact via foreign key constraints:
- arraydesign
- assay
- biomaterial
- contact_relationship
- nd_experiment_contact
- project_contact
- quantification
- stockcollection
- study
</protect>
Table: contact_relationship
<protect>
Table: | contact_relationship |
Module: | Contact |
Model relationships between contacts
FK | Name | Type | Description |
---|---|---|---|
contact_relationship_id | serial | PRIMARY KEY | |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
contact | subject_id | integer | UNIQUE#1 NOT NULL |
contact | object_id | integer | UNIQUE#1 NOT NULL |
Tables referencing contact_relationship via foreign key constraints:
- None.</protect>
Module: Expression
Table: expression
<protect>
Table: | expression |
Module: | Expression |
The expression table is essentially a bridge table.
FK | Name | Type | Description |
---|---|---|---|
expression_id | serial | PRIMARY KEY | |
uniquename | text | UNIQUE NOT NULL | |
md5checksum | character(32) | ||
description | text |
Tables referencing expression via foreign key constraints:
</protect>
Table: expression_cvterm
<protect>
Table: | expression_cvterm |
Module: | Expression |
FK | Name | Type | Description |
---|---|---|---|
expression_cvterm_id | serial | PRIMARY KEY | |
expression | expression_id | integer | UNIQUE#1 NOT NULL |
cvterm | cvterm_id | integer | UNIQUE#1 NOT NULL |
rank | integer | NOT NULL | |
cvterm | cvterm_type_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing expression_cvterm via foreign key constraints:
</protect>
Table: expression_cvtermprop
<protect>
Table: | expression_cvtermprop |
Module: | Expression |
Extensible properties for expression to cvterm associations. Examples: qualifiers.
FK | Name | Type | Description |
---|---|---|---|
expression_cvtermprop_id | serial | PRIMARY KEY | |
expression_cvterm | expression_cvterm_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | 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. | |
rank | integer | UNIQUE#1 NOT NULL |
Tables referencing expression_cvtermprop via foreign key constraints:
- None.</protect>
Table: expressionprop
<protect>
Table: | expressionprop |
Module: | Expression |
FK | Name | Type | Description |
---|---|---|---|
expressionprop_id | serial | PRIMARY KEY | |
expression | expression_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing expressionprop via foreign key constraints:
- None.</protect>
Table: expression_pub
<protect>
Table: | expression_pub |
Module: | Expression |
FK | Name | Type | Description |
---|---|---|---|
expression_pub_id | serial | PRIMARY KEY | |
expression | expression_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing expression_pub via foreign key constraints:
- None.</protect>
Table: feature_expression
<protect>
Table: | feature_expression |
Module: | Expression |
FK | Name | Type | Description |
---|---|---|---|
feature_expression_id | serial | PRIMARY KEY | |
expression | expression_id | integer | UNIQUE#1 NOT NULL |
feature | feature_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing feature_expression via foreign key constraints:
</protect>
Table: feature_expressionprop
<protect>
Table: | feature_expressionprop |
Module: | Expression |
Extensible properties for feature_expression (comments, for example). Modeled on feature_cvtermprop.
FK | Name | Type | Description |
---|---|---|---|
feature_expressionprop_id | serial | PRIMARY KEY | |
feature_expression | feature_expression_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing feature_expressionprop via foreign key constraints:
- None.</protect>
Table: eimage
<protect>
Table: | eimage |
Module: | Expression |
FK | Name | Type | Description |
---|---|---|---|
eimage_id | serial | PRIMARY KEY | |
eimage_data | text | We expect images in eimage_data (e.g. JPEGs) to be uuencoded. | |
eimage_type | character varying(255) | NOT NULL Describes the type of data in eimage_data. | |
image_uri | character varying(255) |
Tables referencing eimage via foreign key constraints:
</protect>
Table: expression_image
<protect>
Table: | expression_image |
Module: | Expression |
FK | Name | Type | Description |
---|---|---|---|
expression_image_id | serial | PRIMARY KEY | |
expression | expression_id | integer | UNIQUE#1 NOT NULL |
eimage | eimage_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing expression_image via foreign key constraints:
- None.</protect>
Module: Genetic
Table: genotype
<protect>
Table: | genotype |
Module: | Genetic |
Genetic context. A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.
FK | Name | Type | Description |
---|---|---|---|
genotype_id | serial | PRIMARY KEY | |
name | text | Optional alternative name for a genotype,
for display purposes. | |
uniquename | text | UNIQUE NOT NULL | |
description | character varying(255) |
Tables referencing genotype via foreign key constraints:
</protect>
Table: feature_genotype
<protect>
Table: | feature_genotype |
Module: | Genetic |
FK | Name | Type | Description |
---|---|---|---|
feature_genotype_id | serial | PRIMARY KEY | |
feature | feature_id | integer | UNIQUE#1 NOT NULL |
genotype | genotype_id | integer | UNIQUE#1 NOT NULL |
feature | chromosome_id | integer | UNIQUE#1 A feature of SO type "chromosome". |
rank | integer | UNIQUE#1 NOT NULL | |
cgroup | integer | UNIQUE#1 NOT NULL | |
cvterm | cvterm_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing feature_genotype via foreign key constraints:
- None.</protect>
Table: environment
<protect>
Table: | environment |
Module: | Genetic |
The environmental component of a phenotype description.
FK | Name | Type | Description |
---|---|---|---|
environment_id | serial | PRIMARY KEY | |
uniquename | text | UNIQUE NOT NULL | |
description | text |
Tables referencing environment via foreign key constraints:
</protect>
Table: environment_cvterm
<protect>
Table: | environment_cvterm |
Module: | Genetic |
FK | Name | Type | Description |
---|---|---|---|
environment_cvterm_id | serial | PRIMARY KEY | |
environment | environment_id | integer | UNIQUE#1 NOT NULL |
cvterm | cvterm_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing environment_cvterm via foreign key constraints:
- None.</protect>
Table: phenstatement
<protect>
Table: | phenstatement |
Module: | Genetic |
Phenotypes are things like "larval lethal". Phenstatements are things like "dpp-1 is recessive larval lethal". So essentially phenstatement is a linking table expressing the relationship between genotype, environment, and phenotype.
FK | Name | Type | Description |
---|---|---|---|
phenstatement_id | serial | PRIMARY KEY | |
genotype | genotype_id | integer | UNIQUE#1 NOT NULL |
environment | environment_id | integer | UNIQUE#1 NOT NULL |
phenotype | phenotype_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing phenstatement via foreign key constraints:
- None.</protect>
Table: phendesc
<protect>
Table: | phendesc |
Module: | Genetic |
A summary of a _set_ of phenotypic statements for any one gcontext made in any one publication.
FK | Name | Type | Description |
---|---|---|---|
phendesc_id | serial | PRIMARY KEY | |
genotype | genotype_id | integer | UNIQUE#1 NOT NULL |
environment | environment_id | integer | UNIQUE#1 NOT NULL |
description | text | NOT NULL | |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing phendesc via foreign key constraints:
- None.</protect>
Table: phenotype_comparison
<protect>
Table: | phenotype_comparison |
Module: | Genetic |
Comparison of phenotypes e.g., genotype1/environment1/phenotype1 "non-suppressible" with respect to genotype2/environment2/phenotype2.
FK | Name | Type | Description |
---|---|---|---|
phenotype_comparison_id | serial | PRIMARY KEY | |
genotype | genotype1_id | integer | UNIQUE#1 NOT NULL |
environment | environment1_id | integer | UNIQUE#1 NOT NULL |
genotype | genotype2_id | integer | UNIQUE#1 NOT NULL |
environment | environment2_id | integer | UNIQUE#1 NOT NULL |
phenotype | phenotype1_id | integer | UNIQUE#1 NOT NULL |
phenotype | phenotype2_id | integer | |
pub | pub_id | integer | UNIQUE#1 NOT NULL |
organism | organism_id | integer | NOT NULL
|
Tables referencing phenotype_comparison via foreign key constraints:
</protect>
Table: phenotype_comparison_cvterm
<protect>
Table: | phenotype_comparison_cvterm |
Module: | Genetic |
FK | Name | Type | Description |
---|---|---|---|
phenotype_comparison_cvterm_id | serial | PRIMARY KEY | |
phenotype_comparison | phenotype_comparison_id | integer | UNIQUE#1 NOT NULL |
cvterm | cvterm_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | NOT NULL |
rank | integer | NOT NULL
|
Tables referencing phenotype_comparison_cvterm via foreign key constraints:
- None.</protect>
Module: Library
Table: library
<protect>
Table: | library |
Module: | Library |
FK | Name | Type | Description |
---|---|---|---|
library_id | serial | PRIMARY KEY | |
organism | organism_id | integer | UNIQUE#1 NOT NULL |
name | character varying(255) | ||
uniquename | text | UNIQUE#1 NOT NULL | |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
is_obsolete | integer | NOT NULL | |
timeaccessioned | timestamp without time zone | NOT NULL DEFAULT now() | |
timelastmodified | timestamp without time zone | NOT NULL DEFAULT now()
|
Tables referencing library via foreign key constraints:
- cell_line_library
- library_cvterm
- library_dbxref
- library_feature
- library_pub
- library_synonym
- libraryprop
</protect>
Table: library_synonym
<protect>
Table: | library_synonym |
Module: | Library |
FK | Name | Type | Description |
---|---|---|---|
library_synonym_id | serial | PRIMARY KEY | |
synonym | synonym_id | integer | UNIQUE#1 NOT NULL |
library | library_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL |
is_current | boolean | NOT NULL DEFAULT true | |
is_internal | boolean | NOT NULL DEFAULT false |
Tables referencing library_synonym via foreign key constraints:
- None.</protect>
Table: library_pub
<protect>
Table: | library_pub |
Module: | Library |
FK | Name | Type | Description |
---|---|---|---|
library_pub_id | serial | PRIMARY KEY | |
library | library_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing library_pub via foreign key constraints:
- None.</protect>
Table: libraryprop
<protect>
Table: | libraryprop |
Module: | Library |
FK | Name | Type | Description |
---|---|---|---|
libraryprop_id | serial | PRIMARY KEY | |
library | library_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing libraryprop via foreign key constraints:
</protect>
Table: libraryprop_pub
<protect>
Table: | libraryprop_pub |
Module: | Library |
FK | Name | Type | Description |
---|---|---|---|
libraryprop_pub_id | serial | PRIMARY KEY | |
libraryprop | libraryprop_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing libraryprop_pub via foreign key constraints:
- None.</protect>
Table: library_cvterm
<protect>
Table: | library_cvterm |
Module: | Library |
The table library_cvterm links a library to controlled vocabularies which describe the library. For instance, there might be a link to the anatomy cv for "head" or "testes" for a head or testes library.
FK | Name | Type | Description |
---|---|---|---|
library_cvterm_id | serial | PRIMARY KEY | |
library | library_id | integer | UNIQUE#1 NOT NULL |
cvterm | cvterm_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing library_cvterm via foreign key constraints:
- None.</protect>
Table: library_feature
<protect>
Table: | library_feature |
Module: | Library |
library_feature links a library to the clones which are contained in the library. Examples of such linked features might be "cDNA_clone" or "genomic_clone".
FK | Name | Type | Description |
---|---|---|---|
library_feature_id | serial | PRIMARY KEY | |
library | library_id | integer | UNIQUE#1 NOT NULL |
feature | feature_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing library_feature via foreign key constraints:
- None.</protect>
Table: library_dbxref
<protect>
Table: | library_dbxref |
Module: | Library |
FK | Name | Type | Description |
---|---|---|---|
library_dbxref_id | serial | PRIMARY KEY | |
library | library_id | integer | UNIQUE#1 NOT NULL |
dbxref | dbxref_id | integer | UNIQUE#1 NOT NULL |
is_current | boolean | NOT NULL DEFAULT true
|
Tables referencing library_dbxref via foreign key constraints:
- None.</protect>
Module: Mage
Table: mageml
<protect>
Table: | mageml |
Module: | Mage |
This table is for storing extra bits of MAGEml in a denormalized form. More normalization would require many more tables.
FK | Name | Type | Description |
---|---|---|---|
mageml_id | serial | PRIMARY KEY | |
mage_package | text | NOT NULL | |
mage_ml | text | NOT NULL
|
Tables referencing mageml via foreign key constraints:
</protect>
Table: magedocumentation
<protect>
Table: | magedocumentation |
Module: | Mage |
FK | Name | Type | Description |
---|---|---|---|
magedocumentation_id | serial | PRIMARY KEY | |
mageml | mageml_id | integer | NOT NULL |
tableinfo | tableinfo_id | integer | NOT NULL |
row_id | integer | NOT NULL | |
mageidentifier | text | NOT NULL
|
Tables referencing magedocumentation via foreign key constraints:
- None.</protect>
Table: protocol
<protect>
Table: | protocol |
Module: | Mage |
Procedural notes on how data was prepared and processed.
FK | Name | Type | Description |
---|---|---|---|
protocol_id | serial | PRIMARY KEY | |
cvterm | type_id | integer | NOT NULL |
pub | pub_id | integer | |
dbxref | dbxref_id | integer | |
name | text | UNIQUE NOT NULL | |
uri | text | ||
protocoldescription | text | ||
hardwaredescription | text | ||
softwaredescription | text |
Tables referencing protocol via foreign key constraints:
</protect>
Table: protocolparam
<protect>
Table: | protocolparam |
Module: | Mage |
Parameters related to a protocol. For example, if the protocol is a soak, this might include attributes of bath temperature and duration.
FK | Name | Type | Description |
---|---|---|---|
protocolparam_id | serial | PRIMARY KEY | |
protocol | protocol_id | integer | NOT NULL |
name | text | NOT NULL | |
cvterm | datatype_id | integer | |
cvterm | unittype_id | integer | |
value | text | ||
rank | integer | NOT NULL
|
Tables referencing protocolparam via foreign key constraints:
- None.</protect>
Table: channel
<protect>
Table: | channel |
Module: | Mage |
Different array platforms can record signals from one or more channels (cDNA arrays typically use two CCD, but Affymetrix uses only one).
FK | Name | Type | Description |
---|---|---|---|
channel_id | serial | PRIMARY KEY | |
name | text | UNIQUE NOT NULL | |
definition | text | NOT NULL
|
Tables referencing channel via foreign key constraints:
</protect>
Table: arraydesign
<protect>
Table: | arraydesign |
Module: | Mage |
General properties about an array. An array is a template used to generate physical slides, etc. It contains layout information, as well as global array properties, such as material (glass, nylon) and spot dimensions (in rows/columns).
FK | Name | Type | Description |
---|---|---|---|
arraydesign_id | serial | PRIMARY KEY | |
contact | manufacturer_id | integer | NOT NULL |
cvterm | platformtype_id | integer | NOT NULL |
cvterm | substratetype_id | integer | |
protocol | protocol_id | integer | |
dbxref | dbxref_id | integer | |
name | text | UNIQUE NOT NULL | |
version | text | ||
description | text | ||
array_dimensions | text | ||
element_dimensions | text | ||
num_of_elements | integer | ||
num_array_columns | integer | ||
num_array_rows | integer | ||
num_grid_columns | integer | ||
num_grid_rows | integer | ||
num_sub_columns | integer | ||
num_sub_rows | integer |
Tables referencing arraydesign via foreign key constraints:
</protect>
Table: arraydesignprop
<protect>
Table: | arraydesignprop |
Module: | Mage |
Extra array design properties that are not accounted for in arraydesign.
FK | Name | Type | Description |
---|---|---|---|
arraydesignprop_id | serial | PRIMARY KEY | |
arraydesign | arraydesign_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing arraydesignprop via foreign key constraints:
- None.</protect>
Table: assay
<protect>
Table: | assay |
Module: | Mage |
An assay consists of a physical instance of an array, combined with the conditions used to create the array (protocols, technician information). The assay can be thought of as a hybridization.
FK | Name | Type | Description |
---|---|---|---|
assay_id | serial | PRIMARY KEY | |
arraydesign | arraydesign_id | integer | NOT NULL |
protocol | protocol_id | integer | |
assaydate | timestamp without time zone | DEFAULT now() | |
arrayidentifier | text | ||
arraybatchidentifier | text | ||
contact | operator_id | integer | NOT NULL |
dbxref | dbxref_id | integer | |
name | text | UNIQUE | |
description | text |
Tables referencing assay via foreign key constraints:
</protect>
Table: assayprop
<protect>
Table: | assayprop |
Module: | Mage |
Extra assay properties that are not accounted for in assay.
FK | Name | Type | Description |
---|---|---|---|
assayprop_id | serial | PRIMARY KEY | |
assay | assay_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing assayprop via foreign key constraints:
- None.</protect>
Table: assay_project
<protect>
Table: | assay_project |
Module: | Mage |
Link assays to projects.
FK | Name | Type | Description |
---|---|---|---|
assay_project_id | serial | PRIMARY KEY | |
assay | assay_id | integer | UNIQUE#1 NOT NULL |
project | project_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing assay_project via foreign key constraints:
- None.</protect>
Table: biomaterial
<protect>
Table: | biomaterial |
Module: | Mage |
A biomaterial represents the MAGE concept of BioSource, BioSample, and LabeledExtract. It is essentially some biological material (tissue, cells, serum) that may have been processed. Processed biomaterials should be traceable back to raw biomaterials via the biomaterialrelationship table.
FK | Name | Type | Description |
---|---|---|---|
biomaterial_id | serial | PRIMARY KEY | |
organism | taxon_id | integer | |
contact | biosourceprovider_id | integer | |
dbxref | dbxref_id | integer | |
name | text | UNIQUE | |
description | text |
Tables referencing biomaterial via foreign key constraints:
- assay_biomaterial
- biomaterial_dbxref
- biomaterial_relationship
- biomaterial_treatment
- biomaterialprop
- treatment
</protect>
Table: biomaterial_relationship
<protect>
Table: | biomaterial_relationship |
Module: | Mage |
Relate biomaterials to one another. This is a way to track a series of treatments or material splits/merges, for instance.
FK | Name | Type | Description |
---|---|---|---|
biomaterial_relationship_id | serial | PRIMARY KEY | |
biomaterial | subject_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
biomaterial | object_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing biomaterial_relationship via foreign key constraints:
- None.</protect>
Table: biomaterialprop
<protect>
Table: | biomaterialprop |
Module: | Mage |
Extra biomaterial properties that are not accounted for in biomaterial.
FK | Name | Type | Description |
---|---|---|---|
biomaterialprop_id | serial | PRIMARY KEY | |
biomaterial | biomaterial_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing biomaterialprop via foreign key constraints:
- None.</protect>
Table: biomaterial_dbxref
<protect>
Table: | biomaterial_dbxref |
Module: | Mage |
FK | Name | Type | Description |
---|---|---|---|
biomaterial_dbxref_id | serial | PRIMARY KEY | |
biomaterial | biomaterial_id | integer | UNIQUE#1 NOT NULL |
dbxref | dbxref_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing biomaterial_dbxref via foreign key constraints:
- None.</protect>
Table: treatment
<protect>
Table: | treatment |
Module: | Mage |
A biomaterial may undergo multiple treatments. Examples of treatments: apoxia, fluorophore and biotin labeling.
FK | Name | Type | Description |
---|---|---|---|
treatment_id | serial | PRIMARY KEY | |
rank | integer | NOT NULL | |
biomaterial | biomaterial_id | integer | NOT NULL |
cvterm | type_id | integer | NOT NULL |
protocol | protocol_id | integer | |
name | text |
Tables referencing treatment via foreign key constraints:
</protect>
Table: biomaterial_treatment
<protect>
Table: | biomaterial_treatment |
Module: | Mage |
Link biomaterials to treatments. Treatments have an order of operations (rank), and associated measurements (unittype_id, value).
FK | Name | Type | Description |
---|---|---|---|
biomaterial_treatment_id | serial | PRIMARY KEY | |
biomaterial | biomaterial_id | integer | UNIQUE#1 NOT NULL |
treatment | treatment_id | integer | UNIQUE#1 NOT NULL |
cvterm | unittype_id | integer | |
value | real | ||
rank | integer | NOT NULL
|
Tables referencing biomaterial_treatment via foreign key constraints:
- None.</protect>
Table: assay_biomaterial
<protect>
Table: | assay_biomaterial |
Module: | Mage |
A biomaterial can be hybridized many times (technical replicates), or combined with other biomaterials in a single hybridization (for two-channel arrays).
FK | Name | Type | Description |
---|---|---|---|
assay_biomaterial_id | serial | PRIMARY KEY | |
assay | assay_id | integer | UNIQUE#1 NOT NULL |
biomaterial | biomaterial_id | integer | UNIQUE#1 NOT NULL |
channel | channel_id | integer | UNIQUE#1 |
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing assay_biomaterial via foreign key constraints:
- None.</protect>
Table: acquisition
<protect>
Table: | acquisition |
Module: | Mage |
This represents the scanning of hybridized material. The output of this process is typically a digital image of an array.
FK | Name | Type | Description |
---|---|---|---|
acquisition_id | serial | PRIMARY KEY | |
assay | assay_id | integer | NOT NULL |
protocol | protocol_id | integer | |
channel | channel_id | integer | |
acquisitiondate | timestamp without time zone | DEFAULT now() | |
name | text | UNIQUE | |
uri | text |
Tables referencing acquisition via foreign key constraints:
</protect>
Table: acquisitionprop
<protect>
Table: | acquisitionprop |
Module: | Mage |
Parameters associated with image acquisition.
FK | Name | Type | Description |
---|---|---|---|
acquisitionprop_id | serial | PRIMARY KEY | |
acquisition | acquisition_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing acquisitionprop via foreign key constraints:
- None.</protect>
Table: acquisition_relationship
<protect>
Table: | acquisition_relationship |
Module: | Mage |
Multiple monochrome images may be merged to form a multi-color image. Red-green images of 2-channel hybridizations are an example of this.
FK | Name | Type | Description |
---|---|---|---|
acquisition_relationship_id | serial | PRIMARY KEY | |
acquisition | subject_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
acquisition | object_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing acquisition_relationship via foreign key constraints:
- None.</protect>
Table: quantification
<protect>
Table: | quantification |
Module: | Mage |
Quantification is the transformation of an image acquisition to numeric data. This typically involves statistical procedures.
FK | Name | Type | Description |
---|---|---|---|
quantification_id | serial | PRIMARY KEY | |
acquisition | acquisition_id | integer | NOT NULL |
contact | operator_id | integer | |
protocol | protocol_id | integer | |
analysis | analysis_id | integer | UNIQUE#1 NOT NULL |
quantificationdate | timestamp without time zone | DEFAULT now() | |
name | text | UNIQUE#1 | |
uri | text |
Tables referencing quantification via foreign key constraints:
</protect>
Table: quantificationprop
<protect>
Table: | quantificationprop |
Module: | Mage |
Extra quantification properties that are not accounted for in quantification.
FK | Name | Type | Description |
---|---|---|---|
quantificationprop_id | serial | PRIMARY KEY | |
quantification | quantification_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing quantificationprop via foreign key constraints:
- None.</protect>
Table: quantification_relationship
<protect>
Table: | quantification_relationship |
Module: | Mage |
There may be multiple rounds of quantification, this allows us to keep an audit trail of what values went where.
FK | Name | Type | Description |
---|---|---|---|
quantification_relationship_id | serial | PRIMARY KEY | |
quantification | subject_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
quantification | object_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing quantification_relationship via foreign key constraints:
- None.</protect>
Table: control
<protect>
Table: | control |
Module: | Mage |
FK | Name | Type | Description |
---|---|---|---|
control_id | serial | PRIMARY KEY | |
cvterm | type_id | integer | NOT NULL |
assay | assay_id | integer | NOT NULL |
tableinfo | tableinfo_id | integer | NOT NULL |
row_id | integer | NOT NULL | |
name | text | ||
value | text | ||
rank | integer | NOT NULL
|
Tables referencing control via foreign key constraints:
- None.</protect>
Table: element
<protect>
Table: | element |
Module: | Mage |
Represents a feature of the array. This is typically a region of the array coated or bound to DNA.
FK | Name | Type | Description |
---|---|---|---|
element_id | serial | PRIMARY KEY | |
feature | feature_id | integer | UNIQUE#1 |
arraydesign | arraydesign_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | |
dbxref | dbxref_id | integer |
Tables referencing element via foreign key constraints:
</protect>
Table: elementresult
<protect>
Table: | elementresult |
Module: | Mage |
An element on an array produces a measurement when hybridized to a biomaterial (traceable through quantification_id). This is the base data from which tables that actually contain data inherit.
FK | Name | Type | Description |
---|---|---|---|
elementresult_id | serial | PRIMARY KEY | |
element | element_id | integer | UNIQUE#1 NOT NULL |
quantification | quantification_id | integer | UNIQUE#1 NOT NULL |
signal | double precision | NOT NULL
|
Tables referencing elementresult via foreign key constraints:
</protect>
Table: element_relationship
<protect>
Table: | element_relationship |
Module: | Mage |
Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.
FK | Name | Type | Description |
---|---|---|---|
element_relationship_id | serial | PRIMARY KEY | |
element | subject_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
element | object_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing element_relationship via foreign key constraints:
- None.</protect>
Table: elementresult_relationship
<protect>
Table: | elementresult_relationship |
Module: | Mage |
Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.
FK | Name | Type | Description |
---|---|---|---|
elementresult_relationship_id | serial | PRIMARY KEY | |
elementresult | subject_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
elementresult | object_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing elementresult_relationship via foreign key constraints:
- None.</protect>
Table: study
<protect>
Table: | study |
Module: | Mage |
FK | Name | Type | Description |
---|---|---|---|
study_id | serial | PRIMARY KEY | |
contact | contact_id | integer | NOT NULL |
pub | pub_id | integer | |
dbxref | dbxref_id | integer | |
name | text | UNIQUE NOT NULL | |
description | text |
Tables referencing study via foreign key constraints:
</protect>
Table: study_assay
<protect>
Table: | study_assay |
Module: | Mage |
FK | Name | Type | Description |
---|---|---|---|
study_assay_id | serial | PRIMARY KEY | |
study | study_id | integer | UNIQUE#1 NOT NULL |
assay | assay_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing study_assay via foreign key constraints:
- None.</protect>
Table: studydesign
<protect>
Table: | studydesign |
Module: | Mage |
FK | Name | Type | Description |
---|---|---|---|
studydesign_id | serial | PRIMARY KEY | |
study | study_id | integer | NOT NULL |
description | text |
Tables referencing studydesign via foreign key constraints:
</protect>
Table: studydesignprop
<protect>
Table: | studydesignprop |
Module: | Mage |
FK | Name | Type | Description |
---|---|---|---|
studydesignprop_id | serial | PRIMARY KEY | |
studydesign | studydesign_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing studydesignprop via foreign key constraints:
- None.</protect>
Table: studyfactor
<protect>
Table: | studyfactor |
Module: | Mage |
FK | Name | Type | Description |
---|---|---|---|
studyfactor_id | serial | PRIMARY KEY | |
studydesign | studydesign_id | integer | NOT NULL |
cvterm | type_id | integer | |
name | text | NOT NULL | |
description | text |
Tables referencing studyfactor via foreign key constraints:
</protect>
Table: studyfactorvalue
<protect>
Table: | studyfactorvalue |
Module: | Mage |
FK | Name | Type | Description |
---|---|---|---|
studyfactorvalue_id | serial | PRIMARY KEY | |
studyfactor | studyfactor_id | integer | NOT NULL |
assay | assay_id | integer | NOT NULL |
factorvalue | text | ||
name | text | ||
rank | integer | NOT NULL
|
Tables referencing studyfactorvalue via foreign key constraints:
- None.</protect>
Table: studyprop
<protect>
Table: | studyprop |
Module: | Mage |
FK | Name | Type | Description |
---|---|---|---|
studyprop_id | serial | PRIMARY KEY | |
study | study_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing studyprop via foreign key constraints:
</protect>
Table: studyprop_feature
<protect>
Table: | studyprop_feature |
Module: | Mage |
FK | Name | Type | Description |
---|---|---|---|
studyprop_feature_id | serial | PRIMARY KEY | |
studyprop | studyprop_id | integer | UNIQUE#1 NOT NULL |
feature | feature_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer |
Tables referencing studyprop_feature via foreign key constraints:
- None.</protect>
Module: Map
Table: featuremap
<protect>
Table: | featuremap |
Module: | Map |
FK | Name | Type | Description |
---|---|---|---|
featuremap_id | serial | PRIMARY KEY | |
name | character varying(255) | UNIQUE | |
description | text | ||
cvterm | unittype_id | integer |
Tables referencing featuremap via foreign key constraints:
</protect>
Table: featurerange
<protect>
Table: | featurerange |
Module: | Map |
In cases where the start and end of a mapped feature is a range, leftendf and rightstartf are populated. leftstartf_id, leftendf_id, rightstartf_id, rightendf_id are the ids of features with respect to which the feature is being mapped. These may be cytological bands.
FK | Name | Type | Description |
---|---|---|---|
featurerange_id | serial | PRIMARY KEY | |
featuremap | featuremap_id | integer | NOT NULL featuremap_id is the id of the feature being mapped. |
feature | feature_id | integer | NOT NULL |
feature | leftstartf_id | integer | NOT NULL |
feature | leftendf_id | integer | |
feature | rightstartf_id | integer | |
feature | rightendf_id | integer | NOT NULL |
rangestr | character varying(255) |
Tables referencing featurerange via foreign key constraints:
- None.</protect>
Table: featurepos
<protect>
Table: | featurepos |
Module: | Map |
FK | Name | Type | Description |
---|---|---|---|
featurepos_id | serial | PRIMARY KEY | |
featuremap | featuremap_id | serial | NOT NULL |
feature | feature_id | integer | NOT NULL |
feature | map_feature_id | integer | NOT NULL map_feature_id links to the feature (map) upon which the feature is being localized. |
mappos | double precision | NOT NULL
|
Tables referencing featurepos via foreign key constraints:
- None.</protect>
Table: featuremap_pub
<protect>
Table: | featuremap_pub |
Module: | Map |
FK | Name | Type | Description |
---|---|---|---|
featuremap_pub_id | serial | PRIMARY KEY | |
featuremap | featuremap_id | integer | NOT NULL |
pub | pub_id | integer | NOT NULL
|
Tables referencing featuremap_pub via foreign key constraints:
- None.</protect>
Module: Natural Diversity
Table: nd_geolocation
<protect>
Table: | nd_geolocation |
Module: | Natural Diversity |
The geo-referencable location of the stock. NOTE: This entity is subject to change as a more general and possibly more OpenGIS-compliant geolocation module may be introduced into Chado.
FK | Name | Type | Description |
---|---|---|---|
nd_geolocation_id | serial | PRIMARY KEY | |
description | character varying(255) | A textual representation of the location, if this is the original georeference. Optional if the original georeference is available in lat/long coordinates. | |
latitude | real | The decimal latitude coordinate of the georeference, using positive and negative sign to indicate N and S, respectively. | |
longitude | real | The decimal longitude coordinate of the georeference, using positive and negative sign to indicate E and W, respectively. | |
geodetic_datum | character varying(32) | The geodetic system on which the geo-reference coordinates are based. For geo-references measured between 1984 and 2010, this will typically be WGS84. | |
altitude | real | The altitude (elevation) of the location in meters. If the altitude is only known as a range, this is the average, and altitude_dev will hold half of the width of the range. |
Tables referencing nd_geolocation via foreign key constraints:
</protect>
Table: nd_experiment
<protect>
Table: | nd_experiment |
Module: | Natural Diversity |
FK | Name | Type | Description |
---|---|---|---|
nd_experiment_id | serial | PRIMARY KEY | |
nd_geolocation | nd_geolocation_id | integer | NOT NULL |
cvterm | type_id | integer | NOT NULL
|
Tables referencing nd_experiment via foreign key constraints:
- nd_experiment_contact
- nd_experiment_dbxref
- nd_experiment_genotype
- nd_experiment_phenotype
- nd_experiment_project
- nd_experiment_protocol
- nd_experiment_pub
- nd_experiment_stock
- nd_experimentprop
</protect>
Table: nd_experiment_project
<protect>
Table: | nd_experiment_project |
Module: | Natural Diversity |
FK | Name | Type | Description |
---|---|---|---|
nd_experiment_project_id | serial | PRIMARY KEY | |
project | project_id | integer | NOT NULL |
nd_experiment | nd_experiment_id | integer | NOT NULL
|
Tables referencing nd_experiment_project via foreign key constraints:
- None.</protect>
Table: nd_experimentprop
<protect>
Table: | nd_experimentprop |
Module: | Natural Diversity |
FK | Name | Type | Description |
---|---|---|---|
nd_experimentprop_id | serial | PRIMARY KEY | |
nd_experiment | nd_experiment_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | character varying(255) | NOT NULL | |
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing nd_experimentprop via foreign key constraints:
- None.</protect>
Table: nd_experiment_pub
<protect>
Table: | nd_experiment_pub |
Module: | Natural Diversity |
Linking nd_experiment(s) to publication(s)
FK | Name | Type | Description |
---|---|---|---|
nd_experiment_pub_id | serial | PRIMARY KEY | |
nd_experiment | nd_experiment_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing nd_experiment_pub via foreign key constraints:
- None.</protect>
Table: nd_geolocationprop
<protect>
Table: | nd_geolocationprop |
Module: | Natural Diversity |
Property/value associations for geolocations. This table can store the properties such as location and environment
FK | Name | Type | Description |
---|---|---|---|
nd_geolocationprop_id | serial | PRIMARY KEY | |
nd_geolocation | nd_geolocation_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | character varying(250) | The value of the property. | |
rank | integer | UNIQUE#1 NOT NULL |
Tables referencing nd_geolocationprop via foreign key constraints:
- None.</protect>
Table: nd_protocol
<protect>
Table: | nd_protocol |
Module: | Natural Diversity |
A protocol can be anything that is done as part of the experiment.
FK | Name | Type | Description |
---|---|---|---|
nd_protocol_id | serial | PRIMARY KEY | |
name | character varying(255) | UNIQUE NOT NULL |
Tables referencing nd_protocol via foreign key constraints:
</protect>
Table: nd_reagent
<protect>
Table: | nd_reagent |
Module: | Natural Diversity |
A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping experiments, or in any other kind of experiment.
FK | Name | Type | Description |
---|---|---|---|
nd_reagent_id | serial | PRIMARY KEY | |
name | character varying(80) | NOT NULL The name of the reagent. The name should be unique for a given type. | |
cvterm | type_id | integer | NOT NULL The type of the reagent, for example linker oligomer, or forward primer. |
feature_id | integer | If the reagent is a primer, the feature that it corresponds to. More generally, the corresponding feature for any reagent that has a sequence that maps to another sequence. |
Tables referencing nd_reagent via foreign key constraints:
</protect>
Table: nd_protocol_reagent
<protect>
Table: | nd_protocol_reagent |
Module: | Natural Diversity |
FK | Name | Type | Description |
---|---|---|---|
nd_protocol_reagent_id | serial | PRIMARY KEY | |
nd_protocol | nd_protocol_id | integer | NOT NULL |
nd_reagent | reagent_id | integer | NOT NULL |
cvterm | type_id | integer | NOT NULL
|
Tables referencing nd_protocol_reagent via foreign key constraints:
- None.</protect>
Table: nd_protocolprop
<protect>
Table: | nd_protocolprop |
Module: | Natural Diversity |
Property/value associations for protocol.
FK | Name | Type | Description |
---|---|---|---|
nd_protocolprop_id | serial | PRIMARY KEY | |
nd_protocol | nd_protocol_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | character varying(255) | The value of the property. | |
rank | integer | UNIQUE#1 NOT NULL |
Tables referencing nd_protocolprop via foreign key constraints:
- None.</protect>
Table: nd_experiment_stock
<protect>
Table: | nd_experiment_stock |
Module: | Natural Diversity |
Part of a stock or a clone of a stock that is used in an experiment
FK | Name | Type | Description |
---|---|---|---|
nd_experiment_stock_id | serial | PRIMARY KEY | |
nd_experiment | nd_experiment_id | integer | NOT NULL |
stock | stock_id | integer | NOT NULL stock used in the extraction or the corresponding stock for the clone |
cvterm | type_id | integer | NOT NULL
|
Tables referencing nd_experiment_stock via foreign key constraints:
</protect>
Table: nd_experiment_protocol
<protect>
Table: | nd_experiment_protocol |
Module: | Natural Diversity |
Linking table: experiments to the protocols they involve.
FK | Name | Type | Description |
---|---|---|---|
nd_experiment_protocol_id | serial | PRIMARY KEY | |
nd_experiment | nd_experiment_id | integer | NOT NULL |
nd_protocol | nd_protocol_id | integer | NOT NULL
|
Tables referencing nd_experiment_protocol via foreign key constraints:
- None.</protect>
Table: nd_experiment_phenotype
<protect>
Table: | nd_experiment_phenotype |
Module: | Natural Diversity |
Linking table: experiments to the phenotypes they produce. There is a one-to-one relationship between an experiment and a phenotype since each phenotype record should point to one experiment. Add a new experiment_id for each phenotype record.
FK | Name | Type | Description |
---|---|---|---|
nd_experiment_phenotype_id | serial | PRIMARY KEY | |
nd_experiment | nd_experiment_id | integer | UNIQUE NOT NULL |
phenotype | phenotype_id | integer | NOT NULL
|
Tables referencing nd_experiment_phenotype via foreign key constraints:
- None.</protect>
Table: nd_experiment_genotype
<protect>
Table: | nd_experiment_genotype |
Module: | Natural Diversity |
Linking table: experiments to the genotypes they produce. There is a one-to-one relationship between an experiment and a genotype since each genotype record should point to one experiment. Add a new experiment_id for each genotype record.
FK | Name | Type | Description |
---|---|---|---|
nd_experiment_genotype_id | serial | PRIMARY KEY | |
nd_experiment | nd_experiment_id | integer | UNIQUE NOT NULL |
genotype | genotype_id | integer | NOT NULL
|
Tables referencing nd_experiment_genotype via foreign key constraints:
- None.</protect>
Table: nd_reagent_relationship
<protect>
Table: | nd_reagent_relationship |
Module: | Natural Diversity |
Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme experiment reagents.
FK | Name | Type | Description |
---|---|---|---|
nd_reagent_relationship_id | serial | PRIMARY KEY | |
nd_reagent | subject_reagent_id | integer | NOT NULL The subject reagent in the relationship. In parent/child terminology, the subject is the child. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object. |
nd_reagent | object_reagent_id | integer | NOT NULL The object reagent in the relationship. In parent/child terminology, the object is the parent. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object. |
cvterm | type_id | integer | NOT NULL The type (or predicate) of the relationship. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object. |
Tables referencing nd_reagent_relationship via foreign key constraints:
- None.</protect>
Table: nd_reagentprop
<protect>
Table: | nd_reagentprop |
Module: | Natural Diversity |
FK | Name | Type | Description |
---|---|---|---|
nd_reagentprop_id | serial | PRIMARY KEY | |
nd_reagent | nd_reagent_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | character varying(255) | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing nd_reagentprop via foreign key constraints:
- None.</protect>
Table: nd_experiment_stockprop
<protect>
Table: | nd_experiment_stockprop |
Module: | Natural Diversity |
Property/value associations for experiment_stocks. This table can store the properties such as treatment
FK | Name | Type | Description |
---|---|---|---|
nd_experiment_stockprop_id | serial | PRIMARY KEY | |
nd_experiment_stock | nd_experiment_stock_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | character varying(255) | The value of the property. | |
rank | integer | UNIQUE#1 NOT NULL |
Tables referencing nd_experiment_stockprop via foreign key constraints:
- None.</protect>
Table: nd_experiment_stock_dbxref
<protect>
Table: | nd_experiment_stock_dbxref |
Module: | Natural Diversity |
Cross-reference experiment_stock to accessions, images, etc
FK | Name | Type | Description |
---|---|---|---|
nd_experiment_stock_dbxref_id | serial | PRIMARY KEY | |
nd_experiment_stock | nd_experiment_stock_id | integer | NOT NULL |
dbxref | dbxref_id | integer | NOT NULL
|
Tables referencing nd_experiment_stock_dbxref via foreign key constraints:
- None.</protect>
Table: nd_experiment_dbxref
<protect>
Table: | nd_experiment_dbxref |
Module: | Natural Diversity |
Cross-reference experiment to accessions, images, etc
FK | Name | Type | Description |
---|---|---|---|
nd_experiment_dbxref_id | serial | PRIMARY KEY | |
nd_experiment | nd_experiment_id | integer | NOT NULL |
dbxref | dbxref_id | integer | NOT NULL
|
Tables referencing nd_experiment_dbxref via foreign key constraints:
- None.</protect>
Table: nd_experiment_contact
<protect>
Table: | nd_experiment_contact |
Module: | Natural Diversity |
FK | Name | Type | Description |
---|---|---|---|
nd_experiment_contact_id | serial | PRIMARY KEY | |
nd_experiment | nd_experiment_id | integer | NOT NULL |
contact | contact_id | integer | NOT NULL
|
Tables referencing nd_experiment_contact via foreign key constraints:
- None.</protect>
Module: Phenotype
Table: phenotype
<protect>
Table: | phenotype |
Module: | Phenotype |
A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function. E.g. Obs=eye, attribute=color, cvalue=red.
FK | Name | Type | Description |
---|---|---|---|
phenotype_id | serial | PRIMARY KEY | |
uniquename | text | UNIQUE NOT NULL | |
cvterm | observable_id | integer | The entity: e.g. anatomy_part, biological_process. |
cvterm | attr_id | integer | Phenotypic attribute (quality, property, attribute, character) - drawn from PATO. |
value | text | Value of attribute - unconstrained free text. Used only if cvalue_id is not appropriate. | |
cvterm | cvalue_id | integer | Phenotype attribute value (state). |
cvterm | assay_id | integer | Evidence type. |
Tables referencing phenotype via foreign key constraints:
</protect>
Table: phenotype_cvterm
<protect>
Table: | phenotype_cvterm |
Module: | Phenotype |
FK | Name | Type | Description |
---|---|---|---|
phenotype_cvterm_id | serial | PRIMARY KEY | |
phenotype | phenotype_id | integer | UNIQUE#1 NOT NULL |
cvterm | cvterm_id | integer | UNIQUE#1 NOT NULL |
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing phenotype_cvterm via foreign key constraints:
- None.</protect>
Table: feature_phenotype
<protect>
Table: | feature_phenotype |
Module: | Phenotype |
FK | Name | Type | Description |
---|---|---|---|
feature_phenotype_id | serial | PRIMARY KEY | |
feature | feature_id | integer | UNIQUE#1 NOT NULL |
phenotype | phenotype_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing feature_phenotype via foreign key constraints:
- None.</protect>
Module: Phylogeny
Table: phylotree
<protect>
Table: | phylotree |
Module: | Phylogeny |
Global anchor for phylogenetic tree.
FK | Name | Type | Description |
---|---|---|---|
phylotree_id | serial | PRIMARY KEY | |
dbxref | dbxref_id | integer | NOT NULL |
name | character varying(255) | ||
cvterm | type_id | integer | Type: protein, nucleotide, taxonomy, for example. The type should be any SO type, or "taxonomy". |
analysis | analysis_id | integer | |
comment | text |
Tables referencing phylotree via foreign key constraints:
</protect>
Table: phylotree_pub
<protect>
Table: | phylotree_pub |
Module: | Phylogeny |
Tracks citations global to the tree e.g. multiple sequence alignment supporting tree construction.
FK | Name | Type | Description |
---|---|---|---|
phylotree_pub_id | serial | PRIMARY KEY | |
phylotree | phylotree_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing phylotree_pub via foreign key constraints:
- None.</protect>
Table: phylonode
<protect>
Table: | phylonode |
Module: | Phylogeny |
This is the most pervasive
element in the phylogeny module, cataloging the "phylonodes" of tree graphs. Edges are implied by the parent_phylonode_id reflexive closure. For all nodes in a nested set implementation the left and right index will be *between* the parents left and right indexes.
FK | Name | Type | Description |
---|---|---|---|
phylonode_id | serial | PRIMARY KEY | |
phylotree | phylotree_id | integer | UNIQUE#1 UNIQUE#2 |
phylonode | parent_phylonode_id | integer | Root phylonode can have null parent_phylonode_id value. |
left_idx | integer | UNIQUE#1 NOT NULL | |
right_idx | integer | UNIQUE#2 NOT NULL | |
cvterm | type_id | integer | Type: e.g. root, interior, leaf. |
feature | feature_id | integer | Phylonodes can have optional features attached to them e.g. a protein or nucleotide sequence usually attached to a leaf of the phylotree for non-leaf nodes, the feature may be a feature that is an instance of SO:match; this feature is the alignment of all leaf features beneath it. |
label | character varying(255) | ||
distance | double precision |
Tables referencing phylonode via foreign key constraints:
</protect>
Table: phylonode_dbxref
<protect>
Table: | phylonode_dbxref |
Module: | Phylogeny |
For example, for orthology, paralogy group identifiers; could also be used for NCBI taxonomy; for sequences, refer to phylonode_feature, feature associated dbxrefs.
FK | Name | Type | Description |
---|---|---|---|
phylonode_dbxref_id | serial | PRIMARY KEY | |
phylonode | phylonode_id | integer | UNIQUE#1 NOT NULL |
dbxref | dbxref_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing phylonode_dbxref via foreign key constraints:
- None.</protect>
Table: phylonode_pub
<protect>
Table: | phylonode_pub |
Module: | Phylogeny |
FK | Name | Type | Description |
---|---|---|---|
phylonode_pub_id | serial | PRIMARY KEY | |
phylonode | phylonode_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing phylonode_pub via foreign key constraints:
- None.</protect>
Table: phylonode_organism
<protect>
Table: | phylonode_organism |
Module: | Phylogeny |
This linking table should only be used for nodes in taxonomy trees; it provides a mapping between the node and an organism. One node can have zero or one organisms, one organism can have zero or more nodes (although typically it should only have one in the standard NCBI taxonomy tree).
FK | Name | Type | Description |
---|---|---|---|
phylonode_organism_id | serial | PRIMARY KEY | |
phylonode | phylonode_id | integer | UNIQUE NOT NULL |
organism | organism_id | integer | NOT NULL
|
Tables referencing phylonode_organism via foreign key constraints:
- None.</protect>
Table: phylonodeprop
<protect>
Table: | phylonodeprop |
Module: | Phylogeny |
FK | Name | Type | Description |
---|---|---|---|
phylonodeprop_id | serial | PRIMARY KEY | |
phylonode | phylonode_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | UNIQUE#1 NOT NULL | |
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing phylonodeprop via foreign key constraints:
- None.</protect>
Table: phylonode_relationship
<protect>
Table: | phylonode_relationship |
Module: | Phylogeny |
This is for relationships that are not strictly hierarchical; for example, horizontal gene transfer. Most phylogenetic trees are strictly hierarchical, nevertheless it is here for completeness.
FK | Name | Type | Description |
---|---|---|---|
phylonode_relationship_id | serial | PRIMARY KEY | |
phylonode | subject_id | integer | UNIQUE#1 NOT NULL |
phylonode | object_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
rank | integer | ||
phylotree | phylotree_id | integer | NOT NULL
|
Tables referencing phylonode_relationship via foreign key constraints:
- None.</protect>
Module: Project
Table: project
<protect>
Table: | project |
Module: | Project |
FK | Name | Type | Description |
---|---|---|---|
project_id | serial | PRIMARY KEY | |
name | character varying(255) | UNIQUE NOT NULL | |
description | character varying(255) | NOT NULL
|
Tables referencing project via foreign key constraints:
</protect>
Table: projectprop
<protect>
Table: | projectprop |
Module: | Project |
FK | Name | Type | Description |
---|---|---|---|
projectprop_id | serial | PRIMARY KEY | |
project | project_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing projectprop via foreign key constraints:
- None.</protect>
Table: project_relationship
<protect>
Table: | project_relationship |
Module: | Project |
A project can be composed of several smaller scale projects
FK | Name | Type | Description |
---|---|---|---|
project_relationship_id | serial | PRIMARY KEY | |
project | subject_project_id | integer | UNIQUE#1 NOT NULL |
project | object_project_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
Tables referencing project_relationship via foreign key constraints:
- None.</protect>
Table: project_pub
<protect>
Table: | project_pub |
Module: | Project |
Linking project(s) to publication(s)
FK | Name | Type | Description |
---|---|---|---|
project_pub_id | serial | PRIMARY KEY | |
project | project_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing project_pub via foreign key constraints:
- None.</protect>
Table: project_contact
<protect>
Table: | project_contact |
Module: | Project |
Linking project(s) to contact(s)
FK | Name | Type | Description |
---|---|---|---|
project_contact_id | serial | PRIMARY KEY | |
project | project_id | integer | UNIQUE#1 NOT NULL |
contact | contact_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing project_contact via foreign key constraints:
- None.</protect>
Module: Stock
Table: stock
<protect>
Table: | stock |
Module: | Stock |
Any stock can be globally identified by the combination of organism, uniquename and stock type. A stock is the physical entities, either living or preserved, held by collections. Stocks belong to a collection; they have IDs, type, organism, description and may have a genotype.
FK | Name | Type | Description |
---|---|---|---|
stock_id | serial | PRIMARY KEY | |
dbxref | dbxref_id | integer | The dbxref_id is an optional primary stable identifier for this stock. Secondary indentifiers and external dbxrefs go in table: stock_dbxref. |
organism | organism_id | integer | UNIQUE#1 The organism_id is the organism to which the stock belongs. This column should only be left blank if the organism cannot be determined. |
name | character varying(255) | The name is a human-readable local name for a stock. | |
uniquename | text | UNIQUE#1 NOT NULL | |
description | text | The description is the genetic description provided in the stock list. | |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
is_obsolete | boolean | NOT NULL DEFAULT false
|
Tables referencing stock via foreign key constraints:
- nd_experiment_stock
- stock_cvterm
- stock_dbxref
- stock_genotype
- stock_pub
- stock_relationship
- stockcollection_stock
- stockprop
</protect>
Table: stock_pub
<protect>
Table: | stock_pub |
Module: | Stock |
Provenance. Linking table between stocks and, for example, a stocklist computer file.
FK | Name | Type | Description |
---|---|---|---|
stock_pub_id | serial | PRIMARY KEY | |
stock | stock_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing stock_pub via foreign key constraints:
- None.</protect>
Table: stockprop
<protect>
Table: | stockprop |
Module: | Stock |
A stock can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stockprop_c1, for the combination of stock_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.
FK | Name | Type | Description |
---|---|---|---|
stockprop_id | serial | PRIMARY KEY | |
stock | stock_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing stockprop via foreign key constraints:
</protect>
Table: stockprop_pub
<protect>
Table: | stockprop_pub |
Module: | Stock |
Provenance. Any stockprop assignment can optionally be supported by a publication.
FK | Name | Type | Description |
---|---|---|---|
stockprop_pub_id | serial | PRIMARY KEY | |
stockprop | stockprop_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing stockprop_pub via foreign key constraints:
- None.</protect>
Table: stock_relationship
<protect>
Table: | stock_relationship |
Module: | Stock |
FK | Name | Type | Description |
---|---|---|---|
stock_relationship_id | serial | PRIMARY KEY | |
stock | subject_id | integer | UNIQUE#1 NOT NULL |
stock | object_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | stock_relationship.value is for additional notes or comments. | |
rank | integer | UNIQUE#1 NOT NULL |
Tables referencing stock_relationship via foreign key constraints:
</protect>
Table: stock_relationship_cvterm
<protect>
Table: | stock_relationship_cvterm |
Module: | Stock |
For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm
FK | Name | Type | Description |
---|---|---|---|
stock_relationship_cvterm_id | serial | PRIMARY KEY | |
stock_relatiohship_id | integer | NOT NULL | |
cvterm | cvterm_id | integer | NOT NULL |
pub | pub_id | integer |
Tables referencing stock_relationship_cvterm via foreign key constraints:
- None.</protect>
Table: stock_relationship_pub
<protect>
Table: | stock_relationship_pub |
Module: | Stock |
Provenance. Attach optional evidence to a stock_relationship in the form of a publication.
FK | Name | Type | Description |
---|---|---|---|
stock_relationship_pub_id | serial | PRIMARY KEY | |
stock_relationship | stock_relationship_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing stock_relationship_pub via foreign key constraints:
- None.</protect>
Table: stock_dbxref
<protect>
Table: | stock_dbxref |
Module: | Stock |
stock_dbxref links a stock to dbxrefs. This is for secondary identifiers; primary identifiers should use stock.dbxref_id.
FK | Name | Type | Description |
---|---|---|---|
stock_dbxref_id | serial | PRIMARY KEY | |
stock | stock_id | integer | UNIQUE#1 NOT NULL |
dbxref | dbxref_id | integer | UNIQUE#1 NOT NULL |
is_current | boolean | NOT NULL DEFAULT true |
Tables referencing stock_dbxref via foreign key constraints:
</protect>
Table: stock_cvterm
<protect>
Table: | stock_cvterm |
Module: | Stock |
stock_cvterm links a stock to cvterms. This is for secondary cvterms; primary cvterms should use stock.type_id.
FK | Name | Type | Description |
---|---|---|---|
stock_cvterm_id | serial | PRIMARY KEY | |
stock | stock_id | integer | UNIQUE#1 NOT NULL |
cvterm | cvterm_id | integer | UNIQUE#1 NOT NULL |
pub | pub_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing stock_cvterm via foreign key constraints:
- None.</protect>
Table: stock_genotype
<protect>
Table: | stock_genotype |
Module: | Stock |
Simple table linking a stock to a genotype. Features with genotypes can be linked to stocks thru feature_genotype -> genotype -> stock_genotype -> stock.
FK | Name | Type | Description |
---|---|---|---|
stock_genotype_id | serial | PRIMARY KEY | |
stock | stock_id | integer | UNIQUE#1 NOT NULL |
genotype | genotype_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing stock_genotype via foreign key constraints:
- None.</protect>
Table: stockcollection
<protect>
Table: | stockcollection |
Module: | Stock |
The lab or stock center distributing the stocks in their collection.
FK | Name | Type | Description |
---|---|---|---|
stockcollection_id | serial | PRIMARY KEY | |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
contact | contact_id | integer | contact_id links to the contact information for the collection. |
name | character varying(255) | name is the collection. | |
uniquename | text | UNIQUE#1 NOT NULL |
Tables referencing stockcollection via foreign key constraints:
</protect>
Table: stockcollectionprop
<protect>
Table: | stockcollectionprop |
Module: | Stock |
The table stockcollectionprop contains the value of the stock collection such as website/email URLs; the value of the stock collection order URLs.
FK | Name | Type | Description |
---|---|---|---|
stockcollectionprop_id | serial | PRIMARY KEY | |
stockcollection | stockcollection_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing stockcollectionprop via foreign key constraints:
- None.</protect>
Table: stockcollection_stock
<protect>
Table: | stockcollection_stock |
Module: | Stock |
stockcollection_stock links a stock collection to the stocks which are contained in the collection.
FK | Name | Type | Description |
---|---|---|---|
stockcollection_stock_id | serial | PRIMARY KEY | |
stockcollection | stockcollection_id | integer | UNIQUE#1 NOT NULL |
stock | stock_id | integer | UNIQUE#1 NOT NULL
|
Tables referencing stockcollection_stock via foreign key constraints:
- None.</protect>
Table: stock_dbxrefprop
<protect>
Table: | stock_dbxrefprop |
Module: | Stock |
A stock_dbxref can have any number of slot-value property tags attached to it. This is useful for storing properties related to dbxref annotations of stocks, such as evidence codes, and references, and metadata, such as create/modify dates. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stock_dbxrefprop_c1, for the combination of stock_dbxref_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.
FK | Name | Type | Description |
---|---|---|---|
stock_dbxrefprop_id | serial | PRIMARY KEY | |
stock_dbxref | stock_dbxref_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL
|
Tables referencing stock_dbxrefprop via foreign key constraints:
- None.</protect>
Module: WWW
Table: wwwuser
Table: wwwuser_project
Template:ChadoTable wwwuser project
Table: wwwuser_author
Template:ChadoTable wwwuser author
Table: wwwuser_cvterm
Template:ChadoTable wwwuser cvterm
Table: wwwuser_expression
Template:ChadoTable wwwuser expression
Table: wwwuser_feature
Template:ChadoTable wwwuser feature
Table: wwwuser_genotype
Template:ChadoTable wwwuser genotype
Table: wwwuser_interaction
Template:ChadoTable wwwuser interaction
Table: wwwuser_organism
Template:ChadoTable wwwuser organism
Table: wwwuser_phenotype
Template:ChadoTable wwwuser phenotype
Table: wwwuser_pub
Template:ChadoTable wwwuser pub
Table: wwwuserrelationship
Template:ChadoTable wwwuserrelationship
Module: Audit
Table: audit_tableinfo
Template:ChadoTable audit tableinfo
Table: audit_db
Table: audit_dbxref
Template:ChadoTable audit dbxref
Table: audit_cv
Table: audit_cvterm
Template:ChadoTable audit cvterm
Table: audit_cvterm_relationship
Template:ChadoTable audit cvterm relationship
Table: audit_cvtermpath
Template:ChadoTable audit cvtermpath
Table: audit_cvtermsynonym
Template:ChadoTable audit cvtermsynonym
Table: audit_cvterm_dbxref
Template:ChadoTable audit cvterm dbxref
Table: audit_cvtermprop
Template:ChadoTable audit cvtermprop
Table: audit_dbxrefprop
Template:ChadoTable audit dbxrefprop
Table: audit_pub
Table: audit_pub_relationship
Template:ChadoTable audit pub relationship
Table: audit_pub_dbxref
Template:ChadoTable audit pub dbxref
Table: audit_pubauthor
Template:ChadoTable audit pubauthor
Table: audit_pubprop
Template:ChadoTable audit pubprop
Table: audit_organism
Template:ChadoTable audit organism
Table: audit_organism_dbxref
Template:ChadoTable audit organism dbxref
Table: audit_organismprop
Template:ChadoTable audit organismprop
Table: audit_feature
Template:ChadoTable audit feature
Table: audit_featureloc
Template:ChadoTable audit featureloc
Table: audit_featureloc_pub
Template:ChadoTable audit featureloc pub
Table: audit_feature_pub
Template:ChadoTable audit feature pub
Table: audit_feature_pubprop
Template:ChadoTable audit feature pubprop
Table: audit_featureprop
Template:ChadoTable audit featureprop
Table: audit_featureprop_pub
Template:ChadoTable audit featureprop pub
Table: audit_feature_dbxref
Template:ChadoTable audit feature dbxref
Table: audit_feature_relationship
Template:ChadoTable audit feature relationship
Table: audit_feature_relationship_pub
Template:ChadoTable audit feature relationship pub
Table: audit_feature_relationshipprop
Template:ChadoTable audit feature relationshipprop
Table: audit_feature_relationshipprop_pub
Template:ChadoTable audit feature relationshipprop pub
Table: audit_feature_cvterm
Template:ChadoTable audit feature cvterm
Table: audit_feature_cvtermprop
Template:ChadoTable audit feature cvtermprop
Table: audit_feature_cvterm_dbxref
Template:ChadoTable audit feature cvterm dbxref
Table: audit_feature_cvterm_pub
Template:ChadoTable audit feature cvterm pub
Table: audit_synonym
Template:ChadoTable audit synonym
Table: audit_feature_synonym
Template:ChadoTable audit feature synonym
Table: audit_gencode
Template:ChadoTable audit gencode
Table: audit_gencode_codon_aa
Template:ChadoTable audit gencode codon aa
Table: audit_gencode_startcodon
Template:ChadoTable audit gencode startcodon
Table: audit_analysis
Template:ChadoTable audit analysis
Table: audit_analysisprop
Template:ChadoTable audit analysisprop
Table: audit_analysisfeature
Template:ChadoTable audit analysisfeature
Table: audit_analysisfeatureprop
Template:ChadoTable audit analysisfeatureprop
Table: audit_phenotype
Template:ChadoTable audit phenotype
Table: audit_phenotype_cvterm
Template:ChadoTable audit phenotype cvterm
Table: audit_feature_phenotype
Template:ChadoTable audit feature phenotype
Table: audit_genotype
Template:ChadoTable audit genotype
Table: audit_feature_genotype
Template:ChadoTable audit feature genotype
Table: audit_environment
Template:ChadoTable audit environment
Table: audit_environment_cvterm
Template:ChadoTable audit environment cvterm
Table: audit_phenstatement
Template:ChadoTable audit phenstatement
Table: audit_phendesc
Template:ChadoTable audit phendesc
Table: audit_phenotype_comparison
Template:ChadoTable audit phenotype comparison
Table: audit_phenotype_comparison_cvterm
Template:ChadoTable audit phenotype comparison cvterm
Table: audit_featuremap
Template:ChadoTable audit featuremap
Table: audit_featurerange
Template:ChadoTable audit featurerange
Table: audit_featurepos
Template:ChadoTable audit featurepos
Table: audit_featuremap_pub
Template:ChadoTable audit featuremap pub
Table: audit_phylotree
Template:ChadoTable audit phylotree
Table: audit_phylotree_pub
Template:ChadoTable audit phylotree pub
Table: audit_phylonode
Template:ChadoTable audit phylonode
Table: audit_phylonode_dbxref
Template:ChadoTable audit phylonode dbxref
Table: audit_phylonode_pub
Template:ChadoTable audit phylonode pub
Table: audit_phylonode_organism
Template:ChadoTable audit phylonode organism
Table: audit_phylonodeprop
Template:ChadoTable audit phylonodeprop
Table: audit_phylonode_relationship
Template:ChadoTable audit phylonode relationship
Table: audit_contact
Template:ChadoTable audit contact
Table: audit_contact_relationship
Template:ChadoTable audit contact relationship
Table: audit_expression
Template:ChadoTable audit expression
Table: audit_expression_cvterm
Template:ChadoTable audit expression cvterm
Table: audit_expression_cvtermprop
Template:ChadoTable audit expression cvtermprop
Table: audit_expressionprop
Template:ChadoTable audit expressionprop
Table: audit_expression_pub
Template:ChadoTable audit expression pub
Table: audit_feature_expression
Template:ChadoTable audit feature expression
Table: audit_feature_expressionprop
Template:ChadoTable audit feature expressionprop
Table: audit_eimage
Template:ChadoTable audit eimage
Table: audit_expression_image
Template:ChadoTable audit expression image
Table: audit_project
Template:ChadoTable audit project
Table: audit_projectprop
Template:ChadoTable audit projectprop
Table: audit_project_relationship
Template:ChadoTable audit project relationship
Table: audit_project_pub
Template:ChadoTable audit project pub
Table: audit_project_contact
Template:ChadoTable audit project contact
Table: audit_mageml
Template:ChadoTable audit mageml
Table: audit_magedocumentation
Template:ChadoTable audit magedocumentation
Table: audit_protocol
Template:ChadoTable audit protocol
Table: audit_protocolparam
Template:ChadoTable audit protocolparam
Table: audit_channel
Template:ChadoTable audit channel
Table: audit_arraydesign
Template:ChadoTable audit arraydesign
Table: audit_arraydesignprop
Template:ChadoTable audit arraydesignprop
Table: audit_assay
Template:ChadoTable audit assay
Table: audit_assayprop
Template:ChadoTable audit assayprop
Table: audit_assay_project
Template:ChadoTable audit assay project
Table: audit_biomaterial
Template:ChadoTable audit biomaterial
Table: audit_biomaterial_relationship
Template:ChadoTable audit biomaterial relationship
Table: audit_biomaterialprop
Template:ChadoTable audit biomaterialprop
Table: audit_biomaterial_dbxref
Template:ChadoTable audit biomaterial dbxref
Table: audit_treatment
Template:ChadoTable audit treatment
Table: audit_biomaterial_treatment
Template:ChadoTable audit biomaterial treatment
Table: audit_assay_biomaterial
Template:ChadoTable audit assay biomaterial
Table: audit_acquisition
Template:ChadoTable audit acquisition
Table: audit_acquisitionprop
Template:ChadoTable audit acquisitionprop
Table: audit_acquisition_relationship
Template:ChadoTable audit acquisition relationship
Table: audit_quantification
Template:ChadoTable audit quantification
Table: audit_quantificationprop
Template:ChadoTable audit quantificationprop
Table: audit_quantification_relationship
Template:ChadoTable audit quantification relationship
Table: audit_control
Template:ChadoTable audit control
Table: audit_element
Template:ChadoTable audit element
Table: audit_elementresult
Template:ChadoTable audit elementresult
Table: audit_element_relationship
Template:ChadoTable audit element relationship
Table: audit_elementresult_relationship
Template:ChadoTable audit elementresult relationship
Table: audit_study
Template:ChadoTable audit study
Table: audit_study_assay
Template:ChadoTable audit study assay
Table: audit_studydesign
Template:ChadoTable audit studydesign
Table: audit_studydesignprop
Template:ChadoTable audit studydesignprop
Table: audit_studyfactor
Template:ChadoTable audit studyfactor
Table: audit_studyfactorvalue
Template:ChadoTable audit studyfactorvalue
Table: audit_studyprop
Template:ChadoTable audit studyprop
Table: audit_studyprop_feature
Template:ChadoTable audit studyprop feature
Table: audit_stock
Template:ChadoTable audit stock
Table: audit_stock_pub
Template:ChadoTable audit stock pub
Table: audit_stockprop
Template:ChadoTable audit stockprop
Table: audit_stockprop_pub
Template:ChadoTable audit stockprop pub
Table: audit_stock_relationship
Template:ChadoTable audit stock relationship
Table: audit_stock_relationship_cvterm
Template:ChadoTable audit stock relationship cvterm
Table: audit_stock_relationship_pub
Template:ChadoTable audit stock relationship pub
Table: audit_stock_dbxref
Template:ChadoTable audit stock dbxref
Table: audit_stock_cvterm
Template:ChadoTable audit stock cvterm
Table: audit_stock_genotype
Template:ChadoTable audit stock genotype
Table: audit_stockcollection
Template:ChadoTable audit stockcollection
Table: audit_stockcollectionprop
Template:ChadoTable audit stockcollectionprop
Table: audit_stockcollection_stock
Template:ChadoTable audit stockcollection stock
Table: audit_stock_dbxrefprop
Template:ChadoTable audit stock dbxrefprop
Table: audit_library
Template:ChadoTable audit library
Table: audit_library_synonym
Template:ChadoTable audit library synonym
Table: audit_library_pub
Template:ChadoTable audit library pub
Table: audit_libraryprop
Template:ChadoTable audit libraryprop
Table: audit_libraryprop_pub
Template:ChadoTable audit libraryprop pub
Table: audit_library_cvterm
Template:ChadoTable audit library cvterm
Table: audit_library_feature
Template:ChadoTable audit library feature
Table: audit_library_dbxref
Template:ChadoTable audit library dbxref
Table: audit_cell_line
Template:ChadoTable audit cell line
Table: audit_cell_line_relationship
Template:ChadoTable audit cell line relationship
Table: audit_cell_line_synonym
Template:ChadoTable audit cell line synonym
Table: audit_cell_line_cvterm
Template:ChadoTable audit cell line cvterm
Table: audit_cell_line_dbxref
Template:ChadoTable audit cell line dbxref
Table: audit_cell_lineprop
Template:ChadoTable audit cell lineprop
Table: audit_cell_lineprop_pub
Template:ChadoTable audit cell lineprop pub
Table: audit_cell_line_feature
Template:ChadoTable audit cell line feature
Table: audit_cell_line_cvtermprop
Template:ChadoTable audit cell line cvtermprop
Table: audit_cell_line_pub
Template:ChadoTable audit cell line pub
Table: audit_cell_line_library
Template:ChadoTable audit cell line library
Table: audit_nd_geolocation
Template:ChadoTable audit nd geolocation
Table: audit_nd_experiment
Template:ChadoTable audit nd experiment
Table: audit_nd_experiment_project
Template:ChadoTable audit nd experiment project
Table: audit_nd_experimentprop
Template:ChadoTable audit nd experimentprop
Table: audit_nd_experiment_pub
Template:ChadoTable audit nd experiment pub
Table: audit_nd_geolocationprop
Template:ChadoTable audit nd geolocationprop
Table: audit_nd_protocol
Template:ChadoTable audit nd protocol
Table: audit_nd_reagent
Template:ChadoTable audit nd reagent
Table: audit_nd_protocol_reagent
Template:ChadoTable audit nd protocol reagent
Table: audit_nd_protocolprop
Template:ChadoTable audit nd protocolprop
Table: audit_nd_experiment_stock
Template:ChadoTable audit nd experiment stock
Table: audit_nd_experiment_protocol
Template:ChadoTable audit nd experiment protocol
Table: audit_nd_experiment_phenotype
Template:ChadoTable audit nd experiment phenotype
Table: audit_nd_experiment_genotype
Template:ChadoTable audit nd experiment genotype
Table: audit_nd_reagent_relationship
Template:ChadoTable audit nd reagent relationship
Table: audit_nd_reagentprop
Template:ChadoTable audit nd reagentprop
Table: audit_nd_experiment_stockprop
Template:ChadoTable audit nd experiment stockprop
Table: audit_nd_experiment_stock_dbxref
Template:ChadoTable audit nd experiment stock dbxref
Table: audit_nd_experiment_dbxref
Template:ChadoTable audit nd experiment dbxref