Description of Schema


Tables

tableinfo
db
dbxref
cv
cvterm
cvterm_relationship
cvtermpath
cvtermsynonym
cvterm_dbxref
cvtermprop
dbxrefprop
cvprop
chadoprop
dbprop
contact
contactprop
contact_relationship
pub
pub_relationship
pub_dbxref
pubauthor
pubprop
pubauthor_contact
organism
organism_dbxref
organismprop
organismprop_pub
organism_pub
organism_cvterm
organism_cvtermprop
organism_relationship
feature
featureloc
featureloc_pub
feature_pub
feature_pubprop
featureprop
featureprop_pub
feature_dbxref
feature_relationship
feature_relationship_pub
feature_relationshipprop
feature_relationshipprop_pub
feature_cvterm
feature_cvtermprop
feature_cvterm_dbxref
feature_cvterm_pub
synonym
feature_synonym
feature_contact
analysis
analysisprop
analysisfeature
analysisfeatureprop
analysis_dbxref
analysis_cvterm
analysis_relationship
analysis_pub
phenotype
phenotype_cvterm
feature_phenotype
phenotypeprop
genotype
feature_genotype
environment
environment_cvterm
phenstatement
phendesc
phenotype_comparison
phenotype_comparison_cvterm
genotypeprop
featuremap
featurerange
featurepos
featureposprop
featuremap_pub
featuremapprop
featuremap_contact
featuremap_dbxref
featuremap_organism
phylotree
phylotree_pub
phylotreeprop
phylonode
phylonode_dbxref
phylonode_pub
phylonode_organism
phylonodeprop
phylonode_relationship
expression
expression_cvterm
expression_cvtermprop
expressionprop
expression_pub
feature_expression
feature_expressionprop
eimage
expression_image
library
library_synonym
library_pub
libraryprop
libraryprop_pub
library_cvterm
library_feature
library_dbxref
library_expression
library_expressionprop
library_featureprop
library_relationship
library_relationship_pub
library_contact
stock
stock_pub
stockprop
stockprop_pub
stock_relationship
stock_relationship_cvterm
stock_relationship_pub
stock_dbxref
stock_cvterm
stock_cvtermprop
stock_genotype
stockcollection
stockcollectionprop
stockcollection_stock
stock_dbxrefprop
stockcollection_db
stock_feature
stock_featuremap
stock_library
project
projectprop
project_relationship
project_pub
project_contact
project_dbxref
project_analysis
project_feature
project_stock
mageml
magedocumentation
protocol
protocolparam
channel
arraydesign
arraydesignprop
assay
assayprop
assay_project
biomaterial
biomaterial_relationship
biomaterialprop
biomaterial_dbxref
treatment
biomaterial_treatment
assay_biomaterial
acquisition
acquisitionprop
acquisition_relationship
quantification
quantificationprop
quantification_relationship
control
element
elementresult
element_relationship
elementresult_relationship
study
study_assay
studydesign
studydesignprop
studyfactor
studyfactorvalue
studyprop
studyprop_feature
cell_line
cell_line_relationship
cell_line_synonym
cell_line_cvterm
cell_line_dbxref
cell_lineprop
cell_lineprop_pub
cell_line_feature
cell_line_cvtermprop
cell_line_pub
cell_line_library
nd_geolocation
nd_experiment
nd_experiment_project
nd_experimentprop
nd_experiment_pub
nd_geolocationprop
nd_protocol
nd_reagent
nd_protocol_reagent
nd_protocolprop
nd_experiment_stock
nd_experiment_protocol
nd_experiment_phenotype
nd_experiment_genotype
nd_reagent_relationship
nd_reagentprop
nd_experiment_stockprop
nd_experiment_stock_dbxref
nd_experiment_dbxref
nd_experiment_contact
nd_experiment_analysis

tableinfo

Top
Comments:

$Id: general.sql,v 1.31 2007-03-01 02:45:54 briano Exp $
==========================================
Chado general module
================================================
TABLE: tableinfo
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
tableinfo_id integer 20 PRIMARY KEY, NOT NULL
name varchar 30 UNIQUE, NOT NULL
primary_key_column varchar 30 NULL
is_view integer 10 0 NOT NULL
view_on_table_id integer 20 NULL
superclass_table_id integer 20 NULL
is_updateable integer 10 1 NOT NULL
modification_date date 0 now() NOT NULL

Constraints

Type Fields
NOT NULLtableinfo_id
NOT NULLname
NOT NULLis_view
NOT NULLis_updateable
NOT NULLmodification_date
UNIQUEname

db

Top
Comments:

================================================
TABLE: db
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
db_id integer 20 PRIMARY KEY, NOT NULL
name varchar 255 UNIQUE, NOT NULL
description varchar 255 NULL contact_id bigint, foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED,
urlprefix varchar 255 NULL
url varchar 255 NULL

Constraints

Type Fields
NOT NULLdb_id
NOT NULLname
UNIQUEname

dbxref

Top
Comments:

================================================
TABLE: dbxref
================================================
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 _dbxref). A dbxref is generally written as : or as ::.
Field Name Data Type Size Default Value Other Foreign Key
dbxref_id integer 20 PRIMARY KEY, NOT NULL
db_id integer 20 UNIQUE, NOT NULL db.db_id
accession varchar 1024 UNIQUE, NOT NULL, The local part of the identifier. Guaranteed by the db authority to be unique for that db.
version varchar 255 UNIQUE, NOT NULL
description text 64000

Indices

Name Fields
dbxref_idx1db_id
dbxref_idx2accession
dbxref_idx3version

Constraints

Type Fields
NOT NULLdbxref_id
NOT NULLdb_id
FOREIGN KEYdb_id
NOT NULLaccession
NOT NULLversion
UNIQUEdb_id, accession, version

cv

Top
Comments:

$Id: cv.sql,v 1.37 2007-02-28 15:08:48 briano Exp $
==========================================
Chado cv module
=================================================================
Dependencies:
:import dbxref from db
=================================================================
================================================
TABLE: 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.
Field Name Data Type Size Default Value Other Foreign Key
cv_id integer 20 PRIMARY KEY, NOT NULL
name varchar 255 UNIQUE, NOT NULL, The name of the ontology. This corresponds to the obo-format -namespace-. cv names uniquely identify the cv. In OBO file format, the cv.name is known as the namespace.
definition text 64000 A text description of the criteria for membership of this ontology.

Constraints

Type Fields
NOT NULLcv_id
NOT NULLname
UNIQUEname

cvterm

Top
Comments:

================================================
TABLE: cvterm
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
cvterm_id integer 20 PRIMARY KEY, NOT NULL
cv_id integer 20 UNIQUE, NOT NULL, The cv or ontology or namespace to which this cvterm belongs. cv.cv_id
name varchar 1024 UNIQUE, NOT NULL, A concise human-readable name or label for the cvterm. Uniquely identifies a cvterm within a cv.
definition text 64000 A human-readable text definition.
dbxref_id integer 20 UNIQUE, NOT NULL, Primary identifier dbxref - The unique global OBO identifier for this cvterm. Note that a cvterm may have multiple secondary dbxrefs - see also table: cvterm_dbxref. dbxref.dbxref_id
is_obsolete integer 10 0 UNIQUE, NOT NULL, Boolean 0=false,1=true; see GO documentation for details of obsoletion. Note that two terms with different primary dbxrefs may exist if one is obsolete.
is_relationshiptype integer 10 0 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.

Indices

Name Fields
cvterm_idx1cv_id
cvterm_idx2name
cvterm_idx3dbxref_id

Constraints

Type Fields
NOT NULLcvterm_id
NOT NULLcv_id
FOREIGN KEYcv_id
NOT NULLname
NOT NULLdbxref_id
FOREIGN KEYdbxref_id
NOT NULLis_obsolete
NOT NULLis_relationshiptype
UNIQUEname, cv_id, is_obsolete
UNIQUEdbxref_id

cvterm_relationship

Top
Comments:

A name can mean different things in different contexts; for example "chromosome" in SO and GO. A name should be unique within an ontology or cv. A name may exist twice in a cv, in both obsolete and non-obsolete forms - these will be for different cvterms with different OBO identifiers; so GO documentation for more details on obsoletion. Note that occasionally multiple obsolete terms with the same name will exist in the same cv. If this is a possibility for the ontology under consideration (e.g. GO) then the ID should be appended to the name to ensure uniqueness.
The OBO identifier is globally unique.
================================================
TABLE: cvterm_relationship
================================================
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".
Field Name Data Type Size Default Value Other Foreign Key
cvterm_relationship_id integer 20 PRIMARY KEY, NOT NULL
type_id integer 20 UNIQUE, NOT NULL, The nature of the relationship between subject and object. Note that relations are also housed in the cvterm table, typically from the OBO relationship ontology, although other relationship types are allowed. cvterm.cvterm_id
subject_id integer 20 UNIQUE, NOT NULL, The subject of the subj-predicate-obj sentence. The cvterm_relationship is about the subject. In a graph, this typically corresponds to the child node. cvterm.cvterm_id
object_id integer 20 UNIQUE, NOT NULL, The object of the subj-predicate-obj sentence. The cvterm_relationship refers to the object. In a graph, this typically corresponds to the parent node. cvterm.cvterm_id

Indices

Name Fields
cvterm_relationship_idx1type_id
cvterm_relationship_idx2subject_id
cvterm_relationship_idx3object_id

Constraints

Type Fields
NOT NULLcvterm_relationship_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLsubject_id
FOREIGN KEYsubject_id
NOT NULLobject_id
FOREIGN KEYobject_id
UNIQUEsubject_id, object_id, type_id

cvtermpath

Top
Comments:

================================================
TABLE: cvtermpath
================================================
The reflexive transitive closure of the cvterm_relationship relation.
Field Name Data Type Size Default Value Other Foreign Key
cvtermpath_id integer 20 PRIMARY KEY, NOT NULL
type_id integer 20 UNIQUE, 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.cvterm_id
subject_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
object_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
cv_id integer 20 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. cv.cv_id
pathdistance integer 10 UNIQUE, The number of steps required to get from the subject cvterm to the object cvterm, counting from zero (reflexive relationship).

Indices

Name Fields
cvtermpath_idx1type_id
cvtermpath_idx2subject_id
cvtermpath_idx3object_id
cvtermpath_idx4cv_id

Constraints

Type Fields
NOT NULLcvtermpath_id
FOREIGN KEYtype_id
NOT NULLsubject_id
FOREIGN KEYsubject_id
NOT NULLobject_id
FOREIGN KEYobject_id
NOT NULLcv_id
FOREIGN KEYcv_id
UNIQUEsubject_id, object_id, type_id, pathdistance

cvtermsynonym

Top
Comments:

================================================
TABLE: cvtermsynonym
================================================
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".
Field Name Data Type Size Default Value Other Foreign Key
cvtermsynonym_id integer 20 PRIMARY KEY, NOT NULL
cvterm_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
synonym varchar 1024 UNIQUE, NOT NULL
type_id integer 20 A synonym can be exact, narrower, or broader than. cvterm.cvterm_id

Indices

Name Fields
cvtermsynonym_idx1cvterm_id

Constraints

Type Fields
NOT NULLcvtermsynonym_id
NOT NULLcvterm_id
FOREIGN KEYcvterm_id
NOT NULLsynonym
FOREIGN KEYtype_id
UNIQUEcvterm_id, synonym

cvterm_dbxref

Top
Comments:

================================================
TABLE: cvterm_dbxref
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
cvterm_dbxref_id integer 20 PRIMARY KEY, NOT NULL
cvterm_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
dbxref_id integer 20 UNIQUE, NOT NULL dbxref.dbxref_id
is_for_definition integer 10 0 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.

Indices

Name Fields
cvterm_dbxref_idx1cvterm_id
cvterm_dbxref_idx2dbxref_id

Constraints

Type Fields
NOT NULLcvterm_dbxref_id
NOT NULLcvterm_id
FOREIGN KEYcvterm_id
NOT NULLdbxref_id
FOREIGN KEYdbxref_id
NOT NULLis_for_definition
UNIQUEcvterm_id, dbxref_id

cvtermprop

Top
Comments:

================================================
TABLE: cvtermprop
================================================
Additional extensible properties can be attached to a cvterm using this table. Corresponds to -AnnotationProperty- in W3C OWL format.
Field Name Data Type Size Default Value Other Foreign Key
cvtermprop_id integer 20 PRIMARY KEY, NOT NULL
cvterm_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
type_id integer 20 UNIQUE, NOT NULL, The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm. cvterm.cvterm_id
value text 64000 UNIQUE, NOT NULL, The value of the property, represented as text. Numeric values are converted to their text representation.
rank integer 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Indices

Name Fields
cvtermprop_idx1cvterm_id
cvtermprop_idx2type_id

Constraints

Type Fields
NOT NULLcvtermprop_id
NOT NULLcvterm_id
FOREIGN KEYcvterm_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLvalue
NOT NULLrank
UNIQUEcvterm_id, type_id, value, rank

dbxrefprop

Top
Comments:

================================================
TABLE: dbxrefprop
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
dbxrefprop_id integer 20 PRIMARY KEY, NOT NULL
dbxref_id integer 20 UNIQUE, NOT NULL dbxref.dbxref_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NOT NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
dbxrefprop_idx1dbxref_id
dbxrefprop_idx2type_id

Constraints

Type Fields
NOT NULLdbxrefprop_id
NOT NULLdbxref_id
FOREIGN KEYdbxref_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLvalue
NOT NULLrank
UNIQUEdbxref_id, type_id, rank

cvprop

Top
Comments:

================================================
TABLE: cvprop
================================================
Additional extensible properties can be attached to a cv using this table. A notable example would be the cv version
Field Name Data Type Size Default Value Other Foreign Key
cvprop_id integer 20 PRIMARY KEY, NOT NULL
cv_id integer 20 UNIQUE, NOT NULL cv.cv_id
type_id integer 20 UNIQUE, NOT NULL, The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm. cvterm.cvterm_id
value text 64000 The value of the property, represented as text. Numeric values are converted to their text representation.
rank integer 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Constraints

Type Fields
NOT NULLcvprop_id
NOT NULLcv_id
FOREIGN KEYcv_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEcv_id, type_id, rank

chadoprop

Top
Comments:

================================================
TABLE: chadoprop
================================================
This table is different from other prop tables in the database, as it is for storing information about the database itself, like schema version
Field Name Data Type Size Default Value Other Foreign Key
chadoprop_id integer 20 PRIMARY KEY, NOT NULL
type_id integer 20 UNIQUE, NOT NULL, The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm. cvterm.cvterm_id
value text 64000 The value of the property, represented as text. Numeric values are converted to their text representation.
rank integer 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Constraints

Type Fields
NOT NULLchadoprop_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEtype_id, rank

dbprop

Top
Comments:

================================================
TABLE: dbprop
================================================
An external database 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, dbprop_c1, for the combination of db_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.
Field Name Data Type Size Default Value Other Foreign Key
dbprop_id integer 20 PRIMARY KEY, NOT NULL
db_id integer 20 UNIQUE, NOT NULL db.db_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
dbprop_idx1db_id
dbprop_idx2type_id

Constraints

Type Fields
NOT NULLdbprop_id
NOT NULLdb_id
NOT NULLtype_id
NOT NULLrank
FOREIGN KEYtype_id
FOREIGN KEYdb_id
UNIQUEdb_id, type_id, rank

contact

Top
Comments:

$Id: contact.sql,v 1.5 2007-02-25 17:00:17 briano Exp $
==========================================
Chado contact module
=================================================================
Dependencies:
:import cvterm from cv
=================================================================
================================================
TABLE: contact
================================================
Model persons, institutes, groups, organizations, etc.
Field Name Data Type Size Default Value Other Foreign Key
contact_id integer 20 PRIMARY KEY, NOT NULL
type_id integer 20 NULL What type of contact is this? E.g. "person", "lab". cvterm.cvterm_id
name varchar 255 UNIQUE, NOT NULL
description varchar 255 NULL

Indices

Name Fields
pubauthor_contact_idx2contact_id
library_contact_idx2contact_id

Constraints

Type Fields
NOT NULLcontact_id
FOREIGN KEYtype_id
NOT NULLname
UNIQUEname

contactprop

Top
Comments:

================================================
TABLE: contactprop
================================================
A contact 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.
Field Name Data Type Size Default Value Other Foreign Key
contactprop_id integer 20 PRIMARY KEY, NOT NULL
contact_id integer 20 UNIQUE, NOT NULL contact.contact_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
contactprop_idx1contact_id
contactprop_idx2type_id

Constraints

Type Fields
NOT NULLcontactprop_id
NOT NULLcontact_id
NOT NULLtype_id
NOT NULLrank
UNIQUEcontact_id, type_id, rank
FOREIGN KEYcontact_id
FOREIGN KEYtype_id

contact_relationship

Top
Comments:

================================================
TABLE: contact_relationship
================================================
Model relationships between contacts
Field Name Data Type Size Default Value Other Foreign Key
contact_relationship_id integer 20 PRIMARY KEY, NOT NULL
type_id integer 20 UNIQUE, NOT NULL, Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. cvterm.cvterm_id
subject_id integer 20 UNIQUE, NOT NULL, The subject of the subj-predicate-obj sentence. In a DAG, this corresponds to the child node. contact.contact_id
object_id integer 20 UNIQUE, NOT NULL, The object of the subj-predicate-obj sentence. In a DAG, this corresponds to the parent node. contact.contact_id

Indices

Name Fields
contact_relationship_idx1type_id
contact_relationship_idx2subject_id
contact_relationship_idx3object_id

Constraints

Type Fields
NOT NULLcontact_relationship_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLsubject_id
FOREIGN KEYsubject_id
NOT NULLobject_id
FOREIGN KEYobject_id
UNIQUEsubject_id, object_id, type_id

pub

Top
Comments:

$Id: pub.sql,v 1.27 2007-02-19 20:50:44 briano Exp $
==========================================
Chado pub module
=================================================================
Dependencies:
:import cvterm from cv
:import dbxref from db
:import analysis from companalysis
:import contact from contact
=================================================================
================================================
TABLE: pub
================================================
A documented provenance artefact - publications, documents, personal communication.
Field Name Data Type Size Default Value Other Foreign Key
pub_id integer 20 PRIMARY KEY, NOT NULL
title text 64000 Descriptive general heading.
volumetitle text 64000 Title of part if one of a series.
volume varchar 255
series_name varchar 255 Full name of (journal) series.
issue varchar 255
pyear varchar 255
pages varchar 255 Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.
miniref varchar 255
uniquename text 64000 UNIQUE, NOT NULL
type_id integer 20 NOT NULL, The type of the publication (book, journal, poem, graffiti, etc). Uses pub cv. cvterm.cvterm_id
is_obsolete boolean 0 false
publisher varchar 255
pubplace varchar 255

Indices

Name Fields
pub_idx1type_id

Constraints

Type Fields
NOT NULLpub_id
NOT NULLuniquename
NOT NULLtype_id
FOREIGN KEYtype_id
UNIQUEuniquename

pub_relationship

Top
Comments:

================================================
TABLE: pub_relationship
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
pub_relationship_id integer 20 PRIMARY KEY, NOT NULL
subject_id integer 20 UNIQUE, NOT NULL pub.pub_id
object_id integer 20 UNIQUE, NOT NULL pub.pub_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id

Indices

Name Fields
pub_relationship_idx1subject_id
pub_relationship_idx2object_id
pub_relationship_idx3type_id

Constraints

Type Fields
NOT NULLpub_relationship_id
NOT NULLsubject_id
FOREIGN KEYsubject_id
NOT NULLobject_id
FOREIGN KEYobject_id
NOT NULLtype_id
FOREIGN KEYtype_id
UNIQUEsubject_id, object_id, type_id

pub_dbxref

Top
Comments:

================================================
TABLE: pub_dbxref
================================================
Handle links to repositories, e.g. Pubmed, Biosis, zoorec, OCLC, Medline, ISSN, coden...
Field Name Data Type Size Default Value Other Foreign Key
pub_dbxref_id integer 20 PRIMARY KEY, NOT NULL
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id
dbxref_id integer 20 UNIQUE, NOT NULL dbxref.dbxref_id
is_current boolean 0 true NOT NULL

Indices

Name Fields
pub_dbxref_idx1pub_id
pub_dbxref_idx2dbxref_id

Constraints

Type Fields
NOT NULLpub_dbxref_id
NOT NULLpub_id
FOREIGN KEYpub_id
NOT NULLdbxref_id
FOREIGN KEYdbxref_id
NOT NULLis_current
UNIQUEpub_id, dbxref_id

pubauthor

Top
Comments:

================================================
TABLE: pubauthor
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
pubauthor_id integer 20 PRIMARY KEY, NOT NULL
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id
rank integer 10 UNIQUE, NOT NULL, Order of author in author list for this pub - order is important.
editor boolean 0 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 varchar 100 NOT NULL
givennames varchar 100 First name, initials
suffix varchar 100 Jr., Sr., etc

Indices

Name Fields
pubauthor_idx2pub_id
pubauthor_contact_idx1pubauthor_id

Constraints

Type Fields
NOT NULLpubauthor_id
NOT NULLpub_id
FOREIGN KEYpub_id
NOT NULLrank
NOT NULLsurname
UNIQUEpub_id, rank

pubprop

Top
Comments:

================================================
TABLE: pubprop
================================================
Property-value pairs for a pub. Follows standard chado pattern.
Field Name Data Type Size Default Value Other Foreign Key
pubprop_id integer 20 PRIMARY KEY, NOT NULL
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NOT NULL
rank integer 10 UNIQUE

Indices

Name Fields
pubprop_idx1pub_id
pubprop_idx2type_id

Constraints

Type Fields
NOT NULLpubprop_id
NOT NULLpub_id
FOREIGN KEYpub_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLvalue
UNIQUEpub_id, type_id, rank

pubauthor_contact

Top
Comments:

================================================
TABLE: pubauthor_contact
================================================
An author on a publication may have a corresponding entry in the contact table and this table can link the two.
Field Name Data Type Size Default Value Other Foreign Key
pubauthor_contact_id integer 20 PRIMARY KEY, NOT NULL
contact_id integer 20 UNIQUE, NOT NULL contact.contact_id
pubauthor_id integer 20 UNIQUE, NOT NULL pubauthor.pubauthor_id

Constraints

Type Fields
NOT NULLpubauthor_contact_id
NOT NULLcontact_id
NOT NULLpubauthor_id
UNIQUEcontact_id, pubauthor_id
FOREIGN KEYpubauthor_id
FOREIGN KEYcontact_id

organism

Top
Comments:

$Id: organism.sql,v 1.19 2007/04/01 18:45:41 briano Exp $
==========================================
Chado organism module
============
DEPENDENCIES
============
:import cvterm from cv
:import dbxref from db
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
================================================
TABLE: 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.
Field Name Data Type Size Default Value Other Foreign Key
organism_id integer 20 PRIMARY KEY, NOT NULL
abbreviation varchar 255 NULL
genus varchar 255 UNIQUE, NOT NULL
species varchar 255 UNIQUE, NOT NULL, A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, this column must be used where it is present, as the common_name column is not always unique (e.g. environmental samples). If a particular strain or subspecies is to be represented, this is appended onto the species name. Follows standard NCBI taxonomy pattern.
common_name varchar 255 NULL
infraspecific_name varchar 1024 NULL UNIQUE, The scientific name for any taxon below the rank of species. The rank should be specified using the type_id field and the name is provided here.
type_id integer 20 null UNIQUE, A controlled vocabulary term that specifies the organism rank below species. It is used when an infraspecific name is provided. Ideally, the rank should be a valid ICN name such as subspecies, varietas, subvarietas, forma and subforma cvterm.cvterm_id
comment text 64000 NULL

Constraints

Type Fields
NOT NULLorganism_id
NOT NULLgenus
NOT NULLspecies
FOREIGN KEYtype_id
UNIQUEgenus, species, type_id, infraspecific_name

organism_dbxref

Top
Comments:

================================================
TABLE: organism_dbxref
================================================
Links an organism to a dbxref.
Field Name Data Type Size Default Value Other Foreign Key
organism_dbxref_id integer 20 PRIMARY KEY, NOT NULL
organism_id integer 20 UNIQUE, NOT NULL organism.organism_id
dbxref_id integer 20 UNIQUE, NOT NULL dbxref.dbxref_id

Indices

Name Fields
organism_dbxref_idx1organism_id
organism_dbxref_idx2dbxref_id

Constraints

Type Fields
NOT NULLorganism_dbxref_id
NOT NULLorganism_id
FOREIGN KEYorganism_id
NOT NULLdbxref_id
FOREIGN KEYdbxref_id
UNIQUEorganism_id, dbxref_id

organismprop

Top
Comments:

================================================
TABLE: organismprop
================================================
Tag-value properties - follows standard chado model.
Field Name Data Type Size Default Value Other Foreign Key
organismprop_id integer 20 PRIMARY KEY, NOT NULL
organism_id integer 20 UNIQUE, NOT NULL organism.organism_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
organismprop_idx1organism_id
organismprop_idx2type_id

Constraints

Type Fields
NOT NULLorganismprop_id
NOT NULLorganism_id
FOREIGN KEYorganism_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEorganism_id, type_id, rank

organismprop_pub

Top
Comments:

================================================
TABLE: organismprop_pub
================================================
Attribution for organismprop.
Field Name Data Type Size Default Value Other Foreign Key
organismprop_pub_id integer 20 PRIMARY KEY, NOT NULL
organismprop_id integer 20 UNIQUE, NOT NULL organismprop.organismprop_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id
value text 64000 NULL
rank integer 10 0 NOT NULL

Indices

Name Fields
organismprop_pub_idx1organismprop_id
organismprop_pub_idx2pub_id

Constraints

Type Fields
NOT NULLorganismprop_pub_id
NOT NULLorganismprop_id
FOREIGN KEYorganismprop_id
NOT NULLpub_id
FOREIGN KEYpub_id
NOT NULLrank
UNIQUEorganismprop_id, pub_id

organism_pub

Top
Comments:

================================================
TABLE: organism_pub
================================================
Attribution for organism.
Field Name Data Type Size Default Value Other Foreign Key
organism_pub_id integer 20 PRIMARY KEY, NOT NULL
organism_id integer 20 UNIQUE, NOT NULL organism.organism_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
organism_pub_idx1organism_id
organism_pub_idx2pub_id

Constraints

Type Fields
NOT NULLorganism_pub_id
NOT NULLorganism_id
FOREIGN KEYorganism_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEorganism_id, pub_id

organism_cvterm

Top
Comments:

================================================
TABLE: organism_cvterm
================================================
organism to cvterm associations. Examples: taxonomic name
Field Name Data Type Size Default Value Other Foreign Key
organism_cvterm_id integer 20 PRIMARY KEY, NOT NULL
organism_id integer 20 UNIQUE, NOT NULL organism.organism_id
cvterm_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
rank integer 10 0 NOT NULL, Property-Value ordering. Any organism_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
organism_cvterm_idx1organism_id
organism_cvterm_idx2cvterm_id

Constraints

Type Fields
NOT NULLorganism_cvterm_id
NOT NULLorganism_id
FOREIGN KEYorganism_id
NOT NULLcvterm_id
FOREIGN KEYcvterm_id
NOT NULLrank
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEorganism_id, cvterm_id, pub_id

organism_cvtermprop

Top
Comments:

================================================
TABLE: organism_cvtermprop
================================================
Extensible properties for organism to cvterm associations. Examples: qualifiers
Field Name Data Type Size Default Value Other Foreign Key
organism_cvtermprop_id integer 20 PRIMARY KEY, NOT NULL
organism_cvterm_id integer 20 UNIQUE, NOT NULL organism_cvterm.organism_cvterm_id
type_id integer 20 UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterm.cvterm_id
value text 64000 NULL 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 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any organism_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used

Indices

Name Fields
organism_cvtermprop_idx1organism_cvterm_id
organism_cvtermprop_idx2type_id

Constraints

Type Fields
NOT NULLorganism_cvtermprop_id
NOT NULLorganism_cvterm_id
FOREIGN KEYorganism_cvterm_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEorganism_cvterm_id, type_id, rank

organism_relationship

Top
Comments:

================================================
TABLE: organism_relationship
================================================
Specifies relationships between organisms that are not taxonomic. For example, in breeding, relationships such as "sterile_with", "incompatible_with", or "fertile_with" would be appropriate. Taxonomic relatinoships should be housed in the phylogeny tables.
Field Name Data Type Size Default Value Other Foreign Key
organism_relationship_id integer 20 PRIMARY KEY, NOT NULL
subject_id integer 20 UNIQUE, NOT NULL organism.organism_id
object_id integer 20 UNIQUE, NOT NULL organism.organism_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
organism_relationship_idx1subject_id
organism_relationship_idx2object_id
organism_relationship_idx3type_id

Constraints

Type Fields
NOT NULLorganism_relationship_id
NOT NULLsubject_id
NOT NULLobject_id
NOT NULLtype_id
NOT NULLrank
UNIQUEsubject_id, object_id, type_id, rank
FOREIGN KEYobject_id
FOREIGN KEYsubject_id
FOREIGN KEYtype_id

feature

Top
Comments:

$Id: sequence.sql,v 1.69 2009-05-14 02:44:23 scottcain Exp $
==========================================
Chado sequence module
=================================================================
Dependencies:
:import cvterm from cv
:import pub from pub
:import organism from organism
:import dbxref from db
:import contact from contact
=================================================================
================================================
TABLE: feature
================================================
A feature is a biological sequence or a section of a biological sequence, or a collection of such sections. Examples include genes, exons, transcripts, regulatory regions, polypeptides, protein domains, chromosome sequences, sequence variations, cross-genome match regions such as hits and HSPs and so on; see the Sequence Ontology for more. The combination of organism_id, uniquename and type_id should be unique.
Field Name Data Type Size Default Value Other Foreign Key
feature_id integer 20 PRIMARY KEY, NOT NULL
dbxref_id integer 20 An optional primary public stable identifier for this feature. Secondary identifiers and external dbxrefs go in the table feature_dbxref. dbxref.dbxref_id
organism_id integer 20 UNIQUE, NOT NULL, The organism to which this feature belongs. This column is mandatory. organism.organism_id
name varchar 255 The optional human-readable common name for a feature, for display purposes.
uniquename text 64000 UNIQUE, NOT NULL, The unique name for a feature; may not be necessarily be particularly human-readable, although this is preferred. This name must be unique for this type of feature within this organism.
residues text 64000 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 20 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 char 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.
type_id integer 20 UNIQUE, NOT NULL, A required reference to a table:cvterm giving the feature type. This will typically be a Sequence Ontology identifier. This column is thus used to subclass the feature table. cvterm.cvterm_id
is_analysis boolean 0 false NOT NULL, Boolean indicating whether this feature is annotated or the result of an automated analysis. Analysis results also use the companalysis module. Note that the dividing line between analysis and annotation may be fuzzy, this should be determined on a per-project basis in a consistent manner. One requirement is that there should only be one non-analysis version of each wild-type gene feature in a genome, whereas the same gene feature can be predicted multiple times in different analyses.
is_obsolete boolean 0 false NOT NULL, Boolean indicating whether this feature has been obsoleted. Some chado instances may choose to simply remove the feature altogether, others may choose to keep an obsolete row in the table.
timeaccessioned timestamp 0 current_timestamp NOT NULL, For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.
timelastmodified timestamp 0 current_timestamp NOT NULL, For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado.

Indices

Name Fields
feature_name_ind1name
feature_idx1dbxref_id
feature_idx2organism_id
feature_idx3type_id
feature_idx4uniquename

Constraints

Type Fields
NOT NULLfeature_id
FOREIGN KEYdbxref_id
NOT NULLorganism_id
FOREIGN KEYorganism_id
NOT NULLuniquename
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLis_analysis
NOT NULLis_obsolete
NOT NULLtimeaccessioned
NOT NULLtimelastmodified
UNIQUEorganism_id, uniquename, type_id

featureloc

Top
Comments:

COMMENT ON INDEX feature_c1 IS 'Any feature can be globally identified
by the combination of organism, uniquename and feature type';
================================================
TABLE: featureloc
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
featureloc_id integer 20 PRIMARY KEY, NOT NULL
feature_id integer 20 UNIQUE, NOT NULL, The feature that is being located. Any feature can have zero or more featurelocs. feature.feature_id
srcfeature_id integer 20 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. feature.feature_id
fmin integer 20 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 0 false NOT NULL, This is typically false, but may be true if the value for column:fmin is inaccurate or the leftmost part of the range is unknown/unbounded.
fmax integer 20 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 0 false NOT NULL, This is typically false, but may be true if the value for column:fmax is inaccurate or the rightmost part of the range is unknown/unbounded.
strand integer 5 The orientation/directionality of the location. Should be 0, -1 or +1.
phase integer 10 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 64000 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 10 0 UNIQUE, NOT NULL, This is used to manifest redundant, derivable extra locations for a feature. The default locgroup=0 is used for the DIRECT location of a feature. Important: most Chado users may never use featurelocs WITH logroup > 0. Transitively derived locations are indicated with locgroup > 0. For example, the position of an exon on a BAC and in global chromosome coordinates. This column is used to differentiate these groupings of locations. The default locgroup 0 is used for the main or primary location, from which the others can be derived via coordinate transformations. Another example of redundant locations is storing ORF coordinates relative to both transcript and genome. Redundant locations open the possibility of the database getting into inconsistent states; this schema gives us the flexibility of both warehouse instantiations with redundant locations (easier for querying) and management instantiations with no redundant locations. An example of using both locgroup and rank: imagine a feature indicating a conserved region between the chromosomes of two different species. We may want to keep redundant locations on both contigs and chromosomes. We would thus have 4 locations for the single conserved region feature - two distinct locgroups (contig level and chromosome level) and two distinct ranks (for the two species).
rank integer 10 0 UNIQUE, NOT NULL, Used when a feature has >1 location, otherwise the default rank 0 is used. Some features (e.g. blast hits and HSPs) have two locations - one on the query and one on the subject. Rank is used to differentiate these. Rank=0 is always used for the query, Rank=1 for the subject. For multiple alignments, assignment of rank is arbitrary. Rank is also used for sequence_variant features, such as SNPs. Rank=0 indicates the wildtype (or baseline) feature, Rank=1 indicates the mutant (or compared) feature.

Indices

Name Fields
featureloc_idx1feature_id
featureloc_idx2srcfeature_id
featureloc_idx3srcfeature_id, fmin, fmax

Constraints

Type Fields
NOT NULLfeatureloc_id
NOT NULLfeature_id
FOREIGN KEYfeature_id
FOREIGN KEYsrcfeature_id
NOT NULLis_fmin_partial
NOT NULLis_fmax_partial
NOT NULLlocgroup
NOT NULLrank
UNIQUEfeature_id, locgroup, rank
CHECK

featureloc_pub

Top
Comments:

COMMENT ON INDEX featureloc_c1 IS 'locgroup and rank serve to uniquely
partition locations for any one feature';
================================================
TABLE: featureloc_pub
================================================
Provenance of featureloc. Linking table between featurelocs and publications that mention them.
Field Name Data Type Size Default Value Other Foreign Key
featureloc_pub_id integer 20 PRIMARY KEY, NOT NULL
featureloc_id integer 20 UNIQUE, NOT NULL featureloc.featureloc_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
featureloc_pub_idx1featureloc_id
featureloc_pub_idx2pub_id

Constraints

Type Fields
NOT NULLfeatureloc_pub_id
NOT NULLfeatureloc_id
FOREIGN KEYfeatureloc_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEfeatureloc_id, pub_id

feature_pub

Top
Comments:

================================================
TABLE: feature_pub
================================================
Provenance. Linking table between features and publications that mention them.
Field Name Data Type Size Default Value Other Foreign Key
feature_pub_id integer 20 PRIMARY KEY, NOT NULL
feature_id integer 20 UNIQUE, NOT NULL feature.feature_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
feature_pub_idx1feature_id
feature_pub_idx2pub_id

Constraints

Type Fields
NOT NULLfeature_pub_id
NOT NULLfeature_id
FOREIGN KEYfeature_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEfeature_id, pub_id

feature_pubprop

Top
Comments:

================================================
TABLE: feature_pubprop
================================================
Property or attribute of a feature_pub link.
Field Name Data Type Size Default Value Other Foreign Key
feature_pubprop_id integer 20 PRIMARY KEY, NOT NULL
feature_pub_id integer 20 UNIQUE, NOT NULL feature_pub.feature_pub_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
feature_pubprop_idx1feature_pub_id

Constraints

Type Fields
NOT NULLfeature_pubprop_id
NOT NULLfeature_pub_id
FOREIGN KEYfeature_pub_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEfeature_pub_id, type_id, rank

featureprop

Top
Comments:

================================================
TABLE: featureprop
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
featureprop_id integer 20 PRIMARY KEY, NOT NULL
feature_id integer 20 UNIQUE, NOT NULL feature.feature_id
type_id integer 20 UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Certain property types will only apply to certain feature types (e.g. the anticodon property will only apply to tRNA features) ; the types here come from the sequence feature property ontology. cvterm.cvterm_id
value text 64000 NULL 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 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any feature can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used

Indices

Name Fields
featureprop_idx1feature_id
featureprop_idx2type_id

Constraints

Type Fields
NOT NULLfeatureprop_id
NOT NULLfeature_id
FOREIGN KEYfeature_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEfeature_id, type_id, rank

featureprop_pub

Top
Comments:

For any one feature, multivalued property-value pairs must be differentiated by rank.
================================================
TABLE: featureprop_pub
================================================
Provenance. Any featureprop assignment can optionally be supported by a publication.
Field Name Data Type Size Default Value Other Foreign Key
featureprop_pub_id integer 20 PRIMARY KEY, NOT NULL
featureprop_id integer 20 UNIQUE, NOT NULL featureprop.featureprop_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
featureprop_pub_idx1featureprop_id
featureprop_pub_idx2pub_id

Constraints

Type Fields
NOT NULLfeatureprop_pub_id
NOT NULLfeatureprop_id
FOREIGN KEYfeatureprop_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEfeatureprop_id, pub_id

feature_dbxref

Top
Comments:

================================================
TABLE: feature_dbxref
================================================
Links a feature to dbxrefs. This is for secondary identifiers; primary identifiers should use feature.dbxref_id.
Links a feature to dbxrefs.
Field Name Data Type Size Default Value Other Foreign Key
feature_dbxref_id integer 20 PRIMARY KEY, NOT NULL
feature_id integer 20 UNIQUE, NOT NULL feature.feature_id
dbxref_id integer 20 UNIQUE, NOT NULL dbxref.dbxref_id
is_current boolean 0 true NOT NULL, True if this secondary dbxref is the most up to date accession in the corresponding db. Retired accessions should set this field to false True if this secondary dbxref is the most up to date accession in the corresponding db. Retired accessions should set this field to false

Indices

Name Fields
feature_dbxref_idx1feature_id
feature_dbxref_idx2dbxref_id

Constraints

Type Fields
NOT NULLfeature_dbxref_id
NOT NULLfeature_id
FOREIGN KEYfeature_id
NOT NULLdbxref_id
FOREIGN KEYdbxref_id
NOT NULLis_current
UNIQUEfeature_id, dbxref_id

feature_relationship

Top
Comments:

================================================
TABLE: feature_relationship
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
feature_relationship_id integer 20 PRIMARY KEY, NOT NULL
subject_id integer 20 UNIQUE, NOT NULL, The subject of the subj-predicate-obj sentence. This is typically the subfeature. feature.feature_id
object_id integer 20 UNIQUE, NOT NULL, The object of the subj-predicate-obj sentence. This is typically the container feature. feature.feature_id
type_id integer 20 UNIQUE, NOT NULL, Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. The most common relationship type is OBO_REL:part_of. Valid relationship types are constrained by the Sequence Ontology. cvterm.cvterm_id
value text 64000 NULL Additional notes or comments.
rank integer 10 0 UNIQUE, NOT NULL, The ordering of subject features with respect to the object feature may be important (for example, exon ordering on a transcript - not always derivable if you take trans spliced genes into consideration). Rank is used to order these; starts from zero.

Indices

Name Fields
feature_relationship_idx1subject_id
feature_relationship_idx2object_id
feature_relationship_idx3type_id

Constraints

Type Fields
NOT NULLfeature_relationship_id
NOT NULLsubject_id
FOREIGN KEYsubject_id
NOT NULLobject_id
FOREIGN KEYobject_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEsubject_id, object_id, type_id, rank

feature_relationship_pub

Top
Comments:

================================================
TABLE: feature_relationship_pub
================================================
Provenance. Attach optional evidence to a feature_relationship in the form of a publication.
Field Name Data Type Size Default Value Other Foreign Key
feature_relationship_pub_id integer 20 PRIMARY KEY, NOT NULL
feature_relationship_id integer 20 UNIQUE, NOT NULL feature_relationship.feature_relationship_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
feature_relationship_pub_idx1feature_relationship_id
feature_relationship_pub_idx2pub_id

Constraints

Type Fields
NOT NULLfeature_relationship_pub_id
NOT NULLfeature_relationship_id
FOREIGN KEYfeature_relationship_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEfeature_relationship_id, pub_id

feature_relationshipprop

Top
Comments:

================================================
TABLE: feature_relationshipprop
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
feature_relationshipprop_id integer 20 PRIMARY KEY, NOT NULL
feature_relationship_id integer 20 UNIQUE, NOT NULL feature_relationship.feature_relationship_id
type_id integer 20 UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Currently there is no standard ontology for feature_relationship property types. cvterm.cvterm_id
value text 64000 NULL 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 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any feature_relationship can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Indices

Name Fields
feature_relationshipprop_idx1feature_relationship_id
feature_relationshipprop_idx2type_id

Constraints

Type Fields
NOT NULLfeature_relationshipprop_id
NOT NULLfeature_relationship_id
FOREIGN KEYfeature_relationship_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEfeature_relationship_id, type_id, rank

feature_relationshipprop_pub

Top
Comments:

================================================
TABLE: feature_relationshipprop_pub
================================================
Provenance for feature_relationshipprop.
Field Name Data Type Size Default Value Other Foreign Key
feature_relationshipprop_pub_id integer 20 PRIMARY KEY, NOT NULL
feature_relationshipprop_id integer 20 UNIQUE, NOT NULL feature_relationshipprop.feature_relationshipprop_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
feature_relationshipprop_pub_idx1feature_relationshipprop_id
feature_relationshipprop_pub_idx2pub_id

Constraints

Type Fields
NOT NULLfeature_relationshipprop_pub_id
NOT NULLfeature_relationshipprop_id
FOREIGN KEYfeature_relationshipprop_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEfeature_relationshipprop_id, pub_id

feature_cvterm

Top
Comments:

================================================
TABLE: feature_cvterm
================================================
Associate a term from a cv with a feature, for example, GO annotation.
Field Name Data Type Size Default Value Other Foreign Key
feature_cvterm_id integer 20 PRIMARY KEY, NOT NULL
feature_id integer 20 UNIQUE, NOT NULL feature.feature_id
cvterm_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 20 UNIQUE, NOT NULL, Provenance for the annotation. Each annotation should have a single primary publication (which may be of the appropriate type for computational analyses) where more details can be found. Additional provenance dbxrefs can be attached using feature_cvterm_dbxref. pub.pub_id
is_not boolean 0 false NOT NULL, If this is set to true, then this annotation is interpreted as a NEGATIVE annotation - i.e. the feature does NOT have the specified function, process, component, part, etc. See GO docs for more details.
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
feature_cvterm_idx1feature_id
feature_cvterm_idx2cvterm_id
feature_cvterm_idx3pub_id

Constraints

Type Fields
NOT NULLfeature_cvterm_id
NOT NULLfeature_id
FOREIGN KEYfeature_id
NOT NULLcvterm_id
FOREIGN KEYcvterm_id
NOT NULLpub_id
FOREIGN KEYpub_id
NOT NULLis_not
NOT NULLrank
UNIQUEfeature_id, cvterm_id, pub_id, rank

feature_cvtermprop

Top
Comments:

================================================
TABLE: feature_cvtermprop
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
feature_cvtermprop_id integer 20 PRIMARY KEY, NOT NULL
feature_cvterm_id integer 20 UNIQUE, NOT NULL feature_cvterm.feature_cvterm_id
type_id integer 20 UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv. cvterm.cvterm_id
value text 64000 NULL 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 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any feature_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Indices

Name Fields
feature_cvtermprop_idx1feature_cvterm_id
feature_cvtermprop_idx2type_id

Constraints

Type Fields
NOT NULLfeature_cvtermprop_id
NOT NULLfeature_cvterm_id
FOREIGN KEYfeature_cvterm_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEfeature_cvterm_id, type_id, rank

feature_cvterm_dbxref

Top
Comments:

================================================
TABLE: feature_cvterm_dbxref
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
feature_cvterm_dbxref_id integer 20 PRIMARY KEY, NOT NULL
feature_cvterm_id integer 20 UNIQUE, NOT NULL feature_cvterm.feature_cvterm_id
dbxref_id integer 20 UNIQUE, NOT NULL dbxref.dbxref_id

Indices

Name Fields
feature_cvterm_dbxref_idx1feature_cvterm_id
feature_cvterm_dbxref_idx2dbxref_id

Constraints

Type Fields
NOT NULLfeature_cvterm_dbxref_id
NOT NULLfeature_cvterm_id
FOREIGN KEYfeature_cvterm_id
NOT NULLdbxref_id
FOREIGN KEYdbxref_id
UNIQUEfeature_cvterm_id, dbxref_id

feature_cvterm_pub

Top
Comments:

================================================
TABLE: feature_cvterm_pub
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
feature_cvterm_pub_id integer 20 PRIMARY KEY, NOT NULL
feature_cvterm_id integer 20 UNIQUE, NOT NULL feature_cvterm.feature_cvterm_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
feature_cvterm_pub_idx1feature_cvterm_id
feature_cvterm_pub_idx2pub_id

Constraints

Type Fields
NOT NULLfeature_cvterm_pub_id
NOT NULLfeature_cvterm_id
FOREIGN KEYfeature_cvterm_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEfeature_cvterm_id, pub_id

synonym

Top
Comments:

================================================
TABLE: synonym
================================================
A synonym for a feature. One feature can have multiple synonyms, and the same synonym can apply to multiple features.
Field Name Data Type Size Default Value Other Foreign Key
synonym_id integer 20 PRIMARY KEY, NOT NULL
name varchar 255 UNIQUE, NOT NULL, The synonym itself. Should be human-readable machine-searchable ascii text.
type_id integer 20 UNIQUE, NOT NULL, Types would be symbol and fullname for now. cvterm.cvterm_id
synonym_sgml varchar 255 NOT NULL, The fully specified synonym, with any non-ascii characters encoded in SGML.

Indices

Name Fields
synonym_idx1type_id

Constraints

Type Fields
NOT NULLsynonym_id
NOT NULLname
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLsynonym_sgml
UNIQUEname, type_id

feature_synonym

Top
Comments:

================================================
TABLE: feature_synonym
================================================
Linking table between feature and synonym.
Field Name Data Type Size Default Value Other Foreign Key
feature_synonym_id integer 20 PRIMARY KEY, NOT NULL
synonym_id integer 20 UNIQUE, NOT NULL synonym.synonym_id
feature_id integer 20 UNIQUE, NOT NULL feature.feature_id
pub_id integer 20 UNIQUE, NOT NULL, The pub_id link is for relating the usage of a given synonym to the publication in which it was used. pub.pub_id
is_current boolean 0 false NOT NULL, The is_current boolean indicates whether the linked synonym is the current -official- symbol for the linked feature.
is_internal boolean 0 false NOT NULL, Typically a synonym exists so that somebody querying the db with an obsolete name can find the object theyre looking for (under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it may also be listed in reports as a synonym. If the synonym was not used deliberately (e.g. there was a typo which went public), then the is_internal boolean may be set to -true- so that it is known that the synonym is -internal- and should be queryable but should not be listed in reports as a valid synonym.

Indices

Name Fields
feature_synonym_idx1synonym_id
feature_synonym_idx2feature_id
feature_synonym_idx3pub_id

Constraints

Type Fields
NOT NULLfeature_synonym_id
NOT NULLsynonym_id
FOREIGN KEYsynonym_id
NOT NULLfeature_id
FOREIGN KEYfeature_id
NOT NULLpub_id
FOREIGN KEYpub_id
NOT NULLis_current
NOT NULLis_internal
UNIQUEsynonym_id, feature_id, pub_id

feature_contact

Top
Comments:

================================================
TABLE: feature_contact
================================================
Links contact(s) with a feature. Used to indicate a particular person or organization responsible for discovery or that can provide more information on a particular feature.
Field Name Data Type Size Default Value Other Foreign Key
feature_contact_id integer 20 PRIMARY KEY, NOT NULL
feature_id integer 20 UNIQUE, NOT NULL feature.feature_id
contact_id integer 20 UNIQUE, NOT NULL contact.contact_id

Indices

Name Fields
feature_contact_idx1feature_id
feature_contact_idx2contact_id

Constraints

Type Fields
NOT NULLfeature_contact_id
NOT NULLfeature_id
NOT NULLcontact_id
UNIQUEfeature_id, contact_id
FOREIGN KEYcontact_id
FOREIGN KEYfeature_id

analysis

Top
Comments:

$Id: companalysis.sql,v 1.37 2007-03-23 15:18:02 scottcain Exp $
==========================================
Chado companalysis module
=================================================================
Dependencies:
:import feature from sequence
:import cvterm from cv
:import dbxref from db
:import pub from pub
=================================================================
================================================
TABLE: analysis
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
analysis_id integer 20 PRIMARY KEY, NOT NULL
name varchar 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 64000
program varchar 255 UNIQUE, NOT NULL, Program name, e.g. blastx, blastp, sim4, genscan.
programversion varchar 255 UNIQUE, NOT NULL, Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000].
algorithm varchar 255 Algorithm name, e.g. blast.
sourcename varchar 255 UNIQUE, Source name, e.g. cDNA, SwissProt.
sourceversion varchar 255
sourceuri text 64000 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 0 current_timestamp NOT NULL

Constraints

Type Fields
NOT NULLanalysis_id
NOT NULLprogram
NOT NULLprogramversion
NOT NULLtimeexecuted
UNIQUEprogram, programversion, sourcename

analysisprop

Top
Comments:

================================================
TABLE: analysisprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
analysisprop_id integer 20 PRIMARY KEY, NOT NULL
analysis_id integer 20 UNIQUE, NOT NULL analysis.analysis_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
analysisprop_idx1analysis_id
analysisprop_idx2type_id

Constraints

Type Fields
NOT NULLanalysisprop_id
NOT NULLanalysis_id
FOREIGN KEYanalysis_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEanalysis_id, type_id, rank

analysisfeature

Top
Comments:

================================================
TABLE: analysisfeature
================================================
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
Field Name Data Type Size Default Value Other Foreign Key
analysisfeature_id integer 20 PRIMARY KEY, NOT NULL
feature_id integer 20 UNIQUE, NOT NULL feature.feature_id
analysis_id integer 20 UNIQUE, NOT NULL analysis.analysis_id
rawscore float 20 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 float 20 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 float 20 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 float 20 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.

Indices

Name Fields
analysisfeature_idx1feature_id
analysisfeature_idx2analysis_id

Constraints

Type Fields
NOT NULLanalysisfeature_id
NOT NULLfeature_id
FOREIGN KEYfeature_id
NOT NULLanalysis_id
FOREIGN KEYanalysis_id
UNIQUEfeature_id, analysis_id

analysisfeatureprop

Top
Comments:

================================================
TABLE: analysisfeatureprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
analysisfeatureprop_id integer 20 PRIMARY KEY, NOT NULL
analysisfeature_id integer 20 UNIQUE, NOT NULL analysisfeature.analysisfeature_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000
rank integer 10 UNIQUE, NOT NULL

Indices

Name Fields
analysisfeatureprop_idx1analysisfeature_id
analysisfeatureprop_idx2type_id

Constraints

Type Fields
NOT NULLanalysisfeature_id
FOREIGN KEYanalysisfeature_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEanalysisfeature_id, type_id, rank
FOREIGN KEYanalysisfeature_id
FOREIGN KEYtype_id

analysis_dbxref

Top
Comments:

================================================
TABLE: analysis_dbxref
================================================
Links an analysis to dbxrefs.
Field Name Data Type Size Default Value Other Foreign Key
analysis_dbxref_id integer 20 PRIMARY KEY, NOT NULL
analysis_id integer 20 UNIQUE, NOT NULL analysis.analysis_id
dbxref_id integer 20 UNIQUE, NOT NULL dbxref.dbxref_id
is_current boolean 0 true NOT NULL, True if this dbxref is the most up to date accession in the corresponding db. Retired accessions should set this field to false

Indices

Name Fields
analysis_dbxref_idx1analysis_id
analysis_dbxref_idx2dbxref_id

Constraints

Type Fields
NOT NULLanalysis_dbxref_id
NOT NULLanalysis_id
NOT NULLdbxref_id
NOT NULLis_current
FOREIGN KEYanalysis_id
FOREIGN KEYdbxref_id
UNIQUEanalysis_id, dbxref_id

analysis_cvterm

Top
Comments:

================================================
TABLE: analysis_cvterm
================================================
Associate a term from a cv with an analysis.
Field Name Data Type Size Default Value Other Foreign Key
analysis_cvterm_id integer 20 PRIMARY KEY, NOT NULL
analysis_id integer 20 UNIQUE, NOT NULL analysis.analysis_id
cvterm_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
is_not boolean 0 false NOT NULL, If this is set to true, then this annotation is interpreted as a NEGATIVE annotation - i.e. the analysis does NOT have the specified term.
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
analysis_cvterm_idx1analysis_id
analysis_cvterm_idx2cvterm_id

Constraints

Type Fields
NOT NULLanalysis_cvterm_id
NOT NULLanalysis_id
NOT NULLcvterm_id
NOT NULLis_not
NOT NULLrank
FOREIGN KEYanalysis_id
FOREIGN KEYcvterm_id
UNIQUEanalysis_id, cvterm_id, rank

analysis_relationship

Top
Comments:

================================================
TABLE: analysis_relationship
================================================
Field Name Data Type Size Default Value Other Foreign Key
analysis_relationship_id integer 20 PRIMARY KEY, NOT NULL
subject_id integer 20 UNIQUE, NOT NULL, analysis_relationship.subject_id i s the subject of the subj-predicate-obj sentence. analysis.analysis_id
object_id integer 20 UNIQUE, NOT NULL, analysis_relationship.object_id is the object of the subj-predicate-obj sentence. analysis.analysis_id
type_id integer 20 UNIQUE, NOT NULL, analysis_relationship.type_id is relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. cvterm.cvterm_id
value text 64000 NULL analysis_relationship.value is for additional notes or comments.
rank integer 10 0 UNIQUE, NOT NULL, analysis_relationship.rank is the ordering of subject analysiss with respect to the object analysis may be important where rank is used to order these; starts from zero.

Indices

Name Fields
analysis_relationship_idx1subject_id
analysis_relationship_idx2object_id
analysis_relationship_idx3type_id

Constraints

Type Fields
NOT NULLanalysis_relationship_id
NOT NULLsubject_id
NOT NULLobject_id
NOT NULLtype_id
NOT NULLrank
FOREIGN KEYsubject_id
FOREIGN KEYobject_id
FOREIGN KEYtype_id
UNIQUEsubject_id, object_id, type_id, rank

analysis_pub

Top
Comments:

================================================
TABLE: analysis_pub
================================================
Provenance. Linking table between analyses and the publications that mention them.
Field Name Data Type Size Default Value Other Foreign Key
analysis_pub_id integer 20 PRIMARY KEY, NOT NULL
analysis_id integer 20 UNIQUE, NOT NULL analysis.analysis_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
analysis_pub_idx1analysis_id
analysis_pub_idx2pub_id

Constraints

Type Fields
NOT NULLanalysis_pub_id
NOT NULLanalysis_id
FOREIGN KEYanalysis_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEanalysis_id, pub_id

phenotype

Top
Comments:

$Id: phenotype.sql,v 1.6 2007-04-27 16:09:46 emmert Exp $
==========================================
Chado phenotype module
05-31-2011
added 'name' column to phenotype. non-unique human readable field.
=================================================================
Dependencies:
:import cvterm from cv
:import feature from sequence
=================================================================
================================================
TABLE: 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.
Field Name Data Type Size Default Value Other Foreign Key
phenotype_id integer 20 PRIMARY KEY, NOT NULL
uniquename text 64000 UNIQUE, NOT NULL
name text 64000 null
observable_id integer 20 The entity: e.g. anatomy_part, biological_process. cvterm.cvterm_id
attr_id integer 20 Phenotypic attribute (quality, property, attribute, character) - drawn from PATO. cvterm.cvterm_id
value text 64000 Value of attribute - unconstrained free text. Used only if cvalue_id is not appropriate.
cvalue_id integer 20 Phenotype attribute value (state). cvterm.cvterm_id
assay_id integer 20 Evidence type. cvterm.cvterm_id

Indices

Name Fields
phenotype_idx1cvalue_id
phenotype_idx2observable_id
phenotype_idx3attr_id

Constraints

Type Fields
NOT NULLphenotype_id
NOT NULLuniquename
FOREIGN KEYobservable_id
FOREIGN KEYattr_id
FOREIGN KEYcvalue_id
FOREIGN KEYassay_id
UNIQUEuniquename

phenotype_cvterm

Top
Comments:

================================================
TABLE: phenotype_cvterm
================================================
phenotype to cvterm associations.
Field Name Data Type Size Default Value Other Foreign Key
phenotype_cvterm_id integer 20 PRIMARY KEY, NOT NULL
phenotype_id integer 20 UNIQUE, NOT NULL phenotype.phenotype_id
cvterm_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
phenotype_cvterm_idx1phenotype_id
phenotype_cvterm_idx2cvterm_id

Constraints

Type Fields
NOT NULLphenotype_cvterm_id
NOT NULLphenotype_id
FOREIGN KEYphenotype_id
NOT NULLcvterm_id
FOREIGN KEYcvterm_id
NOT NULLrank
UNIQUEphenotype_id, cvterm_id, rank

feature_phenotype

Top
Comments:

================================================
TABLE: feature_phenotype
================================================
Linking table between features and phenotypes.
Field Name Data Type Size Default Value Other Foreign Key
feature_phenotype_id integer 20 PRIMARY KEY, NOT NULL
feature_id integer 20 UNIQUE, NOT NULL feature.feature_id
phenotype_id integer 20 UNIQUE, NOT NULL phenotype.phenotype_id

Indices

Name Fields
feature_phenotype_idx1feature_id
feature_phenotype_idx2phenotype_id

Constraints

Type Fields
NOT NULLfeature_phenotype_id
NOT NULLfeature_id
FOREIGN KEYfeature_id
NOT NULLphenotype_id
FOREIGN KEYphenotype_id
UNIQUEfeature_id, phenotype_id

phenotypeprop

Top
Comments:

================================================
TABLE: phenotypeprop
================================================
A phenotype 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, phenotypeprop_c1, for the combination of phenotype_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.
Field Name Data Type Size Default Value Other Foreign Key
phenotypeprop_id integer 20 PRIMARY KEY, NOT NULL
phenotype_id integer 20 UNIQUE, NOT NULL phenotype.phenotype_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
phenotypeprop_idx1phenotype_id
phenotypeprop_idx2type_id

Constraints

Type Fields
NOT NULLphenotypeprop_id
NOT NULLphenotype_id
FOREIGN KEYphenotype_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEphenotype_id, type_id, rank

genotype

Top
Comments:

$Id: genetic.sql,v 1.31 2008-08-25 19:53:14 scottcain Exp $
==========================================
Chado genetics module
changes 2011-05-31
added type_id to genotype (can be null for backward compatibility)
added genotypeprop table
2006-04-11
split out phenotype tables into phenotype module
redesigned 2003-10-28
changes 2003-11-10:
incorporating suggestions to make everything a gcontext; use
gcontext_relationship to make some gcontexts derivable from others. we
would incorporate environment this way - just add the environment
descriptors as properties of the child gcontext
changes 2004-06 (Documented by DE: 10-MAR-2005):
Many, including rename of gcontext to genotype, split
phenstatement into phenstatement & phenotype, created environment
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
============
DEPENDENCIES
============
:import feature from sequence
:import phenotype from phenotype
:import cvterm from cv
:import pub from pub
:import dbxref from db
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
================================================
TABLE: genotype
================================================
Genetic context. A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.
Field Name Data Type Size Default Value Other Foreign Key
genotype_id integer 20 PRIMARY KEY, NOT NULL
name text 64000 Optional alternative name for a genotype, for display purposes.
uniquename text 64000 UNIQUE, NOT NULL, The unique name for a genotype; typically derived from the features making up the genotype.
description text 64000
type_id integer 20 NOT NULL cvterm.cvterm_id

Indices

Name Fields
genotype_idx1uniquename
genotype_idx2name

Constraints

Type Fields
NOT NULLgenotype_id
NOT NULLuniquename
NOT NULLtype_id
FOREIGN KEYtype_id
UNIQUEuniquename

feature_genotype

Top
Comments:

===============================================
TABLE: feature_genotype
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
feature_genotype_id integer 20 PRIMARY KEY, NOT NULL
feature_id integer 20 UNIQUE, NOT NULL feature.feature_id
genotype_id integer 20 UNIQUE, NOT NULL genotype.genotype_id
chromosome_id integer 20 UNIQUE, A feature of SO type "chromosome". feature.feature_id
rank integer 10 UNIQUE, NOT NULL, rank can be used for n-ploid organisms or to preserve order.
cgroup integer 10 UNIQUE, NOT NULL, Spatially distinguishable group. group can be used for distinguishing the chromosomal groups, for example (RNAi products and so on can be treated as different groups, as they do not fall on a particular chromosome).
cvterm_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id

Indices

Name Fields
feature_genotype_idx1feature_id
feature_genotype_idx2genotype_id

Constraints

Type Fields
NOT NULLfeature_genotype_id
NOT NULLfeature_id
FOREIGN KEYfeature_id
NOT NULLgenotype_id
FOREIGN KEYgenotype_id
FOREIGN KEYchromosome_id
NOT NULLrank
NOT NULLcgroup
NOT NULLcvterm_id
FOREIGN KEYcvterm_id
UNIQUEfeature_id, genotype_id, cvterm_id, chromosome_id, rank, cgroup

environment

Top
Comments:

================================================
TABLE: environment
================================================
The environmental component of a phenotype description.
Field Name Data Type Size Default Value Other Foreign Key
environment_id integer 20 PRIMARY KEY, NOT NULL
uniquename text 64000 UNIQUE, NOT NULL
description text 64000

Indices

Name Fields
environment_idx1uniquename

Constraints

Type Fields
NOT NULLenvironment_id
NOT NULLuniquename
UNIQUEuniquename

environment_cvterm

Top
Comments:

================================================
TABLE: environment_cvterm
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
environment_cvterm_id integer 20 PRIMARY KEY, NOT NULL
environment_id integer 20 UNIQUE, NOT NULL environment.environment_id
cvterm_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id

Indices

Name Fields
environment_cvterm_idx1environment_id
environment_cvterm_idx2cvterm_id

Constraints

Type Fields
NOT NULLenvironment_cvterm_id
NOT NULLenvironment_id
FOREIGN KEYenvironment_id
NOT NULLcvterm_id
FOREIGN KEYcvterm_id
UNIQUEenvironment_id, cvterm_id

phenstatement

Top
Comments:

================================================
TABLE: phenstatement
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
phenstatement_id integer 20 PRIMARY KEY, NOT NULL
genotype_id integer 20 UNIQUE, NOT NULL genotype.genotype_id
environment_id integer 20 UNIQUE, NOT NULL environment.environment_id
phenotype_id integer 20 UNIQUE, NOT NULL phenotype.phenotype_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
phenstatement_idx1genotype_id
phenstatement_idx2phenotype_id

Constraints

Type Fields
NOT NULLphenstatement_id
NOT NULLgenotype_id
FOREIGN KEYgenotype_id
NOT NULLenvironment_id
FOREIGN KEYenvironment_id
NOT NULLphenotype_id
FOREIGN KEYphenotype_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEgenotype_id, phenotype_id, environment_id, type_id, pub_id

phendesc

Top
Comments:

================================================
TABLE: phendesc
================================================
A summary of a _set_ of phenotypic statements for any one gcontext made in any one publication.
Field Name Data Type Size Default Value Other Foreign Key
phendesc_id integer 20 PRIMARY KEY, NOT NULL
genotype_id integer 20 UNIQUE, NOT NULL genotype.genotype_id
environment_id integer 20 UNIQUE, NOT NULL environment.environment_id
description text 64000 NOT NULL
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
phendesc_idx1genotype_id
phendesc_idx2environment_id
phendesc_idx3pub_id

Constraints

Type Fields
NOT NULLphendesc_id
NOT NULLgenotype_id
FOREIGN KEYgenotype_id
NOT NULLenvironment_id
FOREIGN KEYenvironment_id
NOT NULLdescription
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEgenotype_id, environment_id, type_id, pub_id

phenotype_comparison

Top
Comments:

================================================
TABLE: phenotype_comparison
================================================
Comparison of phenotypes e.g., genotype1/environment1/phenotype1 "non-suppressible" with respect to genotype2/environment2/phenotype2.
Field Name Data Type Size Default Value Other Foreign Key
phenotype_comparison_id integer 20 PRIMARY KEY, NOT NULL
genotype1_id integer 20 UNIQUE, NOT NULL genotype.genotype_id
environment1_id integer 20 UNIQUE, NOT NULL environment.environment_id
genotype2_id integer 20 UNIQUE, NOT NULL genotype.genotype_id
environment2_id integer 20 UNIQUE, NOT NULL environment.environment_id
phenotype1_id integer 20 UNIQUE, NOT NULL phenotype.phenotype_id
phenotype2_id integer 20 phenotype.phenotype_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id
organism_id integer 20 NOT NULL organism.organism_id

Indices

Name Fields
phenotype_comparison_idx1genotype1_id
phenotype_comparison_idx2genotype2_id
phenotype_comparison_idx4pub_id

Constraints

Type Fields
NOT NULLphenotype_comparison_id
NOT NULLgenotype1_id
FOREIGN KEYgenotype1_id
NOT NULLenvironment1_id
FOREIGN KEYenvironment1_id
NOT NULLgenotype2_id
FOREIGN KEYgenotype2_id
NOT NULLenvironment2_id
FOREIGN KEYenvironment2_id
NOT NULLphenotype1_id
FOREIGN KEYphenotype1_id
FOREIGN KEYphenotype2_id
NOT NULLpub_id
FOREIGN KEYpub_id
NOT NULLorganism_id
FOREIGN KEYorganism_id
UNIQUEgenotype1_id, environment1_id, genotype2_id, environment2_id, phenotype1_id, pub_id

phenotype_comparison_cvterm

Top
Comments:

================================================
TABLE: phenotype_comparison_cvterm
================================================
Field Name Data Type Size Default Value Other Foreign Key
phenotype_comparison_cvterm_id integer 20 PRIMARY KEY, NOT NULL
phenotype_comparison_id integer 20 UNIQUE, NOT NULL phenotype_comparison.phenotype_comparison_id
cvterm_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 20 NOT NULL pub.pub_id
rank integer 10 0 NOT NULL

Indices

Name Fields
phenotype_comparison_cvterm_idx1phenotype_comparison_id
phenotype_comparison_cvterm_idx2cvterm_id

Constraints

Type Fields
NOT NULLphenotype_comparison_cvterm_id
NOT NULLphenotype_comparison_id
FOREIGN KEYphenotype_comparison_id
NOT NULLcvterm_id
FOREIGN KEYcvterm_id
NOT NULLpub_id
FOREIGN KEYpub_id
NOT NULLrank
UNIQUEphenotype_comparison_id, cvterm_id

genotypeprop

Top
Comments:

================================================
TABLE: genotypeprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
genotypeprop_id integer 20 PRIMARY KEY, NOT NULL
genotype_id integer 20 UNIQUE, NOT NULL genotype.genotype_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
genotypeprop_idx1genotype_id
genotypeprop_idx2type_id

Constraints

Type Fields
NOT NULLgenotypeprop_id
NOT NULLgenotype_id
FOREIGN KEYgenotype_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEgenotype_id, type_id, rank

featuremap

Top
Comments:

$Id: map.sql,v 1.14 2007-03-23 15:18:02 scottcain Exp $
==========================================
Chado map module
=================================================================
Dependencies:
:import feature from sequence
:import cvterm from cv
:import pub from pub
:import contact from contact
:import dbxref from db
:import organism from organism
=================================================================
================================================
TABLE: featuremap
================================================
Field Name Data Type Size Default Value Other Foreign Key
featuremap_id integer 20 PRIMARY KEY, NOT NULL
name varchar 255 UNIQUE
description text 64000
unittype_id integer 20 NULL cvterm.cvterm_id

Constraints

Type Fields
NOT NULLfeaturemap_id
FOREIGN KEYunittype_id
UNIQUEname

featurerange

Top
Comments:

================================================
TABLE: featurerange
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
featurerange_id integer 20 PRIMARY KEY, NOT NULL
featuremap_id integer 20 NOT NULL, featuremap_id is the id of the feature being mapped. featuremap.featuremap_id
feature_id integer 20 NOT NULL feature.feature_id
leftstartf_id integer 20 NOT NULL feature.feature_id
leftendf_id integer 20 feature.feature_id
rightstartf_id integer 20 feature.feature_id
rightendf_id integer 20 NOT NULL feature.feature_id
rangestr varchar 255

Indices

Name Fields
featurerange_idx1featuremap_id
featurerange_idx2feature_id
featurerange_idx3leftstartf_id
featurerange_idx4leftendf_id
featurerange_idx5rightstartf_id
featurerange_idx6rightendf_id

Constraints

Type Fields
NOT NULLfeaturerange_id
NOT NULLfeaturemap_id
FOREIGN KEYfeaturemap_id
NOT NULLfeature_id
FOREIGN KEYfeature_id
NOT NULLleftstartf_id
FOREIGN KEYleftstartf_id
FOREIGN KEYleftendf_id
FOREIGN KEYrightstartf_id
NOT NULLrightendf_id
FOREIGN KEYrightendf_id

featurepos

Top
Comments:

================================================
TABLE: featurepos
================================================
Field Name Data Type Size Default Value Other Foreign Key
featurepos_id integer 20 PRIMARY KEY, NOT NULL
featuremap_id integer 20 NOT NULL featuremap.featuremap_id
feature_id integer 20 NOT NULL feature.feature_id
map_feature_id integer 20 NOT NULL, map_feature_id links to the feature (map) upon which the feature is being localized. feature.feature_id
mappos float 20 NOT NULL

Indices

Name Fields
featurepos_idx1featuremap_id
featurepos_idx2feature_id
featurepos_idx3map_feature_id

Constraints

Type Fields
NOT NULLfeaturepos_id
NOT NULLfeaturemap_id
FOREIGN KEYfeaturemap_id
NOT NULLfeature_id
FOREIGN KEYfeature_id
NOT NULLmap_feature_id
FOREIGN KEYmap_feature_id
NOT NULLmappos

featureposprop

Top
Comments:

================================================
TABLE: featureposprop
================================================
Property or attribute of a featurepos record.
Field Name Data Type Size Default Value Other Foreign Key
featureposprop_id integer 20 PRIMARY KEY, NOT NULL
featurepos_id integer 20 UNIQUE, NOT NULL featurepos.featurepos_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
featureposprop_idx1featurepos_id
featureposprop_idx2type_id

Constraints

Type Fields
NOT NULLfeatureposprop_id
NOT NULLfeaturepos_id
NOT NULLtype_id
NOT NULLrank
UNIQUEfeaturepos_id, type_id, rank
FOREIGN KEYfeaturepos_id
FOREIGN KEYtype_id

featuremap_pub

Top
Comments:

================================================
TABLE: featuremap_pub
================================================
Field Name Data Type Size Default Value Other Foreign Key
featuremap_pub_id integer 20 PRIMARY KEY, NOT NULL
featuremap_id integer 20 NOT NULL featuremap.featuremap_id
pub_id integer 20 NOT NULL pub.pub_id

Indices

Name Fields
featuremap_pub_idx1featuremap_id
featuremap_pub_idx2pub_id

Constraints

Type Fields
NOT NULLfeaturemap_pub_id
NOT NULLfeaturemap_id
FOREIGN KEYfeaturemap_id
NOT NULLpub_id
FOREIGN KEYpub_id

featuremapprop

Top
Comments:

================================================
TABLE: featuremapprop
================================================
A featuremap 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.
Field Name Data Type Size Default Value Other Foreign Key
featuremapprop_id integer 20 PRIMARY KEY, NOT NULL
featuremap_id integer 20 UNIQUE, NOT NULL featuremap.featuremap_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
featuremapprop_idx1featuremap_id
featuremapprop_idx2type_id

Constraints

Type Fields
NOT NULLfeaturemapprop_id
NOT NULLfeaturemap_id
NOT NULLtype_id
NOT NULLrank
FOREIGN KEYfeaturemap_id
FOREIGN KEYtype_id
UNIQUEfeaturemap_id, type_id, rank

featuremap_contact

Top
Comments:

================================================
TABLE: featuremap_contact
================================================
Links contact(s) with a featuremap. Used to indicate a particular person or organization responsible for constrution of or that can provide more information on a particular featuremap.
Field Name Data Type Size Default Value Other Foreign Key
featuremap_contact_id integer 20 PRIMARY KEY, NOT NULL
featuremap_id integer 20 UNIQUE, NOT NULL featuremap.featuremap_id
contact_id integer 20 UNIQUE, NOT NULL contact.contact_id

Indices

Name Fields
featuremap_contact_idx1featuremap_id
featuremap_contact_idx2contact_id

Constraints

Type Fields
NOT NULLfeaturemap_contact_id
NOT NULLfeaturemap_id
NOT NULLcontact_id
UNIQUEfeaturemap_id, contact_id
FOREIGN KEYcontact_id
FOREIGN KEYfeaturemap_id

featuremap_dbxref

Top
Comments:

================================================
TABLE: featuremap_dbxref
================================================
Field Name Data Type Size Default Value Other Foreign Key
featuremap_dbxref_id integer 20 PRIMARY KEY, NOT NULL
featuremap_id integer 20 NOT NULL featuremap.featuremap_id
dbxref_id integer 20 NOT NULL dbxref.dbxref_id
is_current boolean 0 true NOT NULL

Indices

Name Fields
featuremap_dbxref_idx1featuremap_id
featuremap_dbxref_idx2dbxref_id

Constraints

Type Fields
NOT NULLfeaturemap_dbxref_id
NOT NULLfeaturemap_id
NOT NULLdbxref_id
NOT NULLis_current
FOREIGN KEYfeaturemap_id
FOREIGN KEYdbxref_id

featuremap_organism

Top
Comments:

================================================
TABLE: featuremap_organism
================================================
Links a featuremap to the organism(s) with which it is associated.
Field Name Data Type Size Default Value Other Foreign Key
featuremap_organism_id integer 20 PRIMARY KEY, NOT NULL
featuremap_id integer 20 UNIQUE, NOT NULL featuremap.featuremap_id
organism_id integer 20 UNIQUE, NOT NULL organism.organism_id

Indices

Name Fields
featuremap_organism_idx1featuremap_id
featuremap_organism_idx2organism_id

Constraints

Type Fields
NOT NULLfeaturemap_organism_id
NOT NULLfeaturemap_id
NOT NULLorganism_id
UNIQUEfeaturemap_id, organism_id
FOREIGN KEYfeaturemap_id
FOREIGN KEYorganism_id

phylotree

Top
Comments:

$Id: phylogeny.sql,v 1.11 2007-04-12 17:00:30 briano Exp $
==========================================
Chado phylogenetics module
Richard Bruskiewich
Chris Mungall
Initial design: 2004-05-27
============
DEPENDENCIES
============
:import feature from sequence
:import cvterm from cv
:import pub from pub
:import organism from organism
:import dbxref from db
:import analysis from companalysis
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
================================================
TABLE: phylotree
================================================
Global anchor for phylogenetic tree.
Field Name Data Type Size Default Value Other Foreign Key
phylotree_id integer 20 PRIMARY KEY, UNIQUE, NOT NULL
dbxref_id integer 20 NOT NULL dbxref.dbxref_id
name varchar 255 NULL
type_id integer 20 Type: protein, nucleotide, taxonomy, for example. The type should be any SO type, or "taxonomy". cvterm.cvterm_id
analysis_id integer 20 NULL analysis.analysis_id
comment text 64000 NULL

Indices

Name Fields
phylotree_idx1phylotree_id

Constraints

Type Fields
NOT NULLphylotree_id
NOT NULLdbxref_id
FOREIGN KEYdbxref_id
FOREIGN KEYtype_id
FOREIGN KEYanalysis_id
UNIQUEphylotree_id

phylotree_pub

Top
Comments:

================================================
TABLE: phylotree_pub
================================================
Tracks citations global to the tree e.g. multiple sequence alignment supporting tree construction.
Field Name Data Type Size Default Value Other Foreign Key
phylotree_pub_id integer 20 PRIMARY KEY, NOT NULL
phylotree_id integer 20 UNIQUE, NOT NULL phylotree.phylotree_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
phylotree_pub_idx1phylotree_id
phylotree_pub_idx2pub_id

Constraints

Type Fields
NOT NULLphylotree_pub_id
NOT NULLphylotree_id
FOREIGN KEYphylotree_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEphylotree_id, pub_id

phylotreeprop

Top
Comments:

================================================
TABLE: phylotreeprop
================================================
A phylotree 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.
Field Name Data Type Size Default Value Other Foreign Key
phylotreeprop_id integer 20 PRIMARY KEY, NOT NULL
phylotree_id integer 20 UNIQUE, NOT NULL phylotree.phylotree_id
type_id integer 20 UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterm.cvterm_id
value text 64000 NULL 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 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any phylotree can have multiple values for any particular property type these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used

Indices

Name Fields
phylotreeprop_idx1phylotree_id
phylotreeprop_idx2type_id

Constraints

Type Fields
NOT NULLphylotreeprop_id
NOT NULLphylotree_id
NOT NULLtype_id
NOT NULLrank
FOREIGN KEYphylotree_id
FOREIGN KEYtype_id
UNIQUEphylotree_id, type_id, rank

phylonode

Top
Comments:

For any one phylotree, multivalued property-value pairs must be differentiated by rank.
================================================
TABLE: phylonode
================================================
Bootstrap float null.
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.
Field Name Data Type Size Default Value Other Foreign Key
phylonode_id integer 20 PRIMARY KEY, NOT NULL
phylotree_id integer 20 UNIQUE, NOT NULL phylotree.phylotree_id
parent_phylonode_id integer 20 NULL Root phylonode can have null parent_phylonode_id value. phylonode.phylonode_id
left_idx integer 10 UNIQUE, NOT NULL
right_idx integer 10 UNIQUE, NOT NULL
type_id integer 20 Type: e.g. root, interior, leaf. cvterm.cvterm_id
feature_id integer 20 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. feature.feature_id
label varchar 255 NULL
distance float 20 NULL

Indices

Name Fields
phylonode_parent_phylonode_id_idxparent_phylonode_id

Constraints

Type Fields
NOT NULLphylonode_id
NOT NULLphylotree_id
FOREIGN KEYphylotree_id
FOREIGN KEYparent_phylonode_id
NOT NULLleft_idx
NOT NULLright_idx
FOREIGN KEYtype_id
FOREIGN KEYfeature_id
UNIQUEphylotree_id, left_idx
UNIQUEphylotree_id, right_idx

phylonode_dbxref

Top
Comments:

================================================
TABLE: phylonode_dbxref
================================================
For example, for orthology, paralogy group identifiers; could also be used for NCBI taxonomy; for sequences, refer to phylonode_feature, feature associated dbxrefs.
Field Name Data Type Size Default Value Other Foreign Key
phylonode_dbxref_id integer 20 PRIMARY KEY, NOT NULL
phylonode_id integer 20 UNIQUE, NOT NULL phylonode.phylonode_id
dbxref_id integer 20 UNIQUE, NOT NULL dbxref.dbxref_id

Indices

Name Fields
phylonode_dbxref_idx1phylonode_id
phylonode_dbxref_idx2dbxref_id

Constraints

Type Fields
NOT NULLphylonode_dbxref_id
NOT NULLphylonode_id
FOREIGN KEYphylonode_id
NOT NULLdbxref_id
FOREIGN KEYdbxref_id
UNIQUEphylonode_id, dbxref_id

phylonode_pub

Top
Comments:

================================================
TABLE: phylonode_pub
================================================
Field Name Data Type Size Default Value Other Foreign Key
phylonode_pub_id integer 20 PRIMARY KEY, NOT NULL
phylonode_id integer 20 UNIQUE, NOT NULL phylonode.phylonode_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
phylonode_pub_idx1phylonode_id
phylonode_pub_idx2pub_id

Constraints

Type Fields
NOT NULLphylonode_pub_id
NOT NULLphylonode_id
FOREIGN KEYphylonode_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEphylonode_id, pub_id

phylonode_organism

Top
Comments:

================================================
TABLE: phylonode_organism
================================================
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).
Field Name Data Type Size Default Value Other Foreign Key
phylonode_organism_id integer 20 PRIMARY KEY, NOT NULL
phylonode_id integer 20 UNIQUE, NOT NULL, One phylonode cannot refer to >1 organism. phylonode.phylonode_id
organism_id integer 20 NOT NULL organism.organism_id

Indices

Name Fields
phylonode_organism_idx1phylonode_id
phylonode_organism_idx2organism_id

Constraints

Type Fields
NOT NULLphylonode_organism_id
NOT NULLphylonode_id
FOREIGN KEYphylonode_id
NOT NULLorganism_id
FOREIGN KEYorganism_id
UNIQUEphylonode_id

phylonodeprop

Top
Comments:

================================================
TABLE: phylonodeprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
phylonodeprop_id integer 20 PRIMARY KEY, NOT NULL
phylonode_id integer 20 UNIQUE, NOT NULL phylonode.phylonode_id
type_id integer 20 UNIQUE, NOT NULL, type_id could designate phylonode hierarchy relationships, for example: species taxonomy (kingdom, order, family, genus, species), "ortholog/paralog", "fold/superfold", etc. cvterm.cvterm_id
value text 64000 UNIQUE, NOT NULL
rank integer 10 0 UNIQUE, NOT NULL, It is not clear how useful the rank concept is here, leave it in for now.

Indices

Name Fields
phylonodeprop_idx1phylonode_id
phylonodeprop_idx2type_id

Constraints

Type Fields
NOT NULLphylonodeprop_id
NOT NULLphylonode_id
FOREIGN KEYphylonode_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLvalue
NOT NULLrank
UNIQUEphylonode_id, type_id, value, rank

phylonode_relationship

Top
Comments:

================================================
TABLE: phylonode_relationship
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
phylonode_relationship_id integer 20 PRIMARY KEY, NOT NULL
subject_id integer 20 UNIQUE, NOT NULL phylonode.phylonode_id
object_id integer 20 UNIQUE, NOT NULL phylonode.phylonode_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
rank integer 10
phylotree_id integer 20 NOT NULL phylotree.phylotree_id

Indices

Name Fields
phylonode_relationship_idx1subject_id
phylonode_relationship_idx2object_id
phylonode_relationship_idx3type_id

Constraints

Type Fields
NOT NULLphylonode_relationship_id
NOT NULLsubject_id
FOREIGN KEYsubject_id
NOT NULLobject_id
FOREIGN KEYobject_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLphylotree_id
FOREIGN KEYphylotree_id
UNIQUEsubject_id, object_id, type_id

expression

Top
Comments:

$Id: expression.sql,v 1.14 2007-03-23 15:18:02 scottcain Exp $
==========================================
Chado expression module
=================================================================
Dependencies:
:import feature from sequence
:import cvterm from cv
:import pub from pub
=================================================================
================================================
TABLE: expression
================================================
The expression table is essentially a bridge table.
Field Name Data Type Size Default Value Other Foreign Key
expression_id integer 20 PRIMARY KEY, NOT NULL
uniquename text 64000 UNIQUE, NOT NULL
md5checksum char 32
description text 64000

Constraints

Type Fields
NOT NULLexpression_id
NOT NULLuniquename
UNIQUEuniquename

expression_cvterm

Top
Comments:

================================================
TABLE: expression_cvterm
================================================
Field Name Data Type Size Default Value Other Foreign Key
expression_cvterm_id integer 20 PRIMARY KEY, NOT NULL
expression_id integer 20 UNIQUE, NOT NULL expression.expression_id
cvterm_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
rank integer 10 0 UNIQUE, NOT NULL
cvterm_type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id

Indices

Name Fields
expression_cvterm_idx1expression_id
expression_cvterm_idx2cvterm_id
expression_cvterm_idx3cvterm_type_id

Constraints

Type Fields
NOT NULLexpression_cvterm_id
NOT NULLexpression_id
FOREIGN KEYexpression_id
NOT NULLcvterm_id
FOREIGN KEYcvterm_id
NOT NULLrank
NOT NULLcvterm_type_id
FOREIGN KEYcvterm_type_id
UNIQUEexpression_id, cvterm_id, rank, cvterm_type_id

expression_cvtermprop

Top
Comments:

================================================
TABLE: expression_cvtermprop
================================================
Extensible properties for expression to cvterm associations. Examples: qualifiers.
Field Name Data Type Size Default Value Other Foreign Key
expression_cvtermprop_id integer 20 PRIMARY KEY, NOT NULL
expression_cvterm_id integer 20 UNIQUE, NOT NULL expression_cvterm.expression_cvterm_id
type_id integer 20 UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. For example, cvterms may come from the FlyBase miscellaneous cv. cvterm.cvterm_id
value text 64000 NULL 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 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any expression_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Indices

Name Fields
expression_cvtermprop_idx1expression_cvterm_id
expression_cvtermprop_idx2type_id

Constraints

Type Fields
NOT NULLexpression_cvtermprop_id
NOT NULLexpression_cvterm_id
FOREIGN KEYexpression_cvterm_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEexpression_cvterm_id, type_id, rank

expressionprop

Top
Comments:

================================================
TABLE: expressionprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
expressionprop_id integer 20 PRIMARY KEY, NOT NULL
expression_id integer 20 UNIQUE, NOT NULL expression.expression_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
expressionprop_idx1expression_id
expressionprop_idx2type_id

Constraints

Type Fields
NOT NULLexpressionprop_id
NOT NULLexpression_id
FOREIGN KEYexpression_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEexpression_id, type_id, rank

expression_pub

Top
Comments:

================================================
TABLE: expression_pub
================================================
Field Name Data Type Size Default Value Other Foreign Key
expression_pub_id integer 20 PRIMARY KEY, NOT NULL
expression_id integer 20 UNIQUE, NOT NULL expression.expression_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
expression_pub_idx1expression_id
expression_pub_idx2pub_id

Constraints

Type Fields
NOT NULLexpression_pub_id
NOT NULLexpression_id
FOREIGN KEYexpression_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEexpression_id, pub_id

feature_expression

Top
Comments:

================================================
TABLE: feature_expression
================================================
Field Name Data Type Size Default Value Other Foreign Key
feature_expression_id integer 20 PRIMARY KEY, NOT NULL
expression_id integer 20 UNIQUE, NOT NULL expression.expression_id
feature_id integer 20 UNIQUE, NOT NULL feature.feature_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
feature_expression_idx1expression_id
feature_expression_idx2feature_id
feature_expression_idx3pub_id

Constraints

Type Fields
NOT NULLfeature_expression_id
NOT NULLexpression_id
FOREIGN KEYexpression_id
NOT NULLfeature_id
FOREIGN KEYfeature_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEexpression_id, feature_id, pub_id

feature_expressionprop

Top
Comments:

================================================
TABLE: feature_expressionprop
================================================
Extensible properties for feature_expression (comments, for example). Modeled on feature_cvtermprop.
Field Name Data Type Size Default Value Other Foreign Key
feature_expressionprop_id integer 20 PRIMARY KEY, NOT NULL
feature_expression_id integer 20 UNIQUE, NOT NULL feature_expression.feature_expression_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
feature_expressionprop_idx1feature_expression_id
feature_expressionprop_idx2type_id

Constraints

Type Fields
NOT NULLfeature_expressionprop_id
NOT NULLfeature_expression_id
FOREIGN KEYfeature_expression_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEfeature_expression_id, type_id, rank

eimage

Top
Comments:

================================================
TABLE: eimage
================================================
Field Name Data Type Size Default Value Other Foreign Key
eimage_id integer 20 PRIMARY KEY, NOT NULL
eimage_data text 64000 We expect images in eimage_data (e.g. JPEGs) to be uuencoded.
eimage_type varchar 255 NOT NULL, Describes the type of data in eimage_data.
image_uri varchar 255

Constraints

Type Fields
NOT NULLeimage_id
NOT NULLeimage_type

expression_image

Top
Comments:

================================================
TABLE: expression_image
================================================
Field Name Data Type Size Default Value Other Foreign Key
expression_image_id integer 20 PRIMARY KEY, NOT NULL
expression_id integer 20 UNIQUE, NOT NULL expression.expression_id
eimage_id integer 20 UNIQUE, NOT NULL eimage.eimage_id

Indices

Name Fields
expression_image_idx1expression_id
expression_image_idx2eimage_id

Constraints

Type Fields
NOT NULLexpression_image_id
NOT NULLexpression_id
FOREIGN KEYexpression_id
NOT NULLeimage_id
FOREIGN KEYeimage_id
UNIQUEexpression_id, eimage_id

library

Top
Comments:

$Id: library.sql,v 1.10 2008-03-25 16:00:43 emmert Exp $
=================================================================
Dependencies:
:import feature from sequence
:import synonym from sequence
:import cvterm from cv
:import pub from pub
:import organism from organism
:import expression from expression
:import dbxref from db
:import contact from contact
=================================================================
================================================
TABLE: library
================================================
Field Name Data Type Size Default Value Other Foreign Key
library_id integer 20 PRIMARY KEY, NOT NULL
organism_id integer 20 UNIQUE, NOT NULL organism.organism_id
name varchar 255
uniquename text 64000 UNIQUE, NOT NULL
type_id integer 20 UNIQUE, NOT NULL, The type_id foreign key links to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library" cvterm.cvterm_id
is_obsolete integer 10 0 NOT NULL
timeaccessioned timestamp 0 current_timestamp NOT NULL
timelastmodified timestamp 0 current_timestamp NOT NULL

Indices

Name Fields
library_name_ind1name
library_idx1organism_id
library_idx2type_id
library_idx3uniquename
library_contact_idx1library_id

Constraints

Type Fields
NOT NULLlibrary_id
NOT NULLorganism_id
FOREIGN KEYorganism_id
NOT NULLuniquename
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLis_obsolete
NOT NULLtimeaccessioned
NOT NULLtimelastmodified
UNIQUEorganism_id, uniquename, type_id

library_synonym

Top
Comments:

================================================
TABLE: library_synonym
================================================
Linking table between library and synonym.
Field Name Data Type Size Default Value Other Foreign Key
library_synonym_id integer 20 PRIMARY KEY, NOT NULL
synonym_id integer 20 UNIQUE, NOT NULL synonym.synonym_id
library_id integer 20 UNIQUE, NOT NULL library.library_id
pub_id integer 20 UNIQUE, NOT NULL, The pub_id link is for relating the usage of a given synonym to the publication in which it was used. pub.pub_id
is_current boolean 0 true NOT NULL, The is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library.
is_internal boolean 0 false NOT NULL, Typically a synonym exists so that somebody querying the database with an obsolete name can find the object they are looking for under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it my also be listed in reports as a synonym. If the synonym was not used deliberately (e.g., there was a typo which went public), then the is_internal bit may be set to "true" so that it is known that the synonym is "internal" and should be queryable but should not be listed in reports as a valid synonym.

Indices

Name Fields
library_synonym_idx1synonym_id
library_synonym_idx2library_id
library_synonym_idx3pub_id

Constraints

Type Fields
NOT NULLlibrary_synonym_id
NOT NULLsynonym_id
FOREIGN KEYsynonym_id
NOT NULLlibrary_id
FOREIGN KEYlibrary_id
NOT NULLpub_id
FOREIGN KEYpub_id
NOT NULLis_current
NOT NULLis_internal
UNIQUEsynonym_id, library_id, pub_id

library_pub

Top
Comments:

================================================
TABLE: library_pub
================================================
Attribution for a library.
Field Name Data Type Size Default Value Other Foreign Key
library_pub_id integer 20 PRIMARY KEY, NOT NULL
library_id integer 20 UNIQUE, NOT NULL library.library_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
library_pub_idx1library_id
library_pub_idx2pub_id

Constraints

Type Fields
NOT NULLlibrary_pub_id
NOT NULLlibrary_id
FOREIGN KEYlibrary_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUElibrary_id, pub_id

libraryprop

Top
Comments:

================================================
TABLE: libraryprop
================================================
Tag-value properties - follows standard chado model.
Field Name Data Type Size Default Value Other Foreign Key
libraryprop_id integer 20 PRIMARY KEY, NOT NULL
library_id integer 20 UNIQUE, NOT NULL library.library_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
libraryprop_idx1library_id
libraryprop_idx2type_id

Constraints

Type Fields
NOT NULLlibraryprop_id
NOT NULLlibrary_id
FOREIGN KEYlibrary_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUElibrary_id, type_id, rank

libraryprop_pub

Top
Comments:

================================================
TABLE: libraryprop_pub
================================================
Attribution for libraryprop.
Field Name Data Type Size Default Value Other Foreign Key
libraryprop_pub_id integer 20 PRIMARY KEY, NOT NULL
libraryprop_id integer 20 UNIQUE, NOT NULL libraryprop.libraryprop_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
libraryprop_pub_idx1libraryprop_id
libraryprop_pub_idx2pub_id

Constraints

Type Fields
NOT NULLlibraryprop_pub_id
NOT NULLlibraryprop_id
FOREIGN KEYlibraryprop_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUElibraryprop_id, pub_id

library_cvterm

Top
Comments:

================================================
TABLE: library_cvterm
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
library_cvterm_id integer 20 PRIMARY KEY, NOT NULL
library_id integer 20 UNIQUE, NOT NULL library.library_id
cvterm_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
library_cvterm_idx1library_id
library_cvterm_idx2cvterm_id
library_cvterm_idx3pub_id

Constraints

Type Fields
NOT NULLlibrary_cvterm_id
NOT NULLlibrary_id
FOREIGN KEYlibrary_id
NOT NULLcvterm_id
FOREIGN KEYcvterm_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUElibrary_id, cvterm_id, pub_id

library_feature

Top
Comments:

================================================
TABLE: library_feature
================================================
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".
Field Name Data Type Size Default Value Other Foreign Key
library_feature_id integer 20 PRIMARY KEY, NOT NULL
library_id integer 20 UNIQUE, NOT NULL library.library_id
feature_id integer 20 UNIQUE, NOT NULL feature.feature_id

Indices

Name Fields
library_feature_idx1library_id
library_feature_idx2feature_id

Constraints

Type Fields
NOT NULLlibrary_feature_id
NOT NULLlibrary_id
FOREIGN KEYlibrary_id
NOT NULLfeature_id
FOREIGN KEYfeature_id
UNIQUElibrary_id, feature_id

library_dbxref

Top
Comments:

================================================
TABLE: library_dbxref
================================================
Links a library to dbxrefs.
Field Name Data Type Size Default Value Other Foreign Key
library_dbxref_id integer 20 PRIMARY KEY, NOT NULL
library_id integer 20 UNIQUE, NOT NULL library.library_id
dbxref_id integer 20 UNIQUE, NOT NULL dbxref.dbxref_id
is_current boolean 0 true NOT NULL

Indices

Name Fields
library_dbxref_idx1library_id
library_dbxref_idx2dbxref_id

Constraints

Type Fields
NOT NULLlibrary_dbxref_id
NOT NULLlibrary_id
FOREIGN KEYlibrary_id
NOT NULLdbxref_id
FOREIGN KEYdbxref_id
NOT NULLis_current
UNIQUElibrary_id, dbxref_id

library_expression

Top
Comments:

================================================
TABLE: library_expression
================================================
Links a library to expression statements.
Field Name Data Type Size Default Value Other Foreign Key
library_expression_id integer 20 PRIMARY KEY, NOT NULL
library_id integer 20 UNIQUE, NOT NULL library.library_id
expression_id integer 20 UNIQUE, NOT NULL expression.expression_id
pub_id integer 20 NOT NULL pub.pub_id

Indices

Name Fields
library_expression_idx1library_id
library_expression_idx2expression_id
library_expression_idx3pub_id

Constraints

Type Fields
NOT NULLlibrary_expression_id
NOT NULLlibrary_id
FOREIGN KEYlibrary_id
NOT NULLexpression_id
FOREIGN KEYexpression_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUElibrary_id, expression_id

library_expressionprop

Top
Comments:

================================================
TABLE: library_expressionprop
================================================
Attributes of a library_expression relationship.
Field Name Data Type Size Default Value Other Foreign Key
library_expressionprop_id integer 20 PRIMARY KEY, NOT NULL
library_expression_id integer 20 UNIQUE, NOT NULL library_expression.library_expression_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
library_expressionprop_idx1library_expression_id
library_expressionprop_idx2type_id

Constraints

Type Fields
NOT NULLlibrary_expressionprop_id
NOT NULLlibrary_expression_id
FOREIGN KEYlibrary_expression_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUElibrary_expression_id, type_id, rank

library_featureprop

Top
Comments:

================================================
TABLE: library_featureprop
================================================
Attributes of a library_feature relationship.
Field Name Data Type Size Default Value Other Foreign Key
library_featureprop_id integer 20 PRIMARY KEY, NOT NULL
library_feature_id integer 20 UNIQUE, NOT NULL library_feature.library_feature_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
library_featureprop_idx1library_feature_id
library_featureprop_idx2type_id

Constraints

Type Fields
NOT NULLlibrary_featureprop_id
NOT NULLlibrary_feature_id
FOREIGN KEYlibrary_feature_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUElibrary_feature_id, type_id, rank

library_relationship

Top
Comments:

================================================
TABLE: library_relationship
================================================
Relationships between libraries.
Field Name Data Type Size Default Value Other Foreign Key
library_relationship_id integer 20 PRIMARY KEY, NOT NULL
subject_id integer 20 UNIQUE, NOT NULL library.library_id
object_id integer 20 UNIQUE, NOT NULL library.library_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id

Indices

Name Fields
library_relationship_idx1subject_id
library_relationship_idx2object_id
library_relationship_idx3type_id

Constraints

Type Fields
NOT NULLlibrary_relationship_id
NOT NULLsubject_id
FOREIGN KEYsubject_id
NOT NULLobject_id
FOREIGN KEYobject_id
NOT NULLtype_id
FOREIGN KEYtype_id
UNIQUEsubject_id, object_id, type_id

library_relationship_pub

Top
Comments:

================================================
TABLE: library_relationship_pub
================================================
Provenance of library_relationship.
Field Name Data Type Size Default Value Other Foreign Key
library_relationship_pub_id integer 20 PRIMARY KEY, NOT NULL
library_relationship_id integer 20 UNIQUE, NOT NULL library_relationship.library_relationship_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
library_relationship_pub_idx1library_relationship_id
library_relationship_pub_idx2pub_id

Constraints

Type Fields
NOT NULLlibrary_relationship_pub_id
NOT NULLlibrary_relationship_id
FOREIGN KEYlibrary_relationship_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUElibrary_relationship_id, pub_id

library_contact

Top
Comments:

================================================
TABLE: library_contact
================================================
Links contact(s) with a library. Used to indicate a particular person or organization responsible for creation of or that can provide more information on a particular library.
Field Name Data Type Size Default Value Other Foreign Key
library_contact_id integer 20 PRIMARY KEY, NOT NULL
library_id integer 20 UNIQUE, NOT NULL library.library_id
contact_id integer 20 UNIQUE, NOT NULL contact.contact_id

Constraints

Type Fields
NOT NULLlibrary_contact_id
NOT NULLlibrary_id
NOT NULLcontact_id
UNIQUElibrary_id, contact_id
FOREIGN KEYlibrary_id
FOREIGN KEYcontact_id

stock

Top
Comments:

$Id: stock.sql,v 1.7 2007-03-23 15:18:03 scottcain Exp $
==========================================
Chado stock module
DEPENDENCIES
============
:import cvterm from cv
:import pub from pub
:import dbxref from db
:import organism from organism
:import genotype from genetic
:import contact from contact
:import feature from sequence
:import featuremap from map
================================================
TABLE: 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.
Field Name Data Type Size Default Value Other Foreign Key
stock_id integer 20 PRIMARY KEY, NOT NULL
dbxref_id integer 20 The dbxref_id is an optional primary stable identifier for this stock. Secondary indentifiers and external dbxrefs go in table: stock_dbxref. dbxref.dbxref_id
organism_id integer 20 UNIQUE, The organism_id is the organism to which the stock belongs. This column should only be left blank if the organism cannot be determined. organism.organism_id
name varchar 255 The name is a human-readable local name for a stock.
uniquename text 64000 UNIQUE, NOT NULL
description text 64000 The description is the genetic description provided in the stock list.
type_id integer 20 UNIQUE, NOT NULL, The type_id foreign key links to a controlled vocabulary of stock types. The would include living stock, genomic DNA, preserved specimen. Secondary cvterms for stocks would go in stock_cvterm. cvterm.cvterm_id
is_obsolete boolean 0 false NOT NULL

Indices

Name Fields
stock_name_ind1name
stock_idx1dbxref_id
stock_idx2organism_id
stock_idx3type_id
stock_idx4uniquename

Constraints

Type Fields
NOT NULLstock_id
FOREIGN KEYdbxref_id
FOREIGN KEYorganism_id
NOT NULLuniquename
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLis_obsolete
UNIQUEorganism_id, uniquename, type_id

stock_pub

Top
Comments:

================================================
TABLE: stock_pub
================================================
Provenance. Linking table between stocks and, for example, a stocklist computer file.
Field Name Data Type Size Default Value Other Foreign Key
stock_pub_id integer 20 PRIMARY KEY, NOT NULL
stock_id integer 20 UNIQUE, NOT NULL stock.stock_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
stock_pub_idx1stock_id
stock_pub_idx2pub_id

Constraints

Type Fields
NOT NULLstock_pub_id
NOT NULLstock_id
FOREIGN KEYstock_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEstock_id, pub_id

stockprop

Top
Comments:

================================================
TABLE: stockprop
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
stockprop_id integer 20 PRIMARY KEY, NOT NULL
stock_id integer 20 UNIQUE, NOT NULL stock.stock_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
stockprop_idx1stock_id
stockprop_idx2type_id

Constraints

Type Fields
NOT NULLstockprop_id
NOT NULLstock_id
FOREIGN KEYstock_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEstock_id, type_id, rank

stockprop_pub

Top
Comments:

================================================
TABLE: stockprop_pub
================================================
Provenance. Any stockprop assignment can optionally be supported by a publication.
Field Name Data Type Size Default Value Other Foreign Key
stockprop_pub_id integer 20 PRIMARY KEY, NOT NULL
stockprop_id integer 20 UNIQUE, NOT NULL stockprop.stockprop_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
stockprop_pub_idx1stockprop_id
stockprop_pub_idx2pub_id

Constraints

Type Fields
NOT NULLstockprop_pub_id
NOT NULLstockprop_id
FOREIGN KEYstockprop_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEstockprop_id, pub_id

stock_relationship

Top
Comments:

================================================
TABLE: stock_relationship
================================================
Field Name Data Type Size Default Value Other Foreign Key
stock_relationship_id integer 20 PRIMARY KEY, NOT NULL
subject_id integer 20 UNIQUE, NOT NULL, stock_relationship.subject_id is the subject of the subj-predicate-obj sentence. This is typically the substock. stock.stock_id
object_id integer 20 UNIQUE, NOT NULL, stock_relationship.object_id is the object of the subj-predicate-obj sentence. This is typically the container stock. stock.stock_id
type_id integer 20 UNIQUE, NOT NULL, stock_relationship.type_id is relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. cvterm.cvterm_id
value text 64000 NULL stock_relationship.value is for additional notes or comments.
rank integer 10 0 UNIQUE, NOT NULL, stock_relationship.rank is the ordering of subject stocks with respect to the object stock may be important where rank is used to order these; starts from zero.

Indices

Name Fields
stock_relationship_idx1subject_id
stock_relationship_idx2object_id
stock_relationship_idx3type_id

Constraints

Type Fields
NOT NULLstock_relationship_id
NOT NULLsubject_id
FOREIGN KEYsubject_id
NOT NULLobject_id
FOREIGN KEYobject_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEsubject_id, object_id, type_id, rank

stock_relationship_cvterm

Top
Comments:

================================================
TABLE: stock_relationship_cvterm
================================================
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
Field Name Data Type Size Default Value Other Foreign Key
stock_relationship_cvterm_id integer 20 PRIMARY KEY, NOT NULL
stock_relationship_id integer 20 NOT NULL stock_relationship.stock_relationship_id
cvterm_id integer 20 NOT NULL cvterm.cvterm_id
pub_id integer 20 pub.pub_id

Constraints

Type Fields
NOT NULLstock_relationship_cvterm_id
NOT NULLstock_relationship_id
FOREIGN KEYstock_relationship_id
NOT NULLcvterm_id
FOREIGN KEYcvterm_id
FOREIGN KEYpub_id

stock_relationship_pub

Top
Comments:

================================================
TABLE: stock_relationship_pub
================================================
Provenance. Attach optional evidence to a stock_relationship in the form of a publication.
Field Name Data Type Size Default Value Other Foreign Key
stock_relationship_pub_id integer 20 PRIMARY KEY, NOT NULL
stock_relationship_id integer 20 UNIQUE, NOT NULL stock_relationship.stock_relationship_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
stock_relationship_pub_idx1stock_relationship_id
stock_relationship_pub_idx2pub_id

Constraints

Type Fields
NOT NULLstock_relationship_pub_id
NOT NULLstock_relationship_id
FOREIGN KEYstock_relationship_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEstock_relationship_id, pub_id

stock_dbxref

Top
Comments:

================================================
TABLE: stock_dbxref
================================================
stock_dbxref links a stock to dbxrefs. This is for secondary identifiers; primary identifiers should use stock.dbxref_id.
Field Name Data Type Size Default Value Other Foreign Key
stock_dbxref_id integer 20 PRIMARY KEY, NOT NULL
stock_id integer 20 UNIQUE, NOT NULL stock.stock_id
dbxref_id integer 20 UNIQUE, NOT NULL dbxref.dbxref_id
is_current boolean 0 true NOT NULL, The is_current boolean indicates whether the linked dbxref is the current -official- dbxref for the linked stock.

Indices

Name Fields
stock_dbxref_idx1stock_id
stock_dbxref_idx2dbxref_id

Constraints

Type Fields
NOT NULLstock_dbxref_id
NOT NULLstock_id
FOREIGN KEYstock_id
NOT NULLdbxref_id
FOREIGN KEYdbxref_id
NOT NULLis_current
UNIQUEstock_id, dbxref_id

stock_cvterm

Top
Comments:

================================================
TABLE: stock_cvterm
================================================
stock_cvterm links a stock to cvterms. This is for secondary cvterms; primary cvterms should use stock.type_id.
Field Name Data Type Size Default Value Other Foreign Key
stock_cvterm_id integer 20 PRIMARY KEY, NOT NULL
stock_id integer 20 UNIQUE, NOT NULL stock.stock_id
cvterm_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id
is_not boolean 0 false NOT NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
stock_cvterm_idx1stock_id
stock_cvterm_idx2cvterm_id
stock_cvterm_idx3pub_id

Constraints

Type Fields
NOT NULLstock_cvterm_id
NOT NULLstock_id
FOREIGN KEYstock_id
NOT NULLcvterm_id
FOREIGN KEYcvterm_id
NOT NULLpub_id
FOREIGN KEYpub_id
NOT NULLis_not
NOT NULLrank
UNIQUEstock_id, cvterm_id, pub_id, rank

stock_cvtermprop

Top
Comments:

================================================
TABLE: stock_cvtermprop
================================================
Extensible properties for stock 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 stockprop table for meanings of type_id, value and rank.
Field Name Data Type Size Default Value Other Foreign Key
stock_cvtermprop_id integer 20 PRIMARY KEY, NOT NULL
stock_cvterm_id integer 20 UNIQUE, NOT NULL stock_cvterm.stock_cvterm_id
type_id integer 20 UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv. cvterm.cvterm_id
value text 64000 NULL 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 10 0 UNIQUE, NOT NULL, Property-Value ordering. Any stock_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

Indices

Name Fields
stock_cvtermprop_idx1stock_cvterm_id
stock_cvtermprop_idx2type_id

Constraints

Type Fields
NOT NULLstock_cvtermprop_id
NOT NULLstock_cvterm_id
FOREIGN KEYstock_cvterm_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEstock_cvterm_id, type_id, rank

stock_genotype

Top
Comments:

================================================
TABLE: stock_genotype
================================================
Simple table linking a stock to a genotype. Features with genotypes can be linked to stocks thru feature_genotype -> genotype -> stock_genotype -> stock.
Field Name Data Type Size Default Value Other Foreign Key
stock_genotype_id integer 20 PRIMARY KEY, NOT NULL
stock_id integer 20 UNIQUE, NOT NULL stock.stock_id
genotype_id integer 20 UNIQUE, NOT NULL genotype.genotype_id

Indices

Name Fields
stock_genotype_idx1stock_id
stock_genotype_idx2genotype_id

Constraints

Type Fields
NOT NULLstock_genotype_id
NOT NULLstock_id
FOREIGN KEYstock_id
NOT NULLgenotype_id
FOREIGN KEYgenotype_id
UNIQUEstock_id, genotype_id

stockcollection

Top
Comments:

================================================
TABLE: stockcollection
================================================
The lab or stock center distributing the stocks in their collection.
Field Name Data Type Size Default Value Other Foreign Key
stockcollection_id integer 20 PRIMARY KEY, NOT NULL
type_id integer 20 UNIQUE, NOT NULL, type_id is the collection type cv. cvterm.cvterm_id
contact_id integer 20 NULL contact_id links to the contact information for the collection. contact.contact_id
name varchar 255 name is the collection.
uniquename text 64000 UNIQUE, NOT NULL, uniqename is the value of the collection cv.

Indices

Name Fields
stockcollection_name_ind1name
stockcollection_idx1contact_id
stockcollection_idx2type_id
stockcollection_idx3uniquename

Constraints

Type Fields
NOT NULLstockcollection_id
NOT NULLtype_id
FOREIGN KEYtype_id
FOREIGN KEYcontact_id
NOT NULLuniquename
UNIQUEuniquename, type_id

stockcollectionprop

Top
Comments:

================================================
TABLE: stockcollectionprop
================================================
The table stockcollectionprop contains the value of the stock collection such as website/email URLs; the value of the stock collection order URLs.
Field Name Data Type Size Default Value Other Foreign Key
stockcollectionprop_id integer 20 PRIMARY KEY, NOT NULL
stockcollection_id integer 20 UNIQUE, NOT NULL stockcollection.stockcollection_id
type_id integer 20 UNIQUE, NOT NULL, The cv for the type_id is "stockcollection property type". cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
stockcollectionprop_idx1stockcollection_id
stockcollectionprop_idx2type_id

Constraints

Type Fields
NOT NULLstockcollectionprop_id
NOT NULLstockcollection_id
FOREIGN KEYstockcollection_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEstockcollection_id, type_id, rank

stockcollection_stock

Top
Comments:

================================================
TABLE: stockcollection_stock
================================================
stockcollection_stock links a stock collection to the stocks which are contained in the collection.
Field Name Data Type Size Default Value Other Foreign Key
stockcollection_stock_id integer 20 PRIMARY KEY, NOT NULL
stockcollection_id integer 20 UNIQUE, NOT NULL stockcollection.stockcollection_id
stock_id integer 20 UNIQUE, NOT NULL stock.stock_id

Indices

Name Fields
stockcollection_stock_idx1stockcollection_id
stockcollection_stock_idx2stock_id

Constraints

Type Fields
NOT NULLstockcollection_stock_id
NOT NULLstockcollection_id
FOREIGN KEYstockcollection_id
NOT NULLstock_id
FOREIGN KEYstock_id
UNIQUEstockcollection_id, stock_id

stock_dbxrefprop

Top
Comments:

================================================
TABLE: stock_dbxrefprop
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
stock_dbxrefprop_id integer 20 PRIMARY KEY, NOT NULL
stock_dbxref_id integer 20 UNIQUE, NOT NULL stock_dbxref.stock_dbxref_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
stock_dbxrefprop_idx1stock_dbxref_id
stock_dbxrefprop_idx2type_id

Constraints

Type Fields
NOT NULLstock_dbxrefprop_id
NOT NULLstock_dbxref_id
FOREIGN KEYstock_dbxref_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEstock_dbxref_id, type_id, rank

stockcollection_db

Top
Comments:

================================================
TABLE: stockcollection_db
================================================
Stock collections may be respresented by an external online database. This table associates a stock collection with a database where its member stocks can be found. Individual stock that are part of this collction should have entries in the stock_dbxref table with the same db_id record
Field Name Data Type Size Default Value Other Foreign Key
stockcollection_db_id integer 20 PRIMARY KEY, NOT NULL
stockcollection_id integer 20 UNIQUE, NOT NULL stockcollection.stockcollection_id
db_id integer 20 UNIQUE, NOT NULL db.db_id

Indices

Name Fields
stockcollection_db_idx1stockcollection_id
stockcollection_db_idx2db_id

Constraints

Type Fields
NOT NULLstockcollection_db_id
NOT NULLstockcollection_id
NOT NULLdb_id
UNIQUEstockcollection_id, db_id
FOREIGN KEYdb_id
FOREIGN KEYstockcollection_id

stock_feature

Top
Comments:

================================================
TABLE: stock_feature
================================================
Links a stock to a feature.
Field Name Data Type Size Default Value Other Foreign Key
stock_feature_id integer 20 PRIMARY KEY, NOT NULL
feature_id integer 20 UNIQUE, NOT NULL feature.feature_id
stock_id integer 20 UNIQUE, NOT NULL stock.stock_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
stock_feature_idx1stock_feature_id
stock_feature_idx2feature_id
stock_feature_idx3stock_id
stock_feature_idx4type_id

Constraints

Type Fields
NOT NULLstock_feature_id
NOT NULLfeature_id
NOT NULLstock_id
NOT NULLtype_id
NOT NULLrank
FOREIGN KEYfeature_id
FOREIGN KEYstock_id
FOREIGN KEYtype_id
UNIQUEfeature_id, stock_id, type_id, rank

stock_featuremap

Top
Comments:

================================================
TABLE: stock_featuremap
================================================
Links a featuremap to a stock.
Field Name Data Type Size Default Value Other Foreign Key
stock_featuremap_id integer 20 PRIMARY KEY, NOT NULL
featuremap_id integer 20 UNIQUE, NOT NULL featuremap.featuremap_id
stock_id integer 20 UNIQUE, NOT NULL stock.stock_id
type_id integer 20 UNIQUE cvterm.cvterm_id

Indices

Name Fields
stock_featuremap_idx1featuremap_id
stock_featuremap_idx2stock_id
stock_featuremap_idx3type_id

Constraints

Type Fields
NOT NULLstock_featuremap_id
NOT NULLfeaturemap_id
NOT NULLstock_id
FOREIGN KEYfeaturemap_id
FOREIGN KEYstock_id
FOREIGN KEYtype_id
UNIQUEfeaturemap_id, stock_id, type_id

stock_library

Top
Comments:

================================================
TABLE: stock_library
================================================
Links a stock with a library.
Field Name Data Type Size Default Value Other Foreign Key
stock_library_id integer 20 PRIMARY KEY, NOT NULL
library_id integer 20 UNIQUE, NOT NULL library.library_id
stock_id integer 20 UNIQUE, NOT NULL stock.stock_id

Indices

Name Fields
stock_library_idx1library_id
stock_library_idx2stock_id

Constraints

Type Fields
NOT NULLstock_library_id
NOT NULLlibrary_id
NOT NULLstock_id
UNIQUElibrary_id, stock_id
FOREIGN KEYlibrary_id
FOREIGN KEYstock_id

project

Top
Comments:

==========================================
Chado project module. Used primarily by other Chado modules to
group experiments, stocks, and so forth that are associated with
eachother administratively or organizationally.
=================================================================
Dependencies:
:import cvterm from cv
:import pub from pub
:import contact from contact
:import dbxref from db
:import analysis from companalysis
:import feature from sequence
:import stock from stock
=================================================================
================================================
TABLE: project
================================================
A project is some kind of planned endeavor. Used primarily by other Chado modules to group experiments, stocks, and so forth that are associated with eachother administratively or organizationally.
Standard Chado flexible property table for projects.
Field Name Data Type Size Default Value Other Foreign Key
project_id integer 20 PRIMARY KEY, NOT NULL
name varchar 255 UNIQUE, NOT NULL
description text 64000

Constraints

Type Fields
NOT NULLproject_id
NOT NULLname
UNIQUEname

projectprop

Top
Comments:

================================================
TABLE: projectprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
projectprop_id integer 20 PRIMARY KEY, NOT NULL
project_id integer 20 UNIQUE, NOT NULL project.project_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000
rank integer 10 0 UNIQUE, NOT NULL

Constraints

Type Fields
NOT NULLprojectprop_id
NOT NULLproject_id
FOREIGN KEYproject_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEproject_id, type_id, rank

project_relationship

Top
Comments:

================================================
TABLE: project_relationship
================================================
Linking table for relating projects to each other. For example, a given project could be composed of several smaller subprojects
Field Name Data Type Size Default Value Other Foreign Key
project_relationship_id integer 20 PRIMARY KEY, NOT NULL
subject_project_id integer 20 UNIQUE, NOT NULL project.project_id
object_project_id integer 20 UNIQUE, NOT NULL project.project_id
type_id integer 20 UNIQUE, NOT NULL, The cvterm type of the relationship being stated, such as "part of". cvterm.cvterm_id

Constraints

Type Fields
NOT NULLproject_relationship_id
NOT NULLsubject_project_id
FOREIGN KEYsubject_project_id
NOT NULLobject_project_id
FOREIGN KEYobject_project_id
NOT NULLtype_id
FOREIGN KEYtype_id
UNIQUEsubject_project_id, object_project_id, type_id

project_pub

Top
Comments:

================================================
TABLE: project_pub
================================================
Linking table for associating projects and publications.
Field Name Data Type Size Default Value Other Foreign Key
project_pub_id integer 20 PRIMARY KEY, NOT NULL
project_id integer 20 UNIQUE, NOT NULL project.project_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
project_pub_idx1project_id
project_pub_idx2pub_id

Constraints

Type Fields
NOT NULLproject_pub_id
NOT NULLproject_id
FOREIGN KEYproject_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEproject_id, pub_id

project_contact

Top
Comments:

================================================
TABLE: project_contact
================================================
Linking table for associating projects and contacts.
Field Name Data Type Size Default Value Other Foreign Key
project_contact_id integer 20 PRIMARY KEY, NOT NULL
project_id integer 20 UNIQUE, NOT NULL project.project_id
contact_id integer 20 UNIQUE, NOT NULL contact.contact_id

Indices

Name Fields
project_contact_idx1project_id
project_contact_idx2contact_id

Constraints

Type Fields
NOT NULLproject_contact_id
NOT NULLproject_id
FOREIGN KEYproject_id
NOT NULLcontact_id
FOREIGN KEYcontact_id
UNIQUEproject_id, contact_id

project_dbxref

Top
Comments:

================================================
TABLE: project_dbxref
================================================
project_dbxref links a project to dbxrefs.
Field Name Data Type Size Default Value Other Foreign Key
project_dbxref_id integer 20 PRIMARY KEY, NOT NULL
project_id integer 20 UNIQUE, NOT NULL project.project_id
dbxref_id integer 20 UNIQUE, NOT NULL dbxref.dbxref_id
is_current boolean 0 true NOT NULL, The is_current boolean indicates whether the linked dbxref is the current -official- dbxref for the linked project.

Indices

Name Fields
project_dbxref_idx1project_id
project_dbxref_idx2dbxref_id

Constraints

Type Fields
NOT NULLproject_dbxref_id
NOT NULLproject_id
NOT NULLdbxref_id
NOT NULLis_current
FOREIGN KEYdbxref_id
FOREIGN KEYproject_id
UNIQUEproject_id, dbxref_id

project_analysis

Top
Comments:

================================================
TABLE: project_analysis
================================================
Links an analysis to a project that may contain multiple analyses. The rank column can be used to specify a simple ordering in which analyses were executed.
Field Name Data Type Size Default Value Other Foreign Key
project_analysis_id integer 20 PRIMARY KEY, NOT NULL
project_id integer 20 UNIQUE, NOT NULL project.project_id
analysis_id integer 20 UNIQUE, NOT NULL analysis.analysis_id
rank integer 10 0 NOT NULL

Indices

Name Fields
project_analysis_idx1project_id
project_analysis_idx2analysis_id

Constraints

Type Fields
NOT NULLproject_analysis_id
NOT NULLproject_id
FOREIGN KEYproject_id
NOT NULLanalysis_id
FOREIGN KEYanalysis_id
NOT NULLrank
UNIQUEproject_id, analysis_id

project_feature

Top
Comments:

================================================
TABLE: project_feature
================================================
This table is intended associate records in the feature table with a project.
Field Name Data Type Size Default Value Other Foreign Key
project_feature_id integer 20 PRIMARY KEY, NOT NULL
feature_id integer 20 UNIQUE, NOT NULL feature.feature_id
project_id integer 20 UNIQUE, NOT NULL project.project_id

Indices

Name Fields
project_feature_idx1feature_id
project_feature_idx2project_id

Constraints

Type Fields
NOT NULLproject_feature_id
NOT NULLfeature_id
NOT NULLproject_id
UNIQUEfeature_id, project_id
FOREIGN KEYfeature_id
FOREIGN KEYproject_id

project_stock

Top
Comments:

================================================
TABLE: project_stock
================================================
This table is intended associate records in the stock table with a project.
Field Name Data Type Size Default Value Other Foreign Key
project_stock_id integer 20 PRIMARY KEY, NOT NULL
stock_id integer 20 UNIQUE, NOT NULL stock.stock_id
project_id integer 20 UNIQUE, NOT NULL project.project_id

Indices

Name Fields
project_stock_idx1stock_id
project_stock_idx2project_id

Constraints

Type Fields
NOT NULLproject_stock_id
NOT NULLstock_id
NOT NULLproject_id
UNIQUEstock_id, project_id
FOREIGN KEYstock_id
FOREIGN KEYproject_id

mageml

Top
Comments:

$Id: mage.sql,v 1.3 2008-03-19 18:32:51 scottcain Exp $
==========================================
Chado mage module
=================================================================
Dependencies:
:import feature from sequence
:import cvterm from cv
:import pub from pub
:import organism from organism
:import contact from contact
:import dbxref from db
:import tableinfo from general
:import project from project
:import analysis from companalysis
=================================================================
================================================
TABLE: mageml
================================================
This table is for storing extra bits of MAGEml in a denormalized form. More normalization would require many more tables.
Field Name Data Type Size Default Value Other Foreign Key
mageml_id integer 20 PRIMARY KEY, NOT NULL
mage_package text 64000 NOT NULL
mage_ml text 64000 NOT NULL

Constraints

Type Fields
NOT NULLmageml_id
NOT NULLmage_package
NOT NULLmage_ml

magedocumentation

Top
Comments:

================================================
TABLE: magedocumentation
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
magedocumentation_id integer 20 PRIMARY KEY, NOT NULL
mageml_id integer 20 NOT NULL mageml.mageml_id
tableinfo_id integer 20 NOT NULL tableinfo.tableinfo_id
row_id integer 10 NOT NULL
mageidentifier text 64000 NOT NULL

Indices

Name Fields
magedocumentation_idx1mageml_id
magedocumentation_idx2tableinfo_id
magedocumentation_idx3row_id

Constraints

Type Fields
NOT NULLmagedocumentation_id
NOT NULLmageml_id
FOREIGN KEYmageml_id
NOT NULLtableinfo_id
FOREIGN KEYtableinfo_id
NOT NULLrow_id
NOT NULLmageidentifier

protocol

Top
Comments:

================================================
TABLE: protocol
================================================
Procedural notes on how data was prepared and processed.
Field Name Data Type Size Default Value Other Foreign Key
protocol_id integer 20 PRIMARY KEY, NOT NULL
type_id integer 20 NOT NULL cvterm.cvterm_id
pub_id integer 20 NULL pub.pub_id
dbxref_id integer 20 NULL dbxref.dbxref_id
name text 64000 UNIQUE, NOT NULL
uri text 64000 NULL
protocoldescription text 64000 NULL
hardwaredescription text 64000 NULL
softwaredescription text 64000 NULL

Indices

Name Fields
protocol_idx1type_id
protocol_idx2pub_id
protocol_idx3dbxref_id

Constraints

Type Fields
NOT NULLprotocol_id
NOT NULLtype_id
FOREIGN KEYtype_id
FOREIGN KEYpub_id
FOREIGN KEYdbxref_id
NOT NULLname
UNIQUEname

protocolparam

Top
Comments:

================================================
TABLE: protocolparam
================================================
Parameters related to a protocol. For example, if the protocol is a soak, this might include attributes of bath temperature and duration.
Field Name Data Type Size Default Value Other Foreign Key
protocolparam_id integer 20 PRIMARY KEY, NOT NULL
protocol_id integer 20 NOT NULL protocol.protocol_id
name text 64000 NOT NULL
datatype_id integer 20 NULL cvterm.cvterm_id
unittype_id integer 20 NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 NOT NULL

Indices

Name Fields
protocolparam_idx1protocol_id
protocolparam_idx2datatype_id
protocolparam_idx3unittype_id

Constraints

Type Fields
NOT NULLprotocolparam_id
NOT NULLprotocol_id
FOREIGN KEYprotocol_id
NOT NULLname
FOREIGN KEYdatatype_id
FOREIGN KEYunittype_id
NOT NULLrank

channel

Top
Comments:

================================================
TABLE: channel
================================================
Different array platforms can record signals from one or more channels (cDNA arrays typically use two CCD, but Affymetrix uses only one).
Field Name Data Type Size Default Value Other Foreign Key
channel_id integer 20 PRIMARY KEY, NOT NULL
name text 64000 UNIQUE, NOT NULL
definition text 64000 NOT NULL

Constraints

Type Fields
NOT NULLchannel_id
NOT NULLname
NOT NULLdefinition
UNIQUEname

arraydesign

Top
Comments:

================================================
TABLE: arraydesign
================================================
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).
Field Name Data Type Size Default Value Other Foreign Key
arraydesign_id integer 20 PRIMARY KEY, NOT NULL
manufacturer_id integer 20 NOT NULL contact.contact_id
platformtype_id integer 20 NOT NULL cvterm.cvterm_id
substratetype_id integer 20 NULL cvterm.cvterm_id
protocol_id integer 20 NULL protocol.protocol_id
dbxref_id integer 20 NULL dbxref.dbxref_id
name text 64000 UNIQUE, NOT NULL
version text 64000 NULL
description text 64000 NULL
array_dimensions text 64000 NULL
element_dimensions text 64000 NULL
num_of_elements integer 10 NULL
num_array_columns integer 10 NULL
num_array_rows integer 10 NULL
num_grid_columns integer 10 NULL
num_grid_rows integer 10 NULL
num_sub_columns integer 10 NULL
num_sub_rows integer 10 NULL

Indices

Name Fields
arraydesign_idx1manufacturer_id
arraydesign_idx2platformtype_id
arraydesign_idx3substratetype_id
arraydesign_idx4protocol_id
arraydesign_idx5dbxref_id

Constraints

Type Fields
NOT NULLarraydesign_id
NOT NULLmanufacturer_id
FOREIGN KEYmanufacturer_id
NOT NULLplatformtype_id
FOREIGN KEYplatformtype_id
FOREIGN KEYsubstratetype_id
FOREIGN KEYprotocol_id
FOREIGN KEYdbxref_id
NOT NULLname
UNIQUEname

arraydesignprop

Top
Comments:

================================================
TABLE: arraydesignprop
================================================
Extra array design properties that are not accounted for in arraydesign.
Field Name Data Type Size Default Value Other Foreign Key
arraydesignprop_id integer 20 PRIMARY KEY, NOT NULL
arraydesign_id integer 20 UNIQUE, NOT NULL arraydesign.arraydesign_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
arraydesignprop_idx1arraydesign_id
arraydesignprop_idx2type_id

Constraints

Type Fields
NOT NULLarraydesignprop_id
NOT NULLarraydesign_id
FOREIGN KEYarraydesign_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEarraydesign_id, type_id, rank

assay

Top
Comments:

================================================
TABLE: assay
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
assay_id integer 20 PRIMARY KEY, NOT NULL
arraydesign_id integer 20 NOT NULL arraydesign.arraydesign_id
protocol_id integer 20 NULL protocol.protocol_id
assaydate timestamp 0 current_timestamp
arrayidentifier text 64000 NULL
arraybatchidentifier text 64000 NULL
operator_id integer 20 NOT NULL contact.contact_id
dbxref_id integer 20 NULL dbxref.dbxref_id
name text 64000 NULL UNIQUE
description text 64000 NULL

Indices

Name Fields
assay_idx1arraydesign_id
assay_idx2protocol_id
assay_idx3operator_id
assay_idx4dbxref_id

Constraints

Type Fields
NOT NULLassay_id
NOT NULLarraydesign_id
FOREIGN KEYarraydesign_id
FOREIGN KEYprotocol_id
NOT NULLoperator_id
FOREIGN KEYoperator_id
FOREIGN KEYdbxref_id
UNIQUEname

assayprop

Top
Comments:

================================================
TABLE: assayprop
================================================
Extra assay properties that are not accounted for in assay.
Field Name Data Type Size Default Value Other Foreign Key
assayprop_id integer 20 PRIMARY KEY, NOT NULL
assay_id integer 20 UNIQUE, NOT NULL assay.assay_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
assayprop_idx1assay_id
assayprop_idx2type_id

Constraints

Type Fields
NOT NULLassayprop_id
NOT NULLassay_id
FOREIGN KEYassay_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEassay_id, type_id, rank

assay_project

Top
Comments:

================================================
TABLE: assay_project
================================================
Link assays to projects.
Field Name Data Type Size Default Value Other Foreign Key
assay_project_id integer 20 PRIMARY KEY, NOT NULL
assay_id integer 20 UNIQUE, NOT NULL assay.assay_id
project_id integer 20 UNIQUE, NOT NULL project.project_id

Indices

Name Fields
assay_project_idx1assay_id
assay_project_idx2project_id

Constraints

Type Fields
NOT NULLassay_project_id
NOT NULLassay_id
FOREIGN KEYassay_id
NOT NULLproject_id
FOREIGN KEYproject_id
UNIQUEassay_id, project_id

biomaterial

Top
Comments:

================================================
TABLE: biomaterial
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
biomaterial_id integer 20 PRIMARY KEY, NOT NULL
taxon_id integer 20 NULL organism.organism_id
biosourceprovider_id integer 20 NULL contact.contact_id
dbxref_id integer 20 NULL dbxref.dbxref_id
name text 64000 NULL UNIQUE
description text 64000 NULL

Indices

Name Fields
biomaterial_idx1taxon_id
biomaterial_idx2biosourceprovider_id
biomaterial_idx3dbxref_id

Constraints

Type Fields
NOT NULLbiomaterial_id
FOREIGN KEYtaxon_id
FOREIGN KEYbiosourceprovider_id
FOREIGN KEYdbxref_id
UNIQUEname

biomaterial_relationship

Top
Comments:

================================================
TABLE: biomaterial_relationship
================================================
Relate biomaterials to one another. This is a way to track a series of treatments or material splits/merges, for instance.
Field Name Data Type Size Default Value Other Foreign Key
biomaterial_relationship_id integer 20 PRIMARY KEY, NOT NULL
subject_id integer 20 UNIQUE, NOT NULL biomaterial.biomaterial_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
object_id integer 20 UNIQUE, NOT NULL biomaterial.biomaterial_id

Indices

Name Fields
biomaterial_relationship_idx1subject_id
biomaterial_relationship_idx2object_id
biomaterial_relationship_idx3type_id

Constraints

Type Fields
NOT NULLbiomaterial_relationship_id
NOT NULLsubject_id
FOREIGN KEYsubject_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLobject_id
FOREIGN KEYobject_id
UNIQUEsubject_id, object_id, type_id

biomaterialprop

Top
Comments:

================================================
TABLE: biomaterialprop
================================================
Extra biomaterial properties that are not accounted for in biomaterial.
Field Name Data Type Size Default Value Other Foreign Key
biomaterialprop_id integer 20 PRIMARY KEY, NOT NULL
biomaterial_id integer 20 UNIQUE, NOT NULL biomaterial.biomaterial_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
biomaterialprop_idx1biomaterial_id
biomaterialprop_idx2type_id

Constraints

Type Fields
NOT NULLbiomaterialprop_id
NOT NULLbiomaterial_id
FOREIGN KEYbiomaterial_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEbiomaterial_id, type_id, rank

biomaterial_dbxref

Top
Comments:

================================================
TABLE: biomaterial_dbxref
================================================
Field Name Data Type Size Default Value Other Foreign Key
biomaterial_dbxref_id integer 20 PRIMARY KEY, NOT NULL
biomaterial_id integer 20 UNIQUE, NOT NULL biomaterial.biomaterial_id
dbxref_id integer 20 UNIQUE, NOT NULL dbxref.dbxref_id

Indices

Name Fields
biomaterial_dbxref_idx1biomaterial_id
biomaterial_dbxref_idx2dbxref_id

Constraints

Type Fields
NOT NULLbiomaterial_dbxref_id
NOT NULLbiomaterial_id
FOREIGN KEYbiomaterial_id
NOT NULLdbxref_id
FOREIGN KEYdbxref_id
UNIQUEbiomaterial_id, dbxref_id

treatment

Top
Comments:

================================================
TABLE: treatment
================================================
A biomaterial may undergo multiple treatments. Examples of treatments: apoxia, fluorophore and biotin labeling.
Field Name Data Type Size Default Value Other Foreign Key
treatment_id integer 20 PRIMARY KEY, NOT NULL
rank integer 10 0 NOT NULL
biomaterial_id integer 20 NOT NULL biomaterial.biomaterial_id
type_id integer 20 NOT NULL cvterm.cvterm_id
protocol_id integer 20 NULL protocol.protocol_id
name text 64000 NULL

Indices

Name Fields
treatment_idx1biomaterial_id
treatment_idx2type_id
treatment_idx3protocol_id

Constraints

Type Fields
NOT NULLtreatment_id
NOT NULLrank
NOT NULLbiomaterial_id
FOREIGN KEYbiomaterial_id
NOT NULLtype_id
FOREIGN KEYtype_id
FOREIGN KEYprotocol_id

biomaterial_treatment

Top
Comments:

================================================
TABLE: biomaterial_treatment
================================================
Link biomaterials to treatments. Treatments have an order of operations (rank), and associated measurements (unittype_id, value).
Field Name Data Type Size Default Value Other Foreign Key
biomaterial_treatment_id integer 20 PRIMARY KEY, NOT NULL
biomaterial_id integer 20 UNIQUE, NOT NULL biomaterial.biomaterial_id
treatment_id integer 20 UNIQUE, NOT NULL treatment.treatment_id
unittype_id integer 20 NULL cvterm.cvterm_id
value float 15 NULL
rank integer 10 0 NOT NULL

Indices

Name Fields
biomaterial_treatment_idx1biomaterial_id
biomaterial_treatment_idx2treatment_id
biomaterial_treatment_idx3unittype_id

Constraints

Type Fields
NOT NULLbiomaterial_treatment_id
NOT NULLbiomaterial_id
FOREIGN KEYbiomaterial_id
NOT NULLtreatment_id
FOREIGN KEYtreatment_id
FOREIGN KEYunittype_id
NOT NULLrank
UNIQUEbiomaterial_id, treatment_id

assay_biomaterial

Top
Comments:

================================================
TABLE: assay_biomaterial
================================================
A biomaterial can be hybridized many times (technical replicates), or combined with other biomaterials in a single hybridization (for two-channel arrays).
Field Name Data Type Size Default Value Other Foreign Key
assay_biomaterial_id integer 20 PRIMARY KEY, NOT NULL
assay_id integer 20 UNIQUE, NOT NULL assay.assay_id
biomaterial_id integer 20 UNIQUE, NOT NULL biomaterial.biomaterial_id
channel_id integer 20 NULL UNIQUE channel.channel_id
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
assay_biomaterial_idx1assay_id
assay_biomaterial_idx2biomaterial_id
assay_biomaterial_idx3channel_id

Constraints

Type Fields
NOT NULLassay_biomaterial_id
NOT NULLassay_id
FOREIGN KEYassay_id
NOT NULLbiomaterial_id
FOREIGN KEYbiomaterial_id
FOREIGN KEYchannel_id
NOT NULLrank
UNIQUEassay_id, biomaterial_id, channel_id, rank

acquisition

Top
Comments:

================================================
TABLE: acquisition
================================================
This represents the scanning of hybridized material. The output of this process is typically a digital image of an array.
Field Name Data Type Size Default Value Other Foreign Key
acquisition_id integer 20 PRIMARY KEY, NOT NULL
assay_id integer 20 NOT NULL assay.assay_id
protocol_id integer 20 NULL protocol.protocol_id
channel_id integer 20 NULL channel.channel_id
acquisitiondate timestamp 0 current_timestamp
name text 64000 NULL UNIQUE
uri text 64000 NULL

Indices

Name Fields
acquisition_idx1assay_id
acquisition_idx2protocol_id
acquisition_idx3channel_id

Constraints

Type Fields
NOT NULLacquisition_id
NOT NULLassay_id
FOREIGN KEYassay_id
FOREIGN KEYprotocol_id
FOREIGN KEYchannel_id
UNIQUEname

acquisitionprop

Top
Comments:

================================================
TABLE: acquisitionprop
================================================
Parameters associated with image acquisition.
Field Name Data Type Size Default Value Other Foreign Key
acquisitionprop_id integer 20 PRIMARY KEY, NOT NULL
acquisition_id integer 20 UNIQUE, NOT NULL acquisition.acquisition_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
acquisitionprop_idx1acquisition_id
acquisitionprop_idx2type_id

Constraints

Type Fields
NOT NULLacquisitionprop_id
NOT NULLacquisition_id
FOREIGN KEYacquisition_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEacquisition_id, type_id, rank

acquisition_relationship

Top
Comments:

================================================
TABLE: acquisition_relationship
================================================
Multiple monochrome images may be merged to form a multi-color image. Red-green images of 2-channel hybridizations are an example of this.
Field Name Data Type Size Default Value Other Foreign Key
acquisition_relationship_id integer 20 PRIMARY KEY, NOT NULL
subject_id integer 20 UNIQUE, NOT NULL acquisition.acquisition_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
object_id integer 20 UNIQUE, NOT NULL acquisition.acquisition_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
acquisition_relationship_idx1subject_id
acquisition_relationship_idx2type_id
acquisition_relationship_idx3object_id

Constraints

Type Fields
NOT NULLacquisition_relationship_id
NOT NULLsubject_id
FOREIGN KEYsubject_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLobject_id
FOREIGN KEYobject_id
NOT NULLrank
UNIQUEsubject_id, object_id, type_id, rank

quantification

Top
Comments:

================================================
TABLE: quantification
================================================
Quantification is the transformation of an image acquisition to numeric data. This typically involves statistical procedures.
Field Name Data Type Size Default Value Other Foreign Key
quantification_id integer 20 PRIMARY KEY, NOT NULL
acquisition_id integer 20 NOT NULL acquisition.acquisition_id
operator_id integer 20 NULL contact.contact_id
protocol_id integer 20 NULL protocol.protocol_id
analysis_id integer 20 UNIQUE, NOT NULL analysis.analysis_id
quantificationdate timestamp 0 current_timestamp
name text 64000 NULL UNIQUE
uri text 64000 NULL

Indices

Name Fields
quantification_idx1acquisition_id
quantification_idx2operator_id
quantification_idx3protocol_id
quantification_idx4analysis_id

Constraints

Type Fields
NOT NULLquantification_id
NOT NULLacquisition_id
FOREIGN KEYacquisition_id
FOREIGN KEYoperator_id
FOREIGN KEYprotocol_id
NOT NULLanalysis_id
FOREIGN KEYanalysis_id
UNIQUEname, analysis_id

quantificationprop

Top
Comments:

================================================
TABLE: quantificationprop
================================================
Extra quantification properties that are not accounted for in quantification.
Field Name Data Type Size Default Value Other Foreign Key
quantificationprop_id integer 20 PRIMARY KEY, NOT NULL
quantification_id integer 20 UNIQUE, NOT NULL quantification.quantification_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
quantificationprop_idx1quantification_id
quantificationprop_idx2type_id

Constraints

Type Fields
NOT NULLquantificationprop_id
NOT NULLquantification_id
FOREIGN KEYquantification_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEquantification_id, type_id, rank

quantification_relationship

Top
Comments:

================================================
TABLE: quantification_relationship
================================================
There may be multiple rounds of quantification, this allows us to keep an audit trail of what values went where.
Field Name Data Type Size Default Value Other Foreign Key
quantification_relationship_id integer 20 PRIMARY KEY, NOT NULL
subject_id integer 20 UNIQUE, NOT NULL quantification.quantification_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
object_id integer 20 UNIQUE, NOT NULL quantification.quantification_id

Indices

Name Fields
quantification_relationship_idx1subject_id
quantification_relationship_idx2type_id
quantification_relationship_idx3object_id

Constraints

Type Fields
NOT NULLquantification_relationship_id
NOT NULLsubject_id
FOREIGN KEYsubject_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLobject_id
FOREIGN KEYobject_id
UNIQUEsubject_id, object_id, type_id

control

Top
Comments:

================================================
TABLE: control
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
control_id integer 20 PRIMARY KEY, NOT NULL
type_id integer 20 NOT NULL cvterm.cvterm_id
assay_id integer 20 NOT NULL assay.assay_id
tableinfo_id integer 20 NOT NULL tableinfo.tableinfo_id
row_id integer 10 NOT NULL
name text 64000 NULL
value text 64000 NULL
rank integer 10 0 NOT NULL

Indices

Name Fields
control_idx1type_id
control_idx2assay_id
control_idx3tableinfo_id
control_idx4row_id

Constraints

Type Fields
NOT NULLcontrol_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLassay_id
FOREIGN KEYassay_id
NOT NULLtableinfo_id
FOREIGN KEYtableinfo_id
NOT NULLrow_id
NOT NULLrank

element

Top
Comments:

================================================
TABLE: element
================================================
Represents a feature of the array. This is typically a region of the array coated or bound to DNA.
Field Name Data Type Size Default Value Other Foreign Key
element_id integer 20 PRIMARY KEY, NOT NULL
feature_id integer 20 NULL UNIQUE feature.feature_id
arraydesign_id integer 20 UNIQUE, NOT NULL arraydesign.arraydesign_id
type_id integer 20 NULL cvterm.cvterm_id
dbxref_id integer 20 NULL dbxref.dbxref_id

Indices

Name Fields
element_idx1feature_id
element_idx2arraydesign_id
element_idx3type_id
element_idx4dbxref_id

Constraints

Type Fields
NOT NULLelement_id
FOREIGN KEYfeature_id
NOT NULLarraydesign_id
FOREIGN KEYarraydesign_id
FOREIGN KEYtype_id
FOREIGN KEYdbxref_id
UNIQUEfeature_id, arraydesign_id

elementresult

Top
Comments:

================================================
TABLE: element_result
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
elementresult_id integer 20 PRIMARY KEY, NOT NULL
element_id integer 20 UNIQUE, NOT NULL element.element_id
quantification_id integer 20 UNIQUE, NOT NULL quantification.quantification_id
signal float 20 NOT NULL

Indices

Name Fields
elementresult_idx1element_id
elementresult_idx2quantification_id
elementresult_idx3signal

Constraints

Type Fields
NOT NULLelementresult_id
NOT NULLelement_id
FOREIGN KEYelement_id
NOT NULLquantification_id
FOREIGN KEYquantification_id
NOT NULLsignal
UNIQUEelement_id, quantification_id

element_relationship

Top
Comments:

================================================
TABLE: element_relationship
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
element_relationship_id integer 20 PRIMARY KEY, NOT NULL
subject_id integer 20 UNIQUE, NOT NULL element.element_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
object_id integer 20 UNIQUE, NOT NULL element.element_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
element_relationship_idx1subject_id
element_relationship_idx2type_id
element_relationship_idx3object_id
element_relationship_idx4value

Constraints

Type Fields
NOT NULLelement_relationship_id
NOT NULLsubject_id
FOREIGN KEYsubject_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLobject_id
FOREIGN KEYobject_id
NOT NULLrank
UNIQUEsubject_id, object_id, type_id, rank

elementresult_relationship

Top
Comments:

================================================
TABLE: elementresult_relationship
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
elementresult_relationship_id integer 20 PRIMARY KEY, NOT NULL
subject_id integer 20 UNIQUE, NOT NULL elementresult.elementresult_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
object_id integer 20 UNIQUE, NOT NULL elementresult.elementresult_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
elementresult_relationship_idx1subject_id
elementresult_relationship_idx2type_id
elementresult_relationship_idx3object_id
elementresult_relationship_idx4value

Constraints

Type Fields
NOT NULLelementresult_relationship_id
NOT NULLsubject_id
FOREIGN KEYsubject_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLobject_id
FOREIGN KEYobject_id
NOT NULLrank
UNIQUEsubject_id, object_id, type_id, rank

study

Top
Comments:

================================================
TABLE: study
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
study_id integer 20 PRIMARY KEY, NOT NULL
contact_id integer 20 NOT NULL contact.contact_id
pub_id integer 20 NULL pub.pub_id
dbxref_id integer 20 NULL dbxref.dbxref_id
name text 64000 UNIQUE, NOT NULL
description text 64000 NULL

Indices

Name Fields
study_idx1contact_id
study_idx2pub_id
study_idx3dbxref_id

Constraints

Type Fields
NOT NULLstudy_id
NOT NULLcontact_id
FOREIGN KEYcontact_id
FOREIGN KEYpub_id
FOREIGN KEYdbxref_id
NOT NULLname
UNIQUEname

study_assay

Top
Comments:

================================================
TABLE: study_assay
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
study_assay_id integer 20 PRIMARY KEY, NOT NULL
study_id integer 20 UNIQUE, NOT NULL study.study_id
assay_id integer 20 UNIQUE, NOT NULL assay.assay_id

Indices

Name Fields
study_assay_idx1study_id
study_assay_idx2assay_id

Constraints

Type Fields
NOT NULLstudy_assay_id
NOT NULLstudy_id
FOREIGN KEYstudy_id
NOT NULLassay_id
FOREIGN KEYassay_id
UNIQUEstudy_id, assay_id

studydesign

Top
Comments:

================================================
TABLE: studydesign
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
studydesign_id integer 20 PRIMARY KEY, NOT NULL
study_id integer 20 NOT NULL study.study_id
description text 64000 NULL

Indices

Name Fields
studydesign_idx1study_id

Constraints

Type Fields
NOT NULLstudydesign_id
NOT NULLstudy_id
FOREIGN KEYstudy_id

studydesignprop

Top
Comments:

================================================
TABLE: studydesignprop
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
studydesignprop_id integer 20 PRIMARY KEY, NOT NULL
studydesign_id integer 20 UNIQUE, NOT NULL studydesign.studydesign_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
studydesignprop_idx1studydesign_id
studydesignprop_idx2type_id

Constraints

Type Fields
NOT NULLstudydesignprop_id
NOT NULLstudydesign_id
FOREIGN KEYstudydesign_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEstudydesign_id, type_id, rank

studyfactor

Top
Comments:

================================================
TABLE: studyfactor
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
studyfactor_id integer 20 PRIMARY KEY, NOT NULL
studydesign_id integer 20 NOT NULL studydesign.studydesign_id
type_id integer 20 NULL cvterm.cvterm_id
name text 64000 NOT NULL
description text 64000 NULL

Indices

Name Fields
studyfactor_idx1studydesign_id
studyfactor_idx2type_id

Constraints

Type Fields
NOT NULLstudyfactor_id
NOT NULLstudydesign_id
FOREIGN KEYstudydesign_id
FOREIGN KEYtype_id
NOT NULLname

studyfactorvalue

Top
Comments:

================================================
TABLE: studyfactorvalue
================================================
NULL
Field Name Data Type Size Default Value Other Foreign Key
studyfactorvalue_id integer 20 PRIMARY KEY, NOT NULL
studyfactor_id integer 20 NOT NULL studyfactor.studyfactor_id
assay_id integer 20 NOT NULL assay.assay_id
factorvalue text 64000 NULL
name text 64000 NULL
rank integer 10 0 NOT NULL

Indices

Name Fields
studyfactorvalue_idx1studyfactor_id
studyfactorvalue_idx2assay_id

Constraints

Type Fields
NOT NULLstudyfactorvalue_id
NOT NULLstudyfactor_id
FOREIGN KEYstudyfactor_id
NOT NULLassay_id
FOREIGN KEYassay_id
NOT NULLrank

studyprop

Top
Comments:

studyprop and studyprop_feature added for Kara Dolinski's group
Here is her description of it:
Both of the tables are used for our YFGdb project
(http://yfgdb.princeton.edu/), which uses chado.
Here is how we use those tables, using the following example:
http://yfgdb.princeton.edu/cgi-bin/display.cgi?db=pmid&id=15575969
The above data set is represented as a row in the STUDY table. We have
lots of attributes that we want to store about each STUDY (status, etc)
and in the official schema, the only prop table we could use was the
STUDYDESIGN_PROP table. This forced us to go through the STUDYDESIGN
table when we often have no real data to store in that table (small
percent of our collection use MAGE-ML unfortunately, and even fewer
provide all the data in the MAGE model, of which STUDYDESIGN is a vestige).
So, we created a STUDYPROP table. I'd think this table would be
generally useful to people storing various types of data sets via the
STUDY table.
The other new table is STUDYPROP_FEATURE. This basically allows us to
group features together per study. For example, we can store microarray
clustering results by saying that the STUDYPROP type is 'cluster' (via
type_id -> CVTERM of course), the value is 'cluster id 123', and then
that cluster would be associated with all the features that are in that
cluster via STUDYPROP_FEATURE. Adding type_id to STUDYPROP_FEATURE is
fine by us!
studyprop
Field Name Data Type Size Default Value Other Foreign Key
studyprop_id integer 20 PRIMARY KEY, NOT NULL
study_id integer 20 UNIQUE, NOT NULL study.study_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
studyprop_idx1study_id
studyprop_idx2type_id

Constraints

Type Fields
NOT NULLstudyprop_id
NOT NULLstudy_id
FOREIGN KEYstudy_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEstudy_id, type_id, rank

studyprop_feature

Top
Comments:

studyprop_feature
Field Name Data Type Size Default Value Other Foreign Key
studyprop_feature_id integer 20 PRIMARY KEY, NOT NULL
studyprop_id integer 20 UNIQUE, NOT NULL studyprop.studyprop_id
feature_id integer 20 UNIQUE, NOT NULL feature.feature_id
type_id integer 20 cvterm.cvterm_id

Indices

Name Fields
studyprop_feature_idx1studyprop_id
studyprop_feature_idx2feature_id

Constraints

Type Fields
NOT NULLstudyprop_feature_id
NOT NULLstudyprop_id
FOREIGN KEYstudyprop_id
NOT NULLfeature_id
FOREIGN KEYfeature_id
FOREIGN KEYtype_id
UNIQUEstudyprop_id, feature_id

cell_line

Top
Comments:

==========================================
Chado cell line module
============
DEPENDENCIES
============
:import feature from sequence
:import synonym from sequence
:import library from library
:import cvterm from cv
:import dbxref from db
:import pub from pub
:import organism from organism
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
================================================
TABLE: cell_line
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_id integer 20 PRIMARY KEY, NOT NULL
name varchar 255 NULL
uniquename varchar 255 UNIQUE, NOT NULL
organism_id integer 20 UNIQUE, NOT NULL organism.organism_id
timeaccessioned timestamp 0 current_timestamp NOT NULL
timelastmodified timestamp 0 current_timestamp NOT NULL

Constraints

Type Fields
NOT NULLcell_line_id
NOT NULLuniquename
NOT NULLorganism_id
FOREIGN KEYorganism_id
NOT NULLtimeaccessioned
NOT NULLtimelastmodified
UNIQUEuniquename, organism_id

cell_line_relationship

Top
Comments:

================================================
TABLE: cell_line_relationship
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_relationship_id integer 20 PRIMARY KEY, NOT NULL
subject_id integer 20 UNIQUE, NOT NULL cell_line.cell_line_id
object_id integer 20 UNIQUE, NOT NULL cell_line.cell_line_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id

Constraints

Type Fields
NOT NULLcell_line_relationship_id
NOT NULLsubject_id
FOREIGN KEYsubject_id
NOT NULLobject_id
FOREIGN KEYobject_id
NOT NULLtype_id
FOREIGN KEYtype_id
UNIQUEsubject_id, object_id, type_id

cell_line_synonym

Top
Comments:

================================================
TABLE: cell_line_synonym
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_synonym_id integer 20 PRIMARY KEY, NOT NULL
cell_line_id integer 20 UNIQUE, NOT NULL cell_line.cell_line_id
synonym_id integer 20 UNIQUE, NOT NULL synonym.synonym_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id
is_current boolean 0 false NOT NULL
is_internal boolean 0 false NOT NULL

Constraints

Type Fields
NOT NULLcell_line_synonym_id
NOT NULLcell_line_id
FOREIGN KEYcell_line_id
NOT NULLsynonym_id
FOREIGN KEYsynonym_id
NOT NULLpub_id
FOREIGN KEYpub_id
NOT NULLis_current
NOT NULLis_internal
UNIQUEsynonym_id, cell_line_id, pub_id

cell_line_cvterm

Top
Comments:

================================================
TABLE: cell_line_cvterm
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_cvterm_id integer 20 PRIMARY KEY, NOT NULL
cell_line_id integer 20 UNIQUE, NOT NULL cell_line.cell_line_id
cvterm_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id
rank integer 10 0 UNIQUE, NOT NULL

Constraints

Type Fields
NOT NULLcell_line_cvterm_id
NOT NULLcell_line_id
FOREIGN KEYcell_line_id
NOT NULLcvterm_id
FOREIGN KEYcvterm_id
NOT NULLpub_id
FOREIGN KEYpub_id
NOT NULLrank
UNIQUEcell_line_id, cvterm_id, pub_id, rank

cell_line_dbxref

Top
Comments:

================================================
TABLE: cell_line_dbxref
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_dbxref_id integer 20 PRIMARY KEY, NOT NULL
cell_line_id integer 20 UNIQUE, NOT NULL cell_line.cell_line_id
dbxref_id integer 20 UNIQUE, NOT NULL dbxref.dbxref_id
is_current boolean 0 true NOT NULL

Constraints

Type Fields
NOT NULLcell_line_dbxref_id
NOT NULLcell_line_id
FOREIGN KEYcell_line_id
NOT NULLdbxref_id
FOREIGN KEYdbxref_id
NOT NULLis_current
UNIQUEcell_line_id, dbxref_id

cell_lineprop

Top
Comments:

================================================
TABLE: cell_lineprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_lineprop_id integer 20 PRIMARY KEY, NOT NULL
cell_line_id integer 20 UNIQUE, NOT NULL cell_line.cell_line_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Constraints

Type Fields
NOT NULLcell_lineprop_id
NOT NULLcell_line_id
FOREIGN KEYcell_line_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEcell_line_id, type_id, rank

cell_lineprop_pub

Top
Comments:

================================================
TABLE: cell_lineprop_pub
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_lineprop_pub_id integer 20 PRIMARY KEY, NOT NULL
cell_lineprop_id integer 20 UNIQUE, NOT NULL cell_lineprop.cell_lineprop_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Constraints

Type Fields
NOT NULLcell_lineprop_pub_id
NOT NULLcell_lineprop_id
FOREIGN KEYcell_lineprop_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEcell_lineprop_id, pub_id

cell_line_feature

Top
Comments:

================================================
TABLE: cell_line_feature
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_feature_id integer 20 PRIMARY KEY, NOT NULL
cell_line_id integer 20 UNIQUE, NOT NULL cell_line.cell_line_id
feature_id integer 20 UNIQUE, NOT NULL feature.feature_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Constraints

Type Fields
NOT NULLcell_line_feature_id
NOT NULLcell_line_id
FOREIGN KEYcell_line_id
NOT NULLfeature_id
FOREIGN KEYfeature_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEcell_line_id, feature_id, pub_id

cell_line_cvtermprop

Top
Comments:

================================================
TABLE: cell_line_cvtermprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_cvtermprop_id integer 20 PRIMARY KEY, NOT NULL
cell_line_cvterm_id integer 20 UNIQUE, NOT NULL cell_line_cvterm.cell_line_cvterm_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Constraints

Type Fields
NOT NULLcell_line_cvtermprop_id
NOT NULLcell_line_cvterm_id
FOREIGN KEYcell_line_cvterm_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEcell_line_cvterm_id, type_id, rank

cell_line_pub

Top
Comments:

================================================
TABLE: cell_line_pub
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_pub_id integer 20 PRIMARY KEY, NOT NULL
cell_line_id integer 20 UNIQUE, NOT NULL cell_line.cell_line_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Constraints

Type Fields
NOT NULLcell_line_pub_id
NOT NULLcell_line_id
FOREIGN KEYcell_line_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEcell_line_id, pub_id

cell_line_library

Top
Comments:

================================================
TABLE: cell_line_library
================================================
Field Name Data Type Size Default Value Other Foreign Key
cell_line_library_id integer 20 PRIMARY KEY, NOT NULL
cell_line_id integer 20 UNIQUE, NOT NULL cell_line.cell_line_id
library_id integer 20 UNIQUE, NOT NULL library.library_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Constraints

Type Fields
NOT NULLcell_line_library_id
NOT NULLcell_line_id
FOREIGN KEYcell_line_id
NOT NULLlibrary_id
FOREIGN KEYlibrary_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEcell_line_id, library_id, pub_id

nd_geolocation

Top
Comments:

=================================================================
Dependencies:
:import feature from sequence
:import cvterm from cv
:import pub from pub
:import phenotype from phenotype
:import organism from organism
:import genotype from genetic
:import contact from contact
:import project from project
:import stock from stock
:import synonym
=================================================================
this probably needs some work, depending on how cross-database we
want to be. In Postgres, at least, there are much better ways to
represent geo information.
================================================
TABLE: nd_geolocation
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
nd_geolocation_id integer 20 PRIMARY KEY, NOT NULL
description text 64000 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 10 The decimal latitude coordinate of the georeference, using positive and negative sign to indicate N and S, respectively.
longitude real 10 The decimal longitude coordinate of the georeference, using positive and negative sign to indicate E and W, respectively.
geodetic_datum varchar 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 10 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.

Indices

Name Fields
nd_geolocation_idx1latitude
nd_geolocation_idx2longitude
nd_geolocation_idx3altitude

Constraints

Type Fields
NOT NULLnd_geolocation_id

nd_experiment

Top
Comments:

================================================
TABLE: nd_experiment
================================================
This is the core table for the natural diversity module, representing each individual assay that is undertaken (this is usually *not* an entire experiment). Each nd_experiment should give rise to a single genotype or phenotype and be described via 1 (or more) protocols. Collections of assays that relate to each other should be linked to the same record in the project table.
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_id integer 20 PRIMARY KEY, NOT NULL
nd_geolocation_id integer 20 NOT NULL nd_geolocation.nd_geolocation_id
type_id integer 20 NOT NULL cvterm.cvterm_id

Indices

Name Fields
nd_experiment_idx1nd_geolocation_id
nd_experiment_idx2type_id

Constraints

Type Fields
NOT NULLnd_experiment_id
NOT NULLnd_geolocation_id
FOREIGN KEYnd_geolocation_id
NOT NULLtype_id
FOREIGN KEYtype_id
FOREIGN KEYnd_geolocation_id
FOREIGN KEYtype_id

nd_experiment_project

Top
Comments:

================================================
TABLE: nd_experiment_project
================================================
used to be nd_diversityexperiment_project
then was nd_assay_project
Used to group together related nd_experiment records. All nd_experiments should be linked to at least one project.
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_project_id integer 20 PRIMARY KEY, NOT NULL
project_id integer 20 UNIQUE, NOT NULL project.project_id
nd_experiment_id integer 20 UNIQUE, NOT NULL nd_experiment.nd_experiment_id

Indices

Name Fields
nd_experiment_project_idx1project_id
nd_experiment_project_idx2nd_experiment_id

Constraints

Type Fields
NOT NULLnd_experiment_project_id
NOT NULLproject_id
FOREIGN KEYproject_id
NOT NULLnd_experiment_id
FOREIGN KEYnd_experiment_id
UNIQUEproject_id, nd_experiment_id
FOREIGN KEYproject_id
FOREIGN KEYnd_experiment_id

nd_experimentprop

Top
Comments:

================================================
TABLE: nd_experimentprop
================================================
An nd_experiment 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.
Field Name Data Type Size Default Value Other Foreign Key
nd_experimentprop_id integer 20 PRIMARY KEY, NOT NULL
nd_experiment_id integer 20 UNIQUE, NOT NULL nd_experiment.nd_experiment_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
nd_experimentprop_idx1nd_experiment_id
nd_experimentprop_idx2type_id

Constraints

Type Fields
NOT NULLnd_experimentprop_id
NOT NULLnd_experiment_id
FOREIGN KEYnd_experiment_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEnd_experiment_id, type_id, rank
FOREIGN KEYnd_experiment_id
FOREIGN KEYtype_id

nd_experiment_pub

Top
Comments:

================================================
TABLE: nd_experiment_pub
================================================
Linking nd_experiment(s) to publication(s)
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_pub_id integer 20 PRIMARY KEY, NOT NULL
nd_experiment_id integer 20 UNIQUE, NOT NULL nd_experiment.nd_experiment_id
pub_id integer 20 UNIQUE, NOT NULL pub.pub_id

Indices

Name Fields
nd_experiment_pub_idx1nd_experiment_id
nd_experiment_pub_idx2pub_id

Constraints

Type Fields
NOT NULLnd_experiment_pub_id
NOT NULLnd_experiment_id
FOREIGN KEYnd_experiment_id
NOT NULLpub_id
FOREIGN KEYpub_id
UNIQUEnd_experiment_id, pub_id

nd_geolocationprop

Top
Comments:

================================================
TABLE: nd_geolocationprop
================================================
Property/value associations for geolocations. This table can store the properties such as location and environment
Field Name Data Type Size Default Value Other Foreign Key
nd_geolocationprop_id integer 20 PRIMARY KEY, NOT NULL
nd_geolocation_id integer 20 UNIQUE, NOT NULL nd_geolocation.nd_geolocation_id
type_id integer 20 UNIQUE, NOT NULL, The name of the property as a reference to a controlled vocabulary term. cvterm.cvterm_id
value text 64000 NULL The value of the property.
rank integer 10 0 UNIQUE, NOT NULL, The rank of the property value, if the property has an array of values.

Indices

Name Fields
nd_geolocationprop_idx1nd_geolocation_id
nd_geolocationprop_idx2type_id

Constraints

Type Fields
NOT NULLnd_geolocationprop_id
NOT NULLnd_geolocation_id
FOREIGN KEYnd_geolocation_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEnd_geolocation_id, type_id, rank
FOREIGN KEYnd_geolocation_id
FOREIGN KEYtype_id

nd_protocol

Top
Comments:

================================================
TABLE: nd_protocol
================================================
A protocol can be anything that is done as part of the experiment.
Field Name Data Type Size Default Value Other Foreign Key
nd_protocol_id integer 20 PRIMARY KEY, NOT NULL
name varchar 255 UNIQUE, NOT NULL, The protocol name.
type_id integer 20 NOT NULL cvterm.cvterm_id

Indices

Name Fields
nd_protocol_idx1type_id

Constraints

Type Fields
NOT NULLnd_protocol_id
NOT NULLname
UNIQUEname
NOT NULLtype_id
FOREIGN KEYtype_id
FOREIGN KEYtype_id

nd_reagent

Top
Comments:

================================================
TABLE: nd_reagent
===============================================
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.
Field Name Data Type Size Default Value Other Foreign Key
nd_reagent_id integer 20 PRIMARY KEY, NOT NULL
name varchar 80 NOT NULL, The name of the reagent. The name should be unique for a given type.
type_id integer 20 NOT NULL, The type of the reagent, for example linker oligomer, or forward primer. cvterm.cvterm_id
feature_id integer 20 NULL 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. feature.feature_id

Indices

Name Fields
nd_reagent_idx1type_id
nd_reagent_idx2feature_id

Constraints

Type Fields
NOT NULLnd_reagent_id
NOT NULLname
NOT NULLtype_id
FOREIGN KEYtype_id
FOREIGN KEYfeature_id
FOREIGN KEYtype_id
FOREIGN KEYfeature_id

nd_protocol_reagent

Top
Comments:

================================================
TABLE: nd_protocol_reagent
================================================
Field Name Data Type Size Default Value Other Foreign Key
nd_protocol_reagent_id integer 20 PRIMARY KEY, NOT NULL
nd_protocol_id integer 20 NOT NULL nd_protocol.nd_protocol_id
reagent_id integer 20 NOT NULL nd_reagent.nd_reagent_id
type_id integer 20 NOT NULL cvterm.cvterm_id

Indices

Name Fields
nd_protocol_reagent_idx1nd_protocol_id
nd_protocol_reagent_idx2reagent_id
nd_protocol_reagent_idx3type_id

Constraints

Type Fields
NOT NULLnd_protocol_reagent_id
NOT NULLnd_protocol_id
FOREIGN KEYnd_protocol_id
NOT NULLreagent_id
FOREIGN KEYreagent_id
NOT NULLtype_id
FOREIGN KEYtype_id
FOREIGN KEYnd_protocol_id
FOREIGN KEYreagent_id
FOREIGN KEYtype_id

nd_protocolprop

Top
Comments:

================================================
TABLE: nd_protocolprop
================================================
Property/value associations for protocol.
Field Name Data Type Size Default Value Other Foreign Key
nd_protocolprop_id integer 20 PRIMARY KEY, NOT NULL
nd_protocol_id integer 20 UNIQUE, NOT NULL, The protocol to which the property applies. nd_protocol.nd_protocol_id
type_id integer 20 UNIQUE, NOT NULL, The name of the property as a reference to a controlled vocabulary term. cvterm.cvterm_id
value text 64000 NULL The value of the property.
rank integer 10 0 UNIQUE, NOT NULL, The rank of the property value, if the property has an array of values.

Indices

Name Fields
nd_protocolprop_idx1nd_protocol_id
nd_protocolprop_idx2type_id

Constraints

Type Fields
NOT NULLnd_protocolprop_id
NOT NULLnd_protocol_id
FOREIGN KEYnd_protocol_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEnd_protocol_id, type_id, rank
FOREIGN KEYnd_protocol_id
FOREIGN KEYtype_id

nd_experiment_stock

Top
Comments:

================================================
TABLE: nd_experiment_stock
================================================
Part of a stock or a clone of a stock that is used in an experiment
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_stock_id integer 20 PRIMARY KEY, NOT NULL
nd_experiment_id integer 20 NOT NULL nd_experiment.nd_experiment_id
stock_id integer 20 NOT NULL, stock used in the extraction or the corresponding stock for the clone stock.stock_id
type_id integer 20 NOT NULL cvterm.cvterm_id

Indices

Name Fields
nd_experiment_stock_idx1nd_experiment_id
nd_experiment_stock_idx2stock_id
nd_experiment_stock_idx3type_id

Constraints

Type Fields
NOT NULLnd_experiment_stock_id
NOT NULLnd_experiment_id
FOREIGN KEYnd_experiment_id
NOT NULLstock_id
FOREIGN KEYstock_id
NOT NULLtype_id
FOREIGN KEYtype_id
FOREIGN KEYnd_experiment_id
FOREIGN KEYstock_id
FOREIGN KEYtype_id

nd_experiment_protocol

Top
Comments:

================================================
TABLE: nd_experiment_protocol
================================================
Linking table: experiments to the protocols they involve.
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_protocol_id integer 20 PRIMARY KEY, NOT NULL
nd_experiment_id integer 20 NOT NULL nd_experiment.nd_experiment_id
nd_protocol_id integer 20 NOT NULL nd_protocol.nd_protocol_id

Indices

Name Fields
nd_experiment_protocol_idx1nd_experiment_id
nd_experiment_protocol_idx2nd_protocol_id

Constraints

Type Fields
NOT NULLnd_experiment_protocol_id
NOT NULLnd_experiment_id
FOREIGN KEYnd_experiment_id
NOT NULLnd_protocol_id
FOREIGN KEYnd_protocol_id
FOREIGN KEYnd_experiment_id
FOREIGN KEYnd_protocol_id

nd_experiment_phenotype

Top
Comments:

================================================
TABLE: nd_experiment_phenotype
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_phenotype_id integer 20 PRIMARY KEY, NOT NULL
nd_experiment_id integer 20 UNIQUE, NOT NULL nd_experiment.nd_experiment_id
phenotype_id integer 20 UNIQUE, NOT NULL phenotype.phenotype_id

Indices

Name Fields
nd_experiment_phenotype_idx1nd_experiment_id
nd_experiment_phenotype_idx2phenotype_id

Constraints

Type Fields
NOT NULLnd_experiment_phenotype_id
NOT NULLnd_experiment_id
FOREIGN KEYnd_experiment_id
NOT NULLphenotype_id
FOREIGN KEYphenotype_id
UNIQUEnd_experiment_id, phenotype_id
FOREIGN KEYnd_experiment_id
FOREIGN KEYphenotype_id

nd_experiment_genotype

Top
Comments:

================================================
TABLE: nd_experiment_genotype
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_genotype_id integer 20 PRIMARY KEY, NOT NULL
nd_experiment_id integer 20 UNIQUE, NOT NULL nd_experiment.nd_experiment_id
genotype_id integer 20 UNIQUE, NOT NULL genotype.genotype_id

Indices

Name Fields
nd_experiment_genotype_idx1nd_experiment_id
nd_experiment_genotype_idx2genotype_id

Constraints

Type Fields
NOT NULLnd_experiment_genotype_id
NOT NULLnd_experiment_id
FOREIGN KEYnd_experiment_id
NOT NULLgenotype_id
FOREIGN KEYgenotype_id
UNIQUEnd_experiment_id, genotype_id
FOREIGN KEYnd_experiment_id
FOREIGN KEYgenotype_id

nd_reagent_relationship

Top
Comments:

================================================
TABLE: nd_reagent_relationship
================================================
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.
Field Name Data Type Size Default Value Other Foreign Key
nd_reagent_relationship_id integer 20 PRIMARY KEY, NOT NULL
subject_reagent_id integer 20 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.nd_reagent_id
object_reagent_id integer 20 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. nd_reagent.nd_reagent_id
type_id integer 20 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. cvterm.cvterm_id

Indices

Name Fields
nd_reagent_relationship_idx1subject_reagent_id
nd_reagent_relationship_idx2object_reagent_id
nd_reagent_relationship_idx3type_id

Constraints

Type Fields
NOT NULLnd_reagent_relationship_id
NOT NULLsubject_reagent_id
FOREIGN KEYsubject_reagent_id
NOT NULLobject_reagent_id
FOREIGN KEYobject_reagent_id
NOT NULLtype_id
FOREIGN KEYtype_id
FOREIGN KEYsubject_reagent_id
FOREIGN KEYobject_reagent_id
FOREIGN KEYtype_id

nd_reagentprop

Top
Comments:

================================================
TABLE: nd_reagentprop
================================================
Field Name Data Type Size Default Value Other Foreign Key
nd_reagentprop_id integer 20 PRIMARY KEY, NOT NULL
nd_reagent_id integer 20 UNIQUE, NOT NULL nd_reagent.nd_reagent_id
type_id integer 20 UNIQUE, NOT NULL cvterm.cvterm_id
value text 64000 NULL
rank integer 10 0 UNIQUE, NOT NULL

Indices

Name Fields
nd_reagentprop_idx1nd_reagent_id
nd_reagentprop_idx2type_id

Constraints

Type Fields
NOT NULLnd_reagentprop_id
NOT NULLnd_reagent_id
FOREIGN KEYnd_reagent_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEnd_reagent_id, type_id, rank
FOREIGN KEYnd_reagent_id
FOREIGN KEYtype_id

nd_experiment_stockprop

Top
Comments:

================================================
TABLE: nd_experiment_stockprop
================================================
Property/value associations for experiment_stocks. This table can store the properties such as treatment
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_stockprop_id integer 20 PRIMARY KEY, NOT NULL
nd_experiment_stock_id integer 20 UNIQUE, NOT NULL, The experiment_stock to which the property applies. nd_experiment_stock.nd_experiment_stock_id
type_id integer 20 UNIQUE, NOT NULL, The name of the property as a reference to a controlled vocabulary term. cvterm.cvterm_id
value text 64000 NULL The value of the property.
rank integer 10 0 UNIQUE, NOT NULL, The rank of the property value, if the property has an array of values.

Indices

Name Fields
nd_experiment_stockprop_idx1nd_experiment_stock_id
nd_experiment_stockprop_idx2type_id

Constraints

Type Fields
NOT NULLnd_experiment_stockprop_id
NOT NULLnd_experiment_stock_id
FOREIGN KEYnd_experiment_stock_id
NOT NULLtype_id
FOREIGN KEYtype_id
NOT NULLrank
UNIQUEnd_experiment_stock_id, type_id, rank
FOREIGN KEYnd_experiment_stock_id
FOREIGN KEYtype_id

nd_experiment_stock_dbxref

Top
Comments:

================================================
TABLE: nd_experiment_stock_dbxref
================================================
Cross-reference experiment_stock to accessions, images, etc
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_stock_dbxref_id integer 20 PRIMARY KEY, NOT NULL
nd_experiment_stock_id integer 20 NOT NULL nd_experiment_stock.nd_experiment_stock_id
dbxref_id integer 20 NOT NULL dbxref.dbxref_id

Indices

Name Fields
nd_experiment_stock_dbxref_idx1nd_experiment_stock_id
nd_experiment_stock_dbxref_idx2dbxref_id

Constraints

Type Fields
NOT NULLnd_experiment_stock_dbxref_id
NOT NULLnd_experiment_stock_id
FOREIGN KEYnd_experiment_stock_id
NOT NULLdbxref_id
FOREIGN KEYdbxref_id
FOREIGN KEYnd_experiment_stock_id
FOREIGN KEYdbxref_id

nd_experiment_dbxref

Top
Comments:

================================================
TABLE: nd_experiment_dbxref
===============================================
Cross-reference experiment to accessions, images, etc
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_dbxref_id integer 20 PRIMARY KEY, NOT NULL
nd_experiment_id integer 20 NOT NULL nd_experiment.nd_experiment_id
dbxref_id integer 20 NOT NULL dbxref.dbxref_id

Indices

Name Fields
nd_experiment_dbxref_idx1nd_experiment_id
nd_experiment_dbxref_idx2dbxref_id

Constraints

Type Fields
NOT NULLnd_experiment_dbxref_id
NOT NULLnd_experiment_id
FOREIGN KEYnd_experiment_id
NOT NULLdbxref_id
FOREIGN KEYdbxref_id
FOREIGN KEYnd_experiment_id
FOREIGN KEYdbxref_id

nd_experiment_contact

Top
Comments:

================================================
TABLE: nd_experiment_contact
================================================
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_contact_id integer 20 PRIMARY KEY, NOT NULL
nd_experiment_id integer 20 NOT NULL nd_experiment.nd_experiment_id
contact_id integer 20 NOT NULL contact.contact_id

Indices

Name Fields
nd_experiment_contact_idx1nd_experiment_id
nd_experiment_contact_idx2contact_id

Constraints

Type Fields
NOT NULLnd_experiment_contact_id
NOT NULLnd_experiment_id
FOREIGN KEYnd_experiment_id
NOT NULLcontact_id
FOREIGN KEYcontact_id
FOREIGN KEYnd_experiment_id
FOREIGN KEYcontact_id

nd_experiment_analysis

Top
Comments:

================================================
TABLE: nd_experiment_analysis
================================================
An analysis that is used in an experiment
Field Name Data Type Size Default Value Other Foreign Key
nd_experiment_analysis_id integer 20 PRIMARY KEY, NOT NULL
nd_experiment_id integer 20 NOT NULL nd_experiment.nd_experiment_id
analysis_id integer 20 NOT NULL analysis.analysis_id
type_id integer 20 NULL cvterm.cvterm_id

Indices

Name Fields
nd_experiment_analysis_idx1nd_experiment_id
nd_experiment_analysis_idx2analysis_id
nd_experiment_analysis_idx3type_id

Constraints

Type Fields
NOT NULLnd_experiment_analysis_id
NOT NULLnd_experiment_id
FOREIGN KEYnd_experiment_id
NOT NULLanalysis_id
FOREIGN KEYanalysis_id
FOREIGN KEYtype_id
FOREIGN KEYnd_experiment_id
FOREIGN KEYanalysis_id
FOREIGN KEYtype_id

Created by
SQL::Translator 0.11020