User:Clements/AllTables

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Contents

Module: General

Table: tableinfo

<protect>

Table: tableinfo
Module: General


tableinfo columns
FK Name Type Description
tableinfo_id serial PRIMARY KEY
name character varying(30) UNIQUE

NOT NULL

primary_key_column character varying(30)
is_view integer NOT NULL
view_on_table_id integer
superclass_table_id integer
is_updateable integer NOT NULL

DEFAULT 1

modification_date date NOT NULL

DEFAULT now()


Tables referencing tableinfo via foreign key constraints:

</protect>

Table: db

<protect>

Table: db
Module: General

A database authority. Typical databases in bioinformatics are FlyBase, GO, UniProt, NCBI, MGI, etc. The authority is generally known by this shortened form, which is unique within the bioinformatics and biomedical realm. To Do - add support for URIs, URNs (e.g. LSIDs). We can do this by treating the URL as a URI - however, some applications may expect this to be resolvable - to be decided.

db columns
FK Name Type Description
db_id serial PRIMARY KEY
name character varying(255) UNIQUE

NOT NULL

description character varying(255)
urlprefix character varying(255)
url character varying(255)

Tables referencing db via foreign key constraints:

</protect>

Table: dbxref

<protect>

Table: dbxref
Module: General

A unique, global, public, stable identifier. Not necessarily an external reference - can reference data items inside the particular chado instance being used. Typically a row in a table can be uniquely identified with a primary identifier (called dbxref_id); a table may also have secondary identifiers (in a linking table <T>_dbxref). A dbxref is generally written as <DB>:<ACCESSION> or as <DB>:<ACCESSION>:<VERSION>.

dbxref columns
FK Name Type Description
dbxref_id serial PRIMARY KEY
db db_id integer UNIQUE#1

NOT NULL

accession character varying(255) UNIQUE#1

NOT NULL
The local part of the identifier. Guaranteed by the db authority to be unique for that db.

version character varying(255) UNIQUE#1

NOT NULL
DEFAULT ''::character varying

description text

Tables referencing dbxref via foreign key constraints:

</protect>

Table: dbxrefprop

<protect>

Table: dbxrefprop
Module: General

Metadata about a dbxref. Note that this is not defined in the dbxref module, as it depends on the cvterm table. This table has a structure analagous to cvtermprop.

dbxrefprop columns
FK Name Type Description
dbxrefprop_id serial PRIMARY KEY
dbxref dbxref_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text NOT NULL

DEFAULT ''::text

rank integer UNIQUE#1

NOT NULL


Tables referencing dbxrefprop via foreign key constraints:

  • None.</protect>

Module: CV

Table: cv

<protect>

Table: cv
Module: CV

A controlled vocabulary or ontology. A cv is composed of cvterms (AKA terms, classes, types, universals - relations and properties are also stored in cvterm) and the relationships between them.

cv columns
FK Name Type Description
cv_id serial PRIMARY KEY
name character varying(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 A text description of the criteria for

membership of this ontology.

Tables referencing cv via foreign key constraints:

</protect>

Table: cvterm

<protect>

Table: cvterm
Module: CV

A term, class, universal or type within an ontology or controlled vocabulary. This table is also used for relations and properties. cvterms constitute nodes in the graph defined by the collection of cvterms and cvterm_relationships.

cvterm columns
FK Name Type Description
cvterm_id serial PRIMARY KEY
cv cv_id integer UNIQUE#1

NOT NULL
The cv or ontology or namespace to which this cvterm belongs.

name character varying(1024) UNIQUE#1

NOT NULL
A concise human-readable name or label for the cvterm. Uniquely identifies a cvterm within a cv.

definition text A human-readable text

definition.

dbxref dbxref_id integer 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.

is_obsolete integer UNIQUE#1

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 NOT NULL

Boolean 0=false,1=true relations or relationship types (also known as Typedefs in OBO format, or as properties or slots) form a cv/ontology in themselves. We use this flag to indicate whether this cvterm is an actual term/class/universal or a relation. Relations may be drawn from the OBO Relations ontology, but are not exclusively drawn from there.

Tables referencing cvterm via foreign key constraints:

</protect>

Table: cvterm_relationship

<protect>

Table: cvterm_relationship
Module: CV

A relationship linking two cvterms. Each cvterm_relationship constitutes an edge in the graph defined by the collection of cvterms and cvterm_relationships. The meaning of the cvterm_relationship depends on the definition of the cvterm R refered to by type_id. However, in general the definitions are such that the statement "all SUBJs REL some OBJ" is true. The cvterm_relationship statement is about the subject, not the object. For example "insect wing part_of thorax".

cvterm_relationship columns
FK Name Type Description
cvterm_relationship_id serial PRIMARY KEY
cvterm type_id integer UNIQUE#1

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 subject_id integer UNIQUE#1

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 object_id integer UNIQUE#1

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.

Tables referencing cvterm_relationship via foreign key constraints:

  • None.</protect>

Table: cvtermpath

<protect>

Table: cvtermpath
Module: CV

The reflexive transitive closure of the cvterm_relationship relation.

cvtermpath columns
FK Name Type Description
cvtermpath_id serial PRIMARY KEY
cvterm type_id integer UNIQUE#1

The relationship type that this is a closure over. If null, then this is a closure over ALL relationship types. If non-null, then this references a relationship cvterm - note that the closure will apply to both this relationship AND the OBO_REL:is_a (subclass) relationship.

cvterm subject_id integer UNIQUE#1

NOT NULL

cvterm object_id integer UNIQUE#1

NOT NULL

cv cv_id integer NOT NULL

Closures will mostly be within one cv. If the closure of a relationship traverses a cv, then this refers to the cv of the object_id cvterm.

pathdistance integer UNIQUE#1

The number of steps required to get from the subject cvterm to the object cvterm, counting from zero (reflexive relationship).

Tables referencing cvtermpath via foreign key constraints:

  • None.</protect>

Table: cvtermsynonym

<protect>

Table: cvtermsynonym
Module: CV

A cvterm actually represents a distinct class or concept. A concept can be refered to by different phrases or names. In addition to the primary name (cvterm.name) there can be a number of alternative aliases or synonyms. For example, "T cell" as a synonym for "T lymphocyte".

cvtermsynonym columns
FK Name Type Description
cvtermsynonym_id serial PRIMARY KEY
cvterm cvterm_id integer UNIQUE#1

NOT NULL

synonym character varying(1024) UNIQUE#1

NOT NULL

cvterm type_id integer A synonym can be exact,

narrower, or broader than.

Tables referencing cvtermsynonym via foreign key constraints:

  • None.</protect>

Table: cvterm_dbxref

<protect>

Table: cvterm_dbxref
Module: CV

In addition to the primary identifier (cvterm.dbxref_id) a cvterm can have zero or more secondary identifiers/dbxrefs, which may refer to records in external databases. The exact semantics of cvterm_dbxref are not fixed. For example: the dbxref could be a pubmed ID that is pertinent to the cvterm, or it could be an equivalent or similar term in another ontology. For example, GO cvterms are typically linked to InterPro IDs, even though the nature of the relationship between them is largely one of statistical association. The dbxref may be have data records attached in the same database instance, or it could be a "hanging" dbxref pointing to some external database. NOTE: If the desired objective is to link two cvterms together, and the nature of the relation is known and holds for all instances of the subject cvterm then consider instead using cvterm_relationship together with a well-defined relation.

cvterm_dbxref columns
FK Name Type Description
cvterm_dbxref_id serial PRIMARY KEY
cvterm cvterm_id integer UNIQUE#1

NOT NULL

dbxref dbxref_id integer UNIQUE#1

NOT NULL

is_for_definition integer NOT NULL

A cvterm.definition should be supported by one or more references. If this column is true, the dbxref is not for a term in an external database - it is a dbxref for provenance information for the definition.

Tables referencing cvterm_dbxref via foreign key constraints:

  • None.</protect>

Table: cvtermprop

<protect>

Table: cvtermprop
Module: CV

Additional extensible properties can be attached to a cvterm using this table. Corresponds to -AnnotationProperty- in W3C OWL format.

cvtermprop columns
FK Name Type Description
cvtermprop_id serial PRIMARY KEY
cvterm cvterm_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL
The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.

value text UNIQUE#1

NOT NULL
DEFAULT ''::text
The value of the property, represented as text. Numeric values are converted to their text representation.

rank integer UNIQUE#1

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.

Tables referencing cvtermprop via foreign key constraints:

  • None.</protect>

Module: Publication

Table: pub

<protect>

Table: pub
Module: Publication

A documented provenance artefact - publications, documents, personal communication.

pub columns
FK Name Type Description
pub_id serial PRIMARY KEY
title text Descriptive general heading.
volumetitle text Title of part if one of a series.
volume character varying(255)
series_name character varying(255) Full name of (journal) series.
issue character varying(255)
pyear character varying(255)
pages character varying(255) Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.
miniref character varying(255)
uniquename text UNIQUE

NOT NULL

cvterm type_id integer NOT NULL

The type of the publication (book, journal, poem, graffiti, etc). Uses pub cv.

is_obsolete boolean DEFAULT false
publisher character varying(255)
pubplace character varying(255)

Tables referencing pub via foreign key constraints:

</protect>

Table: pub_relationship

<protect>

Table: pub_relationship
Module: Publication

Handle relationships between publications, e.g. when one publication makes others obsolete, when one publication contains errata with respect to other publication(s), or when one publication also appears in another pub.

pub_relationship columns
FK Name Type Description
pub_relationship_id serial PRIMARY KEY
pub subject_id integer UNIQUE#1

NOT NULL

pub object_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL


Tables referencing pub_relationship via foreign key constraints:

  • None.</protect>

Table: pub_dbxref

<protect>

Table: pub_dbxref
Module: Publication

Handle links to repositories, e.g. Pubmed, Biosis, zoorec, OCLC, Medline, ISSN, coden...

pub_dbxref columns
FK Name Type Description
pub_dbxref_id serial PRIMARY KEY
pub pub_id integer UNIQUE#1

NOT NULL

dbxref dbxref_id integer UNIQUE#1

NOT NULL

is_current boolean NOT NULL

DEFAULT true


Tables referencing pub_dbxref via foreign key constraints:

  • None.</protect>

Table: pubauthor

<protect>

Table: pubauthor
Module: Publication

An author for a publication. Note the denormalisation (hence lack of _ in table name) - this is deliberate as it is in general too hard to assign IDs to authors.

pubauthor columns
FK Name Type Description
pubauthor_id serial PRIMARY KEY
pub pub_id integer UNIQUE#1

NOT NULL

rank integer UNIQUE#1

NOT NULL
Order of author in author list for this pub - order is important.

editor boolean DEFAULT false

Indicates whether the author is an editor for linked publication. Note: this is a boolean field but does not follow the normal chado convention for naming booleans.

surname character varying(100) NOT NULL
givennames character varying(100) First name, initials
suffix character varying(100) Jr., Sr., etc

Tables referencing pubauthor via foreign key constraints:

  • None.</protect>

Table: pubprop

<protect>

Table: pubprop
Module: Publication

Property-value pairs for a pub. Follows standard chado pattern.

pubprop columns
FK Name Type Description
pubprop_id serial PRIMARY KEY
pub pub_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text NOT NULL
rank integer UNIQUE#1


Tables referencing pubprop via foreign key constraints:

  • None.</protect>

Module: Organism

Table: organism

<protect>

Table: organism
Module: Organism

The organismal taxonomic classification. Note that phylogenies are represented using the phylogeny module, and taxonomies can be represented using the cvterm module or the phylogeny module.

organism columns
FK Name Type Description
organism_id serial PRIMARY KEY
abbreviation character varying(255)
genus character varying(255) UNIQUE#1

NOT NULL

species character varying(255) UNIQUE#1

NOT NULL
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 character varying(255)
comment text

Tables referencing organism via foreign key constraints:

</protect>

Table: organism_dbxref

<protect>

Table: organism_dbxref
Module: Organism


organism_dbxref columns
FK Name Type Description
organism_dbxref_id serial PRIMARY KEY
organism organism_id integer UNIQUE#1

NOT NULL

dbxref dbxref_id integer UNIQUE#1

NOT NULL


Tables referencing organism_dbxref via foreign key constraints:

  • None.</protect>

Table: organismprop

<protect>

Table: organismprop
Module: Organism

Tag-value properties - follows standard chado model.

organismprop columns
FK Name Type Description
organismprop_id serial PRIMARY KEY
organism organism_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing organismprop via foreign key constraints:

  • None.</protect>

Module: Sequence

Table: feature

<protect>

Table: feature
Module: Sequence

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

feature columns
FK Name Type Description
feature_id serial PRIMARY KEY
dbxref dbxref_id integer An optional primary public stable

identifier for this feature. Secondary identifiers and external dbxrefs go in the table feature_dbxref.

organism organism_id integer UNIQUE#1

NOT NULL
The organism to which this feature belongs. This column is mandatory.

name character varying(255) The optional human-readable common name for

a feature, for display purposes.

uniquename text UNIQUE#1

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 A sequence of alphabetic characters

representing biological residues (nucleic acids, amino acids). This column does not need to be manifested for all features; it is optional for features such as exons where the residues can be derived from the featureloc. It is recommended that the value for this column be manifested for features which may may non-contiguous sublocations (e.g. transcripts), since derivation at query time is non-trivial. For expressed sequence, the DNA sequence should be used rather than the RNA sequence. The default storage method for the residues column is EXTERNAL, which will store it uncompressed to make substring operations faster.

seqlen integer The length of the residue feature. See

column:residues. This column is partially redundant with the residues column, and also with featureloc. This column is required because the location may be unknown and the residue sequence may not be manifested, yet it may be desirable to store and query the length of the feature. The seqlen should always be manifested where the length of the sequence is known.

md5checksum character(32) The 32-character checksum of the sequence,

calculated using the MD5 algorithm. This is practically guaranteed to be unique for any feature. This column thus acts as a unique identifier on the mathematical sequence.

cvterm type_id integer UNIQUE#1

NOT NULL
A required reference to a table:cvterm giving the feature type. This will typically be a Sequence Ontology identifier. This column is thus used to subclass the feature table.

is_analysis boolean NOT NULL

DEFAULT false
Boolean indicating whether this feature is annotated or the result of an automated analysis. Analysis results also use the companalysis module. Note that the dividing line between analysis 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 NOT NULL

DEFAULT false
Boolean indicating whether this feature has been obsoleted. Some chado instances may choose to simply remove the feature altogether, others may choose to keep an obsolete row in the table.

timeaccessioned timestamp without time zone NOT NULL

DEFAULT now()
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 without time zone NOT NULL

DEFAULT now()
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.

Tables referencing feature via foreign key constraints:

</protect>

Table: featureloc

<protect>

Table: featureloc
Module: Sequence

The location of a feature relative to another feature. Important: interbase coordinates are used. This is vital as it allows us to represent zero-length features e.g. splice sites, insertion points without an awkward fuzzy system. Features typically have exactly ONE location, but this need not be the case. Some features may not be localized (e.g. a gene that has been characterized genetically but no sequence or molecular information is available). Note on multiple locations: Each feature can have 0 or more locations. Multiple locations do NOT indicate non-contiguous locations (if a feature such as a transcript has a non-contiguous location, then the subfeatures such as exons should always be manifested). Instead, multiple featurelocs for a feature designate alternate locations or grouped locations; for instance, a feature designating a blast hit or hsp will have two locations, one on the query feature, one on the subject feature. Features representing sequence variation could have alternate locations instantiated on a feature on the mutant strain. The column:rank is used to differentiate these different locations. Reflexive locations should never be stored - this is for -proper- (i.e. non-self) locations only; nothing should be located relative to itself.

featureloc columns
FK Name Type Description
featureloc_id serial PRIMARY KEY
feature feature_id integer UNIQUE#1

NOT NULL
The feature that is being located. Any feature can have zero or more featurelocs.

feature srcfeature_id integer The source feature which this location is relative to. Every location is relative to another feature (however, this column is nullable, because the srcfeature may not be known). All locations are -proper- that is, nothing should be located relative to itself. No cycles are allowed in the featureloc graph.
fmin integer The leftmost/minimal boundary in the linear range represented by the featureloc. Sometimes (e.g. in Bioperl) this is called -start- although this is confusing because it does not necessarily represent the 5-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. To convert this to the leftmost position in a base-oriented system (eg GFF, Bioperl), add 1 to fmin.
is_fmin_partial boolean NOT NULL

DEFAULT false
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 The rightmost/maximal boundary in the linear range represented by the featureloc. Sometimes (e.g. in bioperl) this is called -end- although this is confusing because it does not necessarily represent the 3-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. No conversion is required to go from fmax to the rightmost coordinate in a base-oriented system that counts from 1 (e.g. GFF, Bioperl).
is_fmax_partial boolean NOT NULL

DEFAULT false
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 smallint The orientation/directionality of the

location. Should be 0, -1 or +1.

phase integer Phase of translation with

respect to srcfeature_id. Values are 0, 1, 2. It may not be possible to manifest this column for some features such as exons, because the phase is dependant on the spliceform (the same exon can appear in multiple spliceforms). This column is mostly useful for predicted exons and CDSs.

residue_info text Alternative residues,

when these differ from feature.residues. For instance, a SNP feature located on a wild and mutant protein would have different alternative residues. for alignment/similarity features, the alternative residues is used to represent the alignment string (CIGAR format). Note on variation features; even if we do not want to instantiate a mutant chromosome/contig feature, we can still represent a SNP etc with 2 locations, one (rank 0) on the genome, the other (rank 1) would have most fields null, except for alternative residues.

locgroup integer UNIQUE#1

NOT NULL
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 UNIQUE#1

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.

Tables referencing featureloc via foreign key constraints:

</protect>

Table: featureloc_pub

<protect>

Table: featureloc_pub
Module: Sequence

Provenance of featureloc. Linking table between featurelocs and publications that mention them.

featureloc_pub columns
FK Name Type Description
featureloc_pub_id serial PRIMARY KEY
featureloc featureloc_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing featureloc_pub via foreign key constraints:

  • None.</protect>

Table: feature_pub

<protect>

Table: feature_pub
Module: Sequence

Provenance. Linking table between features and publications that mention them.

feature_pub columns
FK Name Type Description
feature_pub_id serial PRIMARY KEY
feature feature_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing feature_pub via foreign key constraints:

</protect>

Table: feature_pubprop

<protect>

Table: feature_pubprop
Module: Sequence

Property or attribute of a feature_pub link.

feature_pubprop columns
FK Name Type Description
feature_pubprop_id serial PRIMARY KEY
feature_pub feature_pub_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing feature_pubprop via foreign key constraints:

  • None.</protect>

Table: featureprop

<protect>

Table: featureprop
Module: Sequence

A feature can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible.

featureprop columns
FK Name Type Description
featureprop_id serial PRIMARY KEY
feature feature_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL
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.

value text The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.
rank integer UNIQUE#1

NOT NULL
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

Tables referencing featureprop via foreign key constraints:

</protect>

Table: featureprop_pub

<protect>

Table: featureprop_pub
Module: Sequence

Provenance. Any featureprop assignment can optionally be supported by a publication.

featureprop_pub columns
FK Name Type Description
featureprop_pub_id serial PRIMARY KEY
featureprop featureprop_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing featureprop_pub via foreign key constraints:

  • None.</protect>

Table: feature_dbxref

<protect>

Table: feature_dbxref
Module: Sequence

Links a feature to dbxrefs. This is for secondary identifiers; primary identifiers should use feature.dbxref_id.

feature_dbxref columns
FK Name Type Description
feature_dbxref_id serial PRIMARY KEY
feature feature_id integer UNIQUE#1

NOT NULL

dbxref dbxref_id integer UNIQUE#1

NOT NULL

is_current boolean NOT NULL

DEFAULT true
True if this secondary dbxref is the most up to date accession in the corresponding db. Retired accessions should set this field to false

Tables referencing feature_dbxref via foreign key constraints:

  • None.</protect>

Table: feature_relationship

<protect>

Table: feature_relationship
Module: Sequence

Features can be arranged in graphs, e.g. "exon part_of transcript part_of gene"; If type is thought of as a verb, the each arc or edge makes a statement [Subject Verb Object]. The object can also be thought of as parent (containing feature), and subject as child (contained feature or subfeature). We include the relationship rank/order, because even though most of the time we can order things implicitly by sequence coordinates, we can not always do this - e.g. transpliced genes. It is also useful for quickly getting implicit introns.

feature_relationship columns
FK Name Type Description
feature_relationship_id serial PRIMARY KEY
feature subject_id integer UNIQUE#1

NOT NULL
The subject of the subj-predicate-obj sentence. This is typically the subfeature.

feature object_id integer UNIQUE#1

NOT NULL
The object of the subj-predicate-obj sentence. This is typically the container feature.

cvterm type_id integer UNIQUE#1

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.

value text Additional notes or comments.
rank integer UNIQUE#1

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.

Tables referencing feature_relationship via foreign key constraints:

</protect>

Table: feature_relationship_pub

<protect>

Table: feature_relationship_pub
Module: Sequence

Provenance. Attach optional evidence to a feature_relationship in the form of a publication.

feature_relationship_pub columns
FK Name Type Description
feature_relationship_pub_id serial PRIMARY KEY
feature_relationship feature_relationship_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing feature_relationship_pub via foreign key constraints:

  • None.</protect>

Table: feature_relationshipprop

<protect>

Table: feature_relationshipprop
Module: Sequence

Extensible properties for feature_relationships. Analagous structure to featureprop. This table is largely optional and not used with a high frequency. Typical scenarios may be if one wishes to attach additional data to a feature_relationship - for example to say that the feature_relationship is only true in certain contexts.

feature_relationshipprop columns
FK Name Type Description
feature_relationshipprop_id serial PRIMARY KEY
feature_relationship feature_relationship_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL
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.

value text The value of the

property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.

rank integer UNIQUE#1

NOT NULL
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.

Tables referencing feature_relationshipprop via foreign key constraints:

</protect>

Table: feature_relationshipprop_pub

<protect>

Table: feature_relationshipprop_pub
Module: Sequence

Provenance for feature_relationshipprop.

feature_relationshipprop_pub columns
FK Name Type Description
feature_relationshipprop_pub_id serial PRIMARY KEY
feature_relationshipprop feature_relationshipprop_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing feature_relationshipprop_pub via foreign key constraints:

  • None.</protect>

Table: feature_cvterm

<protect>

Table: feature_cvterm
Module: Sequence

Associate a term from a cv with a feature, for example, GO annotation.

feature_cvterm columns
FK Name Type Description
feature_cvterm_id serial PRIMARY KEY
feature feature_id integer UNIQUE#1

NOT NULL

cvterm cvterm_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL
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.

is_not boolean NOT NULL

DEFAULT false
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 UNIQUE#1

NOT NULL


Tables referencing feature_cvterm via foreign key constraints:

</protect>

Table: feature_cvtermprop

<protect>

Table: feature_cvtermprop
Module: Sequence

Extensible properties for feature to cvterm associations. Examples: GO evidence codes; qualifiers; metadata such as the date on which the entry was curated and the source of the association. See the featureprop table for meanings of type_id, value and rank.

feature_cvtermprop columns
FK Name Type Description
feature_cvtermprop_id serial PRIMARY KEY
feature_cvterm feature_cvterm_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL
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.

value text The value of the

property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.

rank integer UNIQUE#1

NOT NULL
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.

Tables referencing feature_cvtermprop via foreign key constraints:

  • None.</protect>

Table: feature_cvterm_dbxref

<protect>

Table: feature_cvterm_dbxref
Module: Sequence

Additional dbxrefs for an association. Rows in the feature_cvterm table may be backed up by dbxrefs. For example, a feature_cvterm association that was inferred via a protein-protein interaction may be backed by by refering to the dbxref for the alternate protein. Corresponds to the WITH column in a GO gene association file (but can also be used for other analagous associations). See http://www.geneontology.org/doc/GO.annotation.shtml#file for more details.

feature_cvterm_dbxref columns
FK Name Type Description
feature_cvterm_dbxref_id serial PRIMARY KEY
feature_cvterm feature_cvterm_id integer UNIQUE#1

NOT NULL

dbxref dbxref_id integer UNIQUE#1

NOT NULL


Tables referencing feature_cvterm_dbxref via foreign key constraints:

  • None.</protect>

Table: feature_cvterm_pub

<protect>

Table: feature_cvterm_pub
Module: Sequence

Secondary pubs for an association. Each feature_cvterm association is supported by a single primary publication. Additional secondary pubs can be added using this linking table (in a GO gene association file, these corresponding to any IDs after the pipe symbol in the publications column.

feature_cvterm_pub columns
FK Name Type Description
feature_cvterm_pub_id serial PRIMARY KEY
feature_cvterm feature_cvterm_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing feature_cvterm_pub via foreign key constraints:

  • None.</protect>

Table: synonym

<protect>

Table: synonym
Module: Sequence

A synonym for a feature. One feature can have multiple synonyms, and the same synonym can apply to multiple features.

synonym columns
FK Name Type Description
synonym_id serial PRIMARY KEY
name character varying(255) UNIQUE#1

NOT NULL
The synonym itself. Should be human-readable machine-searchable ascii text.

cvterm type_id integer UNIQUE#1

NOT NULL
Types would be symbol and fullname for now.

synonym_sgml character varying(255) NOT NULL

The fully specified synonym, with any non-ascii characters encoded in SGML.

Tables referencing synonym via foreign key constraints:

</protect>

Table: feature_synonym

<protect>

Table: feature_synonym
Module: Sequence

Linking table between feature and synonym.

feature_synonym columns
FK Name Type Description
feature_synonym_id serial PRIMARY KEY
synonym synonym_id integer UNIQUE#1

NOT NULL

feature feature_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL
The pub_id link is for relating the usage of a given synonym to the publication in which it was used.

is_current boolean NOT NULL

DEFAULT false
The is_current boolean indicates whether the linked synonym is the current -official- symbol for the linked feature.

is_internal boolean NOT NULL

DEFAULT false
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.

Tables referencing feature_synonym via foreign key constraints:

  • None.</protect>

Table: gencode

<protect>

Table: gencode
Module: Sequence


gencode columns
FK Name Type Description
gencode_id integer PRIMARY KEY
organismstr character varying(512) NOT NULL


Tables referencing gencode via foreign key constraints:

</protect>

Table: gencode_codon_aa

<protect>

Table: gencode_codon_aa
Module: Sequence


gencode_codon_aa columns
FK Name Type Description
gencode gencode_id integer NOT NULL
codon character(3) NOT NULL
aa character(1) NOT NULL


Tables referencing gencode_codon_aa via foreign key constraints:

  • None.</protect>

Table: gencode_startcodon

<protect>

Table: gencode_startcodon
Module: Sequence


gencode_startcodon columns
FK Name Type Description
gencode gencode_id integer NOT NULL
codon character(3)

Tables referencing gencode_startcodon via foreign key constraints:

  • None.</protect>

Module: Companalysis

Table: analysis

<protect>

Table: analysis
Module: Companalysis

An analysis is a particular type of a

   computational analysis; it may be a blast of one sequence against
   another, or an all by all blast, or a different kind of analysis
   altogether. It is a single unit of computation.
analysis columns
FK Name Type Description
analysis_id serial PRIMARY KEY
name character varying(255) A way of grouping analyses. This
   should be a handy short identifier that can help people find an
   analysis they want. For instance "tRNAscan", "cDNA", "FlyPep",
   "SwissProt", and it should not be assumed to be unique. For instance, there may be lots of separate analyses done against a cDNA database.
description text
program character varying(255) UNIQUE#1

NOT NULL
Program name, e.g. blastx, blastp, sim4, genscan.

programversion character varying(255) UNIQUE#1

NOT NULL
Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000].

algorithm character varying(255) Algorithm name, e.g. blast.
sourcename character varying(255) UNIQUE#1

Source name, e.g. cDNA, SwissProt.

sourceversion character varying(255)
sourceuri text This is an optional, permanent URL or URI for the source of the analysis. The idea is that someone could recreate the analysis directly by going to this URI and fetching the source data (e.g. the blast database, or the training model).
timeexecuted timestamp without time zone NOT NULL

DEFAULT now()


Tables referencing analysis via foreign key constraints:

</protect>

Table: analysisprop

<protect>

Table: analysisprop
Module: Companalysis


analysisprop columns
FK Name Type Description
analysisprop_id serial PRIMARY KEY
analysis analysis_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing analysisprop via foreign key constraints:

  • None.</protect>

Table: analysisfeature

<protect>

Table: analysisfeature
Module: Companalysis

Computational analyses generate features (e.g. Genscan generates transcripts and exons; sim4 alignments generate similarity/match features). analysisfeatures are stored using the feature table from the sequence module. The analysisfeature table is used to decorate these features, with analysis specific attributes. A feature is an analysisfeature if and only if there is a corresponding entry in the analysisfeature table. analysisfeatures will have two or more featureloc entries,

with rank indicating query/subject
analysisfeature columns
FK Name Type Description
analysisfeature_id serial PRIMARY KEY
feature feature_id integer UNIQUE#1

NOT NULL

analysis analysis_id integer UNIQUE#1

NOT NULL

rawscore double precision This is the native score generated by the program; for example, the bitscore generated by blast, sim4 or genscan scores. One should not assume that high is necessarily better than low.
normscore double precision This is the rawscore but
   semi-normalized. Complete normalization to allow comparison of
   features generated by different programs would be nice but too
   difficult. Instead the normalization should strive to enforce the
   following semantics: * normscores are floating point numbers >= 0,
   * high normscores are better than low one. For most programs, it would be sufficient to make the normscore the same as this rawscore, providing these semantics are satisfied.
significance double precision This is some kind of expectation or probability metric, representing the probability that the analysis would appear randomly given the model. As such, any program or person querying this table can assume the following semantics:
  * 0 <= significance <= n, where n is a positive number, theoretically unbounded but unlikely to be more than 10
 * low numbers are better than high numbers.
identity double precision Percent identity between the locations compared. Note that these 4 metrics do not cover the full range of scores possible; it would be undesirable to list every score possible, as this should be kept extensible. instead, for non-standard scores, use the analysisprop table.

Tables referencing analysisfeature via foreign key constraints:

</protect>

Table: analysisfeatureprop

<protect>

Table: analysisfeatureprop
Module: Companalysis


analysisfeatureprop columns
FK Name Type Description
analysisfeatureprop_id serial PRIMARY KEY
analysisfeature analysisfeature_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing analysisfeatureprop via foreign key constraints:

  • None.</protect>

Module: Cell Line

Table: cell_line

<protect>

Table: cell_line
Module: Cell Line


cell_line columns
FK Name Type Description
cell_line_id serial PRIMARY KEY
name character varying(255)
uniquename character varying(255) UNIQUE#1

NOT NULL

organism organism_id integer UNIQUE#1

NOT NULL

timeaccessioned timestamp without time zone NOT NULL

DEFAULT now()

timelastmodified timestamp without time zone NOT NULL

DEFAULT now()


Tables referencing cell_line via foreign key constraints:

</protect>

Table: cell_line_relationship

<protect>

Table: cell_line_relationship
Module: Cell Line


cell_line_relationship columns
FK Name Type Description
cell_line_relationship_id serial PRIMARY KEY
cell_line subject_id integer UNIQUE#1

NOT NULL

cell_line object_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL


Tables referencing cell_line_relationship via foreign key constraints:

  • None.</protect>

Table: cell_line_synonym

<protect>

Table: cell_line_synonym
Module: Cell Line


cell_line_synonym columns
FK Name Type Description
cell_line_synonym_id serial PRIMARY KEY
cell_line cell_line_id integer UNIQUE#1

NOT NULL

synonym synonym_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL

is_current boolean NOT NULL

DEFAULT false

is_internal boolean NOT NULL

DEFAULT false


Tables referencing cell_line_synonym via foreign key constraints:

  • None.</protect>

Table: cell_line_cvterm

<protect>

Table: cell_line_cvterm
Module: Cell Line


cell_line_cvterm columns
FK Name Type Description
cell_line_cvterm_id serial PRIMARY KEY
cell_line cell_line_id integer UNIQUE#1

NOT NULL

cvterm cvterm_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL

rank integer UNIQUE#1

NOT NULL


Tables referencing cell_line_cvterm via foreign key constraints:

</protect>

Table: cell_line_dbxref

<protect>

Table: cell_line_dbxref
Module: Cell Line


cell_line_dbxref columns
FK Name Type Description
cell_line_dbxref_id serial PRIMARY KEY
cell_line cell_line_id integer UNIQUE#1

NOT NULL

dbxref dbxref_id integer UNIQUE#1

NOT NULL

is_current boolean NOT NULL

DEFAULT true


Tables referencing cell_line_dbxref via foreign key constraints:

  • None.</protect>

Table: cell_lineprop

<protect>

Table: cell_lineprop
Module: Cell Line


cell_lineprop columns
FK Name Type Description
cell_lineprop_id serial PRIMARY KEY
cell_line cell_line_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing cell_lineprop via foreign key constraints:

</protect>

Table: cell_lineprop_pub

<protect>

Table: cell_lineprop_pub
Module: Cell Line


cell_lineprop_pub columns
FK Name Type Description
cell_lineprop_pub_id serial PRIMARY KEY
cell_lineprop cell_lineprop_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing cell_lineprop_pub via foreign key constraints:

  • None.</protect>

Table: cell_line_feature

<protect>

Table: cell_line_feature
Module: Cell Line


cell_line_feature columns
FK Name Type Description
cell_line_feature_id serial PRIMARY KEY
cell_line cell_line_id integer UNIQUE#1

NOT NULL

feature feature_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing cell_line_feature via foreign key constraints:

  • None.</protect>

Table: cell_line_cvtermprop

<protect>

Table: cell_line_cvtermprop
Module: Cell Line


cell_line_cvtermprop columns
FK Name Type Description
cell_line_cvtermprop_id serial PRIMARY KEY
cell_line_cvterm cell_line_cvterm_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing cell_line_cvtermprop via foreign key constraints:

  • None.</protect>

Table: cell_line_pub

<protect>

Table: cell_line_pub
Module: Cell Line


cell_line_pub columns
FK Name Type Description
cell_line_pub_id serial PRIMARY KEY
cell_line cell_line_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing cell_line_pub via foreign key constraints:

  • None.</protect>

Table: cell_line_library

<protect>

Table: cell_line_library
Module: Cell Line


cell_line_library columns
FK Name Type Description
cell_line_library_id serial PRIMARY KEY
cell_line cell_line_id integer UNIQUE#1

NOT NULL

library library_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing cell_line_library via foreign key constraints:

  • None.</protect>

Module: Contact

Table: contactprop

Table: contact

<protect>

Table: contact
Module: Contact

Model persons, institutes, groups, organizations, etc.

contact columns
FK Name Type Description
contact_id serial PRIMARY KEY
cvterm type_id integer What type of contact is this? E.g. "person", "lab".
name character varying(255) UNIQUE

NOT NULL

description character varying(255)

Tables referencing contact via foreign key constraints:

</protect>

Table: contact_relationship

<protect>

Table: contact_relationship
Module: Contact

Model relationships between contacts

contact_relationship columns
FK Name Type Description
contact_relationship_id serial PRIMARY KEY
cvterm type_id integer UNIQUE#1

NOT NULL
Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed.

contact subject_id integer UNIQUE#1

NOT NULL
The subject of the subj-predicate-obj sentence. In a DAG, this corresponds to the child node.

contact object_id integer UNIQUE#1

NOT NULL
The object of the subj-predicate-obj sentence. In a DAG, this corresponds to the parent node.

Tables referencing contact_relationship via foreign key constraints:

  • None.</protect>

Module: Expression

Table: expression

<protect>

Table: expression
Module: Expression

The expression table is essentially a bridge table.

expression columns
FK Name Type Description
expression_id serial PRIMARY KEY
uniquename text UNIQUE

NOT NULL

md5checksum character(32)
description text

Tables referencing expression via foreign key constraints:

</protect>

Table: expression_cvterm

<protect>

Table: expression_cvterm
Module: Expression


expression_cvterm columns
FK Name Type Description
expression_cvterm_id serial PRIMARY KEY
expression expression_id integer UNIQUE#1

NOT NULL

cvterm cvterm_id integer UNIQUE#1

NOT NULL

rank integer NOT NULL
cvterm cvterm_type_id integer UNIQUE#1

NOT NULL


Tables referencing expression_cvterm via foreign key constraints:

</protect>

Table: expression_cvtermprop

<protect>

Table: expression_cvtermprop
Module: Expression

Extensible properties for expression to cvterm associations. Examples: qualifiers.

expression_cvtermprop columns
FK Name Type Description
expression_cvtermprop_id serial PRIMARY KEY
expression_cvterm expression_cvterm_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL
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.

value text The value of the

property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query.

rank integer UNIQUE#1

NOT NULL
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.

Tables referencing expression_cvtermprop via foreign key constraints:

  • None.</protect>

Table: expressionprop

<protect>

Table: expressionprop
Module: Expression


expressionprop columns
FK Name Type Description
expressionprop_id serial PRIMARY KEY
expression expression_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing expressionprop via foreign key constraints:

  • None.</protect>

Table: expression_pub

<protect>

Table: expression_pub
Module: Expression


expression_pub columns
FK Name Type Description
expression_pub_id serial PRIMARY KEY
expression expression_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing expression_pub via foreign key constraints:

  • None.</protect>

Table: feature_expression

<protect>

Table: feature_expression
Module: Expression


feature_expression columns
FK Name Type Description
feature_expression_id serial PRIMARY KEY
expression expression_id integer UNIQUE#1

NOT NULL

feature feature_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing feature_expression via foreign key constraints:

</protect>

Table: feature_expressionprop

<protect>

Table: feature_expressionprop
Module: Expression

Extensible properties for feature_expression (comments, for example). Modeled on feature_cvtermprop.

feature_expressionprop columns
FK Name Type Description
feature_expressionprop_id serial PRIMARY KEY
feature_expression feature_expression_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing feature_expressionprop via foreign key constraints:

  • None.</protect>

Table: eimage

<protect>

Table: eimage
Module: Expression


eimage columns
FK Name Type Description
eimage_id serial PRIMARY KEY
eimage_data text We expect images in eimage_data (e.g. JPEGs) to be uuencoded.
eimage_type character varying(255) NOT NULL

Describes the type of data in eimage_data.

image_uri character varying(255)

Tables referencing eimage via foreign key constraints:

</protect>

Table: expression_image

<protect>

Table: expression_image
Module: Expression


expression_image columns
FK Name Type Description
expression_image_id serial PRIMARY KEY
expression expression_id integer UNIQUE#1

NOT NULL

eimage eimage_id integer UNIQUE#1

NOT NULL


Tables referencing expression_image via foreign key constraints:

  • None.</protect>

Module: Genetic

Table: genotype

<protect>

Table: genotype
Module: Genetic

Genetic context. A genotype is defined by a collection of features, mutations, balancers, deficiencies, haplotype blocks, or engineered constructs.

genotype columns
FK Name Type Description
genotype_id serial PRIMARY KEY
name text Optional alternative name for a genotype,

for display purposes.

uniquename text UNIQUE

NOT NULL
The unique name for a genotype; typically derived from the features making up the genotype.

description character varying(255)

Tables referencing genotype via foreign key constraints:

</protect>

Table: feature_genotype

<protect>

Table: feature_genotype
Module: Genetic


feature_genotype columns
FK Name Type Description
feature_genotype_id serial PRIMARY KEY
feature feature_id integer UNIQUE#1

NOT NULL

genotype genotype_id integer UNIQUE#1

NOT NULL

feature chromosome_id integer UNIQUE#1

A feature of SO type "chromosome".

rank integer UNIQUE#1

NOT NULL
rank can be used for n-ploid organisms or to preserve order.

cgroup integer UNIQUE#1

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 cvterm_id integer UNIQUE#1

NOT NULL


Tables referencing feature_genotype via foreign key constraints:

  • None.</protect>

Table: environment

<protect>

Table: environment
Module: Genetic

The environmental component of a phenotype description.

environment columns
FK Name Type Description
environment_id serial PRIMARY KEY
uniquename text UNIQUE

NOT NULL

description text

Tables referencing environment via foreign key constraints:

</protect>

Table: environment_cvterm

<protect>

Table: environment_cvterm
Module: Genetic


environment_cvterm columns
FK Name Type Description
environment_cvterm_id serial PRIMARY KEY
environment environment_id integer UNIQUE#1

NOT NULL

cvterm cvterm_id integer UNIQUE#1

NOT NULL


Tables referencing environment_cvterm via foreign key constraints:

  • None.</protect>

Table: phenstatement

<protect>

Table: phenstatement
Module: Genetic

Phenotypes are things like "larval lethal". Phenstatements are things like "dpp-1 is recessive larval lethal". So essentially phenstatement is a linking table expressing the relationship between genotype, environment, and phenotype.

phenstatement columns
FK Name Type Description
phenstatement_id serial PRIMARY KEY
genotype genotype_id integer UNIQUE#1

NOT NULL

environment environment_id integer UNIQUE#1

NOT NULL

phenotype phenotype_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing phenstatement via foreign key constraints:

  • None.</protect>

Table: phendesc

<protect>

Table: phendesc
Module: Genetic

A summary of a _set_ of phenotypic statements for any one gcontext made in any one publication.

phendesc columns
FK Name Type Description
phendesc_id serial PRIMARY KEY
genotype genotype_id integer UNIQUE#1

NOT NULL

environment environment_id integer UNIQUE#1

NOT NULL

description text NOT NULL
cvterm type_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing phendesc via foreign key constraints:

  • None.</protect>

Table: phenotype_comparison

<protect>

Table: phenotype_comparison
Module: Genetic

Comparison of phenotypes e.g., genotype1/environment1/phenotype1 "non-suppressible" with respect to genotype2/environment2/phenotype2.

phenotype_comparison columns
FK Name Type Description
phenotype_comparison_id serial PRIMARY KEY
genotype genotype1_id integer UNIQUE#1

NOT NULL

environment environment1_id integer UNIQUE#1

NOT NULL

genotype genotype2_id integer UNIQUE#1

NOT NULL

environment environment2_id integer UNIQUE#1

NOT NULL

phenotype phenotype1_id integer UNIQUE#1

NOT NULL

phenotype phenotype2_id integer
pub pub_id integer UNIQUE#1

NOT NULL

organism organism_id integer NOT NULL


Tables referencing phenotype_comparison via foreign key constraints:

</protect>

Table: phenotype_comparison_cvterm

<protect>

Table: phenotype_comparison_cvterm
Module: Genetic


phenotype_comparison_cvterm columns
FK Name Type Description
phenotype_comparison_cvterm_id serial PRIMARY KEY
phenotype_comparison phenotype_comparison_id integer UNIQUE#1

NOT NULL

cvterm cvterm_id integer UNIQUE#1

NOT NULL

pub pub_id integer NOT NULL
rank integer NOT NULL


Tables referencing phenotype_comparison_cvterm via foreign key constraints:

  • None.</protect>

Module: Library

Table: library

<protect>

Table: library
Module: Library


library columns
FK Name Type Description
library_id serial PRIMARY KEY
organism organism_id integer UNIQUE#1

NOT NULL

name character varying(255)
uniquename text UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL
The type_id foreign key links to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library"

is_obsolete integer NOT NULL
timeaccessioned timestamp without time zone NOT NULL

DEFAULT now()

timelastmodified timestamp without time zone NOT NULL

DEFAULT now()


Tables referencing library via foreign key constraints:

</protect>

Table: library_synonym

<protect>

Table: library_synonym
Module: Library


library_synonym columns
FK Name Type Description
library_synonym_id serial PRIMARY KEY
synonym synonym_id integer UNIQUE#1

NOT NULL

library library_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL
The pub_id link is for relating the usage of a given synonym to the publication in which it was used.

is_current boolean NOT NULL

DEFAULT true
The is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library.

is_internal boolean NOT NULL

DEFAULT false
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.

Tables referencing library_synonym via foreign key constraints:

  • None.</protect>

Table: library_pub

<protect>

Table: library_pub
Module: Library


library_pub columns
FK Name Type Description
library_pub_id serial PRIMARY KEY
library library_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing library_pub via foreign key constraints:

  • None.</protect>

Table: libraryprop

<protect>

Table: libraryprop
Module: Library


libraryprop columns
FK Name Type Description
libraryprop_id serial PRIMARY KEY
library library_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing libraryprop via foreign key constraints:

</protect>

Table: libraryprop_pub

<protect>

Table: libraryprop_pub
Module: Library


libraryprop_pub columns
FK Name Type Description
libraryprop_pub_id serial PRIMARY KEY
libraryprop libraryprop_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing libraryprop_pub via foreign key constraints:

  • None.</protect>

Table: library_cvterm

<protect>

Table: library_cvterm
Module: Library

The table library_cvterm links a library to controlled vocabularies which describe the library. For instance, there might be a link to the anatomy cv for "head" or "testes" for a head or testes library.

library_cvterm columns
FK Name Type Description
library_cvterm_id serial PRIMARY KEY
library library_id integer UNIQUE#1

NOT NULL

cvterm cvterm_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing library_cvterm via foreign key constraints:

  • None.</protect>

Table: library_feature

<protect>

Table: library_feature
Module: Library

library_feature links a library to the clones which are contained in the library. Examples of such linked features might be "cDNA_clone" or "genomic_clone".

library_feature columns
FK Name Type Description
library_feature_id serial PRIMARY KEY
library library_id integer UNIQUE#1

NOT NULL

feature feature_id integer UNIQUE#1

NOT NULL


Tables referencing library_feature via foreign key constraints:

  • None.</protect>

Table: library_dbxref

<protect>

Table: library_dbxref
Module: Library


library_dbxref columns
FK Name Type Description
library_dbxref_id serial PRIMARY KEY
library library_id integer UNIQUE#1

NOT NULL

dbxref dbxref_id integer UNIQUE#1

NOT NULL

is_current boolean NOT NULL

DEFAULT true


Tables referencing library_dbxref via foreign key constraints:

  • None.</protect>

Module: Mage

Table: mageml

<protect>

Table: mageml
Module: Mage

This table is for storing extra bits of MAGEml in a denormalized form. More normalization would require many more tables.

mageml columns
FK Name Type Description
mageml_id serial PRIMARY KEY
mage_package text NOT NULL
mage_ml text NOT NULL


Tables referencing mageml via foreign key constraints:

</protect>

Table: magedocumentation

<protect>

Table: magedocumentation
Module: Mage


magedocumentation columns
FK Name Type Description
magedocumentation_id serial PRIMARY KEY
mageml mageml_id integer NOT NULL
tableinfo tableinfo_id integer NOT NULL
row_id integer NOT NULL
mageidentifier text NOT NULL


Tables referencing magedocumentation via foreign key constraints:

  • None.</protect>

Table: protocol

<protect>

Table: protocol
Module: Mage

Procedural notes on how data was prepared and processed.

protocol columns
FK Name Type Description
protocol_id serial PRIMARY KEY
cvterm type_id integer NOT NULL
pub pub_id integer
dbxref dbxref_id integer
name text UNIQUE

NOT NULL

uri text
protocoldescription text
hardwaredescription text
softwaredescription text

Tables referencing protocol via foreign key constraints:

</protect>

Table: protocolparam

<protect>

Table: protocolparam
Module: Mage

Parameters related to a protocol. For example, if the protocol is a soak, this might include attributes of bath temperature and duration.

protocolparam columns
FK Name Type Description
protocolparam_id serial PRIMARY KEY
protocol protocol_id integer NOT NULL
name text NOT NULL
cvterm datatype_id integer
cvterm unittype_id integer
value text
rank integer NOT NULL


Tables referencing protocolparam via foreign key constraints:

  • None.</protect>

Table: channel

<protect>

Table: channel
Module: Mage

Different array platforms can record signals from one or more channels (cDNA arrays typically use two CCD, but Affymetrix uses only one).

channel columns
FK Name Type Description
channel_id serial PRIMARY KEY
name text UNIQUE

NOT NULL

definition text NOT NULL


Tables referencing channel via foreign key constraints:

</protect>

Table: arraydesign

<protect>

Table: arraydesign
Module: Mage

General properties about an array. An array is a template used to generate physical slides, etc. It contains layout information, as well as global array properties, such as material (glass, nylon) and spot dimensions (in rows/columns).

arraydesign columns
FK Name Type Description
arraydesign_id serial PRIMARY KEY
contact manufacturer_id integer NOT NULL
cvterm platformtype_id integer NOT NULL
cvterm substratetype_id integer
protocol protocol_id integer
dbxref dbxref_id integer
name text UNIQUE

NOT NULL

version text
description text
array_dimensions text
element_dimensions text
num_of_elements integer
num_array_columns integer
num_array_rows integer
num_grid_columns integer
num_grid_rows integer
num_sub_columns integer
num_sub_rows integer

Tables referencing arraydesign via foreign key constraints:

</protect>

Table: arraydesignprop

<protect>

Table: arraydesignprop
Module: Mage

Extra array design properties that are not accounted for in arraydesign.

arraydesignprop columns
FK Name Type Description
arraydesignprop_id serial PRIMARY KEY
arraydesign arraydesign_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing arraydesignprop via foreign key constraints:

  • None.</protect>

Table: assay

<protect>

Table: assay
Module: Mage

An assay consists of a physical instance of an array, combined with the conditions used to create the array (protocols, technician information). The assay can be thought of as a hybridization.

assay columns
FK Name Type Description
assay_id serial PRIMARY KEY
arraydesign arraydesign_id integer NOT NULL
protocol protocol_id integer
assaydate timestamp without time zone DEFAULT now()
arrayidentifier text
arraybatchidentifier text
contact operator_id integer NOT NULL
dbxref dbxref_id integer
name text UNIQUE
description text

Tables referencing assay via foreign key constraints:

</protect>

Table: assayprop

<protect>

Table: assayprop
Module: Mage

Extra assay properties that are not accounted for in assay.

assayprop columns
FK Name Type Description
assayprop_id serial PRIMARY KEY
assay assay_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing assayprop via foreign key constraints:

  • None.</protect>

Table: assay_project

<protect>

Table: assay_project
Module: Mage

Link assays to projects.

assay_project columns
FK Name Type Description
assay_project_id serial PRIMARY KEY
assay assay_id integer UNIQUE#1

NOT NULL

project project_id integer UNIQUE#1

NOT NULL


Tables referencing assay_project via foreign key constraints:

  • None.</protect>

Table: biomaterial

<protect>

Table: biomaterial
Module: Mage

A biomaterial represents the MAGE concept of BioSource, BioSample, and LabeledExtract. It is essentially some biological material (tissue, cells, serum) that may have been processed. Processed biomaterials should be traceable back to raw biomaterials via the biomaterialrelationship table.

biomaterial columns
FK Name Type Description
biomaterial_id serial PRIMARY KEY
organism taxon_id integer
contact biosourceprovider_id integer
dbxref dbxref_id integer
name text UNIQUE
description text

Tables referencing biomaterial via foreign key constraints:

</protect>

Table: biomaterial_relationship

<protect>

Table: biomaterial_relationship
Module: Mage

Relate biomaterials to one another. This is a way to track a series of treatments or material splits/merges, for instance.

biomaterial_relationship columns
FK Name Type Description
biomaterial_relationship_id serial PRIMARY KEY
biomaterial subject_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

biomaterial object_id integer UNIQUE#1

NOT NULL


Tables referencing biomaterial_relationship via foreign key constraints:

  • None.</protect>

Table: biomaterialprop

<protect>

Table: biomaterialprop
Module: Mage

Extra biomaterial properties that are not accounted for in biomaterial.

biomaterialprop columns
FK Name Type Description
biomaterialprop_id serial PRIMARY KEY
biomaterial biomaterial_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing biomaterialprop via foreign key constraints:

  • None.</protect>

Table: biomaterial_dbxref

<protect>

Table: biomaterial_dbxref
Module: Mage


biomaterial_dbxref columns
FK Name Type Description
biomaterial_dbxref_id serial PRIMARY KEY
biomaterial biomaterial_id integer UNIQUE#1

NOT NULL

dbxref dbxref_id integer UNIQUE#1

NOT NULL


Tables referencing biomaterial_dbxref via foreign key constraints:

  • None.</protect>

Table: treatment

<protect>

Table: treatment
Module: Mage

A biomaterial may undergo multiple treatments. Examples of treatments: apoxia, fluorophore and biotin labeling.

treatment columns
FK Name Type Description
treatment_id serial PRIMARY KEY
rank integer NOT NULL
biomaterial biomaterial_id integer NOT NULL
cvterm type_id integer NOT NULL
protocol protocol_id integer
name text

Tables referencing treatment via foreign key constraints:

</protect>

Table: biomaterial_treatment

<protect>

Table: biomaterial_treatment
Module: Mage

Link biomaterials to treatments. Treatments have an order of operations (rank), and associated measurements (unittype_id, value).

biomaterial_treatment columns
FK Name Type Description
biomaterial_treatment_id serial PRIMARY KEY
biomaterial biomaterial_id integer UNIQUE#1

NOT NULL

treatment treatment_id integer UNIQUE#1

NOT NULL

cvterm unittype_id integer
value real
rank integer NOT NULL


Tables referencing biomaterial_treatment via foreign key constraints:

  • None.</protect>

Table: assay_biomaterial

<protect>

Table: assay_biomaterial
Module: Mage

A biomaterial can be hybridized many times (technical replicates), or combined with other biomaterials in a single hybridization (for two-channel arrays).

assay_biomaterial columns
FK Name Type Description
assay_biomaterial_id serial PRIMARY KEY
assay assay_id integer UNIQUE#1

NOT NULL

biomaterial biomaterial_id integer UNIQUE#1

NOT NULL

channel channel_id integer UNIQUE#1
rank integer UNIQUE#1

NOT NULL


Tables referencing assay_biomaterial via foreign key constraints:

  • None.</protect>

Table: acquisition

<protect>

Table: acquisition
Module: Mage

This represents the scanning of hybridized material. The output of this process is typically a digital image of an array.

acquisition columns
FK Name Type Description
acquisition_id serial PRIMARY KEY
assay assay_id integer NOT NULL
protocol protocol_id integer
channel channel_id integer
acquisitiondate timestamp without time zone DEFAULT now()
name text UNIQUE
uri text

Tables referencing acquisition via foreign key constraints:

</protect>

Table: acquisitionprop

<protect>

Table: acquisitionprop
Module: Mage

Parameters associated with image acquisition.

acquisitionprop columns
FK Name Type Description
acquisitionprop_id serial PRIMARY KEY
acquisition acquisition_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing acquisitionprop via foreign key constraints:

  • None.</protect>

Table: acquisition_relationship

<protect>

Table: acquisition_relationship
Module: Mage

Multiple monochrome images may be merged to form a multi-color image. Red-green images of 2-channel hybridizations are an example of this.

acquisition_relationship columns
FK Name Type Description
acquisition_relationship_id serial PRIMARY KEY
acquisition subject_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

acquisition object_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing acquisition_relationship via foreign key constraints:

  • None.</protect>

Table: quantification

<protect>

Table: quantification
Module: Mage

Quantification is the transformation of an image acquisition to numeric data. This typically involves statistical procedures.

quantification columns
FK Name Type Description
quantification_id serial PRIMARY KEY
acquisition acquisition_id integer NOT NULL
contact operator_id integer
protocol protocol_id integer
analysis analysis_id integer UNIQUE#1

NOT NULL

quantificationdate timestamp without time zone DEFAULT now()
name text UNIQUE#1
uri text

Tables referencing quantification via foreign key constraints:

</protect>

Table: quantificationprop

<protect>

Table: quantificationprop
Module: Mage

Extra quantification properties that are not accounted for in quantification.

quantificationprop columns
FK Name Type Description
quantificationprop_id serial PRIMARY KEY
quantification quantification_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing quantificationprop via foreign key constraints:

  • None.</protect>

Table: quantification_relationship

<protect>

Table: quantification_relationship
Module: Mage

There may be multiple rounds of quantification, this allows us to keep an audit trail of what values went where.

quantification_relationship columns
FK Name Type Description
quantification_relationship_id serial PRIMARY KEY
quantification subject_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

quantification object_id integer UNIQUE#1

NOT NULL


Tables referencing quantification_relationship via foreign key constraints:

  • None.</protect>

Table: control

<protect>

Table: control
Module: Mage


control columns
FK Name Type Description
control_id serial PRIMARY KEY
cvterm type_id integer NOT NULL
assay assay_id integer NOT NULL
tableinfo tableinfo_id integer NOT NULL
row_id integer NOT NULL
name text
value text
rank integer NOT NULL


Tables referencing control via foreign key constraints:

  • None.</protect>

Table: element

<protect>

Table: element
Module: Mage

Represents a feature of the array. This is typically a region of the array coated or bound to DNA.

element columns
FK Name Type Description
element_id serial PRIMARY KEY
feature feature_id integer UNIQUE#1
arraydesign arraydesign_id integer UNIQUE#1

NOT NULL

cvterm type_id integer
dbxref dbxref_id integer

Tables referencing element via foreign key constraints:

</protect>

Table: elementresult

<protect>

Table: elementresult
Module: Mage

An element on an array produces a measurement when hybridized to a biomaterial (traceable through quantification_id). This is the base data from which tables that actually contain data inherit.

elementresult columns
FK Name Type Description
elementresult_id serial PRIMARY KEY
element element_id integer UNIQUE#1

NOT NULL

quantification quantification_id integer UNIQUE#1

NOT NULL

signal double precision NOT NULL


Tables referencing elementresult via foreign key constraints:

</protect>

Table: element_relationship

<protect>

Table: element_relationship
Module: Mage

Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.

element_relationship columns
FK Name Type Description
element_relationship_id serial PRIMARY KEY
element subject_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

element object_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing element_relationship via foreign key constraints:

  • None.</protect>

Table: elementresult_relationship

<protect>

Table: elementresult_relationship
Module: Mage

Sometimes we want to combine measurements from multiple elements to get a composite value. Affymetrix combines many probes to form a probeset measurement, for instance.

elementresult_relationship columns
FK Name Type Description
elementresult_relationship_id serial PRIMARY KEY
elementresult subject_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

elementresult object_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing elementresult_relationship via foreign key constraints:

  • None.</protect>

Table: study

<protect>

Table: study
Module: Mage


study columns
FK Name Type Description
study_id serial PRIMARY KEY
contact contact_id integer NOT NULL
pub pub_id integer
dbxref dbxref_id integer
name text UNIQUE

NOT NULL

description text

Tables referencing study via foreign key constraints:

</protect>

Table: study_assay

<protect>

Table: study_assay
Module: Mage


study_assay columns
FK Name Type Description
study_assay_id serial PRIMARY KEY
study study_id integer UNIQUE#1

NOT NULL

assay assay_id integer UNIQUE#1

NOT NULL


Tables referencing study_assay via foreign key constraints:

  • None.</protect>

Table: studydesign

<protect>

Table: studydesign
Module: Mage


studydesign columns
FK Name Type Description
studydesign_id serial PRIMARY KEY
study study_id integer NOT NULL
description text

Tables referencing studydesign via foreign key constraints:

</protect>

Table: studydesignprop

<protect>

Table: studydesignprop
Module: Mage


studydesignprop columns
FK Name Type Description
studydesignprop_id serial PRIMARY KEY
studydesign studydesign_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing studydesignprop via foreign key constraints:

  • None.</protect>

Table: studyfactor

<protect>

Table: studyfactor
Module: Mage


studyfactor columns
FK Name Type Description
studyfactor_id serial PRIMARY KEY
studydesign studydesign_id integer NOT NULL
cvterm type_id integer
name text NOT NULL
description text

Tables referencing studyfactor via foreign key constraints:

</protect>

Table: studyfactorvalue

<protect>

Table: studyfactorvalue
Module: Mage


studyfactorvalue columns
FK Name Type Description
studyfactorvalue_id serial PRIMARY KEY
studyfactor studyfactor_id integer NOT NULL
assay assay_id integer NOT NULL
factorvalue text
name text
rank integer NOT NULL


Tables referencing studyfactorvalue via foreign key constraints:

  • None.</protect>

Table: studyprop

<protect>

Table: studyprop
Module: Mage


studyprop columns
FK Name Type Description
studyprop_id serial PRIMARY KEY
study study_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing studyprop via foreign key constraints:

</protect>

Table: studyprop_feature

<protect>

Table: studyprop_feature
Module: Mage


studyprop_feature columns
FK Name Type Description
studyprop_feature_id serial PRIMARY KEY
studyprop studyprop_id integer UNIQUE#1

NOT NULL

feature feature_id integer UNIQUE#1

NOT NULL

cvterm type_id integer

Tables referencing studyprop_feature via foreign key constraints:

  • None.</protect>

Module: Map

Table: featuremap

<protect>

Table: featuremap
Module: Map


featuremap columns
FK Name Type Description
featuremap_id serial PRIMARY KEY
name character varying(255) UNIQUE
description text
cvterm unittype_id integer

Tables referencing featuremap via foreign key constraints:

</protect>

Table: featurerange

<protect>

Table: featurerange
Module: Map

In cases where the start and end of a mapped feature is a range, leftendf and rightstartf are populated. leftstartf_id, leftendf_id, rightstartf_id, rightendf_id are the ids of features with respect to which the feature is being mapped. These may be cytological bands.

featurerange columns
FK Name Type Description
featurerange_id serial PRIMARY KEY
featuremap featuremap_id integer NOT NULL

featuremap_id is the id of the feature being mapped.

feature feature_id integer NOT NULL
feature leftstartf_id integer NOT NULL
feature leftendf_id integer
feature rightstartf_id integer
feature rightendf_id integer NOT NULL
rangestr character varying(255)

Tables referencing featurerange via foreign key constraints:

  • None.</protect>

Table: featurepos

<protect>

Table: featurepos
Module: Map


featurepos columns
FK Name Type Description
featurepos_id serial PRIMARY KEY
featuremap featuremap_id serial NOT NULL
feature feature_id integer NOT NULL
feature map_feature_id integer NOT NULL

map_feature_id links to the feature (map) upon which the feature is being localized.

mappos double precision NOT NULL


Tables referencing featurepos via foreign key constraints:

  • None.</protect>

Table: featuremap_pub

<protect>

Table: featuremap_pub
Module: Map


featuremap_pub columns
FK Name Type Description
featuremap_pub_id serial PRIMARY KEY
featuremap featuremap_id integer NOT NULL
pub pub_id integer NOT NULL


Tables referencing featuremap_pub via foreign key constraints:

  • None.</protect>

Module: Natural Diversity

Table: nd_geolocation

<protect>

Table: nd_geolocation
Module: Natural Diversity

The geo-referencable location of the stock. NOTE: This entity is subject to change as a more general and possibly more OpenGIS-compliant geolocation module may be introduced into Chado.

nd_geolocation columns
FK Name Type Description
nd_geolocation_id serial PRIMARY KEY
description character varying(255) A textual representation of the location, if this is the original georeference. Optional if the original georeference is available in lat/long coordinates.
latitude real The decimal latitude coordinate of the georeference, using positive and negative sign to indicate N and S, respectively.
longitude real The decimal longitude coordinate of the georeference, using positive and negative sign to indicate E and W, respectively.
geodetic_datum character varying(32) The geodetic system on which the geo-reference coordinates are based. For geo-references measured between 1984 and 2010, this will typically be WGS84.
altitude real The altitude (elevation) of the location in meters. If the altitude is only known as a range, this is the average, and altitude_dev will hold half of the width of the range.

Tables referencing nd_geolocation via foreign key constraints:

</protect>

Table: nd_experiment

<protect>

Table: nd_experiment
Module: Natural Diversity


nd_experiment columns
FK Name Type Description
nd_experiment_id serial PRIMARY KEY
nd_geolocation nd_geolocation_id integer NOT NULL
cvterm type_id integer NOT NULL


Tables referencing nd_experiment via foreign key constraints:

</protect>

Table: nd_experiment_project

<protect>

Table: nd_experiment_project
Module: Natural Diversity


nd_experiment_project columns
FK Name Type Description
nd_experiment_project_id serial PRIMARY KEY
project project_id integer NOT NULL
nd_experiment nd_experiment_id integer NOT NULL


Tables referencing nd_experiment_project via foreign key constraints:

  • None.</protect>

Table: nd_experimentprop

<protect>

Table: nd_experimentprop
Module: Natural Diversity


nd_experimentprop columns
FK Name Type Description
nd_experimentprop_id serial PRIMARY KEY
nd_experiment nd_experiment_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value character varying(255) NOT NULL
rank integer UNIQUE#1

NOT NULL


Tables referencing nd_experimentprop via foreign key constraints:

  • None.</protect>

Table: nd_experiment_pub

<protect>

Table: nd_experiment_pub
Module: Natural Diversity

Linking nd_experiment(s) to publication(s)

nd_experiment_pub columns
FK Name Type Description
nd_experiment_pub_id serial PRIMARY KEY
nd_experiment nd_experiment_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing nd_experiment_pub via foreign key constraints:

  • None.</protect>

Table: nd_geolocationprop

<protect>

Table: nd_geolocationprop
Module: Natural Diversity

Property/value associations for geolocations. This table can store the properties such as location and environment

nd_geolocationprop columns
FK Name Type Description
nd_geolocationprop_id serial PRIMARY KEY
nd_geolocation nd_geolocation_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL
The name of the property as a reference to a controlled vocabulary term.

value character varying(250) The value of the property.
rank integer UNIQUE#1

NOT NULL
The rank of the property value, if the property has an array of values.

Tables referencing nd_geolocationprop via foreign key constraints:

  • None.</protect>

Table: nd_protocol

<protect>

Table: nd_protocol
Module: Natural Diversity

A protocol can be anything that is done as part of the experiment.

nd_protocol columns
FK Name Type Description
nd_protocol_id serial PRIMARY KEY
name character varying(255) UNIQUE

NOT NULL
The protocol name.

Tables referencing nd_protocol via foreign key constraints:

</protect>

Table: nd_reagent

<protect>

Table: nd_reagent
Module: Natural Diversity

A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping experiments, or in any other kind of experiment.

nd_reagent columns
FK Name Type Description
nd_reagent_id serial PRIMARY KEY
name character varying(80) NOT NULL

The name of the reagent. The name should be unique for a given type.

cvterm type_id integer NOT NULL

The type of the reagent, for example linker oligomer, or forward primer.

feature_id integer If the reagent is a primer, the feature that it corresponds to. More generally, the corresponding feature for any reagent that has a sequence that maps to another sequence.

Tables referencing nd_reagent via foreign key constraints:

</protect>

Table: nd_protocol_reagent

<protect>

Table: nd_protocol_reagent
Module: Natural Diversity


nd_protocol_reagent columns
FK Name Type Description
nd_protocol_reagent_id serial PRIMARY KEY
nd_protocol nd_protocol_id integer NOT NULL
nd_reagent reagent_id integer NOT NULL
cvterm type_id integer NOT NULL


Tables referencing nd_protocol_reagent via foreign key constraints:

  • None.</protect>

Table: nd_protocolprop

<protect>

Table: nd_protocolprop
Module: Natural Diversity

Property/value associations for protocol.

nd_protocolprop columns
FK Name Type Description
nd_protocolprop_id serial PRIMARY KEY
nd_protocol nd_protocol_id integer UNIQUE#1

NOT NULL
The protocol to which the property applies.

cvterm type_id integer UNIQUE#1

NOT NULL
The name of the property as a reference to a controlled vocabulary term.

value character varying(255) The value of the property.
rank integer UNIQUE#1

NOT NULL
The rank of the property value, if the property has an array of values.

Tables referencing nd_protocolprop via foreign key constraints:

  • None.</protect>

Table: nd_experiment_stock

<protect>

Table: nd_experiment_stock
Module: Natural Diversity

Part of a stock or a clone of a stock that is used in an experiment

nd_experiment_stock columns
FK Name Type Description
nd_experiment_stock_id serial PRIMARY KEY
nd_experiment nd_experiment_id integer NOT NULL
stock stock_id integer NOT NULL

stock used in the extraction or the corresponding stock for the clone

cvterm type_id integer NOT NULL


Tables referencing nd_experiment_stock via foreign key constraints:

</protect>

Table: nd_experiment_protocol

<protect>

Table: nd_experiment_protocol
Module: Natural Diversity

Linking table: experiments to the protocols they involve.

nd_experiment_protocol columns
FK Name Type Description
nd_experiment_protocol_id serial PRIMARY KEY
nd_experiment nd_experiment_id integer NOT NULL
nd_protocol nd_protocol_id integer NOT NULL


Tables referencing nd_experiment_protocol via foreign key constraints:

  • None.</protect>

Table: nd_experiment_phenotype

<protect>

Table: nd_experiment_phenotype
Module: Natural Diversity

Linking table: experiments to the phenotypes they produce. There is a one-to-one relationship between an experiment and a phenotype since each phenotype record should point to one experiment. Add a new experiment_id for each phenotype record.

nd_experiment_phenotype columns
FK Name Type Description
nd_experiment_phenotype_id serial PRIMARY KEY
nd_experiment nd_experiment_id integer UNIQUE

NOT NULL

phenotype phenotype_id integer NOT NULL


Tables referencing nd_experiment_phenotype via foreign key constraints:

  • None.</protect>

Table: nd_experiment_genotype

<protect>

Table: nd_experiment_genotype
Module: Natural Diversity

Linking table: experiments to the genotypes they produce. There is a one-to-one relationship between an experiment and a genotype since each genotype record should point to one experiment. Add a new experiment_id for each genotype record.

nd_experiment_genotype columns
FK Name Type Description
nd_experiment_genotype_id serial PRIMARY KEY
nd_experiment nd_experiment_id integer UNIQUE

NOT NULL

genotype genotype_id integer NOT NULL


Tables referencing nd_experiment_genotype via foreign key constraints:

  • None.</protect>

Table: nd_reagent_relationship

<protect>

Table: nd_reagent_relationship
Module: Natural Diversity

Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme experiment reagents.

nd_reagent_relationship columns
FK Name Type Description
nd_reagent_relationship_id serial PRIMARY KEY
nd_reagent subject_reagent_id integer NOT NULL

The subject reagent in the relationship. In parent/child terminology, the subject is the child. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.

nd_reagent object_reagent_id integer NOT NULL

The object reagent in the relationship. In parent/child terminology, the object is the parent. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.

cvterm type_id integer NOT NULL

The type (or predicate) of the relationship. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.

Tables referencing nd_reagent_relationship via foreign key constraints:

  • None.</protect>

Table: nd_reagentprop

<protect>

Table: nd_reagentprop
Module: Natural Diversity


nd_reagentprop columns
FK Name Type Description
nd_reagentprop_id serial PRIMARY KEY
nd_reagent nd_reagent_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value character varying(255)
rank integer UNIQUE#1

NOT NULL


Tables referencing nd_reagentprop via foreign key constraints:

  • None.</protect>

Table: nd_experiment_stockprop

<protect>

Table: nd_experiment_stockprop
Module: Natural Diversity

Property/value associations for experiment_stocks. This table can store the properties such as treatment

nd_experiment_stockprop columns
FK Name Type Description
nd_experiment_stockprop_id serial PRIMARY KEY
nd_experiment_stock nd_experiment_stock_id integer UNIQUE#1

NOT NULL
The experiment_stock to which the property applies.

cvterm type_id integer UNIQUE#1

NOT NULL
The name of the property as a reference to a controlled vocabulary term.

value character varying(255) The value of the property.
rank integer UNIQUE#1

NOT NULL
The rank of the property value, if the property has an array of values.

Tables referencing nd_experiment_stockprop via foreign key constraints:

  • None.</protect>

Table: nd_experiment_stock_dbxref

<protect>

Table: nd_experiment_stock_dbxref
Module: Natural Diversity

Cross-reference experiment_stock to accessions, images, etc

nd_experiment_stock_dbxref columns
FK Name Type Description
nd_experiment_stock_dbxref_id serial PRIMARY KEY
nd_experiment_stock nd_experiment_stock_id integer NOT NULL
dbxref dbxref_id integer NOT NULL


Tables referencing nd_experiment_stock_dbxref via foreign key constraints:

  • None.</protect>

Table: nd_experiment_dbxref

<protect>

Table: nd_experiment_dbxref
Module: Natural Diversity

Cross-reference experiment to accessions, images, etc

nd_experiment_dbxref columns
FK Name Type Description
nd_experiment_dbxref_id serial PRIMARY KEY
nd_experiment nd_experiment_id integer NOT NULL
dbxref dbxref_id integer NOT NULL


Tables referencing nd_experiment_dbxref via foreign key constraints:

  • None.</protect>

Table: nd_experiment_contact

<protect>

Table: nd_experiment_contact
Module: Natural Diversity


nd_experiment_contact columns
FK Name Type Description
nd_experiment_contact_id serial PRIMARY KEY
nd_experiment nd_experiment_id integer NOT NULL
contact contact_id integer NOT NULL


Tables referencing nd_experiment_contact via foreign key constraints:

  • None.</protect>

Module: Phenotype

Table: phenotype

<protect>

Table: phenotype
Module: Phenotype

A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function. E.g. Obs=eye, attribute=color, cvalue=red.

phenotype columns
FK Name Type Description
phenotype_id serial PRIMARY KEY
uniquename text UNIQUE

NOT NULL

cvterm observable_id integer The entity: e.g. anatomy_part, biological_process.
cvterm attr_id integer Phenotypic attribute (quality, property, attribute, character) - drawn from PATO.
value text Value of attribute - unconstrained free text. Used only if cvalue_id is not appropriate.
cvterm cvalue_id integer Phenotype attribute value (state).
cvterm assay_id integer Evidence type.

Tables referencing phenotype via foreign key constraints:

</protect>

Table: phenotype_cvterm

<protect>

Table: phenotype_cvterm
Module: Phenotype


phenotype_cvterm columns
FK Name Type Description
phenotype_cvterm_id serial PRIMARY KEY
phenotype phenotype_id integer UNIQUE#1

NOT NULL

cvterm cvterm_id integer UNIQUE#1

NOT NULL

rank integer UNIQUE#1

NOT NULL


Tables referencing phenotype_cvterm via foreign key constraints:

  • None.</protect>

Table: feature_phenotype

<protect>

Table: feature_phenotype
Module: Phenotype


feature_phenotype columns
FK Name Type Description
feature_phenotype_id serial PRIMARY KEY
feature feature_id integer UNIQUE#1

NOT NULL

phenotype phenotype_id integer UNIQUE#1

NOT NULL


Tables referencing feature_phenotype via foreign key constraints:

  • None.</protect>

Module: Phylogeny

Table: phylotree

<protect>

Table: phylotree
Module: Phylogeny

Global anchor for phylogenetic tree.

phylotree columns
FK Name Type Description
phylotree_id serial PRIMARY KEY
dbxref dbxref_id integer NOT NULL
name character varying(255)
cvterm type_id integer Type: protein, nucleotide, taxonomy, for example. The type should be any SO type, or "taxonomy".
analysis analysis_id integer
comment text

Tables referencing phylotree via foreign key constraints:

</protect>

Table: phylotree_pub

<protect>

Table: phylotree_pub
Module: Phylogeny

Tracks citations global to the tree e.g. multiple sequence alignment supporting tree construction.

phylotree_pub columns
FK Name Type Description
phylotree_pub_id serial PRIMARY KEY
phylotree phylotree_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing phylotree_pub via foreign key constraints:

  • None.</protect>

Table: phylonode

<protect>

Table: phylonode
Module: Phylogeny

This is the most pervasive

      element in the phylogeny module, cataloging the "phylonodes" of
      tree graphs. Edges are implied by the parent_phylonode_id
      reflexive closure. For all nodes in a nested set implementation the left and right index will be *between* the parents left and right indexes.
phylonode columns
FK Name Type Description
phylonode_id serial PRIMARY KEY
phylotree phylotree_id integer UNIQUE#1

UNIQUE#2
NOT NULL

phylonode parent_phylonode_id integer Root phylonode can have null parent_phylonode_id value.
left_idx integer UNIQUE#1

NOT NULL

right_idx integer UNIQUE#2

NOT NULL

cvterm type_id integer Type: e.g. root, interior, leaf.
feature feature_id integer Phylonodes can have optional features attached to them e.g. a protein or nucleotide sequence usually attached to a leaf of the phylotree for non-leaf nodes, the feature may be a feature that is an instance of SO:match; this feature is the alignment of all leaf features beneath it.
label character varying(255)
distance double precision

Tables referencing phylonode via foreign key constraints:

</protect>

Table: phylonode_dbxref

<protect>

Table: phylonode_dbxref
Module: Phylogeny

For example, for orthology, paralogy group identifiers; could also be used for NCBI taxonomy; for sequences, refer to phylonode_feature, feature associated dbxrefs.

phylonode_dbxref columns
FK Name Type Description
phylonode_dbxref_id serial PRIMARY KEY
phylonode phylonode_id integer UNIQUE#1

NOT NULL

dbxref dbxref_id integer UNIQUE#1

NOT NULL


Tables referencing phylonode_dbxref via foreign key constraints:

  • None.</protect>

Table: phylonode_pub

<protect>

Table: phylonode_pub
Module: Phylogeny


phylonode_pub columns
FK Name Type Description
phylonode_pub_id serial PRIMARY KEY
phylonode phylonode_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing phylonode_pub via foreign key constraints:

  • None.</protect>

Table: phylonode_organism

<protect>

Table: phylonode_organism
Module: Phylogeny

This linking table should only be used for nodes in taxonomy trees; it provides a mapping between the node and an organism. One node can have zero or one organisms, one organism can have zero or more nodes (although typically it should only have one in the standard NCBI taxonomy tree).

phylonode_organism columns
FK Name Type Description
phylonode_organism_id serial PRIMARY KEY
phylonode phylonode_id integer UNIQUE

NOT NULL
One phylonode cannot refer to >1 organism.

organism organism_id integer NOT NULL


Tables referencing phylonode_organism via foreign key constraints:

  • None.</protect>

Table: phylonodeprop

<protect>

Table: phylonodeprop
Module: Phylogeny


phylonodeprop columns
FK Name Type Description
phylonodeprop_id serial PRIMARY KEY
phylonode phylonode_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL
type_id could designate phylonode hierarchy relationships, for example: species taxonomy (kingdom, order, family, genus, species), "ortholog/paralog", "fold/superfold", etc.

value text UNIQUE#1

NOT NULL
DEFAULT ''::text

rank integer UNIQUE#1

NOT NULL


Tables referencing phylonodeprop via foreign key constraints:

  • None.</protect>

Table: phylonode_relationship

<protect>

Table: phylonode_relationship
Module: Phylogeny

This is for relationships that are not strictly hierarchical; for example, horizontal gene transfer. Most phylogenetic trees are strictly hierarchical, nevertheless it is here for completeness.

phylonode_relationship columns
FK Name Type Description
phylonode_relationship_id serial PRIMARY KEY
phylonode subject_id integer UNIQUE#1

NOT NULL

phylonode object_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

rank integer
phylotree phylotree_id integer NOT NULL


Tables referencing phylonode_relationship via foreign key constraints:

  • None.</protect>

Module: Project

Table: project

<protect>

Table: project
Module: Project


project columns
FK Name Type Description
project_id serial PRIMARY KEY
name character varying(255) UNIQUE

NOT NULL

description character varying(255) NOT NULL


Tables referencing project via foreign key constraints:

</protect>

Table: projectprop

<protect>

Table: projectprop
Module: Project


projectprop columns
FK Name Type Description
projectprop_id serial PRIMARY KEY
project project_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing projectprop via foreign key constraints:

  • None.</protect>

Table: project_relationship

<protect>

Table: project_relationship
Module: Project

A project can be composed of several smaller scale projects

project_relationship columns
FK Name Type Description
project_relationship_id serial PRIMARY KEY
project subject_project_id integer UNIQUE#1

NOT NULL

project object_project_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL
The type of relationship being stated, such as "is part of".

Tables referencing project_relationship via foreign key constraints:

  • None.</protect>

Table: project_pub

<protect>

Table: project_pub
Module: Project

Linking project(s) to publication(s)

project_pub columns
FK Name Type Description
project_pub_id serial PRIMARY KEY
project project_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing project_pub via foreign key constraints:

  • None.</protect>

Table: project_contact

<protect>

Table: project_contact
Module: Project

Linking project(s) to contact(s)

project_contact columns
FK Name Type Description
project_contact_id serial PRIMARY KEY
project project_id integer UNIQUE#1

NOT NULL

contact contact_id integer UNIQUE#1

NOT NULL


Tables referencing project_contact via foreign key constraints:

  • None.</protect>

Module: Stock

Table: stock

<protect>

Table: stock
Module: Stock

Any stock can be globally identified by the combination of organism, uniquename and stock type. A stock is the physical entities, either living or preserved, held by collections. Stocks belong to a collection; they have IDs, type, organism, description and may have a genotype.

stock columns
FK Name Type Description
stock_id serial PRIMARY KEY
dbxref dbxref_id integer The dbxref_id is an optional primary stable identifier for this stock. Secondary indentifiers and external dbxrefs go in table: stock_dbxref.
organism organism_id integer UNIQUE#1

The organism_id is the organism to which the stock belongs. This column should only be left blank if the organism cannot be determined.

name character varying(255) The name is a human-readable local name for a stock.
uniquename text UNIQUE#1

NOT NULL

description text The description is the genetic description provided in the stock list.
cvterm type_id integer UNIQUE#1

NOT NULL
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.

is_obsolete boolean NOT NULL

DEFAULT false


Tables referencing stock via foreign key constraints:

</protect>

Table: stock_pub

<protect>

Table: stock_pub
Module: Stock

Provenance. Linking table between stocks and, for example, a stocklist computer file.

stock_pub columns
FK Name Type Description
stock_pub_id serial PRIMARY KEY
stock stock_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing stock_pub via foreign key constraints:

  • None.</protect>

Table: stockprop

<protect>

Table: stockprop
Module: Stock

A stock can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stockprop_c1, for the combination of stock_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.

stockprop columns
FK Name Type Description
stockprop_id serial PRIMARY KEY
stock stock_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing stockprop via foreign key constraints:

</protect>

Table: stockprop_pub

<protect>

Table: stockprop_pub
Module: Stock

Provenance. Any stockprop assignment can optionally be supported by a publication.

stockprop_pub columns
FK Name Type Description
stockprop_pub_id serial PRIMARY KEY
stockprop stockprop_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing stockprop_pub via foreign key constraints:

  • None.</protect>

Table: stock_relationship

<protect>

Table: stock_relationship
Module: Stock


stock_relationship columns
FK Name Type Description
stock_relationship_id serial PRIMARY KEY
stock subject_id integer UNIQUE#1

NOT NULL
stock_relationship.subject_id is the subject of the subj-predicate-obj sentence. This is typically the substock.

stock object_id integer UNIQUE#1

NOT NULL
stock_relationship.object_id is the object of the subj-predicate-obj sentence. This is typically the container stock.

cvterm type_id integer UNIQUE#1

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.

value text stock_relationship.value is for additional notes or comments.
rank integer UNIQUE#1

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.

Tables referencing stock_relationship via foreign key constraints:

</protect>

Table: stock_relationship_cvterm

<protect>

Table: stock_relationship_cvterm
Module: Stock

For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm

stock_relationship_cvterm columns
FK Name Type Description
stock_relationship_cvterm_id serial PRIMARY KEY
stock_relatiohship_id integer NOT NULL
cvterm cvterm_id integer NOT NULL
pub pub_id integer

Tables referencing stock_relationship_cvterm via foreign key constraints:

  • None.</protect>

Table: stock_relationship_pub

<protect>

Table: stock_relationship_pub
Module: Stock

Provenance. Attach optional evidence to a stock_relationship in the form of a publication.

stock_relationship_pub columns
FK Name Type Description
stock_relationship_pub_id serial PRIMARY KEY
stock_relationship stock_relationship_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing stock_relationship_pub via foreign key constraints:

  • None.</protect>

Table: stock_dbxref

<protect>

Table: stock_dbxref
Module: Stock

stock_dbxref links a stock to dbxrefs. This is for secondary identifiers; primary identifiers should use stock.dbxref_id.

stock_dbxref columns
FK Name Type Description
stock_dbxref_id serial PRIMARY KEY
stock stock_id integer UNIQUE#1

NOT NULL

dbxref dbxref_id integer UNIQUE#1

NOT NULL

is_current boolean NOT NULL

DEFAULT true
The is_current boolean indicates whether the linked dbxref is the current -official- dbxref for the linked stock.

Tables referencing stock_dbxref via foreign key constraints:

</protect>

Table: stock_cvterm

<protect>

Table: stock_cvterm
Module: Stock

stock_cvterm links a stock to cvterms. This is for secondary cvterms; primary cvterms should use stock.type_id.

stock_cvterm columns
FK Name Type Description
stock_cvterm_id serial PRIMARY KEY
stock stock_id integer UNIQUE#1

NOT NULL

cvterm cvterm_id integer UNIQUE#1

NOT NULL

pub pub_id integer UNIQUE#1

NOT NULL


Tables referencing stock_cvterm via foreign key constraints:

  • None.</protect>

Table: stock_genotype

<protect>

Table: stock_genotype
Module: Stock

Simple table linking a stock to a genotype. Features with genotypes can be linked to stocks thru feature_genotype -> genotype -> stock_genotype -> stock.

stock_genotype columns
FK Name Type Description
stock_genotype_id serial PRIMARY KEY
stock stock_id integer UNIQUE#1

NOT NULL

genotype genotype_id integer UNIQUE#1

NOT NULL


Tables referencing stock_genotype via foreign key constraints:

  • None.</protect>

Table: stockcollection

<protect>

Table: stockcollection
Module: Stock

The lab or stock center distributing the stocks in their collection.

stockcollection columns
FK Name Type Description
stockcollection_id serial PRIMARY KEY
cvterm type_id integer UNIQUE#1

NOT NULL
type_id is the collection type cv.

contact contact_id integer contact_id links to the contact information for the collection.
name character varying(255) name is the collection.
uniquename text UNIQUE#1

NOT NULL
uniqename is the value of the collection cv.

Tables referencing stockcollection via foreign key constraints:

</protect>

Table: stockcollectionprop

<protect>

Table: stockcollectionprop
Module: Stock

The table stockcollectionprop contains the value of the stock collection such as website/email URLs; the value of the stock collection order URLs.

stockcollectionprop columns
FK Name Type Description
stockcollectionprop_id serial PRIMARY KEY
stockcollection stockcollection_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL
The cv for the type_id is "stockcollection property type".

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing stockcollectionprop via foreign key constraints:

  • None.</protect>

Table: stockcollection_stock

<protect>

Table: stockcollection_stock
Module: Stock

stockcollection_stock links a stock collection to the stocks which are contained in the collection.

stockcollection_stock columns
FK Name Type Description
stockcollection_stock_id serial PRIMARY KEY
stockcollection stockcollection_id integer UNIQUE#1

NOT NULL

stock stock_id integer UNIQUE#1

NOT NULL


Tables referencing stockcollection_stock via foreign key constraints:

  • None.</protect>

Table: stock_dbxrefprop

<protect>

Table: stock_dbxrefprop
Module: Stock

A stock_dbxref can have any number of slot-value property tags attached to it. This is useful for storing properties related to dbxref annotations of stocks, such as evidence codes, and references, and metadata, such as create/modify dates. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, stock_dbxrefprop_c1, for the combination of stock_dbxref_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.

stock_dbxrefprop columns
FK Name Type Description
stock_dbxrefprop_id serial PRIMARY KEY
stock_dbxref stock_dbxref_id integer UNIQUE#1

NOT NULL

cvterm type_id integer UNIQUE#1

NOT NULL

value text
rank integer UNIQUE#1

NOT NULL


Tables referencing stock_dbxrefprop via foreign key constraints:

  • None.</protect>

Module: WWW

Table: wwwuser

Template:ChadoTable wwwuser

Table: wwwuser_project

Template:ChadoTable wwwuser project

Table: wwwuser_author

Template:ChadoTable wwwuser author

Table: wwwuser_cvterm

Template:ChadoTable wwwuser cvterm

Table: wwwuser_expression

Template:ChadoTable wwwuser expression

Table: wwwuser_feature

Template:ChadoTable wwwuser feature

Table: wwwuser_genotype

Template:ChadoTable wwwuser genotype

Table: wwwuser_interaction

Template:ChadoTable wwwuser interaction

Table: wwwuser_organism

Template:ChadoTable wwwuser organism

Table: wwwuser_phenotype

Template:ChadoTable wwwuser phenotype

Table: wwwuser_pub

Template:ChadoTable wwwuser pub

Table: wwwuserrelationship

Template:ChadoTable wwwuserrelationship

Module: Audit

Table: audit_tableinfo

Template:ChadoTable audit tableinfo

Table: audit_db

Template:ChadoTable audit db

Table: audit_dbxref

Template:ChadoTable audit dbxref

Table: audit_cv

Template:ChadoTable audit cv

Table: audit_cvterm

Template:ChadoTable audit cvterm

Table: audit_cvterm_relationship

Template:ChadoTable audit cvterm relationship

Table: audit_cvtermpath

Template:ChadoTable audit cvtermpath

Table: audit_cvtermsynonym

Template:ChadoTable audit cvtermsynonym

Table: audit_cvterm_dbxref

Template:ChadoTable audit cvterm dbxref

Table: audit_cvtermprop

Template:ChadoTable audit cvtermprop

Table: audit_dbxrefprop

Template:ChadoTable audit dbxrefprop

Table: audit_pub

Template:ChadoTable audit pub

Table: audit_pub_relationship

Template:ChadoTable audit pub relationship

Table: audit_pub_dbxref

Template:ChadoTable audit pub dbxref

Table: audit_pubauthor

Template:ChadoTable audit pubauthor

Table: audit_pubprop

Template:ChadoTable audit pubprop

Table: audit_organism

Template:ChadoTable audit organism

Table: audit_organism_dbxref

Template:ChadoTable audit organism dbxref

Table: audit_organismprop

Template:ChadoTable audit organismprop

Table: audit_feature

Template:ChadoTable audit feature

Table: audit_featureloc

Template:ChadoTable audit featureloc

Table: audit_featureloc_pub

Template:ChadoTable audit featureloc pub

Table: audit_feature_pub

Template:ChadoTable audit feature pub

Table: audit_feature_pubprop

Template:ChadoTable audit feature pubprop

Table: audit_featureprop

Template:ChadoTable audit featureprop

Table: audit_featureprop_pub

Template:ChadoTable audit featureprop pub

Table: audit_feature_dbxref

Template:ChadoTable audit feature dbxref

Table: audit_feature_relationship

Template:ChadoTable audit feature relationship

Table: audit_feature_relationship_pub

Template:ChadoTable audit feature relationship pub

Table: audit_feature_relationshipprop

Template:ChadoTable audit feature relationshipprop

Table: audit_feature_relationshipprop_pub

Template:ChadoTable audit feature relationshipprop pub

Table: audit_feature_cvterm

Template:ChadoTable audit feature cvterm

Table: audit_feature_cvtermprop

Template:ChadoTable audit feature cvtermprop

Table: audit_feature_cvterm_dbxref

Template:ChadoTable audit feature cvterm dbxref

Table: audit_feature_cvterm_pub

Template:ChadoTable audit feature cvterm pub

Table: audit_synonym

Template:ChadoTable audit synonym

Table: audit_feature_synonym

Template:ChadoTable audit feature synonym

Table: audit_gencode

Template:ChadoTable audit gencode

Table: audit_gencode_codon_aa

Template:ChadoTable audit gencode codon aa

Table: audit_gencode_startcodon

Template:ChadoTable audit gencode startcodon

Table: audit_analysis

Template:ChadoTable audit analysis

Table: audit_analysisprop

Template:ChadoTable audit analysisprop

Table: audit_analysisfeature

Template:ChadoTable audit analysisfeature

Table: audit_analysisfeatureprop

Template:ChadoTable audit analysisfeatureprop

Table: audit_phenotype

Template:ChadoTable audit phenotype

Table: audit_phenotype_cvterm

Template:ChadoTable audit phenotype cvterm

Table: audit_feature_phenotype

Template:ChadoTable audit feature phenotype

Table: audit_genotype

Template:ChadoTable audit genotype

Table: audit_feature_genotype

Template:ChadoTable audit feature genotype

Table: audit_environment

Template:ChadoTable audit environment

Table: audit_environment_cvterm

Template:ChadoTable audit environment cvterm

Table: audit_phenstatement

Template:ChadoTable audit phenstatement

Table: audit_phendesc

Template:ChadoTable audit phendesc

Table: audit_phenotype_comparison

Template:ChadoTable audit phenotype comparison

Table: audit_phenotype_comparison_cvterm

Template:ChadoTable audit phenotype comparison cvterm

Table: audit_featuremap

Template:ChadoTable audit featuremap

Table: audit_featurerange

Template:ChadoTable audit featurerange

Table: audit_featurepos

Template:ChadoTable audit featurepos

Table: audit_featuremap_pub

Template:ChadoTable audit featuremap pub

Table: audit_phylotree

Template:ChadoTable audit phylotree

Table: audit_phylotree_pub

Template:ChadoTable audit phylotree pub

Table: audit_phylonode

Template:ChadoTable audit phylonode

Table: audit_phylonode_dbxref

Template:ChadoTable audit phylonode dbxref

Table: audit_phylonode_pub

Template:ChadoTable audit phylonode pub

Table: audit_phylonode_organism

Template:ChadoTable audit phylonode organism

Table: audit_phylonodeprop

Template:ChadoTable audit phylonodeprop

Table: audit_phylonode_relationship

Template:ChadoTable audit phylonode relationship

Table: audit_contact

Template:ChadoTable audit contact

Table: audit_contact_relationship

Template:ChadoTable audit contact relationship

Table: audit_expression

Template:ChadoTable audit expression

Table: audit_expression_cvterm

Template:ChadoTable audit expression cvterm

Table: audit_expression_cvtermprop

Template:ChadoTable audit expression cvtermprop

Table: audit_expressionprop

Template:ChadoTable audit expressionprop

Table: audit_expression_pub

Template:ChadoTable audit expression pub

Table: audit_feature_expression

Template:ChadoTable audit feature expression

Table: audit_feature_expressionprop

Template:ChadoTable audit feature expressionprop

Table: audit_eimage

Template:ChadoTable audit eimage

Table: audit_expression_image

Template:ChadoTable audit expression image

Table: audit_project

Template:ChadoTable audit project

Table: audit_projectprop

Template:ChadoTable audit projectprop

Table: audit_project_relationship

Template:ChadoTable audit project relationship

Table: audit_project_pub

Template:ChadoTable audit project pub

Table: audit_project_contact

Template:ChadoTable audit project contact

Table: audit_mageml

Template:ChadoTable audit mageml

Table: audit_magedocumentation

Template:ChadoTable audit magedocumentation

Table: audit_protocol

Template:ChadoTable audit protocol

Table: audit_protocolparam

Template:ChadoTable audit protocolparam

Table: audit_channel

Template:ChadoTable audit channel

Table: audit_arraydesign

Template:ChadoTable audit arraydesign

Table: audit_arraydesignprop

Template:ChadoTable audit arraydesignprop

Table: audit_assay

Template:ChadoTable audit assay

Table: audit_assayprop

Template:ChadoTable audit assayprop

Table: audit_assay_project

Template:ChadoTable audit assay project

Table: audit_biomaterial

Template:ChadoTable audit biomaterial

Table: audit_biomaterial_relationship

Template:ChadoTable audit biomaterial relationship

Table: audit_biomaterialprop

Template:ChadoTable audit biomaterialprop

Table: audit_biomaterial_dbxref

Template:ChadoTable audit biomaterial dbxref

Table: audit_treatment

Template:ChadoTable audit treatment

Table: audit_biomaterial_treatment

Template:ChadoTable audit biomaterial treatment

Table: audit_assay_biomaterial

Template:ChadoTable audit assay biomaterial

Table: audit_acquisition

Template:ChadoTable audit acquisition

Table: audit_acquisitionprop

Template:ChadoTable audit acquisitionprop

Table: audit_acquisition_relationship

Template:ChadoTable audit acquisition relationship

Table: audit_quantification

Template:ChadoTable audit quantification

Table: audit_quantificationprop

Template:ChadoTable audit quantificationprop

Table: audit_quantification_relationship

Template:ChadoTable audit quantification relationship

Table: audit_control

Template:ChadoTable audit control

Table: audit_element

Template:ChadoTable audit element

Table: audit_elementresult

Template:ChadoTable audit elementresult

Table: audit_element_relationship

Template:ChadoTable audit element relationship

Table: audit_elementresult_relationship

Template:ChadoTable audit elementresult relationship

Table: audit_study

Template:ChadoTable audit study

Table: audit_study_assay

Template:ChadoTable audit study assay

Table: audit_studydesign

Template:ChadoTable audit studydesign

Table: audit_studydesignprop

Template:ChadoTable audit studydesignprop

Table: audit_studyfactor

Template:ChadoTable audit studyfactor

Table: audit_studyfactorvalue

Template:ChadoTable audit studyfactorvalue

Table: audit_studyprop

Template:ChadoTable audit studyprop

Table: audit_studyprop_feature

Template:ChadoTable audit studyprop feature

Table: audit_stock

Template:ChadoTable audit stock

Table: audit_stock_pub

Template:ChadoTable audit stock pub

Table: audit_stockprop

Template:ChadoTable audit stockprop

Table: audit_stockprop_pub

Template:ChadoTable audit stockprop pub

Table: audit_stock_relationship

Template:ChadoTable audit stock relationship

Table: audit_stock_relationship_cvterm

Template:ChadoTable audit stock relationship cvterm

Table: audit_stock_relationship_pub

Template:ChadoTable audit stock relationship pub

Table: audit_stock_dbxref

Template:ChadoTable audit stock dbxref

Table: audit_stock_cvterm

Template:ChadoTable audit stock cvterm

Table: audit_stock_genotype

Template:ChadoTable audit stock genotype

Table: audit_stockcollection

Template:ChadoTable audit stockcollection

Table: audit_stockcollectionprop

Template:ChadoTable audit stockcollectionprop

Table: audit_stockcollection_stock

Template:ChadoTable audit stockcollection stock

Table: audit_stock_dbxrefprop

Template:ChadoTable audit stock dbxrefprop

Table: audit_library

Template:ChadoTable audit library

Table: audit_library_synonym

Template:ChadoTable audit library synonym

Table: audit_library_pub

Template:ChadoTable audit library pub

Table: audit_libraryprop

Template:ChadoTable audit libraryprop

Table: audit_libraryprop_pub

Template:ChadoTable audit libraryprop pub

Table: audit_library_cvterm

Template:ChadoTable audit library cvterm

Table: audit_library_feature

Template:ChadoTable audit library feature

Table: audit_library_dbxref

Template:ChadoTable audit library dbxref

Table: audit_cell_line

Template:ChadoTable audit cell line

Table: audit_cell_line_relationship

Template:ChadoTable audit cell line relationship

Table: audit_cell_line_synonym

Template:ChadoTable audit cell line synonym

Table: audit_cell_line_cvterm

Template:ChadoTable audit cell line cvterm

Table: audit_cell_line_dbxref

Template:ChadoTable audit cell line dbxref

Table: audit_cell_lineprop

Template:ChadoTable audit cell lineprop

Table: audit_cell_lineprop_pub

Template:ChadoTable audit cell lineprop pub

Table: audit_cell_line_feature

Template:ChadoTable audit cell line feature

Table: audit_cell_line_cvtermprop

Template:ChadoTable audit cell line cvtermprop

Table: audit_cell_line_pub

Template:ChadoTable audit cell line pub

Table: audit_cell_line_library

Template:ChadoTable audit cell line library

Table: audit_nd_geolocation

Template:ChadoTable audit nd geolocation

Table: audit_nd_experiment

Template:ChadoTable audit nd experiment

Table: audit_nd_experiment_project

Template:ChadoTable audit nd experiment project

Table: audit_nd_experimentprop

Template:ChadoTable audit nd experimentprop

Table: audit_nd_experiment_pub

Template:ChadoTable audit nd experiment pub

Table: audit_nd_geolocationprop

Template:ChadoTable audit nd geolocationprop

Table: audit_nd_protocol

Template:ChadoTable audit nd protocol

Table: audit_nd_reagent

Template:ChadoTable audit nd reagent

Table: audit_nd_protocol_reagent

Template:ChadoTable audit nd protocol reagent

Table: audit_nd_protocolprop

Template:ChadoTable audit nd protocolprop

Table: audit_nd_experiment_stock

Template:ChadoTable audit nd experiment stock

Table: audit_nd_experiment_protocol

Template:ChadoTable audit nd experiment protocol

Table: audit_nd_experiment_phenotype

Template:ChadoTable audit nd experiment phenotype

Table: audit_nd_experiment_genotype

Template:ChadoTable audit nd experiment genotype

Table: audit_nd_reagent_relationship

Template:ChadoTable audit nd reagent relationship

Table: audit_nd_reagentprop

Template:ChadoTable audit nd reagentprop

Table: audit_nd_experiment_stockprop

Template:ChadoTable audit nd experiment stockprop

Table: audit_nd_experiment_stock_dbxref

Template:ChadoTable audit nd experiment stock dbxref

Table: audit_nd_experiment_dbxref

Template:ChadoTable audit nd experiment dbxref

Table: audit_nd_experiment_contact

Template:ChadoTable audit nd experiment contact