tableinfo |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| tableinfo_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| name | varchar | 30 | UNIQUE, NOT NULL | ||
| primary_key_column | varchar | 30 | NULL | ||
| is_view | integer | 10 | 0 | NOT NULL | |
| view_on_table_id | integer | 10 | NULL | ||
| superclass_table_id | integer | 10 | NULL | ||
| is_updateable | integer | 10 | 1 | NOT NULL | |
| modification_date | date | 0 | now() | NOT NULL |
| Type | Fields |
|---|---|
| NOT NULL | tableinfo_id |
| NOT NULL | name |
| NOT NULL | is_view |
| NOT NULL | is_updateable |
| NOT NULL | modification_date |
| UNIQUE | name |
db |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| db_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| name | varchar | 255 | UNIQUE, NOT NULL | ||
| description | varchar | 255 | NULL | contact_id int, | |
| urlprefix | varchar | 255 | NULL | ||
| url | varchar | 255 | NULL |
| Type | Fields |
|---|---|
| NOT NULL | db_id |
| NOT NULL | name |
| UNIQUE | name |
dbxref |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| dbxref_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| db_id | integer | 10 | UNIQUE, NOT NULL | db.db_id | |
| accession | varchar | 255 | UNIQUE, NOT NULL, The local part of the identifier. Guaranteed by the db authority to be unique for that db. | ||
| version | varchar | 255 | UNIQUE, NOT NULL | ||
| description | text | 64000 |
| Name | Fields |
|---|---|
| dbxref_idx1 | db_id |
| dbxref_idx2 | accession |
| dbxref_idx3 | version |
| Type | Fields |
|---|---|
| NOT NULL | dbxref_id |
| NOT NULL | db_id |
| FOREIGN KEY | db_id |
| NOT NULL | accession |
| NOT NULL | version |
| UNIQUE | db_id, accession, version |
cv |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| cv_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| name | varchar | 255 | UNIQUE, NOT NULL, The name of the ontology. This corresponds to the obo-format -namespace-. cv names uniquely identify the cv. In OBO file format, the cv.name is known as the namespace. | ||
| definition | text | 64000 | A text description of the criteria for membership of this ontology. |
| Type | Fields |
|---|---|
| NOT NULL | cv_id |
| NOT NULL | name |
| UNIQUE | name |
cvterm |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| cvterm_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| cv_id | integer | 10 | UNIQUE, NOT NULL, The cv or ontology or namespace to which this cvterm belongs. | cv.cv_id | |
| name | varchar | 1024 | UNIQUE, NOT NULL, A concise human-readable name or label for the cvterm. Uniquely identifies a cvterm within a cv. | ||
| definition | text | 64000 | A human-readable text definition. | ||
| dbxref_id | integer | 10 | UNIQUE, NOT NULL, Primary identifier dbxref - The unique global OBO identifier for this cvterm. Note that a cvterm may have multiple secondary dbxrefs - see also table: cvterm_dbxref. | dbxref.dbxref_id | |
| is_obsolete | integer | 10 | 0 | UNIQUE, NOT NULL, Boolean 0=false,1=true; see GO documentation for details of obsoletion. Note that two terms with different primary dbxrefs may exist if one is obsolete. | |
| is_relationshiptype | integer | 10 | 0 | NOT NULL, Boolean 0=false,1=true relations or relationship types (also known as Typedefs in OBO format, or as properties or slots) form a cv/ontology in themselves. We use this flag to indicate whether this cvterm is an actual term/class/universal or a relation. Relations may be drawn from the OBO Relations ontology, but are not exclusively drawn from there. |
| Name | Fields |
|---|---|
| cvterm_idx1 | cv_id |
| cvterm_idx2 | name |
| cvterm_idx3 | dbxref_id |
| Type | Fields |
|---|---|
| NOT NULL | cvterm_id |
| NOT NULL | cv_id |
| FOREIGN KEY | cv_id |
| NOT NULL | name |
| NOT NULL | dbxref_id |
| FOREIGN KEY | dbxref_id |
| NOT NULL | is_obsolete |
| NOT NULL | is_relationshiptype |
| UNIQUE | name, cv_id, is_obsolete |
| UNIQUE | dbxref_id |
cvterm_relationship |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| cvterm_relationship_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| type_id | integer | 10 | UNIQUE, NOT NULL, The nature of the relationship between subject and object. Note that relations are also housed in the cvterm table, typically from the OBO relationship ontology, although other relationship types are allowed. | cvterm.cvterm_id | |
| subject_id | integer | 10 | UNIQUE, NOT NULL, The subject of the subj-predicate-obj sentence. The cvterm_relationship is about the subject. In a graph, this typically corresponds to the child node. | cvterm.cvterm_id | |
| object_id | integer | 10 | UNIQUE, NOT NULL, The object of the subj-predicate-obj sentence. The cvterm_relationship refers to the object. In a graph, this typically corresponds to the parent node. | cvterm.cvterm_id |
| Name | Fields |
|---|---|
| cvterm_relationship_idx1 | type_id |
| cvterm_relationship_idx2 | subject_id |
| cvterm_relationship_idx3 | object_id |
| Type | Fields |
|---|---|
| NOT NULL | cvterm_relationship_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | subject_id |
| FOREIGN KEY | subject_id |
| NOT NULL | object_id |
| FOREIGN KEY | object_id |
| UNIQUE | subject_id, object_id, type_id |
cvtermpath |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| cvtermpath_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| type_id | integer | 10 | UNIQUE, The relationship type that this is a closure over. If null, then this is a closure over ALL relationship types. If non-null, then this references a relationship cvterm - note that the closure will apply to both this relationship AND the OBO_REL:is_a (subclass) relationship. | cvterm.cvterm_id | |
| subject_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| object_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| cv_id | integer | 10 | NOT NULL, Closures will mostly be within one cv. If the closure of a relationship traverses a cv, then this refers to the cv of the object_id cvterm. | cv.cv_id | |
| pathdistance | integer | 10 | UNIQUE, The number of steps required to get from the subject cvterm to the object cvterm, counting from zero (reflexive relationship). |
| Name | Fields |
|---|---|
| cvtermpath_idx1 | type_id |
| cvtermpath_idx2 | subject_id |
| cvtermpath_idx3 | object_id |
| cvtermpath_idx4 | cv_id |
| Type | Fields |
|---|---|
| NOT NULL | cvtermpath_id |
| FOREIGN KEY | type_id |
| NOT NULL | subject_id |
| FOREIGN KEY | subject_id |
| NOT NULL | object_id |
| FOREIGN KEY | object_id |
| NOT NULL | cv_id |
| FOREIGN KEY | cv_id |
| UNIQUE | subject_id, object_id, type_id, pathdistance |
cvtermsynonym |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| cvtermsynonym_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| cvterm_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| synonym | varchar | 1024 | UNIQUE, NOT NULL | ||
| type_id | integer | 10 | A synonym can be exact, narrower, or broader than. | cvterm.cvterm_id |
| Name | Fields |
|---|---|
| cvtermsynonym_idx1 | cvterm_id |
| Type | Fields |
|---|---|
| NOT NULL | cvtermsynonym_id |
| NOT NULL | cvterm_id |
| FOREIGN KEY | cvterm_id |
| NOT NULL | synonym |
| FOREIGN KEY | type_id |
| UNIQUE | cvterm_id, synonym |
cvterm_dbxref |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| cvterm_dbxref_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| cvterm_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| dbxref_id | integer | 10 | UNIQUE, NOT NULL | dbxref.dbxref_id | |
| is_for_definition | integer | 10 | 0 | NOT NULL, A cvterm.definition should be supported by one or more references. If this column is true, the dbxref is not for a term in an external database - it is a dbxref for provenance information for the definition. |
| Name | Fields |
|---|---|
| cvterm_dbxref_idx1 | cvterm_id |
| cvterm_dbxref_idx2 | dbxref_id |
| Type | Fields |
|---|---|
| NOT NULL | cvterm_dbxref_id |
| NOT NULL | cvterm_id |
| FOREIGN KEY | cvterm_id |
| NOT NULL | dbxref_id |
| FOREIGN KEY | dbxref_id |
| NOT NULL | is_for_definition |
| UNIQUE | cvterm_id, dbxref_id |
cvtermprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| cvtermprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| cvterm_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL, The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm. | cvterm.cvterm_id | |
| value | text | 64000 | UNIQUE, NOT NULL, The value of the property, represented as text. Numeric values are converted to their text representation. | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL, Property-Value ordering. Any cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used. |
| Name | Fields |
|---|---|
| cvtermprop_idx1 | cvterm_id |
| cvtermprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | cvtermprop_id |
| NOT NULL | cvterm_id |
| FOREIGN KEY | cvterm_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | value |
| NOT NULL | rank |
| UNIQUE | cvterm_id, type_id, value, rank |
dbxrefprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| dbxrefprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| dbxref_id | integer | 10 | UNIQUE, NOT NULL | dbxref.dbxref_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| value | text | 64000 | NOT NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| dbxrefprop_idx1 | dbxref_id |
| dbxrefprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | dbxrefprop_id |
| NOT NULL | dbxref_id |
| FOREIGN KEY | dbxref_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | value |
| NOT NULL | rank |
| UNIQUE | dbxref_id, type_id, rank |
cvprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| cvprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| cv_id | integer | 10 | UNIQUE, NOT NULL | cv.cv_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL, The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm. | cvterm.cvterm_id | |
| value | text | 64000 | The value of the property, represented as text. Numeric values are converted to their text representation. | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL, Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used. |
| Type | Fields |
|---|---|
| NOT NULL | cvprop_id |
| NOT NULL | cv_id |
| FOREIGN KEY | cv_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | cv_id, type_id, rank |
chadoprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| chadoprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| type_id | integer | 10 | UNIQUE, NOT NULL, The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm. | cvterm.cvterm_id | |
| value | text | 64000 | The value of the property, represented as text. Numeric values are converted to their text representation. | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL, Property-Value ordering. Any cv can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used. |
| Type | Fields |
|---|---|
| NOT NULL | chadoprop_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | type_id, rank |
pub |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| pub_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| title | text | 64000 | Descriptive general heading. | ||
| volumetitle | text | 64000 | Title of part if one of a series. | ||
| volume | varchar | 255 | |||
| series_name | varchar | 255 | Full name of (journal) series. | ||
| issue | varchar | 255 | |||
| pyear | varchar | 255 | |||
| pages | varchar | 255 | Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii. | ||
| miniref | varchar | 255 | |||
| uniquename | text | 64000 | UNIQUE, NOT NULL | ||
| type_id | integer | 10 | NOT NULL, The type of the publication (book, journal, poem, graffiti, etc). Uses pub cv. | cvterm.cvterm_id | |
| is_obsolete | boolean | 0 | false | ||
| publisher | varchar | 255 | |||
| pubplace | varchar | 255 |
| Name | Fields |
|---|---|
| pub_idx1 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | pub_id |
| NOT NULL | uniquename |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| UNIQUE | uniquename |
pub_relationship |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| pub_relationship_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| subject_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id | |
| object_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id |
| Name | Fields |
|---|---|
| pub_relationship_idx1 | subject_id |
| pub_relationship_idx2 | object_id |
| pub_relationship_idx3 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | pub_relationship_id |
| NOT NULL | subject_id |
| FOREIGN KEY | subject_id |
| NOT NULL | object_id |
| FOREIGN KEY | object_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| UNIQUE | subject_id, object_id, type_id |
pub_dbxref |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| pub_dbxref_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id | |
| dbxref_id | integer | 10 | UNIQUE, NOT NULL | dbxref.dbxref_id | |
| is_current | boolean | 0 | true | NOT NULL |
| Name | Fields |
|---|---|
| pub_dbxref_idx1 | pub_id |
| pub_dbxref_idx2 | dbxref_id |
| Type | Fields |
|---|---|
| NOT NULL | pub_dbxref_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| NOT NULL | dbxref_id |
| FOREIGN KEY | dbxref_id |
| NOT NULL | is_current |
| UNIQUE | pub_id, dbxref_id |
pubauthor |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| pubauthor_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id | |
| rank | integer | 10 | UNIQUE, NOT NULL, Order of author in author list for this pub - order is important. | ||
| editor | boolean | 0 | false | Indicates whether the author is an editor for linked publication. Note: this is a boolean field but does not follow the normal chado convention for naming booleans. | |
| surname | varchar | 100 | NOT NULL | ||
| givennames | varchar | 100 | First name, initials | ||
| suffix | varchar | 100 | Jr., Sr., etc |
| Name | Fields |
|---|---|
| pubauthor_idx2 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | pubauthor_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| NOT NULL | rank |
| NOT NULL | surname |
| UNIQUE | pub_id, rank |
pubprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| pubprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| value | text | 64000 | NOT NULL | ||
| rank | integer | 10 | UNIQUE |
| Name | Fields |
|---|---|
| pubprop_idx1 | pub_id |
| pubprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | pubprop_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | value |
| UNIQUE | pub_id, type_id, rank |
organism |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| organism_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| abbreviation | varchar | 255 | NULL | ||
| genus | varchar | 255 | UNIQUE, NOT NULL | ||
| species | varchar | 255 | UNIQUE, NOT NULL, A type of organism is always uniquely identified by genus and species. When mapping from the NCBI taxonomy names.dmp file, this column must be used where it is present, as the common_name column is not always unique (e.g. environmental samples). If a particular strain or subspecies is to be represented, this is appended onto the species name. Follows standard NCBI taxonomy pattern. | ||
| common_name | varchar | 255 | NULL | ||
| comment | text | 64000 | NULL |
| Type | Fields |
|---|---|
| NOT NULL | organism_id |
| NOT NULL | genus |
| NOT NULL | species |
| UNIQUE | genus, species |
organism_dbxref |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| organism_dbxref_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| organism_id | integer | 10 | UNIQUE, NOT NULL | organism.organism_id | |
| dbxref_id | integer | 10 | UNIQUE, NOT NULL | dbxref.dbxref_id |
| Name | Fields |
|---|---|
| organism_dbxref_idx1 | organism_id |
| organism_dbxref_idx2 | dbxref_id |
| Type | Fields |
|---|---|
| NOT NULL | organism_dbxref_id |
| NOT NULL | organism_id |
| FOREIGN KEY | organism_id |
| NOT NULL | dbxref_id |
| FOREIGN KEY | dbxref_id |
| UNIQUE | organism_id, dbxref_id |
organismprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| organismprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| organism_id | integer | 10 | UNIQUE, NOT NULL | organism.organism_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| value | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| organismprop_idx1 | organism_id |
| organismprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | organismprop_id |
| NOT NULL | organism_id |
| FOREIGN KEY | organism_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | organism_id, type_id, rank |
feature |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| feature_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| dbxref_id | integer | 10 | An optional primary public stable identifier for this feature. Secondary identifiers and external dbxrefs go in the table feature_dbxref. | dbxref.dbxref_id | |
| organism_id | integer | 10 | UNIQUE, NOT NULL, The organism to which this feature belongs. This column is mandatory. | organism.organism_id | |
| name | varchar | 255 | The optional human-readable common name for a feature, for display purposes. | ||
| uniquename | text | 64000 | UNIQUE, NOT NULL, The unique name for a feature; may not be necessarily be particularly human-readable, although this is preferred. This name must be unique for this type of feature within this organism. | ||
| residues | text | 64000 | A sequence of alphabetic characters representing biological residues (nucleic acids, amino acids). This column does not need to be manifested for all features; it is optional for features such as exons where the residues can be derived from the featureloc. It is recommended that the value for this column be manifested for features which may may non-contiguous sublocations (e.g. transcripts), since derivation at query time is non-trivial. For expressed sequence, the DNA sequence should be used rather than the RNA sequence. The default storage method for the residues column is EXTERNAL, which will store it uncompressed to make substring operations faster. | ||
| seqlen | integer | 10 | The length of the residue feature. See column:residues. This column is partially redundant with the residues column, and also with featureloc. This column is required because the location may be unknown and the residue sequence may not be manifested, yet it may be desirable to store and query the length of the feature. The seqlen should always be manifested where the length of the sequence is known. | ||
| md5checksum | char | 32 | The 32-character checksum of the sequence, calculated using the MD5 algorithm. This is practically guaranteed to be unique for any feature. This column thus acts as a unique identifier on the mathematical sequence. | ||
| type_id | integer | 10 | UNIQUE, NOT NULL, A required reference to a table:cvterm giving the feature type. This will typically be a Sequence Ontology identifier. This column is thus used to subclass the feature table. | cvterm.cvterm_id | |
| is_analysis | boolean | 0 | false | NOT NULL, Boolean indicating whether this feature is annotated or the result of an automated analysis. Analysis results also use the companalysis module. Note that the dividing line between analysis and annotation may be fuzzy, this should be determined on a per-project basis in a consistent manner. One requirement is that there should only be one non-analysis version of each wild-type gene feature in a genome, whereas the same gene feature can be predicted multiple times in different analyses. | |
| is_obsolete | boolean | 0 | false | NOT NULL, Boolean indicating whether this feature has been obsoleted. Some chado instances may choose to simply remove the feature altogether, others may choose to keep an obsolete row in the table. | |
| timeaccessioned | timestamp | 0 | current_timestamp | NOT NULL, For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado. | |
| timelastmodified | timestamp | 0 | current_timestamp | NOT NULL, For handling object accession or modification timestamps (as opposed to database auditing data, handled elsewhere). The expectation is that these fields would be available to software interacting with chado. |
| Name | Fields |
|---|---|
| feature_name_ind1 | name |
| feature_idx1 | dbxref_id |
| feature_idx2 | organism_id |
| feature_idx3 | type_id |
| feature_idx4 | uniquename |
| Type | Fields |
|---|---|
| NOT NULL | feature_id |
| FOREIGN KEY | dbxref_id |
| NOT NULL | organism_id |
| FOREIGN KEY | organism_id |
| NOT NULL | uniquename |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | is_analysis |
| NOT NULL | is_obsolete |
| NOT NULL | timeaccessioned |
| NOT NULL | timelastmodified |
| UNIQUE | organism_id, uniquename, type_id |
featureloc |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| featureloc_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| feature_id | integer | 10 | UNIQUE, NOT NULL, The feature that is being located. Any feature can have zero or more featurelocs. | feature.feature_id | |
| srcfeature_id | integer | 10 | The source feature which this location is relative to. Every location is relative to another feature (however, this column is nullable, because the srcfeature may not be known). All locations are -proper- that is, nothing should be located relative to itself. No cycles are allowed in the featureloc graph. | feature.feature_id | |
| fmin | integer | 10 | The leftmost/minimal boundary in the linear range represented by the featureloc. Sometimes (e.g. in Bioperl) this is called -start- although this is confusing because it does not necessarily represent the 5-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. To convert this to the leftmost position in a base-oriented system (eg GFF, Bioperl), add 1 to fmin. | ||
| is_fmin_partial | boolean | 0 | false | NOT NULL, This is typically false, but may be true if the value for column:fmin is inaccurate or the leftmost part of the range is unknown/unbounded. | |
| fmax | integer | 10 | The rightmost/maximal boundary in the linear range represented by the featureloc. Sometimes (e.g. in bioperl) this is called -end- although this is confusing because it does not necessarily represent the 3-prime coordinate. Important: This is space-based (interbase) coordinates, counting from zero. No conversion is required to go from fmax to the rightmost coordinate in a base-oriented system that counts from 1 (e.g. GFF, Bioperl). | ||
| is_fmax_partial | boolean | 0 | false | NOT NULL, This is typically false, but may be true if the value for column:fmax is inaccurate or the rightmost part of the range is unknown/unbounded. | |
| strand | integer | 5 | The orientation/directionality of the location. Should be 0, -1 or +1. | ||
| phase | integer | 10 | Phase of translation with respect to srcfeature_id. Values are 0, 1, 2. It may not be possible to manifest this column for some features such as exons, because the phase is dependant on the spliceform (the same exon can appear in multiple spliceforms). This column is mostly useful for predicted exons and CDSs. | ||
| residue_info | text | 64000 | Alternative residues, when these differ from feature.residues. For instance, a SNP feature located on a wild and mutant protein would have different alternative residues. for alignment/similarity features, the alternative residues is used to represent the alignment string (CIGAR format). Note on variation features; even if we do not want to instantiate a mutant chromosome/contig feature, we can still represent a SNP etc with 2 locations, one (rank 0) on the genome, the other (rank 1) would have most fields null, except for alternative residues. | ||
| locgroup | integer | 10 | 0 | UNIQUE, NOT NULL, This is used to manifest redundant, derivable extra locations for a feature. The default locgroup=0 is used for the DIRECT location of a feature. Important: most Chado users may never use featurelocs WITH logroup > 0. Transitively derived locations are indicated with locgroup > 0. For example, the position of an exon on a BAC and in global chromosome coordinates. This column is used to differentiate these groupings of locations. The default locgroup 0 is used for the main or primary location, from which the others can be derived via coordinate transformations. Another example of redundant locations is storing ORF coordinates relative to both transcript and genome. Redundant locations open the possibility of the database getting into inconsistent states; this schema gives us the flexibility of both warehouse instantiations with redundant locations (easier for querying) and management instantiations with no redundant locations. An example of using both locgroup and rank: imagine a feature indicating a conserved region between the chromosomes of two different species. We may want to keep redundant locations on both contigs and chromosomes. We would thus have 4 locations for the single conserved region feature - two distinct locgroups (contig level and chromosome level) and two distinct ranks (for the two species). | |
| rank | integer | 10 | 0 | UNIQUE, NOT NULL, Used when a feature has >1 location, otherwise the default rank 0 is used. Some features (e.g. blast hits and HSPs) have two locations - one on the query and one on the subject. Rank is used to differentiate these. Rank=0 is always used for the query, Rank=1 for the subject. For multiple alignments, assignment of rank is arbitrary. Rank is also used for sequence_variant features, such as SNPs. Rank=0 indicates the wildtype (or baseline) feature, Rank=1 indicates the mutant (or compared) feature. |
| Name | Fields |
|---|---|
| featureloc_idx1 | feature_id |
| featureloc_idx2 | srcfeature_id |
| featureloc_idx3 | srcfeature_id, fmin, fmax |
| Type | Fields |
|---|---|
| NOT NULL | featureloc_id |
| NOT NULL | feature_id |
| FOREIGN KEY | feature_id |
| FOREIGN KEY | srcfeature_id |
| NOT NULL | is_fmin_partial |
| NOT NULL | is_fmax_partial |
| NOT NULL | locgroup |
| NOT NULL | rank |
| UNIQUE | feature_id, locgroup, rank |
| CHECK |
featureloc_pub |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| featureloc_pub_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| featureloc_id | integer | 10 | UNIQUE, NOT NULL | featureloc.featureloc_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id |
| Name | Fields |
|---|---|
| featureloc_pub_idx1 | featureloc_id |
| featureloc_pub_idx2 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | featureloc_pub_id |
| NOT NULL | featureloc_id |
| FOREIGN KEY | featureloc_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| UNIQUE | featureloc_id, pub_id |
feature_pub |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| feature_pub_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| feature_id | integer | 10 | UNIQUE, NOT NULL | feature.feature_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id |
| Name | Fields |
|---|---|
| feature_pub_idx1 | feature_id |
| feature_pub_idx2 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | feature_pub_id |
| NOT NULL | feature_id |
| FOREIGN KEY | feature_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| UNIQUE | feature_id, pub_id |
feature_pubprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| feature_pubprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| feature_pub_id | integer | 10 | UNIQUE, NOT NULL | feature_pub.feature_pub_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| value | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| feature_pubprop_idx1 | feature_pub_id |
| Type | Fields |
|---|---|
| NOT NULL | feature_pubprop_id |
| NOT NULL | feature_pub_id |
| FOREIGN KEY | feature_pub_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | feature_pub_id, type_id, rank |
featureprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| featureprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| feature_id | integer | 10 | UNIQUE, NOT NULL | feature.feature_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Certain property types will only apply to certain feature types (e.g. the anticodon property will only apply to tRNA features) ; the types here come from the sequence feature property ontology. | cvterm.cvterm_id | |
| value | text | 64000 | NULL | The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query. | |
| rank | integer | 10 | 0 | UNIQUE, NOT NULL, Property-Value ordering. Any feature can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used |
| Name | Fields |
|---|---|
| featureprop_idx1 | feature_id |
| featureprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | featureprop_id |
| NOT NULL | feature_id |
| FOREIGN KEY | feature_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | feature_id, type_id, rank |
featureprop_pub |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| featureprop_pub_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| featureprop_id | integer | 10 | UNIQUE, NOT NULL | featureprop.featureprop_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id |
| Name | Fields |
|---|---|
| featureprop_pub_idx1 | featureprop_id |
| featureprop_pub_idx2 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | featureprop_pub_id |
| NOT NULL | featureprop_id |
| FOREIGN KEY | featureprop_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| UNIQUE | featureprop_id, pub_id |
feature_dbxref |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| feature_dbxref_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| feature_id | integer | 10 | UNIQUE, NOT NULL | feature.feature_id | |
| dbxref_id | integer | 10 | UNIQUE, NOT NULL | dbxref.dbxref_id | |
| is_current | boolean | 0 | true | NOT NULL, True if this secondary dbxref is the most up to date accession in the corresponding db. Retired accessions should set this field to false |
| Name | Fields |
|---|---|
| feature_dbxref_idx1 | feature_id |
| feature_dbxref_idx2 | dbxref_id |
| Type | Fields |
|---|---|
| NOT NULL | feature_dbxref_id |
| NOT NULL | feature_id |
| FOREIGN KEY | feature_id |
| NOT NULL | dbxref_id |
| FOREIGN KEY | dbxref_id |
| NOT NULL | is_current |
| UNIQUE | feature_id, dbxref_id |
feature_relationship |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| feature_relationship_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| subject_id | integer | 10 | UNIQUE, NOT NULL, The subject of the subj-predicate-obj sentence. This is typically the subfeature. | feature.feature_id | |
| object_id | integer | 10 | UNIQUE, NOT NULL, The object of the subj-predicate-obj sentence. This is typically the container feature. | feature.feature_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL, Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. The most common relationship type is OBO_REL:part_of. Valid relationship types are constrained by the Sequence Ontology. | cvterm.cvterm_id | |
| value | text | 64000 | NULL | Additional notes or comments. | |
| rank | integer | 10 | 0 | UNIQUE, NOT NULL, The ordering of subject features with respect to the object feature may be important (for example, exon ordering on a transcript - not always derivable if you take trans spliced genes into consideration). Rank is used to order these; starts from zero. |
| Name | Fields |
|---|---|
| feature_relationship_idx1 | subject_id |
| feature_relationship_idx2 | object_id |
| feature_relationship_idx3 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | feature_relationship_id |
| NOT NULL | subject_id |
| FOREIGN KEY | subject_id |
| NOT NULL | object_id |
| FOREIGN KEY | object_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | subject_id, object_id, type_id, rank |
feature_relationship_pub |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| feature_relationship_pub_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| feature_relationship_id | integer | 10 | UNIQUE, NOT NULL | feature_relationship.feature_relationship_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id |
| Name | Fields |
|---|---|
| feature_relationship_pub_idx1 | feature_relationship_id |
| feature_relationship_pub_idx2 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | feature_relationship_pub_id |
| NOT NULL | feature_relationship_id |
| FOREIGN KEY | feature_relationship_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| UNIQUE | feature_relationship_id, pub_id |
feature_relationshipprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| feature_relationshipprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| feature_relationship_id | integer | 10 | UNIQUE, NOT NULL | feature_relationship.feature_relationship_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. Currently there is no standard ontology for feature_relationship property types. | cvterm.cvterm_id | |
| value | text | 64000 | NULL | The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query. | |
| rank | integer | 10 | 0 | UNIQUE, NOT NULL, Property-Value ordering. Any feature_relationship can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used. |
| Name | Fields |
|---|---|
| feature_relationshipprop_idx1 | feature_relationship_id |
| feature_relationshipprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | feature_relationshipprop_id |
| NOT NULL | feature_relationship_id |
| FOREIGN KEY | feature_relationship_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | feature_relationship_id, type_id, rank |
feature_relationshipprop_pub |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| feature_relationshipprop_pub_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| feature_relationshipprop_id | integer | 10 | UNIQUE, NOT NULL | feature_relationshipprop.feature_relationshipprop_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id |
| Name | Fields |
|---|---|
| feature_relationshipprop_pub_idx1 | feature_relationshipprop_id |
| feature_relationshipprop_pub_idx2 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | feature_relationshipprop_pub_id |
| NOT NULL | feature_relationshipprop_id |
| FOREIGN KEY | feature_relationshipprop_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| UNIQUE | feature_relationshipprop_id, pub_id |
feature_cvterm |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| feature_cvterm_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| feature_id | integer | 10 | UNIQUE, NOT NULL | feature.feature_id | |
| cvterm_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL, Provenance for the annotation. Each annotation should have a single primary publication (which may be of the appropriate type for computational analyses) where more details can be found. Additional provenance dbxrefs can be attached using feature_cvterm_dbxref. | pub.pub_id | |
| is_not | boolean | 0 | false | NOT NULL, If this is set to true, then this annotation is interpreted as a NEGATIVE annotation - i.e. the feature does NOT have the specified function, process, component, part, etc. See GO docs for more details. | |
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| feature_cvterm_idx1 | feature_id |
| feature_cvterm_idx2 | cvterm_id |
| feature_cvterm_idx3 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | feature_cvterm_id |
| NOT NULL | feature_id |
| FOREIGN KEY | feature_id |
| NOT NULL | cvterm_id |
| FOREIGN KEY | cvterm_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| NOT NULL | is_not |
| NOT NULL | rank |
| UNIQUE | feature_id, cvterm_id, pub_id, rank |
feature_cvtermprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| feature_cvtermprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| feature_cvterm_id | integer | 10 | UNIQUE, NOT NULL | feature_cvterm.feature_cvterm_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv. | cvterm.cvterm_id | |
| value | text | 64000 | NULL | The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query. | |
| rank | integer | 10 | 0 | UNIQUE, NOT NULL, Property-Value ordering. Any feature_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used. |
| Name | Fields |
|---|---|
| feature_cvtermprop_idx1 | feature_cvterm_id |
| feature_cvtermprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | feature_cvtermprop_id |
| NOT NULL | feature_cvterm_id |
| FOREIGN KEY | feature_cvterm_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | feature_cvterm_id, type_id, rank |
feature_cvterm_dbxref |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| feature_cvterm_dbxref_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| feature_cvterm_id | integer | 10 | UNIQUE, NOT NULL | feature_cvterm.feature_cvterm_id | |
| dbxref_id | integer | 10 | UNIQUE, NOT NULL | dbxref.dbxref_id |
| Name | Fields |
|---|---|
| feature_cvterm_dbxref_idx1 | feature_cvterm_id |
| feature_cvterm_dbxref_idx2 | dbxref_id |
| Type | Fields |
|---|---|
| NOT NULL | feature_cvterm_dbxref_id |
| NOT NULL | feature_cvterm_id |
| FOREIGN KEY | feature_cvterm_id |
| NOT NULL | dbxref_id |
| FOREIGN KEY | dbxref_id |
| UNIQUE | feature_cvterm_id, dbxref_id |
feature_cvterm_pub |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| feature_cvterm_pub_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| feature_cvterm_id | integer | 10 | UNIQUE, NOT NULL | feature_cvterm.feature_cvterm_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id |
| Name | Fields |
|---|---|
| feature_cvterm_pub_idx1 | feature_cvterm_id |
| feature_cvterm_pub_idx2 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | feature_cvterm_pub_id |
| NOT NULL | feature_cvterm_id |
| FOREIGN KEY | feature_cvterm_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| UNIQUE | feature_cvterm_id, pub_id |
synonym |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| synonym_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| name | varchar | 255 | UNIQUE, NOT NULL, The synonym itself. Should be human-readable machine-searchable ascii text. | ||
| type_id | integer | 10 | UNIQUE, NOT NULL, Types would be symbol and fullname for now. | cvterm.cvterm_id | |
| synonym_sgml | varchar | 255 | NOT NULL, The fully specified synonym, with any non-ascii characters encoded in SGML. |
| Name | Fields |
|---|---|
| synonym_idx1 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | synonym_id |
| NOT NULL | name |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | synonym_sgml |
| UNIQUE | name, type_id |
feature_synonym |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| feature_synonym_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| synonym_id | integer | 10 | UNIQUE, NOT NULL | synonym.synonym_id | |
| feature_id | integer | 10 | UNIQUE, NOT NULL | feature.feature_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL, The pub_id link is for relating the usage of a given synonym to the publication in which it was used. | pub.pub_id | |
| is_current | boolean | 0 | false | NOT NULL, The is_current boolean indicates whether the linked synonym is the current -official- symbol for the linked feature. | |
| is_internal | boolean | 0 | false | NOT NULL, Typically a synonym exists so that somebody querying the db with an obsolete name can find the object theyre looking for (under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it may also be listed in reports as a synonym. If the synonym was not used deliberately (e.g. there was a typo which went public), then the is_internal boolean may be set to -true- so that it is known that the synonym is -internal- and should be queryable but should not be listed in reports as a valid synonym. |
| Name | Fields |
|---|---|
| feature_synonym_idx1 | synonym_id |
| feature_synonym_idx2 | feature_id |
| feature_synonym_idx3 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | feature_synonym_id |
| NOT NULL | synonym_id |
| FOREIGN KEY | synonym_id |
| NOT NULL | feature_id |
| FOREIGN KEY | feature_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| NOT NULL | is_current |
| NOT NULL | is_internal |
| UNIQUE | synonym_id, feature_id, pub_id |
analysis |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| analysis_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| name | varchar | 255 | A way of grouping analyses. This should be a handy short identifier that can help people find an analysis they want. For instance "tRNAscan", "cDNA", "FlyPep", "SwissProt", and it should not be assumed to be unique. For instance, there may be lots of separate analyses done against a cDNA database. | ||
| description | text | 64000 | |||
| program | varchar | 255 | UNIQUE, NOT NULL, Program name, e.g. blastx, blastp, sim4, genscan. | ||
| programversion | varchar | 255 | UNIQUE, NOT NULL, Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000]. | ||
| algorithm | varchar | 255 | Algorithm name, e.g. blast. | ||
| sourcename | varchar | 255 | UNIQUE, Source name, e.g. cDNA, SwissProt. | ||
| sourceversion | varchar | 255 | |||
| sourceuri | text | 64000 | This is an optional, permanent URL or URI for the source of the analysis. The idea is that someone could recreate the analysis directly by going to this URI and fetching the source data (e.g. the blast database, or the training model). | ||
| timeexecuted | timestamp | 0 | current_timestamp | NOT NULL |
| Type | Fields |
|---|---|
| NOT NULL | analysis_id |
| NOT NULL | program |
| NOT NULL | programversion |
| NOT NULL | timeexecuted |
| UNIQUE | program, programversion, sourcename |
analysisprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| analysisprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| analysis_id | integer | 10 | UNIQUE, NOT NULL | analysis.analysis_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| value | text | 64000 | |||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| analysisprop_idx1 | analysis_id |
| analysisprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | analysisprop_id |
| NOT NULL | analysis_id |
| FOREIGN KEY | analysis_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | analysis_id, type_id, rank |
analysisfeature |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| analysisfeature_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| feature_id | integer | 10 | UNIQUE, NOT NULL | feature.feature_id | |
| analysis_id | integer | 10 | UNIQUE, NOT NULL | analysis.analysis_id | |
| rawscore | float | 20 | This is the native score generated by the program; for example, the bitscore generated by blast, sim4 or genscan scores. One should not assume that high is necessarily better than low. | ||
| normscore | float | 20 | This is the rawscore but semi-normalized. Complete normalization to allow comparison of features generated by different programs would be nice but too difficult. Instead the normalization should strive to enforce the following semantics: * normscores are floating point numbers >= 0, * high normscores are better than low one. For most programs, it would be sufficient to make the normscore the same as this rawscore, providing these semantics are satisfied. | ||
| significance | float | 20 | This is some kind of expectation or probability metric, representing the probability that the analysis would appear randomly given the model. As such, any program or person querying this table can assume the following semantics: * 0 <= significance <= n, where n is a positive number, theoretically unbounded but unlikely to be more than 10 * low numbers are better than high numbers. | ||
| identity | float | 20 | Percent identity between the locations compared. Note that these 4 metrics do not cover the full range of scores possible; it would be undesirable to list every score possible, as this should be kept extensible. instead, for non-standard scores, use the analysisprop table. |
| Name | Fields |
|---|---|
| analysisfeature_idx1 | feature_id |
| analysisfeature_idx2 | analysis_id |
| Type | Fields |
|---|---|
| NOT NULL | analysisfeature_id |
| NOT NULL | feature_id |
| FOREIGN KEY | feature_id |
| NOT NULL | analysis_id |
| FOREIGN KEY | analysis_id |
| UNIQUE | feature_id, analysis_id |
analysisfeatureprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| analysisfeatureprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| analysisfeature_id | integer | 10 | UNIQUE, NOT NULL | analysisfeature.analysisfeature_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| value | text | 64000 | |||
| rank | integer | 10 | UNIQUE, NOT NULL |
| Type | Fields |
|---|---|
| NOT NULL | analysisfeature_id |
| FOREIGN KEY | analysisfeature_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | analysisfeature_id, type_id, rank |
| FOREIGN KEY | analysisfeature_id |
| FOREIGN KEY | type_id |
phenotype |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phenotype_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| uniquename | text | 64000 | UNIQUE, NOT NULL | ||
| name | text | 64000 | null | ||
| observable_id | integer | 10 | The entity: e.g. anatomy_part, biological_process. | cvterm.cvterm_id | |
| attr_id | integer | 10 | Phenotypic attribute (quality, property, attribute, character) - drawn from PATO. | cvterm.cvterm_id | |
| value | text | 64000 | Value of attribute - unconstrained free text. Used only if cvalue_id is not appropriate. | ||
| cvalue_id | integer | 10 | Phenotype attribute value (state). | cvterm.cvterm_id | |
| assay_id | integer | 10 | Evidence type. | cvterm.cvterm_id |
| Name | Fields |
|---|---|
| phenotype_idx1 | cvalue_id |
| phenotype_idx2 | observable_id |
| phenotype_idx3 | attr_id |
| Type | Fields |
|---|---|
| NOT NULL | phenotype_id |
| NOT NULL | uniquename |
| FOREIGN KEY | observable_id |
| FOREIGN KEY | attr_id |
| FOREIGN KEY | cvalue_id |
| FOREIGN KEY | assay_id |
| UNIQUE | uniquename |
phenotype_cvterm |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phenotype_cvterm_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| phenotype_id | integer | 10 | UNIQUE, NOT NULL | phenotype.phenotype_id | |
| cvterm_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| phenotype_cvterm_idx1 | phenotype_id |
| phenotype_cvterm_idx2 | cvterm_id |
| Type | Fields |
|---|---|
| NOT NULL | phenotype_cvterm_id |
| NOT NULL | phenotype_id |
| FOREIGN KEY | phenotype_id |
| NOT NULL | cvterm_id |
| FOREIGN KEY | cvterm_id |
| NOT NULL | rank |
| UNIQUE | phenotype_id, cvterm_id, rank |
feature_phenotype |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| feature_phenotype_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| feature_id | integer | 10 | UNIQUE, NOT NULL | feature.feature_id | |
| phenotype_id | integer | 10 | UNIQUE, NOT NULL | phenotype.phenotype_id |
| Name | Fields |
|---|---|
| feature_phenotype_idx1 | feature_id |
| feature_phenotype_idx2 | phenotype_id |
| Type | Fields |
|---|---|
| NOT NULL | feature_phenotype_id |
| NOT NULL | feature_id |
| FOREIGN KEY | feature_id |
| NOT NULL | phenotype_id |
| FOREIGN KEY | phenotype_id |
| UNIQUE | feature_id, phenotype_id |
genotype |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| genotype_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| name | text | 64000 | Optional alternative name for a genotype, for display purposes. | ||
| uniquename | text | 64000 | UNIQUE, NOT NULL, The unique name for a genotype; typically derived from the features making up the genotype. | ||
| description | varchar | 255 | |||
| type_id | integer | 10 | NOT NULL | cvterm.cvterm_id |
| Name | Fields |
|---|---|
| genotype_idx1 | uniquename |
| genotype_idx2 | name |
| Type | Fields |
|---|---|
| NOT NULL | genotype_id |
| NOT NULL | uniquename |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| UNIQUE | uniquename |
feature_genotype |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| feature_genotype_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| feature_id | integer | 10 | UNIQUE, NOT NULL | feature.feature_id | |
| genotype_id | integer | 10 | UNIQUE, NOT NULL | genotype.genotype_id | |
| chromosome_id | integer | 10 | UNIQUE, A feature of SO type "chromosome". | feature.feature_id | |
| rank | integer | 10 | UNIQUE, NOT NULL, rank can be used for n-ploid organisms or to preserve order. | ||
| cgroup | integer | 10 | UNIQUE, NOT NULL, Spatially distinguishable group. group can be used for distinguishing the chromosomal groups, for example (RNAi products and so on can be treated as different groups, as they do not fall on a particular chromosome). | ||
| cvterm_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id |
| Name | Fields |
|---|---|
| feature_genotype_idx1 | feature_id |
| feature_genotype_idx2 | genotype_id |
| Type | Fields |
|---|---|
| NOT NULL | feature_genotype_id |
| NOT NULL | feature_id |
| FOREIGN KEY | feature_id |
| NOT NULL | genotype_id |
| FOREIGN KEY | genotype_id |
| FOREIGN KEY | chromosome_id |
| NOT NULL | rank |
| NOT NULL | cgroup |
| NOT NULL | cvterm_id |
| FOREIGN KEY | cvterm_id |
| UNIQUE | feature_id, genotype_id, cvterm_id, chromosome_id, rank, cgroup |
environment |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| environment_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| uniquename | text | 64000 | UNIQUE, NOT NULL | ||
| description | text | 64000 |
| Name | Fields |
|---|---|
| environment_idx1 | uniquename |
| Type | Fields |
|---|---|
| NOT NULL | environment_id |
| NOT NULL | uniquename |
| UNIQUE | uniquename |
environment_cvterm |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| environment_cvterm_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| environment_id | integer | 10 | UNIQUE, NOT NULL | environment.environment_id | |
| cvterm_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id |
| Name | Fields |
|---|---|
| environment_cvterm_idx1 | environment_id |
| environment_cvterm_idx2 | cvterm_id |
| Type | Fields |
|---|---|
| NOT NULL | environment_cvterm_id |
| NOT NULL | environment_id |
| FOREIGN KEY | environment_id |
| NOT NULL | cvterm_id |
| FOREIGN KEY | cvterm_id |
| UNIQUE | environment_id, cvterm_id |
phenstatement |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phenstatement_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| genotype_id | integer | 10 | UNIQUE, NOT NULL | genotype.genotype_id | |
| environment_id | integer | 10 | UNIQUE, NOT NULL | environment.environment_id | |
| phenotype_id | integer | 10 | UNIQUE, NOT NULL | phenotype.phenotype_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id |
| Name | Fields |
|---|---|
| phenstatement_idx1 | genotype_id |
| phenstatement_idx2 | phenotype_id |
| Type | Fields |
|---|---|
| NOT NULL | phenstatement_id |
| NOT NULL | genotype_id |
| FOREIGN KEY | genotype_id |
| NOT NULL | environment_id |
| FOREIGN KEY | environment_id |
| NOT NULL | phenotype_id |
| FOREIGN KEY | phenotype_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| UNIQUE | genotype_id, phenotype_id, environment_id, type_id, pub_id |
phendesc |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phendesc_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| genotype_id | integer | 10 | UNIQUE, NOT NULL | genotype.genotype_id | |
| environment_id | integer | 10 | UNIQUE, NOT NULL | environment.environment_id | |
| description | text | 64000 | NOT NULL | ||
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id |
| Name | Fields |
|---|---|
| phendesc_idx1 | genotype_id |
| phendesc_idx2 | environment_id |
| phendesc_idx3 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | phendesc_id |
| NOT NULL | genotype_id |
| FOREIGN KEY | genotype_id |
| NOT NULL | environment_id |
| FOREIGN KEY | environment_id |
| NOT NULL | description |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| UNIQUE | genotype_id, environment_id, type_id, pub_id |
phenotype_comparison |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phenotype_comparison_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| genotype1_id | integer | 10 | UNIQUE, NOT NULL | genotype.genotype_id | |
| environment1_id | integer | 10 | UNIQUE, NOT NULL | environment.environment_id | |
| genotype2_id | integer | 10 | UNIQUE, NOT NULL | genotype.genotype_id | |
| environment2_id | integer | 10 | UNIQUE, NOT NULL | environment.environment_id | |
| phenotype1_id | integer | 10 | UNIQUE, NOT NULL | phenotype.phenotype_id | |
| phenotype2_id | integer | 10 | phenotype.phenotype_id | ||
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id | |
| organism_id | integer | 10 | NOT NULL | organism.organism_id |
| Name | Fields |
|---|---|
| phenotype_comparison_idx1 | genotype1_id |
| phenotype_comparison_idx2 | genotype2_id |
| phenotype_comparison_idx4 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | phenotype_comparison_id |
| NOT NULL | genotype1_id |
| FOREIGN KEY | genotype1_id |
| NOT NULL | environment1_id |
| FOREIGN KEY | environment1_id |
| NOT NULL | genotype2_id |
| FOREIGN KEY | genotype2_id |
| NOT NULL | environment2_id |
| FOREIGN KEY | environment2_id |
| NOT NULL | phenotype1_id |
| FOREIGN KEY | phenotype1_id |
| FOREIGN KEY | phenotype2_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| NOT NULL | organism_id |
| FOREIGN KEY | organism_id |
| UNIQUE | genotype1_id, environment1_id, genotype2_id, environment2_id, phenotype1_id, pub_id |
phenotype_comparison_cvterm |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phenotype_comparison_cvterm_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| phenotype_comparison_id | integer | 10 | UNIQUE, NOT NULL | phenotype_comparison.phenotype_comparison_id | |
| cvterm_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| pub_id | integer | 10 | NOT NULL | pub.pub_id | |
| rank | integer | 10 | 0 | NOT NULL |
| Name | Fields |
|---|---|
| phenotype_comparison_cvterm_idx1 | phenotype_comparison_id |
| phenotype_comparison_cvterm_idx2 | cvterm_id |
| Type | Fields |
|---|---|
| NOT NULL | phenotype_comparison_cvterm_id |
| NOT NULL | phenotype_comparison_id |
| FOREIGN KEY | phenotype_comparison_id |
| NOT NULL | cvterm_id |
| FOREIGN KEY | cvterm_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| NOT NULL | rank |
| UNIQUE | phenotype_comparison_id, cvterm_id |
genotypeprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| genotypeprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| genotype_id | integer | 10 | UNIQUE, NOT NULL | genotype.genotype_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| value | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| genotypeprop_idx1 | genotype_id |
| genotypeprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | genotypeprop_id |
| NOT NULL | genotype_id |
| FOREIGN KEY | genotype_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | genotype_id, type_id, rank |
featuremap |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| featuremap_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| name | varchar | 255 | UNIQUE | ||
| description | text | 64000 | |||
| unittype_id | integer | 10 | NULL | cvterm.cvterm_id |
| Type | Fields |
|---|---|
| NOT NULL | featuremap_id |
| FOREIGN KEY | unittype_id |
| UNIQUE | name |
featurerange |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| featurerange_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| featuremap_id | integer | 10 | NOT NULL, featuremap_id is the id of the feature being mapped. | featuremap.featuremap_id | |
| feature_id | integer | 10 | NOT NULL | feature.feature_id | |
| leftstartf_id | integer | 10 | NOT NULL | feature.feature_id | |
| leftendf_id | integer | 10 | feature.feature_id | ||
| rightstartf_id | integer | 10 | feature.feature_id | ||
| rightendf_id | integer | 10 | NOT NULL | feature.feature_id | |
| rangestr | varchar | 255 |
| Name | Fields |
|---|---|
| featurerange_idx1 | featuremap_id |
| featurerange_idx2 | feature_id |
| featurerange_idx3 | leftstartf_id |
| featurerange_idx4 | leftendf_id |
| featurerange_idx5 | rightstartf_id |
| featurerange_idx6 | rightendf_id |
| Type | Fields |
|---|---|
| NOT NULL | featurerange_id |
| NOT NULL | featuremap_id |
| FOREIGN KEY | featuremap_id |
| NOT NULL | feature_id |
| FOREIGN KEY | feature_id |
| NOT NULL | leftstartf_id |
| FOREIGN KEY | leftstartf_id |
| FOREIGN KEY | leftendf_id |
| FOREIGN KEY | rightstartf_id |
| NOT NULL | rightendf_id |
| FOREIGN KEY | rightendf_id |
featurepos |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| featurepos_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| featuremap_id | integer | 11 | NOT NULL | featuremap.featuremap_id | |
| feature_id | integer | 10 | NOT NULL | feature.feature_id | |
| map_feature_id | integer | 10 | NOT NULL, map_feature_id links to the feature (map) upon which the feature is being localized. | feature.feature_id | |
| mappos | float | 20 | NOT NULL |
| Name | Fields |
|---|---|
| featurepos_idx1 | featuremap_id |
| featurepos_idx2 | feature_id |
| featurepos_idx3 | map_feature_id |
| Type | Fields |
|---|---|
| NOT NULL | featurepos_id |
| NOT NULL | featuremap_id |
| FOREIGN KEY | featuremap_id |
| NOT NULL | feature_id |
| FOREIGN KEY | feature_id |
| NOT NULL | map_feature_id |
| FOREIGN KEY | map_feature_id |
| NOT NULL | mappos |
featuremap_pub |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| featuremap_pub_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| featuremap_id | integer | 10 | NOT NULL | featuremap.featuremap_id | |
| pub_id | integer | 10 | NOT NULL | pub.pub_id |
| Name | Fields |
|---|---|
| featuremap_pub_idx1 | featuremap_id |
| featuremap_pub_idx2 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | featuremap_pub_id |
| NOT NULL | featuremap_id |
| FOREIGN KEY | featuremap_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
phylotree |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phylotree_id | integer | 11 | PRIMARY KEY, UNIQUE, NOT NULL | ||
| dbxref_id | integer | 10 | NOT NULL | dbxref.dbxref_id | |
| name | varchar | 255 | NULL | ||
| type_id | integer | 10 | Type: protein, nucleotide, taxonomy, for example. The type should be any SO type, or "taxonomy". | cvterm.cvterm_id | |
| analysis_id | integer | 10 | NULL | analysis.analysis_id | |
| comment | text | 64000 | NULL |
| Name | Fields |
|---|---|
| phylotree_idx1 | phylotree_id |
| Type | Fields |
|---|---|
| NOT NULL | phylotree_id |
| NOT NULL | dbxref_id |
| FOREIGN KEY | dbxref_id |
| FOREIGN KEY | type_id |
| FOREIGN KEY | analysis_id |
| UNIQUE | phylotree_id |
phylotree_pub |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phylotree_pub_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| phylotree_id | integer | 10 | UNIQUE, NOT NULL | phylotree.phylotree_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id |
| Name | Fields |
|---|---|
| phylotree_pub_idx1 | phylotree_id |
| phylotree_pub_idx2 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | phylotree_pub_id |
| NOT NULL | phylotree_id |
| FOREIGN KEY | phylotree_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| UNIQUE | phylotree_id, pub_id |
phylonode |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phylonode_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| phylotree_id | integer | 10 | UNIQUE, NOT NULL | phylotree.phylotree_id | |
| parent_phylonode_id | integer | 10 | NULL | Root phylonode can have null parent_phylonode_id value. | phylonode.phylonode_id |
| left_idx | integer | 10 | UNIQUE, NOT NULL | ||
| right_idx | integer | 10 | UNIQUE, NOT NULL | ||
| type_id | integer | 10 | Type: e.g. root, interior, leaf. | cvterm.cvterm_id | |
| feature_id | integer | 10 | Phylonodes can have optional features attached to them e.g. a protein or nucleotide sequence usually attached to a leaf of the phylotree for non-leaf nodes, the feature may be a feature that is an instance of SO:match; this feature is the alignment of all leaf features beneath it. | feature.feature_id | |
| label | varchar | 255 | NULL | ||
| distance | float | 20 | NULL |
| Type | Fields |
|---|---|
| NOT NULL | phylonode_id |
| NOT NULL | phylotree_id |
| FOREIGN KEY | phylotree_id |
| FOREIGN KEY | parent_phylonode_id |
| NOT NULL | left_idx |
| NOT NULL | right_idx |
| FOREIGN KEY | type_id |
| FOREIGN KEY | feature_id |
| UNIQUE | phylotree_id, left_idx |
| UNIQUE | phylotree_id, right_idx |
phylonode_dbxref |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phylonode_dbxref_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| phylonode_id | integer | 10 | UNIQUE, NOT NULL | phylonode.phylonode_id | |
| dbxref_id | integer | 10 | UNIQUE, NOT NULL | dbxref.dbxref_id |
| Name | Fields |
|---|---|
| phylonode_dbxref_idx1 | phylonode_id |
| phylonode_dbxref_idx2 | dbxref_id |
| Type | Fields |
|---|---|
| NOT NULL | phylonode_dbxref_id |
| NOT NULL | phylonode_id |
| FOREIGN KEY | phylonode_id |
| NOT NULL | dbxref_id |
| FOREIGN KEY | dbxref_id |
| UNIQUE | phylonode_id, dbxref_id |
phylonode_pub |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phylonode_pub_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| phylonode_id | integer | 10 | UNIQUE, NOT NULL | phylonode.phylonode_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id |
| Name | Fields |
|---|---|
| phylonode_pub_idx1 | phylonode_id |
| phylonode_pub_idx2 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | phylonode_pub_id |
| NOT NULL | phylonode_id |
| FOREIGN KEY | phylonode_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| UNIQUE | phylonode_id, pub_id |
phylonode_organism |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phylonode_organism_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| phylonode_id | integer | 10 | UNIQUE, NOT NULL, One phylonode cannot refer to >1 organism. | phylonode.phylonode_id | |
| organism_id | integer | 10 | NOT NULL | organism.organism_id |
| Name | Fields |
|---|---|
| phylonode_organism_idx1 | phylonode_id |
| phylonode_organism_idx2 | organism_id |
| Type | Fields |
|---|---|
| NOT NULL | phylonode_organism_id |
| NOT NULL | phylonode_id |
| FOREIGN KEY | phylonode_id |
| NOT NULL | organism_id |
| FOREIGN KEY | organism_id |
| UNIQUE | phylonode_id |
phylonodeprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phylonodeprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| phylonode_id | integer | 10 | UNIQUE, NOT NULL | phylonode.phylonode_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL, type_id could designate phylonode hierarchy relationships, for example: species taxonomy (kingdom, order, family, genus, species), "ortholog/paralog", "fold/superfold", etc. | cvterm.cvterm_id | |
| value | text | 64000 | UNIQUE, NOT NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL, It is not clear how useful the rank concept is here, leave it in for now. |
| Name | Fields |
|---|---|
| phylonodeprop_idx1 | phylonode_id |
| phylonodeprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | phylonodeprop_id |
| NOT NULL | phylonode_id |
| FOREIGN KEY | phylonode_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | value |
| NOT NULL | rank |
| UNIQUE | phylonode_id, type_id, value, rank |
phylonode_relationship |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| phylonode_relationship_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| subject_id | integer | 10 | UNIQUE, NOT NULL | phylonode.phylonode_id | |
| object_id | integer | 10 | UNIQUE, NOT NULL | phylonode.phylonode_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| rank | integer | 10 | |||
| phylotree_id | integer | 10 | NOT NULL | phylotree.phylotree_id |
| Name | Fields |
|---|---|
| phylonode_relationship_idx1 | subject_id |
| phylonode_relationship_idx2 | object_id |
| phylonode_relationship_idx3 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | phylonode_relationship_id |
| NOT NULL | subject_id |
| FOREIGN KEY | subject_id |
| NOT NULL | object_id |
| FOREIGN KEY | object_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | phylotree_id |
| FOREIGN KEY | phylotree_id |
| UNIQUE | subject_id, object_id, type_id |
contact |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| contact_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| type_id | integer | 10 | NULL | What type of contact is this? E.g. "person", "lab". | cvterm.cvterm_id |
| name | varchar | 255 | UNIQUE, NOT NULL | ||
| description | varchar | 255 | NULL |
| Type | Fields |
|---|---|
| NOT NULL | contact_id |
| FOREIGN KEY | type_id |
| NOT NULL | name |
| UNIQUE | name |
contact_relationship |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| contact_relationship_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| type_id | integer | 10 | UNIQUE, NOT NULL, Relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. | cvterm.cvterm_id | |
| subject_id | integer | 10 | UNIQUE, NOT NULL, The subject of the subj-predicate-obj sentence. In a DAG, this corresponds to the child node. | contact.contact_id | |
| object_id | integer | 10 | UNIQUE, NOT NULL, The object of the subj-predicate-obj sentence. In a DAG, this corresponds to the parent node. | contact.contact_id |
| Name | Fields |
|---|---|
| contact_relationship_idx1 | type_id |
| contact_relationship_idx2 | subject_id |
| contact_relationship_idx3 | object_id |
| Type | Fields |
|---|---|
| NOT NULL | contact_relationship_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | subject_id |
| FOREIGN KEY | subject_id |
| NOT NULL | object_id |
| FOREIGN KEY | object_id |
| UNIQUE | subject_id, object_id, type_id |
expression |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| expression_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| uniquename | text | 64000 | UNIQUE, NOT NULL | ||
| md5checksum | char | 32 | |||
| description | text | 64000 |
| Type | Fields |
|---|---|
| NOT NULL | expression_id |
| NOT NULL | uniquename |
| UNIQUE | uniquename |
expression_cvterm |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| expression_cvterm_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| expression_id | integer | 10 | UNIQUE, NOT NULL | expression.expression_id | |
| cvterm_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| rank | integer | 10 | 0 | NOT NULL | |
| cvterm_type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id |
| Name | Fields |
|---|---|
| expression_cvterm_idx1 | expression_id |
| expression_cvterm_idx2 | cvterm_id |
| expression_cvterm_idx3 | cvterm_type_id |
| Type | Fields |
|---|---|
| NOT NULL | expression_cvterm_id |
| NOT NULL | expression_id |
| FOREIGN KEY | expression_id |
| NOT NULL | cvterm_id |
| FOREIGN KEY | cvterm_id |
| NOT NULL | rank |
| NOT NULL | cvterm_type_id |
| FOREIGN KEY | cvterm_type_id |
| UNIQUE | expression_id, cvterm_id, cvterm_type_id |
expression_cvtermprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| expression_cvtermprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| expression_cvterm_id | integer | 10 | UNIQUE, NOT NULL | expression_cvterm.expression_cvterm_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. For example, cvterms may come from the FlyBase miscellaneous cv. | cvterm.cvterm_id | |
| value | text | 64000 | NULL | The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query. | |
| rank | integer | 10 | 0 | UNIQUE, NOT NULL, Property-Value ordering. Any expression_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used. |
| Name | Fields |
|---|---|
| expression_cvtermprop_idx1 | expression_cvterm_id |
| expression_cvtermprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | expression_cvtermprop_id |
| NOT NULL | expression_cvterm_id |
| FOREIGN KEY | expression_cvterm_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | expression_cvterm_id, type_id, rank |
expressionprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| expressionprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| expression_id | integer | 10 | UNIQUE, NOT NULL | expression.expression_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| value | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| expressionprop_idx1 | expression_id |
| expressionprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | expressionprop_id |
| NOT NULL | expression_id |
| FOREIGN KEY | expression_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | expression_id, type_id, rank |
expression_pub |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| expression_pub_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| expression_id | integer | 10 | UNIQUE, NOT NULL | expression.expression_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id |
| Name | Fields |
|---|---|
| expression_pub_idx1 | expression_id |
| expression_pub_idx2 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | expression_pub_id |
| NOT NULL | expression_id |
| FOREIGN KEY | expression_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| UNIQUE | expression_id, pub_id |
feature_expression |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| feature_expression_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| expression_id | integer | 10 | UNIQUE, NOT NULL | expression.expression_id | |
| feature_id | integer | 10 | UNIQUE, NOT NULL | feature.feature_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id |
| Name | Fields |
|---|---|
| feature_expression_idx1 | expression_id |
| feature_expression_idx2 | feature_id |
| feature_expression_idx3 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | feature_expression_id |
| NOT NULL | expression_id |
| FOREIGN KEY | expression_id |
| NOT NULL | feature_id |
| FOREIGN KEY | feature_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| UNIQUE | expression_id, feature_id, pub_id |
feature_expressionprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| feature_expressionprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| feature_expression_id | integer | 10 | UNIQUE, NOT NULL | feature_expression.feature_expression_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| value | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| feature_expressionprop_idx1 | feature_expression_id |
| feature_expressionprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | feature_expressionprop_id |
| NOT NULL | feature_expression_id |
| FOREIGN KEY | feature_expression_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | feature_expression_id, type_id, rank |
eimage |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| eimage_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| eimage_data | text | 64000 | We expect images in eimage_data (e.g. JPEGs) to be uuencoded. | ||
| eimage_type | varchar | 255 | NOT NULL, Describes the type of data in eimage_data. | ||
| image_uri | varchar | 255 |
| Type | Fields |
|---|---|
| NOT NULL | eimage_id |
| NOT NULL | eimage_type |
expression_image |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| expression_image_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| expression_id | integer | 10 | UNIQUE, NOT NULL | expression.expression_id | |
| eimage_id | integer | 10 | UNIQUE, NOT NULL | eimage.eimage_id |
| Name | Fields |
|---|---|
| expression_image_idx1 | expression_id |
| expression_image_idx2 | eimage_id |
| Type | Fields |
|---|---|
| NOT NULL | expression_image_id |
| NOT NULL | expression_id |
| FOREIGN KEY | expression_id |
| NOT NULL | eimage_id |
| FOREIGN KEY | eimage_id |
| UNIQUE | expression_id, eimage_id |
project |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| project_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| name | varchar | 255 | UNIQUE, NOT NULL | ||
| description | varchar | 255 | NOT NULL |
| Type | Fields |
|---|---|
| NOT NULL | project_id |
| NOT NULL | name |
| NOT NULL | description |
| UNIQUE | name |
projectprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| projectprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| project_id | integer | 10 | UNIQUE, NOT NULL | project.project_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| value | text | 64000 | |||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Type | Fields |
|---|---|
| NOT NULL | projectprop_id |
| NOT NULL | project_id |
| FOREIGN KEY | project_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | project_id, type_id, rank |
project_relationship |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| project_relationship_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| subject_project_id | integer | 10 | UNIQUE, NOT NULL | project.project_id | |
| object_project_id | integer | 10 | UNIQUE, NOT NULL | project.project_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL, The type of relationship being stated, such as "is part of". | cvterm.cvterm_id |
| Type | Fields |
|---|---|
| NOT NULL | project_relationship_id |
| NOT NULL | subject_project_id |
| FOREIGN KEY | subject_project_id |
| NOT NULL | object_project_id |
| FOREIGN KEY | object_project_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| UNIQUE | subject_project_id, object_project_id, type_id |
project_pub |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| project_pub_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| project_id | integer | 10 | UNIQUE, NOT NULL | project.project_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id |
| Name | Fields |
|---|---|
| project_pub_idx1 | project_id |
| project_pub_idx2 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | project_pub_id |
| NOT NULL | project_id |
| FOREIGN KEY | project_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| UNIQUE | project_id, pub_id |
project_contact |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| project_contact_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| project_id | integer | 10 | UNIQUE, NOT NULL | project.project_id | |
| contact_id | integer | 10 | UNIQUE, NOT NULL | contact.contact_id |
| Name | Fields |
|---|---|
| project_contact_idx1 | project_id |
| project_contact_idx2 | contact_id |
| Type | Fields |
|---|---|
| NOT NULL | project_contact_id |
| NOT NULL | project_id |
| FOREIGN KEY | project_id |
| NOT NULL | contact_id |
| FOREIGN KEY | contact_id |
| UNIQUE | project_id, contact_id |
mageml |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| mageml_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| mage_package | text | 64000 | NOT NULL | ||
| mage_ml | text | 64000 | NOT NULL |
| Type | Fields |
|---|---|
| NOT NULL | mageml_id |
| NOT NULL | mage_package |
| NOT NULL | mage_ml |
magedocumentation |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| magedocumentation_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| mageml_id | integer | 10 | NOT NULL | mageml.mageml_id | |
| tableinfo_id | integer | 10 | NOT NULL | tableinfo.tableinfo_id | |
| row_id | integer | 10 | NOT NULL | ||
| mageidentifier | text | 64000 | NOT NULL |
| Name | Fields |
|---|---|
| magedocumentation_idx1 | mageml_id |
| magedocumentation_idx2 | tableinfo_id |
| magedocumentation_idx3 | row_id |
| Type | Fields |
|---|---|
| NOT NULL | magedocumentation_id |
| NOT NULL | mageml_id |
| FOREIGN KEY | mageml_id |
| NOT NULL | tableinfo_id |
| FOREIGN KEY | tableinfo_id |
| NOT NULL | row_id |
| NOT NULL | mageidentifier |
protocol |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| protocol_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| type_id | integer | 10 | NOT NULL | cvterm.cvterm_id | |
| pub_id | integer | 10 | NULL | pub.pub_id | |
| dbxref_id | integer | 10 | NULL | dbxref.dbxref_id | |
| name | text | 64000 | UNIQUE, NOT NULL | ||
| uri | text | 64000 | NULL | ||
| protocoldescription | text | 64000 | NULL | ||
| hardwaredescription | text | 64000 | NULL | ||
| softwaredescription | text | 64000 | NULL |
| Name | Fields |
|---|---|
| protocol_idx1 | type_id |
| protocol_idx2 | pub_id |
| protocol_idx3 | dbxref_id |
| Type | Fields |
|---|---|
| NOT NULL | protocol_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| FOREIGN KEY | pub_id |
| FOREIGN KEY | dbxref_id |
| NOT NULL | name |
| UNIQUE | name |
protocolparam |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| protocolparam_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| protocol_id | integer | 10 | NOT NULL | protocol.protocol_id | |
| name | text | 64000 | NOT NULL | ||
| datatype_id | integer | 10 | NULL | cvterm.cvterm_id | |
| unittype_id | integer | 10 | NULL | cvterm.cvterm_id | |
| value | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | NOT NULL |
| Name | Fields |
|---|---|
| protocolparam_idx1 | protocol_id |
| protocolparam_idx2 | datatype_id |
| protocolparam_idx3 | unittype_id |
| Type | Fields |
|---|---|
| NOT NULL | protocolparam_id |
| NOT NULL | protocol_id |
| FOREIGN KEY | protocol_id |
| NOT NULL | name |
| FOREIGN KEY | datatype_id |
| FOREIGN KEY | unittype_id |
| NOT NULL | rank |
channel |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| channel_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| name | text | 64000 | UNIQUE, NOT NULL | ||
| definition | text | 64000 | NOT NULL |
| Type | Fields |
|---|---|
| NOT NULL | channel_id |
| NOT NULL | name |
| NOT NULL | definition |
| UNIQUE | name |
arraydesign |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| arraydesign_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| manufacturer_id | integer | 10 | NOT NULL | contact.contact_id | |
| platformtype_id | integer | 10 | NOT NULL | cvterm.cvterm_id | |
| substratetype_id | integer | 10 | NULL | cvterm.cvterm_id | |
| protocol_id | integer | 10 | NULL | protocol.protocol_id | |
| dbxref_id | integer | 10 | NULL | dbxref.dbxref_id | |
| name | text | 64000 | UNIQUE, NOT NULL | ||
| version | text | 64000 | NULL | ||
| description | text | 64000 | NULL | ||
| array_dimensions | text | 64000 | NULL | ||
| element_dimensions | text | 64000 | NULL | ||
| num_of_elements | integer | 10 | NULL | ||
| num_array_columns | integer | 10 | NULL | ||
| num_array_rows | integer | 10 | NULL | ||
| num_grid_columns | integer | 10 | NULL | ||
| num_grid_rows | integer | 10 | NULL | ||
| num_sub_columns | integer | 10 | NULL | ||
| num_sub_rows | integer | 10 | NULL |
| Name | Fields |
|---|---|
| arraydesign_idx1 | manufacturer_id |
| arraydesign_idx2 | platformtype_id |
| arraydesign_idx3 | substratetype_id |
| arraydesign_idx4 | protocol_id |
| arraydesign_idx5 | dbxref_id |
| Type | Fields |
|---|---|
| NOT NULL | arraydesign_id |
| NOT NULL | manufacturer_id |
| FOREIGN KEY | manufacturer_id |
| NOT NULL | platformtype_id |
| FOREIGN KEY | platformtype_id |
| FOREIGN KEY | substratetype_id |
| FOREIGN KEY | protocol_id |
| FOREIGN KEY | dbxref_id |
| NOT NULL | name |
| UNIQUE | name |
arraydesignprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| arraydesignprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| arraydesign_id | integer | 10 | UNIQUE, NOT NULL | arraydesign.arraydesign_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| value | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| arraydesignprop_idx1 | arraydesign_id |
| arraydesignprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | arraydesignprop_id |
| NOT NULL | arraydesign_id |
| FOREIGN KEY | arraydesign_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | arraydesign_id, type_id, rank |
assay |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| assay_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| arraydesign_id | integer | 10 | NOT NULL | arraydesign.arraydesign_id | |
| protocol_id | integer | 10 | NULL | protocol.protocol_id | |
| assaydate | timestamp | 0 | current_timestamp | ||
| arrayidentifier | text | 64000 | NULL | ||
| arraybatchidentifier | text | 64000 | NULL | ||
| operator_id | integer | 10 | NOT NULL | contact.contact_id | |
| dbxref_id | integer | 10 | NULL | dbxref.dbxref_id | |
| name | text | 64000 | NULL | UNIQUE | |
| description | text | 64000 | NULL |
| Name | Fields |
|---|---|
| assay_idx1 | arraydesign_id |
| assay_idx2 | protocol_id |
| assay_idx3 | operator_id |
| assay_idx4 | dbxref_id |
| Type | Fields |
|---|---|
| NOT NULL | assay_id |
| NOT NULL | arraydesign_id |
| FOREIGN KEY | arraydesign_id |
| FOREIGN KEY | protocol_id |
| NOT NULL | operator_id |
| FOREIGN KEY | operator_id |
| FOREIGN KEY | dbxref_id |
| UNIQUE | name |
assayprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| assayprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| assay_id | integer | 10 | UNIQUE, NOT NULL | assay.assay_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| value | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| assayprop_idx1 | assay_id |
| assayprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | assayprop_id |
| NOT NULL | assay_id |
| FOREIGN KEY | assay_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | assay_id, type_id, rank |
assay_project |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| assay_project_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| assay_id | integer | 10 | UNIQUE, NOT NULL | assay.assay_id | |
| project_id | integer | 10 | UNIQUE, NOT NULL | project.project_id |
| Name | Fields |
|---|---|
| assay_project_idx1 | assay_id |
| assay_project_idx2 | project_id |
| Type | Fields |
|---|---|
| NOT NULL | assay_project_id |
| NOT NULL | assay_id |
| FOREIGN KEY | assay_id |
| NOT NULL | project_id |
| FOREIGN KEY | project_id |
| UNIQUE | assay_id, project_id |
biomaterial |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| biomaterial_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| taxon_id | integer | 10 | NULL | organism.organism_id | |
| biosourceprovider_id | integer | 10 | NULL | contact.contact_id | |
| dbxref_id | integer | 10 | NULL | dbxref.dbxref_id | |
| name | text | 64000 | NULL | UNIQUE | |
| description | text | 64000 | NULL |
| Name | Fields |
|---|---|
| biomaterial_idx1 | taxon_id |
| biomaterial_idx2 | biosourceprovider_id |
| biomaterial_idx3 | dbxref_id |
| Type | Fields |
|---|---|
| NOT NULL | biomaterial_id |
| FOREIGN KEY | taxon_id |
| FOREIGN KEY | biosourceprovider_id |
| FOREIGN KEY | dbxref_id |
| UNIQUE | name |
biomaterial_relationship |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| biomaterial_relationship_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| subject_id | integer | 10 | UNIQUE, NOT NULL | biomaterial.biomaterial_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| object_id | integer | 10 | UNIQUE, NOT NULL | biomaterial.biomaterial_id |
| Name | Fields |
|---|---|
| biomaterial_relationship_idx1 | subject_id |
| biomaterial_relationship_idx2 | object_id |
| biomaterial_relationship_idx3 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | biomaterial_relationship_id |
| NOT NULL | subject_id |
| FOREIGN KEY | subject_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | object_id |
| FOREIGN KEY | object_id |
| UNIQUE | subject_id, object_id, type_id |
biomaterialprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| biomaterialprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| biomaterial_id | integer | 10 | UNIQUE, NOT NULL | biomaterial.biomaterial_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| value | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| biomaterialprop_idx1 | biomaterial_id |
| biomaterialprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | biomaterialprop_id |
| NOT NULL | biomaterial_id |
| FOREIGN KEY | biomaterial_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | biomaterial_id, type_id, rank |
biomaterial_dbxref |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| biomaterial_dbxref_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| biomaterial_id | integer | 10 | UNIQUE, NOT NULL | biomaterial.biomaterial_id | |
| dbxref_id | integer | 10 | UNIQUE, NOT NULL | dbxref.dbxref_id |
| Name | Fields |
|---|---|
| biomaterial_dbxref_idx1 | biomaterial_id |
| biomaterial_dbxref_idx2 | dbxref_id |
| Type | Fields |
|---|---|
| NOT NULL | biomaterial_dbxref_id |
| NOT NULL | biomaterial_id |
| FOREIGN KEY | biomaterial_id |
| NOT NULL | dbxref_id |
| FOREIGN KEY | dbxref_id |
| UNIQUE | biomaterial_id, dbxref_id |
treatment |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| treatment_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| rank | integer | 10 | 0 | NOT NULL | |
| biomaterial_id | integer | 10 | NOT NULL | biomaterial.biomaterial_id | |
| type_id | integer | 10 | NOT NULL | cvterm.cvterm_id | |
| protocol_id | integer | 10 | NULL | protocol.protocol_id | |
| name | text | 64000 | NULL |
| Name | Fields |
|---|---|
| treatment_idx1 | biomaterial_id |
| treatment_idx2 | type_id |
| treatment_idx3 | protocol_id |
| Type | Fields |
|---|---|
| NOT NULL | treatment_id |
| NOT NULL | rank |
| NOT NULL | biomaterial_id |
| FOREIGN KEY | biomaterial_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| FOREIGN KEY | protocol_id |
biomaterial_treatment |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| biomaterial_treatment_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| biomaterial_id | integer | 10 | UNIQUE, NOT NULL | biomaterial.biomaterial_id | |
| treatment_id | integer | 10 | UNIQUE, NOT NULL | treatment.treatment_id | |
| unittype_id | integer | 10 | NULL | cvterm.cvterm_id | |
| value | float | 15 | NULL | ||
| rank | integer | 10 | 0 | NOT NULL |
| Name | Fields |
|---|---|
| biomaterial_treatment_idx1 | biomaterial_id |
| biomaterial_treatment_idx2 | treatment_id |
| biomaterial_treatment_idx3 | unittype_id |
| Type | Fields |
|---|---|
| NOT NULL | biomaterial_treatment_id |
| NOT NULL | biomaterial_id |
| FOREIGN KEY | biomaterial_id |
| NOT NULL | treatment_id |
| FOREIGN KEY | treatment_id |
| FOREIGN KEY | unittype_id |
| NOT NULL | rank |
| UNIQUE | biomaterial_id, treatment_id |
assay_biomaterial |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| assay_biomaterial_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| assay_id | integer | 10 | UNIQUE, NOT NULL | assay.assay_id | |
| biomaterial_id | integer | 10 | UNIQUE, NOT NULL | biomaterial.biomaterial_id | |
| channel_id | integer | 10 | NULL | UNIQUE | channel.channel_id |
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| assay_biomaterial_idx1 | assay_id |
| assay_biomaterial_idx2 | biomaterial_id |
| assay_biomaterial_idx3 | channel_id |
| Type | Fields |
|---|---|
| NOT NULL | assay_biomaterial_id |
| NOT NULL | assay_id |
| FOREIGN KEY | assay_id |
| NOT NULL | biomaterial_id |
| FOREIGN KEY | biomaterial_id |
| FOREIGN KEY | channel_id |
| NOT NULL | rank |
| UNIQUE | assay_id, biomaterial_id, channel_id, rank |
acquisition |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| acquisition_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| assay_id | integer | 10 | NOT NULL | assay.assay_id | |
| protocol_id | integer | 10 | NULL | protocol.protocol_id | |
| channel_id | integer | 10 | NULL | channel.channel_id | |
| acquisitiondate | timestamp | 0 | current_timestamp | ||
| name | text | 64000 | NULL | UNIQUE | |
| uri | text | 64000 | NULL |
| Name | Fields |
|---|---|
| acquisition_idx1 | assay_id |
| acquisition_idx2 | protocol_id |
| acquisition_idx3 | channel_id |
| Type | Fields |
|---|---|
| NOT NULL | acquisition_id |
| NOT NULL | assay_id |
| FOREIGN KEY | assay_id |
| FOREIGN KEY | protocol_id |
| FOREIGN KEY | channel_id |
| UNIQUE | name |
acquisitionprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| acquisitionprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| acquisition_id | integer | 10 | UNIQUE, NOT NULL | acquisition.acquisition_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| value | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| acquisitionprop_idx1 | acquisition_id |
| acquisitionprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | acquisitionprop_id |
| NOT NULL | acquisition_id |
| FOREIGN KEY | acquisition_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | acquisition_id, type_id, rank |
acquisition_relationship |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| acquisition_relationship_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| subject_id | integer | 10 | UNIQUE, NOT NULL | acquisition.acquisition_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| object_id | integer | 10 | UNIQUE, NOT NULL | acquisition.acquisition_id | |
| value | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| acquisition_relationship_idx1 | subject_id |
| acquisition_relationship_idx2 | type_id |
| acquisition_relationship_idx3 | object_id |
| Type | Fields |
|---|---|
| NOT NULL | acquisition_relationship_id |
| NOT NULL | subject_id |
| FOREIGN KEY | subject_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | object_id |
| FOREIGN KEY | object_id |
| NOT NULL | rank |
| UNIQUE | subject_id, object_id, type_id, rank |
quantification |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| quantification_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| acquisition_id | integer | 10 | NOT NULL | acquisition.acquisition_id | |
| operator_id | integer | 10 | NULL | contact.contact_id | |
| protocol_id | integer | 10 | NULL | protocol.protocol_id | |
| analysis_id | integer | 10 | UNIQUE, NOT NULL | analysis.analysis_id | |
| quantificationdate | timestamp | 0 | current_timestamp | ||
| name | text | 64000 | NULL | UNIQUE | |
| uri | text | 64000 | NULL |
| Name | Fields |
|---|---|
| quantification_idx1 | acquisition_id |
| quantification_idx2 | operator_id |
| quantification_idx3 | protocol_id |
| quantification_idx4 | analysis_id |
| Type | Fields |
|---|---|
| NOT NULL | quantification_id |
| NOT NULL | acquisition_id |
| FOREIGN KEY | acquisition_id |
| FOREIGN KEY | operator_id |
| FOREIGN KEY | protocol_id |
| NOT NULL | analysis_id |
| FOREIGN KEY | analysis_id |
| UNIQUE | name, analysis_id |
quantificationprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| quantificationprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| quantification_id | integer | 10 | UNIQUE, NOT NULL | quantification.quantification_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| value | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| quantificationprop_idx1 | quantification_id |
| quantificationprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | quantificationprop_id |
| NOT NULL | quantification_id |
| FOREIGN KEY | quantification_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | quantification_id, type_id, rank |
quantification_relationship |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| quantification_relationship_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| subject_id | integer | 10 | UNIQUE, NOT NULL | quantification.quantification_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| object_id | integer | 10 | UNIQUE, NOT NULL | quantification.quantification_id |
| Name | Fields |
|---|---|
| quantification_relationship_idx1 | subject_id |
| quantification_relationship_idx2 | type_id |
| quantification_relationship_idx3 | object_id |
| Type | Fields |
|---|---|
| NOT NULL | quantification_relationship_id |
| NOT NULL | subject_id |
| FOREIGN KEY | subject_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | object_id |
| FOREIGN KEY | object_id |
| UNIQUE | subject_id, object_id, type_id |
control |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| control_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| type_id | integer | 10 | NOT NULL | cvterm.cvterm_id | |
| assay_id | integer | 10 | NOT NULL | assay.assay_id | |
| tableinfo_id | integer | 10 | NOT NULL | tableinfo.tableinfo_id | |
| row_id | integer | 10 | NOT NULL | ||
| name | text | 64000 | NULL | ||
| value | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | NOT NULL |
| Name | Fields |
|---|---|
| control_idx1 | type_id |
| control_idx2 | assay_id |
| control_idx3 | tableinfo_id |
| control_idx4 | row_id |
| Type | Fields |
|---|---|
| NOT NULL | control_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | assay_id |
| FOREIGN KEY | assay_id |
| NOT NULL | tableinfo_id |
| FOREIGN KEY | tableinfo_id |
| NOT NULL | row_id |
| NOT NULL | rank |
element |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| element_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| feature_id | integer | 10 | NULL | UNIQUE | feature.feature_id |
| arraydesign_id | integer | 10 | UNIQUE, NOT NULL | arraydesign.arraydesign_id | |
| type_id | integer | 10 | NULL | cvterm.cvterm_id | |
| dbxref_id | integer | 10 | NULL | dbxref.dbxref_id |
| Name | Fields |
|---|---|
| element_idx1 | feature_id |
| element_idx2 | arraydesign_id |
| element_idx3 | type_id |
| element_idx4 | dbxref_id |
| Type | Fields |
|---|---|
| NOT NULL | element_id |
| FOREIGN KEY | feature_id |
| NOT NULL | arraydesign_id |
| FOREIGN KEY | arraydesign_id |
| FOREIGN KEY | type_id |
| FOREIGN KEY | dbxref_id |
| UNIQUE | feature_id, arraydesign_id |
elementresult |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| elementresult_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| element_id | integer | 10 | UNIQUE, NOT NULL | element.element_id | |
| quantification_id | integer | 10 | UNIQUE, NOT NULL | quantification.quantification_id | |
| signal | float | 20 | NOT NULL |
| Name | Fields |
|---|---|
| elementresult_idx1 | element_id |
| elementresult_idx2 | quantification_id |
| elementresult_idx3 | signal |
| Type | Fields |
|---|---|
| NOT NULL | elementresult_id |
| NOT NULL | element_id |
| FOREIGN KEY | element_id |
| NOT NULL | quantification_id |
| FOREIGN KEY | quantification_id |
| NOT NULL | signal |
| UNIQUE | element_id, quantification_id |
element_relationship |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| element_relationship_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| subject_id | integer | 10 | UNIQUE, NOT NULL | element.element_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| object_id | integer | 10 | UNIQUE, NOT NULL | element.element_id | |
| value | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| element_relationship_idx1 | subject_id |
| element_relationship_idx2 | type_id |
| element_relationship_idx3 | object_id |
| element_relationship_idx4 | value |
| Type | Fields |
|---|---|
| NOT NULL | element_relationship_id |
| NOT NULL | subject_id |
| FOREIGN KEY | subject_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | object_id |
| FOREIGN KEY | object_id |
| NOT NULL | rank |
| UNIQUE | subject_id, object_id, type_id, rank |
elementresult_relationship |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| elementresult_relationship_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| subject_id | integer | 10 | UNIQUE, NOT NULL | elementresult.elementresult_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| object_id | integer | 10 | UNIQUE, NOT NULL | elementresult.elementresult_id | |
| value | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| elementresult_relationship_idx1 | subject_id |
| elementresult_relationship_idx2 | type_id |
| elementresult_relationship_idx3 | object_id |
| elementresult_relationship_idx4 | value |
| Type | Fields |
|---|---|
| NOT NULL | elementresult_relationship_id |
| NOT NULL | subject_id |
| FOREIGN KEY | subject_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | object_id |
| FOREIGN KEY | object_id |
| NOT NULL | rank |
| UNIQUE | subject_id, object_id, type_id, rank |
study |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| study_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| contact_id | integer | 10 | NOT NULL | contact.contact_id | |
| pub_id | integer | 10 | NULL | pub.pub_id | |
| dbxref_id | integer | 10 | NULL | dbxref.dbxref_id | |
| name | text | 64000 | UNIQUE, NOT NULL | ||
| description | text | 64000 | NULL |
| Name | Fields |
|---|---|
| study_idx1 | contact_id |
| study_idx2 | pub_id |
| study_idx3 | dbxref_id |
| Type | Fields |
|---|---|
| NOT NULL | study_id |
| NOT NULL | contact_id |
| FOREIGN KEY | contact_id |
| FOREIGN KEY | pub_id |
| FOREIGN KEY | dbxref_id |
| NOT NULL | name |
| UNIQUE | name |
study_assay |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| study_assay_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| study_id | integer | 10 | UNIQUE, NOT NULL | study.study_id | |
| assay_id | integer | 10 | UNIQUE, NOT NULL | assay.assay_id |
| Name | Fields |
|---|---|
| study_assay_idx1 | study_id |
| study_assay_idx2 | assay_id |
| Type | Fields |
|---|---|
| NOT NULL | study_assay_id |
| NOT NULL | study_id |
| FOREIGN KEY | study_id |
| NOT NULL | assay_id |
| FOREIGN KEY | assay_id |
| UNIQUE | study_id, assay_id |
studydesign |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| studydesign_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| study_id | integer | 10 | NOT NULL | study.study_id | |
| description | text | 64000 | NULL |
| Name | Fields |
|---|---|
| studydesign_idx1 | study_id |
| Type | Fields |
|---|---|
| NOT NULL | studydesign_id |
| NOT NULL | study_id |
| FOREIGN KEY | study_id |
studydesignprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| studydesignprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| studydesign_id | integer | 10 | UNIQUE, NOT NULL | studydesign.studydesign_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| value | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| studydesignprop_idx1 | studydesign_id |
| studydesignprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | studydesignprop_id |
| NOT NULL | studydesign_id |
| FOREIGN KEY | studydesign_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | studydesign_id, type_id, rank |
studyfactor |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| studyfactor_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| studydesign_id | integer | 10 | NOT NULL | studydesign.studydesign_id | |
| type_id | integer | 10 | NULL | cvterm.cvterm_id | |
| name | text | 64000 | NOT NULL | ||
| description | text | 64000 | NULL |
| Name | Fields |
|---|---|
| studyfactor_idx1 | studydesign_id |
| studyfactor_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | studyfactor_id |
| NOT NULL | studydesign_id |
| FOREIGN KEY | studydesign_id |
| FOREIGN KEY | type_id |
| NOT NULL | name |
studyfactorvalue |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| studyfactorvalue_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| studyfactor_id | integer | 10 | NOT NULL | studyfactor.studyfactor_id | |
| assay_id | integer | 10 | NOT NULL | assay.assay_id | |
| factorvalue | text | 64000 | NULL | ||
| name | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | NOT NULL |
| Name | Fields |
|---|---|
| studyfactorvalue_idx1 | studyfactor_id |
| studyfactorvalue_idx2 | assay_id |
| Type | Fields |
|---|---|
| NOT NULL | studyfactorvalue_id |
| NOT NULL | studyfactor_id |
| FOREIGN KEY | studyfactor_id |
| NOT NULL | assay_id |
| FOREIGN KEY | assay_id |
| NOT NULL | rank |
studyprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| studyprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| study_id | integer | 10 | UNIQUE, NOT NULL | study.study_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| value | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| studyprop_idx1 | study_id |
| studyprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | studyprop_id |
| NOT NULL | study_id |
| FOREIGN KEY | study_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | study_id, type_id, rank |
studyprop_feature |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| studyprop_feature_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| studyprop_id | integer | 10 | UNIQUE, NOT NULL | studyprop.studyprop_id | |
| feature_id | integer | 10 | UNIQUE, NOT NULL | feature.feature_id | |
| type_id | integer | 10 | cvterm.cvterm_id |
| Name | Fields |
|---|---|
| studyprop_feature_idx1 | studyprop_id |
| studyprop_feature_idx2 | feature_id |
| Type | Fields |
|---|---|
| NOT NULL | studyprop_feature_id |
| NOT NULL | studyprop_id |
| FOREIGN KEY | studyprop_id |
| NOT NULL | feature_id |
| FOREIGN KEY | feature_id |
| FOREIGN KEY | type_id |
| UNIQUE | studyprop_id, feature_id |
stock |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| stock_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| dbxref_id | integer | 10 | The dbxref_id is an optional primary stable identifier for this stock. Secondary indentifiers and external dbxrefs go in table: stock_dbxref. | dbxref.dbxref_id | |
| organism_id | integer | 10 | UNIQUE, The organism_id is the organism to which the stock belongs. This column should only be left blank if the organism cannot be determined. | organism.organism_id | |
| name | varchar | 255 | The name is a human-readable local name for a stock. | ||
| uniquename | text | 64000 | UNIQUE, NOT NULL | ||
| description | text | 64000 | The description is the genetic description provided in the stock list. | ||
| type_id | integer | 10 | UNIQUE, NOT NULL, The type_id foreign key links to a controlled vocabulary of stock types. The would include living stock, genomic DNA, preserved specimen. Secondary cvterms for stocks would go in stock_cvterm. | cvterm.cvterm_id | |
| is_obsolete | boolean | 0 | false | NOT NULL |
| Name | Fields |
|---|---|
| stock_name_ind1 | name |
| stock_idx1 | dbxref_id |
| stock_idx2 | organism_id |
| stock_idx3 | type_id |
| stock_idx4 | uniquename |
| Type | Fields |
|---|---|
| NOT NULL | stock_id |
| FOREIGN KEY | dbxref_id |
| FOREIGN KEY | organism_id |
| NOT NULL | uniquename |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | is_obsolete |
| UNIQUE | organism_id, uniquename, type_id |
stock_pub |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| stock_pub_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| stock_id | integer | 10 | UNIQUE, NOT NULL | stock.stock_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id |
| Name | Fields |
|---|---|
| stock_pub_idx1 | stock_id |
| stock_pub_idx2 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | stock_pub_id |
| NOT NULL | stock_id |
| FOREIGN KEY | stock_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| UNIQUE | stock_id, pub_id |
stockprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| stockprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| stock_id | integer | 10 | UNIQUE, NOT NULL | stock.stock_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| value | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| stockprop_idx1 | stock_id |
| stockprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | stockprop_id |
| NOT NULL | stock_id |
| FOREIGN KEY | stock_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | stock_id, type_id, rank |
stockprop_pub |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| stockprop_pub_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| stockprop_id | integer | 10 | UNIQUE, NOT NULL | stockprop.stockprop_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id |
| Name | Fields |
|---|---|
| stockprop_pub_idx1 | stockprop_id |
| stockprop_pub_idx2 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | stockprop_pub_id |
| NOT NULL | stockprop_id |
| FOREIGN KEY | stockprop_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| UNIQUE | stockprop_id, pub_id |
stock_relationship |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| stock_relationship_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| subject_id | integer | 10 | UNIQUE, NOT NULL, stock_relationship.subject_id is the subject of the subj-predicate-obj sentence. This is typically the substock. | stock.stock_id | |
| object_id | integer | 10 | UNIQUE, NOT NULL, stock_relationship.object_id is the object of the subj-predicate-obj sentence. This is typically the container stock. | stock.stock_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL, stock_relationship.type_id is relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed. | cvterm.cvterm_id | |
| value | text | 64000 | NULL | stock_relationship.value is for additional notes or comments. | |
| rank | integer | 10 | 0 | UNIQUE, NOT NULL, stock_relationship.rank is the ordering of subject stocks with respect to the object stock may be important where rank is used to order these; starts from zero. |
| Name | Fields |
|---|---|
| stock_relationship_idx1 | subject_id |
| stock_relationship_idx2 | object_id |
| stock_relationship_idx3 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | stock_relationship_id |
| NOT NULL | subject_id |
| FOREIGN KEY | subject_id |
| NOT NULL | object_id |
| FOREIGN KEY | object_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | subject_id, object_id, type_id, rank |
stock_relationship_cvterm |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| stock_relationship_cvterm_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| stock_relationship_id | integer | 10 | NOT NULL | stock_relationship.stock_relationship_id | |
| cvterm_id | integer | 10 | NOT NULL | cvterm.cvterm_id | |
| pub_id | integer | 10 | pub.pub_id |
| Type | Fields |
|---|---|
| NOT NULL | stock_relationship_cvterm_id |
| NOT NULL | stock_relationship_id |
| FOREIGN KEY | stock_relationship_id |
| NOT NULL | cvterm_id |
| FOREIGN KEY | cvterm_id |
| FOREIGN KEY | pub_id |
stock_relationship_pub |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| stock_relationship_pub_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| stock_relationship_id | integer | 10 | UNIQUE, NOT NULL | stock_relationship.stock_relationship_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id |
| Name | Fields |
|---|---|
| stock_relationship_pub_idx1 | stock_relationship_id |
| stock_relationship_pub_idx2 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | stock_relationship_pub_id |
| NOT NULL | stock_relationship_id |
| FOREIGN KEY | stock_relationship_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| UNIQUE | stock_relationship_id, pub_id |
stock_dbxref |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| stock_dbxref_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| stock_id | integer | 10 | UNIQUE, NOT NULL | stock.stock_id | |
| dbxref_id | integer | 10 | UNIQUE, NOT NULL | dbxref.dbxref_id | |
| is_current | boolean | 0 | true | NOT NULL, The is_current boolean indicates whether the linked dbxref is the current -official- dbxref for the linked stock. |
| Name | Fields |
|---|---|
| stock_dbxref_idx1 | stock_id |
| stock_dbxref_idx2 | dbxref_id |
| Type | Fields |
|---|---|
| NOT NULL | stock_dbxref_id |
| NOT NULL | stock_id |
| FOREIGN KEY | stock_id |
| NOT NULL | dbxref_id |
| FOREIGN KEY | dbxref_id |
| NOT NULL | is_current |
| UNIQUE | stock_id, dbxref_id |
stock_cvterm |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| stock_cvterm_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| stock_id | integer | 10 | UNIQUE, NOT NULL | stock.stock_id | |
| cvterm_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id | |
| is_not | boolean | 0 | false | NOT NULL | |
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| stock_cvterm_idx1 | stock_id |
| stock_cvterm_idx2 | cvterm_id |
| stock_cvterm_idx3 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | stock_cvterm_id |
| NOT NULL | stock_id |
| FOREIGN KEY | stock_id |
| NOT NULL | cvterm_id |
| FOREIGN KEY | cvterm_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| NOT NULL | is_not |
| NOT NULL | rank |
| UNIQUE | stock_id, cvterm_id, pub_id, rank |
stock_cvtermprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| stock_cvtermprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| stock_cvterm_id | integer | 10 | UNIQUE, NOT NULL | stock_cvterm.stock_cvterm_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL, The name of the property/slot is a cvterm. The meaning of the property is defined in that cvterm. cvterms may come from the OBO evidence code cv. | cvterm.cvterm_id | |
| value | text | 64000 | NULL | The value of the property, represented as text. Numeric values are converted to their text representation. This is less efficient than using native database types, but is easier to query. | |
| rank | integer | 10 | 0 | UNIQUE, NOT NULL, Property-Value ordering. Any stock_cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used. |
| Name | Fields |
|---|---|
| stock_cvtermprop_idx1 | stock_cvterm_id |
| stock_cvtermprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | stock_cvtermprop_id |
| NOT NULL | stock_cvterm_id |
| FOREIGN KEY | stock_cvterm_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | stock_cvterm_id, type_id, rank |
stock_genotype |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| stock_genotype_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| stock_id | integer | 10 | UNIQUE, NOT NULL | stock.stock_id | |
| genotype_id | integer | 10 | UNIQUE, NOT NULL | genotype.genotype_id |
| Name | Fields |
|---|---|
| stock_genotype_idx1 | stock_id |
| stock_genotype_idx2 | genotype_id |
| Type | Fields |
|---|---|
| NOT NULL | stock_genotype_id |
| NOT NULL | stock_id |
| FOREIGN KEY | stock_id |
| NOT NULL | genotype_id |
| FOREIGN KEY | genotype_id |
| UNIQUE | stock_id, genotype_id |
stockcollection |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| stockcollection_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| type_id | integer | 10 | UNIQUE, NOT NULL, type_id is the collection type cv. | cvterm.cvterm_id | |
| contact_id | integer | 10 | NULL | contact_id links to the contact information for the collection. | contact.contact_id |
| name | varchar | 255 | name is the collection. | ||
| uniquename | text | 64000 | UNIQUE, NOT NULL, uniqename is the value of the collection cv. |
| Name | Fields |
|---|---|
| stockcollection_name_ind1 | name |
| stockcollection_idx1 | contact_id |
| stockcollection_idx2 | type_id |
| stockcollection_idx3 | uniquename |
| Type | Fields |
|---|---|
| NOT NULL | stockcollection_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| FOREIGN KEY | contact_id |
| NOT NULL | uniquename |
| UNIQUE | uniquename, type_id |
stockcollectionprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| stockcollectionprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| stockcollection_id | integer | 10 | UNIQUE, NOT NULL | stockcollection.stockcollection_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL, The cv for the type_id is "stockcollection property type". | cvterm.cvterm_id | |
| value | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| stockcollectionprop_idx1 | stockcollection_id |
| stockcollectionprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | stockcollectionprop_id |
| NOT NULL | stockcollection_id |
| FOREIGN KEY | stockcollection_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | stockcollection_id, type_id, rank |
stockcollection_stock |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| stockcollection_stock_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| stockcollection_id | integer | 10 | UNIQUE, NOT NULL | stockcollection.stockcollection_id | |
| stock_id | integer | 10 | UNIQUE, NOT NULL | stock.stock_id |
| Name | Fields |
|---|---|
| stockcollection_stock_idx1 | stockcollection_id |
| stockcollection_stock_idx2 | stock_id |
| Type | Fields |
|---|---|
| NOT NULL | stockcollection_stock_id |
| NOT NULL | stockcollection_id |
| FOREIGN KEY | stockcollection_id |
| NOT NULL | stock_id |
| FOREIGN KEY | stock_id |
| UNIQUE | stockcollection_id, stock_id |
stock_dbxrefprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| stock_dbxrefprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| stock_dbxref_id | integer | 10 | UNIQUE, NOT NULL | stock_dbxref.stock_dbxref_id | |
| type_id | integer | 10 | UNIQUE, NOT NULL | cvterm.cvterm_id | |
| value | text | 64000 | NULL | ||
| rank | integer | 10 | 0 | UNIQUE, NOT NULL |
| Name | Fields |
|---|---|
| stock_dbxrefprop_idx1 | stock_dbxref_id |
| stock_dbxrefprop_idx2 | type_id |
| Type | Fields |
|---|---|
| NOT NULL | stock_dbxrefprop_id |
| NOT NULL | stock_dbxref_id |
| FOREIGN KEY | stock_dbxref_id |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | rank |
| UNIQUE | stock_dbxref_id, type_id, rank |
library |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| library_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| organism_id | integer | 10 | UNIQUE, NOT NULL | organism.organism_id | |
| name | varchar | 255 | |||
| uniquename | text | 64000 | UNIQUE, NOT NULL | ||
| type_id | integer | 10 | UNIQUE, NOT NULL, The type_id foreign key links to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library" | cvterm.cvterm_id | |
| is_obsolete | integer | 10 | 0 | NOT NULL | |
| timeaccessioned | timestamp | 0 | current_timestamp | NOT NULL | |
| timelastmodified | timestamp | 0 | current_timestamp | NOT NULL |
| Name | Fields |
|---|---|
| library_name_ind1 | name |
| library_idx1 | organism_id |
| library_idx2 | type_id |
| library_idx3 | uniquename |
| Type | Fields |
|---|---|
| NOT NULL | library_id |
| NOT NULL | organism_id |
| FOREIGN KEY | organism_id |
| NOT NULL | uniquename |
| NOT NULL | type_id |
| FOREIGN KEY | type_id |
| NOT NULL | is_obsolete |
| NOT NULL | timeaccessioned |
| NOT NULL | timelastmodified |
| UNIQUE | organism_id, uniquename, type_id |
library_synonym |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| library_synonym_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| synonym_id | integer | 10 | UNIQUE, NOT NULL | synonym.synonym_id | |
| library_id | integer | 10 | UNIQUE, NOT NULL | library.library_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL, The pub_id link is for relating the usage of a given synonym to the publication in which it was used. | pub.pub_id | |
| is_current | boolean | 0 | true | NOT NULL, The is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library. | |
| is_internal | boolean | 0 | false | NOT NULL, Typically a synonym exists so that somebody querying the database with an obsolete name can find the object they are looking for under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it my also be listed in reports as a synonym. If the synonym was not used deliberately (e.g., there was a typo which went public), then the is_internal bit may be set to "true" so that it is known that the synonym is "internal" and should be queryable but should not be listed in reports as a valid synonym. |
| Name | Fields |
|---|---|
| library_synonym_idx1 | synonym_id |
| library_synonym_idx2 | library_id |
| library_synonym_idx3 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | library_synonym_id |
| NOT NULL | synonym_id |
| FOREIGN KEY | synonym_id |
| NOT NULL | library_id |
| FOREIGN KEY | library_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| NOT NULL | is_current |
| NOT NULL | is_internal |
| UNIQUE | synonym_id, library_id, pub_id |
library_pub |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| library_pub_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| library_id | integer | 10 | UNIQUE, NOT NULL | library.library_id | |
| pub_id | integer | 10 | UNIQUE, NOT NULL | pub.pub_id |
| Name | Fields |
|---|---|
| library_pub_idx1 | library_id |
| library_pub_idx2 | pub_id |
| Type | Fields |
|---|---|
| NOT NULL | library_pub_id |
| NOT NULL | library_id |
| FOREIGN KEY | library_id |
| NOT NULL | pub_id |
| FOREIGN KEY | pub_id |
| UNIQUE | library_id, pub_id |
libraryprop |
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| Field Name | Data Type | Size | Default Value | Other | Foreign Key |
|---|---|---|---|---|---|
| libraryprop_id | integer | 11 | PRIMARY KEY, NOT NULL | ||
| library_id | integer | 10 | UNIQUE, NOT NULL | library.library_id | |