Dumped on 2011-10-24

Index of database - golddoc

Schema gaf

Table: gaf.bioentity

A gene, gene product, or collection of gene products (i.e. macromolecular complex). A bioentity is capable of performing some kind of biological function, either by itself, or as a member of a larger object or complex.

gaf.bioentity Structure
F-Key Name Type Description
id character varying PRIMARY KEY

A unique identifier for the bioentity. MAPPINGS: GAF: c1:c2 LEAD: gene_product.dbxref.(xref_dbname+":"+xref_key)
symbol character varying NOT NULL

A concise label identifying the bioentity. This should be unique within the db, but this is not mandated. MAPPINGS: GAF: c3 LEAD: gene_product.symbol
full_name character varying NOT NULL

A descriptive label describing the bioentity. This should be unique within the db, but this is not mandated. MAPPINGS: GAF: c10 LEAD: gene_product.full_name
ontol.cls.id type_cls character varying NOT NULL

An ontology identifier referencing the cls table, providing the bioentity type. The referenced ontology should be SO in the majority of cases, unless the type is "complex" in which case GO should be used. MAPPINGS: GAF: c12->class LEAD: gene_product.type_id
ontol.cls.id taxon_cls character varying NOT NULL

An ontology identifier referencing the cls table, providing the organism type (e.g. NCBI Taxon class) MAPPINGS: GAF: c13 LEAD: "NCBITaxon:" + gene_product.species.ncbi_taxa_id
db character varying

Database from which this bioentity ID comes from. MUST be the same as the prefix part of the id column. Note this is partly redundant with the id column. MAPPINGS: GAF: c11 LEAD: gene_product.dbxref.xref_dbname
gaf.gaf_document.id gaf_document character varying

Tables referencing this one via Foreign Key Constraints:

Index - Schema gaf

Table: gaf.bioentity_relationship

gaf.bioentity_relationship Structure
F-Key Name Type Description
gaf.bioentity.id bioentity character varying
ontol.relation.id relation character varying
gaf.bioentity.id parent_bioentity character varying

Index - Schema gaf

Table: gaf.composite_qualifier

gaf.composite_qualifier Structure
F-Key Name Type Description
id character varying PRIMARY KEY
qualifier_obj character varying

Tables referencing this one via Foreign Key Constraints:

Index - Schema gaf

Table: gaf.extension_expression

gaf.extension_expression Structure
F-Key Name Type Description
id character varying PRIMARY KEY
ontol.relation.id relation character varying
ontol.cls.id cls character varying

Tables referencing this one via Foreign Key Constraints:

Index - Schema gaf

Table: gaf.gaf_document

gaf.gaf_document Structure
F-Key Name Type Description
id character varying PRIMARY KEY
document_path character varying

Tables referencing this one via Foreign Key Constraints:

Index - Schema gaf

Table: gaf.gene_annotation

An association between a gene, gene-product or similar bioentity (e.g. a protein complex) and an ontology class that describes an attribute of that entity (e.g. its function or location), together with associated provenance metadata. Corresponds to a line in a GPAD or GAF file.

gaf.gene_annotation Structure
F-Key Name Type Description
gaf.bioentity.id bioentity character varying NOT NULL
gaf.composite_qualifier.id composite_qualifier character varying

Identical to col 4 in the GAF. StringBlob. This can be viewed as a composite expression describing the relationship between the bioentity and the GO cls. Typically this will be a single qualifier (e.g. "contributes_to"), but may be a pipe-separated list of qualifiers. These are decomposed in the composite_qualifier table. note: negative annotations to go in separate table.
is_contributes_to boolean
is_integral_to boolean
ontol.cls.id cls character varying NOT NULL
reference_id character varying

The ontology class that describes an attribute of the bioentity
ontol.cls.id evidence_cls character varying
gaf.with_info.id with_expression character varying

Identical to GAF col 8. StringBlob. Example: CGSC:pabA|CGSC:pabB
ontol.cls.id acts_on_taxon_id character varying
last_update_date character varying
assigned_by character varying
gaf.extension_expression.id extension_expression character varying

Examples:
  • occurs_in(CL:0000123)
  • occurs_in(CL:0000123)|occurs_in(MA:9999999)
gene_product_form character varying
gaf_document character varying

Index - Schema gaf

Table: gaf.id_mapping

gaf.id_mapping Structure
F-Key Name Type Description
source_id character varying NOT NULL
target_id character varying NOT NULL
relationship character varying
mapping_source character varying

Index - Schema gaf

Table: gaf.with_info

gaf.with_info Structure
F-Key Name Type Description
id character varying PRIMARY KEY
with_xref character varying

Tables referencing this one via Foreign Key Constraints:

Index - Schema gaf

Schema ontol

Table: ontol.all_only_relationship

holds iff: cls SubClassOf rel Only tgt EXAMPLE: lactation only_in_taxon Mammalia ==> lactation SubClassOf in_taxon only Mammalia

ontol.all_only_relationship Structure
F-Key Name Type Description
ontol.cls.id cls character varying PRIMARY KEY
ontol.relation.id relation character varying PRIMARY KEY
ontol.cls.id target_cls character varying PRIMARY KEY
ontol.ontology.id ontology character varying PRIMARY KEY

Index - Schema ontol

Table: ontol.all_some_relationship

holds iff: cls SubClassOf rel Some tgt

ontol.all_some_relationship Structure
F-Key Name Type Description
ontol.cls.id cls character varying PRIMARY KEY
ontol.relation.id relation character varying PRIMARY KEY
ontol.cls.id target_cls character varying PRIMARY KEY
ontol.ontology.id ontology character varying PRIMARY KEY

Index - Schema ontol

Table: ontol.annotation_assertion

A non-logical relationship between two objects (classes or relations). When an obo consider tag is being used, relation=consider When an obo replaced_by tag is being used, relation=replaced_by MAPPINGS: OBO: property_value (also: consider, replaced_by) OWL: AnnotationAssertion(relation obj target_obj) LEAD: term2term_metadata

ontol.annotation_assertion Structure
F-Key Name Type Description
ontol.relation.id relation character varying PRIMARY KEY
obj character varying PRIMARY KEY
target_obj character varying PRIMARY KEY
ontol.ontology.id ontology character varying PRIMARY KEY

Index - Schema ontol

Table: ontol.annotation_property

A non-logical relation/tag that can connect objects or objects and values. TYPICAL ENTRIES: consider, replaced_by TODO: use separate table? MAPPINGS: OBO: Typedef[is_metadata_tag=true] OWL: AnnotationProperty LEAD: term (overloaded)

ontol.annotation_property Structure
F-Key Name Type Description
id character varying PRIMARY KEY
label character varying
ontol.ontology.id ontology character varying
obo_namespace character varying
text_comment text
text_definition text
is_obsolete boolean

Index - Schema ontol

Table: ontol.axiom_cache

This table contains a cache of all axioms in the ontology, and their relationship to an object (a class, property or individual)

ontol.axiom_cache Structure
F-Key Name Type Description
obj character varying

ID for the entity that is associated with the axiom. E.g. GO:0008150
axiom character varying

A formatted string encoding an axiom. E.g. SubClassOf(GO_000001 GO_0000002). TODO - QName scheme
ontol.ontology.id ontology character varying

The ontology to which the axiom belongs. Note that the axiom can belong to a different ontology from the class declaration
is_directly_about boolean

True if the axiom is directly about obj. This corresponds to what you would see on the main display in Protege vs under the "about" tab
owlformat character varying

The syntax used in axiom_cache.axiom. One of: functional, manchester, owlxml

Index - Schema ontol

Table: ontol.cls

An ontology class (aka term).
MAPPINGS: 

 OBO: Term stanza.
 OWL: Class
 LEAD: term

ontol.cls Structure
F-Key Name Type Description
id character varying PRIMARY KEY

A unique identifier for this class.
Example: GO:0008150
MAPPINGS:
OBO: Term.id
OWL: URI for class, with obo2owl transform. E.g. GO_nnnnnnn -> GO:nnnnnnn
LEAD: term.acc
label character varying

A descriptive label for this class. Should be unique within the ontology, but this is not enforced. Example: "lung development" MAPPINGS: 
 OBO: term.name
 OWL: rdfs:label
 LEAD: term.name
ontol.ontology.id ontology character varying

The ontology to which this class belongs. Examples: "GO", "CL". References ontology.id MAPPINGS: 
 OBO: the idspace for the term id
 OWL: ontology
 LEAD: n/a
obo_namespace character varying

An obo namespace is similar to an ontology. The GO is split into 3 namespaces. Most ontologies have a 1:1 association between ontology and obo_namespace. MAPPINGS: 
 OBO: term.namespace
 OWL: n/a
 LEAD: term.term_type
Example: "biological_process".
text_comment text
text_definition text

A textual definition uniquely defining the class. MAPPINGS: 
 OBO: term.definition
 OWL: see obo2owl guide
 LEAD: term_definition.term_definition
 API: getDef()
is_obsolete boolean

True if this is an obsolete/deprecated class MAPPINGS: OBO: term.is_obsolete OWL: AnnotationProperty(owl:deprecated cls true) [TBD: obo obsoletion may be stronger] LEAD: term.is_obsolete

Tables referencing this one via Foreign Key Constraints:

Index - Schema ontol

Table: ontol.cls_intersection_of

A shorthand for stating necessary and sufficient definitions. For any cls, the set of all_intersection_of tuples are collected. This constitutes a conjunctive expression that is equivalent to cls. E.g. 

[Term]
id: blue_car
intersection_of: car
intersection_of: has_color blue
==> [gold]
cls_intersection_of(blue_car,null,car)
cls_intersection_of(blue_car,has_color,blue)
==> [owl]
EquivalentTo (blue_car IntersectionOf(car SomeValuesFrom(has_color blue)))
// Limitation: only a single such equivalence relation is allowed per class // Note that there should never be a cls that only has a single cls_intersection_of. MAPPINGS: OBO: intersection_of OWL: EquivalentTo(cls IntersectionOf( {...} ) -- see obo2owl doc LEAD: term2term[completes=1]

ontol.cls_intersection_of Structure
F-Key Name Type Description
cls character varying UNIQUE#1
relation character varying UNIQUE#1
target_cls character varying UNIQUE#1
ontology character varying UNIQUE#1

Index - Schema ontol

Table: ontol.cls_union_of

A shorthand declaring a class to be equivalent to a union of other classes. For any cls, the set of all_union_of tuples are collected. This constitutes a conjunctive expression that is equivalent to cls. E.g. 

[Term]
id: prokaryote
union_of: eubacteria
union_of: archaea
==> [gold]
cls_union_of(prokaryote,eubacteria)
cls_union_of(prokaryote,archaea)
==> [owl]
EquivalentTo (prokaryote UnionOf(eubacteria archaea))
// Limitation: only a single such equivalence relation is allowed per class // Note that there should never be a cls that only has a single cls_union_of. MAPPINGS: 
 OBO: union_of
 OWL: EquivalentTo(cls UnionOf( {...} ) -- see obo2owl doc
 LEAD: n/a

ontol.cls_union_of Structure
F-Key Name Type Description
cls character varying PRIMARY KEY
target_cls character varying PRIMARY KEY
ontology character varying PRIMARY KEY

Index - Schema ontol

Table: ontol.disjoint_with

Two classes are disjoint if they share no instances or subclasses in common. MAPPINGS: OBO: Term.disjoint_from OWL: DisjointClasses(cls disjoint_cls) LEAD: n/a

ontol.disjoint_with Structure
F-Key Name Type Description
cls character varying PRIMARY KEY
disjoint_cls character varying PRIMARY KEY
ontology character varying PRIMARY KEY

Index - Schema ontol

Table: ontol.equivalent_to

ontol.equivalent_to Structure
F-Key Name Type Description
cls character varying PRIMARY KEY
equivalent_cls character varying PRIMARY KEY
ontology character varying PRIMARY KEY

Index - Schema ontol

Table: ontol.inferred_all_only_relationship

holds iff: cls SubClassOf rel Only tgt EXAMPLE: lactation only_in_taxon Mammalia ==> lactation SubClassOf in_taxon only Mammalia

ontol.inferred_all_only_relationship Structure
F-Key Name Type Description
cls character varying PRIMARY KEY
relation character varying PRIMARY KEY
target_cls character varying PRIMARY KEY
is_direct boolean
is_reflexive boolean
quantifier character varying
ontology character varying PRIMARY KEY

Index - Schema ontol

Table: ontol.inferred_all_some_relationship

holds iff: cls SubClassOf rel Some tgt

ontol.inferred_all_some_relationship Structure
F-Key Name Type Description
cls character varying PRIMARY KEY
relation character varying PRIMARY KEY
target_cls character varying PRIMARY KEY
is_direct boolean
is_reflexive boolean
quantifier character varying
ontology character varying PRIMARY KEY

Index - Schema ontol

Table: ontol.inferred_never_some_relationship

holds iff: cls SubClassOf ComplementOf(rel Some tgt) EXAMPLE: odontogenesis never_in_taxon Aves ==> odontogenesis SubClassOf ComplementOf(in_taxon some Aves) [taxon_go_triggers]

ontol.inferred_never_some_relationship Structure
F-Key Name Type Description
cls character varying PRIMARY KEY
target_cls character varying PRIMARY KEY
relation character varying PRIMARY KEY
is_direct boolean
is_reflexive boolean
quantifier character varying
ontology character varying PRIMARY KEY

Index - Schema ontol

Table: ontol.inferred_subclass_of

holds iff: cls SubClassOf tgt, where both cls and tgt are named classes.

ontol.inferred_subclass_of Structure
F-Key Name Type Description
cls character varying PRIMARY KEY
target_cls character varying PRIMARY KEY
is_direct boolean
is_reflexive boolean
relation character varying
quantifier character varying
ontology character varying PRIMARY KEY

Index - Schema ontol

Table: ontol.inferred_subrelation_of

holds iff: cls SubObjectPropertyOf super_cls

ontol.inferred_subrelation_of Structure
F-Key Name Type Description
relation character varying PRIMARY KEY
super_relation character varying PRIMARY KEY
is_direct boolean
is_reflexive boolean
ontology character varying PRIMARY KEY

Index - Schema ontol

Table: ontol.never_some_relationship

holds iff: cls SubClassOf ComplementOf(rel Some tgt) EXAMPLE: odontogenesis never_in_taxon Aves ==> odontogenesis SubClassOf ComplementOf(in_taxon some Aves) [taxon_go_triggers]

ontol.never_some_relationship Structure
F-Key Name Type Description
cls character varying PRIMARY KEY
target_cls character varying PRIMARY KEY
relation character varying PRIMARY KEY
ontology character varying PRIMARY KEY

Index - Schema ontol

Table: ontol.obj_alternate_id

An alternive identifier for a class or relation, typically arising from class merges. MAPPINGS: OBO: alt_id OWL: see obo2owl spec LEAD: term_synonym (overloaded)

ontol.obj_alternate_id Structure
F-Key Name Type Description
obj character varying PRIMARY KEY
id character varying PRIMARY KEY

Index - Schema ontol

Table: ontol.obj_alternate_label

Synonyms and alternative labels. TODO - denormalize synonym_xrefs MAPPINGS: OBO: synonym OWL: see obo2owl spec LEAD: term_synonym

ontol.obj_alternate_label Structure
F-Key Name Type Description
obj character varying UNIQUE#1

class or relation that owns the alternate label.
label character varying UNIQUE#1
synonym_scope character varying UNIQUE#1
synonym_type character varying UNIQUE#1
synonym_xref character varying UNIQUE#1

Index - Schema ontol

Table: ontol.obj_definition_xref

Provenance for a class or relation textual definition MAPPINGS: OBO: term.def.xrefs OWL: see obo2owl spec LEAD: term_dbxref[is_for_definition=1]

ontol.obj_definition_xref Structure
F-Key Name Type Description
obj character varying PRIMARY KEY
xref character varying PRIMARY KEY

Identifier for def xref. EXAMPLE: PMID:123456 EXAMPLE: http://en/wikipedia.org/wiki/Transcription OBO: term.def.xrefs OWL: see obo2owl spec LEAD: term_dbxref[is_for_definition=1].dbxref.{xref_dbname:xref_key}

Index - Schema ontol

Table: ontol.obj_subset

Relates an ontology class or relation to an ontology_subset. MAPPINGS: OBO: term.subset OWL: see obo2owl spec LEAD: term_subset

ontol.obj_subset Structure
F-Key Name Type Description
obj character varying PRIMARY KEY
ontology_subset character varying PRIMARY KEY

Index - Schema ontol

Table: ontol.obj_xref

ontol.obj_xref Structure
F-Key Name Type Description
obj character varying PRIMARY KEY
xref character varying PRIMARY KEY
xref_description character varying

Index - Schema ontol

Table: ontol.ontology

A collection of classes, relations and relationships.
MAPPINGS: OBO: header.ontology (introduced in obof1.4) OWL: Ontology LEAD: n/a

ontol.ontology Structure
F-Key Name Type Description
id character varying PRIMARY KEY
label character varying
versioniri character varying
creation_date character varying

Tables referencing this one via Foreign Key Constraints:

Index - Schema ontol

Table: ontol.ontology_alternate_label_type

ontol.ontology_alternate_label_type Structure
F-Key Name Type Description
id character varying PRIMARY KEY
description character varying
default_scope character varying

Index - Schema ontol

Table: ontol.ontology_annotation

A property of an ontology
MAPPINGS: 

 OBO: header.
 OWL: OntologyAnnotation(ontology property value)
 LEAD: n/a
Example properties: saved_by

ontol.ontology_annotation Structure
F-Key Name Type Description
ontology character varying PRIMARY KEY
property character varying PRIMARY KEY
annotation_value character varying PRIMARY KEY

Index - Schema ontol

Table: ontol.ontology_changes_history

This table maintains history of chages of an ontology when the ontology is updated preiodically. This table is on experimental basis. Its structure can be changed in future.

ontol.ontology_changes_history Structure
F-Key Name Type Description
table_name character varying
col character varying
ontology character varying
versioniri character varying
new_value character varying

Index - Schema ontol

Table: ontol.ontology_imports

ontol.ontology_imports Structure
F-Key Name Type Description
ontology character varying PRIMARY KEY
imports_ontology character varying

Index - Schema ontol

Table: ontol.ontology_subset

A named subset of the ontology EXAMPLE: goslim_prok MAPPINGS: OBO: header.subsetdef OWL: see obo2owl spec LEAD: term (term table is overloaded)

ontol.ontology_subset Structure
F-Key Name Type Description
id character varying PRIMARY KEY
label character varying

Index - Schema ontol

Table: ontol.relation

An ontology relation MAPPINGS:
OBO: Typedef stanza.
OWL: ObjectProperty
LEAD: term (the term table is overloaded)

ontol.relation Structure
F-Key Name Type Description
id character varying PRIMARY KEY

A unique identifier for this relation. Example: part_of MAPPINGS: OBO: Term.id OWL: URI for relation, with obo2owl transform. LEAD: term.acc
label character varying

A descriptive label for this relation. Should be unique within the ontology, but this is not enforced. Example: "is part of" MAPPINGS: OBO: term.name OWL: rdfs:label LEAD: term.name
ontology character varying

The ontology to which this relation belongs. Examples: "RO", "GO". References ontology.id MAPPINGS: OBO: the idspace for the term id OWL: ontology LEAD: n/a
obo_namespace character varying

See comments for cls.namespace MAPPINGS: OBO: term.namespace OWL: n/a LEAD: term.term_type Example: "biological_process".
text_comment text
text_definition text

A textual definition uniquely defining the relation. MAPPINGS: OBO: term.definition OWL: see obo2owl guide LEAD: term_definition.term_definition
is_transitive boolean
is_symmetric boolean
is_reflexive boolean
is_obsolete boolean

Tables referencing this one via Foreign Key Constraints:

Index - Schema ontol

Table: ontol.relation_chain

A rule defining how two relations are composed. SEMANTICS: SubObjectPropertyOf(inferred_relation PropertyChain(relation1 relation2)) note this table cannot be used for property chains of length >2, GO should not have these. if this is desired then the property chain should be broken into pairs. EXAMPLE: SubObjectPropertOf(regulates PropertyChain(regulates part_of)) (in obof, this is encoded using transitive_over). EXAMPLE: has_part o part_of --> overlaps EXAMPLE: regulates o part_of --> regulates MAPPINGS: OBO: typedef.holds_over_chain OWL: SubObjectPropertyOf(inferred_relation PropertyChain(relation1 relation2)) LEAD: n/a

ontol.relation_chain Structure
F-Key Name Type Description
inferred_relation character varying PRIMARY KEY
relation1 character varying PRIMARY KEY
relation2 character varying PRIMARY KEY
is_bidirectional boolean

True if the implication is bidirectional. MAPPINGS: OBO: true for typedef.equivalent_to_chain, false for typedef.holds_over_chain OWL: n/a LEAD: n/a

Index - Schema ontol

Table: ontol.relation_disjoint_with

holds iff: DisjointObjectProperties(relation disjoint_relation)

ontol.relation_disjoint_with Structure
F-Key Name Type Description
relation character varying PRIMARY KEY
disjoint_relation character varying PRIMARY KEY
ontology character varying PRIMARY KEY

Index - Schema ontol

Table: ontol.relation_equivalent_to

holds iff: EquivalentObjectProperties(relation equivalent_relation)

ontol.relation_equivalent_to Structure
F-Key Name Type Description
relation character varying PRIMARY KEY
equivalent_relation character varying PRIMARY KEY
ontology character varying PRIMARY KEY

Index - Schema ontol

Table: ontol.subclass_of

holds iff: cls SubClassOf super_cls

ontol.subclass_of Structure
F-Key Name Type Description
cls character varying PRIMARY KEY
super_cls character varying PRIMARY KEY
ontology character varying PRIMARY KEY

Index - Schema ontol

Table: ontol.subrelation_of

holds iff: cls SubObjectPropertyOf super_cls

ontol.subrelation_of Structure
F-Key Name Type Description
relation character varying PRIMARY KEY
super_relation character varying PRIMARY KEY
ontology character varying PRIMARY KEY

Index - Schema ontol

Schema phylo

Table: phylo.family

phylo.family Structure
F-Key Name Type Description
id character varying PRIMARY KEY
label character varying
versioniri character varying
creation_date character varying

Index - Schema phylo

Table: phylo.family_ancestry

phylo.family_ancestry Structure
F-Key Name Type Description
bioentity character varying
ancestor_bioentity character varying
branch_length_sum double precision
family character varying

Index - Schema phylo

Table: phylo.family_branch

phylo.family_branch Structure
F-Key Name Type Description
bioentity character varying
parent_bioentity character varying
branch_length double precision
family character varying

Index - Schema phylo

Table: phylo.family_data_dump

phylo.family_data_dump Structure
F-Key Name Type Description
family character varying
data_source text
data_dump text
data_format character varying

Index - Schema phylo

Table: phylo.family_member

phylo.family_member Structure
F-Key Name Type Description
family character varying
bioentity character varying

Index - Schema phylo

Table: phylo.homology_relationship

phylo.homology_relationship Structure
F-Key Name Type Description
bioentity1 character varying
bioentity2 character varying
relationship_type character varying
ancestor_taxon character varying
family character varying

Index - Schema phylo

Schema public

standard public schema

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