GO database schema

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The Gene Ontology consortium developed a structured, common, controlled vocabulary for describing the roles of genes and gene products in any organism. Here is the schema.

Contents

Table: association

association Structure
F-Key Name Type Description
gene_product gene_product_id INT4 NOT NULL
  Id SERIAL NOT NULL PRIMARY KEY
  is_not INT4  
  role_group INT4  
term term_id INT4 NOT NULL

Tables referencing this one via Foreign Key Constraints:

  • evidence

Table: category

category Structure
F-Key Name Type Description
  description TEXT  
  id SERIAL NOT NULL PRIMARY KEY
  name   NOT NULL

Tables referencing this one via Foreign Key Constraints:

  • term_category

Table: dbxref

dbxref Structure
F-Key Name Type Description
  id SERIAL NOT NULL PRIMARY KEY
  xref_dbname   NOT NULL
  xref_desc    
  xref_key   NOT NULL
  xref_keytype    


dbxref Constraints
Name Constraint
dbxref_xref_key_key UNIQUE (xref_key, xref_dbname)


Tables referencing this one via Foreign Key Constraints:

  • evidence
  • gene_product
  • seq_dbxref
  • term_dbxref

Table: edit_session

edit_session Structure
F-Key Name Type Description
  id SERIAL NOT NULL PRIMARY KEY
  mod_time INT4 NOT NULL
  person VARCHAR(32) NOT NULL
  session_comment TEXT  

Tables referencing this one via Foreign Key Constraints:

  • node_operation

Table: evidence

evidence Structure
F-Key Name Type Description
association association_id INT4 NOT NULL
  code   NOT NULL
dbxref dbxref_id INT4 NOT NULL
  id SERIAL NOT NULL PRIMARY KEY
  seq_acc    


evidence Constraints
Name Constraint
evidence_association_id_key UNIQUE (association_id, dbxref_id, code, seq_acc)

Table: gene_product

gene_product Structure
F-Key Name Type Description
dbxref dbxref_id INT4 NOT NULL
  full_name TEXT  
  id SERIAL NOT NULL PRIMARY KEY
species species_id INT4 NOT NULL
  symbol   NOT NULL


gene_product Constraints
Name Constraint
gene_product_symbol_key UNIQUE (symbol, dbxref_id)

Tables referencing this one via Foreign Key Constraints:

  • association
  • gene_product_synonym

Table: gene_product_count

gene_product_count Structure
F-Key Name Type Description
  Code    
  product_count INT4 NOT NULL
  Speciesdbname   NOT NULL
term term_id INT4 NOT NULL

Table: gene_product_synonym

gene_product_synonym Structure
F-Key Name Type Description
gene_product gene_product_id INT4 NOT NULL
  product_synonym   NOT NULL


gene_product_synonym Constraints
Name Constraint

Table: godb_meta_data

godb_meta_data Structure
F-Key Name Type Description
  created_by VARCHAR(64) NOT NULL
  creation_comment TEXT  
  current_id INT4 NOT NULL
  date_created INT4 NOT NULL
  Version VARCHAR(64) NOT NULL


Table:graph_path

graph_path Structure
F-Key Name Type Description
  distance INT4 NOT NULL
  id SERIAL NOT NULL PRIMARY KEY
term term1_id INT4 NOT NULL
term term2_id INT4 NOT NULL

Tables referencing this one via Foreign Key Constraints:

  • graph_path2term

Table: graph_path2term

graph_path2term Structure
F-Key Name Type Description
graph_path graph_path_id INT4 NOT NULL
  rank INT4 NOT NULL
term term_id INT4 NOT NULL

Table: mod_comment

mod_comment Structure
F-Key Name Type Description
  mod_comment TEXT  
modification modification_id INT4 NOT NULL

Table: modification

modification Structure
F-Key Name Type Description
  id SERIAL NOT NULL PRIMARY KEY
  mod_time INT4 NOT NULL
  mod_type   NOT NULL
  person   NOT NULL
  rank INT4 NOT NULL

Tables referencing this one via Foreign Key Constraints:

  • mod_comment
  • term2term
  • term_history

Table: node_operation

node_operation Structure
F-Key Name Type Description
edit_session edit_session_id INT4 NOT NULL
  id SERIAL NOT NULL PRIMARY KEY
term term_id INT4 NOT NULL
  type INT4  

Tables referencing this one via Foreign Key Constraints:

  • synonym_edit
  • term_dbxref_edit
  • term_text_edit

Table: relationship_type

relationship_type Structure
F-Key Name Type Description
  id SERIAL NOT NULL PRIMARY KEY
  type_desc   NOT NULL
  type_name   NOT NULL

Table: seq

seq Structure
F-Key Name Type Description
  description    
  display_id    
  id SERIAL NOT NULL PRIMARY KEY
  md5checksum    
  moltype    
  seq TEXT  
  seq_len INT4  
  timestamp INT4  


seq Constraints
Name Constraint
seq_display_id_key UNIQUE (display_id, md5checksum)

Tables referencing this one via Foreign Key Constraints:

  • seq_dbxref
  • seq_property

Table: seq_dbxref

seq_dbxref Structure
F-Key Name Type Description
dbxref dbxref_id INT4 NOT NULL
seq seq_id INT4 NOT NULL


seq_dbxref Constraints
Name Constraint
seq_dbxref_seq_id_key UNIQUE (seq_id, dbxref_id)

Table: seq_property

seq_property Structure
F-Key Name Type Description
  id SERIAL NOT NULL PRIMARY KEY
  property_key   NOT NULL
  property_val   NOT NULL
seq seq_id INT4 NOT NULL


seq_property Constraints
Name Constraint
seq_property_seq_id_key UNIQUE (seq_id, property_key, property_val)

Table: species

species Structure
F-Key Name Type Description
  common_name    
  genus    
  id SERIAL NOT NULL PRIMARY KEY
  lineage_string TEXT  
  ncbi_taxa_id INT4  
  species    

Tables referencing this one via Foreign Key Constraints:

  • gene_product

Table: synonym_edit

synonym_edit Structure
F-Key Name Type Description
  acc INT4  
  edit_type   NOT NULL
  new_acc INT4  
  new_synonym    
node_operation operation_id INT4  
  synonym_text    

Table: term

term Structure
F-Key Name Type Description
  acc INT4 NOT NULL UNIQUE
  id SERIAL NOT NULL PRIMARY KEY
  is_obsolete INT4 NOT NULL
  is_root INT4 NOT NULL
  name   NOT NULL
  term_type   NOT NULL

Tables referencing this one via Foreign Key Constraints:

  • association
  • gene_product_count
  • graph_path
  • graph_path
  • graph_path2term
  • node_operation
  • term2term
  • term2term
  • term_category
  • term_dbxref
  • term_definition
  • term_history
  • term_history
  • term_synonym
  • wordunit2term

Table: term2term

term2term Structure
F-Key Name Type Description
  Id SERIAL NOT NULL PRIMARY KEY
  Is_inheritance INT4 NOT NULL
  Is_obsolete INT4 NOT NULL
modification modification_id INT4 NOT NULL
  relationship_type    
  relationship_type_id INT4 NOT NULL
term term1_id INT4 NOT NULL
term term2_id INT4 NOT NULL


term2term Constraints
Name Constraint
term2term_term1_id_key UNIQUE (term1_id, term2_id)

Table: term_category

term_category Structure
F-Key Name Type Description
category category_id INT4 NOT NULL
term term_id INT4 NOT NULL


term_category Constraints
Name Constraint
term_category_term_id_key UNIQUE (term_id, category_id)

Table: term_dbxref

term_dbxref Structure
F-Key Name Type Description
dbxref dbxref_id INT4 NOT NULL
term term_id INT4 NOT NULL


term_dbxref Constraints
Name Constraint
term_dbxref_term_id_key UNIQUE (term_id, dbxref_id)

Table: term_dbxref_edit

term_dbxref_edit Structure
F-Key Name Type Description
  edit_type   NOT NULL
  new_xref_dbname    
  new_xref_key    
  new_xref_type    
node_operation operation_id INT4 NOT NULL
  xref_dbname    
  xref_key    
  xref_type    

Table: term_definition

term_definition Structure
F-Key Name Type Description
  term_definition TEXT NOT NULL
term term_id INT4 NOT NULL UNIQUE

Index

Table: term_history

term_history Structure
F-Key Name Type Description
modification modification_id INT4 NOT NULL
term term1_id INT4 NOT NULL
term term2_id INT4  

Index

Table: term_synonym

term_synonym Structure
F-Key Name Type Description
  acc_synonym INT4  
term term_id INT4 NOT NULL
  term_synonym    


term_synonym Constraints
Name Constraint
term_synonym_term_id_key UNIQUE (term_id, term_synonym)

Table: term_text_edit

term_text_edit Structure
F-Key Name Type Description
  comment_text TEXT  
  name    
node_operation operation_id INT4 NOT NULL
  term_definition TEXT  

Table: wordunit2term

wordunit2term Structure
F-Key Name Type Description
  is_definition INT4 NOT NULL
  is_synonym INT4 NOT NULL
term term_id INT4 NOT NULL
  wordsound    
  wordtype    
  wordunit    
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