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Unified Medical Language System® (UMLS®)

2012AB Gene Ontology Source Information




Skip to: Notes, Summary of Changes, Summary of Source-Provided Files Source-Provided File Details

Notes

GO is updated daily, however only the version from the first day of the month is archived (http://www.geneontology.org/ontology-archive/).  For tracking and consistency purposes, the UMLS uses an officially archived version.

GO "terms" are analagous to the Metathesaurus idea of "descriptors," i.e. a collection of closely related but not necessarily synonymous names.  In the documentation below, the word "Term" is used in the the GO sense of the word in order to describe the original GO data in the language used by the source itself.

Summary of Changes:

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New RELAs:
results_in/result_of_regulation

Some of these relationships are included in the obo file with tag = "relationship";  others have tag = "intersection_of".  All "intersection_of" relationships from GO are represented using relationship groups in MRREL.RRF.

In addition, the "occurs_in" relationship is now present with tag = "relationship" in the obo file.  Previously, it was only present with tag = "intersection_of".  Therefore, in previous versions all relationships with RELA = occurs_in/has_occurence had a relationship group value;  now, these relationships may or may not have a relationship group value.

Source-Provided Files: Summary

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Data files in various formats and extensive documentation is available at:  http://www.geneontology.org/

Documentation and Reference

File Name Description
ene_ontology_edit.obo (2012_04_03) OBO format documentation

Data Files

File Name Description
http://www.geneontology.org/ontology-archive/gene_ontology_edit.obo.20112-06-01.gz
OBO data file


Not included:
* Certain fields and data elements may not be directly processed because they contain redundant data.

Source-Provided Files: Details

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Details on format of input files and representation of source data. In OBO, content is structured as tag-value pairs, with optional trailing modifiers.  Tag-value pairs consist of a tag name, an unescaped colon, the tag value, and a newline.

Consult the GO OBO format documentation for additional details.

file:gene_ontology_edit.obo.<YYYY-DD-MM>

  return to Data Files

For inclusion in the Metathesaurus, all tags in a [Term] Stanza, are processed, as described in the OBO format documentation.

Required tags:

Tag Name Description Representation
id
Unique identifier
MRCONSO.CODE, MRCONSO.SDUI
name
Term name
MRCONSO.STR

TTY = "PT" if there is no is_obsolete flag
TTY = "OP" if is_obsolete = true
namespace
Ontology (domain) name.  Valid values are: 
biological_process
cellular_component
molecular_function
MRSAT.ATN = "GO_NAMESPACE"



Optional tags:  the following table lists only tags actually present in the data processed for inclusion in this version of the Metathesaurus. Tags are presented in the order in which they appear in a [Term] Stanza.  For information on all optional OBO tags, including deprecated tags, please consult the OBO format documentation.

Tag Name Description Representation
alt_id
Alternate identifier MRSAT.ATN = "SID"
def
Definition MRDEF.DEF
comment
Comment
MRSAT.ATN = "GO_COMMENT"
subset
Subset.  Valid values are:
goslim_candida
goslim_generic
goslim_goa
goslim_pir
goslim_plant
goslim_pombe
goslim_yeast
gosubset_prok
MRSAT.ATN = "GO_SUBSET"

synonym
Synonym
MRCONSO.STR
TTYs are assigned based on the value of the scope identifier and the presence or absence of the "is_obsolete" tag.

MRREL.REL
REL values are assigned based on the value of the scope identifier

Scope identifier
is_obsolete
MRCONSO.TTY
MRREL.REL
EXACT
(no value)
SY
SY
EXACT
true
IS
SY
NARROW
(no value)
ET
RN
NARROW
true
OET
RB
BROAD
(no value)
ET
RB
BROAD
true
OET
RN
RELATED
(no value)
ET
RO
RELATED
true
OET
RO

Optional dbxref lists included in synonym tags are represented in MRSAT.ATN = "REF"

When present on "EXACT" synonyms, the modifier "systematic_synonym" is represented in MRSAT.ATN ="SYN_QUALIFIER,"  MRSAT.ATV="systematic_synonym"
xref
Cross-reference (dbxref) describing an analagous term in another vocabulary
MRSAT.ATN = "GXR"
is_a
Indicates a subclassing relationship between one term and another
Used to create a hierarchy, represented in MRHIER.RRF and MRREL.RRF (REL = "PAR," "CHD," "SIB"; RELA = "isa")
relationship
Describes a relationship between one term and another.  Valid values are:
has_part
negatively_regulates
occurs_in
part_of
positively_regulates
regulates
results_in
MRREL.RELA

For part_of, MRREL.REL = "RN/RB"
For all other relationship tag values, MRREL.REL = "RO"
is_obsolete
Indicates if a term is obsolete
Used to compute termtype assignments
replaced_by
Gives a term which replaces an obsolete term
MRREL.REL = "RO"
MRREL.RELA = "replaced_by/replaces"
consider
Gives a term which may be an appropriate substitute or an obsolete term, but requires human review
MRREL.REL = "RO"
MRREL.RELA = "consider/consider_from"
disjoint_from
Indicates that a term is disjoint from another, meaning that the two terms have no instances or subclasses in common. The value is the id of the term from which the current term is disjoint. MRSAT.ATN = "DISJOINT_FROM"
intersection_of
Indicates that this term is equivalent to the intersection of several other terms. The value is either a term id, or a relationship type id, a space, and a term id. If the value is a GO term id:  MRREL.REL = "RN/RB";  MRREL.RELA = "isa/inverse_isa"
If the value includes a relationship type:  MRREL.REL and MRREL.RELA are populated appropriately based on the value of the relationship type.  Relationship groups are used tolink pairs (or groups) of intersecting relationship.
creation_date
Indicates the creation time and date of the term MRSAT.ATN = "DATE_CREATED"