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Unified Medical Language System® (UMLS®)

2015AB UMLS Gene Ontology Source Information

This page lists UMLS Metathesaurus data elements and traces them back to the specific source data that populates them.




Skip to: Atoms, Attributes, Definitions, Relationships, Mappings

VSAB: GO2015_04_04

Summary of Changes

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New REL/RELA

RRF Field(s) Value
REL
RELA/Inverse RELA
RO
happens_during/inverse_happens_during

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
http://oboformat.googlecode.com/svn/trunk/doc/GO.format.obo-1_2.html OBO format documentation

Data Files

File Name Description
gene_ontology_ext_20150404.obo
OBO data file

Identifiers:

Identifiers are assigned as follows:

Identifier Origin
CODE tag = "id"
SAUI Not Applicable
SCUI Not Applicable
SDUI tag = "id"

Atoms (MRCONSO):

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Term Type Origin
ET CODE: tag = "id"
STR: tag = "synonym"
SDUI: tag = "id"
TTY = "ET" is assigned to the value of tag = "synonym" where the scope identifier is "BROAD," "NARROW," or "RELATED" in records where there is no "is_obsolete" tag.
IS CODE: tag = "id"
STR: tag = "synonym"
SDUI: tag = "id"
TTY = "IS" is assigned to the value of tag = "synonym" where the scope identifier = "EXACT" and tag="is_obsolete" has a value of "true."
MTH_ET CODE: tag = "id"
STR: tag = "synonym," with the word "location" included for clarification of selected strings from the Cellular Component Ontology.
SDUI: tag = "id"
TTY = "ET" is assigned to the value of tag = "synonym" where the scope identifier is "BROAD," "NARROW," or "RELATED" in records where there is no "is_obsolete" tag. For the GO Cellular Component Ontology, additional atoms are created for selected strings by including the word "location" in the STR, and prepending the TTY with "MTH_." This data is added during Metathesaurus source processing.
MTH_IS CODE: tag = "id"
STR: tag = "synonym" with the word "location" included for clarification of selected strings from the Cellular Component Ontology.
SDUI: tag = "id"
TTY = "IS" is assigned to the value of tag = "synonym" where the scope identifier = "EXACT" and tag="is_obsolete" has a value of "true." For the GO Cellular Component Ontology, additional atoms are created for selected strings by including the word "location" in the STR, and prepending the TTY with "MTH_." This data is added during Metathesaurus source processing
MTH_OP CODE: tag = "id"
STR: tag = "name" with the word "location" included for clarification of selected strings from the Cellular Component Ontology.
SDUI: tag = "id"
TTY = "OP" is assigned to the value of tag = "name" where tag = "is_obsolete" has a value of "true." For the GO Cellular Component Ontology, additional atoms are created for selected strings by including the word "location" in the STR, and prepending the TTY with "MTH_." This data is added during Metathesaurus source processing
MTH_PT CODE: tag = "id"
STR: tag = "name" with the word "location" included for clarification of selected strings from the Cellular Component Ontology.
SDUI: tag = "id"
TTY = "PT" is assigned to the value of tag = "name" in records where there is no "is_obsolete" tag. For the GO Cellular Component Ontology, additional atoms are created for selected strings by including the word "location" in the STR, and prepending the TTY with "MTH_." This data is added during Metathesaurus source processing
MTH_OET CODE: tag = "id"
STR: tag = "synonym," with the word "location" included for clarification of selected strings from the Cellular Component Ontology
SDUI: tag = "id"
TTY = "OET" is assigned to the value of tag = "synonym" where the scope identifier is "BROAD," "NARROW," or "RELATED" in records where is_obsolete has a value of "true." For the GO Cellular Component Ontology, additional atoms are created for selected strings by including the word "location" in the STR, and prepending the TTY with "MTH_." This data is added during Metathesaurus source processing.
MTH_SY CODE: tag = "id"
STR: tag = "synonym" with the word "location" included for clarification of selected strings from the Cellular Component Ontology.
SDUI: tag = "id"
TTY = "SY" is assigned to the value of tag = "synonym" where the scope identifier is "EXACT" in records where ethere is no "is_obsolete" tag. For the GO Cellular Component Ontology, additional atoms are created for selected strings by including the word "location" in the STR, and prepending the TTY with "MTH_." This data is added during Metathesaurus source processing
OET CODE: tag = "id"
STR: tag = "synonym"
SDUI: tag = "id"
TTY = "OET" is assigned to the value of tag = "synonym" where the scope identifier is "BROAD," "NARROW," or "RELATED" in records where is_obsolete has a value of "true."
OP CODE: tag = "id"
STR: tag = "synonym"
SDUI: tag = "id"
TTY = "OP" is assigned to the value of tag = "name" in records where is_obsolete has a value of "true."
PT CODE: tag = "id"
STR: tag = "synonym"
SDUI: tag = "id"
TTY = "PT" is assigned to the value of tag = "name" in reocrds with no "is_obsolete" tag.
SY CODE: tag = "id"
STR: tag = "synonym"
SDUI: tag = "id"
TTY = "SY" is assigned to hte value of tag = synonyn where the scope identifier is "EXACT" in records where there is no "is_obsolete" tag.

Attributes (MRSAT):

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Attribute Name Origin
DATE_CREATED tag = "creation_date"
DISJOINT_FROM tag = "disjoint_from"
GO_COMMENT tag = "comment"
GO_NAMESPACE tag = "namespace"
GO_SUBSET tag = "subset"
GXR tag = "xref""
REF tag = "synonym," dbxref list (information extracted from square brackets at the end of the field)
SID
tag = "alt_id"
SYN_QUALIFIER tag = "synonym," qualifier (information following the scope identifier; currently the only value is "systematic synonym")

Definitions (MRDEF):

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Definitions are created from data with the "def" tag in the OBO format.


Relationships (MRREL):

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REL RELA
Inverse RELA
ORIGIN
CHD
PAR
SIB
isa
inverse_isa
hierarchy created from tag = "is_a"
RN
RB
(no rela) Connects an atom created from tag = "synonym" with a scope identifier of "BROAD" or "NARROW" with the preferred atom of the GO [term] record.
RN
RB
part_of
has_part
tag = "relationship"; value = "part_of"
RN
RB
isa
inverse_isa
used to reprsent the intersection_of tags where the value is a GO term_id. A relationship group is used to link pairs (or groups) of intersecting relationships.
RO (no rela) Connects an atom created from tag = "synonym" with a scope identifier of "RELATED" with the preferred atom of the GO [term] record.
RO happens_during
inverse_happens_during
tag = "relationship"; value = "happens_during"
RO negatively_regulates
negatively_regulated_by
tag = "relationship"; value = "negatively_regulates"
RO occurs_in
has_occurrence
tag = "relationship"; value = "occurs_in"
tag = "intersection_of"; relationship_type = "occurs_in". A relationships group is used to link pairs (or groups) of intersecting relationships.
RO positively_regulates
positively_regulated_by
tag = "relationship"; value = "positively_regulates"
RO regulates
regulated_by
tag = "relationship"; value = "regulates"
RQ consider
consider_from
created from tag = "consider"
RQ replaced_by
replaces
created from tag = "replaced_by"
SY (no rela) Connects an atom created from tag = "synonym" with a scope identifier of "EXACT" with the preferred atom of the GO [term] record.
SY expanded_form_of
has_expanded_form
Connects atoms with TTY = "MTH_*" with their original form

Mappings (MRMAP):

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No mappings are represented for GO. Cross Reference to external databases (e.g. MetaCyc:TRNA-CHARGING-PWY) are represented in MRSAT.RRF (ATN = "GXR").