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Unified Medical Language System® (UMLS®)

2013AB 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: GO2013_04_06

Summary of Changes

New TTY:  MTH_OET (suppressible = "O")

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.

Source Provided Files:


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

The file used for 2013AB is:

gene_ontology_edit.obo (2013_04_06)

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.

Identifiers:

Identifiers are assigned as follows:
  • 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
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"
RO
results_in
result_of_regulation
tag = "relationship"; value = "results_in"
tag = "intersection_of"; relationship_type = "results_in".  A relationships group is used to link pairs (or groups) of intersecting relationships.
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").