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Unified Medical Language System (UMLS)

UMLS Vocabularies

HPO (Human Phenotype Ontology) - Metathesaurus Representation


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

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Atoms
Attributes
Definitions
Relationships
Mappings

VSAB:HPO2022_10_05

Summary of Changes

There were no changes to the source file format or Metathesaurus source processing.

Source-Provided Files: Summary

HPO is released in both owl and obo formats. The obo format is processed for the UMLS Metathesaurus.

Data Files

File Name Description
hp.obo.txt 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):

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."
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" and tag="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 the value of tag = synonym where the scope identifier is "EXACT" in records where there is no "is_obsolete" tag.

Attributes (MRSAT):

Attribute Name Origin
DATE_CREATED tag = "creation_date"
HPO_COMMENT tag = "comment"
REF tag = "synonym," dbxref list (information extracted from square brackets at the end of the field)
SID tag = "alt_id"
SYN_QUALIFIER tag = "synonym" synonymtypedef value

Definitions (MRDEF):


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

Relationships (MRREL):

REL RELA
Inverse RELA		 ORIGIN
CHD
PAR		 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 HPO [term] record.
RO (no rela) Connects an atom created from tag = "synonym" with a scope identifier of "RELATED" with the preferred atom of the HPO [term] record.
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 HPO [term] record.

Mappings (MRMAP):


No mappings are represented for HPO.