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Unified Medical Language System (UMLS)

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.

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

VSAB: HPO2017_10_05

Summary of Changes

There are no changes to the source data 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 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 hte 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"
HXR 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" 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
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 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. Cross Reference to external databases (e.g. MeSH) are represented in MRSAT.RRF (ATN = "HXR").