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Unified Medical Language System (UMLS)

UMLS Vocabularies

HPO (Human Phenotype Ontology) - Source Representation


This page lists specific source data elements and provides information on their representation in the UMLS Metathesaurus.

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VSAB:HPO2020_06_08

Summary of Changes:

No changes were made to the source format or Metathesaurus source processing

Source-Provided Files: Summary

Documentation on the obo format is available at: http://www.geneontology.org/

Data Files

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

File Name Description
2020_06_08_hp.obo.txt obo format data file

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

Source-Provided Files: Details

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 at www.geneontology.org for additional details.

file:2020_06_08_hp.obo.txt

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

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
def Definition MRDEF.DEF
comment Comment MRSAT.ATN = "HPO_COMMENT"
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
BROAD (no value) ET RB
RELATED (no value) ET RO

Optional dbxref lists included in synonym tags are represented in MRSAT.ATN = "REF"
Optional synonymtypedef values in synonym tags are represented in MRSAT.ATN = SYN_QUALIFIER
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")
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"
creation_date Indicates the creation time and date of the term MRSAT.ATN = "DATE_CREATED"
alt_id An alternative (secondary) identifier MRSAT.ATN = "SID"