This page lists specific source data elements and provides information on their representation in the UMLS Metathesaurus.
Documentation on the obo format is available at: http://www.geneontology.org/
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.
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.
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 |
Tag Name | Description | Representation | ||||||||||||||||||||||||
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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
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 |
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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is_obsolete | Indicates if a term is obsolete | Used to compute termtype assignments | ||||||||||||||||||||||||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" |
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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" |
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creation_date | Indicates the creation time and date of the term | MRSAT.ATN = "DATE_CREATED" | ||||||||||||||||||||||||
alt_id | An alternative (secondary) identifier | MRSAT.ATN = "SID" |