HPO (Human Phenotype Ontology) - Source Representation

Data Files

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

File Name	Description
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.

file: 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 RELATED true OET 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"; 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is_obsolete	Indicates if a term is obsolete	Used to compute termtype assignments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"