HPOTerm¶

HPOTerm¶

class pyhpo.term.HPOTerm[source]¶

Represents an HPO Term with all metadata

Note

An HPOTerm is initialized as an empty object. Attributes are added line by line from an OBO file

all_parents¶

set of HPOTerm

Set of direct and indirect parent HPOTerms

Note

This property is read-only

children¶

list of HPOTerm

List of direct children HPOTerms

comment¶

str

Comments from HPO Team

Example:

Multicystic kidney dysplasia is the result of
abnormal fetal renal development in which the affected kidney
is replaced by multiple cysts and has little or no residual
function. The vast majority of multicystic kidneys are unilateral.
Multicystic kidney can be diagnosed on prenatal ultrasound.

definition¶

str

HPO Term Definition

Example:

"Multicystic dysplasia of the kidney is characterized by
multiple cysts of varying size in the kidney and the absence of a
normal pelvicaliceal system. The condition is associated with
ureteral or ureteropelvic atresia, and the affected kidney is
nonfunctional." [HPO:curators]

Warning

The string contains double-quote enclosed sections

genes¶

set of pyhpo.annotations.Gene

All genes associated with the term or its children

Note

The set is recursively calcualted the first time it is requested by retrieving all children genes as well. The updated set is then cached.

It is not possibe to remove genes from the set. Any updates will only allow addition of new genes.

Warning

Updating the associated gene set causes a recalculation of the cache and the caches of all parents, so this is a quite expensive operation and should be avoided.

id¶

str

HPO Term ID

Example:

'HP:0000003'

information_content¶

dict

The information content of the HPO term for:

• gene: float
• omim: float
• orpha: float
• decipher: float

Example:

{
    'gene': 0.24,
    'omim': 0.84,
    'orpha': 0.43,
    'decipher': 0.12
}

name¶

str

HPO Term name

Example:

'Abnormality of body height'

omim_diseases¶

set of pyhpo.annotations.Omim

All OMIM diseases associated with the term or its children

Note

The set is recursively calcualted the first time it is requested by retrieving all children OMIM diseases as well. The updated set is then cached.

It is not possibe to remove OMIM diseases from the set. Any updates will only allow addition of new omim-diseases.

Warning

Updating the associated OMIM disease set causes a recalculation of the cache and the caches of all parents, so this is a quite expensive operation and should be avoided.

omim_excluded_diseases¶

set of pyhpo.annotations.Omim

All OMIM diseases that are excluded from the term

Note

Since excluded diseased do not follow the general model of ontology inheritance, the associated annotations are not inherited from or passed on to parents or children

orpha_diseases¶

set of pyhpo.annotations.Orpha

All Orphanet diseases associated with the term or its children

Note

The set is recursively calcualted the first time it is requested by retrieving all children Orphanet diseases as well. The updated set is then cached.

It is not possibe to remove Orphanet diseases from the set. Any updates will only allow addition of new orphanet-diseases.

Warning

Updating the associated Orphanet disease set causes a recalculation of the cache and the caches of all parents, so this is a quite expensive operation and should be avoided.

decipher_diseases¶

set of pyhpo.annotations.Decipher

All Decipher diseases associated with the term or its children

Note

The set is recursively calcualted the first time it is requested by retrieving all children Decipher diseases as well. The updated set is then cached.

It is not possibe to remove Decipher diseases from the set. Any updates will only allow addition of new decipher-diseases.

Warning

Updating the associated Decipher disease set causes a recalculation of the cache and the caches of all parents, so this is a quite expensive operation and should be avoided.

parents¶

list of HPOTerm

List of direct parent HPOTerms

synonym¶

list of str

List of synonymous names

Example:

['Multicystic dysplastic kidney', 'Multicystic kidneys',
'Multicystic renal dysplasia']

xref¶

list

List of xref attributes

is_a¶

list of str

List of parent HPO terms

Example:

['HP:0000107 ! Renal cyst']

is_obsolete¶

bool

Indicates if the HPO term is obsolete and should not be used anymore.

Note

Check the replaced_by attribute which HPO term to use instead.

replaced_by¶

str (HPOTerm.id)

Specifies which HPO term to use instead if self is obsolete.

Example:

'HP:0008665'

Warning

It is not guaranteed that this attribute is present - even for obsolete terms.

is_modifier¶

bool

Indicates whether the HPO is a child of a mooifier term. (read only) Modifier terms are specified in HPOTerm._modifier_ids

• Mode of inheritance - 'HP:0000005'
• Clinical modifier - 'HP:0012823'
• Frequency - 'HP:0040279'
• Clinical course - 'HP:0031797'
• Blood group - 'HP:0032223'
• Past medical history - 'HP:0032443'

_index¶

int

Integer representation of ID

Example:

3

Class methods¶