HPOTerm

class HPOTerm

all_parents

A set of all parents

Returns: All direct and indirect parents
Return type: Set[HPOTerm]

Examples

from pyhpo import Ontology
Ontology()
term = Ontology.hpo(108)
term.all_parents  # >> {large set}

categories

A list of the root phenotypical or modifier categories the term belongs to

Returns

The root phenotypical terms or modifier categories

Return type

Set[HPOTerm]

Raises

NameError – Ontology not yet constructed
KeyError – No HPO term is found for the provided query

Examples

from pyhpo import Ontology
Ontology()
term = Ontology.hpo(10049)
for cat in term.categories:
    print(cat.name)

child_of(other)

Returns true if the term is a child of other

Parameters: other (HPOTerm) – The other HPOTerm
Returns: Whether the term is a child of other
Return type: bool

Examples

from pyhpo import Ontology
Ontology()
term = Ontology[10049]
term2 = Ontology[118]

term.child_of(term2)
# >> True

children

A set of direct children

Returns: All direct children
Return type: Set[HPOTerm]

Examples

from pyhpo import Ontology
Ontology()
term = Ontology.hpo(1)
term.children  # >> {<HpoTerm (HP:0000005)>, <HpoTerm (HP:0000118)>, <HpoTerm (HP:0012823)>, <HpoTerm (HP:0032443)>, <HpoTerm (HP:0040279)>, <HpoTerm (HP:0032223)>}

common_ancestors(other)

Returns common ancestor HPOTerm

Parameters: other (HPOTerm) – The other HPOTerm
Returns: All terms that are common ancestors
Return type: set[HPOTerm]

Examples

from pyhpo import Ontology
Ontology()
term = Ontology[2650]
term2 = Ontology[9121]

term.common_ancestors(term2)
# >> {<HpoTerm (HP:0000001)>, <HpoTerm (HP:0011842)>,
# >> <HpoTerm (HP:0033127)>, <HpoTerm (HP:0000118)>,
# >> <HpoTerm (HP:0000924)>}

count_parents()

Returns the number of direct parents of the term

Returns: The number of parents of the term
Return type: int

Examples

from pyhpo import Ontology
Ontology()
Ontology[100490].count_parents()
# >> 3

genes

Returns a set of associated genes

The list includes “inherited” genes that are not directly linked to the term, but to one of its children

Returns: All associated genes
Return type: Set[pyhpo.Gene]

Examples

from pyhpo import Ontology
Ontology()
term = Ontology.hpo(188)
for gene in term.genes:
    print(gene.name)

id

Returns the HPO Term ID

Returns: The term identifier, e.g.: HP:0011968
Return type: str

Examples

from pyhpo import Ontology
Ontology()
term = Ontology.hpo(11968)
term.id    # >> 'HP:0011968'

information_content

Returns the Information Content of the HPO Term

Returns: The term’s information content
Return type: pyhpo.types.InformationContent

Examples

from pyhpo import Ontology
Ontology()
term = Ontology.hpo(11968)
term.information_content.omim  # >> 2.5363943576812744
term.information_content.gene  # >> 1.457185983657837

is_obsolete

Indicates if the term is flagged as obsolete

Obsolete terms are ususally not linked to parents or children and should not be used.

In most cases, you can find a replacement using HPOTerm::replaced_by()

Returns: True if the term is obsolete
Return type: bool

Examples

from pyhpo import Ontology
Ontology()
term = Ontology[10049]
term.is_obsolete # ==> False

name

Returns the name of the HPO Term

Returns: The term name, e.g.: Feeding difficulties
Return type: str

Examples

from pyhpo import Ontology
Ontology()
term = Ontology.hpo(11968)
term.name  # >> 'Feeding difficulties'

omim_diseases

Returns a set of associated OMIM diseases

The list includes “inherited” diseases that are not directly linked to the term, but to one of its children

Returns: All associated Omim diseases
Return type: Set[pyhpo.Omim]

Examples

from pyhpo import Ontology
Ontology()
term = Ontology.hpo(188)
for disease in term.omim_diseases:
    print(disease.name)

parent_ids()

Returns a list of all direct parent’s HPO-IDs

Returns: A list of int representations of the parent terms
Return type: List[int]

Examples

from pyhpo import Ontology
Ontology()
term = Ontology[10049]

term.parent_ids()
# >> [3026, 5914]

parent_of(other)

Returns true if the term is a parent of other

Parameters: other (HPOTerm) – The other HPOTerm
Returns: Whether the term is a parent of other
Return type: bool

Examples

from pyhpo import Ontology
Ontology()
term = Ontology[10049]
term2 = Ontology[118]

term2.parent_of(term)
# >> True

parents

A set of direct parents

Returns: All direct parents
Return type: Set[HPOTerm]

Examples

from pyhpo import Ontology
Ontology()
term = Ontology.hpo(108)
term.parents  # >> {<HpoTerm (HP:0011035)>, <HpoTerm (HP:0000107)>, <HpoTerm (HP:0100957)>}

path_to_other(other)

Calculates the shortest path to another HPO Term

Note

This method is not correctly implemented: It will always return 0 for the sub-paths distances.

Parameters

other (HPOTerm) – The other HPOTerm

Returns

int – The number of terms between self and the other term (excluding self, but including other)
List[HPOTerm] – The terms between and including self and other
int – Always 0
int – Always 0

Examples

from pyhpo import Ontology
Ontology()
term = Ontology[40064]
term2 = Ontology[769]
term.path_to_other(term2)
# >> (
# >>    2,
# >>    [<HpoTerm (HP:0040064)>, <HpoTerm (HP:0000118)>, <HpoTerm (HP:0000769)>],
# >>    0,
# >>    0
# >> )

replace()

Returns the replacement term, if the term is obsolete

Returns: The HPOterm
Return type: HPOTerm

Examples

from pyhpo import Ontology
Ontology()
term = Ontology[100637]
replacement = term.replace()
replacement.id # >> 'HP:0012720'

replaced_by

Returns the replacement term name, if the term is obsolete

Returns: The HPO term id, e.g. HP:0003026
Return type: str

Examples

from pyhpo import Ontology
Ontology()
term = Ontology[100637]
term.replaced_by # >> 'HP:0012720'

shortest_path_to_parent(other)

Calculates the shortest path to an ancestor HPO Term

If other is not a parent term, the distance will be Inf.

As a minor difference to PyHPO, this method does not return a Tuple, but a list of terms.

Parameters

other (HPOTerm) – The other HPOTerm

Returns

float – The number of terms between self and the other term. If other is not a parent, it returns Inf
List[HPOTerm] – The terms between self and other

Examples

from pyhpo import Ontology
Ontology()
term = Ontology[100490]
term2 = Ontology[1]
term.shortest_path_to_parent(term2)
# >> (
# >>    8.0,
# >>    [
# >>        <HpoTerm (HP:0006261)>, <HpoTerm (HP:0005918)>,
# >>        <HpoTerm (HP:0001167)>, <HpoTerm (HP:0001155)>,
# >>        <HpoTerm (HP:0002817)>, <HpoTerm (HP:0040064)>,
# >>        <HpoTerm (HP:0000118)>, <HpoTerm (HP:0000001)>
# >>    ]
# >> )

shortest_path_to_root()

Returns the number of terms between self and the root term

Returns: The number of terms between self and the root term
Return type: int

Examples

from pyhpo import Ontology
Ontology()
Ontology[100490].shortest_path_to_root()
# >> 8

similarity_score(other, kind, method)

Calculates the similarity score of two HPO Terms

Parameters

other (HPOTerm) – The other HPOTerm
kind (str, default: omim) –
Which kind of information content to use for similarity calculation

Available options:
- omim
- gene
method (str, default graphic) –
The method to use to calculate the similarity.

Available options:
- resnik - Resnik P, Proceedings of the 14th IJCAI, (1995)
- lin - Lin D, Proceedings of the 15th ICML, (1998)
- jc - Jiang J, Conrath D, ROCLING X, (1997) This is different to PyHPO
- jc2 - Jiang J, Conrath D, ROCLING X, (1997) Same as jc, but kept for backwards compatibility
- rel - Relevance measure - Schlicker A, et.al., BMC Bioinformatics, (2006)
- ic - Information coefficient - Li B, et. al., arXiv, (2010)
- graphic - Graph based Information coefficient - Deng Y, et. al., PLoS One, (2015)
- dist - Distance between terms

Returns

The similarity score

Return type

float

Raises

KeyError – Invalid kind
RuntimeError – Invalid method

Examples

from pyhpo import Ontology

Ontology()
term = Ontology[11968]

term.similarity_score(Ontology[1743])

# compare HP:0011968 and HP:0001743 using Gene
term.similarity_score(Ontology[1743], kind="gene")

similarity_scores(others, kind, method)

Calculates the similarity score between the term and a batch of other terms

This method is useful if you want to compare the term to thousands of other terms. It will utilize all avaible CPU for parallel processing.

Parameters

others (List[HPOTerm]) – Lost of HPOTerm to calculate similarity to
kind (str, default: omim) –
Which kind of information content to use for similarity calculation

Available options:
- omim
- gene
method (str, default graphic) –
The method to use to calculate the similarity.

Available options:
- resnik - Resnik P, Proceedings of the 14th IJCAI, (1995)
- lin - Lin D, Proceedings of the 15th ICML, (1998)
- jc - Jiang J, Conrath D, ROCLING X, (1997) This is different to PyHPO
- jc2 - Jiang J, Conrath D, ROCLING X, (1997) Same as jc, but kept for backwards compatibility
- rel - Relevance measure - Schlicker A, et.al., BMC Bioinformatics, (2006)
- ic - Information coefficient - Li B, et. al., arXiv, (2010)
- graphic - Graph based Information coefficient - Deng Y, et. al., PLoS One, (2015)
- dist - Distance between terms

Returns

The similarity scores

Return type

List[float]

Raises

KeyError – Invalid kind
RuntimeError – Invalid method

Examples

from pyhpo import Ontology

Ontology()
term = Ontology[11968]

term.similarity_scores(list(Ontology))

toJSON(verbose)

Returns a dict/JSON representation the HPOTerm

Parameters

verbose (bool) – if extra attributes should be included

Returns

Dict representation of the HPOTerm with the following keys:

namestr
The name of the HPO term
idstr
The HPO term ID e.g.: HP:0000265
intint
Integer of the term ID, e.g.: 265
synonymlist[str]
Not implemented, will always be []
commentstr
Not implemented, will always be ""
definitionstr
Not implemented, will always be ""
xreflist[str]
Not implemented, will always be []
is_alist[str]
Not implemented, will always be []
icdict[str, float]
The information content scores, see pyhpo.InformationContent

Return type

Dict

Examples

from pyhpo import Ontology
Ontology()
term = Ontology[118]
term.toJSON()
# >> {'name': 'Phenotypic abnormality', 'id': 'HP:0000118', 'int': 118}

Ontology[265].toJSON(True)
# >> {
# >>     'name': 'Mastoiditis',
# >>     'id': 'HP:0000265',
# >>     'int': 265,
# >>     'synonym': [],
# >>     'comment': '',
# >>     'definition': '',
# >>     'xref': [],
# >>     'is_a': [],
# >>     'ic': {
# >>         'gene': 6.7086944580078125,
# >>         'omim': 7.392647743225098,
# >>         'orpha': 0.0,
# >>         'decipher': 0.0
# >>     }
# >> }

class InformationContent

Holds the information content for an HPOTerm

gene: Returns the gene - based information content

omim: Returns the Omim disease - based information content