Ontology¶
The Ontology
contains all HPOTerm
s and thus reflects the full ontology including links and information about inheritance
Ontology
class¶
-
class
pyhpo.ontology.
OntologyClass
[source]¶ A linked and indexed list of interconnected
HPOTerm
s.-
genes
¶ set
Set of all genes associated with the HPOTerms
-
omim_diseases
¶ set
Set of all OMIM-diseases associated with the HPOTerms
-
omim_excluded_diseases
¶ set
Set of all excluded OMIM-diseases associated with the HPOTerms
-
get_hpo_object¶
-
OntologyClass.
get_hpo_object
(query)[source]¶ Matches a single HPO term based on its name, synonym or id
Parameters: query (str or int) – - str HPO term
Scoliosis
- str synonym
Curved spine
- str HPO-ID
HP:0002650
- int HPO term id
2650
Returns: A single matching HPO term instance Return type: HPOTerm Example
# Search by ID (int) >>> ontology.get_hpo_object(3) HP:0000003 | Multicystic kidney dysplasia # Search by HPO-ID (string) >>> ontology.get_hpo_object('HP:0000003') HP:0000003 | Multicystic kidney dysplasia # Search by term (string) >>> ontology.get_hpo_object('Multicystic kidney dysplasia') HP:0000003 | Multicystic kidney dysplasia # Search by synonym (string) >>> ontology.get_hpo_object('Multicystic renal dysplasia') HP:0000003 | Multicystic kidney dysplasia
- str HPO term
match¶
path¶
-
OntologyClass.
path
(query1, query2)[source]¶ Returns the shortest connection between two HPO terms
Parameters: - query1 (str or int) – HPO term 1, synonym or HPO-ID (HP:00001) to match HPO term id (Integer based) e.g: Abnormality of the nervous system
- query2 (str or int) – HPO term 2, synonym or HPO-ID (HP:00001) to match HPO term id (Integer based) e.g: Abnormality of the nervous system
Returns: - int – Length of path
- tuple – Tuple of HPOTerms in the path
- int – Number of steps from term-1 to the common parent
- int – Number of steps from term-2 to the common parent
search¶
synonym_match¶
-
OntologyClass.
synonym_match
(query)[source]¶ Searches for actual and synonym term matches If a match is found in any term, that one is returned If no actual match is found, the first match with synonyms is considered
Parameters: query (str) – Term to search for Returns: A single HPO term instance Return type: HPOTerm
synonym_search¶
to_dataframe¶
-
OntologyClass.
to_dataframe
()[source]¶ Creates a Pandas DataFrame from the most important features
Each HPO term is one row, the features are present in columns
Returns: The DataFrame of HPO-Terms and their attributes in the following columns - id
str
The HPO Term ID “HP:0000003” (used as index) - name
str
The HPO Term name “Multicystic kidney dysplasia” - parents
str
Concatenated list of direct parents of HPO terms. Separated by|
- children
str
Concatenated list of direct children of HPO terms. Separated by|
- ic_omim
float
Information-content (based on associated OMIM diseases) - ic_gene
float
Information-content (based on associated genes) - dTop_l
int
Maximum distance to root term (viapyhpo.term.longest_path_to_root()
) - dTop_s
int
Shortest distance to root term (viapyhpo.term.shortest_path_to_root()
) - dBottom
int
Longest graph of children nodes (viapyhpo.term.longest_path_to_bottom()
) - genes
str
Concatenated list of associated genes. Separated by|
- diseases
str
Concatenated list of associated OMIM diseases. Separated by|
Return type: DataFrame
- id