Ontoma Interface

main interface class

class ontoma.interface.OnToma

Open Targets ontology mapping wrapper

The output should always be a EFO/OpenTargets ontology URI.

Example

Initialize the class (which will download EFO,OBO and others):

>>> t=OnToma()

We can now lookup “asthma” and get:

>>> t.efo_lookup('asthma')
'http://www.ebi.ac.uk/efo/EFO_0000270'

Notice we always tend to return a full IRI

Search by synonyms coming from the OBO file is also supported

>>> t.efo_lookup('Asthma unspecified')
'http://www.ebi.ac.uk/efo/EFO_0000270'

Reverse lookups uses the get_efo_label() method

>>> t.get_efo_label('EFO_0000270')
'asthma'
>>> t.get_efo_label('EFO:0000270')
'asthma'
>>> t.get_efo_label('http://www.ebi.ac.uk/efo/EFO_0000270')
'asthma'

Similarly, we can now lookup “Phenotypic abnormality” on HP OBO:

>>> t.hp_lookup('Phenotypic abnormality')
'http://purl.obolibrary.org/obo/HP_0000118'
>>> t.hp_lookup('Narrow nasal tip')
'http://purl.obolibrary.org/obo/HP_0011832'

OMIM code lookup

>>> t.omim_lookup('230650')
'http://www.orpha.net/ORDO/Orphanet_354'

>>> t.zooma_lookup('asthma')
'http://www.ebi.ac.uk/efo/EFO_0000270'

Searching the ICD9 code for ‘other dermatoses’ returns EFO’s skin disease:

>>> t.icd9_lookup('696')
'EFO:0000676'

There is also a semi-intelligent wrapper, which tries to guess the best matching strategy:

>>> t.find_term('asthma')
'http://www.ebi.ac.uk/efo/EFO_0000270'
>>> t.find_term('615877',code='OMIM')
'http://www.orpha.net/ORDO/Orphanet_202948'

It returns None if it cannot find an EFO id:

>>> t.find_term('notadisease') is None
True

efo_lookup(name)

Searches the EFO OBO file for a direct match

efo_to_name

find_term(query, code=None)

Finds the most likely EFO code for a given string or ontology code.

If the code argument is passed, it will attempt to perform an exact match amongst the mappings available.

If only a string is passed, it will attempt to match it against mappings, but will try using the EBI SPOT APIs if no match is found, until a likely code is identified

TODO suggestions and fuzzy search should be returned. A specific exception should be crafted and handled.

Parameters:

• query (str) – the disease/phenotype to be matched to an EFO code
• code – accepts one of “ICD9CM”, “OMIM” TODO expand to more ontologies If a code is passed, it will attempt to find the code in one of our curated mapping datasources. Defaults to None.

Returns:

A valid OT ontology URI. None if no EFO code was found

get_efo_label(efocode)

Given an EFO short form code, returns the label as taken from the OBO

hp_lookup(name)

Searches the HP OBO file for a direct match

hp_to_name

icd9_lookup(icd9code)

Searches the ICD9CM <=> EFO mappings returned from the OXO API

logger = None

Initialize API clients

name_to_efo

name_to_hp

omim_lookup(omimcode)

Searches our own curated OMIM <=> EFO mappings #FIXME assumes the first is the best hit. is this ok?

otzooma_map_lookup(name)

Searches against the curated OpenTargets mapping we submitted to zooma.

These mappings are usually stored on github. NOTE: this is not a lookup to zooma API

oxo_lookup(other_ontology_id, input_source='ICD9CM')

Searches in the mappings returned from the EBI OXO API.

The function should return an EFO code for any given xref, if one exists.

Parameters:

• other_ontology_id – the code that should be mapped to EFO
• input_source – an ontology code. Defaults to ‘ICD9CM’. Available ontologies are listed at https://www.ebi.ac.uk/spot/oxo/api/datasources?fields=preferredPrefix

Returns:

the EFO code

Return type:

str

zooma_lookup(name)

Searches against the EBI Zooma service for an high confidence mapping

ontoma.interface.make_uri(ontology_short_form)

Transform a short form ontology code in a full URI. Currently works for EFO, HPO, ORDO and MP.

Parameters:ontology_short_form – An ontology code in the short format, like ‘EFO:0000270’. The function won’t break if a valid URI is passed. Returns:A full URI. Raises a ValueError if the short form code was not one of the supported ones.

Example

>>> make_uri('EFO:0000270')
'http://www.ebi.ac.uk/efo/EFO_0000270'

>>> make_uri('HP_0000270')
'http://purl.obolibrary.org/obo/HP_0000270'

>>> make_uri('http://purl.obolibrary.org/obo/HP_0000270')
'http://purl.obolibrary.org/obo/HP_0000270'

>>> make_uri('TEST_0000270')
Traceback (most recent call last):
    ...
ValueError: Could not build an URI. Short form: TEST_0000270 not recognized