OLS wrapper

OLS API wrapper

Original code borrowed from

https://github.com/cthoyt/ols-client/blob/master/src/ols_client/client.py

• Removed ontology and term methods.
• Added details/parameters for all search methods

TODO: check input parameters are valid TODO: handle requests.exceptions.ConnectionError when traffic is too high and API goes down

class ontoma.ols.OlsClient(ols_base=None, ontology=None, field_list=None, query_fields=None)

Wraps the functions to query the Ontology Lookup Service.

>>> ols = OlsClient()
>>> ols.search('asthma')[0]['iri']
'http://purl.obolibrary.org/obo/NCIT_C28397'

You can search in other ontologies and pass all other parameters accepted by OLS

>>> ols.search('lung',ontology='uberon')[0]['iri']
'http://purl.obolibrary.org/obo/UBERON_0002048'

besthit() simply returns the first element:

>>> ols.besthit('lung',ontology='uberon')['iri']
'http://purl.obolibrary.org/obo/UBERON_0002048'

exact=True forces an exact match:

>>> ols.besthit('hypogammaglobulinemia',ontology='efo')['label']
'Osteopetrosis - hypogammaglobulinemia'

>>> ols.besthit('hypogammaglobulinemia',ontology='efo',exact=True)['label']
'Agammaglobulinemia'

>>> r = ols.search('asthma',ontology=['efo'],query_fields=['synonym'],field_list=['iri','label'])
>>> 'http://www.ebi.ac.uk/efo/EFO_0004591' in [syn['iri'] for syn in r]
True

Find the label of its first ancestor:

>>> a = ols.get_ancestors('efo',r[0]['iri'])
>>> a[0]['label']
'asthma'

>>> r = ols.suggest('asthma', ontology=['efo','ordo','hpo'])
>>> r[0]['autosuggest']
'asthma'

>>> r= ols.select('asthma', ontology=['efo','ordo','hpo'],field_list=['iri'])
>>> r[0]['iri']
'http://www.ebi.ac.uk/efo/EFO_0000270'

>>> ols.search('Myofascial Pain Syndrome',ontology=['efo'])[0]['short_form']
'EFO_1001054'

>>> [x['short_form'] for x in ols.select('alzheimer')[:2]]
['PW_0000015', 'DOID_0080348']

You can also pass your favourite parameters at class instantiation:

>>> ot_ols = OlsClient(ontology=['efo'],field_list=['short_form'])
>>> ot_ols.search('asthma')[0]['short_form']
'EFO_0000270'
>>> ot_ols.besthit('asthma')['short_form']
'EFO_0000270'

besthit(name, **kwargs)

select first element of the /search API response

get_ancestors(ont, iri)

Gets the data for a given term

Parameters:

• ontology – The name of the ontology
• iri – The IRI of a term

get_term(ontology, iri)

Gets the data for a given term

Parameters:

• ontology – The name of the ontology
• iri – The IRI of a term

search(name, query_fields=None, ontology=None, field_list=None, exact=None, bytype='class')

Searches the OLS with the given term

Parameters:

• query_fields – By default the search is performed over term labels, synonyms, descriptions, identifiers and annotation properties. This option allows to specify the fields to query, the defaults are {label, synonym, description, short_form, obo_id, annotations, logical_description, iri}
• exact – Forces exact match if not None
• bytype – restrict to terms one of {class,property,individual,ontology}

select(name, ontology=None, field_list=None)

Select terms, Tuned specifically to support applications such as autocomplete.

See also

https://www.ebi.ac.uk/ols/docs/api#_select

suggest(name, ontology=None)

Suggest terms from an optional list of ontologies

See also

https://www.ebi.ac.uk/ols/docs/api#_suggest_term