OnToma is a Python module which maps the disease or phenotype terms to EFO, the ontology used in the Open Targets platform.
More precisely, only a subset of EFO is used in the Open Targets platform, called EFO slim. It is released alongside with every new version of EFO.
OnToma supports two kinds of inputs: either identifiers from other ontologies (e.g.
OMIM:102900), or strings (e.g.
pyruvate kinase hyperactivity).
The way OnToma operates is by trying a series of lookups in EFO and also querying tools from the EBI ontology stack such as OxO and ZOOMA.
For each input, it will return anywhere from zero to multiple matches in EFO. This version of OnToma only returns mappings which are considered of high quality.
For each input type, you can run OnToma from command line or directly from other Python code.
pip install --upgrade ontoma
Running OnToma from CLI¶
In this mode, the input is a file or STDIN, with one input per line:
echo -e 'asthma\npyruvate kinase hyperactivity' | ontoma --input-type string echo -e 'OMIM:102900\nOMIM:104310' | ontoma --input-type ontology
The output format is a TSV file, containing one query-to-EFO mapping per line. The columns to include are configurable via the
--columns flag and can include the following:
query: The original query, e.g. asthma
id_normalised: The EFO term ID in the internal normalised CURIE representation as used by OnToma, e.g. EFO:0000270.
id_ot_schema: The EFO term ID as supported by the Open Targets JSON schema, e.g. EFO_0000270.
id_full_uri: The full EFO term URI, e.g. http://www.ebi.ac.uk/efo/EFO_0000270.
label: The normalised (lower case) label as specified in EFO, e.g. asthma.
By default, two columns are included:
In case no results were found, the query will be missing from the output. In case multiple results were found, the query will appear multiple times in the output.
You can read about additional flags by running
Running OnToma from Python code¶
from ontoma import OnToma otmap = OnToma() result_code = otmap.find_term('OMIM:102900', code=True) result_string = otmap.find_term('asthma') # Columns are available as attributes. print(result.id_ot_schema) # Prints 'EFO_0000270'.
Speeding up subsequent OnToma runs¶
When you initialise an OnToma client, it needs to download and parse the latest EFO OT slim release. Depending on your internet connection, it may take anywhere from 10 seconds to a few minutes.
To speed up subsequent OnToma runs, you can specify a cache directory to avoid doing this every time. This can be supplied by a
--cache-dir option in the CLI or by a
cache_dir parameter in the Python interface.