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OnToma is a python module that helps you map your disease/phenotype terms to the ontology we use in the Open Targets platform.

The ontology we use in the Open Targets platform is a subset (aka. slim) of the EFO ontology plus any HPO terms for which a valid EFO mapping could not be found.

features

  • Wrap OLS, OXO, Zooma in a pythonic API
  • Always tries to output full URI
  • Tries to find mappings iteratively using the faster methods first
  • Checks if mapping is in the subset of EFO that gets included in the Open Targets platform
  • tries to follow the procedure highlighted in https://github.com/opentargets/data_release/blob/master/diagram.jpg

Usage

Installing

pip install ontoma

Quickstart

Looking for a disease or phenotype string is simple:

from ontoma import OnToma

otmap = OnToma()
print(otmap.find_term('asthma'))

#outputs:
'http://www.ebi.ac.uk/efo/EFO_0000270'

you can obtain more details using the verbose flag:

print(otmap.find_term('asthma',verbose=True))

#outputs something similar to:
{'term':'http://www.ebi.ac.uk/efo/EFO_0000270','label':'asthma',
'source':'EFO OBO','quality':'match' ...}

From the command line

The command line version can be invoked with ontoma (type ontoma --help to find out about the usage):

ontoma <input_file> <output_file>

where input file can be replaced with - to read from stdin and write to stdout.

Which means that to read from a previous command, using pipes:

echo 'asthma' | ontoma - <output_file>

will output a file test.txt containing the result, where it came from and the degree of confidence of the match (one of {match, fuzzy, check}):

http://www.ebi.ac.uk/efo/EFO_0000270    asthma  EFO OBO     match

Piping also works for the output. If you want to find the string "mymatch" from the results, you can:

ontoma <input_file> - | grep "mymatch"

More detailed documentation is at Documentation Status http://ontoma.readthedocs.io/en/stable/

Developing

set up your environment

First clone this repo

git clone https://github.com/opentargets/OnToma.git

Install pipenv and then run

pipenv install --dev

to get all development dependencies installed.

Test everything is working:

pipenv run pytest

if you don't like pipenv you can stick with the more traditional setuptools/virtualenv setup:

git clone https://github.com/opentargets/OnToma.git
virtualenv -p python3 venv
source venv/bin/activate
pip install --editable .

How to add a dependency

Add to both pipenv AND setup.py

To add a dep for a library, add it by hand to setup.py, then add it separately to Pipfile, so that it shows up both as a transitive dependency and in your locked dev environment

Release to PyPi

Simply run ./bumpversion.sh

The script will tag, push and trigger a new CI run. The package will be automatically uploaded to pypi.

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Map your disease and phenotype terms to the Open Targets platform ontology

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