ontoma 0.0.11

Ontology mapping for Open Targets

This software was developed as part of the Open Targets project. For more information please see:

http://www.opentargets.org
Target Validation platform

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

See the License for the specific language governing permissions and
limitations under the License.
Description: 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 [our wiki](https://github.com/opentargets/data_release/wiki/EFO-Ontology-Annotation-Process)


# Usage

## Installing

`pip install ontoma`

## Quickstart

Looking for a disease or phenotype string is simple:

```python
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:

```python
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):

```sh
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:
```sh
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:
```sh
ontoma <input_file> - | grep "mymatch"
```



More detailed documentation is at [](http://ontoma.readthedocs.io/en/stable/?badge=stable)
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](https://pipenv.readthedocs.io/en/latest/install/#homebrew-installation-of-pipenv) and then run
```sh
pipenv install --dev
```
to get all development dependencies installed.

Test everything is working:
```sh
pipenv run pytest
```

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

```sh
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.

Keywords: opentargets ontology efo mapper
Platform: UNKNOWN
Classifier: Intended Audience :: Developers
Classifier: Operating System :: OS Independent
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3 :: Only
Requires-Python: >=3.2
Description-Content-Type: text/markdown