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https://github.com/althonos/pronto
A Python frontend to (Open Biomedical) Ontologies.
https://github.com/althonos/pronto
bioinformatics obo obo-graphs obofoundry ontology owl parser python semantic-web
Last synced: 7 days ago
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A Python frontend to (Open Biomedical) Ontologies.
- Host: GitHub
- URL: https://github.com/althonos/pronto
- Owner: althonos
- License: mit
- Created: 2016-07-01T23:02:01.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2024-04-24T13:37:45.000Z (8 months ago)
- Last Synced: 2024-06-11T18:24:00.438Z (6 months ago)
- Topics: bioinformatics, obo, obo-graphs, obofoundry, ontology, owl, parser, python, semantic-web
- Language: Python
- Homepage: https://pronto.readthedocs.io
- Size: 10.1 MB
- Stars: 224
- Watchers: 12
- Forks: 46
- Open Issues: 40
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: COPYING
Awesome Lists containing this project
README
# `pronto` [](https://github.com/althonos/pronto/stargazers)
*A Python frontend to ontologies.*
[](https://github.com/althonos/pronto/actions)
[](https://choosealicense.com/licenses/mit/)
[](https://github.com/althonos/pronto/)
[](http://pronto.readthedocs.io/en/stable/?badge=stable)
[](https://codecov.io/gh/althonos/pronto/)
[](https://codacy.com/app/althonos/pronto)
[](https://pypi.python.org/pypi/pronto)
[](https://anaconda.org/bioconda/pronto)
[](https://pypi.org/project/pronto/#files)
[](https://pypi.org/project/pronto/#files)
[](https://github.com/althonos/pronto/blob/master/CHANGELOG.md)
[](https://github.com/althonos/pronto/issues)
[](https://doi.org/10.5281/zenodo.595572)
[](https://pepy.tech/project/pronto)
## 🚩 Table of Contents
- [Overview](#%EF%B8%8F-overview)
- [Supported Languages](#%EF%B8%8F-supported-languages)
- [Installing](#-installing)
- [Examples](#-examples)
- [API Reference](#-api-reference)
- [License](#-license)
## 🗺️ Overview
Pronto is a Python library to parse, browse, create, and export
ontologies, supporting several ontology languages and formats. It
implement the specifications of the
[Open Biomedical Ontologies 1.4](http://owlcollab.github.io/oboformat/doc/obo-syntax.html)
in the form of an safe high-level interface. *If you're only interested in
parsing OBO or OBO Graphs document, you may wish to consider
[`fastobo`](https://pypi.org/project/fastobo) instead.*
## 🏳️ Supported Languages
- [Open Biomedical Ontologies 1.4](http://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html).
*Because this format is fairly new, not all OBO ontologies can be parsed at the
moment. See the [OBO Foundry roadmap](https://github.com/orgs/fastobo/projects/2)
listing the compliant ontologies, and don't hesitate to contact their developers
to push adoption forward.*
- [OBO Graphs](https://github.com/geneontology/obographs) in [JSON](http://json.org/)
format. *The format is not yet stabilized to the results may change from file
to file.*
- [Ontology Web Language 2](https://www.w3.org/TR/owl2-overview/)
in [RDF/XML format](https://www.w3.org/TR/2012/REC-owl2-mapping-to-rdf-20121211/).
*OWL2 ontologies are reverse translated to OBO using the mapping defined in the
[OBO 1.4 Semantics](http://owlcollab.github.io/oboformat/doc/obo-syntax.html).*
## 🔧 Installing
Installing with `pip` is the easiest:
```console
# pip install pronto # if you have the admin rights
$ pip install pronto --user # install it in a user-site directory
```
There is also a `conda` recipe in the `bioconda` channel:
```console
$ conda install -c bioconda pronto
```
Finally, a development version can be installed from GitHub
using `setuptools`, provided you have the right dependencies
installed already:
```console
$ git clone https://github.com/althonos/pronto
$ cd pronto
# python setup.py install
```
## 💡 Examples
If you're only reading ontologies, you'll only use the `Ontology`
class, which is the main entry point.
```python
>>> from pronto import Ontology
```
It can be instantiated from a path to an ontology in one of the supported
formats, even if the file is compressed:
```python
>>> go = Ontology("tests/data/go.obo.gz")
```
Loading a file from a persistent URL is also supported, although you may also
want to use the `Ontology.from_obo_library` method if you're using persistent
URLs a lot:
```python
>>> cl = Ontology("http://purl.obolibrary.org/obo/cl.obo")
>>> stato = Ontology.from_obo_library("stato.owl")
```
### 🏷️ Get a term by accession
`Ontology` objects can be used as mappings to access any entity
they contain from their identifier in compact form:
```python
>>> cl['CL:0002116']
Term('CL:0002116', name='B220-low CD38-positive unswitched memory B cell')
```
Note that when loading an OWL ontology, URIs will be compacted to CURIEs
whenever possible:
```python
>>> aeo = Ontology.from_obo_library("aeo.owl")
>>> aeo["AEO:0000078"]
Term('AEO:0000078', name='lumen of tube')
```
### 🖊️ Create a new term from scratch
We can load an ontology, and edit it locally. Here, we add a new protein class
to the Protein Ontology.
```python
>>> pr = Ontology.from_obo_library("pr.obo")
>>> brh = ms.create_term("PR:XXXXXXXX")
>>> brh.name = "Bacteriorhodopsin"
>>> brh.superclasses().add(pr["PR:000001094"]) # is a rhodopsin-like G-protein
>>> brh.disjoint_from.add(pr["PR:000036194"]) # disjoint from eukaryotic proteins
```
### ✏️ Convert an OWL ontology to OBO format
The `Ontology.dump` method can be used to serialize an ontology to any of the
supported formats (currently OBO and OBO JSON):
```python
>>> edam = Ontology("http://edamontology.org/EDAM.owl")
>>> with open("edam.obo", "wb") as f:
... edam.dump(f, format="obo")
```
### 🌿 Find ontology terms without subclasses
The `terms` method of `Ontology` instances can be used to
iterate over all the terms in the ontology (including the
ones that are imported). We can then use the `is_leaf`
method of `Term` objects to check is the term is a leaf in the
class inclusion graph.
```python
>>> ms = Ontology("ms.obo")
>>> for term in ms.terms():
... if term.is_leaf():
... print(term.id)
MS:0000000
MS:1000001
...
```
### 🤫 Silence warnings
`pronto` is explicit about the parts of the code that are doing
non-standard assumptions, or missing capabilities to handle certain
constructs. It does so by raising warnings with the `warnings` module,
which can get quite verbose.
If you are fine with the inconsistencies, you can manually disable
warning reports in your consumer code with the `filterwarnings` function:
```python
import warnings
import pronto
warnings.filterwarnings("ignore", category=pronto.warnings.ProntoWarning)
```
## 📖 API Reference
A complete API reference can be found in the
[online documentation](https://pronto.readthedocs.io/en/latest/api.html), or
directly from the command line using `pydoc`:
```console
$ pydoc pronto.Ontology
```
## 📜 License
This library is provided under the open-source
[MIT license](https://choosealicense.com/licenses/mit/).
Please cite this library if you are using it in a scientific
context using the following DOI:
[**10.5281/zenodo.595572**](https://doi.org/10.5281/zenodo.595572)