# `pronto` [](https://github.com/althonos/pronto/stargazers)
*A Python frontend to ontologies.*
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[](https://github.com/althonos/pronto/blob/master/CHANGELOG.md)
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[](https://doi.org/10.5281/zenodo.595572)
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## 🚩 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)
```
<!-- ### 🤝 Merging several ontologies -->
## 📖 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)
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"description": "# `pronto` [](https://github.com/althonos/pronto/stargazers)\n\n*A Python frontend to ontologies.*\n\n[](https://github.com/althonos/pronto/actions)\n[](https://choosealicense.com/licenses/mit/)\n[](https://github.com/althonos/pronto/)\n[](http://pronto.readthedocs.io/en/stable/?badge=stable)\n[](https://codecov.io/gh/althonos/pronto/)\n[](https://codacy.com/app/althonos/pronto)\n[](https://pypi.python.org/pypi/pronto)\n[](https://anaconda.org/bioconda/pronto)\n[](https://pypi.org/project/pronto/#files)\n[](https://pypi.org/project/pronto/#files)\n[](https://github.com/althonos/pronto/blob/master/CHANGELOG.md)\n[](https://github.com/althonos/pronto/issues)\n[](https://doi.org/10.5281/zenodo.595572)\n[](https://pepy.tech/project/pronto)\n\n## \ud83d\udea9 Table of Contents\n\n- [Overview](#%EF%B8%8F-overview)\n- [Supported Languages](#%EF%B8%8F-supported-languages)\n- [Installing](#-installing)\n- [Examples](#-examples)\n- [API Reference](#-api-reference)\n- [License](#-license)\n\n## \ud83d\uddfa\ufe0f Overview\n\nPronto is a Python library to parse, browse, create, and export\nontologies, supporting several ontology languages and formats. It\nimplement the specifications of the\n[Open Biomedical Ontologies 1.4](http://owlcollab.github.io/oboformat/doc/obo-syntax.html)\nin the form of an safe high-level interface. *If you're only interested in\nparsing OBO or OBO Graphs document, you may wish to consider\n[`fastobo`](https://pypi.org/project/fastobo) instead.*\n\n\n## \ud83c\udff3\ufe0f Supported Languages\n\n- [Open Biomedical Ontologies 1.4](http://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html).\n *Because this format is fairly new, not all OBO ontologies can be parsed at the\n moment. See the [OBO Foundry roadmap](https://github.com/orgs/fastobo/projects/2)\n listing the compliant ontologies, and don't hesitate to contact their developers\n to push adoption forward.*\n- [OBO Graphs](https://github.com/geneontology/obographs) in [JSON](http://json.org/)\n format. *The format is not yet stabilized to the results may change from file\n to file.*\n- [Ontology Web Language 2](https://www.w3.org/TR/owl2-overview/)\n in [RDF/XML format](https://www.w3.org/TR/2012/REC-owl2-mapping-to-rdf-20121211/).\n *OWL2 ontologies are reverse translated to OBO using the mapping defined in the\n [OBO 1.4 Semantics](http://owlcollab.github.io/oboformat/doc/obo-syntax.html).*\n\n## \ud83d\udd27 Installing\n\n\nInstalling with `pip` is the easiest:\n```console\n# pip install pronto # if you have the admin rights\n$ pip install pronto --user # install it in a user-site directory\n```\n\nThere is also a `conda` recipe in the `bioconda` channel:\n```console\n$ conda install -c bioconda pronto\n```\n\nFinally, a development version can be installed from GitHub\nusing `setuptools`, provided you have the right dependencies\ninstalled already:\n```console\n$ git clone https://github.com/althonos/pronto\n$ cd pronto\n# python setup.py install\n```\n\n## \ud83d\udca1 Examples\n\nIf you're only reading ontologies, you'll only use the `Ontology`\nclass, which is the main entry point.\n\n```python\n>>> from pronto import Ontology\n```\n\nIt can be instantiated from a path to an ontology in one of the supported\nformats, even if the file is compressed:\n```python\n>>> go = Ontology(\"tests/data/go.obo.gz\")\n```\n\nLoading a file from a persistent URL is also supported, although you may also\nwant to use the `Ontology.from_obo_library` method if you're using persistent\nURLs a lot:\n```python\n>>> cl = Ontology(\"http://purl.obolibrary.org/obo/cl.obo\")\n>>> stato = Ontology.from_obo_library(\"stato.owl\")\n```\n\n### \ud83c\udff7\ufe0f Get a term by accession\n\n`Ontology` objects can be used as mappings to access any entity\nthey contain from their identifier in compact form:\n```python\n>>> cl['CL:0002116']\nTerm('CL:0002116', name='B220-low CD38-positive unswitched memory B cell')\n```\n\nNote that when loading an OWL ontology, URIs will be compacted to CURIEs\nwhenever possible:\n\n```python\n>>> aeo = Ontology.from_obo_library(\"aeo.owl\")\n>>> aeo[\"AEO:0000078\"]\nTerm('AEO:0000078', name='lumen of tube')\n```\n\n### \ud83d\udd8a\ufe0f Create a new term from scratch\n\nWe can load an ontology, and edit it locally. Here, we add a new protein class\nto the Protein Ontology.\n```python\n>>> pr = Ontology.from_obo_library(\"pr.obo\")\n>>> brh = ms.create_term(\"PR:XXXXXXXX\")\n>>> brh.name = \"Bacteriorhodopsin\"\n>>> brh.superclasses().add(pr[\"PR:000001094\"]) # is a rhodopsin-like G-protein\n>>> brh.disjoint_from.add(pr[\"PR:000036194\"]) # disjoint from eukaryotic proteins\n```\n\n### \u270f\ufe0f Convert an OWL ontology to OBO format\n\nThe `Ontology.dump` method can be used to serialize an ontology to any of the\nsupported formats (currently OBO and OBO JSON):\n```python\n>>> edam = Ontology(\"http://edamontology.org/EDAM.owl\")\n>>> with open(\"edam.obo\", \"wb\") as f:\n... edam.dump(f, format=\"obo\")\n```\n\n### \ud83c\udf3f Find ontology terms without subclasses\n\nThe `terms` method of `Ontology` instances can be used to\niterate over all the terms in the ontology (including the\nones that are imported). 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