| Name | pronto JSON |
| Version |
2.7.1
JSON |
| download |
| home_page | None |
| Summary | Python frontend to ontologies. |
| upload_time | 2025-10-25 20:06:23 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.7 |
| license | MIT License
Copyright (c) 2016-2025 Martin Larralde <martin.larralde@embl.de>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
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The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
|
| keywords |
bioinformatics
ontology
obo
owl
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
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# `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)
```
<!-- ### 🤝 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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