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Repository
A Python frontend to (Open Biomedical) Ontologies.
Basic Info
- Host: GitHub
- Owner: althonos
- License: mit
- Language: Python
- Default Branch: master
- Homepage: https://pronto.readthedocs.io
- Size: 10.1 MB
Statistics
- Stars: 242
- Watchers: 11
- Forks: 49
- Open Issues: 34
- Releases: 61
Topics
Metadata Files
README.md
pronto 
A Python frontend to ontologies.
🚩 Table of Contents
🗺️ 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
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 instead.
🏳️ Supported Languages
- Open Biomedical Ontologies 1.4. Because this format is fairly new, not all OBO ontologies can be parsed at the moment. See the OBO Foundry roadmap listing the compliant ontologies, and don't hesitate to contact their developers to push adoption forward.
- OBO Graphs in JSON format. The format is not yet stabilized to the results may change from file to file.
- Ontology Web Language 2 in RDF/XML format. OWL2 ontologies are reverse translated to OBO using the mapping defined in the OBO 1.4 Semantics.
🔧 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.fromobolibrary("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.fromobolibrary("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.fromobolibrary("pr.obo") brh = ms.createterm("PR:XXXXXXXX") brh.name = "Bacteriorhodopsin" brh.superclasses().add(pr["PR:000001094"]) # is a rhodopsin-like G-protein brh.disjointfrom.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, or
directly from the command line using pydoc:
console
$ pydoc pronto.Ontology
📜 License
This library is provided under the open-source MIT license. Please cite this library if you are using it in a scientific context using the following DOI: 10.5281/zenodo.595572
Owner
- Name: Martin Larralde
- Login: althonos
- Kind: user
- Location: Heidelberg, Germany
- Company: EMBL / LUMC, @zellerlab
- Twitter: althonos
- Repositories: 91
- Profile: https://github.com/althonos
PhD candidate in Bioinformatics, passionate about programming, SIMD-enthusiast, Pythonista, Rustacean. I write poems, and sometimes they are executable.
GitHub Events
Total
- Create event: 8
- Release event: 1
- Issues event: 15
- Watch event: 10
- Delete event: 6
- Issue comment event: 27
- Push event: 10
- Pull request event: 11
- Fork event: 1
Last Year
- Create event: 8
- Release event: 1
- Issues event: 15
- Watch event: 10
- Delete event: 6
- Issue comment event: 27
- Push event: 10
- Pull request event: 11
- Fork event: 1
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Martin Larralde | m****e@e****r | 550 |
| Martin Larralde | m****e@e****r | 283 |
| dependabot-preview[bot] | 2****] | 5 |
| Philipp A | f****p@w****e | 3 |
| Alex Henrie | a****4@g****m | 2 |
| Chris Morris | c****s | 1 |
| Daniel Himmelstein | d****n@g****m | 1 |
| Dave Lawrence | d****w@g****m | 1 |
| Rafal Wojdyla | r****a@g****m | 1 |
| Spencer Mitchell | s****6@g****m | 1 |
| dependabot[bot] | 4****] | 1 |
| imgbot[bot] | 3****] | 1 |
| Erik Bakke | b****k@g****m | 1 |
| tatsu | t****1@g****m | 1 |
| Martin Larralde | m****e@a****r | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 71
- Total pull requests: 73
- Average time to close issues: 6 months
- Average time to close pull requests: 4 months
- Total issue authors: 45
- Total pull request authors: 13
- Average comments per issue: 2.24
- Average comments per pull request: 1.3
- Merged pull requests: 10
- Bot issues: 0
- Bot pull requests: 63
Past Year
- Issues: 5
- Pull requests: 12
- Average time to close issues: about 1 month
- Average time to close pull requests: 3 days
- Issue authors: 5
- Pull request authors: 2
- Average comments per issue: 2.2
- Average comments per pull request: 0.58
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 11
Top Authors
Issue Authors
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- cthoyt (4)
- dhimmel (3)
- Zethson (3)
- CarMoreno (3)
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- njoannin (2)
- ali3assi (2)
- manulera (2)
- mukund109 (2)
- theArsalanM (1)
- dgolden96 (1)
Pull Request Authors
- dependabot[bot] (49)
- dependabot-preview[bot] (11)
- chrishmorris (2)
- imgbot[bot] (2)
- manvikri22 (2)
- dhimmel (1)
- davmlaw (1)
- ebakke (1)
- ravwojdyla (1)
- flying-sheep (1)
- jday1 (1)
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Top Labels
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Packages
- Total packages: 2
-
Total downloads:
- pypi 45,855 last-month
- Total docker downloads: 5,930
-
Total dependent packages: 19
(may contain duplicates) -
Total dependent repositories: 93
(may contain duplicates) - Total versions: 150
- Total maintainers: 1
pypi.org: pronto
Python frontend to ontologies.
- Documentation: https://pronto.readthedocs.io/en/latest/
- 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 furnished to do so, subject to the following conditions: 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.
-
Latest release: 2.7.0
published 12 months ago
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Maintainers (1)
proxy.golang.org: github.com/althonos/pronto
- Documentation: https://pkg.go.dev/github.com/althonos/pronto#section-documentation
- License: mit
-
Latest release: v2.7.0+incompatible
published 12 months ago
Rankings
Dependencies
- actions/checkout v1 composite
- actions/setup-python v2 composite
- actions/setup-python v1 composite
- codecov/codecov-action v1 composite
- pypa/gh-action-pypi-publish master composite
- rasmus-saks/release-a-changelog-action v1.0.1 composite
- fastobo *
- ipython *
- nbsphinx *
- pygments *
- pygments-style-monokailight *
- recommonmark *
- semantic_version *
- sphinx *