<!--
<p align="center">
<img src="https://github.com/biopragmatics/pyobo/raw/main/docs/source/logo.png" height="150">
</p>
-->
<h1 align="center">
PyOBO
</h1>
<p align="center">
<a href="https://github.com/biopragmatics/pyobo/actions/workflows/tests.yml">
<img alt="Tests" src="https://github.com/biopragmatics/pyobo/actions/workflows/tests.yml/badge.svg" /></a>
<a href="https://pypi.org/project/pyobo">
<img alt="PyPI" src="https://img.shields.io/pypi/v/pyobo" /></a>
<a href="https://pypi.org/project/pyobo">
<img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/pyobo" /></a>
<a href="https://github.com/biopragmatics/pyobo/blob/main/LICENSE">
<img alt="PyPI - License" src="https://img.shields.io/pypi/l/pyobo" /></a>
<a href='https://pyobo.readthedocs.io/en/latest/?badge=latest'>
<img src='https://readthedocs.org/projects/pyobo/badge/?version=latest' alt='Documentation Status' /></a>
<a href="https://codecov.io/gh/biopragmatics/pyobo/branch/main">
<img src="https://codecov.io/gh/biopragmatics/pyobo/branch/main/graph/badge.svg" alt="Codecov status" /></a>
<a href="https://github.com/cthoyt/cookiecutter-python-package">
<img alt="Cookiecutter template from @cthoyt" src="https://img.shields.io/badge/Cookiecutter-snekpack-blue" /></a>
<a href="https://github.com/astral-sh/ruff">
<img src="https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json" alt="Ruff" style="max-width:100%;"></a>
<a href="https://github.com/biopragmatics/pyobo/blob/main/.github/CODE_OF_CONDUCT.md">
<img src="https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg" alt="Contributor Covenant"/></a>
<a href="https://doi.org/10.5281/zenodo.3381961">
<img src="https://zenodo.org/badge/DOI/10.5281/zenodo.3381961.svg" alt="DOI"></a>
</p>
Tools for biological identifiers, names, synonyms, xrefs, hierarchies,
relations, and properties through the perspective of OBO.
## Example Usage
Note! PyOBO is no-nonsense. This means that there's no repetitive prefixes in
identifiers. It also means all identifiers are strings, no exceptions.
Note! The first time you run these, they have to download and cache all
resources. We're not in the business of redistributing data, so all scripts
should be completely reproducible.
### Mapping Identifiers and CURIEs
Get mapping of ChEBI identifiers to names:
```python
import pyobo
chebi_id_to_name = pyobo.get_id_name_mapping("chebi")
assert "fluazifop-P-butyl" == chebi_id_to_name["132964"]
# or more directly
assert "fluazifop-P-butyl" == pyobo.get_name("chebi", "132964")
```
Get reverse mapping of ChEBI names to identifiers:
```python
import pyobo
chebi_name_to_id = pyobo.get_name_id_mapping("chebi")
assert "132964" == chebi_name_to_id["fluazifop-P-butyl"]
```
Maybe you live in CURIE world and just want to normalize something like
`CHEBI:132964`:
```python
import pyobo
assert "fluazifop-P-butyl" == pyobo.get_name_by_curie("CHEBI:132964")
```
Sometimes you accidentally got an old CURIE. It can be mapped to the more recent
one using alternative identifiers listed in the underlying OBO with:
```python
import pyobo
from pyobo import Reference
# Look up DNA-binding transcription factor activity (go:0003700)
# based on an old id
primary_curie = pyobo.get_primary_curie("go:0001071")
assert primary_curie == "go:0003700"
# If it's already the primary, it just gets returned
assert Reference.from_curie("go:0003700") == pyobo.get_primary_curie("go:0003700")
```
### Mapping Species
Some resources have species information for their term. Get a mapping of
WikiPathway identifiers to species (as NCBI taxonomy identifiers):
```python
import pyobo
wikipathways_id_to_species = pyobo.get_id_species_mapping("wikipathways")
# Apoptosis (Homo sapiens)
assert "9606" == wikipathways_id_to_species["WP254"]
```
Or, you don't have time for two lines:
```python
import pyobo
# Apoptosis (Homo sapiens)
taxonomy_id = pyobo.get_species("wikipathways", "WP254")
assert taxonomy_id == "9606"
```
### Grounding
Maybe you've got names/synonyms you want to try and map back to ChEBI synonyms.
Given the brand name `Fusilade II` of `CHEBI:132964`, it should be able to look
it up and its preferred label.
```python
import pyobo
reference = pyobo.ground("chebi", "Fusilade II")
assert reference.prefix == "chebi"
assert reference.identifier == "132964"
assert reference.name == "fluazifop-P-butyl"
# When failure happens...
reference = pyobo.ground("chebi", "Definitely not a real name")
assert reference is None
```
If you're not really sure which namespace a name might belong to, you can try a
few in a row (prioritize by ones that cover the appropriate entity type to avoid
false positives in case of conflicts):
```python
import pyobo
# looking for phenotypes/pathways
reference = pyobo.ground(["efo", "go"], "ERAD")
assert reference.prefix == "go"
assert reference.identifier == "0030433"
assert reference.name == "ubiquitin-dependent ERAD pathway"
```
### Cross-referencing
Get xrefs from ChEBI to PubChem:
```python
import pyobo
chebi_id_to_pubchem_compound_id = pyobo.get_filtered_xrefs("chebi", "pubchem.compound")
pubchem_compound_id = chebi_id_to_pubchem_compound_id["132964"]
assert pubchem_compound_id == "3033674"
```
If you don't have time for two lines:
```python
import pyobo
pubchem_compound_id = pyobo.get_xref("chebi", "132964", "pubchem.compound")
assert pubchem_compound_id == "3033674"
```
Get xrefs from Entrez to HGNC, but they're only available through HGNC, so you
need to flip them:
```python
import pyobo
hgnc_id_to_ncbigene_id = pyobo.get_filtered_xrefs("hgnc", "ncbigene")
ncbigene_id_to_hgnc_id = {
ncbigene_id: hgnc_id
for hgnc_id, ncbigene_id in hgnc_id_to_ncbigene_id.items()
}
mapt_hgnc = ncbigene_id_to_hgnc_id["4137"]
assert mapt_hgnc == "6893"
```
Since this is a common pattern, there's a keyword argument `flip` that does this
for you:
```python
import pyobo
ncbigene_id_to_hgnc_id = pyobo.get_filtered_xrefs("hgnc", "ncbigene", flip=True)
mapt_hgnc_id = ncbigene_id_to_hgnc_id["4137"]
assert mapt_hgnc_id == "6893"
```
If you don't have time for two lines (I admit this one is a bit confusing) and
need to flip it:
```python
import pyobo
hgnc_id = pyobo.get_xref("hgnc", "4137", "ncbigene", flip=True)
assert hgnc_id == "6893"
```
### Properties
Get properties, like SMILES. The semantics of these are defined on an OBO-OBO
basis.
```python
import pyobo
# I don't make the rules. I wouldn't have chosen this as the key for this property. It could be any string
chebi_smiles_property = "http://purl.obolibrary.org/obo/chebi/smiles"
chebi_id_to_smiles = pyobo.get_filtered_properties_mapping("chebi", chebi_smiles_property)
smiles = chebi_id_to_smiles["132964"]
assert smiles == "C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F"
```
If you don't have time for two lines:
```python
import pyobo
smiles = pyobo.get_property("chebi", "132964", "http://purl.obolibrary.org/obo/chebi/smiles")
assert smiles == "C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F"
```
### Hierarchy
Check if an entity is in the hierarchy:
```python
import pyobo
from pyobo import Reference
# check that go:0008219 ! cell death is an ancestor of go:0006915 ! apoptotic process
assert Reference.from_curie("go:0008219") in pyobo.get_ancestors("go", "0006915")
# check that go:0070246 ! natural killer cell apoptotic process is a
# descendant of go:0006915 ! apoptotic process
apopototic_process_descendants = pyobo.get_descendants("go", "0006915")
assert Reference.from_curie("go:0070246") in apopototic_process_descendants
```
Get the sub-hierarchy below a given node:
```python
import pyobo
from pyobo import Reference
# get the descendant graph of go:0006915 ! apoptotic process
apopototic_process_subhierarchy = pyobo.get_subhierarchy("go", "0006915")
# check that go:0070246 ! natural killer cell apoptotic process is a
# descendant of go:0006915 ! apoptotic process through the subhierarchy
assert Reference.from_curie("go:0070246") in apopototic_process_subhierarchy
```
Get a hierarchy with properties preloaded in the node data dictionaries:
```python
import pyobo
from pyobo import Reference
prop = "http://purl.obolibrary.org/obo/chebi/smiles"
chebi_hierarchy = pyobo.get_hierarchy("chebi", properties=[prop])
assert Reference.from_curie("chebi:132964") in chebi_hierarchy
assert prop in chebi_hierarchy.nodes["chebi:132964"]
assert chebi_hierarchy.nodes["chebi:132964"][prop] == "C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F"
```
### Relations
Get all orthologies (`ro:HOM0000017`) between HGNC and MGI (note: this is one
way)
```python
>>> import pyobo
>>> human_mapt_hgnc_id = "6893"
>>> mouse_mapt_mgi_id = "97180"
>>> hgnc_mgi_orthology_mapping = pyobo.get_relation_mapping("hgnc", "ro:HOM0000017", "mgi")
>>> assert mouse_mapt_mgi_id == hgnc_mgi_orthology_mapping[human_mapt_hgnc_id]
```
If you want to do it in one line, use:
```python
>>> import pyobo
>>> human_mapt_hgnc_id = "6893"
>>> mouse_mapt_mgi_id = "97180"
>>> assert mouse_mapt_mgi_id == pyobo.get_relation("hgnc", "ro:HOM0000017", "mgi", human_mapt_hgnc_id)
```
### Writings Tests that Use PyOBO
If you're writing your own code that relies on PyOBO, and unit testing it (as
you should) in a continuous integration setting, you've probably realized that
loading all the resources on each build is not so fast. In those scenarios, you
can use some of the pre-build patches like in the following:
```python
import unittest
import pyobo
from pyobo.mocks import get_mock_id_name_mapping
mock_id_name_mapping = get_mock_id_name_mapping({
"chebi": {
"132964": "fluazifop-P-butyl",
},
})
class MyTestCase(unittest.TestCase):
def my_test(self):
with mock_id_name_mapping:
# use functions directly, or use your functions that wrap them
pyobo.get_name("chebi", "1234")
```
## Troubleshooting
The OBO Foundry seems to be pretty unstable with respect to the URLs to OBO
resources. If you get an error like:
```
pyobo.getters.MissingOboBuild: OBO Foundry is missing a build for: mondo
```
Then you should check the corresponding page on the OBO Foundry (in this case,
http://www.obofoundry.org/ontology/mondo.html) and make update to the `url`
entry for that namespace in the Bioregistry.
## 🚀 Installation
The most recent release can be installed from
[PyPI](https://pypi.org/project/pyobo/) with uv:
```console
$ uv pip install pyobo
```
or with pip:
```console
$ python3 -m pip install pyobo
```
The most recent code and data can be installed directly from GitHub with uv:
```console
$ uv pip install git+https://github.com/biopragmatics/pyobo.git
```
or with pip:
```console
$ python3 -m pip install git+https://github.com/biopragmatics/pyobo.git
```
## 👐 Contributing
Contributions, whether filing an issue, making a pull request, or forking, are
appreciated. See
[CONTRIBUTING.md](https://github.com/biopragmatics/pyobo/blob/master/.github/CONTRIBUTING.md)
for more information on getting involved.
## 👋 Attribution
### ⚖️ License
The code in this package is licensed under the MIT License.
<!--
### 📖 Citation
Citation goes here!
-->
<!--
### 🎁 Support
This project has been supported by the following organizations (in alphabetical order):
- [Biopragmatics Lab](https://biopragmatics.github.io)
-->
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### 💰 Funding
This project has been supported by the following grants:
| Funding Body | Program | Grant Number |
|---------------|--------------------------------------------------------------|--------------|
| Funder | [Grant Name (GRANT-ACRONYM)](https://example.com/grant-link) | ABCXYZ |
-->
### 🍪 Cookiecutter
This package was created with
[@audreyfeldroy](https://github.com/audreyfeldroy)'s
[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using
[@cthoyt](https://github.com/cthoyt)'s
[cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack)
template.
## 🛠️ For Developers
<details>
<summary>See developer instructions</summary>
The final section of the README is for if you want to get involved by making a
code contribution.
### Development Installation
To install in development mode, use the following:
```console
$ git clone git+https://github.com/biopragmatics/pyobo.git
$ cd pyobo
$ uv pip install -e .
```
Alternatively, install using pip:
```console
$ python3 -m pip install -e .
```
### Updating Package Boilerplate
This project uses `cruft` to keep boilerplate (i.e., configuration, contribution
guidelines, documentation configuration) up-to-date with the upstream
cookiecutter package. Install cruft with either `uv tool install cruft` or
`python3 -m pip install cruft` then run:
```console
$ cruft update
```
More info on Cruft's update command is available
[here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).
### 🥼 Testing
After cloning the repository and installing `tox` with
`uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, the
unit tests in the `tests/` folder can be run reproducibly with:
```console
$ tox -e py
```
Additionally, these tests are automatically re-run with each commit in a
[GitHub Action](https://github.com/biopragmatics/pyobo/actions?query=workflow%3ATests).
### 📖 Building the Documentation
The documentation can be built locally using the following:
```console
$ git clone git+https://github.com/biopragmatics/pyobo.git
$ cd pyobo
$ tox -e docs
$ open docs/build/html/index.html
```
The documentation automatically installs the package as well as the `docs` extra
specified in the [`pyproject.toml`](pyproject.toml). `sphinx` plugins like
`texext` can be added there. Additionally, they need to be added to the
`extensions` list in [`docs/source/conf.py`](docs/source/conf.py).
The documentation can be deployed to [ReadTheDocs](https://readthedocs.io) using
[this guide](https://docs.readthedocs.io/en/stable/intro/import-guide.html). The
[`.readthedocs.yml`](.readthedocs.yml) YAML file contains all the configuration
you'll need. You can also set up continuous integration on GitHub to check not
only that Sphinx can build the documentation in an isolated environment (i.e.,
with `tox -e docs-test`) but also that
[ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html).
#### Configuring ReadTheDocs
1. Log in to ReadTheDocs with your GitHub account to install the integration at
https://readthedocs.org/accounts/login/?next=/dashboard/
2. Import your project by navigating to https://readthedocs.org/dashboard/import
then clicking the plus icon next to your repository
3. You can rename the repository on the next screen using a more stylized name
(i.e., with spaces and capital letters)
4. Click next, and you're good to go!
### 📦 Making a Release
#### Configuring Zenodo
[Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI
to each release of your package.
1. Log in to Zenodo via GitHub with this link:
https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a page
that lists all of your organizations and asks you to approve installing the
Zenodo app on GitHub. Click "grant" next to any organizations you want to
enable the integration for, then click the big green "approve" button. This
step only needs to be done once.
2. Navigate to https://zenodo.org/account/settings/github/, which lists all of
your GitHub repositories (both in your username and any organizations you
enabled). Click the on/off toggle for any relevant repositories. When you
make a new repository, you'll have to come back to this
After these steps, you're ready to go! After you make "release" on GitHub (steps
for this are below), you can navigate to
https://zenodo.org/account/settings/github/repository/biopragmatics/pyobo to see
the DOI for the release and link to the Zenodo record for it.
#### Registering with the Python Package Index (PyPI)
You only have to do the following steps once.
1. Register for an account on the
[Python Package Index (PyPI)](https://pypi.org/account/register)
2. Navigate to https://pypi.org/manage/account and make sure you have verified
your email address. A verification email might not have been sent by default,
so you might have to click the "options" dropdown next to your address to get
to the "re-send verification email" button
3. 2-Factor authentication is required for PyPI since the end of 2023 (see this
[blog post from PyPI](https://blog.pypi.org/posts/2023-05-25-securing-pypi-with-2fa/)).
This means you have to first issue account recovery codes, then set up
2-factor authentication
4. Issue an API token from https://pypi.org/manage/account/token
#### Configuring your machine's connection to PyPI
You have to do the following steps once per machine.
```console
$ uv tool install keyring
$ keyring set https://upload.pypi.org/legacy/ __token__
$ keyring set https://test.pypi.org/legacy/ __token__
```
Note that this deprecates previous workflows using `.pypirc`.
#### Uploading to PyPI
After installing the package in development mode and installing `tox` with
`uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, run
the following from the console:
```console
$ tox -e finish
```
This script does the following:
1. Uses [bump-my-version](https://github.com/callowayproject/bump-my-version) to
switch the version number in the `pyproject.toml`, `CITATION.cff`,
`src/pyobo/version.py`, and [`docs/source/conf.py`](docs/source/conf.py) to
not have the `-dev` suffix
2. Packages the code in both a tar archive and a wheel using
[`uv build`](https://docs.astral.sh/uv/guides/publish/#building-your-package)
3. Uploads to PyPI using
[`uv publish`](https://docs.astral.sh/uv/guides/publish/#publishing-your-package).
4. Push to GitHub. You'll need to make a release going with the commit where the
version was bumped.
5. Bump the version to the next patch. If you made big changes and want to bump
the version by minor, you can use `tox -e bumpversion -- minor` after.
#### Releasing on GitHub
1. Navigate to https://github.com/biopragmatics/pyobo/releases/new to draft a
new release
2. Click the "Choose a Tag" dropdown and select the tag corresponding to the
release you just made
3. Click the "Generate Release Notes" button to get a quick outline of recent
changes. Modify the title and description as you see fit
4. Click the big green "Publish Release" button
This will trigger Zenodo to assign a DOI to your release as well.
</details>
Raw data
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"maintainer_email": "Charles Tapley Hoyt <cthoyt@gmail.com>",
"keywords": "snekpack, cookiecutter, ontologies, biomedical ontologies, life sciences, natural sciences, bioinformatics, cheminformatics, Open Biomedical Ontologies, OBO",
"author": "Charles Tapley Hoyt",
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"description": "<!--\n<p align=\"center\">\n <img src=\"https://github.com/biopragmatics/pyobo/raw/main/docs/source/logo.png\" height=\"150\">\n</p>\n-->\n\n<h1 align=\"center\">\n PyOBO\n</h1>\n\n<p align=\"center\">\n <a href=\"https://github.com/biopragmatics/pyobo/actions/workflows/tests.yml\">\n <img alt=\"Tests\" src=\"https://github.com/biopragmatics/pyobo/actions/workflows/tests.yml/badge.svg\" /></a>\n <a href=\"https://pypi.org/project/pyobo\">\n <img alt=\"PyPI\" src=\"https://img.shields.io/pypi/v/pyobo\" /></a>\n <a href=\"https://pypi.org/project/pyobo\">\n <img alt=\"PyPI - Python Version\" src=\"https://img.shields.io/pypi/pyversions/pyobo\" /></a>\n <a href=\"https://github.com/biopragmatics/pyobo/blob/main/LICENSE\">\n <img alt=\"PyPI - License\" src=\"https://img.shields.io/pypi/l/pyobo\" /></a>\n <a href='https://pyobo.readthedocs.io/en/latest/?badge=latest'>\n <img src='https://readthedocs.org/projects/pyobo/badge/?version=latest' alt='Documentation Status' /></a>\n <a href=\"https://codecov.io/gh/biopragmatics/pyobo/branch/main\">\n <img src=\"https://codecov.io/gh/biopragmatics/pyobo/branch/main/graph/badge.svg\" alt=\"Codecov status\" /></a> \n <a href=\"https://github.com/cthoyt/cookiecutter-python-package\">\n <img alt=\"Cookiecutter template from @cthoyt\" src=\"https://img.shields.io/badge/Cookiecutter-snekpack-blue\" /></a>\n <a href=\"https://github.com/astral-sh/ruff\">\n <img src=\"https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json\" alt=\"Ruff\" style=\"max-width:100%;\"></a>\n <a href=\"https://github.com/biopragmatics/pyobo/blob/main/.github/CODE_OF_CONDUCT.md\">\n <img src=\"https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg\" alt=\"Contributor Covenant\"/></a>\n <a href=\"https://doi.org/10.5281/zenodo.3381961\">\n <img src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.3381961.svg\" alt=\"DOI\"></a>\n</p>\n\nTools for biological identifiers, names, synonyms, xrefs, hierarchies,\nrelations, and properties through the perspective of OBO.\n\n## Example Usage\n\nNote! PyOBO is no-nonsense. This means that there's no repetitive prefixes in\nidentifiers. It also means all identifiers are strings, no exceptions.\n\nNote! The first time you run these, they have to download and cache all\nresources. We're not in the business of redistributing data, so all scripts\nshould be completely reproducible.\n\n### Mapping Identifiers and CURIEs\n\nGet mapping of ChEBI identifiers to names:\n\n```python\nimport pyobo\n\nchebi_id_to_name = pyobo.get_id_name_mapping(\"chebi\")\nassert \"fluazifop-P-butyl\" == chebi_id_to_name[\"132964\"]\n\n# or more directly\nassert \"fluazifop-P-butyl\" == pyobo.get_name(\"chebi\", \"132964\")\n```\n\nGet reverse mapping of ChEBI names to identifiers:\n\n```python\nimport pyobo\n\nchebi_name_to_id = pyobo.get_name_id_mapping(\"chebi\")\nassert \"132964\" == chebi_name_to_id[\"fluazifop-P-butyl\"]\n```\n\nMaybe you live in CURIE world and just want to normalize something like\n`CHEBI:132964`:\n\n```python\nimport pyobo\n\nassert \"fluazifop-P-butyl\" == pyobo.get_name_by_curie(\"CHEBI:132964\")\n```\n\nSometimes you accidentally got an old CURIE. It can be mapped to the more recent\none using alternative identifiers listed in the underlying OBO with:\n\n```python\nimport pyobo\nfrom pyobo import Reference\n\n# Look up DNA-binding transcription factor activity (go:0003700)\n# based on an old id\nprimary_curie = pyobo.get_primary_curie(\"go:0001071\")\nassert primary_curie == \"go:0003700\"\n\n# If it's already the primary, it just gets returned\nassert Reference.from_curie(\"go:0003700\") == pyobo.get_primary_curie(\"go:0003700\")\n```\n\n### Mapping Species\n\nSome resources have species information for their term. Get a mapping of\nWikiPathway identifiers to species (as NCBI taxonomy identifiers):\n\n```python\nimport pyobo\n\nwikipathways_id_to_species = pyobo.get_id_species_mapping(\"wikipathways\")\n\n# Apoptosis (Homo sapiens)\nassert \"9606\" == wikipathways_id_to_species[\"WP254\"]\n```\n\nOr, you don't have time for two lines:\n\n```python\nimport pyobo\n\n# Apoptosis (Homo sapiens)\ntaxonomy_id = pyobo.get_species(\"wikipathways\", \"WP254\")\nassert taxonomy_id == \"9606\"\n```\n\n### Grounding\n\nMaybe you've got names/synonyms you want to try and map back to ChEBI synonyms.\nGiven the brand name `Fusilade II` of `CHEBI:132964`, it should be able to look\nit up and its preferred label.\n\n```python\nimport pyobo\n\nreference = pyobo.ground(\"chebi\", \"Fusilade II\")\nassert reference.prefix == \"chebi\"\nassert reference.identifier == \"132964\"\nassert reference.name == \"fluazifop-P-butyl\"\n\n# When failure happens...\nreference = pyobo.ground(\"chebi\", \"Definitely not a real name\")\nassert reference is None\n```\n\nIf you're not really sure which namespace a name might belong to, you can try a\nfew in a row (prioritize by ones that cover the appropriate entity type to avoid\nfalse positives in case of conflicts):\n\n```python\nimport pyobo\n\n# looking for phenotypes/pathways\nreference = pyobo.ground([\"efo\", \"go\"], \"ERAD\")\nassert reference.prefix == \"go\"\nassert reference.identifier == \"0030433\"\nassert reference.name == \"ubiquitin-dependent ERAD pathway\"\n```\n\n### Cross-referencing\n\nGet xrefs from ChEBI to PubChem:\n\n```python\nimport pyobo\n\nchebi_id_to_pubchem_compound_id = pyobo.get_filtered_xrefs(\"chebi\", \"pubchem.compound\")\n\npubchem_compound_id = chebi_id_to_pubchem_compound_id[\"132964\"]\nassert pubchem_compound_id == \"3033674\"\n```\n\nIf you don't have time for two lines:\n\n```python\nimport pyobo\n\npubchem_compound_id = pyobo.get_xref(\"chebi\", \"132964\", \"pubchem.compound\")\nassert pubchem_compound_id == \"3033674\"\n```\n\nGet xrefs from Entrez to HGNC, but they're only available through HGNC, so you\nneed to flip them:\n\n```python\nimport pyobo\n\nhgnc_id_to_ncbigene_id = pyobo.get_filtered_xrefs(\"hgnc\", \"ncbigene\")\nncbigene_id_to_hgnc_id = {\n ncbigene_id: hgnc_id\n for hgnc_id, ncbigene_id in hgnc_id_to_ncbigene_id.items()\n}\nmapt_hgnc = ncbigene_id_to_hgnc_id[\"4137\"]\nassert mapt_hgnc == \"6893\"\n```\n\nSince this is a common pattern, there's a keyword argument `flip` that does this\nfor you:\n\n```python\nimport pyobo\n\nncbigene_id_to_hgnc_id = pyobo.get_filtered_xrefs(\"hgnc\", \"ncbigene\", flip=True)\nmapt_hgnc_id = ncbigene_id_to_hgnc_id[\"4137\"]\nassert mapt_hgnc_id == \"6893\"\n```\n\nIf you don't have time for two lines (I admit this one is a bit confusing) and\nneed to flip it:\n\n```python\nimport pyobo\n\nhgnc_id = pyobo.get_xref(\"hgnc\", \"4137\", \"ncbigene\", flip=True)\nassert hgnc_id == \"6893\"\n```\n\n### Properties\n\nGet properties, like SMILES. The semantics of these are defined on an OBO-OBO\nbasis.\n\n```python\nimport pyobo\n\n# I don't make the rules. I wouldn't have chosen this as the key for this property. It could be any string\nchebi_smiles_property = \"http://purl.obolibrary.org/obo/chebi/smiles\"\nchebi_id_to_smiles = pyobo.get_filtered_properties_mapping(\"chebi\", chebi_smiles_property)\n\nsmiles = chebi_id_to_smiles[\"132964\"]\nassert smiles == \"C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F\"\n```\n\nIf you don't have time for two lines:\n\n```python\nimport pyobo\n\nsmiles = pyobo.get_property(\"chebi\", \"132964\", \"http://purl.obolibrary.org/obo/chebi/smiles\")\nassert smiles == \"C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F\"\n```\n\n### Hierarchy\n\nCheck if an entity is in the hierarchy:\n\n```python\nimport pyobo\nfrom pyobo import Reference\n\n# check that go:0008219 ! cell death is an ancestor of go:0006915 ! apoptotic process\nassert Reference.from_curie(\"go:0008219\") in pyobo.get_ancestors(\"go\", \"0006915\")\n\n# check that go:0070246 ! natural killer cell apoptotic process is a\n# descendant of go:0006915 ! apoptotic process\napopototic_process_descendants = pyobo.get_descendants(\"go\", \"0006915\")\nassert Reference.from_curie(\"go:0070246\") in apopototic_process_descendants\n```\n\nGet the sub-hierarchy below a given node:\n\n```python\nimport pyobo\nfrom pyobo import Reference\n\n# get the descendant graph of go:0006915 ! apoptotic process\napopototic_process_subhierarchy = pyobo.get_subhierarchy(\"go\", \"0006915\")\n\n# check that go:0070246 ! natural killer cell apoptotic process is a\n# descendant of go:0006915 ! apoptotic process through the subhierarchy\nassert Reference.from_curie(\"go:0070246\") in apopototic_process_subhierarchy\n```\n\nGet a hierarchy with properties preloaded in the node data dictionaries:\n\n```python\nimport pyobo\nfrom pyobo import Reference\n\nprop = \"http://purl.obolibrary.org/obo/chebi/smiles\"\nchebi_hierarchy = pyobo.get_hierarchy(\"chebi\", properties=[prop])\n\nassert Reference.from_curie(\"chebi:132964\") in chebi_hierarchy\nassert prop in chebi_hierarchy.nodes[\"chebi:132964\"]\nassert chebi_hierarchy.nodes[\"chebi:132964\"][prop] == \"C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F\"\n```\n\n### Relations\n\nGet all orthologies (`ro:HOM0000017`) between HGNC and MGI (note: this is one\nway)\n\n```python\n>>> import pyobo\n>>> human_mapt_hgnc_id = \"6893\"\n>>> mouse_mapt_mgi_id = \"97180\"\n>>> hgnc_mgi_orthology_mapping = pyobo.get_relation_mapping(\"hgnc\", \"ro:HOM0000017\", \"mgi\")\n>>> assert mouse_mapt_mgi_id == hgnc_mgi_orthology_mapping[human_mapt_hgnc_id]\n```\n\nIf you want to do it in one line, use:\n\n```python\n\n>>> import pyobo\n>>> human_mapt_hgnc_id = \"6893\"\n>>> mouse_mapt_mgi_id = \"97180\"\n>>> assert mouse_mapt_mgi_id == pyobo.get_relation(\"hgnc\", \"ro:HOM0000017\", \"mgi\", human_mapt_hgnc_id)\n```\n\n### Writings Tests that Use PyOBO\n\nIf you're writing your own code that relies on PyOBO, and unit testing it (as\nyou should) in a continuous integration setting, you've probably realized that\nloading all the resources on each build is not so fast. In those scenarios, you\ncan use some of the pre-build patches like in the following:\n\n```python\nimport unittest\nimport pyobo\nfrom pyobo.mocks import get_mock_id_name_mapping\n\nmock_id_name_mapping = get_mock_id_name_mapping({\n \"chebi\": {\n \"132964\": \"fluazifop-P-butyl\",\n },\n})\n\nclass MyTestCase(unittest.TestCase):\n def my_test(self):\n with mock_id_name_mapping:\n # use functions directly, or use your functions that wrap them\n pyobo.get_name(\"chebi\", \"1234\")\n```\n\n## Troubleshooting\n\nThe OBO Foundry seems to be pretty unstable with respect to the URLs to OBO\nresources. If you get an error like:\n\n```\npyobo.getters.MissingOboBuild: OBO Foundry is missing a build for: mondo\n```\n\nThen you should check the corresponding page on the OBO Foundry (in this case,\nhttp://www.obofoundry.org/ontology/mondo.html) and make update to the `url`\nentry for that namespace in the Bioregistry.\n\n## \ud83d\ude80 Installation\n\nThe most recent release can be installed from\n[PyPI](https://pypi.org/project/pyobo/) with uv:\n\n```console\n$ uv pip install pyobo\n```\n\nor with pip:\n\n```console\n$ python3 -m pip install pyobo\n```\n\nThe most recent code and data can be installed directly from GitHub with uv:\n\n```console\n$ uv pip install git+https://github.com/biopragmatics/pyobo.git\n```\n\nor with pip:\n\n```console\n$ python3 -m pip install git+https://github.com/biopragmatics/pyobo.git\n```\n\n## \ud83d\udc50 Contributing\n\nContributions, whether filing an issue, making a pull request, or forking, are\nappreciated. See\n[CONTRIBUTING.md](https://github.com/biopragmatics/pyobo/blob/master/.github/CONTRIBUTING.md)\nfor more information on getting involved.\n\n## \ud83d\udc4b Attribution\n\n### \u2696\ufe0f License\n\nThe code in this package is licensed under the MIT License.\n\n<!--\n### \ud83d\udcd6 Citation\n\nCitation goes here!\n-->\n\n<!--\n### \ud83c\udf81 Support\n\nThis project has been supported by the following organizations (in alphabetical order):\n\n- [Biopragmatics Lab](https://biopragmatics.github.io)\n\n-->\n\n<!--\n### \ud83d\udcb0 Funding\n\nThis project has been supported by the following grants:\n\n| Funding Body | Program | Grant Number |\n|---------------|--------------------------------------------------------------|--------------|\n| Funder | [Grant Name (GRANT-ACRONYM)](https://example.com/grant-link) | ABCXYZ |\n-->\n\n### \ud83c\udf6a Cookiecutter\n\nThis package was created with\n[@audreyfeldroy](https://github.com/audreyfeldroy)'s\n[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using\n[@cthoyt](https://github.com/cthoyt)'s\n[cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack)\ntemplate.\n\n## \ud83d\udee0\ufe0f For Developers\n\n<details>\n <summary>See developer instructions</summary>\n\nThe final section of the README is for if you want to get involved by making a\ncode contribution.\n\n### Development Installation\n\nTo install in development mode, use the following:\n\n```console\n$ git clone git+https://github.com/biopragmatics/pyobo.git\n$ cd pyobo\n$ uv pip install -e .\n```\n\nAlternatively, install using pip:\n\n```console\n$ python3 -m pip install -e .\n```\n\n### Updating Package Boilerplate\n\nThis project uses `cruft` to keep boilerplate (i.e., configuration, contribution\nguidelines, documentation configuration) up-to-date with the upstream\ncookiecutter package. Install cruft with either `uv tool install cruft` or\n`python3 -m pip install cruft` then run:\n\n```console\n$ cruft update\n```\n\nMore info on Cruft's update command is available\n[here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).\n\n### \ud83e\udd7c Testing\n\nAfter cloning the repository and installing `tox` with\n`uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, the\nunit tests in the `tests/` folder can be run reproducibly with:\n\n```console\n$ tox -e py\n```\n\nAdditionally, these tests are automatically re-run with each commit in a\n[GitHub Action](https://github.com/biopragmatics/pyobo/actions?query=workflow%3ATests).\n\n### \ud83d\udcd6 Building the Documentation\n\nThe documentation can be built locally using the following:\n\n```console\n$ git clone git+https://github.com/biopragmatics/pyobo.git\n$ cd pyobo\n$ tox -e docs\n$ open docs/build/html/index.html\n```\n\nThe documentation automatically installs the package as well as the `docs` extra\nspecified in the [`pyproject.toml`](pyproject.toml). `sphinx` plugins like\n`texext` can be added there. Additionally, they need to be added to the\n`extensions` list in [`docs/source/conf.py`](docs/source/conf.py).\n\nThe documentation can be deployed to [ReadTheDocs](https://readthedocs.io) using\n[this guide](https://docs.readthedocs.io/en/stable/intro/import-guide.html). The\n[`.readthedocs.yml`](.readthedocs.yml) YAML file contains all the configuration\nyou'll need. You can also set up continuous integration on GitHub to check not\nonly that Sphinx can build the documentation in an isolated environment (i.e.,\nwith `tox -e docs-test`) but also that\n[ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html).\n\n#### Configuring ReadTheDocs\n\n1. Log in to ReadTheDocs with your GitHub account to install the integration at\n https://readthedocs.org/accounts/login/?next=/dashboard/\n2. Import your project by navigating to https://readthedocs.org/dashboard/import\n then clicking the plus icon next to your repository\n3. You can rename the repository on the next screen using a more stylized name\n (i.e., with spaces and capital letters)\n4. Click next, and you're good to go!\n\n### \ud83d\udce6 Making a Release\n\n#### Configuring Zenodo\n\n[Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI\nto each release of your package.\n\n1. Log in to Zenodo via GitHub with this link:\n https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a page\n that lists all of your organizations and asks you to approve installing the\n Zenodo app on GitHub. Click \"grant\" next to any organizations you want to\n enable the integration for, then click the big green \"approve\" button. This\n step only needs to be done once.\n2. Navigate to https://zenodo.org/account/settings/github/, which lists all of\n your GitHub repositories (both in your username and any organizations you\n enabled). Click the on/off toggle for any relevant repositories. When you\n make a new repository, you'll have to come back to this\n\nAfter these steps, you're ready to go! After you make \"release\" on GitHub (steps\nfor this are below), you can navigate to\nhttps://zenodo.org/account/settings/github/repository/biopragmatics/pyobo to see\nthe DOI for the release and link to the Zenodo record for it.\n\n#### Registering with the Python Package Index (PyPI)\n\nYou only have to do the following steps once.\n\n1. Register for an account on the\n [Python Package Index (PyPI)](https://pypi.org/account/register)\n2. Navigate to https://pypi.org/manage/account and make sure you have verified\n your email address. A verification email might not have been sent by default,\n so you might have to click the \"options\" dropdown next to your address to get\n to the \"re-send verification email\" button\n3. 2-Factor authentication is required for PyPI since the end of 2023 (see this\n [blog post from PyPI](https://blog.pypi.org/posts/2023-05-25-securing-pypi-with-2fa/)).\n This means you have to first issue account recovery codes, then set up\n 2-factor authentication\n4. Issue an API token from https://pypi.org/manage/account/token\n\n#### Configuring your machine's connection to PyPI\n\nYou have to do the following steps once per machine.\n\n```console\n$ uv tool install keyring\n$ keyring set https://upload.pypi.org/legacy/ __token__\n$ keyring set https://test.pypi.org/legacy/ __token__\n```\n\nNote that this deprecates previous workflows using `.pypirc`.\n\n#### Uploading to PyPI\n\nAfter installing the package in development mode and installing `tox` with\n`uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, run\nthe following from the console:\n\n```console\n$ tox -e finish\n```\n\nThis script does the following:\n\n1. Uses [bump-my-version](https://github.com/callowayproject/bump-my-version) to\n switch the version number in the `pyproject.toml`, `CITATION.cff`,\n `src/pyobo/version.py`, and [`docs/source/conf.py`](docs/source/conf.py) to\n not have the `-dev` suffix\n2. Packages the code in both a tar archive and a wheel using\n [`uv build`](https://docs.astral.sh/uv/guides/publish/#building-your-package)\n3. Uploads to PyPI using\n [`uv publish`](https://docs.astral.sh/uv/guides/publish/#publishing-your-package).\n4. Push to GitHub. You'll need to make a release going with the commit where the\n version was bumped.\n5. Bump the version to the next patch. If you made big changes and want to bump\n the version by minor, you can use `tox -e bumpversion -- minor` after.\n\n#### Releasing on GitHub\n\n1. Navigate to https://github.com/biopragmatics/pyobo/releases/new to draft a\n new release\n2. Click the \"Choose a Tag\" dropdown and select the tag corresponding to the\n release you just made\n3. Click the \"Generate Release Notes\" button to get a quick outline of recent\n changes. Modify the title and description as you see fit\n4. Click the big green \"Publish Release\" button\n\nThis will trigger Zenodo to assign a DOI to your release as well.\n\n</details>\n",
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