biosynonyms

☎️ A decentralized database of synonyms for biomedical concepts

https://github.com/biopragmatics/biosynonyms

Keywords

biology chemistry ontology

Last synced: 6 months ago · JSON representation ·

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☎️ A decentralized database of synonyms for biomedical concepts

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Host: GitHub
Owner: biopragmatics
License: cc0-1.0
Language: Jupyter Notebook
Default Branch: main
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biology chemistry ontology

Created almost 4 years ago · Last pushed 8 months ago

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Readme Contributing License Code of conduct Citation

Biosynonyms

A decentralized database of synonyms for biomedical entities and concepts. This resource is meant to be complementary to ontologies, databases, and other controlled vocabularies that provide synonyms. It's released under a permissive license (CC0), so they can be easily adopted by/contributed back to upstream resources.

Here's how to get the data:

```python import biosynonyms

Uses an internal data structure

positivesynonyms = biosynonyms.getpositivesynonyms() negativesynonyms = biosynonyms.getnegativesynonyms()

Get ready for use in NER with Gilda, only using positive synonyms

gildaterms = biosynonyms.getgilda_terms() ```

Synonyms

The data are also accessible directly through TSV such that anyone can consume them from any programming language.

The positives.tsv has the following columns:

text the synonym text itself
curie the compact uniform resource identifier (CURIE) for a biomedical entity or concept, standardized using the Bioregistry
name the standard name for the concept
predicate the predicate which encodes the synonym scope, written as a CURIE from the OBO in OWL (oboInOWL) or RDFS controlled vocabularies, e.g., one of:
- rdfs:label
- oboInOwl:hasExactSynonym
- oboInOwl:hasNarrowSynonym (i.e., the synonym represents a narrower term)
- oboInOwl:hasBroadSynonym (i.e., the synonym represents a broader term)
- oboInOwl:hasRelatedSynonym (use this if the scope is unknown)
type the (optional) synonym property type, written as a CURIE from the OBO Metadata Ontology (omo) controlled vocabulary, e.g., one of:
- OMO:0003000 (abbreviation)
- OMO:0003001 (ambiguous synonym)
- OMO:0003002 (dubious synonym)
- OMO:0003003 (layperson synonym)
- OMO:0003004 (plural form)
- ...
provenance a comma-delimited list of CURIEs corresponding to publications that use the given synonym (ideally using highly actionable identifiers from semantic spaces like pubmed, pmc, doi)
contributor a CURIE with the ORCID identifier of the contributor
date the optional date when the row was curated in YYYY-MM-DD format
language the (optional) ISO 2-letter language code. If missing, assumed to be American English.
comment an optional comment
source the source of the synonyms, usually biosynonyms unless imported from elsewhere

Here's an example of some rows in the synonyms table (with linkified CURIEs):

| text | curie | predicate | provenance | contributor | language | | --------------- | --------------------------------------------------- | --------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------- | -------- | | alsterpaullone | CHEBI:138488 | rdfs:label | pubmed:30655881 | orcid:0000-0003-4423-4370 | en | | 9-nitropaullone | CHEBI:138488 | oboInOwl:hasExactSynonym | pubmed:11597333, pubmed:10911915 | orcid:0000-0003-4423-4370 | en |

Under the hood, biosynonyms uses ssslm for the underlying data model.

Incorrect Synonyms

The negatives.tsv has the following columns for non-trivial examples of text strings that aren't synonyms. This document doesn't address the same issues as context-based disambiguation, but rather helps describe issues like incorrect sub-string matching:

text the non-synonym text itself
curie the compact uniform resource identifier (CURIE) for a biomedical entity or concept that does not match the following text, standardized using the Bioregistry
references same as for positives.tsv, illustrating documents where this string appears
contributor the ORCID identifier of the contributor
language the (optional) ISO 2-letter language code. If missing, assumed to be American English.

Here's an example of some rows in the negative synonyms table (with linkified CURIEs):

| text | curie | provenance | contributor | language | | ----------- | ----------------------------------------------- | -------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------- | -------- | | PI(3,4,5)P3 | hgnc:22979 | pubmed:29623928, pubmed:20817957 | orcid:0000-0003-4423-4370 | en |

Known Limitations

It's hard to know which exact matches between different vocabularies could be used to deduplicate synonyms. Right now, this isn't covered but some partial solutions already exist that could be adopted.

🚀 Installation

The most recent release can be installed from PyPI with:

shell pip install biosynonyms

The most recent code and data can be installed directly from GitHub with:

shell pip install git+https://github.com/biopragmatics/biosynonyms.git

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.

👋 Attribution

⚖️ License

The code in this package is licensed under the MIT License. The data is licensed under CC0.

🍪 Cookiecutter

This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.

🛠️ For Developers

See developer instructions

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: ```bash git clone git+https://github.com/biopragmatics/biosynonyms.git cd biosynonyms 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. Update with the following: ```shell pip install cruft 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 `pip install tox tox-uv`, the unit tests in the `tests/` folder can be run reproducibly with: ```shell tox -e py ``` Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/biopragmatics/biosynonyms/actions?query=workflow%3ATests). ### 📖 Building the Documentation The documentation can be built locally using the following: ```shell git clone git+https://github.com/biopragmatics/biosynonyms.git cd biosynonyms 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`](../../Desktop/biosynonyms/.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/biosynonyms 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. Create a file in your home directory called `.pypirc` and include the following: ```ini [distutils] index-servers = pypi testpypi [pypi] username = __token__ password = # This block is optional in case you want to be able to make test releases to the Test PyPI server [testpypi] repository = https://test.pypi.org/legacy/ username = __token__ password = ``` Note that since PyPI is requiring token-based authentication, we use `__token__` as the user, verbatim. If you already have a `.pypirc` file with a `[distutils]` section, just make sure that there is an `index-servers` key and that `pypi` is in its associated list. More information on configuring the `.pypirc` file can be found [here](https://packaging.python.org/en/latest/specifications/pypirc). #### Uploading to PyPI After installing the package in development mode and installing `tox` with `pip install tox tox-uv`, run the following from the shell: ```shell 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/biosynonyms/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 [`twine`](https://github.com/pypa/twine). 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/biosynonyms/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.

Owner

Name: Biopragmatics Stack
Login: biopragmatics
Kind: organization

Website: https://biopragmatics.github.io
Twitter: biopragmatics
Repositories: 9
Profile: https://github.com/biopragmatics

Software supporting biomedical semantics and pragmatics

Citation (CITATION.cff)

cff-version: 1.0.2
message: "If you use this software, please cite it as below."
title: "Biosynonyms"
authors:
  - name: "Charles Tapley Hoyt"
version: 0.4.2-dev
doi:
url: "https://github.com/biopragmatics/biosynonyms"

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pypi.org: biosynonyms

Decentralized database of biomedical synonyms

Homepage: https://github.com/biopragmatics/biosynonyms
Documentation: https://biosynonyms.readthedocs.io
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Latest release: 0.4.1
published about 1 year ago

Versions: 12
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cthoyt