Simple Standard for Sharing Literal Mappings

A simple standard for sharing literal mappings (SSSLM).

This repository implements a data model for literal mappings that supports encoding labels, synonyms, synonym types, internationalization, and other important information for curation, construction of lexica, and population of NER/NEN tools.

SSSLM echos the name of SSSOM, which is a related standard for ontological mappings. SSSLM can be pronounced S-S-S-L-M, sess-lem, or however brings joy to you.

💪 Getting Started

import ssslm
from ssslm import LiteralMapping
from curies import NamedReference

# Construct a mapping using Pydantic objects
m1 = LiteralMapping(
   reference=NamedReference(prefix="NCBITaxon", identifier="9606", name="Homo sapiens"),
   text="human",
)

# get a pandas dataframe
df = ssslm.literal_mappings_to_df([m1])

# Write mappings to TSV
ssslm.write_literal_mappings([m1], "literal_mappings.tsv")

# Read mappings from TSV
mappings = ssslm.read_literal_mappings("literal_mappings.tsv")

Note that references are standardized using the curies package. It's up to you to use a meaningful set of prefixes, so consider adopting the Bioregistry as a standard.

Data Model

The SSSLM data model is defined using Pydantic, and corresponds to the following columns in a TSV file:

1. text the label/synonym text itself
2. curie the compact uniform resource identifier (CURIE) for a biomedical entity or concept
3. name the standard name for the concept
4. 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)
5. 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)
   • ...
6. 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)
7. contributor a CURIE with the ORCID identifier of the contributor
8. date the optional date when the row was curated in YYYY-MM-DD format
9. language the (optional) ISO 2-letter language code. If missing, assumed to be American English.
10. comment an optional comment
11. source the source of the synonyms, usually biosynonyms unless imported from elsewhere
12. taxon the optional NCBITaxon CURIE, if the term is taxon-specific, like NCBITaxon:9606 for humans

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

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.
• This doesn't keep track of NER annotations, such as when you want to keep track of the start and end position in a full sentence or paragraph
• This doesn't keep track of transformations done to make mappings. It's more oriented towards curation.

🚀 Installation

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

$ uv pip install git+https://github.com/cthoyt/ssslm.git

or with pip:

$ python3 -m pip install git+https://github.com/cthoyt/ssslm.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.

🍪 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:

$ git clone git+https://github.com/cthoyt/ssslm.git
$ cd ssslm
$ uv pip install -e .

Alternatively, install using pip:

$ python3 -m pip install -e .

🥼 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:

$ tox -e py

Additionally, these tests are automatically re-run with each commit in a GitHub Action.

📖 Building the Documentation

The documentation can be built locally using the following:

$ git clone git+https://github.com/cthoyt/ssslm.git
$ cd ssslm
$ 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. sphinx plugins like texext can be added there. Additionally, they need to be added to the extensions list in docs/source/conf.py.

The documentation can be deployed to ReadTheDocs using this guide. The .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.

🧑‍💻 For Maintainers

See maintainer instructions

Initial Configuration

Configuring ReadTheDocs

ReadTheDocs is an external documentation hosting service that integrates with GitHub's CI/CD. Do the following for each repository:

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!

Configuring Archival on Zenodo

Zenodo is a long-term archival system that assigns a DOI to each release of your package. Do the following for each repository:

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/cthoyt/ssslm to see the DOI for the release and link to the Zenodo record for it.

Registering with the Python Package Index (PyPI)

The Python Package Index (PyPI) hosts packages so they can be easily installed with pip, uv, and equivalent tools.

1. Register for an account here
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). 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

This only needs to be done once per developer.

Configuring your machine's connection to PyPI

This needs to be done once per machine.

$ 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.

📦 Making a Release

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:

$ tox -e finish

This script does the following:

1. Uses bump-my-version to switch the version number in the pyproject.toml, CITATION.cff, src/ssslm/version.py, and 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
3. Uploads to PyPI using uv publish.
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/cthoyt/ssslm/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.

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:

$ cruft update

More info on Cruft's update command is available here.