gocam
gocam is a Python data model and command-line interface for working with Gene Ontology Causal
Activity Models (GO-CAMs). It provides Pydantic models for validated GO-CAM data, tools for fetching
published models, and optional translations to formats such as CX2 and gene-centered networks.
Learn more about GO-CAMs or explore published models in the GO-CAM browser.
Installation
Install gocam from PyPI:
pip install gocam
This installs both the Python package and the gocam command.
Quick start
Fetch a published model as YAML from the command line:
gocam fetch 5b91dbd100002057 > model.yaml
Fetch and translate a published model from Python:
from gocam.translation import MinervaWrapper
model = MinervaWrapper().fetch_model("5b91dbd100002057")
print(model.title)
Load and validate a local JSON model:
from pathlib import Path
from gocam.datamodel import Model
model = Model.model_validate_json(Path("model.json").read_text())
print(model.id)
See the getting-started guide for JSON output, local YAML loading, serialization, and more complete examples.
Documentation
Development
The source schema is src/gocam/schema/gocam.yaml. This repository also contains reusable Python
code and internal scripts used by the GO Release pipeline. One-off and exploratory analyses belong
in the gocam-analysis repository.
Install uv, clone the repository, and create the complete development environment:
git clone https://github.com/geneontology/gocam-py.git
cd gocam-py
uv sync --all-extras
CX2-related development requires Graphviz to be installed on the system before syncing the optional dependencies.
Run the standard project checks:
make test
make lint-python
make type-check
Regenerate schema-derived outputs when intentionally changing the schema:
make src/gocam/datamodel/gocam.py
make gen-project
make gendoc
The generated project/ directory is disposable local output. Versioned generated schema artifacts
are distributed through GitHub Releases.
2 maintainers
Metadata
2 maintainers
Release files for gocam 0.13.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| gocam-0.13.0.tar.gz | 422.5 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| gocam-0.13.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 488.8 kB
Release files / gocam-0.13.0.tar.gz
| Download URL | gocam-0.13.0.tar.gz |
|---|---|
| Size | 422.5 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
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PyPI Publish Attestation
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Signed by GitHub Actions, verified by PyPI on Oct 15, 2026.
Transparency logRelease files / gocam-0.13.0-py3-none-any.whl
| Download URL | gocam-0.13.0-py3-none-any.whl |
|---|---|
| Size | 66.3 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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|
BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 15, 2026.
Transparency log
