OntoGPT may be installed through
pip or used directly from the GitHub repository. In the latter case, you will need to install the
poetry dependency manager and precede commands with
poetry run. See the poetry installation documentation for more details.
Additional requirements and options
OpenAI API key: necessary for using OpenAI's GPT models. This is a paid API and you will be charged based on usage. If you do not have an OpenAI account, you may sign up here.
You may also set additional API keys for optional resources:
- BioPortal account (for grounding). The BioPortal key is necessary for using ontologies from BioPortal. You may get a key by signing up for an account on their web site.
- NCBI E-utilities. The NCBI email address and API key are used for retrieving text and metadata from PubMed. You may still access these resources without identifying yourself, but you may encounter rate limiting and errors.
- HuggingFace Hub. This API key is necessary to retrieve models from the HuggingFace Hub service.
To simply start using the package in your workspace:
pip install ontogpt
Note that some features require installing additional, optional dependencies. These may be installed as:
pip install ontogpt[extra_name]
extra_name is one of the following:
docs- dependencies for building documentation
gpt4all- dependencies for running local models
huggingface- dependencies for accessing LLMs from HuggingFace Hub, remotely or locally
recipes- dependencies for recipe scraping and parsing
textract- the textract plugin
web- dependencies for the web application
For installation from the GitHub repository, particularly if you plan to contribute to feature development or other package code:
git clone https://github.com/monarch-initiative/ontogpt.git
Extras listed above may be installed as:
poetry install --extras extra_name
All commands should then be preceded by
poetry run, or simply run
poetry shell to create and enter a virtual environment for the project.
Setting API keys
One OntoGPT and all of its dependencies are installed, you will need to set your API keys using the Ontology Access Kit:
runoak set-apikey -e openai <your openai api key>
The optional keys may be set as follows:
runoak set-apikey -e bioportal <your bioportal api key>
runoak set-apikey -e ncbi-email <your email address>
runoak set-apikey -e ncbi-key <your NCBI api key>
runoak set-apikey -e hfhub-key <your HuggingFace Hub api key>
Running local models
Using local models currently depends upon using the
gpt4all package and may require additional setup steps specific to your computing environment.
See the gpt4all documentation for more details.