phenospy 0.12

Tools for making and processing computable phenotype descriptions

Phenospy (= Phenoscript Python tools)

Phenospy is a Python package that facilitates the automatic analysis and comparison of ontology-based (= semantic) descriptions of species and phenotypes. Phenospy works with descriptions written in Phenoscript, a computer language designed for describing species (support for other semantic approaches is under development).

The Phenoscript language allows rapid coding of morphological and ecological traits using an individual-based approach (ontology's A-box). You can efficiently code Phenoscript by using the VS Code Phenoscript extension that provides syntax highlighting and snippet support. It can be installed from the Marketplace from within the VS Code. Its GitHub repository can be accessed here. Afterward, Phenospy can be used to analyze and process the semantic descriptions.

What can I do with Phenospy?

• Create snippets based on selected ontologies for writing semantic phenotypes with the VS Code Phenoscript extension.
• Convert the Phenoscript description into an OWL file.
• Convert the Phenoscript description into an annotated Natural Language description (Markdown format).
• Automatically compare species and phenotypes (under development).

Requirements

• Python >=3.0

If you are a new user with Python 2 installed, you should uninstall it and install Python 3 instead. For more information, please refer to this discussion.

Install

Phenospy can be installed directly from the PyPI repository by running the following command in your terminal (macOS) or a command prompt (Windows):

pip install phenospy

Troubleshooting

Pip is usually pre-installed with Python on macOS and Windows. However, if pip is not installed or you want to upgrade it to the latest version, you can follow these steps:

For macOS:

1. In your terminal type the following command to download the get-pip.py script:

curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py

2. Type the following command to run the get-pip.py script and install pip:

sudo python get-pip.py

3. Verify that pip is installed by typing the following command:

pip --version

For Windows:

Open a command prompt by clicking on the "Start" menu, typing "cmd" into the search box, and selecting "Command Prompt" from the search results.

1. Type the following command to install pip:

py -m ensurepip --default-pip

2. Type the following command to upgrade pip to the latest version:

py -m pip install --upgrade pip

Quick start guide

Coming soon.

Let's create snippets

Coming soon.

Let's convert Phenoscript into OWL

Coming soon.