An introduction to computable phenotype descriptions of Hymenoptera

Workshop Schedule

• 15:30 - 15:45: Self-introductions.
• 15:45 - 16:15: Talk. Introduction to Ontologies, Phenoscript, and semantic descriptions.
• 16:15 - 16:30: Quick demonstration of the workflow using Phenoscript.
• 16:30 - 17:30: Hands-on activity. Writing your own semantic descriptions with Phenoscript.
• 17:30 - 17:45: Questions and feedback.

Getting ready for the workshop

• First, you need to install a few software and packages.

Casual users

If you want to just write phenoscripts without the ability to convert phenoscripts to hyperlinked text, then you need only to install VS Code and Phenoscript for VS Code. Detailed instructions for installing the Phenoscript extension for VS Code can be found here.

Advanced users

For more advanced users with Python experience who want to convert phenoscripts to OWL files and produce hyperlinked descriptions using Markdown, then you also need to install Python, pip, and Phenospy. Detailed instructions for installing Python, pip, and Phenospy can be found here. Advanced users may also want to personalize snippets by importing a different set of ontologies. Phenoscript already includes precooked snippets to describe insect phenotypes by default, but if you want to customize your own, you can change the YAML configuration file following the instructions indicated here.

• Then, it would be a good idea to get familiar with some concepts related to ontologies by reading this wiki page.

• Finally, you can also take a look at the Introduction to Phenoscript Language to get familiar with the Phenoscript syntax. But do not worry! We will go through this during the workshop.

During the workshop: General Workflow

• First, create a folder called workshop_ish2023 on your computer.

• Download this YAML configuration file: phs-config.yaml. Save it in the workshop_ish2023 folder.

• Open VS Code and go to "File", then "Open Folder" and select the workshop_ish2023 folder. VS Code will ask "Do you trust the authors of the files in this folder?", just click "Yes, I trust the authors".

• Open the YAML file on VS Code by clicking on "File" and then "Open File". Configure the YAML file following these instructions. You only need to do the steps from the section "Setup phs-config.yaml".

• Go to "File", then "New File" and create a new file called my_description.phs. This will be the file where you will be writing your first semantic species description!

• Then, follow the instructions presented here. Do not worry! We will go through them together!

Content

• Install Phenoscript

• Install Phenospy

• Configure snippets

• About Semantic Descriptions

• Intro to Phenoscript Language

• Quick Start

• Issues

Funding and Sponsorship

• Academy of Finland (grants: 346294 and 339576)

• International Society of Hymenopterists