Cell Ontology Training

A free virtual training session for the Cell Ontology. This training session is open to all, please register in advance. All skills levels are welcome, prior experience with ontologies is not necessaary.

Dates: Thursday, Sept 24, 2020 and Oct 01, 2020

Time: 8-11am PT / 11-2pm ET / 4-7pm UK

Zoom: https://zoom.us/j/95194536310
Password: Please register to obtain the password.

Note - the practical application session will be recorded.

Agenda:

1. History and Structure of the Cell Ontology (Alex Diehl)
   • Decisions that have gone into why the structure is the way it is
   • Imported ontologies, such as Uberon, GO, PRO
   • Who has been using the CL
2. Basic introduction to ontologies and ontology logic - why do we build ontologies and what we can do with them? (David Osumi-Sutherland)
   • Why we build the logic and how we do that
3. Practical application (Nicole Vasilevsky, Alex Diehl, David Osumi-Sutherland)
   • How to use GitHub to request terms
   • Browsing, searching and querying in Protege
   • Cell Ontology Practical Training materials are here

----- DAY 2 ----

1. Intro/Recap:
   • Intro to Ontologies quick recap
   • A guide to what relations to use where in the Cell Ontology
   • Intro to GitHub workflows
2. Practical application
   • Editing in Protege
   • Pull Requests
   • Cell Ontology Practical Training materials are here
3. Use cases
   • Participant use cases - how do participants want to use the CL?
   • High throughput data - what should be captured in a Cell Ontology term
   • When to add a term, when will it be accepted?

Preparation

Participants will need to have access to the following resources and tools prior to the training:

• GitHub account - register for a free GitHub account here
• Protege - Please install Protege 5.5, download it here
• Please try and install ELK 0.5 (_For a video showing how to install Elk, click here._)
  • Click here to get the latest Protege Plugin latest build (this is available on the bottom of ELK pages. This will download a zipped file.)
  • When downloaded, unzip and copy puli and elk jars (two .jar files) in the unpacked directory.
  • Paste these files in your Protege plugin directory. This is in one of two locations:
  • ~/.Protege/plugins (note this is usually hidden from finder, but you can see it in the terminal) or
  • Go to Protege in Applications (Finder), right click, 'Show package contents' -> Java -> plugins
  • Restart Protege. You should see ELK 0.5 installed in your Reasoner menu.
  • Important: it seems Elk 0.5. Does not work with all versions of Protege, in particular, 5.2 and below. These instructions were only tested with Protege 5.5!
• Optional GitHub Desktop - Please make sure you have some kind of git client installed on your Machine. If you are new to Git, please install GitHub Desktop
• Set your preferences in Protege, find your ID range here

Related Workshop: CELLS 2020 Workshop

4th International Cells in Experimental Life Science Workshop, CELLS 2020
A virtual workshop associated with ICBO 2020 and JOWO 2020
Friday, September 25, 2020, 11 am to 1:30 pm, US Eastern Time Zone

Resources

Cell Ontology

• Cell Ontology Repository
• A guide to what relations to use where in the Cell Ontology

General Resources

• How to Write a Git Commit Message
• Ontology tutorials and Resources: Includes links to ontology browsers, past tutorials and slides, links to ontology tools and relevant publications.
• Monkeying around with OWL: Musings on building and using ontologies: Blog posts by Chris Mungall.
• Managing Translational Informatics Projects (MTIP): Includes GitHub tutorials.

Slides, Chat and Recordings:

• History and Structure of the Cell Ontology (Alex Diehl)
• Basic introduction to ontologies and ontology logic (David Osumi-Sutherland)
• Chat transcript from Day 1 is here
• Chat transcript from Day 2 is here
• Day 1 Recording (Pracical application) (Nicole Vasilevsky, David Osumi-Sutherland, Alex Diehl). On Day 1 we covered:
  • create a ticket in the Cell Ontology GitHub repository
  • create a fork from GitHub
  • browsing, searching and querying the Cell Ontology
  • set up preferences in Protege. Note - you can find your ID range here
• Day 2 Recording (Nicole Vasilevsky, David Osumi-Sutherland, Alex Diehl, Nico Matentzoglu). On Day 2 we covered:
  • Version control and GitHub
  • Creating a branch on GitHub and doing a Pull Request (see video here)
  • Creating new entities and editing terms

Contact

Register here.

Slack: Join the anatomy-and-cell-ontologies workspace here.

For questions, please contact cl_edit@googlegroups.com.