EDAM ontology

[matuskalas]

Project Lead: @matuskalas

Mentor: @bgruening

Welcome to OLS-1! This issue will be used to track your project and progress during the program. Please use this checklist over the next few weeks as you start Open Life Science program :tada:.

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Before Week 1 (Jan 20): Meet your mentor!

• [x] Create an account on GitHub

• [x] Complete your own copy of the open leadership self-assessment and share it to your mentor

  If you're a group, each teammate should complete this assessment individually. This is here to help you set your own personal goals during the program. No need to share your results, but be ready to share your thoughts with your mentor.

• [x] Make sure you know when and how you'll be meeting with your mentor.

Before Week 2 (Jan 27): Cohort Call (Welcome to Open Life Science!)

• [x] Create an issue on the OLS-1 GitHub repository for your OLS work and share the link to your mentor.

• [x] Draft a brief vision statement using your goals

  This lesson from the Open Leadership Training Series (OLTS) might be helpful

• [x] Leave a comment on this issue with your draft vision statement & be ready to share this on the call

• [x] Check the Syllabus for notes and connection info for all the cohort calls.

Before Week 3 (Feb 3): Meet your mentor!

• [ ] Look up two other projects and comment on their issues with feedback on their vision statement
• [ ] Complete this compare and contrast assignment about current and desired community interactions and value exchanges
• [ ] Complete your Open Canvas (instructions, canvas)
• [ ] Share a link to your Open Canvas in your GitHub issue
• [ ] Start your Roadmap
• [ ] Comment on your issue with your draft Roadmap
• [x] Suggest a cohort name at the bottom of the shared notes and vote on your favorite with a +1

Before Week 4 (Feb 10): Cohort Call (Tooling and roadmapping for Open projects)

• [ ] Look up two other projects and comment on their issues with feedback on their open canvas.

Week 5 and more

• [x] Create a GitHub repository for your project
• [ ] Add the link to your repository in your issue
• [ ] Use your canvas to start writing a README.md file, or landing page, for your project
• [ ] Link to your README in a comment on this issue
• [x] Add an open license to your repository as a file called LICENSE.md
• [ ] Add a Code of Conduct to your repository as a file called CODE_OF_CONDUCT.md
• [ ] Invite new contributors to into your work!

This issue is here to help you keep track of work as you start Open Life Science program. Please refer to the OLS-1 Syllabus for more detailed weekly notes and assignments past week 4.

[matuskalas]

Draft vision statement

Short version:

I'm working with experts in analysing scientific data, to create domain ontologies, so that researchers can find suitable software tools, services, training materials, terminology, etc.

Longer version:

I'm working with experts in analysing scientific data, to create domain ontologies, so that e-infrastructure developers can implement categorisation of resources of their concern using a controlled taxonomy, and researchers can then find suitable software tools, services, training materials, terminology, etc.

In order for a domain ontology to capture the concepts and needs of a scientific domain in a representative, consensed way, a broad active participation of the scientific community is a necessity, as well as openness to contribution. Only openness can enable the participation necessary to achieve representative consensus using realistic resources.

[cassgvp]

Your project sounds so cool (I love finding tools!), but I'm not sure I understand what it means? Software tools suitable for what? What is a "domain ontology"? What's e-infrastucture?

[billbrod]

I have a similar response, I think. I agree this sounds great, and am also confused.

To me, "domain ontology" sounds like you're going to put together an ontology of different scientific concepts (like Cognitive atlas, so "feature search is a type of visual search is a type of search) and then relate those to tools? Something along the lines of, "Tools related to visual search: PsychToolbox, PsychoPy, etc"

Is that correct? Or is the ontology an ontology of tools and services? So "data management is a type of "research management*, and related tools are: DataLad, git annex, etc"

And is your target all of science or are you starting with one research community in mind? This also sounds like the kind of work that research librarians, the people who run High-Performance Compute clusters at universities, and similar folks would be really interested in, if you're not already talking to them.

[dlebauer]

This does sound like a cool project. Would a brief version like the following accurately convey your vision?

"I'm working with scientific analysts to create domain-specific ontologies that will help scientists discover ... "

by ... I wasn't sure if it is computational tools or resources or software or?

[matuskalas]

Vision statement according to Hemingway Editor

I'm working with experts in analysing scientific data, to create domain ontologies. These domain ontologies cover concepts related to data analysis: e.g. types of data or topics. In scientific web portals, they help researchers find suitable tools for their research. A domain ontology can also help finding suitable training materials, terminology, etc.

... a bit choppy sentences in the 2nd half, needs a bit more work

Using Up-Goer 5 Editor

... I gave up, left hopeless without words like science, research, web, community, analyse, software, program 😔 ... Indeed, our special terminology 🤔

[malvikasharan]

Hi Project Lead,

This is your project report file: https://hackmd.io/jH1GvA1FTrW76KzKCQOvoQ Please start working on it for the final presentation. We will send more info in the weekly email.



Best, 
OLS team