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Pathway: Semantic engineer #313

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3 changes: 2 additions & 1 deletion .gitignore
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.idea/
site/
.DS_Store
11-KnowledgeGraphs/person.owl
11-KnowledgeGraphs/Untitled.owl
docs/resources/fhkb.zip
docs/tutorial/project-ontology
.env
.env
9 changes: 1 addition & 8 deletions docs/pathways/ontology-engineer.md
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Expand Up @@ -29,7 +29,6 @@ As a ontology engineer, it would be useful for you to know how curators work, as
1. [Setting up a ODK repository](../tutorial/setting-up-project-odk.md)
1. [Developing an obo ontology](../lesson/developing-an-obo-ontology.md)
1. [Understanding product variants](../explanation/owl-format-variants.md)
1. [Dealing with large ontologies](../howto/deal-with-large-ontologies.md)
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@joeflack4 joeflack4 Nov 29, 2022

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Removed this from "learning..." section because it was in the "how to..." section.

1. [ROBOT tutorial pt. 1](../tutorial/robot-tutorial-1.md)
1. [ROBOT tutorial pt. 2](../tutorial/robot-tutorial-2.md)
1. [Templates](../lesson/templates-for-obo.md)
Expand All @@ -45,17 +44,11 @@ This section is a non-ordered collection of how to documents that an engineer mi

- [Adding taxon restrictions](../howto/add-taxon-restrictions.md)
- [Changing files in pull requests](../howto/change-files-pull-request.md)
- [Cloning a repo](../howto/clone-mondo-repo.md)
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@joeflack4 joeflack4 Nov 29, 2022

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For the other ones I removed from the Ontology Engineer "how to" section, it's either because (a) it is very basic, e.g. cloning, and a quick google search away if really needed, or (b) it's already in another section of the same page.

- [Creating new terms](../howto/create-new-term.md)
- [Daily Curator Workflow](../howto/daily-curator-workflow.md)
- [Daily Git Workflow (Curators and Engineers)](../howto/daily-curator-workflow.md)
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@joeflack4 joeflack4 Nov 29, 2022

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Changed this because even though the page is curator focused, it is a useful workflow to know for engineers as well. Added word 'Git' because it seems focused on largely on that.

- [Fixing Conflicts](../howto/fixing-conflicts.md)
- [Creating a github fork](../howto/github-create-fork.md)
- [Creating a github pull request](../howto/github-create-pull-request.md)
- [Setting up your ID range](../howto/idrange.md)
- [Setting up ELK reasoner in protege](../howto/installing-elk-in-protege.md)
- [Obsoleting terms](../howto/obsolete-term.md)
- [Merging terms](../howto/merge-terms.md)
- [Creating slims](../howto/add-new-slim.md)
- [Setting up ODK](../howto/odk-setup.md)
- [Switching ontologies](../howto/switching-ontologies.md)
- [Dealing with large ontologies](../howto/deal-with-large-ontologies.md)
49 changes: 49 additions & 0 deletions docs/pathways/semantic-engineer.md
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# Semantic Engineer Pathway

## Getting Set-up
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@joeflack4 joeflack4 Nov 29, 2022

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For this section, I kept everything from Ontology Engineer except for this:

4. [Setting up your ID range](../howto/idrange.md)


1. Download and install [GitHub Desktop](https://desktop.github.com/)
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@joeflack4 joeflack4 Nov 29, 2022

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I don't use GitHub Desktop, but it's not bad. I have seen data managers and similar roles use it more often.

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@joeflack4 joeflack4 Nov 29, 2022

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For a lot of these as well, I feel like if you have the title engineer or developer, a lot of this stuff will be mastered already, such as GitHub, or CLI. But for a junior engineer just starting out, or someone looking to become an engineer, I suppose it is indeed good to have some of these things in the list.

2. Download and install [Protege](https://protege.stanford.edu/products.php)
3. Install [ELK reasoner in protege](../howto/installing-elk-in-protege.md)
4. [Setting up ODK](../howto/odk-setup.md)

## Learning

As a semantic engineer, it would be useful for you to know how curators work, as such, it would be useful to be familiar with all the concepts in the [ontology curator pathways document](ontology-curator.md). This pathways will however be focusing on the engineering side of things.

### Very basics

1. [Basic introduction to CLI 1](../tutorial/intro-cli-1.md)
1. [Basic introduction to CLI 2](../tutorial/intro-cli-2.md)

### Learning Git and GitHub

1. [Fundamentals of GitHub](../tutorial/github-fundamentals.md)
1. [Github issues](../tutorial/github-issues.md)
1. [Cloning a Repo](../howto/clone-mondo-repo.md)
1. [Creating pull requests](../howto/github-create-pull-request.md)

### Learning semantic engineering

1. [ROBOT tutorial pt. 1](../tutorial/robot-tutorial-1.md)
1. [ROBOT tutorial pt. 2](../tutorial/robot-tutorial-2.md)
1. [Templates](../lesson/templates-for-obo.md)
1. [Getting started with DOSDP templates](../tutorial/dosdp-overview.md)
1. [DOSDP Templates Basic Tutorial](../tutorial/dosdp-template.md)
1. [Introduction to Managing DOSDP Templates in ODK](../tutorial/dosdp-odk.md)
1. [Basics of SPARQL](../tutorial/sparql.md)
1. OAK
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@joeflack4 joeflack4 Nov 29, 2022

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@matentzn I probably got to the most important value-add right at the end, and didn't have much time to think/write about it. I added these 5 bullet points to the bottom of "learning semantic engineering", but I did not yet create pages for these.

1. SSSOM
1. makefile (introduction, pipelines, syntax, optional flags, run.sh)
1. Docker
1. Some common ontologies, properties, and relationships (RDF, RDFS, oboInOwl, etc)

## Semantic Engineer How To Collection

This section is a non-ordered collection of how to documents that an engineer might need (this includes everything from the curators list as they may be pertinent knowledge to an engineer).

- [Changing files in pull requests](../howto/change-files-pull-request.md)
- [Creating new terms](../howto/create-new-term.md)
- [Daily Git Workflow (Curators and Engineers)](../howto/daily-curator-workflow.md)
- [Fixing Conflicts](../howto/fixing-conflicts.md)
- [Dealing with large ontologies](../howto/deal-with-large-ontologies.md)
1 change: 1 addition & 0 deletions mkdocs.yml
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Expand Up @@ -19,6 +19,7 @@ nav:
- Ontology Curator GO-style: pathways/ontology-curator-go-style.md
- Ontology Curator OBI-style: pathways/ontology-curator-obi-style.md
- Ontology Engineer/Developer: pathways/ontology-engineer.md
- Semantic Engineer: pathways/semantic-engineer.md
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@joeflack4 joeflack4 Nov 29, 2022 •
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I think there is a lot of overlap between "semantic engineer" and "ontology engineer". I used that one as a template instead of the "ontology curator: go" page. There's only one section in that page that isn't in "ontology engineer", and it is the "mindset" section.

I removed some items from these lists if it's something I haven't done/used before, but I wouldn't be surprised if that changes!

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@shawntanzk shawntanzk Nov 30, 2022

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could we merge ontology engineer with semantic engineer then?

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@shawntanzk shawntanzk Nov 30, 2022

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PS I didn't over think this pathway (was focusing on curator one) so happy for it to be fully revamped as semnatic engineer and taken over as so :)

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@matentzn matentzn Nov 30, 2022

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There will always be a lot of overlap, but for me, the ontology engineer is focused on design patterns, modelling, logic, while the Semantic Software Engineer is focused on using ontologies in Software and Data pipelines.

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@joeflack4 joeflack4 Nov 30, 2022

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Ontology Engineer sounds like Ontology/Semantic Architect! (I actually don't like to use 'architect' usually; sounds very Java)

- Ontology contributor: pathways/ontology-contributor.md
- Lessons:
- Contributing to OBO ontologies: lesson/contributing-to-obo-ontologies.md
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