diff --git a/.gitignore b/.gitignore index 41ce8a627..61b4ea581 100644 --- a/.gitignore +++ b/.gitignore @@ -1,7 +1,8 @@ +.idea/ site/ .DS_Store 11-KnowledgeGraphs/person.owl 11-KnowledgeGraphs/Untitled.owl docs/resources/fhkb.zip docs/tutorial/project-ontology -.env \ No newline at end of file +.env diff --git a/docs/pathways/ontology-engineer.md b/docs/pathways/ontology-engineer.md index 66b26fb9c..22fc12685 100644 --- a/docs/pathways/ontology-engineer.md +++ b/docs/pathways/ontology-engineer.md @@ -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) 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) @@ -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) - [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) - [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) diff --git a/docs/pathways/semantic-engineer.md b/docs/pathways/semantic-engineer.md new file mode 100644 index 000000000..8d6010a33 --- /dev/null +++ b/docs/pathways/semantic-engineer.md @@ -0,0 +1,49 @@ +# Semantic Engineer Pathway + +## Getting Set-up + +1. Download and install [GitHub Desktop](https://desktop.github.com/) +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 +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) diff --git a/mkdocs.yml b/mkdocs.yml index 00bdafce1..620103324 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -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 - Ontology contributor: pathways/ontology-contributor.md - Lessons: - Contributing to OBO ontologies: lesson/contributing-to-obo-ontologies.md