From dded3adb8ae82d6cbe3def44b0ac074cf702ef0d Mon Sep 17 00:00:00 2001 From: bvarner-ebi Date: Wed, 30 Mar 2022 10:34:22 -0400 Subject: [PATCH 01/15] Update getting-started.md --- docs/getting-started.md | 75 ++++++++++++++++++++--------------------- 1 file changed, 37 insertions(+), 38 deletions(-) diff --git a/docs/getting-started.md b/docs/getting-started.md index d4fcc172e..288824ad6 100644 --- a/docs/getting-started.md +++ b/docs/getting-started.md @@ -1,53 +1,52 @@ -# How to start with the lessons +# Getting started with the training -Before you start with the lessons of this course, keep the following in mind: +Here are some points to keep in mind whilst working through the lessons and other semantic engineering training materials. -1. The materials in this course are all intended to be used for self-study. We sometimes offer [flipped-classroom](https://en.wikipedia.org/wiki/Flipped_classroom) sessions for new members on our teams - this means that we expect them to work through the entire course themselves and then come to use with questions and requests for clarifications. -2. There is no need to reinvent the wheel: there are a lot of great materials out there already. Providing references to these these external resources is an essential part of the course - some lessons primarily comprise external tutorials, blog articles and more - please make sure you take advantage of them. -3. Some of the materials developed by us are a bit rough around the edges, and we need your help to fix and improve them. To that end, we appreciate anything from [suggestions for improvement](#issues) to [pull requests](#pulls). -4. Depending on your specific role and interest, you can choose which lessons are relevant to you. There is no specific order, but if you want to start somewhere, we recommend [Contributing to OBO ontologies: Protege and Github](lesson/contributing-to-obo-ontologies.md) and/or [Using Ontologies and Ontology Terms](lesson/ontology-term-use.md) +1. The course materials are designed for self-study. [Flipped-classroom](https://en.wikipedia.org/wiki/Flipped_classroom) sessions are offered on occassion and are generally intended to onboard new contributors. The expectation is that new recruits will work through the course themselves and come to sessions with questions and requests for clarifications. +2. There are a lot of great materials out there already. Some lessons primarily comprise external tutorials, blog articles and more. Reviewing these external resources is an essential part of the course. +3. These training materials are constantly evolving and your help with improving them would be greatly appreciated. Please feel free to submit [suggestions for improvement](#issues) and/or [pull requests](#pulls). +4. Depending on your specific role and interest, some lessons may be more or less relevant for your use case. There is no specific order, but if you are new to OBO ontologies, here are some recommended starting points: +- [Contributing to OBO ontologies: Protégé and Github](lesson/contributing-to-obo-ontologies.md) +- [Using Ontologies and Ontology Terms](lesson/ontology-term-use.md) ## The different roles of OBO Semantic Engineering -There are a wide variety of entry points into the OBO world, for example: +Some learning pathways are geared towards specific roles within the OBO Semantic Engineering space. Below are some of the typical roles and their typical tasks. -### *Database Curator*: You are +### *Database Curator*: +- uses ontologies for annotating datasets, experiments and publications +- requests new terms to be added to ontologies +- suggests corrections to existing ontologies, e.g., incorrect synonyms, missing definitions, typos, modelling inconsistencies -- using ontologies for annotating datasets, experiments and publications -- requesting new terms from ontologies -- Suggest corrections to existing ontologies, such as wrong or missing synonyms, typos and definitions +### *Ontology Curator*: +- develops and maintains ontologies +- adds terms to ontologies +- edits ontologies, such as adding synonyms and correcting typos +- publishes ontology releases -### *Ontology Curator*: You are -- developing and maintaining ontologies -- adding terms to ontologies -- performing changes to ontologies, like adding or correcting synonyms -- responsible for ontology releases - -### *Ontology Engineer/Developer*: You are -- developing design patterns for ontologies, specifying the logical structure of terms -- responsible for ensuring the specification and consistent application of metadata in your ontologies (which annotation properties to use, minimal metadata standards) +### *Ontology Engineer/Developer*: +- develops design patterns for ontologies, specifies the logical structure of terms +- ensures the specification and consistent application of metadata in ontologies, e.g., defining minimal metadata standards and which annotation properties to use - defining quality control checks -### *Ontology Pipeline Specialist*: You are -- developing ontology pipelines with `make` and `ROBOT` -- building the release and quality control architecture that *Engineers* and *Curators* need to do their work. -- building infrastructure for application ontologies, implementing dynamic imports modules, transformations of and mappings to other ontologies. - -### *Semantic ETL Engineer*: You are - -- Building ingests from public life science resources such as Bgee, Panther, UniProt and many more -- You use ontologies to glue together data from different sources -- You use ontologies to augment your the information in your data sources through inference +### *Ontology Pipeline Specialist*: +- develops ontology pipelines with `make` and `ROBOT` commands +- builds the release and quality control architecture that *Engineers* and *Curators* need to do their work +- builds infrastructure for application ontologies, implements dynamic imports modules, facilitates transformations of and mappings to other ontologies -### *(Semantic) Software Engineer*: You are +### *Semantic ETL Engineer*: +- builds incoming pipelines from public life science resources such as Bgee, Panther, UniProt and many others +- leverages ontologies to glue together data from different sources +- leverages inferences derived from ontologies to augment information in proprietary data sources -- using ontologies to generate value to end-user applications (user interfaces, semantic facetted search) -- building widgets that exploit the logical and graph structure of ontologies, for example phenotypic profile matching -- building ontology term browsers such as [OLS](https://www.ebi.ac.uk/ols/index). +### *(Semantic) Software Engineer*: +- uses ontologies to generate value to end-user applications, e.g., user interfaces, semantic facetted search +- builds widgets that exploit the logical and graph structure of ontologies, e.g., phenotypic profile matching +- builds ontology term browsers such as [OLS](https://www.ebi.ac.uk/ols/index) -Of course, many of you will occupy more than one of the above "hats" or roles. While they all require specialised training, many shared skill requirements exist. This course is being developed to: +Of course, many of you will not be confined to only one of the above roles. While they all require specialised training, many shared skill requirements exist. The OBO Semantic Engineering course is intended to: -- Provide basic training for OBO Semantic Engineers of any of the above flavours -- Provide an entry point for people new to the field, for example as part of onboarding activities for projects working with ontologies -- Capture some of the typical pitfalls and how-to's guides to address common problems across the OBO-sphere +- Provide basic training for OBO Semantic Engineers performing any of the tasks mentioned above +- Provide an entry point for users new to the field, e.g., as part of onboarding activities for projects working with ontologies +- Capture some of the typical pitfalls and provide guides to address common problems across the OBO-sphere From 9c1da012fc40ca876293905fe14ee8e96e00547a Mon Sep 17 00:00:00 2001 From: bvarner-ebi Date: Wed, 30 Mar 2022 10:53:43 -0400 Subject: [PATCH 02/15] Update getting-started.md --- docs/getting-started.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/getting-started.md b/docs/getting-started.md index 288824ad6..39df4b7b1 100644 --- a/docs/getting-started.md +++ b/docs/getting-started.md @@ -2,7 +2,7 @@ Here are some points to keep in mind whilst working through the lessons and other semantic engineering training materials. -1. The course materials are designed for self-study. [Flipped-classroom](https://en.wikipedia.org/wiki/Flipped_classroom) sessions are offered on occassion and are generally intended to onboard new contributors. The expectation is that new recruits will work through the course themselves and come to sessions with questions and requests for clarifications. +1. The course materials are designed for self-study. [Flipped-classroom](https://en.wikipedia.org/wiki/Flipped_classroom) sessions are offered on occassion and are generally intended to onboard new contributors. The expectation is that new recruits will work through the course themselves and come to sessions with questions and requests for clarifications. 2. There are a lot of great materials out there already. Some lessons primarily comprise external tutorials, blog articles and more. Reviewing these external resources is an essential part of the course. 3. These training materials are constantly evolving and your help with improving them would be greatly appreciated. Please feel free to submit [suggestions for improvement](#issues) and/or [pull requests](#pulls). 4. Depending on your specific role and interest, some lessons may be more or less relevant for your use case. There is no specific order, but if you are new to OBO ontologies, here are some recommended starting points: From cafc574a274109ae0f33d9db5993fb06dd6499b1 Mon Sep 17 00:00:00 2001 From: bvarner-ebi Date: Thu, 21 Apr 2022 09:19:37 -0400 Subject: [PATCH 03/15] Create training-contents.md --- docs/training-contents.md | 102 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 102 insertions(+) create mode 100644 docs/training-contents.md diff --git a/docs/training-contents.md b/docs/training-contents.md new file mode 100644 index 000000000..c090da4c7 --- /dev/null +++ b/docs/training-contents.md @@ -0,0 +1,102 @@ +# Training Contents + +Prerequisites (required for training) + +GitHub Desktop +Protégé +ELK reasoner (Protégé plug-in) +Ontology contributor ID range +Docker and the Ontology Development Kit (ODK)* +ROBOT* +* Required for engineers, optional for curators + + +Primers (introduction to fundamental concepts and applications) + +Ontologies +Fundamentals of Ontologies + +Git and GitHub +Fundamentals of GitHub +Github issues +Cloning a Repo +Creating pull requests + +Protégé +Protégé interface +Browse and search +DL query +Editing terms +Creating new terms +Adding disjointness +Logical axiomatization of classes & use of reasoning +Ontology relations +OBO-style term annotation +Obsoleting terms +Merging terms + +Ontology Engineering +Setting up a ODK repository +Developing an OBO ontology +Understanding product variants +Dealing with large ontologies +ROBOT tutorial pt. 1 +ROBOT tutorial pt. 2 +Templates +Getting started with DOSDP templates +DOSDP Templates Basic Tutorial +Introduction to Managing DOSDP Templates in ODK +Basics of SPARQL +Setting up slims + + +Lessons (formalised training) (?is there a sequence to these?) + +Contributing to OBO ontologies +Ontology Pipelines with ROBOT +Analysing Linked Data +Automating Ontology Workflows +Developing an OBO Ontology +Ontology Design +Templates for OBO ontologies +Ontology Fundamentals +Modelling with Object Properties +Ontology Term Use +RDF Fundamentals +Disease and Phenotype Ontologies + + +How Tos + +Adding taxon restrictions +Changing files in pull requests +Cloning a repo +Creating new terms +Daily Curator Workflow +Fixing Conflicts +Creating a github fork +Creating a github pull request +Setting up your ID range +Setting up ELK reasoner in protege +Obsoleting terms +Merging terms +Creating slims +Setting up ODK +Switching ontologies +Dealing with large ontologies* +*Geared towards Engineers + + +Curated resources + +For the Ontology Curator + +Pathways +Ontology Curator (list of ontologies that are Go-style) +Ontology Curator (list of ontologies that are OBI-style) + + +For the Ontology Engineer/Developer + +Pathways +Ontology Engineer/Developer \ No newline at end of file From 27eaaacb3e2fc519548fb31663d855d51f4d264b Mon Sep 17 00:00:00 2001 From: bvarner-ebi Date: Thu, 21 Apr 2022 09:21:17 -0400 Subject: [PATCH 04/15] Update training-contents.md --- docs/training-contents.md | 44 +++++++++++++++++++-------------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/docs/training-contents.md b/docs/training-contents.md index c090da4c7..c127d6cec 100644 --- a/docs/training-contents.md +++ b/docs/training-contents.md @@ -1,28 +1,28 @@ # Training Contents -Prerequisites (required for training) +##Prerequisites (required for training) -GitHub Desktop -Protégé -ELK reasoner (Protégé plug-in) -Ontology contributor ID range -Docker and the Ontology Development Kit (ODK)* -ROBOT* -* Required for engineers, optional for curators +[GitHub Desktop](https://desktop.github.com/) +[Protégé](https://protege.stanford.edu/products.php) +[ELK reasoner](../howto/installing-elk-in-protege.md) (Protégé plug-in) +[Ontology contributor ID range](../howto/idrange.md) +[Docker and the Ontology Development Kit (ODK)](../howto/odk-setup.md) + +[ROBOT](http://robot.obolibrary.org) + ++ Required for engineers, optional for curators -Primers (introduction to fundamental concepts and applications) +##Primers (introduction to fundamental concepts and applications) -Ontologies +###Ontologies Fundamentals of Ontologies -Git and GitHub +###Git and GitHub Fundamentals of GitHub Github issues Cloning a Repo Creating pull requests -Protégé +###Protégé Protégé interface Browse and search DL query @@ -35,7 +35,7 @@ OBO-style term annotation Obsoleting terms Merging terms -Ontology Engineering +###Ontology Engineering Setting up a ODK repository Developing an OBO ontology Understanding product variants @@ -50,7 +50,7 @@ Basics of SPARQL Setting up slims -Lessons (formalised training) (?is there a sequence to these?) +##Lessons (formalised training) (?is there a sequence to these?) Contributing to OBO ontologies Ontology Pipelines with ROBOT @@ -66,7 +66,7 @@ RDF Fundamentals Disease and Phenotype Ontologies -How Tos +##How Tos Adding taxon restrictions Changing files in pull requests @@ -83,20 +83,20 @@ Merging terms Creating slims Setting up ODK Switching ontologies -Dealing with large ontologies* -*Geared towards Engineers +Dealing with large ontologies+ ++ Geared towards Engineers -Curated resources +##Curated resources -For the Ontology Curator +###For the Ontology Curator -Pathways +####Pathways Ontology Curator (list of ontologies that are Go-style) Ontology Curator (list of ontologies that are OBI-style) -For the Ontology Engineer/Developer +###For the Ontology Engineer/Developer -Pathways +####Pathways Ontology Engineer/Developer \ No newline at end of file From b64b753e74ddd1a1c3a8ce53e2a1bc1ec55c0e1b Mon Sep 17 00:00:00 2001 From: bvarner-ebi Date: Thu, 21 Apr 2022 09:26:02 -0400 Subject: [PATCH 05/15] Update training-contents.md --- docs/training-contents.md | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/docs/training-contents.md b/docs/training-contents.md index c127d6cec..8c3c8e045 100644 --- a/docs/training-contents.md +++ b/docs/training-contents.md @@ -1,6 +1,6 @@ # Training Contents -##Prerequisites (required for training) +## Prerequisites (required for training) [GitHub Desktop](https://desktop.github.com/) [Protégé](https://protege.stanford.edu/products.php) @@ -11,18 +11,18 @@ + Required for engineers, optional for curators -##Primers (introduction to fundamental concepts and applications) +## Primers (introduction to fundamental concepts and applications) -###Ontologies +### Ontologies Fundamentals of Ontologies -###Git and GitHub -Fundamentals of GitHub -Github issues -Cloning a Repo -Creating pull requests +### 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) -###Protégé +### Protégé Protégé interface Browse and search DL query @@ -35,7 +35,7 @@ OBO-style term annotation Obsoleting terms Merging terms -###Ontology Engineering +### Ontology Engineering Setting up a ODK repository Developing an OBO ontology Understanding product variants @@ -50,7 +50,7 @@ Basics of SPARQL Setting up slims -##Lessons (formalised training) (?is there a sequence to these?) +## Lessons (formalised training) (?is there a sequence to these?) Contributing to OBO ontologies Ontology Pipelines with ROBOT @@ -66,7 +66,7 @@ RDF Fundamentals Disease and Phenotype Ontologies -##How Tos +## How Tos Adding taxon restrictions Changing files in pull requests @@ -87,16 +87,16 @@ Dealing with large ontologies+ + Geared towards Engineers -##Curated resources +## Curated resources -###For the Ontology Curator +### For the Ontology Curator -####Pathways +#### Pathways Ontology Curator (list of ontologies that are Go-style) Ontology Curator (list of ontologies that are OBI-style) -###For the Ontology Engineer/Developer +###F or the Ontology Engineer/Developer -####Pathways +#### Pathways Ontology Engineer/Developer \ No newline at end of file From f23ba0121efda3b6f038a27492361b23f64f57cc Mon Sep 17 00:00:00 2001 From: bvarner-ebi Date: Thu, 21 Apr 2022 09:44:25 -0400 Subject: [PATCH 06/15] Update training-contents.md --- docs/training-contents.md | 120 +++++++++++++++++++------------------- 1 file changed, 60 insertions(+), 60 deletions(-) diff --git a/docs/training-contents.md b/docs/training-contents.md index 8c3c8e045..1c125081b 100644 --- a/docs/training-contents.md +++ b/docs/training-contents.md @@ -14,76 +14,76 @@ ## Primers (introduction to fundamental concepts and applications) ### Ontologies -Fundamentals of Ontologies +- [Fundamentals of Ontologies](../explanation/intro-to-ontologies.md) ### 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) +- [Fundamentals of GitHub](../tutorial/github-fundamentals.md) +- [Github issues](../tutorial/github-issues.md) +- [Cloning a Repo](../howto/clone-mondo-repo.md) +- [Creating pull requests](../howto/github-create-pull-request.md) ### Protégé -Protégé interface -Browse and search -DL query -Editing terms -Creating new terms -Adding disjointness -Logical axiomatization of classes & use of reasoning -Ontology relations -OBO-style term annotation -Obsoleting terms -Merging terms +- [Protégé interface](../reference/protege-interface.md) +- [Browse and Search](../howto/protege-browse-search.md) +- [DL query](../tutorial/basic-dl-query.md) +- [Editing Terms](../howto/edit-in-protege.md) +- [Creating New Terms](../howto/create-new-term.md) +- [Adding disjointness](../tutorial/disjointness.md) +- [Logical axiomatization of classes & use of reasoning](../explanation/logical-axiomatization.md) +- [Ontology Relations](../lesson/modelling-with-object-properties.md) +- [OBO-style term annotation](../reference/go-style-annotation-property-practice.md) +- [Obsoleting terms](../howto/obsolete-term.md) +- [Merging terms](../howto/merge-terms.md) ### Ontology Engineering -Setting up a ODK repository -Developing an OBO ontology -Understanding product variants -Dealing with large ontologies -ROBOT tutorial pt. 1 -ROBOT tutorial pt. 2 -Templates -Getting started with DOSDP templates -DOSDP Templates Basic Tutorial -Introduction to Managing DOSDP Templates in ODK -Basics of SPARQL -Setting up slims +- [Setting up a ODK repository](../tutorial/setting-up-project-odk.md) +- [Developing an obo ontology](../lesson/developing-an-obo-ontology.md) +- [Understanding product variants](../explanation/owl-format-variants.md) +- [Dealing with large ontologies](../howto/deal-with-large-ontologies.md) +- [ROBOT tutorial pt. 1](../tutorial/robot-tutorial-1.md) +- [ROBOT tutorial pt. 2](../tutorial/robot-tutorial-2.md) +- [Templates](../lesson/templates-for-obo.md) +- [Getting started with DOSDP templates](../tutorial/dosdp-overview.md) +- [DOSDP Templates Basic Tutorial](../tutorial/dosdp-template.md) +- [Introduction to Managing DOSDP Templates in ODK](../tutorial/dosdp-odk.md) +- [Basics of SPARQL](../tutorial/sparql.md) +- [Setting up slims](../howto/add-new-slim.md) ## Lessons (formalised training) (?is there a sequence to these?) -Contributing to OBO ontologies -Ontology Pipelines with ROBOT -Analysing Linked Data -Automating Ontology Workflows -Developing an OBO Ontology -Ontology Design -Templates for OBO ontologies -Ontology Fundamentals -Modelling with Object Properties -Ontology Term Use -RDF Fundamentals -Disease and Phenotype Ontologies +- [Contributing to OBO ontologies](https://oboacademy.github.io/obook/lesson/contributing-to-obo-ontologies/) +- [Ontology Pipelines with ROBOT](https://oboacademy.github.io/obook/lesson/ontology-pipelines/) +- [Analysing Linked Data](https://oboacademy.github.io/obook/lesson/analysing-linked-data/) +- [Automating Ontology Workflows](https://oboacademy.github.io/obook/lesson/automating-ontology-workflows/) +- [Developing an OBO Ontology](https://oboacademy.github.io/obook/lesson/developing-an-obo-ontology/) +- [Ontology Design](https://oboacademy.github.io/obook/lesson/ontology-design/) +- [Templates for OBO ontologies](https://oboacademy.github.io/obook/lesson/templates-for-obo/) +- [Ontology Fundamentals](https://oboacademy.github.io/obook/lesson/ontology-fundamentals/) +- [Modelling with Object Properties](https://oboacademy.github.io/obook/lesson/modelling-with-object-properties/) +- [Ontology Term Use](https://oboacademy.github.io/obook/lesson/ontology-term-use/) +- [RDF Fundamentals](https://oboacademy.github.io/obook/lesson/rdf/) +- [Disease and Phenotype Ontologies](https://oboacademy.github.io/obook/lesson/using-disease-and-phenotype-ontologies/) ## How Tos -Adding taxon restrictions -Changing files in pull requests -Cloning a repo -Creating new terms -Daily Curator Workflow -Fixing Conflicts -Creating a github fork -Creating a github pull request -Setting up your ID range -Setting up ELK reasoner in protege -Obsoleting terms -Merging terms -Creating slims -Setting up ODK -Switching ontologies -Dealing with large ontologies+ +- [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) +- [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) + + Geared towards Engineers @@ -92,11 +92,11 @@ Dealing with large ontologies+ ### For the Ontology Curator #### Pathways -Ontology Curator (list of ontologies that are Go-style) -Ontology Curator (list of ontologies that are OBI-style) +- [Ontology Curator](https://oboacademy.github.io/obook/pathways/ontology-curator-go-style/) (list of ontologies that are Go-style) +- [Ontology Curator](https://oboacademy.github.io/obook/pathways/ontology-curator-obi-style/) (list of ontologies that are OBI-style) -###F or the Ontology Engineer/Developer +### For the Ontology Engineer/Developer #### Pathways -Ontology Engineer/Developer \ No newline at end of file +- [Ontology Engineer/Developer](https://oboacademy.github.io/obook/pathways/ontology-engineer/) \ No newline at end of file From beca075d14926cccdf570264c04e26cedea49bee Mon Sep 17 00:00:00 2001 From: bvarner-ebi Date: Thu, 21 Apr 2022 10:39:03 -0400 Subject: [PATCH 07/15] Update training-contents.md --- docs/training-contents.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/training-contents.md b/docs/training-contents.md index 1c125081b..19ce6714a 100644 --- a/docs/training-contents.md +++ b/docs/training-contents.md @@ -2,12 +2,12 @@ ## Prerequisites (required for training) -[GitHub Desktop](https://desktop.github.com/) -[Protégé](https://protege.stanford.edu/products.php) -[ELK reasoner](../howto/installing-elk-in-protege.md) (Protégé plug-in) -[Ontology contributor ID range](../howto/idrange.md) -[Docker and the Ontology Development Kit (ODK)](../howto/odk-setup.md) + -[ROBOT](http://robot.obolibrary.org) + +- [GitHub Desktop](https://desktop.github.com/) +- [Protégé](https://protege.stanford.edu/products.php) +- [ELK reasoner](../howto/installing-elk-in-protege.md) (Protégé plug-in) +- [Ontology contributor ID range](../howto/idrange.md) +- [Docker and the Ontology Development Kit (ODK)](../howto/odk-setup.md) + +- [ROBOT](http://robot.obolibrary.org) + + Required for engineers, optional for curators From 4f1d3c30bf9bb2b5bb6b4f62e99fe18d86472826 Mon Sep 17 00:00:00 2001 From: bvarner-ebi Date: Thu, 21 Apr 2022 11:10:16 -0400 Subject: [PATCH 08/15] Update training-contents.md --- docs/training-contents.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/training-contents.md b/docs/training-contents.md index 19ce6714a..14c987394 100644 --- a/docs/training-contents.md +++ b/docs/training-contents.md @@ -8,7 +8,7 @@ - [Ontology contributor ID range](../howto/idrange.md) - [Docker and the Ontology Development Kit (ODK)](../howto/odk-setup.md) + - [ROBOT](http://robot.obolibrary.org) + -+ Required for engineers, optional for curators +'+' Required for engineers, optional for curators ## Primers (introduction to fundamental concepts and applications) @@ -84,7 +84,7 @@ - [Setting up ODK](../howto/odk-setup.md) - [Switching ontologies](../howto/switching-ontologies.md) - [Dealing with large ontologies](../howto/deal-with-large-ontologies.md) + -+ Geared towards Engineers +'+' Geared towards Engineers ## Curated resources From ac30a3ec1b1fa711da0a676600b54633ddaaf7c6 Mon Sep 17 00:00:00 2001 From: bvarner-ebi Date: Thu, 21 Apr 2022 11:11:49 -0400 Subject: [PATCH 09/15] Update training-contents.md --- docs/training-contents.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/training-contents.md b/docs/training-contents.md index 14c987394..ee4df6f3b 100644 --- a/docs/training-contents.md +++ b/docs/training-contents.md @@ -8,7 +8,7 @@ - [Ontology contributor ID range](../howto/idrange.md) - [Docker and the Ontology Development Kit (ODK)](../howto/odk-setup.md) + - [ROBOT](http://robot.obolibrary.org) + -'+' Required for engineers, optional for curators +- '+' Required for engineers, optional for curators ## Primers (introduction to fundamental concepts and applications) @@ -84,7 +84,7 @@ - [Setting up ODK](../howto/odk-setup.md) - [Switching ontologies](../howto/switching-ontologies.md) - [Dealing with large ontologies](../howto/deal-with-large-ontologies.md) + -'+' Geared towards Engineers +- '+' Geared towards Engineers ## Curated resources From 68a4be285df51a12c733b63b88d23d9170537482 Mon Sep 17 00:00:00 2001 From: bvarner-ebi Date: Thu, 21 Apr 2022 11:13:34 -0400 Subject: [PATCH 10/15] Update training-contents.md --- docs/training-contents.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/training-contents.md b/docs/training-contents.md index ee4df6f3b..98fbbd8ad 100644 --- a/docs/training-contents.md +++ b/docs/training-contents.md @@ -8,7 +8,7 @@ - [Ontology contributor ID range](../howto/idrange.md) - [Docker and the Ontology Development Kit (ODK)](../howto/odk-setup.md) + - [ROBOT](http://robot.obolibrary.org) + -- '+' Required for engineers, optional for curators +\+ Required for engineers, optional for curators ## Primers (introduction to fundamental concepts and applications) @@ -84,7 +84,7 @@ - [Setting up ODK](../howto/odk-setup.md) - [Switching ontologies](../howto/switching-ontologies.md) - [Dealing with large ontologies](../howto/deal-with-large-ontologies.md) + -- '+' Geared towards Engineers +\+ Geared towards Engineers ## Curated resources From 9b152510a08775f85808d0b534139b359a483dab Mon Sep 17 00:00:00 2001 From: bvarner-ebi Date: Thu, 21 Apr 2022 11:14:14 -0400 Subject: [PATCH 11/15] Update training-contents.md --- docs/training-contents.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/training-contents.md b/docs/training-contents.md index 98fbbd8ad..5ef251af4 100644 --- a/docs/training-contents.md +++ b/docs/training-contents.md @@ -7,7 +7,7 @@ - [ELK reasoner](../howto/installing-elk-in-protege.md) (Protégé plug-in) - [Ontology contributor ID range](../howto/idrange.md) - [Docker and the Ontology Development Kit (ODK)](../howto/odk-setup.md) + -- [ROBOT](http://robot.obolibrary.org) + +- [ROBOT](http://robot.obolibrary.org) + \n \+ Required for engineers, optional for curators @@ -83,7 +83,7 @@ - [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) + +- [Dealing with large ontologies](../howto/deal-with-large-ontologies.md) + \n \+ Geared towards Engineers From 8a09b97fbc05e12d0effa0365f6d64bbf7b3b0ec Mon Sep 17 00:00:00 2001 From: bvarner-ebi Date: Thu, 21 Apr 2022 11:15:06 -0400 Subject: [PATCH 12/15] Update training-contents.md --- docs/training-contents.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/training-contents.md b/docs/training-contents.md index 5ef251af4..4119b8bca 100644 --- a/docs/training-contents.md +++ b/docs/training-contents.md @@ -7,7 +7,7 @@ - [ELK reasoner](../howto/installing-elk-in-protege.md) (Protégé plug-in) - [Ontology contributor ID range](../howto/idrange.md) - [Docker and the Ontology Development Kit (ODK)](../howto/odk-setup.md) + -- [ROBOT](http://robot.obolibrary.org) + \n +- [ROBOT](http://robot.obolibrary.org) +
\+ Required for engineers, optional for curators @@ -83,7 +83,7 @@ - [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) + \n +- [Dealing with large ontologies](../howto/deal-with-large-ontologies.md) +
\+ Geared towards Engineers From f7678df44f93e72304d6ec996f4481195cf54212 Mon Sep 17 00:00:00 2001 From: bvarner-ebi Date: Thu, 21 Apr 2022 11:16:52 -0400 Subject: [PATCH 13/15] Update training-contents.md --- docs/training-contents.md | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/docs/training-contents.md b/docs/training-contents.md index 4119b8bca..7dd54ca4e 100644 --- a/docs/training-contents.md +++ b/docs/training-contents.md @@ -7,8 +7,10 @@ - [ELK reasoner](../howto/installing-elk-in-protege.md) (Protégé plug-in) - [Ontology contributor ID range](../howto/idrange.md) - [Docker and the Ontology Development Kit (ODK)](../howto/odk-setup.md) + -- [ROBOT](http://robot.obolibrary.org) +
-\+ Required for engineers, optional for curators +- [ROBOT](http://robot.obolibrary.org) + +
+
+ \+ Required for engineers, optional for curators ## Primers (introduction to fundamental concepts and applications) @@ -83,8 +85,10 @@ - [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) +
-\+ Geared towards Engineers +- [Dealing with large ontologies](../howto/deal-with-large-ontologies.md) + +
+
+ \+ Geared towards Engineers ## Curated resources From 2bc9e6534661c1c50c878cdb4f3e372357597322 Mon Sep 17 00:00:00 2001 From: bvarner-ebi Date: Thu, 21 Apr 2022 11:17:19 -0400 Subject: [PATCH 14/15] Update training-contents.md --- docs/training-contents.md | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/docs/training-contents.md b/docs/training-contents.md index 7dd54ca4e..005f54057 100644 --- a/docs/training-contents.md +++ b/docs/training-contents.md @@ -8,9 +8,7 @@ - [Ontology contributor ID range](../howto/idrange.md) - [Docker and the Ontology Development Kit (ODK)](../howto/odk-setup.md) + - [ROBOT](http://robot.obolibrary.org) + -
-
- \+ Required for engineers, optional for curators + + Required for engineers, optional for curators ## Primers (introduction to fundamental concepts and applications) @@ -86,9 +84,7 @@ - [Setting up ODK](../howto/odk-setup.md) - [Switching ontologies](../howto/switching-ontologies.md) - [Dealing with large ontologies](../howto/deal-with-large-ontologies.md) + -
-
- \+ Geared towards Engineers + + Geared towards Engineers ## Curated resources From 7b5f3200c9d5bc8bb38796c84d4b564743528964 Mon Sep 17 00:00:00 2001 From: bvarner-ebi Date: Thu, 21 Apr 2022 11:17:46 -0400 Subject: [PATCH 15/15] Update training-contents.md --- docs/training-contents.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/training-contents.md b/docs/training-contents.md index 005f54057..05462d823 100644 --- a/docs/training-contents.md +++ b/docs/training-contents.md @@ -7,7 +7,8 @@ - [ELK reasoner](../howto/installing-elk-in-protege.md) (Protégé plug-in) - [Ontology contributor ID range](../howto/idrange.md) - [Docker and the Ontology Development Kit (ODK)](../howto/odk-setup.md) + -- [ROBOT](http://robot.obolibrary.org) + +- [ROBOT](http://robot.obolibrary.org) + +
+ Required for engineers, optional for curators @@ -84,6 +85,7 @@ - [Setting up ODK](../howto/odk-setup.md) - [Switching ontologies](../howto/switching-ontologies.md) - [Dealing with large ontologies](../howto/deal-with-large-ontologies.md) + +
+ Geared towards Engineers