What

This repository contains a template for writing OWL ontologies as Org Mode documents, with supporting functions and scripts. ELOT works on Windows, MacOS, and Linux.

Literate programming is a paradigm where the creator of some technical artefact focuses on the explanation and readability of each technical construct, rather than its formal machine-readable definition. The machine-readable artefacts are then extracted through a process called "tangling".

ELOT takes inspiration from this paradigm and uses the excellent Emacs Orgmode plain-text format to create an author- and reader-friendly ontology authoring environment. Ontological constructs are generated from headlines and description lists. Export to OWL (OMN or Turtle) and documentation (HTML or PDF). Diagrams are generated from Turtle blocks or SPARQL queries using the rdfpuml tool.

NEW April 2025: Minimalistic templating from tables – handy when you need to add many similar-looking classes and don't need complex template expansion.

NEW March 2025:

• Convert OWL files to ELOT's org-mode format. Download the jar binary from releases, store as elot-exporter.jar in your bin/ and open existing OWL files with function elot-open-owl.

• VS Code support: For instructions on how to run ELOT commands directly from within VS Code on your own projects, please see the detailed README.

• Prerequisites in brief

• Installation

  • Get Emacs
  • Install ELOT in Emacs
  • Install ELOT auxiliaries

• Quick start using ELOT

  • Adding an ontology
  • Adding classes and relations
  • Adding annotations
  • Querying the ontology
  • Making a diagram
  • Display labels instead of identifiers

Prerequisites in brief

• Download ELOT using Git to easily obtain updates
• Use a recent version (29+) of Emacs
• For viewing your ontologies, install Protégé Desktop
• Install Java to enable advanced features
  • Turtle output, ontology metrics, and more: install ROBOT
  • Ontology diagrams: install PlantUML and rdfpuml
  • Open OWL files: Download elot-exporter from releases

Installation

Get Emacs

See the GNU Emacs download page.

For new Windows users: download Emacs from a GNU mirror; the latest version is in the emacs-30 directory. The package named emacs-30.1-installer.exe will work fine (as of 2025-03-11). It's preferable to install into a folder that doesn't contain spaces.

If you are new to Emacs, the book Mastering Emacs is highly recommended.

Install ELOT in Emacs

ELOT is in active development. For easy access to updates, you should clone the ELOT repository using Git.

1. Create a directory for local Emacs add-ons in your home folder, named elisp (on Windows, that will likely mean c:\Users\myname�lisp\).

2. Clone ELOT into the elisp folder using your Git client. If using a terminal for Git, the following will do it.

   cd elisp
   git clone https://github.com/johanwk/elot.git
   

   You should now have a subfolder of elisp called elot.

3. Ensure ELOT is loaded when Emacs starts up.

   • For new Emacs users: find the file elot-init.el inside the elot folder, and copy it to a new file named .emacs in your home folder, then restart Emacs. You should now be looking at a basic, working Emacs configuration.
   • Experienced Emacs users should open elot-init.el and look at the list of packages that are required. Add ~/elisp/elot/elot-package/ to your load-path.

Install ELOT auxiliaries

ELOT relies on external software programs to query your ontologies and produce diagrams. These need to be downloaded.

Preparatory steps, if needed:

1. Create a directory named bin in your home folder: you will download programs to this folder. On Windows, that will mean c:\Users\myname�in\; also ensure the environment variable HOME is set (check issue 83).
2. Ensure the bin folder is on your PATH, so the programs can be found by ELOT. On Windows, use the Control Panel to edit Local Environment Variables and add c:\Users\myname�in\ to the list.

Get the tools:

1. The ROBOT tool is highly recommended for ELOT. Download robot.jar from the ROBOT releases page to your bin folder.
2. The PlantUML tool is needed for diagrams. Download the latest version from PlantUML Downloads (tested with plantuml-1.2024.3.jar) to your bin folder. For convenience, rename it as just plantuml.jar (on Linux, make a symlink).
3. The rdfpuml tool will produce great-looking diagrams for ontologies.

   • On Windows, download rdfpuml.exe to your bin folder.

   • On Linux or MacOS, clone the repository to your bin folder, then add ~/bin/rdf2rml/bin/ to your PATH. Install Perl modules as listed in the rdfpuml installation guide.

     cd ~/bin
     git clone https://github.com/VladimirAlexiev/rdf2rml.git
     

4. The elot-exporter tool converts existing OWL ontologies to ELOT's org-mode format. Once downloaded, you can open an OWL ontology from a local file, or from a URL, with M-x elot-open-owl.
   • download the latest Java JAR from releases and save it as elot-exporter.jar in your bin folder.

Quick start using ELOT

Adding an ontology

Open the familiar Pizza ontology from elisp/elot/examples/pizza.org for an example of what an ELOT file will look like. Check the menu bar to locate the ELOT menu.

To create a new ontology, do this in Emacs:

• Select a directory that you want to work in. Open a new Org Mode file, for instance myontology.org.

• Insert the ELOT template for a document header. From the bottom of the ELOT menu, select Insert New Ontology Document Header. Answer the prompts, and a header is produced, like the following.

  # -*- eval: (load-library "elot-defaults") -*-
  #+title: My new ontology
  #+subtitle: An OWL ontology
  #+author: John Doe
  #+date: WIP (version of 2024-04-04 12:34)
  

• Insert the ELOT template for an ontology skeleton: menu entry Insert New Ontology Skeleton. Answer the prompts – be ready to provide namespaces/prefixes for your ontology and the resources it will contain. You should see something like this screenshot:

Now create an OWL file from your new document.

• Menu entry Export to OWL will "tangle" the ontology to a file in OWL Manchester Syntax, e.g., with filename myontology.omn.
• If you have installed ROBOT, a Turtle file named myontology.ttl will also be generated.
• Have Protégé ready, and open the ontology file to inspect it.

• Export to an HTML document with menu entry Export to HTML. The document will open in your web browser.

Adding classes and relations

• Navigate to the Classes heading
• Select Insert Primitive/Defined Class template from the menu to declare a class. Some appropriate annotation properties from the Industrial Ontology Foundry Annotation Vocabulary (IOF-AV) are included.
• Navigate to the Object properties heading
• Select Insert Property template for an object, data, or annotation property.
• The screenshot shows how checkboxes are included for tracking progress. These are completely optional and won't appear in output.

Adding annotations

ELOT makes it easy to add annotations to both annotations and axioms: just put them in a description list (~ - term :: value~). In this screenshot, two annotations are added to the "transitive" characteristic axiom:

Querying the ontology

• Navigate to the Prefixes heading and insert a new heading named "Queries".
• Select menu item Insert SPARQL Select Block, then write a query over the ontology.
• Hit C-c C-c to run the query.

Making a diagram

• A SPARQL construct query will produce Turtle code for a diagram. Select Insert SPARQL Construct Block.
• Write a query and hit C-c C-c to run it.

• Select Insert RDFPUML Diagram Block.
• When prompted, provide the name of the Turtle source (the name of the construct query) and a figure caption.
• Place the cursor on the row of the #+call: and hit C-c C-c. A diagram is generated.

• Select Export to HTML to view your ontology in a browser.

Display labels instead of identifiers

ELOT can display readable labels instead of prefixed identifiers (which are unreadable if the identifiers are not informative), and offers quick search across the ontology resources. Hit F5 to toggle.

Navigating Ontologies with Xref

ELOT supports cross-referencing and navigation using Emacs’s built-in xref system. This allows users to find where a resource is used and to jump directly to its definition from anywhere in an ELOT buffer.

To find all references to a CURIE (e.g., :BFO_0000015), place the cursor on it and type M-? (xref-find-references). The *xref* buffer will open and show each occurrence, along with the heading and flattened description list entry for context.

Inside the *xref* buffer:

• Press RET to jump to the occurrence.
• Move the cursor to any other CURIE and press M-. (xref-find-definitions) to jump to its definition (typically the Org headline where it's declared).

Label overlays are enabled automatically in the *xref* buffer, so identifiers appear with readable labels if available. This makes it easier to explore large ontologies interactively.

This functionality is activated automatically for Org files exported with ELOT startup code and does not require additional setup.

HTML style

HTML output from ELOT produces stable anchors for ontology resources, and shows readable labels with internal, clickable links.