OBO Foundry Registry and Website

What is this?

This is the registry and website for the OBO Foundry.

It uses GitHub pages and can be visible here: http://obofoundry.github.io/

We map http://obofoundry.org to this address.

How does it work?

The source can be found on https://github.com/OBOFoundry/OBOFoundry.github.io

It uses GitHub Pages/Jekyll, a popular static site generator.

GitHub pages are integrated with github which means that the entire site can be seen on http://obofoundry.github.io (we don't run a dedicated webserver)

For more details see: README-sitedev.md

I have some comments

You can use the issue tracker but you may want to hold off til things are more stable

I want to contribute

Please do! Anyone can fork and make PR, or create an issue in the tracker.

Note that most members of the community will do this via the obofoundry.org website - each ontology page has links for editing the metadata.

See CONTRIBUTING.md

Repo Organization

• registry/ <-- DERIVED yaml, json and RDF. DO NOT EDIT
  • registry/ontologies.yaml <-- READONLY
  • registry/ontologies.jsonld <-- generated from yaml
  • registry/ontologies.rdf <-- TODO generated from jsonld
• ontology/ <-- source for ontology metadata. EDIT IN HERE
  • ontology/obi.md <-- metadata (yml) and markdown for display. EDIT THIS
  • ontology/uberon.md
  • ...
• Makefile <-- For compiling derived artefacts and running tests
• .travis.yml <-- continuous integration config
• _posts/ <-- Blog posts/news
• _layouts/ <-- Jekyll layouts
• _includes/ <-- Jekyll includes
• _util/ <-- scripts etc
  • _util/extract-metadata.py <-- tool for working with .md files

Instructions for Registry Curators

See this FAQ entry for simple web-based editing of metadata

Please edit the source files in the ontology/ directory only.

For example:

• ontology/uberon.md
• ontology/bfo.md

Each md file consists of

• YAML metadata
• Markdown text to be shown on the page for that ontology

For example:

---
layout: ontology_detail
id: aeo
title: Anatomical Entity Ontology
contact: 
  email: J.Bard@ed.ac.uk
  label: Jonathan Bard
description: AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology
domain: anatomy
homepage: http://www.obofoundry.org/wiki/index.php/AEO:Main_Page
products: 
  - id: aeo.owl
---

AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology, to about 200 classes using the is_a relationship; it thus provides a detailed type classification for tissues. The new classes were chosen for their use in categorizing the major vertebrate and invertebrate anatomy ontologies at a granularity adequate for tissues of a single cell type. The ontology should be useful in increasing the amount of knowledge in anatomy ontologies, facilitating annotation and enabling interoperability across anatomy ontologies

The aeo page shows the structured info on the right and the formatted text on the right. (THIS IS A BAD EXAMPLE IT HAS NO FORMATTING)

The YAML data is strictly vetted by OBO team. The Makefile takes care of syntactic validation (the travis job runs make test). The OBO team ensures the content is correct, up to date and accurate.

You can put any HTML or Markdown in the lower section - customize each ontology page!

Note that each md file is the primary source for the metadata for each ontology. It may seem odd to mix the markdown in with the yaml, but in practice this works well and is easy to mainpulate using the python script in the util/ directory.

The one piece of visual info in the md is the layout field, which is necessary for Jekyll.

Generation of downstream artefacts

OBO admins should periodically

git pull
make
jekyll server
## open 127.0.0.1:4000 in a web browser and spot-check changes
git commit -m 'regenerated derived files' -a
git push origin master

See the Makefile for details. This will have the effect of regenerating the main ontologies yaml (used by external consumers such as OLS, as well as the central OBO library build), as well as the GitHub pages _config.yml file. This last step is necessary to update the front page.

RDF

The yaml is all "YAML-LD" and can compile down to RDF/OWL using a generic translator (eg JENA) plus our context file.

Community Contributions

Note that general OBO users are free to edit via the github web interface and make a pull request. They can update their own entries, but they are also welcome to suggest changes elsewhere.

On the live site, each page has links to view source and edit source. This makes use of githubs builtin editing facility

For example:

• view ontology/uberon.md
• edit ontology/uberon.md

Note that joe randoms cannot just come in and update things. Anyone with a github ID can make pull request (aka PR). It is up to the OBO team whether the PR may be merged or rejected.

Note that if you make a syntax error whilst editing, then the travis check will fail. Your PR will have a big red X next to it, in which case the OBO team will not merge your PR. Don't worry, all you have to do is make further edits to fix the syntax error.

TODO: add a quick guide to yaml, and the tags we use.

Central OBO library build

(see also the FAQ entry on this)

The central OBO build runs here:

• http://build.berkeleybop.org/job/simple-build-obo-all/

It takes as metadata input the yml file from this repository. It makes use of the build object.

The output of this job is a set of obo and owl files deposited in

• http://berkeleybop.org/ontologies/

Depending on the build configuration, this may also make additional files. See for example:

• http://berkeleybop.org/ontologies/uberon/

A http://berkeleybop.org/ontologies/ URL should never be handed out directly. This service exists so that:

• Un PURL-registered ontologies will have a fall-through
• Registered PURL ontologies that do not want to take charge of either OBO or OWL generation will have a place to 302-redirect to

This job will fail if ontologies marked as infallible fail. To debug, the full log of the last build can be examined:

• https://build.berkeleybop.org/job/simple-build-obo-all/lastBuild/consoleFull

(Look for the text "should not fail")

Adding news

Simply add a post to the _posts/ directory - copy an exiting one if you like

Posts can also be edited via the GH web interface, all posts are here:

https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/_posts

Instructions for WebSite developers

Consult online Jekyll docs for details. Basically you just do

gem install jekyll

(I am currently using Jekyll 2.5.3)

You can run a local test install from the top level directory

jekyll serve

Then open http://127.0.0.1:4000

Every commit is visible within a few minutes on: http://obofoundry.github.io

You may want to work on a branch to avoid disrupting the live site. Exact procedures for accepting changes back into master have yet to be determined. See CONTRIBUTING.md for a draft.

The setup is fairly standard for Jekyll. We use Jekyll bootstrap (bootstrap 3). We try and keep things minimal so that the site will work on github. Even if you have no knowledge of Jekyll, it is fairly easy to introspect what is going on if you have done much CMS work or web development.

Basics:

• source can be markdown or html
• Different styles of pages go in _layouts
• ...

Site FAQ

See also the main FAQ on the website: this FAQ is for OBO internal people

It's missing feature X from the old site

File an issue! Or better yet, make a change on a fork and make a PR!

Shouldn't we pull project data from the ontologies themselves?

We should definitely have some mechanism for syncing these or allowing this option. However, for the majority of ontologies for which I (cjm) are de-facto administrating, the expertise and time to do this in OWL is not there, and many groups prefer to have this centralized.