Developers Github Guide

Plant Ontology: Developers guide to GitHub access

Get an account from GitHub administrator

To be granted developer access to the GitHub Plant-ontology repository you need to have a GitHub account and password. Follow on-screen instructions at https://github.com/

To get developer access, please email your GitHub username to Justin Elser and by mentioning the following:

Request for GitHub developers account on: Planteome/plant-ontology/repository Your name: Institution: Email address: Office or lab telephone number:(xxx)-xxx-xxxx GitHub account name:

If you already have one, do not worry, it will work. Once you have developer status, start with the following set of instructions. The terminal you use with vary depending on the type of machine from which you will be using.

GitHub access via command-line interface

If you prefer a command line access via a unix or linux machines, try this.

Set up a directory on your home box:

mkdir plant-ontology

cd plant-ontology

Get the files by cloning the repository:

git clone https://github.com/Planteome/plant-ontology.git

In order to update an ontology, do this:

git pull

Make your changes to the ontology files, then stage your modified file to your local repository before committing it.

git add name_of_file_that_has_been_changed.obo

To commit your changes:

git commit

This will open your terminal's default text editor (vi, nano, etc...) Enter in your commit message, and save.

To make your committed changes on the Github master, type

git push

It is good practice always to pull a file before revising it.

At any time you can check the status of your local repository vs. the master on Github by typing:

git status

There is a helpful guide on Github's help page. If you need help in depositing your files, please contact one of us: Pankaj Jaiswal,Laurel Cooper, Justin Elser

Ontology editing software:

Obo-Edit software

OBO-Edit is an open source ontology editor written in Java that can be used to browse, search, or edit the PO (or any .obo) files.

OBO-Edit features an easy to use editing interface, a simple but fast reasoner, and powerful search capabilities. It is optimized for reading and writing ontologies in the OBO biological ontology file format.

OBO-Edit is developed by the Berkeley Bioinformatics and Open Source Projects, and is funded by the Gene Ontology Consortium.

The latest version of OBO-Edit can be downloaded from SourceForge.

Protégé software

Protégé is a free, open source ontology editor and knowledge-base framework that is useful if you want to edite ontlogies in RDF(S), OWL, or XML Schema.

Protégé is based on Java, is extensible, and provides a plug-and-play environment that makes it a flexible base for rapid prototyping and application development.

Ontology development

The PO Developers Guide provides details on the standard practices and principles used in development of the Plant Ontology.