Developers GitHub Guide
From Plant Ontology Wiki
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 Laurel Cooper or Justin Elser and provide the following information:
Request for GitHub developers account on: Planteome/plant-ontology/repository
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 on a Mac, unix, or linux machines, try this.
Set up a directory on your local computer, with a name of your choice (such as '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:
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:
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
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:
There is a helpful guide on GitHub's help page.
Ontology editing 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 is a free, open source ontology editor and knowledge-base framework that is useful if you want to edit ontologies 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.
The PO Developers Guide provides details on the standard practices and principles used in development of the Plant Ontology.