Ensembl glossary as an OWL ontology.
git clone https://github.com/Ensembl/ensembl-glossary.git
The command will create ensembl-glossary
in your working directory. You may need to switch to using the SSH version of the repository URL git@github.com:Ensembl/ensembl-glossary.git.
First always pull in the latest changes from the repository origin. If you do this before each edit you'll avoid edit conflicts later on.
git pull
Now open the file ensembl-glossary/src/templates/ontology.tsv
in Excel (or another spreadsheet engine), import as tab delimited data, edit and save.
Once saved check what Git thinks you'll be committing back on the command line by using the git diff
command. You can also use git status
to get a summary of the changes.
$ git status
On branch master
Your branch is up to date with 'origin/master'.
Changes not staged for commit:
(use "git add <file>..." to update what will be committed)
(use "git checkout -- <file>..." to discard changes in working directory)
modified: src/templates/ontology.tsv
no changes added to commit (use "git add" and/or "git commit -a")
$ git diff src/templates/ontology.tsv
diff --git a/src/templates/ontology.tsv b/src/templates/ontology.tsv
index 6fb6ef5..a72a359 100644
--- a/src/templates/ontology.tsv
+++ b/src/templates/ontology.tsv
..... AFTER THIS YOU WILL SEE THE ACTUAL CHANGES ......
git add src/templates/ontology.tsv
git commit -m 'Enter your change message here'
git push origin
This will add the changes to ontology.tsv
into your local Git repository and push those changes back to the GitHub hosted version.
This step need only be run if you are building the ontology file locally and committing this into the repo. This should normally be handled by Travis-CI.
cd src/ontology
make
make prepare_release
You will need Java8+ to run this builder.
The ontology file is built from a spreadsheet template in src/template/ontology.tsv
Editors of this ontology should use the edit version, src/ontology/ensembl-glossary-edit.owl
Please use this GitHub repository's Issue tracker to request new terms/classes or report errors or specific concerns related to the ontology.
This ontology repository was created using the ontology starter kit