ensembl/ensembl-glossary

ensembl-glossary

Ensembl glossary as an OWL ontology.

How To Edit

Clone for the first time

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 [email protected]:Ensembl/ensembl-glossary.git.

Editing The File

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 ......

Committing your changes and pushing these changes back

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.

Building the ontology file (optional step)

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.

Other Repository Information

Template

The ontology file is built from a spreadsheet template in src/template/ontology.tsv

Editors' version

Editors of this ontology should use the edit version, src/ontology/ensembl-glossary-edit.owl

Contact

Please use this GitHub repository's Issue tracker to request new terms/classes or report errors or specific concerns related to the ontology.

Acknowledgements

This ontology repository was created using the ontology starter kit