Setup before editing
- Join phenotype-ontologies slack
- Invite to join the obo-community workspace (slack) here: https://join.slack.com/t/obo-communitygroup/shared_invite/zt-i0cim9vk-yUxCjyPRpsXjiMAjwiBzMg
- and for http://anatomy-and-cell-onto.slack.com/ invite is https://join.slack.com/t/anatomy-and-cell-onto/shared_invite/zt-h8mtt4s3-d4gymfzyflYJUE_K_IGnpw
- Install docker.
- Install Protege. See obook website with full instructions on how to install protege and the ELK reasoner.
- Get a copy of the repository in your machine:
- You will need to authenticate with your github account, the easiest way is to use the GitHub command line interface: installation instructions
- Then you can authenticate with the command
gh auth login - Clone the repository:
git clone https://github.com/pombase/fypo
Because there can be several editors of the ontology, everyone gets a range of IDs, so that there are no clashes if two editors work at the same time. For example at some point @ValWoord had ranges from (8000 to 9000) and @manulera (9000 to 10000), so new terms added by @ValWood started from FYPO:0008000, FYPO:0008001, etc.
This is explained in the obook switching ontologies and setting id ranges tutorials. A brief summary is given below.
Obsoleted setting of ranges in Protégé
You should indicate your idrange in the file src/ontology/fypo-idranges.owl
In Protege go to Protege > Preference (in Mac) or File > Preferences (in Windows -I think-). Go to the tab New entities and set:
- 'Specified IRI': http://purl.obolibrary.org/obo/
- /
- Auto-generated ID
- Same as label renderer
- Numeric (iterative)
- Prefix:
FYPO_ - Digit Count:
7 - Start: your starting id from your id range in
src/ontology/fypo-idranges.owl - End: the end id of your range in
src/ontology/fypo-idranges.owl.
This is how the settings should look:
You can also set the following in the "renderer" tab:
More important Protege configuration can be found in the section "setting preferences for user details" and next sections from OBO tutorials. These settings make it so that protege marks you as an author of every term you add, otherwise you have to do this manually. If your user name in Protege matches the name in the fypo-idranges.owl file, your id range will be picked up directly from the file. Otherwise, Protege will ask you to pick up a user from the list.