Molecular Interactions Controlled Vocabulary
If you need a new entity added to the PSI-MI ontology, you can create a new issue on https://github.com/HUPO-PSI/psi-mi-CV/issues.
Otherwise, you can make you own contributions to the PSI-MI controlled vocabulary using Protege, which you can download from https://protege.stanford.edu/.
The first time you use Protege, you must update the settings.
Go to Settings, and to tab 'New entities' and set the different properties as follows.
Then, go to tab 'New entities metadata' and set the properties as follows.
Go to 'File > Open...', and open the 'psi-mi.owl' file.
On the 'Entities' tab you can find all the PSI-MI entities. Here you can update any of them, delete existing entities or add new ones.
To add a new entity, as a child entity of an existing entity, right-click on the parent entity, and click 'Add subclass...'. Set a name for the new entity and leave the IRI field empty, as it should be auto-generated. The new entity will be created with label, created_by and creation_date annotations.
If the MI Id is not correct (it is not the expected next Id), then you need to change the Auto-generated ID Start value in 'Settings > New Entities'.
Sometimes labels have a language tab added to them.
This is not needed and it may cause issues, so make sure to keep the language tag empty.
Similarly, creation_date annotations sometimes have a Datatype added to them.
Also make sure this is left empty.
If you're gonna create an entity similar to an existing one, you can right-click on an existing entity, and then click 'Duplicate class...'. Then, you can update all the annotations that need updating. Also check that you don't have duplicated created_by and creation_date annotations.
To add a new annotation for an entity, click the plus button.
To update an annotation value, click the circle button (on the right).
To delete an annotation, click the 'X' button (in the middle).
To add or edit nested annotations to an existing annotation, click the '@' button (on the left).
Then, click the plus button to add annotations, or click the circle or 'X' buttons to edit or delete annotations.
Some fields, like 'label', use a literal value.
Other fields, like 'has_synonym_type', refer to other entries in the ontology, and use 'Entity IRI'.
To save your changes, go to 'File > Save as ...', select 'RDF/XML Syntax' format, and save it with the name 'psi-mi.owl', overwriting the existing file.
Then, go again to 'File > Save as ...', select 'OBO Format', and save it with the name 'psi-mi.obo', overwriting the existing file.
Make sure file 'last-id.txt' has been updated with the MI id of the latest entry added to the ontology.
OLS updates their entries weekly, reading the PSI-MI controlled vocabulary terms from the master branch https://github.com/HUPO-PSI/psi-mi-CV/tree/master.
To commit your changes and propagate them to OLS, make your changes on a different branch (or fork), develop if you have the right access to it, or a different branch. Then, create a pull request to merge the changes to the master branch. These changes will be reviewed and either the team will ask for changes, or they will be approved and merged.