I have build a couple of ontologies in Protege. I want to find/extract the links where those specifications are stored in the web. I am trying googling, but either I ask it the wrong way, or such information does not exist.....Thanks
You need to modify a file hosted on a web site (assuming the original ontology is stored as a plain file).
What is essential is that you have write access to the location. If so, all you have to do is write the new file in the correct location.
If the ontology is not just served as a plain file, you need to provide more details. The update will depend on how the original ontology is served.
The version IRI can be anything you wish; the ontology IRI can be (for example) a GitHub repository URL and a file name, and match an existing GitHub file, but that's not necessary. These are not used to decide where to ave the ontology. If you try to save an ontology loaded from an URL, the URL used to load the ontology will be the document URL, and will be used to try and save the changes, but it does not need to match the ontology IRI.