Brief Zotero is an impressive free and open-source app that lets you collect organize cite and share research. You can also instantly create references and bibliographies for your documents with Zotero.
Usually you can use any note taking app on Linux to collect and share your ideas. But here I want to share something tailored specifically to help you collect organize and share your research i.e. Zotero.
Zotero is a completely open-source project that you can find on GitHub. It aims to help you easily collect organize add notes and share your research.
And all of that without being a cloud-based service it is completely offline. So your research notes belong to you. Of course unless you want to sync it for collaboration purpose for which you may have to refer the documentation.
To give you a head start you can either opt for a WebDAV storage or just create a Zotero account to sync and share your research easily.