Most of the suggestions here involve organized, and perhaps structured, note taking. This is good and makes sense for personal knowledge/research.

That said when I saw ‘personal knowledge base’ my first thought was ‘personal knowledge graph.’ An advantage of knowledge graphs is the ability to start with public data sources and combine in your own information. Like, customizing DBPedia with your own scheme and data.

For organizations, ontology development, defined vocabularies, etc. make sense, but not for most individuals.