I am the developer of Uberon and I would be happy to help you with what you need, either from Uberon, or from the FMA.
You mentioned you need something simpler than FMA. There are a variety of tools for creating custom subsets. Additionally, some ontologies provide ready-made subsets for particular purposes.
For example, we make a subset called 'basic.obo' from Uberon:
You can examine this directly in either oboedit or Protege5 (note Protege5 parses obo so you don't need to convert).
From your question, you didn't indicate you needed programmatic access, but if you do there are a variety of options, as well as more programmer-friendly JSON exports.
Most ontologies have a number of different options for web-browsing, you can see some of the options for Uberon here:
You mentioned annotating disease sites. There may be a tools (either desktop or web-based) for helping with this - e.g. providing autocomplete over a desired subset of an ontology.
You may also want to ask your question on a mailing list like obo-discuss. Unfortunately many ontology developers don't read stackexchange, but most are always keen to hear of community requirements, to help them provide better and more useful products.