You can find out more about available ontologies for use during annotation with Phenote software:

NCBO Bioportal

On this page you can find a listing of biomedical ontologies that have been submitted to the NCBO. From there you can link to their project websites, download the ontology files, and search their contents.

OBO Foundry

The OBO Foundry is an open, inclusive, and collaborative core of interoperable ontologies developed by the research community. The goal is to facilitate the creation of consistent, compatible, and unambiguous ontologies thereby supporting the biomedical research community. The contributors are those biological researchers and ontology developers who have agreed to work together on an evolving set of design principles that can foster interoperability of ontologies, and ensure a gradual improvement of quality and formal rigor in ontologies, in ways designed to meet the increasing needs of data and information integration in the biomedical domain.

Ontology Lookup Service (OLS)

The Ontology Lookup Service is a spin-off of the PRIDE project, which required a centralized query interface for ontology and controlled vocabulary lookup. While many of the ontologies queriable by the OLS are available online, each has its own query interface and output format. The OLS provides a web service interface to query multiple ontologies from a single location with a unified output format.