software

Software related questions (e.g. AmiGO, OBO-Edit, database, scripts, OWL, file formats...).

What is the status of the GO MySQL database?

While the GO MySQL database is currently considered to be in "legacy" mode, meaning that there will likely not be any new developments on it, it is a widely used and convenient resource for many types of queries. More information about it can be found on its main page.

Where can I find software to allow me to edit the GO terms?

  • Protege: Protege is a free, open-source ontology editor and framework for building intelligent systems. At this time, all ontology editors for GO use this program.
  • OBO-Edit - now deprecated: OBO-Edit was developed by the software group at the Berkeley Drosophila Genome Project (BDGP), specifically for ontology editing; it ensured that file syntax remained correct. Until recently, it was also used for editing GO, but its use has been deprecated.

How do I install AmiGO locally?

Full documentation for downloading and installing AmiGO is available here .