A GPI - Gene Product Information file is used to submit gene and gene product information to the GO Consortium. The specification is here. Please note that annotation information relationships between GO terms and annotations made to them uses GPAD format files
AmiGO is under constant development and our suggestion is that you frequently check back for the most recent information (and code, accordingly). The most recent proposal for a stable API is available from the
AmiGO 2 wiki manual.
The OBO file format is one of the formats that the Gene Ontology is made available in. The most recent version is OBO 1.2. The OBO format is designed to be more human readable than XML based formats. GO can be accessed in this format here.
The ontologies are initially produced in the specially designed OBO flat file format. They are converted to XML once a month for the convenience of users who require this facility. Both formats and many others are available in the GO downloads section. We use the OBO flat file format because it is human-readable, and also because the file is much smaller without the XML tags.
The GO RDF-XML format was originally developed some time ago, before the advent of OWL. It has a few unusual features that render it more of a pseudo-rdf format. The actual RDF is embedded within a xml element - this should be stripped out before handing to RDF parsers. Note that the GO RDF-XML conforms to a DTD, something that is not normally a requirement of RDF. This is because most people parse the file using conventional XML parsers rather than XML tools. We are working on a more up to date RDF representation of GO.