software

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

How can I do term enrichment analysis for a species that is not present in the list from AmiGO?

The Term Enrichment tool on the GO and AmiGO websites center only on data from the genomes available on the PANTHER Classification System Database (http://go.pantherdb.org). Details about how to use the tools available on AmiGO and how to interpret the results is available on our website at http://geneontology.org/page/go-enrichment-analysis.

How do I find all annotations for species X that I can't find in AmiGO?

  1. Open the QuickGO web-page http://www.ebi.ac.uk/QuickGO/
  2. Click on the Search and Filter GO annotation sets link located beneath the search box
  3. This will lead you to an Annotation download page where you can click the filter icon (Located to the right hand side of the page)

What is a GPI file?

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

What is the best way to link into AmiGO?

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.

What is OBO file format?

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.

Why are the ontologies initially produced in OBO flat file format instead of XML?

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.

Why won't the RDF-XML file parse using RDF parsers?

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.

How can I generate files in the old GO flat file format?

As of August 1, 2009, the original GO flat file format was deprecated and is no longer be provided by the GO Consortium.

The OBO-Edit project, which used to generate the flat file format, has been mothballed.