ontology

Ontology related questions (e.g. structure, relations, subsets/slims...).

Can a single gene product be annotated with more than one GO term?

Yes!

It is possible and usually expected for a single gene / gene product to be associated with more than one GO term. The fact that you may have found that there are two or more different GO terms associated with a single gene / gene product in your results should not be a cause for concern.

The Gene Ontology allows users to describe a gene / gene product in detail, considering three main aspects: its molecular function, the biological process in which it participates, and its cellular location:

How can I programmatically get a list of GO terms associated with a gene identifier?

This very useful BIOSTARS thread clarifies "How Do I Do Simple GO Term Lookup Given A Gene (Or mRNA) Identifier?" You might find these responses useful when trying to simply create a list of GO terms associated with a given ID- and when you are not looking to conduct enrichment analyses - using a programatic approach. https://www.biostars.org/p/1226/

How do I get the term names for my list of GO ids?

You can use the YeastMine tool available at SGD to retrieve the GO term names for each ID. Here is how-
  1. Go to - http://yeastmine.yeastgenome.org/yeastmine/bag.do
  2. In the Select Type pull down, scroll down and select GO term
  3. Enter your GO ids or upload a list in the full format (GO:0016020, GO:0016301..)
  4. Click on Create List and you should be able to create a list of GO IDs, Term name, Definition, aspect. The tool offers several options to download the list.

Where can I find the number of terms in each of the ontologies?

You can find the number of terms on each of the ontologies by going to AmiGO:

  • Under the 'Advanced Search' section in the middle of the page, use the drop-down menu to choose "Ontology". You don't need to type anything on the 'Quick search' box.
  • This action will send you to the 'Information about Ontology search' page. There, open the 'Ontology source' filter menu on the left. You will see that as of October-27-2015 the number of terms on per ontology were:

How can I contribute to GO?

We welcome your contributions!

The GO project is constantly evolving, and we welcome feedback from all users. Research groups may contribute to the GOC by either providing suggestions for updating the ontology (e.g. requests for new terms) or by providing annotations, that is, associations between genes or gene products and ontology terms. Suggested edits are reviewed by the ontology editors and implemented where appropriate.

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.

Can I download the ontologies as an Excel spreadsheet?

It is not possible to download the ontologies as a tabulated spreadsheet. The complex graph structure of GO, where terms can have one or more parent terms, makes it impractical to be rendered as a spreadsheet. It would probably also be too big for software packages such as Excel to cope with.

How can I calculate the "level" of a GO term?

GO terms do not occupy strict fixed levels in the hierarchy. Because GO is structured as a graph, terms would appear at different 'levels' if different paths were followed through the graph. This is especially true if one mixes the different relations used to connect terms. Thus it is more proper to ask: "what is the maximum depth of such and such a term" (or minimum, average, etc.).

Where have the 'unknown' terms gone?

Good principles of ontological design state that terms should represent biological entities that actually exist, e.g., functional activities that are catalyzed by enzymes, biological processes that are carried out in cells, specific locations or complexes in cells, etc. To adhere to these principles the Gene Ontology Consortium has removed the terms, "biological process unknown" (GO:0000004), "molecular function unknown" (GO:0005554) and "cellular component unknown" (GO:0008372) from the ontology.