CGD Frequently Asked Questions (FAQ)

This page provides answers to some common questions.


FAQs about CGD

Why hasn't CGD cited my paper?

How do I propose a gene name?

How can I find more information about sequences in CGD?

How should I cite CGD?

How can I get more help?

FAQs about Gene Ontology at CGD

What is Gene Ontology (GO)?

GO is a collaborative project, involving CGD and other model organism databases, to provide controlled vocabularies that are used to describe the molecular function and cellular location of gene products and the biological process in which they are involved. The three ontologies that comprise GO (Molecular Function, Cellular Component, and Biological Process) are used by multiple databases to annotate gene products, so that this common vocabulary can be used to compare gene products across species. The development of the ontologies is ongoing in order to incorporate new information.
Where can I learn more about the GO project?

The GO Consortium website is the central repository for GO information and documentation, and for the ontologies themselves. SGD's GO Help page provides a brief introduction to GO, and the SGD GO tutorial is a guided tour of GO annotations and of the GO tools that are used at SGD and at CGD.

How do I find which genes or proteins are annotated to a GO term?

Whenever a GO term is displayed on an CGD Locus page, that term is hyperlinked to a list of all gene products annotated to that term in CGD. You can search for a particular GO term by typing all or part of the term into the Quick Search box at the top of most CGD pages. This will return a list of all terms matching the search criterion, along with lists of gene products annotated to each term. CGD GO annotations may be downloaded in bulk from the Download directories.

How can I analyze the GO terms assigned to a set of genes?

CGD has two tools for analysis of GO classifications of groups of genes. The GO Term Mapper tool takes a set of genes specified by the user and maps each to higher-level GO-Slim terms. The GO Term Finder tool takes the user's set of genes of interest and finds GO terms that are shared within the set. Detailed documentation is available on the GO Term Mapper help page and the GO Term Finder help page, provided by SGD.

How does CGD assign references for GO terms?

In assigning Gene Ontology (GO) terms, our aim is to annotate each function, process, and location of the gene product with the full set of references that establish the classification. If your paper has not been cited, feel free to send us an email, and we will add the information as quickly as possible.

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