How research communities can contribute data to the GOC
The GO project is constantly evolving, and we welcome feedback from all users. Research groups may contribute to the Gene Ontology Consortium (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.
Please contact the GOC before carrying out any annotation work you intend to submit; this will ensure that GOC mentors and trainers can be of assistance in producing data sets in agreement with the GOC annotation policies and format requirements.
We welcome your contributions!
1. Contributing GO Annotations
If your research group has GO annotations for a species that is not currently included in the GO, whether or not these annotations cover the entire genome, or if your research team has identified gaps or inaccuracies in the current set of GO annotations, this guide is for you. Choose the scenario that best describes your research group and follow the steps as indicated below.
If you are contributing data from:
- Human & Model Organism Databases: Your research group should follow the steps outlined on the guide to Submitting GO Annotations. This involves the preparation and submission of a formatted file that complies with the specifications of the GOC.
- Special Interest Research Groups: If your research group has a specific focus for GO annotations, for example genes or gene products localized in "synapse" (cellular component), then you should first contact the GOC to discuss the best approach for your annotations, and then follow the steps outlined on the guide to Submitting GO Annotations.
- Non-MOD Genome Projects: If you belong to a research community conducting a genome sequencing project for a "non-model" organism (for example species of butterflies, passerine birds, other vertebrates, etc.), and you:
- have conducted automated annotations using tools such as InterProScan, Emsembl Compara, or have conducted Hidden Markov Model-based searches (e.g. with tools such as Just_Annotate_My_proteins (JAMps)), please follow the steps outlined on the guide to Submitting GO Annotations to prepare a formatted file for submission.
- have conducted manual annotations, associating GO terms to genes or gene products, with or without the assistance of genome annotation editing tools (e.g. Apollo), submit your annotations using the GO curator request tracker on Github. Each of your annotations should include an identifier as well as literature references in support of these annotations (if available).
- Ad hoc curation efforts: If you are conducting annotation efforts of smaller magnitude than genome projects, or focused on just a handful of genes and gene products (e.g. annotations from the Community Assessment of Community Annotation with Ontologies (CACAO)), you should submit your annotations using the GO curator request tracker on Github. Be sure to include the following information in your request:
- An identifier for the gene or gene product of interest
- A citation to a publicly available reference supporting the need for improving the annotation (e.g. PubMed ID)
- Details on the specific annotations that should be reviewed or added.
- Other bioinformatics analyses: If you are conducting automated annotation efforts across an entire genome or across a number of genomes, follow the steps outlined on the guide to Submitting GO Annotations to learn about file format specifications. Contacting the GOC to discuss the best approach for your annotations and where to submit your file.
2. Contributing to the Ontology
If you have suggestions for a new ontology term, first make sure the term doesn't exist, either as a primary term or a synonym term. To do this, search the ontology using the AmiGO browser. Requests for new synonyms or clarification of textual definitions are also welcomed. Please choose the scenario that best describes your research group and follow the steps as indicated below.
If you are:
- Very familiar with the ontology and with the use of TermGenie: If you curate the ontology regularly and are familiar with the tools and resources of the GOC, we invite you to use one of the templates available from TermGenie. If the term you are looking for is not available, you may enter a request using the GO curator request tracker on Github. Additional information on how to submit requests for new terms are available from our site at "Submitting Term Suggestions to GO".
- Familiar with the ontology, but do not use TermGenie: whether you are already well acquainted with the ontology or are just becoming involved, if you have not yet become familiar with TermGenie, we suggest that you submit your ontology updates using the the GO curator request tracker on Github. As it is the case with TermGenie, you will need to sign up for a username.
- Ready to contribute, but not familiar with TermGenie or GitHub: If you are ready to submit your suggestions for improving the ontology but are not familiar with either of the tools mentioned above, please Contacting the GOC HelpDesk.