Some GO terms have special usage notes, like those we use for grouping, and may not be intended for direct annotation (more about this later). There’s also a very important set of terms that have a distinct meaning when you see them in an annotation: the root nodes.
These terms are the root ontology term for each of the three GO domains; every term in the GO will map up to (is_a) one of these. When you find them used in a direct annotation, they will have the evidence “No biological Data available” (ND). These annotations mean curators have looked through all resources, but cannot find any peer-reviewed literature that supports making a manual annotation to this aspect. There may be papers that mention these gene products, but not enough evidence to support an annotation to any GO term. Some curation groups will retain these root annotations when electronic, sequence-based, or other non-curator-reviewed annotations exist- but remember that evidence codes describe the evidence, not make statements of the quality of the annotation.
A term can have many annotations in one aspect, and still have an annotation to the root node in another aspect. A lack of knowledge about one aspect does not indicate there is a lack of knowledge about the other aspects. A gene product can have annotations to the root node in one, two, or all three aspects. In this example of a putative protein in Saccharomyces cerevisiae, curators were unable to find any literature to support annotation to any term in any of the 3 aspects:
How can this help you? These root annotations might help you guide your research to investigate unexplored gene products. Be aware that these root annotations should not be used in enrichment studies, etc. as they are more ‘curator notes’ than conclusive statements about the gene product.
How can you help GO? If you find a root annotation but believe you know a peer-reviewed publication that might support an annotation in that aspect, pass this on to a MOD if applicable, or directly to GO and we’ll get it to the correct team of curators! Not all papers/experiments can be used to support GO annotations, but we appreciate any help in keeping GO current and complete. When GO curators come across appropriate papers, they remove the root annotation and replace it with the “more helpful” GO term.