Most annotations in association files are electronically inferred (IEA). As with all types of annotations, IEAs change over time, with an overall increasing trend. However, in the specific case of IEAs, significant fluctuations in numbers may sometimes be observed over a short period of time. Nearly always, these are not due to bugs, but rather to the following reasons and/or to a combination thereof:
- All IEA annotations that are over one year old are removed from association files. This is part of quality control procedures. Another procedure the GO started implementing in mid-2014 are taxonomic checks. A technical summary of annotation QC checks may be found here: http://geneontology.org/page/annotation-quality-control
- Electronic annotations are provided to UniProt-GOA by various groups, including Ensembl, InterPro and UniProt. UniProt-GOA then includes these in their annotation files that they submit to the GO Consortium. There are numerous reasons why electronic annotations can fluctuate; e.g., InterPro may have changed a mapping that affected a large number of annotations; a mapping between a GO term and a UniProt keyword may have been added or removed; Ensembl may have changed their orthology sets; new quality checking procedures may have been introduced; a supplying group may have had a problem providing the annotations. Since electronic annotations tend to hit a large number of proteins, it is more likely to observe larger fluctuations than one would in a manual annotation set. UniProt-GOA aims to record all the known changes to the datasets they provide in the release notes here: http://www.ebi.ac.uk/GOA/news
- New genome assemblies for various species are periodically released, and that may contribute to changes in gene annotations.
- Changes are good. Our knowledge foundation is growing and increasing and information is continuing to be added based on existing, older literature.
- Relevant paper: Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt.