gocentral
commented
20 years ago Logged In: YES user_id=436423
Hi,
In the annotation sets provided by GO Consortium members, biological process terms are used only for gene products that actively participate in the process, not for gene products that are targets or substrates (or otherwise acted upon) by the process. So in the bacterial secretion system example, we would annotate the gene products that make up the injection apparatus, but not those transported by it.
If you wish to annotate gene products that are transported by the type III system internally, you are free to do so, but the annotations should be distinguished (e.g. by a tag in your database) from those that are part of the secretory apparatus, and the former should be removed from any set of annotations that you submit to the GO repository.
Midori
Original comment by: mah11
Hello this is Candace Collmer (email: ccollmer@wells.edu) from the PAMGO (Plant-Associated Microbe Gene Ontology) interest group. We are beginning the work of developing suggested GO terms for the Biological Process ontology that could be used to annotate gene products of different plant pathogens bacteria, fungi, oomycetes, nematodes, etc. We are currently working on an outline of higher order terms (and definitions) that we hope will be applicable to both plant and animal pathogens as well as to microbes that enter into various types of symbiotic relationships with hosts. We are also trying to find a way to integrate these suggested new terms into existing categories in the GO Biological Process ontology (e.g. host-pathogen interactions, pathogenesis, etc.), and will soon send a proposed scheme for your evaluation. In the meantime, as we are working on this project, we have a question about what gene products are appropriate to annotate to an existing term in the GO biological process ontology, GO:0030254 = type III protein secretion system (definition: a bacterial secretion system in which secretion occurs in a continuous process without the distinct presence of periplasmic intermediates; does not involve proteolytic processing of secreted proteins). Given this is a biological process term, can we annotate gene products to it that are transported via the type III system as well as those gene products that make up the injection apparatus itself?
Reported by: ccollmer
Original Ticket: "geneontology/annotation-issues/9":https://sourceforge.net/p/geneontology/annotation-issues/9