Virus terms (Completed 2012)
The aim of this project is to completely overhaul all the terms related to viruses in GO, mainly processes. Term phrasing and tree structures will be standardized, and new terms will be added with the aim of giving a broad coverage for all species of virus.
UPDATE: This work is now published (http://www.ncbi.nlm.nih.gov/pubmed/26215368).
Status - July 2012
- Jane Lomax, Rebecca Foulger, Brenley McIntosh - July 2012
- Michelle Gwinn Giglio, Candace Collmer, Ariane Toussaint, Alexander Diehl, Fiona McCarthy, Marcus Chibucos
- Now deprecated. Instead use the general go-discuss list (email@example.com), and precede subject with VIRUSES
- The archive of the old list is available here
The most recent file of terms is available to download here:
The keyword mappings from SIB are available here:
We should probably aim for several virtual meetings via WebEx and phone, and perhaps one face-to-face meeting, budget allowing in 2009.
The discussion can be viewed in the meeting minutes and on the mailing list archive, but we have so far all agreed to the following principles for developing the viral terms in GO:
- viruses should be classed as organisms
- virus-host interactions should be classed as symbiotic interactions, even when they result in the demise of the host
- viral-host processes should be regarded as 'normal' from the perspective of both the host and the virus
- Are viruses organisms or not? This is important because it will determine whether the virus will live under the multi-organism process node or not.
I disagree. The Gene Ontology is about classifying gene function. Viruses have genes, therefore these viral gene products should be included in the GO. However, if you really need to decide if viruses are "organisms" then I would say that they contain genetic material and are capable of reproducing, evolving and responding to their environment. They are organisms without baggage. - Fiona
The developers of the Infectious Disease Ontology favor defining viruses as organisms, and would like the GO to do so as well, to ensure that this issue is handled in the same way across the OBO Foundry ontologies, so that IDO can import GO terms without modification in their ontological placements. - Alex
- Most of the existing virus terms in GO were added for the annotation of HPV1, so the existing structure may not be optimal for organising all viral processes. We may need to obsolete many of these terms (note: there are very few annotations to these terms because the HPV1 annotation file went out of date).
- It is not always obvious with these terms whether they describe the host or the symbiont process or both. We'll need to make sure that's made clear.
- transduction SF:2532011
- viral genome replication SF:1774586
- recombinases SF:1742920
- children of viral genome replication SF:1883849
- obsolete 'provirus' SF:2930856
This is a list of all the terms currently in GO relating to viruses. I've removed the obsolete terms, and the molecular function terms.
Ariane: some of the 'component' terms are in fact SO terms (provirus and the genomes). Where should virion (and phage in my case) fit with a sequence/nucleic acid AND proteins?
- Suggestion from Fiona for structuring the process terms:
Hi Jane, I see that you are involved with editing the viral GO terms. For viral genome replication it would make the most biological sense to have children based on the type of genome because (1)this will affect functionality, including is a's for all the child terms and (2) it is how virologists think of the function. For example: 1. dsDNA viruses 2. ssDNA viruses (+)sense DNA 3. dsRNA viruses 4. ssRNA viruses 4.1. (+)ssRNA viruses (+)sense RNA 4.2. (-)ssRNA viruses (-)sense RNA (includes the "ambisense" viruses like bunyaviruses) 5. ssRNA-RT viruses (+)sense RNA with DNA intermediate in life-cycle 6. dsDNA-RT viruses So instead of having a child term "Flaviridae viral genome replication" you would want to have "positive sense, single stranded RNA genome replication" and etc. Then I think you will find that all these terms will just fall out naturally and you will be able to make child terms to these in a very systematic way. The ds DNA viruses (Pox & Herpes) will be a part of regular DNA replication but they also have rolling circle replication, exactly as you would describe for plasmids. Etc, etc. Anyway, my 2 cents. Fiona
- Here's a link to the phage and plasmid protein database ACLAME where you shall see a link to the MeGO ontology. The phage ontology PhiGO is now part of MeGO.